Query psy13443
Match_columns 188
No_of_seqs 147 out of 1277
Neff 10.8
Searched_HMMs 46136
Date Fri Aug 16 19:33:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13443.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13443hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 4.9E-30 1.1E-34 179.0 4.2 134 12-157 129-266 (279)
2 KOG2462|consensus 99.9 1.7E-25 3.8E-30 156.3 7.3 128 42-178 131-259 (279)
3 KOG1074|consensus 99.8 3.9E-22 8.5E-27 157.1 1.2 85 77-161 604-695 (958)
4 KOG1074|consensus 99.8 1.5E-21 3.3E-26 153.8 4.3 58 107-164 880-937 (958)
5 KOG3608|consensus 99.8 9.3E-22 2E-26 141.7 2.7 161 1-162 195-380 (467)
6 KOG3623|consensus 99.8 3.2E-21 6.9E-26 150.1 3.5 82 74-155 890-971 (1007)
7 KOG3608|consensus 99.7 1.2E-17 2.6E-22 120.7 3.9 156 14-170 178-360 (467)
8 KOG3576|consensus 99.7 2.8E-17 6E-22 110.4 3.0 115 11-162 115-240 (267)
9 KOG3576|consensus 99.6 5.2E-17 1.1E-21 109.1 1.1 85 76-160 115-199 (267)
10 KOG3623|consensus 99.6 1.4E-16 3E-21 124.6 2.4 111 13-158 210-333 (1007)
11 PLN03086 PRLI-interacting fact 99.3 1.3E-11 2.9E-16 96.8 6.8 128 15-169 409-548 (567)
12 PLN03086 PRLI-interacting fact 99.3 4.3E-11 9.3E-16 93.9 9.4 120 14-159 434-565 (567)
13 PHA00733 hypothetical protein 99.2 6.4E-12 1.4E-16 81.1 3.7 83 76-160 38-125 (128)
14 PHA00733 hypothetical protein 99.0 4.9E-10 1.1E-14 72.4 4.8 56 74-131 69-124 (128)
15 PHA02768 hypothetical protein; 99.0 1.8E-10 3.8E-15 61.9 1.8 39 107-147 6-44 (55)
16 PHA02768 hypothetical protein; 98.9 7.5E-10 1.6E-14 59.5 2.2 43 78-122 5-47 (55)
17 PF13465 zf-H2C2_2: Zinc-finge 98.8 1.6E-09 3.5E-14 49.9 1.0 25 1-25 2-26 (26)
18 PF13465 zf-H2C2_2: Zinc-finge 98.8 3.5E-09 7.6E-14 48.7 2.1 24 122-145 2-25 (26)
19 PHA00616 hypothetical protein 98.7 1.4E-08 3E-13 52.0 1.8 33 134-166 1-33 (44)
20 KOG3993|consensus 98.5 2.5E-08 5.4E-13 74.6 1.4 86 76-161 354-485 (500)
21 KOG3993|consensus 98.5 1.8E-08 3.9E-13 75.4 -0.4 86 79-164 268-386 (500)
22 PHA00616 hypothetical protein 98.5 4.3E-08 9.3E-13 50.2 1.1 33 78-110 1-33 (44)
23 PHA00732 hypothetical protein 98.4 2.4E-07 5.3E-12 54.5 2.3 46 78-129 1-47 (79)
24 PHA00732 hypothetical protein 98.3 1.1E-06 2.3E-11 51.8 3.1 47 106-158 1-48 (79)
25 PF05605 zf-Di19: Drought indu 98.2 4.9E-06 1.1E-10 45.5 4.3 49 107-158 3-53 (54)
26 PF05605 zf-Di19: Drought indu 98.1 6E-06 1.3E-10 45.1 4.4 50 78-130 2-53 (54)
27 PF00096 zf-C2H2: Zinc finger, 98.0 4.1E-06 9E-11 37.2 1.8 22 135-156 1-22 (23)
28 PF13894 zf-C2H2_4: C2H2-type 98.0 5E-06 1.1E-10 37.2 2.1 24 135-158 1-24 (24)
29 PF00096 zf-C2H2: Zinc finger, 98.0 5.4E-06 1.2E-10 36.8 1.7 22 79-100 1-22 (23)
30 PF12756 zf-C2H2_2: C2H2 type 97.9 7.7E-06 1.7E-10 50.6 2.3 73 80-157 1-73 (100)
31 COG5189 SFP1 Putative transcri 97.8 5.9E-06 1.3E-10 60.1 0.5 52 104-155 347-419 (423)
32 PF13894 zf-C2H2_4: C2H2-type 97.8 2.8E-05 6.1E-10 34.6 2.3 24 14-37 1-24 (24)
33 PF13912 zf-C2H2_6: C2H2-type 97.7 1.3E-05 2.8E-10 37.1 1.0 25 134-158 1-25 (27)
34 PF13912 zf-C2H2_6: C2H2-type 97.7 2.8E-05 6.1E-10 35.9 1.7 25 13-37 1-25 (27)
35 PF12756 zf-C2H2_2: C2H2 type 97.6 6.8E-05 1.5E-09 46.3 2.7 73 15-101 1-73 (100)
36 PF09237 GAGA: GAGA factor; I 97.4 0.00021 4.5E-09 37.5 2.6 31 132-162 22-52 (54)
37 PF13909 zf-H2C2_5: C2H2-type 97.3 0.00019 4.1E-09 32.1 1.9 24 135-159 1-24 (24)
38 COG5189 SFP1 Putative transcri 97.2 0.0001 2.3E-09 53.8 0.8 52 76-127 347-419 (423)
39 smart00355 ZnF_C2H2 zinc finge 97.2 0.00036 7.7E-09 31.4 2.3 23 135-157 1-23 (26)
40 PF09237 GAGA: GAGA factor; I 97.2 0.00048 1E-08 36.2 2.6 37 5-41 15-52 (54)
41 smart00355 ZnF_C2H2 zinc finge 97.1 0.00067 1.4E-08 30.5 2.4 22 80-101 2-23 (26)
42 PF13909 zf-H2C2_5: C2H2-type 97.0 0.00086 1.9E-08 29.8 2.3 24 14-38 1-24 (24)
43 PRK04860 hypothetical protein; 96.9 0.00078 1.7E-08 45.3 2.7 37 106-146 119-155 (160)
44 PF12874 zf-met: Zinc-finger o 96.9 0.00083 1.8E-08 30.2 1.7 21 14-34 1-21 (25)
45 PF12874 zf-met: Zinc-finger o 96.8 0.00072 1.6E-08 30.4 1.3 21 79-99 1-21 (25)
46 PRK04860 hypothetical protein; 96.7 0.0014 3.1E-08 44.0 2.5 41 76-120 117-157 (160)
47 PF12171 zf-C2H2_jaz: Zinc-fin 95.8 0.002 4.2E-08 29.6 -0.3 21 135-155 2-22 (27)
48 PF12171 zf-C2H2_jaz: Zinc-fin 95.7 0.0033 7.2E-08 28.8 0.3 22 79-100 2-23 (27)
49 PF13913 zf-C2HC_2: zinc-finge 95.4 0.017 3.6E-07 26.0 2.1 21 135-156 3-23 (25)
50 KOG1146|consensus 95.3 0.0033 7E-08 54.5 -0.9 81 8-100 460-540 (1406)
51 KOG2231|consensus 95.2 0.044 9.6E-07 44.9 5.1 103 16-130 118-236 (669)
52 smart00451 ZnF_U1 U1-like zinc 94.9 0.026 5.7E-07 27.4 2.1 23 12-34 2-24 (35)
53 KOG1146|consensus 94.8 0.011 2.5E-07 51.3 0.9 56 101-156 460-540 (1406)
54 COG5236 Uncharacterized conser 94.7 0.095 2.1E-06 39.4 5.3 134 13-159 151-306 (493)
55 PF12013 DUF3505: Protein of u 94.6 0.088 1.9E-06 33.1 4.5 83 76-159 9-109 (109)
56 COG4049 Uncharacterized protei 94.6 0.016 3.5E-07 31.0 0.8 34 5-38 9-42 (65)
57 cd00350 rubredoxin_like Rubred 94.6 0.031 6.7E-07 26.9 1.8 24 107-142 2-25 (33)
58 TIGR00622 ssl1 transcription f 94.5 0.078 1.7E-06 33.3 3.9 24 106-129 81-104 (112)
59 COG2888 Predicted Zn-ribbon RN 94.4 0.062 1.3E-06 29.3 2.8 46 64-114 12-58 (61)
60 KOG2785|consensus 94.4 0.17 3.7E-06 38.5 6.0 57 107-163 167-250 (390)
61 smart00451 ZnF_U1 U1-like zinc 94.3 0.048 1E-06 26.4 2.2 22 78-99 3-24 (35)
62 KOG2482|consensus 94.1 0.084 1.8E-06 39.5 3.9 49 107-155 280-355 (423)
63 KOG4173|consensus 94.0 0.037 7.9E-07 38.3 1.8 79 78-159 79-171 (253)
64 COG4049 Uncharacterized protei 94.0 0.028 6.2E-07 30.1 1.0 30 131-160 14-43 (65)
65 KOG2893|consensus 93.3 0.032 6.9E-07 39.6 0.6 42 80-125 12-53 (341)
66 PRK14890 putative Zn-ribbon RN 92.8 0.15 3.3E-06 27.9 2.6 12 76-87 23-34 (59)
67 PF06524 NOA36: NOA36 protein; 91.5 0.062 1.3E-06 38.7 0.3 27 103-129 206-232 (314)
68 cd00729 rubredoxin_SM Rubredox 91.4 0.17 3.7E-06 24.5 1.7 11 107-117 3-13 (34)
69 PF12013 DUF3505: Protein of u 91.2 0.8 1.7E-05 28.7 5.1 25 107-131 81-109 (109)
70 COG5048 FOG: Zn-finger [Genera 90.6 0.051 1.1E-06 42.4 -0.9 65 106-170 289-359 (467)
71 KOG2893|consensus 90.3 0.06 1.3E-06 38.2 -0.7 48 108-159 12-59 (341)
72 PF07754 DUF1610: Domain of un 89.9 0.34 7.3E-06 21.4 1.8 10 76-85 14-23 (24)
73 PF13719 zinc_ribbon_5: zinc-r 89.3 0.37 8E-06 23.8 1.9 13 108-120 4-16 (37)
74 COG5048 FOG: Zn-finger [Genera 89.2 0.093 2E-06 40.9 -0.5 63 77-139 288-356 (467)
75 PF10571 UPF0547: Uncharacteri 88.6 0.36 7.7E-06 21.8 1.4 10 80-89 16-25 (26)
76 COG1592 Rubrerythrin [Energy p 88.4 0.65 1.4E-05 31.5 3.2 25 105-142 133-157 (166)
77 smart00659 RPOLCX RNA polymera 88.4 0.4 8.7E-06 24.7 1.7 26 107-143 3-28 (44)
78 TIGR00622 ssl1 transcription f 88.1 1.7 3.7E-05 27.4 4.6 82 11-102 13-105 (112)
79 PF13717 zinc_ribbon_4: zinc-r 87.7 0.65 1.4E-05 22.8 2.2 13 108-120 4-16 (36)
80 KOG2186|consensus 87.0 0.49 1.1E-05 34.1 2.0 47 78-127 3-49 (276)
81 TIGR02098 MJ0042_CXXC MJ0042 f 86.8 0.59 1.3E-05 23.1 1.8 10 135-144 26-35 (38)
82 KOG2482|consensus 86.4 1.2 2.7E-05 33.6 3.9 51 79-129 280-357 (423)
83 PF15135 UPF0515: Uncharacteri 86.3 1.3 2.7E-05 32.0 3.7 51 42-92 113-169 (278)
84 PF09986 DUF2225: Uncharacteri 86.2 0.13 2.9E-06 36.5 -1.1 13 135-147 49-61 (214)
85 COG5236 Uncharacterized conser 86.1 1.2 2.5E-05 33.8 3.6 24 79-102 152-177 (493)
86 PF09538 FYDLN_acid: Protein o 85.9 0.53 1.1E-05 29.6 1.6 29 80-119 11-39 (108)
87 PF09723 Zn-ribbon_8: Zinc rib 85.9 0.48 1E-05 24.1 1.2 11 42-52 6-17 (42)
88 PF02892 zf-BED: BED zinc fing 85.6 0.61 1.3E-05 23.9 1.5 26 133-158 15-44 (45)
89 smart00531 TFIIE Transcription 85.2 0.93 2E-05 30.2 2.6 35 11-49 97-131 (147)
90 smart00834 CxxC_CXXC_SSSS Puta 84.8 0.63 1.4E-05 23.3 1.3 8 42-49 6-13 (41)
91 TIGR00373 conserved hypothetic 84.2 1 2.2E-05 30.4 2.5 31 10-49 106-136 (158)
92 PF09986 DUF2225: Uncharacteri 84.1 0.17 3.8E-06 35.9 -1.3 13 107-119 49-61 (214)
93 COG1996 RPC10 DNA-directed RNA 83.8 0.68 1.5E-05 24.4 1.2 11 106-116 6-16 (49)
94 PF06524 NOA36: NOA36 protein; 83.4 0.32 7E-06 35.1 -0.2 26 132-157 207-232 (314)
95 PF05443 ROS_MUCR: ROS/MUCR tr 82.3 0.7 1.5E-05 30.1 1.0 25 134-161 72-96 (132)
96 TIGR00373 conserved hypothetic 81.3 1.9 4.2E-05 29.1 2.9 32 103-143 106-137 (158)
97 PRK00464 nrdR transcriptional 80.6 0.33 7.2E-06 32.5 -0.9 17 106-122 28-44 (154)
98 smart00614 ZnF_BED BED zinc fi 80.6 1.8 3.9E-05 22.8 2.1 23 136-158 20-47 (50)
99 smart00531 TFIIE Transcription 80.5 4.1 8.8E-05 27.1 4.3 37 104-144 97-133 (147)
100 smart00734 ZnF_Rad18 Rad18-lik 80.4 1.8 4E-05 19.4 1.8 19 136-155 3-21 (26)
101 PF12907 zf-met2: Zinc-binding 79.9 1.2 2.6E-05 22.5 1.2 27 135-161 2-31 (40)
102 TIGR02605 CxxC_CxxC_SSSS putat 79.1 1.2 2.7E-05 23.6 1.2 11 14-24 6-16 (52)
103 PRK06266 transcription initiat 78.5 1.6 3.5E-05 30.1 1.9 29 12-49 116-144 (178)
104 KOG2186|consensus 78.3 1.2 2.6E-05 32.2 1.2 54 107-163 4-57 (276)
105 KOG2231|consensus 78.2 3.9 8.5E-05 34.1 4.2 69 24-110 160-240 (669)
106 PRK06266 transcription initiat 78.2 1.7 3.7E-05 30.0 1.9 30 105-143 116-145 (178)
107 PHA00626 hypothetical protein 77.8 1.8 4E-05 23.4 1.5 11 79-89 24-34 (59)
108 TIGR02300 FYDLN_acid conserved 76.4 1.8 3.8E-05 27.9 1.5 15 105-119 25-39 (129)
109 KOG2807|consensus 76.3 4.9 0.00011 30.3 3.9 25 133-157 344-368 (378)
110 KOG2785|consensus 75.9 4.4 9.5E-05 31.2 3.6 52 77-128 165-242 (390)
111 PF02176 zf-TRAF: TRAF-type zi 75.1 2.5 5.4E-05 23.1 1.7 41 105-145 8-53 (60)
112 COG5151 SSL1 RNA polymerase II 74.6 1.4 3.1E-05 32.8 0.8 91 63-158 310-412 (421)
113 PF15269 zf-C2H2_7: Zinc-finge 74.1 3.1 6.7E-05 21.3 1.7 22 13-34 20-41 (54)
114 COG1198 PriA Primosomal protei 74.0 3 6.5E-05 35.4 2.6 29 100-143 456-484 (730)
115 PRK00398 rpoP DNA-directed RNA 73.8 2.2 4.7E-05 22.1 1.2 8 42-49 4-11 (46)
116 PF14353 CpXC: CpXC protein 73.5 2.2 4.7E-05 27.6 1.4 14 78-91 38-51 (128)
117 COG1571 Predicted DNA-binding 72.9 1.9 4.1E-05 33.8 1.2 30 63-92 352-381 (421)
118 smart00661 RPOL9 RNA polymeras 71.3 3.3 7.2E-05 21.8 1.6 11 78-88 20-30 (52)
119 PRK09678 DNA-binding transcrip 70.5 1.3 2.7E-05 25.6 -0.2 14 133-146 26-41 (72)
120 PF15135 UPF0515: Uncharacteri 70.4 4.3 9.2E-05 29.4 2.3 61 74-147 108-168 (278)
121 COG3357 Predicted transcriptio 69.9 3 6.6E-05 25.0 1.3 13 106-118 58-70 (97)
122 PF12760 Zn_Tnp_IS1595: Transp 69.4 4.9 0.00011 20.8 1.9 28 106-142 18-45 (46)
123 PRK04023 DNA polymerase II lar 68.7 5.5 0.00012 34.9 3.0 8 135-142 664-671 (1121)
124 PF04959 ARS2: Arsenite-resist 68.3 3.6 7.9E-05 29.3 1.7 29 132-160 75-103 (214)
125 PF03604 DNA_RNApol_7kD: DNA d 68.0 3.1 6.8E-05 19.8 0.9 6 80-85 19-24 (32)
126 KOG1280|consensus 66.4 11 0.00023 28.9 3.8 22 78-99 79-100 (381)
127 KOG2593|consensus 66.0 4.9 0.00011 31.5 2.1 37 9-49 124-161 (436)
128 cd00730 rubredoxin Rubredoxin; 66.0 2 4.3E-05 22.9 0.0 11 14-24 2-12 (50)
129 KOG4118|consensus 65.8 3.2 6.9E-05 23.2 0.8 31 135-165 39-69 (74)
130 PF13240 zinc_ribbon_2: zinc-r 63.0 5.2 0.00011 17.4 1.1 6 81-86 16-21 (23)
131 PRK00432 30S ribosomal protein 62.4 4.9 0.00011 21.3 1.1 10 106-115 37-46 (50)
132 KOG2593|consensus 62.0 8.1 0.00018 30.4 2.6 38 101-141 123-160 (436)
133 PF12773 DZR: Double zinc ribb 61.9 6.4 0.00014 20.6 1.5 8 79-86 30-37 (50)
134 PRK14714 DNA polymerase II lar 61.2 12 0.00025 33.9 3.6 34 42-87 668-701 (1337)
135 TIGR00595 priA primosomal prot 61.1 6.4 0.00014 32.1 2.1 16 100-115 234-249 (505)
136 KOG1280|consensus 60.4 10 0.00022 28.9 2.8 40 10-49 76-117 (381)
137 smart00440 ZnF_C2C2 C2C2 Zinc 60.3 11 0.00023 18.9 2.1 13 77-89 27-39 (40)
138 smart00154 ZnF_AN1 AN1-like Zi 60.2 7.9 0.00017 19.3 1.6 13 78-90 12-24 (39)
139 PRK04023 DNA polymerase II lar 59.5 12 0.00026 33.0 3.4 8 42-49 627-634 (1121)
140 TIGR01206 lysW lysine biosynth 59.2 7.3 0.00016 21.1 1.4 10 14-23 3-12 (54)
141 KOG3408|consensus 57.5 6.1 0.00013 25.2 1.1 25 132-156 55-79 (129)
142 COG4957 Predicted transcriptio 56.7 7.2 0.00016 25.4 1.3 25 135-162 77-101 (148)
143 PRK14873 primosome assembly pr 56.5 7.5 0.00016 32.8 1.8 26 102-143 406-431 (665)
144 PF13451 zf-trcl: Probable zin 56.2 7 0.00015 20.7 1.0 10 107-116 5-14 (49)
145 KOG3214|consensus 55.6 7.4 0.00016 23.9 1.2 13 107-119 48-60 (109)
146 KOG2907|consensus 54.2 4.6 9.9E-05 25.4 0.2 38 107-146 75-114 (116)
147 PRK14714 DNA polymerase II lar 53.1 17 0.00036 33.0 3.3 53 14-89 668-720 (1337)
148 COG4888 Uncharacterized Zn rib 53.0 7.6 0.00016 23.9 0.9 8 42-49 23-30 (104)
149 PF01096 TFIIS_C: Transcriptio 52.7 6.3 0.00014 19.6 0.5 12 77-88 27-38 (39)
150 COG1571 Predicted DNA-binding 52.6 9.9 0.00021 30.0 1.8 29 108-147 352-380 (421)
151 COG3364 Zn-ribbon containing p 52.6 11 0.00023 23.3 1.5 16 105-120 1-16 (112)
152 COG5151 SSL1 RNA polymerase II 52.2 32 0.0007 26.0 4.2 25 105-129 387-411 (421)
153 KOG4173|consensus 52.1 9.1 0.0002 27.0 1.3 51 105-158 78-130 (253)
154 PRK00420 hypothetical protein; 51.9 11 0.00024 23.8 1.6 11 78-88 40-50 (112)
155 KOG3408|consensus 51.4 10 0.00023 24.2 1.4 25 10-34 54-78 (129)
156 COG1198 PriA Primosomal protei 51.0 11 0.00025 32.1 2.0 21 63-87 464-484 (730)
157 PF04959 ARS2: Arsenite-resist 50.9 9.5 0.00021 27.2 1.3 30 10-39 74-103 (214)
158 PF07649 C1_3: C1-like domain; 50.4 11 0.00025 17.3 1.2 10 77-86 14-23 (30)
159 PF08274 PhnA_Zn_Ribbon: PhnA 50.3 7.2 0.00016 18.3 0.5 8 106-113 19-26 (30)
160 PF07975 C1_4: TFIIH C1-like d 50.3 6 0.00013 21.1 0.2 20 78-97 21-40 (51)
161 PF07282 OrfB_Zn_ribbon: Putat 49.8 16 0.00034 20.6 1.9 10 106-115 46-55 (69)
162 COG1655 Uncharacterized protei 49.2 3.2 6.8E-05 29.7 -1.2 39 105-143 18-71 (267)
163 PTZ00255 60S ribosomal protein 49.0 12 0.00026 22.6 1.4 14 77-90 53-66 (90)
164 PF13878 zf-C2H2_3: zinc-finge 48.4 25 0.00054 17.7 2.3 23 135-157 14-38 (41)
165 KOG4167|consensus 48.3 4.8 0.0001 33.8 -0.5 27 11-37 790-816 (907)
166 PF04780 DUF629: Protein of un 48.1 17 0.00037 29.2 2.5 32 8-39 52-83 (466)
167 KOG2636|consensus 47.5 15 0.00032 29.1 2.0 27 8-34 396-423 (497)
168 PF04780 DUF629: Protein of un 47.2 15 0.00032 29.6 2.0 28 134-161 57-84 (466)
169 PF08792 A2L_zn_ribbon: A2L zi 46.7 12 0.00026 17.9 0.9 11 78-88 21-31 (33)
170 PF03833 PolC_DP2: DNA polymer 45.5 7 0.00015 33.6 0.0 8 42-49 656-663 (900)
171 TIGR00100 hypA hydrogenase nic 45.3 13 0.00029 23.6 1.3 12 78-89 70-81 (115)
172 KOG3002|consensus 45.1 61 0.0013 24.6 4.8 109 42-160 49-165 (299)
173 TIGR00280 L37a ribosomal prote 44.4 15 0.00032 22.3 1.3 12 78-89 53-64 (91)
174 COG1327 Predicted transcriptio 44.3 5.8 0.00013 26.4 -0.5 14 107-120 29-42 (156)
175 PF07191 zinc-ribbons_6: zinc- 44.2 8.9 0.00019 22.0 0.3 10 78-87 17-26 (70)
176 KOG2807|consensus 43.7 57 0.0012 25.0 4.4 31 105-141 344-374 (378)
177 PF14311 DUF4379: Domain of un 43.5 22 0.00048 19.0 1.8 12 107-118 29-40 (55)
178 COG3091 SprT Zn-dependent meta 43.4 21 0.00045 23.9 1.9 33 77-114 116-148 (156)
179 PRK03681 hypA hydrogenase nick 43.3 13 0.00027 23.7 0.9 12 78-89 70-81 (114)
180 TIGR00244 transcriptional regu 43.3 5.7 0.00012 26.4 -0.7 16 107-122 29-44 (147)
181 PRK12380 hydrogenase nickel in 42.7 17 0.00036 23.1 1.4 11 79-89 71-81 (113)
182 COG0068 HypF Hydrogenase matur 42.4 4.8 0.0001 33.8 -1.3 74 63-143 103-182 (750)
183 PF02084 Bindin: Bindin; Inte 41.8 14 0.00031 26.3 1.1 12 148-159 131-142 (238)
184 COG0068 HypF Hydrogenase matur 41.5 2.8 6E-05 35.1 -2.7 33 80-118 153-185 (750)
185 PF01428 zf-AN1: AN1-like Zinc 41.4 9.5 0.00021 19.4 0.1 15 12-26 12-26 (43)
186 PF01363 FYVE: FYVE zinc finge 41.3 15 0.00033 20.6 1.0 6 80-85 27-32 (69)
187 KOG1701|consensus 41.1 24 0.00053 27.9 2.3 13 106-118 427-439 (468)
188 PF05495 zf-CHY: CHY zinc fing 41.1 6.3 0.00014 22.6 -0.6 30 106-143 41-70 (71)
189 COG3677 Transposase and inacti 41.0 13 0.00029 24.2 0.8 12 134-145 53-64 (129)
190 COG4530 Uncharacterized protei 40.7 17 0.00036 22.8 1.1 12 105-116 25-36 (129)
191 PF04423 Rad50_zn_hook: Rad50 40.6 27 0.00059 18.6 1.9 11 108-118 22-32 (54)
192 PF12647 RNHCP: RNHCP domain; 39.6 24 0.00051 21.5 1.6 8 42-49 5-12 (92)
193 PRK03976 rpl37ae 50S ribosomal 39.6 17 0.00037 22.0 1.0 9 41-49 36-44 (90)
194 PRK14559 putative protein seri 38.6 45 0.00098 28.3 3.6 24 63-89 29-52 (645)
195 PRK03564 formate dehydrogenase 38.4 16 0.00035 27.7 1.0 13 134-146 252-264 (309)
196 KOG4377|consensus 37.8 53 0.0012 26.0 3.6 21 139-159 408-428 (480)
197 COG1675 TFA1 Transcription ini 37.8 27 0.0006 24.1 1.9 17 103-119 110-126 (176)
198 cd04476 RPA1_DBD_C RPA1_DBD_C: 37.5 24 0.00053 23.8 1.7 26 63-88 36-61 (166)
199 PRK10220 hypothetical protein; 37.2 29 0.00063 21.8 1.8 15 77-91 19-33 (111)
200 PRK00564 hypA hydrogenase nick 37.1 18 0.00039 23.1 0.9 16 76-91 69-84 (117)
201 PRK03824 hypA hydrogenase nick 36.8 17 0.00037 23.8 0.8 16 76-91 68-83 (135)
202 COG1773 Rubredoxin [Energy pro 36.8 17 0.00037 19.7 0.7 15 106-120 3-17 (55)
203 KOG4124|consensus 36.6 4.6 9.9E-05 30.8 -2.1 50 105-154 348-418 (442)
204 KOG1842|consensus 36.6 21 0.00046 28.4 1.4 28 134-161 15-42 (505)
205 PF14803 Nudix_N_2: Nudix N-te 36.5 24 0.00052 17.0 1.1 9 78-86 22-30 (34)
206 COG2331 Uncharacterized protei 36.5 9.4 0.0002 22.2 -0.4 28 14-49 13-41 (82)
207 COG1997 RPL43A Ribosomal prote 36.3 26 0.00057 21.0 1.4 13 77-89 52-64 (89)
208 PF11931 DUF3449: Domain of un 35.3 12 0.00027 26.2 0.0 24 11-34 99-123 (196)
209 KOG4167|consensus 34.9 9.1 0.0002 32.3 -0.8 25 106-130 792-816 (907)
210 PF01780 Ribosomal_L37ae: Ribo 34.6 11 0.00023 22.9 -0.4 9 41-49 35-43 (90)
211 TIGR00686 phnA alkylphosphonat 34.6 24 0.00053 22.1 1.2 13 78-90 19-31 (109)
212 PF13824 zf-Mss51: Zinc-finger 33.8 40 0.00086 18.4 1.8 11 133-143 13-23 (55)
213 KOG2272|consensus 33.4 6.1 0.00013 28.7 -1.8 43 42-84 100-143 (332)
214 PF14369 zf-RING_3: zinc-finge 33.3 27 0.00058 16.9 1.0 8 81-88 24-31 (35)
215 PF07503 zf-HYPF: HypF finger; 33.3 4 8.7E-05 19.9 -1.9 12 134-145 21-32 (35)
216 PF01286 XPA_N: XPA protein N- 33.3 29 0.00064 16.8 1.1 6 44-49 6-11 (34)
217 PRK05978 hypothetical protein; 33.3 31 0.00068 23.1 1.6 8 42-49 34-41 (148)
218 KOG0717|consensus 33.1 27 0.00059 28.0 1.5 34 135-168 461-495 (508)
219 KOG0717|consensus 33.0 31 0.00068 27.7 1.8 22 79-100 293-314 (508)
220 PRK12496 hypothetical protein; 33.0 23 0.00051 24.1 1.0 11 79-89 128-138 (164)
221 PF00130 C1_1: Phorbol esters/ 32.8 33 0.00072 17.9 1.4 11 76-86 26-36 (53)
222 COG1326 Uncharacterized archae 32.6 45 0.00097 23.4 2.3 11 134-144 30-40 (201)
223 cd00065 FYVE FYVE domain; Zinc 32.3 32 0.0007 18.3 1.4 9 81-89 5-13 (57)
224 smart00731 SprT SprT homologue 32.1 34 0.00074 22.6 1.7 11 78-88 112-122 (146)
225 PF08646 Rep_fac-A_C: Replicat 32.1 16 0.00035 24.1 0.2 26 63-88 20-47 (146)
226 KOG4727|consensus 31.9 33 0.00071 23.5 1.5 24 11-34 73-96 (193)
227 COG5188 PRP9 Splicing factor 3 31.7 33 0.00072 26.4 1.7 27 7-33 368-395 (470)
228 PF03107 C1_2: C1 domain; Int 31.5 40 0.00087 15.5 1.4 8 78-85 15-22 (30)
229 COG1594 RPB9 DNA-directed RNA 31.4 41 0.00088 21.4 1.8 16 11-26 20-35 (113)
230 PF01155 HypA: Hydrogenase exp 31.4 8.5 0.00019 24.3 -1.2 14 78-91 70-83 (113)
231 PLN03238 probable histone acet 31.3 49 0.0011 24.8 2.5 26 133-158 47-72 (290)
232 PF14446 Prok-RING_1: Prokaryo 31.3 64 0.0014 17.5 2.3 8 79-86 22-29 (54)
233 TIGR00627 tfb4 transcription f 31.0 41 0.0009 25.2 2.1 11 107-117 256-266 (279)
234 TIGR01384 TFS_arch transcripti 30.8 44 0.00095 20.6 1.9 36 107-145 63-101 (104)
235 KOG2636|consensus 30.8 48 0.001 26.5 2.4 23 105-127 400-423 (497)
236 PF11789 zf-Nse: Zinc-finger o 30.4 36 0.00079 18.5 1.3 13 77-89 23-35 (57)
237 PF08790 zf-LYAR: LYAR-type C2 30.3 7.7 0.00017 17.8 -1.1 9 108-116 2-10 (28)
238 PF10276 zf-CHCC: Zinc-finger 30.1 18 0.00039 18.2 0.1 11 134-144 29-39 (40)
239 PHA02998 RNA polymerase subuni 30.1 58 0.0012 22.5 2.4 14 78-91 171-184 (195)
240 PF06397 Desulfoferrod_N: Desu 29.9 22 0.00047 17.5 0.3 11 13-23 6-16 (36)
241 PF03811 Zn_Tnp_IS1: InsA N-te 29.8 18 0.00039 17.7 0.0 13 100-112 23-35 (36)
242 PLN02294 cytochrome c oxidase 29.8 28 0.0006 23.8 0.9 16 132-147 139-154 (174)
243 PF08271 TF_Zn_Ribbon: TFIIB z 29.6 39 0.00084 17.0 1.3 7 43-49 2-8 (43)
244 cd00924 Cyt_c_Oxidase_Vb Cytoc 29.3 29 0.00062 21.4 0.9 13 133-145 78-90 (97)
245 PF01927 Mut7-C: Mut7-C RNAse 29.0 36 0.00077 22.6 1.4 11 78-88 124-134 (147)
246 PF10263 SprT-like: SprT-like 29.0 21 0.00045 23.8 0.2 11 78-88 123-133 (157)
247 TIGR01562 FdhE formate dehydro 28.8 23 0.0005 26.8 0.5 12 75-86 207-218 (305)
248 PF08209 Sgf11: Sgf11 (transcr 28.8 39 0.00084 16.2 1.1 21 78-99 4-24 (33)
249 KOG3507|consensus 28.7 34 0.00074 18.8 1.0 10 106-115 37-46 (62)
250 PRK04351 hypothetical protein; 28.6 33 0.00071 23.0 1.1 11 106-116 132-142 (149)
251 PF10013 DUF2256: Uncharacteri 28.4 45 0.00098 17.0 1.3 16 15-30 10-25 (42)
252 PF05191 ADK_lid: Adenylate ki 28.3 33 0.00072 16.7 0.8 9 15-23 3-11 (36)
253 KOG0320|consensus 28.2 11 0.00023 26.0 -1.2 7 42-48 132-138 (187)
254 COG4306 Uncharacterized protei 28.1 14 0.0003 23.7 -0.6 13 79-91 69-81 (160)
255 PF00301 Rubredoxin: Rubredoxi 28.1 28 0.00061 18.2 0.6 36 107-143 2-43 (47)
256 PF09845 DUF2072: Zn-ribbon co 27.9 30 0.00066 22.5 0.8 12 135-146 2-13 (131)
257 COG2879 Uncharacterized small 27.9 73 0.0016 17.8 2.2 19 146-164 24-42 (65)
258 PF13453 zf-TFIIB: Transcripti 27.5 90 0.0019 15.4 2.5 15 80-94 21-35 (41)
259 PF07295 DUF1451: Protein of u 27.4 30 0.00064 23.1 0.8 7 107-113 113-119 (146)
260 PF11781 RRN7: RNA polymerase 27.3 39 0.00084 16.5 1.0 11 75-85 22-32 (36)
261 PF00628 PHD: PHD-finger; Int 27.2 55 0.0012 16.9 1.7 14 75-88 11-24 (51)
262 PF04606 Ogr_Delta: Ogr/Delta- 26.7 41 0.00089 17.4 1.1 6 44-49 2-7 (47)
263 COG4896 Uncharacterized protei 26.5 34 0.00073 19.0 0.7 18 15-32 4-22 (68)
264 KOG1842|consensus 26.3 40 0.00087 26.9 1.4 28 13-40 15-42 (505)
265 PF09332 Mcm10: Mcm10 replicat 26.1 16 0.00035 28.1 -0.7 37 13-49 252-293 (344)
266 PRK14892 putative transcriptio 25.9 33 0.00072 21.2 0.7 12 107-118 43-54 (99)
267 COG1998 RPS31 Ribosomal protei 25.5 48 0.001 17.6 1.2 10 106-115 37-46 (51)
268 TIGR00570 cdk7 CDK-activating 25.5 49 0.0011 25.1 1.7 11 79-89 44-54 (309)
269 cd00029 C1 Protein kinase C co 25.4 49 0.0011 16.8 1.3 7 79-85 29-35 (50)
270 COG1645 Uncharacterized Zn-fin 25.2 43 0.00093 21.9 1.2 8 42-49 29-36 (131)
271 TIGR03830 CxxCG_CxxCG_HTH puta 25.2 88 0.0019 19.8 2.7 22 77-98 30-51 (127)
272 PF06677 Auto_anti-p27: Sjogre 24.7 51 0.0011 16.7 1.2 7 43-49 19-25 (41)
273 PRK05580 primosome assembly pr 24.6 55 0.0012 28.0 2.0 21 63-87 410-430 (679)
274 PF15616 TerY-C: TerY-C metal 24.6 51 0.0011 21.6 1.4 10 106-115 105-114 (131)
275 PF06220 zf-U1: U1 zinc finger 24.2 62 0.0013 15.9 1.4 21 13-33 3-25 (38)
276 PF05129 Elf1: Transcription e 24.2 30 0.00065 20.5 0.3 8 42-49 23-30 (81)
277 PF09963 DUF2197: Uncharacteri 24.2 38 0.00081 18.5 0.6 9 134-142 31-39 (56)
278 PF14255 Cys_rich_CPXG: Cystei 24.1 39 0.00085 18.1 0.7 11 135-145 1-11 (52)
279 PF10122 Mu-like_Com: Mu-like 23.8 27 0.00058 18.6 0.0 7 43-49 6-12 (51)
280 KOG1940|consensus 23.8 1.4E+02 0.0029 22.5 3.6 19 14-33 197-215 (276)
281 smart00064 FYVE Protein presen 23.1 79 0.0017 17.5 1.9 10 80-89 12-21 (68)
282 TIGR00319 desulf_FeS4 desulfof 23.0 37 0.0008 16.1 0.4 11 13-23 7-17 (34)
283 cd00974 DSRD Desulforedoxin (D 22.9 38 0.00083 16.0 0.5 10 13-22 4-13 (34)
284 smart00249 PHD PHD zinc finger 22.7 81 0.0018 15.3 1.8 13 76-88 12-24 (47)
285 PF10083 DUF2321: Uncharacteri 22.7 75 0.0016 21.5 1.9 15 77-91 67-81 (158)
286 KOG0978|consensus 22.7 13 0.00027 31.5 -2.0 13 107-119 679-691 (698)
287 PF02591 DUF164: Putative zinc 22.6 76 0.0016 17.0 1.7 11 104-114 44-54 (56)
288 PF02150 RNA_POL_M_15KD: RNA p 22.5 27 0.00058 16.9 -0.1 8 80-87 22-29 (35)
289 PF04810 zf-Sec23_Sec24: Sec23 22.5 81 0.0018 15.6 1.7 10 77-86 23-32 (40)
290 PF11023 DUF2614: Protein of u 22.3 63 0.0014 20.5 1.4 15 107-121 86-100 (114)
291 PF14569 zf-UDP: Zinc-binding 22.0 1.8E+02 0.004 17.1 3.4 6 80-85 30-35 (80)
292 PHA02942 putative transposase; 21.9 74 0.0016 25.0 2.1 14 105-118 341-354 (383)
293 COG5112 UFD2 U1-like Zn-finger 21.1 38 0.00083 21.1 0.3 23 134-156 55-77 (126)
294 PTZ00448 hypothetical protein; 21.0 74 0.0016 24.8 1.9 24 78-101 314-337 (373)
295 KOG0782|consensus 20.8 12 0.00026 30.7 -2.3 51 93-148 240-290 (1004)
296 KOG2906|consensus 20.8 51 0.0011 20.3 0.8 15 77-91 20-34 (105)
297 PTZ00303 phosphatidylinositol 20.7 81 0.0017 27.5 2.1 9 16-24 463-471 (1374)
298 TIGR01385 TFSII transcription 20.5 1.9E+02 0.0041 22.0 3.9 13 77-89 285-297 (299)
299 COG1656 Uncharacterized conser 20.3 73 0.0016 21.8 1.6 13 107-119 131-143 (165)
300 PLN00104 MYST -like histone ac 20.2 70 0.0015 25.8 1.7 30 133-162 197-226 (450)
301 PTZ00064 histone acetyltransfe 20.2 80 0.0017 25.9 1.9 29 134-162 280-308 (552)
No 1
>KOG2462|consensus
Probab=99.96 E-value=4.9e-30 Score=179.01 Aligned_cols=134 Identities=26% Similarity=0.514 Sum_probs=120.2
Q ss_pred CccccCCCcccccCHHHHHHHHHhhhcC--Cc-ccCCCCCC-cccccccccccccccccccccccCCCCceeecCCCCCC
Q psy13443 12 QQFECDFCPYGAKQAADVHNHVQQIHMG--VN-FVCVHCKQ-FEVVPTRKTQTLEHCATCVDMVRPDASYTYMCYLCNYH 87 (188)
Q Consensus 12 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~--~~-~~C~~C~~-~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~C~~C~~~ 87 (188)
..|+|+.|++.+.+..+|.+|.|.|-.. ++ +.|..|++ +.+...++.|++. ...++.|.+||+.
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirT------------H~l~c~C~iCGKa 196 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRT------------HTLPCECGICGKA 196 (279)
T ss_pred CceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhc------------cCCCccccccccc
Confidence 4599999999999999999998544432 22 99999999 7777778888774 3568999999999
Q ss_pred CCCHHHHHHHHHhcCCCCceecccCccccCCchhHHHHHHhhcCCCCccCCCCcccccCcHHHHHHHHHh
Q psy13443 88 TPTRKYMRTHIDTHNGEKPFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYECAQGSQLMQHLRKV 157 (188)
Q Consensus 88 f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 157 (188)
|...+.|+.|+++|+|+|||.|+.|+++|...++|+.|+++|.+.++|+|..|+++|...+.|.+|.+..
T Consensus 197 FSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES~ 266 (279)
T KOG2462|consen 197 FSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSESA 266 (279)
T ss_pred ccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhhc
Confidence 9999999999999999999999999999999999999999999999999999999999999999998754
No 2
>KOG2462|consensus
Probab=99.92 E-value=1.7e-25 Score=156.32 Aligned_cols=128 Identities=25% Similarity=0.471 Sum_probs=116.1
Q ss_pred ccCCCCCC-cccccccccccccccccccccccCCCCceeecCCCCCCCCCHHHHHHHHHhcCCCCceecccCccccCCch
Q psy13443 42 FVCVHCKQ-FEVVPTRKTQTLEHCATCVDMVRPDASYTYMCYLCNYHTPTRKYMRTHIDTHNGEKPFRCALCAYSARRKT 120 (188)
Q Consensus 42 ~~C~~C~~-~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~ 120 (188)
|+|+.|++ ......+..|...+|+. +..+.+.|+.|++.|.+-..|.+|+++|+ .+..|.+||+.|.+.+
T Consensus 131 ~~c~eCgk~ysT~snLsrHkQ~H~~~-------~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPW 201 (279)
T KOG2462|consen 131 YKCPECGKSYSTSSNLSRHKQTHRSL-------DSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPW 201 (279)
T ss_pred eeccccccccccccccchhhcccccc-------cccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchH
Confidence 89999999 77777788888877766 44677899999999999999999999998 5799999999999999
Q ss_pred hHHHHHHhhcCCCCccCCCCcccccCcHHHHHHHHHhcCCCCCCCCcchhhhHHhhhh
Q psy13443 121 HLDDHMRRHTGEKPHACGMCGYECAQGSQLMQHLRKVHKVDKKGGEEEEEEEEEEEEE 178 (188)
Q Consensus 121 ~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~~~~~~~~ 178 (188)
.|+.|+|+|+|+|||.|+.|+++|..+++|..|+++|...+.|.|..+-..+.-.+-.
T Consensus 202 LLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyL 259 (279)
T KOG2462|consen 202 LLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYL 259 (279)
T ss_pred HhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999988776655543
No 3
>KOG1074|consensus
Probab=99.84 E-value=3.9e-22 Score=157.06 Aligned_cols=85 Identities=26% Similarity=0.523 Sum_probs=77.9
Q ss_pred ceeecCCCCCCCCCHHHHHHHHHhcCCCCceecccCccccCCchhHHHHHHhhcCCC----CccCC---CCcccccCcHH
Q psy13443 77 YTYMCYLCNYHTPTRKYMRTHIDTHNGEKPFRCALCAYSARRKTHLDDHMRRHTGEK----PHACG---MCGYECAQGSQ 149 (188)
Q Consensus 77 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~----~~~C~---~C~~~f~~~~~ 149 (188)
.|.+|-+|.++...++.|+.|.++|+|++||+|.+||++|.++.+|+.|+.+|.... ++.|+ +|.+.|...-.
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~ 683 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVT 683 (958)
T ss_pred CccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccccccc
Confidence 468899999999999999999999999999999999999999999999999987543 38899 99999999999
Q ss_pred HHHHHHHhcCCC
Q psy13443 150 LMQHLRKVHKVD 161 (188)
Q Consensus 150 l~~H~~~~h~~~ 161 (188)
|..|++.|.++.
T Consensus 684 lpQhIriH~~~~ 695 (958)
T KOG1074|consen 684 LPQHIRIHLGGQ 695 (958)
T ss_pred ccceEEeecCCC
Confidence 999999988543
No 4
>KOG1074|consensus
Probab=99.84 E-value=1.5e-21 Score=153.81 Aligned_cols=58 Identities=28% Similarity=0.485 Sum_probs=54.4
Q ss_pred eecccCccccCCchhHHHHHHhhcCCCCccCCCCcccccCcHHHHHHHHHhcCCCCCC
Q psy13443 107 FRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYECAQGSQLMQHLRKVHKVDKKG 164 (188)
Q Consensus 107 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~ 164 (188)
..|.+|++.|...+.|+.|+++|++++||.|.+|++.|.+...|+.|+.+|+...++.
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~s 937 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPS 937 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCc
Confidence 6899999999999999999999999999999999999999999999999998766653
No 5
>KOG3608|consensus
Probab=99.84 E-value=9.3e-22 Score=141.70 Aligned_cols=161 Identities=22% Similarity=0.450 Sum_probs=132.5
Q ss_pred ChhHHhhccCCCccccCCCcccccCHHHHHHHHHhhhcC--CcccCCCCCC-ccccccccccccc-----cccccccccc
Q psy13443 1 MLRHVRTHLAKQQFECDFCPYGAKQAADVHNHVQQIHMG--VNFVCVHCKQ-FEVVPTRKTQTLE-----HCATCVDMVR 72 (188)
Q Consensus 1 l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~--~~~~C~~C~~-~~~~~~~~~~~~~-----~c~~c~~~~~ 72 (188)
|+.|+++|++++...|+.||.-|.++..|..|+++.... .+|+|..|.+ |.....+..|... .|+.|..+..
T Consensus 195 LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~ 274 (467)
T KOG3608|consen 195 LREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCS 274 (467)
T ss_pred HHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCC
Confidence 578999999999999999999999999999998654432 3499999988 7776655555544 6777755544
Q ss_pred C------------CCCceeecCCCCCCCCCHHHHHHHHHhcCCCCceeccc--CccccCCchhHHHHHHhhc-C--CCCc
Q psy13443 73 P------------DASYTYMCYLCNYHTPTRKYMRTHIDTHNGEKPFRCAL--CAYSARRKTHLDDHMRRHT-G--EKPH 135 (188)
Q Consensus 73 ~------------~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~--C~~~~~~~~~l~~H~~~h~-~--~~~~ 135 (188)
. ..++||+|..|++.|...+.|..|+.+|. +-.|.|.. |..++.+..++..|++.++ | ..+|
T Consensus 275 ~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y 353 (467)
T KOG3608|consen 275 SASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILY 353 (467)
T ss_pred ChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCce
Confidence 3 66889999999999999999999999888 55789977 9999999999999988765 4 3459
Q ss_pred cCCCCcccccCcHHHHHHHHHhcCCCC
Q psy13443 136 ACGMCGYECAQGSQLMQHLRKVHKVDK 162 (188)
Q Consensus 136 ~C~~C~~~f~~~~~l~~H~~~~h~~~~ 162 (188)
.|-.|++.|++..+|..|+...|+-+.
T Consensus 354 ~CH~Cdr~ft~G~~L~~HL~kkH~f~~ 380 (467)
T KOG3608|consen 354 ACHCCDRFFTSGKSLSAHLMKKHGFRL 380 (467)
T ss_pred eeecchhhhccchhHHHHHHHhhcccC
Confidence 999999999999999999998887554
No 6
>KOG3623|consensus
Probab=99.82 E-value=3.2e-21 Score=150.09 Aligned_cols=82 Identities=28% Similarity=0.640 Sum_probs=77.4
Q ss_pred CCCceeecCCCCCCCCCHHHHHHHHHhcCCCCceecccCccccCCchhHHHHHHhhcCCCCccCCCCcccccCcHHHHHH
Q psy13443 74 DASYTYMCYLCNYHTPTRKYMRTHIDTHNGEKPFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYECAQGSQLMQH 153 (188)
Q Consensus 74 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H 153 (188)
+.+..|.|.+|+++|.-.+.|.+|.--|+|++||.|.+|.++|..+-.|..|+|.|.|++||+|+.|+++|...+....|
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQH 969 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQH 969 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhh
Confidence 44456999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HH
Q psy13443 154 LR 155 (188)
Q Consensus 154 ~~ 155 (188)
+.
T Consensus 970 MN 971 (1007)
T KOG3623|consen 970 MN 971 (1007)
T ss_pred hc
Confidence 84
No 7
>KOG3608|consensus
Probab=99.69 E-value=1.2e-17 Score=120.69 Aligned_cols=156 Identities=22% Similarity=0.451 Sum_probs=120.6
Q ss_pred ccc--CCCcccccCHHHHHHHHHhhhcCCcccCCCCCC-ccccccccccccc---------ccccccccccC--------
Q psy13443 14 FEC--DFCPYGAKQAADVHNHVQQIHMGVNFVCVHCKQ-FEVVPTRKTQTLE---------HCATCVDMVRP-------- 73 (188)
Q Consensus 14 ~~C--~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~-~~~~~~~~~~~~~---------~c~~c~~~~~~-------- 73 (188)
+.| ..|-+.|.++..|..|++.+.+++...|+.|+. |.....+..|.+. .|..|.+.|..
T Consensus 178 ~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv 257 (467)
T KOG3608|consen 178 TMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHV 257 (467)
T ss_pred eeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHH
Confidence 456 468899999999999995554555599999999 6665555555443 68888877776
Q ss_pred -CCCceeecCCCCCCCCCHHHHHHHHH-hcCCCCceecccCccccCCchhHHHHHHhhcCCCCccCCC--CcccccCcHH
Q psy13443 74 -DASYTYMCYLCNYHTPTRKYMRTHID-THNGEKPFRCALCAYSARRKTHLDDHMRRHTGEKPHACGM--CGYECAQGSQ 149 (188)
Q Consensus 74 -~~~~~~~C~~C~~~f~~~~~l~~H~~-~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~~ 149 (188)
.....|+|+.|+.+....++|..|++ .|...|||+|..|...+.+.+.|..|...|. +..|+|.. |.+.|.+..+
T Consensus 258 ~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q 336 (467)
T KOG3608|consen 258 VRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQ 336 (467)
T ss_pred HHhhhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHH
Confidence 33345888888888888888888887 5667888888888888888888888888886 56688887 8888888888
Q ss_pred HHHHHHHhc-C--CCCCCCCcchh
Q psy13443 150 LMQHLRKVH-K--VDKKGGEEEEE 170 (188)
Q Consensus 150 l~~H~~~~h-~--~~~~~~~~~~~ 170 (188)
|.+|++.+| + .-+|+|-.++.
T Consensus 337 ~~~H~~evhEg~np~~Y~CH~Cdr 360 (467)
T KOG3608|consen 337 MRRHFLEVHEGNNPILYACHCCDR 360 (467)
T ss_pred HHHHHHHhccCCCCCceeeecchh
Confidence 888888877 3 33467766654
No 8
>KOG3576|consensus
Probab=99.67 E-value=2.8e-17 Score=110.39 Aligned_cols=115 Identities=23% Similarity=0.528 Sum_probs=88.6
Q ss_pred CCccccCCCcccccCHHHHHHHHHhhhcCCcccCCCCCCcccccccccccccccccccccccCCCCceeecCCCCCCCCC
Q psy13443 11 KQQFECDFCPYGAKQAADVHNHVQQIHMGVNFVCVHCKQFEVVPTRKTQTLEHCATCVDMVRPDASYTYMCYLCNYHTPT 90 (188)
Q Consensus 11 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~C~~C~~~f~~ 90 (188)
...|.|.+|++.|....-|.+|+ ..|.. .+.+.|..||++|..
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~-kch~~------------------------------------vkr~lct~cgkgfnd 157 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHL-KCHSD------------------------------------VKRHLCTFCGKGFND 157 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHh-hhccH------------------------------------HHHHHHhhccCcccc
Confidence 34578888888888888888887 44432 234567778888888
Q ss_pred HHHHHHHHHhcCCCCceecccCccccCCchhHHHHHHhhcC-----------CCCccCCCCcccccCcHHHHHHHHHhcC
Q psy13443 91 RKYMRTHIDTHNGEKPFRCALCAYSARRKTHLDDHMRRHTG-----------EKPHACGMCGYECAQGSQLMQHLRKVHK 159 (188)
Q Consensus 91 ~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~-----------~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 159 (188)
...|..|+++|+|.+||+|..|+++|...-.|..|++.-+| .+-|.|..||.+-.....+..|+..+|+
T Consensus 158 tfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 158 TFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred hhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 88888888888888888888888888888888888764332 4558888898888888888888888886
Q ss_pred CCC
Q psy13443 160 VDK 162 (188)
Q Consensus 160 ~~~ 162 (188)
..+
T Consensus 238 ~Sp 240 (267)
T KOG3576|consen 238 FSP 240 (267)
T ss_pred CCH
Confidence 554
No 9
>KOG3576|consensus
Probab=99.63 E-value=5.2e-17 Score=109.09 Aligned_cols=85 Identities=28% Similarity=0.594 Sum_probs=81.5
Q ss_pred CceeecCCCCCCCCCHHHHHHHHHhcCCCCceecccCccccCCchhHHHHHHhhcCCCCccCCCCcccccCcHHHHHHHH
Q psy13443 76 SYTYMCYLCNYHTPTRKYMRTHIDTHNGEKPFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYECAQGSQLMQHLR 155 (188)
Q Consensus 76 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 155 (188)
...|.|.+|++.|....-|..|++-|...+.+-|..||+.|...-.|.+|+++|+|-+||+|..|+++|++.-.|..|++
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~ 194 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLK 194 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHH
Confidence 45699999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCC
Q psy13443 156 KVHKV 160 (188)
Q Consensus 156 ~~h~~ 160 (188)
..|+.
T Consensus 195 kvhgv 199 (267)
T KOG3576|consen 195 KVHGV 199 (267)
T ss_pred HHcCc
Confidence 99973
No 10
>KOG3623|consensus
Probab=99.62 E-value=1.4e-16 Score=124.65 Aligned_cols=111 Identities=26% Similarity=0.620 Sum_probs=92.2
Q ss_pred ccccCCCcccccCHHHHHHHHHhhhcCCcccCCCCCCcccccccccccccccccccccccCCCCceeecCCCCCCCCCHH
Q psy13443 13 QFECDFCPYGAKQAADVHNHVQQIHMGVNFVCVHCKQFEVVPTRKTQTLEHCATCVDMVRPDASYTYMCYLCNYHTPTRK 92 (188)
Q Consensus 13 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~C~~C~~~f~~~~ 92 (188)
...|+.|.+.+.....|+.|+...|... +..|.|.+|.++|..+.
T Consensus 210 lltcpycdrgykrltslkeHikyrhekn-----------------------------------e~nfsC~lCsytFAyRt 254 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKYRHEKN-----------------------------------EPNFSCMLCSYTFAYRT 254 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHHHhhC-----------------------------------CCCCcchhhhhhhhhHH
Confidence 4689999999999999999997766422 33467888888999999
Q ss_pred HHHHHHHhcCCC-------------CceecccCccccCCchhHHHHHHhhcCCCCccCCCCcccccCcHHHHHHHHHhc
Q psy13443 93 YMRTHIDTHNGE-------------KPFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYECAQGSQLMQHLRKVH 158 (188)
Q Consensus 93 ~l~~H~~~h~~~-------------~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h 158 (188)
.|.+|+.+|... +.|+|..|+++|..+-.|..|+|+|.|++||.|+.|+++|...+.+..|+....
T Consensus 255 QLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSSKK 333 (1007)
T KOG3623|consen 255 QLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSSKK 333 (1007)
T ss_pred HHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccccc
Confidence 999998877532 458999999999999999999999999999999999999999999888885443
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.26 E-value=1.3e-11 Score=96.76 Aligned_cols=128 Identities=18% Similarity=0.301 Sum_probs=80.4
Q ss_pred ccCCCcccccCHHHHHHHHHhhhcCCcccCCC--CCCcccccccccccccccccccccccCCCCceeecCCCCCCCCCHH
Q psy13443 15 ECDFCPYGAKQAADVHNHVQQIHMGVNFVCVH--CKQFEVVPTRKTQTLEHCATCVDMVRPDASYTYMCYLCNYHTPTRK 92 (188)
Q Consensus 15 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~--C~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~C~~C~~~f~~~~ 92 (188)
.|+.|..... ..+|..|. .......-.|+. |+.......+ ++.+.|+.|++.|. ..
T Consensus 409 ~C~NC~~~i~-l~~l~lHe-~~C~r~~V~Cp~~~Cg~v~~r~el-------------------~~H~~C~~Cgk~f~-~s 466 (567)
T PLN03086 409 ECRNCKHYIP-SRSIALHE-AYCSRHNVVCPHDGCGIVLRVEEA-------------------KNHVHCEKCGQAFQ-QG 466 (567)
T ss_pred ECCCCCCccc-hhHHHHHH-hhCCCcceeCCcccccceeecccc-------------------ccCccCCCCCCccc-hH
Confidence 5777776543 44555675 344444456663 6662222222 23356777777775 56
Q ss_pred HHHHHHHhcCCCCceecccCccccCCchhHHHHHHhhcCCCCccCCCCcccccC----------cHHHHHHHHHhcCCCC
Q psy13443 93 YMRTHIDTHNGEKPFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYECAQ----------GSQLMQHLRKVHKVDK 162 (188)
Q Consensus 93 ~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~----------~~~l~~H~~~~h~~~~ 162 (188)
.|..|+..++ +++.|+ |+..+ ....|..|+.+|.+.+++.|..|+..|.. ...|..|... .+.++
T Consensus 467 ~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~-CG~rt 541 (567)
T PLN03086 467 EMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESI-CGSRT 541 (567)
T ss_pred HHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHh-cCCcc
Confidence 6777777764 567777 77644 45677777777777777788888777741 2467777666 37777
Q ss_pred CCCCcch
Q psy13443 163 KGGEEEE 169 (188)
Q Consensus 163 ~~~~~~~ 169 (188)
+.|..|.
T Consensus 542 ~~C~~Cg 548 (567)
T PLN03086 542 APCDSCG 548 (567)
T ss_pred eEccccC
Confidence 7776654
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.25 E-value=4.3e-11 Score=93.94 Aligned_cols=120 Identities=18% Similarity=0.356 Sum_probs=92.0
Q ss_pred cccCC--CcccccCHHHHHHHHHhhhcCCcccCCCCCCcccccccccccccccccccccccCCCCceeecCCCCCCCCCH
Q psy13443 14 FECDF--CPYGAKQAADVHNHVQQIHMGVNFVCVHCKQFEVVPTRKTQTLEHCATCVDMVRPDASYTYMCYLCNYHTPTR 91 (188)
Q Consensus 14 ~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~C~~C~~~f~~~ 91 (188)
-.|+. |+..|. +..+..| +.|+.|++......+..|.... ..++.|+ |++.+ .+
T Consensus 434 V~Cp~~~Cg~v~~-r~el~~H---------~~C~~Cgk~f~~s~LekH~~~~------------Hkpv~Cp-Cg~~~-~R 489 (567)
T PLN03086 434 VVCPHDGCGIVLR-VEEAKNH---------VHCEKCGQAFQQGEMEKHMKVF------------HEPLQCP-CGVVL-EK 489 (567)
T ss_pred eeCCcccccceee-ccccccC---------ccCCCCCCccchHHHHHHHHhc------------CCCccCC-CCCCc-ch
Confidence 35874 888873 3334444 5899999833445566665431 2578999 99755 67
Q ss_pred HHHHHHHHhcCCCCceecccCccccC----------CchhHHHHHHhhcCCCCccCCCCcccccCcHHHHHHHHHhcC
Q psy13443 92 KYMRTHIDTHNGEKPFRCALCAYSAR----------RKTHLDDHMRRHTGEKPHACGMCGYECAQGSQLMQHLRKVHK 159 (188)
Q Consensus 92 ~~l~~H~~~h~~~~~~~C~~C~~~~~----------~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 159 (188)
..|..|+.+|...+++.|+.|+..+. ....|..|...+ |.+++.|..|++.+.. ..|..|+-..|.
T Consensus 490 ~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrl-rdm~~H~~~~h~ 565 (567)
T PLN03086 490 EQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVML-KEMDIHQIAVHQ 565 (567)
T ss_pred hHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeee-hhHHHHHHHhhc
Confidence 89999999999999999999999985 235899998885 8999999999999876 478899887774
No 13
>PHA00733 hypothetical protein
Probab=99.24 E-value=6.4e-12 Score=81.14 Aligned_cols=83 Identities=19% Similarity=0.409 Sum_probs=67.6
Q ss_pred CceeecCCCCCCCCCHHHHHHH--HH---hcCCCCceecccCccccCCchhHHHHHHhhcCCCCccCCCCcccccCcHHH
Q psy13443 76 SYTYMCYLCNYHTPTRKYMRTH--ID---THNGEKPFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYECAQGSQL 150 (188)
Q Consensus 76 ~~~~~C~~C~~~f~~~~~l~~H--~~---~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l 150 (188)
.+++.|.+|.+.|..+..|..+ +. .+.+.++|.|+.|++.|.+...|..|++.+ ..++.|+.|++.|.....|
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL 115 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDST 115 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHH
Confidence 4567788888777777666655 21 333578999999999999999999999976 4579999999999999999
Q ss_pred HHHHHHhcCC
Q psy13443 151 MQHLRKVHKV 160 (188)
Q Consensus 151 ~~H~~~~h~~ 160 (188)
..|+...|+.
T Consensus 116 ~~H~~~~h~~ 125 (128)
T PHA00733 116 LDHVCKKHNI 125 (128)
T ss_pred HHHHHHhcCc
Confidence 9999998863
No 14
>PHA00733 hypothetical protein
Probab=99.02 E-value=4.9e-10 Score=72.43 Aligned_cols=56 Identities=21% Similarity=0.412 Sum_probs=49.6
Q ss_pred CCCceeecCCCCCCCCCHHHHHHHHHhcCCCCceecccCccccCCchhHHHHHHhhcC
Q psy13443 74 DASYTYMCYLCNYHTPTRKYMRTHIDTHNGEKPFRCALCAYSARRKTHLDDHMRRHTG 131 (188)
Q Consensus 74 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~ 131 (188)
.+..+|.|+.|++.|.+...|..|++.+. .+|.|+.|++.|.....|..|+...++
T Consensus 69 ~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~--~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 69 KAVSPYVCPLCLMPFSSSVSLKQHIRYTE--HSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCCccCCCCCCcCCCHHHHHHHHhcCC--cCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 34678999999999999999999999773 569999999999999999999987654
No 15
>PHA02768 hypothetical protein; Provisional
Probab=99.00 E-value=1.8e-10 Score=61.92 Aligned_cols=39 Identities=15% Similarity=0.418 Sum_probs=19.0
Q ss_pred eecccCccccCCchhHHHHHHhhcCCCCccCCCCcccccCc
Q psy13443 107 FRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYECAQG 147 (188)
Q Consensus 107 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 147 (188)
|.|+.||+.|.....|..|+++|. +|++|..|++.|...
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~ 44 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRT 44 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccc
Confidence 445555555555555555555544 344555555544433
No 16
>PHA02768 hypothetical protein; Provisional
Probab=98.91 E-value=7.5e-10 Score=59.49 Aligned_cols=43 Identities=28% Similarity=0.453 Sum_probs=39.4
Q ss_pred eeecCCCCCCCCCHHHHHHHHHhcCCCCceecccCccccCCchhH
Q psy13443 78 TYMCYLCNYHTPTRKYMRTHIDTHNGEKPFRCALCAYSARRKTHL 122 (188)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l 122 (188)
.|.|+.||+.|...+.|..|+++|+ +++.|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 4899999999999999999999999 689999999999877655
No 17
>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=98.81 E-value=1.6e-09 Score=49.89 Aligned_cols=25 Identities=28% Similarity=0.756 Sum_probs=22.7
Q ss_pred ChhHHhhccCCCccccCCCcccccC
Q psy13443 1 MLRHVRTHLAKQQFECDFCPYGAKQ 25 (188)
Q Consensus 1 l~~h~~~h~~~~~~~C~~C~~~f~~ 25 (188)
|..|+++|++++||.|+.|+++|..
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEESS
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 5789999999999999999999863
No 18
>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=98.80 E-value=3.5e-09 Score=48.74 Aligned_cols=24 Identities=54% Similarity=0.989 Sum_probs=15.4
Q ss_pred HHHHHHhhcCCCCccCCCCccccc
Q psy13443 122 LDDHMRRHTGEKPHACGMCGYECA 145 (188)
Q Consensus 122 l~~H~~~h~~~~~~~C~~C~~~f~ 145 (188)
|..|+++|++++||.|+.|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 556666666666666666666664
No 19
>PHA00616 hypothetical protein
Probab=98.65 E-value=1.4e-08 Score=51.98 Aligned_cols=33 Identities=30% Similarity=0.397 Sum_probs=24.7
Q ss_pred CccCCCCcccccCcHHHHHHHHHhcCCCCCCCC
Q psy13443 134 PHACGMCGYECAQGSQLMQHLRKVHKVDKKGGE 166 (188)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~~ 166 (188)
||+|+.||+.|...+.|..|++.+|+.+++.++
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 577777777777777777777777777776654
No 20
>KOG3993|consensus
Probab=98.54 E-value=2.5e-08 Score=74.63 Aligned_cols=86 Identities=19% Similarity=0.236 Sum_probs=57.8
Q ss_pred CceeecCCCCCCCCCHHHHHHHHHhcCCCC----------------------------------------------ceec
Q psy13443 76 SYTYMCYLCNYHTPTRKYMRTHIDTHNGEK----------------------------------------------PFRC 109 (188)
Q Consensus 76 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~----------------------------------------------~~~C 109 (188)
+.-|.|..|++.|+....|..|+.+|...- ...+
T Consensus 354 ~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~sael~~p 433 (500)
T KOG3993|consen 354 SGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGSAELELP 433 (500)
T ss_pred CceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeeccccccCC
Confidence 346999999999999999999987765320 0123
Q ss_pred ccCccccCCchhHHHHHHhhcCCCCccCCCCcccccCcHHHHHHHHHhcCCC
Q psy13443 110 ALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYECAQGSQLMQHLRKVHKVD 161 (188)
Q Consensus 110 ~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 161 (188)
+.++..+.++..--.+.+.-.....|.|.+|.-+|.+...|.+|+...|..+
T Consensus 434 p~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~Hpse 485 (500)
T KOG3993|consen 434 PYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCHPSE 485 (500)
T ss_pred CCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcChHH
Confidence 3444444333332222222222344889999999999999999998888543
No 21
>KOG3993|consensus
Probab=98.50 E-value=1.8e-08 Score=75.40 Aligned_cols=86 Identities=20% Similarity=0.339 Sum_probs=65.7
Q ss_pred eecCCCCCCCCCHHHHHHHHHhcCCCCceecccCccccCCchhHHHHHHhhcC---------------------------
Q psy13443 79 YMCYLCNYHTPTRKYMRTHIDTHNGEKPFRCALCAYSARRKTHLDDHMRRHTG--------------------------- 131 (188)
Q Consensus 79 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~--------------------------- 131 (188)
|.|.+|...|.....|.+|.-.--...-|+|+.|++.|+..++|..|.|.|..
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~r 347 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAER 347 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccc
Confidence 78888888888888888886321111238888888888888888888887741
Q ss_pred ------CCCccCCCCcccccCcHHHHHHHHHhcCCCCCC
Q psy13443 132 ------EKPHACGMCGYECAQGSQLMQHLRKVHKVDKKG 164 (188)
Q Consensus 132 ------~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~ 164 (188)
+.-|.|.+|++.|.....|.+|+-+|+.....+
T Consensus 348 sg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k 386 (500)
T KOG3993|consen 348 SGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAK 386 (500)
T ss_pred cCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccch
Confidence 123899999999999999999999998654433
No 22
>PHA00616 hypothetical protein
Probab=98.50 E-value=4.3e-08 Score=50.19 Aligned_cols=33 Identities=15% Similarity=0.275 Sum_probs=21.5
Q ss_pred eeecCCCCCCCCCHHHHHHHHHhcCCCCceecc
Q psy13443 78 TYMCYLCNYHTPTRKYMRTHIDTHNGEKPFRCA 110 (188)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~ 110 (188)
||+|+.||+.|...+.|..|++.|++++++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 356666666666666666666666666666554
No 23
>PHA00732 hypothetical protein
Probab=98.37 E-value=2.4e-07 Score=54.49 Aligned_cols=46 Identities=26% Similarity=0.604 Sum_probs=34.1
Q ss_pred eeecCCCCCCCCCHHHHHHHHHh-cCCCCceecccCccccCCchhHHHHHHhh
Q psy13443 78 TYMCYLCNYHTPTRKYMRTHIDT-HNGEKPFRCALCAYSARRKTHLDDHMRRH 129 (188)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~C~~C~~~~~~~~~l~~H~~~h 129 (188)
||.|..|++.|.+...|..|++. |. ++.|+.|++.|. .+..|..++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhccc
Confidence 47788888888888888888874 44 357888888887 356676554
No 24
>PHA00732 hypothetical protein
Probab=98.25 E-value=1.1e-06 Score=51.81 Aligned_cols=47 Identities=30% Similarity=0.627 Sum_probs=39.3
Q ss_pred ceecccCccccCCchhHHHHHHh-hcCCCCccCCCCcccccCcHHHHHHHHHhc
Q psy13443 106 PFRCALCAYSARRKTHLDDHMRR-HTGEKPHACGMCGYECAQGSQLMQHLRKVH 158 (188)
Q Consensus 106 ~~~C~~C~~~~~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h 158 (188)
||.|..|++.|.+...|..|++. |. ++.|+.|++.|. .|..|.+++-
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---ChhhhhcccC
Confidence 58899999999999999999985 54 368999999997 4788885543
No 25
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.15 E-value=4.9e-06 Score=45.47 Aligned_cols=49 Identities=27% Similarity=0.622 Sum_probs=20.9
Q ss_pred eecccCccccCCchhHHHHHHh-hcC-CCCccCCCCcccccCcHHHHHHHHHhc
Q psy13443 107 FRCALCAYSARRKTHLDDHMRR-HTG-EKPHACGMCGYECAQGSQLMQHLRKVH 158 (188)
Q Consensus 107 ~~C~~C~~~~~~~~~l~~H~~~-h~~-~~~~~C~~C~~~f~~~~~l~~H~~~~h 158 (188)
|.||.|++ ..+...|..|... |.. .+.+.|++|...+. ..|..|+...|
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 44555554 2333444444433 222 12345555554322 24555555444
No 26
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.14 E-value=6e-06 Score=45.11 Aligned_cols=50 Identities=18% Similarity=0.472 Sum_probs=38.7
Q ss_pred eeecCCCCCCCCCHHHHHHHHHh-cCC-CCceecccCccccCCchhHHHHHHhhc
Q psy13443 78 TYMCYLCNYHTPTRKYMRTHIDT-HNG-EKPFRCALCAYSARRKTHLDDHMRRHT 130 (188)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H~~~-h~~-~~~~~C~~C~~~~~~~~~l~~H~~~h~ 130 (188)
.|.|+.|++. .+...|..|... |.. .+.+.||+|...+. .+|..|+...+
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 4789999994 557789999774 443 35799999998655 48899988765
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.00 E-value=4.1e-06 Score=37.18 Aligned_cols=22 Identities=32% Similarity=0.736 Sum_probs=15.2
Q ss_pred ccCCCCcccccCcHHHHHHHHH
Q psy13443 135 HACGMCGYECAQGSQLMQHLRK 156 (188)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~~ 156 (188)
|.|+.|++.|.+...|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 4567777777777777777665
No 28
>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=98.00 E-value=5e-06 Score=37.17 Aligned_cols=24 Identities=38% Similarity=0.729 Sum_probs=17.3
Q ss_pred ccCCCCcccccCcHHHHHHHHHhc
Q psy13443 135 HACGMCGYECAQGSQLMQHLRKVH 158 (188)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~~~h 158 (188)
|.|++|++.|.+...|..|++.+|
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 568888888888888888887765
No 29
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.95 E-value=5.4e-06 Score=36.80 Aligned_cols=22 Identities=18% Similarity=0.631 Sum_probs=12.5
Q ss_pred eecCCCCCCCCCHHHHHHHHHh
Q psy13443 79 YMCYLCNYHTPTRKYMRTHIDT 100 (188)
Q Consensus 79 ~~C~~C~~~f~~~~~l~~H~~~ 100 (188)
|.|+.|++.|.....|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 4555555555555555555554
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.90 E-value=7.7e-06 Score=50.64 Aligned_cols=73 Identities=15% Similarity=0.309 Sum_probs=21.8
Q ss_pred ecCCCCCCCCCHHHHHHHHHhcCCCCceecccCccccCCchhHHHHHHhhcCCCCccCCCCcccccCcHHHHHHHHHh
Q psy13443 80 MCYLCNYHTPTRKYMRTHIDTHNGEKPFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYECAQGSQLMQHLRKV 157 (188)
Q Consensus 80 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 157 (188)
+|..|+..|.+...|..|+...++-.. + ....+.....+..+.+... ...+.|..|+..|.+...|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~---~-~~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDI---P-DQKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -----------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Ccccccccccccccccccccccccccc---c-ccccccccccccccccccc-CCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 489999999999999999975554321 1 1112223334444443322 23689999999999999999999875
No 31
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.79 E-value=5.9e-06 Score=60.10 Aligned_cols=52 Identities=25% Similarity=0.547 Sum_probs=42.2
Q ss_pred CCceeccc--CccccCCchhHHHHHHhhc-------------------CCCCccCCCCcccccCcHHHHHHHH
Q psy13443 104 EKPFRCAL--CAYSARRKTHLDDHMRRHT-------------------GEKPHACGMCGYECAQGSQLMQHLR 155 (188)
Q Consensus 104 ~~~~~C~~--C~~~~~~~~~l~~H~~~h~-------------------~~~~~~C~~C~~~f~~~~~l~~H~~ 155 (188)
+|||.|++ |.+.|.....|..|+..-+ ..+||+|.+|++.++.-..|+.|..
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 37888877 8888888888888876422 3589999999999999999998864
No 32
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.75 E-value=2.8e-05 Score=34.61 Aligned_cols=24 Identities=21% Similarity=0.677 Sum_probs=19.5
Q ss_pred cccCCCcccccCHHHHHHHHHhhh
Q psy13443 14 FECDFCPYGAKQAADVHNHVQQIH 37 (188)
Q Consensus 14 ~~C~~C~~~f~~~~~l~~H~~~~~ 37 (188)
|.|++|++.|.+...|..|+..+|
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 689999999999999999996553
No 33
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.74 E-value=1.3e-05 Score=37.07 Aligned_cols=25 Identities=32% Similarity=0.541 Sum_probs=14.1
Q ss_pred CccCCCCcccccCcHHHHHHHHHhc
Q psy13443 134 PHACGMCGYECAQGSQLMQHLRKVH 158 (188)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~~h 158 (188)
||.|..|++.|.+...|..|++.|+
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 3555556666666666666655443
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=97.68 E-value=2.8e-05 Score=35.90 Aligned_cols=25 Identities=24% Similarity=0.438 Sum_probs=22.0
Q ss_pred ccccCCCcccccCHHHHHHHHHhhh
Q psy13443 13 QFECDFCPYGAKQAADVHNHVQQIH 37 (188)
Q Consensus 13 ~~~C~~C~~~f~~~~~l~~H~~~~~ 37 (188)
||.|..|++.|.+...|..|++.++
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 6899999999999999999985443
No 35
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.55 E-value=6.8e-05 Score=46.31 Aligned_cols=73 Identities=16% Similarity=0.243 Sum_probs=16.3
Q ss_pred ccCCCcccccCHHHHHHHHHhhhcCCcccCCCCCCcccccccccccccccccccccccCCCCceeecCCCCCCCCCHHHH
Q psy13443 15 ECDFCPYGAKQAADVHNHVQQIHMGVNFVCVHCKQFEVVPTRKTQTLEHCATCVDMVRPDASYTYMCYLCNYHTPTRKYM 94 (188)
Q Consensus 15 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~C~~C~~~f~~~~~l 94 (188)
.|..|+..|.+...|..|+...|+-.. +....+.....+...... .....+.|..|++.|.+...|
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~---~~~~~l~~~~~~~~~~~~-----------~~~~~~~C~~C~~~f~s~~~l 66 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDI---PDQKYLVDPNRLLNYLRK-----------KVKESFRCPYCNKTFRSREAL 66 (100)
T ss_dssp --------------------------------------------------------------SSEEBSSSS-EESSHHHH
T ss_pred Ccccccccccccccccccccccccccc---cccccccccccccccccc-----------ccCCCCCCCccCCCCcCHHHH
Confidence 489999999999999999977775321 100011111111111100 111246677777777777777
Q ss_pred HHHHHhc
Q psy13443 95 RTHIDTH 101 (188)
Q Consensus 95 ~~H~~~h 101 (188)
..|++.+
T Consensus 67 ~~Hm~~~ 73 (100)
T PF12756_consen 67 QEHMRSK 73 (100)
T ss_dssp HHHHHHT
T ss_pred HHHHcCc
Confidence 7777654
No 36
>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=97.36 E-value=0.00021 Score=37.54 Aligned_cols=31 Identities=32% Similarity=0.558 Sum_probs=17.6
Q ss_pred CCCccCCCCcccccCcHHHHHHHHHhcCCCC
Q psy13443 132 EKPHACGMCGYECAQGSQLMQHLRKVHKVDK 162 (188)
Q Consensus 132 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 162 (188)
+.|-.|++|+..+.+..+|.+|++..|+.+|
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 4556777777777777777777777776654
No 37
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.32 E-value=0.00019 Score=32.05 Aligned_cols=24 Identities=33% Similarity=0.711 Sum_probs=16.2
Q ss_pred ccCCCCcccccCcHHHHHHHHHhcC
Q psy13443 135 HACGMCGYECAQGSQLMQHLRKVHK 159 (188)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~~~h~ 159 (188)
|+|+.|++... ...|..|++.+|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 56777877776 7778888777764
No 38
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.23 E-value=0.0001 Score=53.82 Aligned_cols=52 Identities=23% Similarity=0.537 Sum_probs=43.7
Q ss_pred CceeecCC--CCCCCCCHHHHHHHHHhcC-------------------CCCceecccCccccCCchhHHHHHH
Q psy13443 76 SYTYMCYL--CNYHTPTRKYMRTHIDTHN-------------------GEKPFRCALCAYSARRKTHLDDHMR 127 (188)
Q Consensus 76 ~~~~~C~~--C~~~f~~~~~l~~H~~~h~-------------------~~~~~~C~~C~~~~~~~~~l~~H~~ 127 (188)
.+||.|++ |++.+.....|+-|+.--+ ..|||+|++|++.|.....|..|..
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 48999976 9999999999999985322 1279999999999999999988864
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.21 E-value=0.00036 Score=31.40 Aligned_cols=23 Identities=30% Similarity=0.508 Sum_probs=19.2
Q ss_pred ccCCCCcccccCcHHHHHHHHHh
Q psy13443 135 HACGMCGYECAQGSQLMQHLRKV 157 (188)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~~~ 157 (188)
|.|..|++.|.+...|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 57888999999999999998744
No 40
>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=97.17 E-value=0.00048 Score=36.23 Aligned_cols=37 Identities=16% Similarity=0.337 Sum_probs=24.5
Q ss_pred HhhccC-CCccccCCCcccccCHHHHHHHHHhhhcCCc
Q psy13443 5 VRTHLA-KQQFECDFCPYGAKQAADVHNHVQQIHMGVN 41 (188)
Q Consensus 5 ~~~h~~-~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~ 41 (188)
.+++.. +.|-.|++|+..+....+|.+|+...|..+|
T Consensus 15 ~k~~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 15 PKSKSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp -CCCCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred HHHhhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 333433 5689999999999999999999988887654
No 41
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.05 E-value=0.00067 Score=30.45 Aligned_cols=22 Identities=23% Similarity=0.502 Sum_probs=14.0
Q ss_pred ecCCCCCCCCCHHHHHHHHHhc
Q psy13443 80 MCYLCNYHTPTRKYMRTHIDTH 101 (188)
Q Consensus 80 ~C~~C~~~f~~~~~l~~H~~~h 101 (188)
.|..|++.|.....|..|++.|
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHHh
Confidence 4666666666666666666644
No 42
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.98 E-value=0.00086 Score=29.83 Aligned_cols=24 Identities=21% Similarity=0.772 Sum_probs=19.0
Q ss_pred cccCCCcccccCHHHHHHHHHhhhc
Q psy13443 14 FECDFCPYGAKQAADVHNHVQQIHM 38 (188)
Q Consensus 14 ~~C~~C~~~f~~~~~l~~H~~~~~~ 38 (188)
|.|+.|+.... ...|..|++.+|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 68999999988 9999999977663
No 43
>PRK04860 hypothetical protein; Provisional
Probab=96.92 E-value=0.00078 Score=45.33 Aligned_cols=37 Identities=30% Similarity=0.617 Sum_probs=22.3
Q ss_pred ceecccCccccCCchhHHHHHHhhcCCCCccCCCCcccccC
Q psy13443 106 PFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYECAQ 146 (188)
Q Consensus 106 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 146 (188)
+|.|. |+. ....+..|.+++.++++|.|..|+..|..
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEE
Confidence 46665 655 44555666666666666666666665543
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.85 E-value=0.00083 Score=30.16 Aligned_cols=21 Identities=24% Similarity=0.651 Sum_probs=19.6
Q ss_pred cccCCCcccccCHHHHHHHHH
Q psy13443 14 FECDFCPYGAKQAADVHNHVQ 34 (188)
Q Consensus 14 ~~C~~C~~~f~~~~~l~~H~~ 34 (188)
|.|.+|++.|.+...|..|++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 689999999999999999984
No 45
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.82 E-value=0.00072 Score=30.38 Aligned_cols=21 Identities=24% Similarity=0.705 Sum_probs=12.2
Q ss_pred eecCCCCCCCCCHHHHHHHHH
Q psy13443 79 YMCYLCNYHTPTRKYMRTHID 99 (188)
Q Consensus 79 ~~C~~C~~~f~~~~~l~~H~~ 99 (188)
|.|.+|+..|.+...|.+|++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 345666666666666666654
No 46
>PRK04860 hypothetical protein; Provisional
Probab=96.67 E-value=0.0014 Score=44.04 Aligned_cols=41 Identities=27% Similarity=0.563 Sum_probs=35.1
Q ss_pred CceeecCCCCCCCCCHHHHHHHHHhcCCCCceecccCccccCCch
Q psy13443 76 SYTYMCYLCNYHTPTRKYMRTHIDTHNGEKPFRCALCAYSARRKT 120 (188)
Q Consensus 76 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~ 120 (188)
..+|.|. |+. ....+..|.++++++++|.|..|+..|....
T Consensus 117 ~~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 117 TFPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 3579998 997 6678899999999999999999999887543
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=95.83 E-value=0.002 Score=29.59 Aligned_cols=21 Identities=29% Similarity=0.564 Sum_probs=14.0
Q ss_pred ccCCCCcccccCcHHHHHHHH
Q psy13443 135 HACGMCGYECAQGSQLMQHLR 155 (188)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~ 155 (188)
|.|..|++.|.+...|..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 456677777777777766654
No 48
>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=95.73 E-value=0.0033 Score=28.80 Aligned_cols=22 Identities=14% Similarity=0.561 Sum_probs=15.1
Q ss_pred eecCCCCCCCCCHHHHHHHHHh
Q psy13443 79 YMCYLCNYHTPTRKYMRTHIDT 100 (188)
Q Consensus 79 ~~C~~C~~~f~~~~~l~~H~~~ 100 (188)
|.|..|++.|.+...+.+|+++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 5577777777777777776653
No 49
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.44 E-value=0.017 Score=25.96 Aligned_cols=21 Identities=24% Similarity=0.569 Sum_probs=14.5
Q ss_pred ccCCCCcccccCcHHHHHHHHH
Q psy13443 135 HACGMCGYECAQGSQLMQHLRK 156 (188)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~~ 156 (188)
..|+.|++.| ....|..|+..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4677788887 55677777653
No 50
>KOG1146|consensus
Probab=95.30 E-value=0.0033 Score=54.47 Aligned_cols=81 Identities=23% Similarity=0.374 Sum_probs=53.6
Q ss_pred ccCCCccccCCCcccccCHHHHHHHHHhhhcCCcccCCCCCCcccccccccccccccccccccccCCCCceeecCCCCCC
Q psy13443 8 HLAKQQFECDFCPYGAKQAADVHNHVQQIHMGVNFVCVHCKQFEVVPTRKTQTLEHCATCVDMVRPDASYTYMCYLCNYH 87 (188)
Q Consensus 8 h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~C~~C~~~ 87 (188)
++..+.|+|+.|+..|+....|..|++..|.+-.- ..|.. ... ++..-+..+...+-++|.|..|..+
T Consensus 460 ~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~--~~c~~------gq~----~~~~arg~~~~~~~~p~~C~~C~~s 527 (1406)
T KOG1146|consen 460 HSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS--AYCKA------GQN----HPRLARGEVYRCPGKPYPCRACNYS 527 (1406)
T ss_pred ecccccccCCccchhhhhHHHhhhcccccccccch--hHhHh------ccc----cccccccccccCCCCcccceeeeee
Confidence 45557899999999999999999999766643221 22211 000 1111111222245578999999999
Q ss_pred CCCHHHHHHHHHh
Q psy13443 88 TPTRKYMRTHIDT 100 (188)
Q Consensus 88 f~~~~~l~~H~~~ 100 (188)
+.....|..|+.+
T Consensus 528 tttng~LsihlqS 540 (1406)
T KOG1146|consen 528 TTTNGNLSIHLQS 540 (1406)
T ss_pred eecchHHHHHHHH
Confidence 9999999999863
No 51
>KOG2231|consensus
Probab=95.17 E-value=0.044 Score=44.93 Aligned_cols=103 Identities=18% Similarity=0.335 Sum_probs=61.9
Q ss_pred cCCCcccccCHHHHHHHHHhhhcCCcccCCCCCC----ccc------ccccccccccccccccccccCCCCceeecCCCC
Q psy13443 16 CDFCPYGAKQAADVHNHVQQIHMGVNFVCVHCKQ----FEV------VPTRKTQTLEHCATCVDMVRPDASYTYMCYLCN 85 (188)
Q Consensus 16 C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~----~~~------~~~~~~~~~~~c~~c~~~~~~~~~~~~~C~~C~ 85 (188)
|.+| ..|.....|..|+...|.. +.|..|-. |+. ...++.|+..-++ +...+. + --.|..|.
T Consensus 118 ~~~c-~~~~s~~~Lk~H~~~~H~~--~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~-d~~s~r--G--hp~C~~C~ 189 (669)
T KOG2231|consen 118 CLHC-TEFKSVENLKNHMRDQHKL--HLCSLCLQNLKIFINERKLYTRAELNLHLMFGDP-DDESCR--G--HPLCKFCH 189 (669)
T ss_pred Cccc-cchhHHHHHHHHHHHhhhh--hccccccccceeeeeeeehehHHHHHHHHhcCCC-cccccc--C--Cccchhhh
Confidence 4444 4445889999999666643 56777732 322 2223333332222 111111 1 24688899
Q ss_pred CCCCCHHHHHHHHHhcCCCCceecccC------ccccCCchhHHHHHHhhc
Q psy13443 86 YHTPTRKYMRTHIDTHNGEKPFRCALC------AYSARRKTHLDDHMRRHT 130 (188)
Q Consensus 86 ~~f~~~~~l~~H~~~h~~~~~~~C~~C------~~~~~~~~~l~~H~~~h~ 130 (188)
..|.....|..|++.++ |.|..| +..|.....|..|.+.++
T Consensus 190 ~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 190 ERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred hhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcC
Confidence 99999999999988765 555555 345677788888877654
No 52
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=94.94 E-value=0.026 Score=27.38 Aligned_cols=23 Identities=22% Similarity=0.521 Sum_probs=20.5
Q ss_pred CccccCCCcccccCHHHHHHHHH
Q psy13443 12 QQFECDFCPYGAKQAADVHNHVQ 34 (188)
Q Consensus 12 ~~~~C~~C~~~f~~~~~l~~H~~ 34 (188)
.+|.|..|+..|.+...+..|++
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHC
Confidence 36899999999999999999984
No 53
>KOG1146|consensus
Probab=94.80 E-value=0.011 Score=51.31 Aligned_cols=56 Identities=29% Similarity=0.564 Sum_probs=43.6
Q ss_pred cCCCCceecccCccccCCchhHHHHHHhhc-------------------------CCCCccCCCCcccccCcHHHHHHHH
Q psy13443 101 HNGEKPFRCALCAYSARRKTHLDDHMRRHT-------------------------GEKPHACGMCGYECAQGSQLMQHLR 155 (188)
Q Consensus 101 h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~-------------------------~~~~~~C~~C~~~f~~~~~l~~H~~ 155 (188)
+...+.+.|+.|+..|.....|..|+|..+ +.++|.|..|...+.....|..|+.
T Consensus 460 ~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 460 HSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred ecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHH
Confidence 334466778888888888777777777621 3467999999999999999999986
Q ss_pred H
Q psy13443 156 K 156 (188)
Q Consensus 156 ~ 156 (188)
.
T Consensus 540 S 540 (1406)
T KOG1146|consen 540 S 540 (1406)
T ss_pred H
Confidence 4
No 54
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.72 E-value=0.095 Score=39.35 Aligned_cols=134 Identities=19% Similarity=0.363 Sum_probs=83.0
Q ss_pred ccccCC--CcccccCHHHHHHHHHhhhcCCcccCCCCC--C--ccc------ccccccccccccccccccccCCCCceee
Q psy13443 13 QFECDF--CPYGAKQAADVHNHVQQIHMGVNFVCVHCK--Q--FEV------VPTRKTQTLEHCATCVDMVRPDASYTYM 80 (188)
Q Consensus 13 ~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~--~--~~~------~~~~~~~~~~~c~~c~~~~~~~~~~~~~ 80 (188)
.|.|+. |..+...+..|+.|....|. .+.|..|- + |.. ...++.|...- .-+.+| +.--.
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~--~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G--~~e~GF----KGHP~ 222 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHG--FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGG--LEEEGF----KGHPL 222 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcC--cEEhHhhhcCcccCccceeeeecccccccccCC--ccccCc----CCCch
Confidence 367764 77777778899999865554 36788882 2 332 23333333210 000011 11236
Q ss_pred cCCCCCCCCCHHHHHHHHHhcCCCCceecccCc----cccCCchhHHHHHHhhcCCCCccCCC--Cc----ccccCcHHH
Q psy13443 81 CYLCNYHTPTRKYMRTHIDTHNGEKPFRCALCA----YSARRKTHLDDHMRRHTGEKPHACGM--CG----YECAQGSQL 150 (188)
Q Consensus 81 C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~----~~~~~~~~l~~H~~~h~~~~~~~C~~--C~----~~f~~~~~l 150 (188)
|..|...|.+...|..|.+.-+. +-|.|..-+ .-|.+..+|..|.+.- -|.|.. |. ..|.....|
T Consensus 223 C~FC~~~FYdDDEL~~HcR~~HE-~ChICD~v~p~~~QYFK~Y~~Le~HF~~~----hy~ct~qtc~~~k~~vf~~~~el 297 (493)
T COG5236 223 CIFCKIYFYDDDELRRHCRLRHE-ACHICDMVGPIRYQYFKSYEDLEAHFRNA----HYCCTFQTCRVGKCYVFPYHTEL 297 (493)
T ss_pred hhhccceecChHHHHHHHHhhhh-hhhhhhccCccchhhhhCHHHHHHHhhcC----ceEEEEEEEecCcEEEeccHHHH
Confidence 99999999999999999985442 234443322 3367777888776542 356543 32 568899999
Q ss_pred HHHHHHhcC
Q psy13443 151 MQHLRKVHK 159 (188)
Q Consensus 151 ~~H~~~~h~ 159 (188)
..|+-..|+
T Consensus 298 ~~h~~~~h~ 306 (493)
T COG5236 298 LEHLTRFHK 306 (493)
T ss_pred HHHHHHHhh
Confidence 999988885
No 55
>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=94.62 E-value=0.088 Score=33.11 Aligned_cols=83 Identities=18% Similarity=0.300 Sum_probs=47.0
Q ss_pred CceeecCCCCCCCCCHHHHHHHHHhcCCCC-ceecccCccccCCchhH-HH--HHHh-hcC---------CCCccC----
Q psy13443 76 SYTYMCYLCNYHTPTRKYMRTHIDTHNGEK-PFRCALCAYSARRKTHL-DD--HMRR-HTG---------EKPHAC---- 137 (188)
Q Consensus 76 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~-~~~C~~C~~~~~~~~~l-~~--H~~~-h~~---------~~~~~C---- 137 (188)
-+...|..|..+... +.+..|++..+... ...-..-...+.....+ .. .... ..+ -..|.|
T Consensus 9 ~~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gLp~~~G~~C~~~~ 87 (109)
T PF12013_consen 9 YRVLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGLPVYDGYRCQCDP 87 (109)
T ss_pred CCEEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCCCCCCCCeeeecCC
Confidence 345789999988776 88999998443221 11000000000000000 00 0000 000 122899
Q ss_pred CCCcccccCcHHHHHHHHHhcC
Q psy13443 138 GMCGYECAQGSQLMQHLRKVHK 159 (188)
Q Consensus 138 ~~C~~~f~~~~~l~~H~~~~h~ 159 (188)
..|++.+.+...|.+|++.+|+
T Consensus 88 ~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 88 PHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCCcEeccHHHHHHHHHHhcC
Confidence 9999999999999999999885
No 56
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=94.56 E-value=0.016 Score=31.04 Aligned_cols=34 Identities=24% Similarity=0.372 Sum_probs=29.0
Q ss_pred HhhccCCCccccCCCcccccCHHHHHHHHHhhhc
Q psy13443 5 VRTHLAKQQFECDFCPYGAKQAADVHNHVQQIHM 38 (188)
Q Consensus 5 ~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 38 (188)
+++.-|+..+.|+-|+..|.+..+..+|....|+
T Consensus 9 v~~RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 9 VRDRDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred eeccCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 3455678889999999999999999999987775
No 57
>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=94.56 E-value=0.031 Score=26.94 Aligned_cols=24 Identities=29% Similarity=0.919 Sum_probs=13.0
Q ss_pred eecccCccccCCchhHHHHHHhhcCCCCccCCCCcc
Q psy13443 107 FRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGY 142 (188)
Q Consensus 107 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 142 (188)
|.|.+||..+.... .++.|+.|+.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 45666665554322 4556666654
No 58
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.53 E-value=0.078 Score=33.29 Aligned_cols=24 Identities=21% Similarity=0.314 Sum_probs=14.5
Q ss_pred ceecccCccccCCchhHHHHHHhh
Q psy13443 106 PFRCALCAYSARRKTHLDDHMRRH 129 (188)
Q Consensus 106 ~~~C~~C~~~~~~~~~l~~H~~~h 129 (188)
.|+|+.|...|-..=++-.|..+|
T Consensus 81 ~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 81 RYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred ceeCCCCCCccccccchhhhhhcc
Confidence 466666666666655555555555
No 59
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=94.38 E-value=0.062 Score=29.34 Aligned_cols=46 Identities=20% Similarity=0.507 Sum_probs=23.0
Q ss_pred cccccccc-cCCCCceeecCCCCCCCCCHHHHHHHHHhcCCCCceecccCcc
Q psy13443 64 CATCVDMV-RPDASYTYMCYLCNYHTPTRKYMRTHIDTHNGEKPFRCALCAY 114 (188)
Q Consensus 64 c~~c~~~~-~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 114 (188)
|..|+..+ .......|.|+.||.....+...- +. ...+|+|+.||+
T Consensus 12 CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~C---Rk--~g~~Y~Cp~CGF 58 (61)
T COG2888 12 CTSCGREIAPGETAVKFPCPNCGEVEIYRCAKC---RK--LGNPYRCPKCGF 58 (61)
T ss_pred eccCCCEeccCCceeEeeCCCCCceeeehhhhH---HH--cCCceECCCcCc
Confidence 33444444 223344577888886554433211 11 124677777774
No 60
>KOG2785|consensus
Probab=94.36 E-value=0.17 Score=38.54 Aligned_cols=57 Identities=18% Similarity=0.248 Sum_probs=44.0
Q ss_pred eecccCccccCCchhHHHHHHhhcCC-----------------------CCccCCCCc---ccccCcHHHHHHHHH-hcC
Q psy13443 107 FRCALCAYSARRKTHLDDHMRRHTGE-----------------------KPHACGMCG---YECAQGSQLMQHLRK-VHK 159 (188)
Q Consensus 107 ~~C~~C~~~~~~~~~l~~H~~~h~~~-----------------------~~~~C~~C~---~~f~~~~~l~~H~~~-~h~ 159 (188)
-.|..|+..+.+......||..++|- .-+.|-.|. +.|.+-...+.|+.. -|.
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K~HC 246 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDKGHC 246 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhccCc
Confidence 45788999999999999999877641 226788888 999999999999964 444
Q ss_pred CCCC
Q psy13443 160 VDKK 163 (188)
Q Consensus 160 ~~~~ 163 (188)
.-+|
T Consensus 247 kl~y 250 (390)
T KOG2785|consen 247 KLPY 250 (390)
T ss_pred ccCC
Confidence 4444
No 61
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=94.30 E-value=0.048 Score=26.41 Aligned_cols=22 Identities=23% Similarity=0.566 Sum_probs=17.2
Q ss_pred eeecCCCCCCCCCHHHHHHHHH
Q psy13443 78 TYMCYLCNYHTPTRKYMRTHID 99 (188)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H~~ 99 (188)
+|.|.+|+..|.+...+.+|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4678888888888888888875
No 62
>KOG2482|consensus
Probab=94.06 E-value=0.084 Score=39.52 Aligned_cols=49 Identities=20% Similarity=0.396 Sum_probs=35.4
Q ss_pred eecccCccccCCchhHHHHHHhhcC---------------------------CCCccCCCCcccccCcHHHHHHHH
Q psy13443 107 FRCALCAYSARRKTHLDDHMRRHTG---------------------------EKPHACGMCGYECAQGSQLMQHLR 155 (188)
Q Consensus 107 ~~C~~C~~~~~~~~~l~~H~~~h~~---------------------------~~~~~C~~C~~~f~~~~~l~~H~~ 155 (188)
..|-.|...+.+...|..||.+-+. .....|..|.-.|-.+..|..|+.
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~ 355 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMV 355 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcc
Confidence 3677788888888888888875331 112467788888888888888874
No 63
>KOG4173|consensus
Probab=94.00 E-value=0.037 Score=38.33 Aligned_cols=79 Identities=20% Similarity=0.391 Sum_probs=59.5
Q ss_pred eeecCC--CCCCCCCHHHHHHHHHhcCCCCceecccCccccCCchhHHHHHHhhc----------CCCCccCC--CCccc
Q psy13443 78 TYMCYL--CNYHTPTRKYMRTHIDTHNGEKPFRCALCAYSARRKTHLDDHMRRHT----------GEKPHACG--MCGYE 143 (188)
Q Consensus 78 ~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~----------~~~~~~C~--~C~~~ 143 (188)
.|.|++ |-+.|.....+..|..+-++ ..|..|.+.|.+...|..|+...+ |...|+|- .|+..
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~K 155 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEK 155 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhh
Confidence 466766 66677777777777765443 379999999999988888886543 33458885 49999
Q ss_pred ccCcHHHHHHHHHhcC
Q psy13443 144 CAQGSQLMQHLRKVHK 159 (188)
Q Consensus 144 f~~~~~l~~H~~~~h~ 159 (188)
|.+..+-..|+-..|+
T Consensus 156 FkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 156 FKTSRDRKDHMIRMHK 171 (253)
T ss_pred hhhhhhhhhHHHHhcc
Confidence 9999999999877774
No 64
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.97 E-value=0.028 Score=30.12 Aligned_cols=30 Identities=27% Similarity=0.524 Sum_probs=24.6
Q ss_pred CCCCccCCCCcccccCcHHHHHHHHHhcCC
Q psy13443 131 GEKPHACGMCGYECAQGSQLMQHLRKVHKV 160 (188)
Q Consensus 131 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 160 (188)
|+..++|+.|+..|....+..+|+...|+.
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKaH~~ 43 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKAHGW 43 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHHhhh
Confidence 566688999999999988888998877753
No 65
>KOG2893|consensus
Probab=93.32 E-value=0.032 Score=39.57 Aligned_cols=42 Identities=24% Similarity=0.518 Sum_probs=31.3
Q ss_pred ecCCCCCCCCCHHHHHHHHHhcCCCCceecccCccccCCchhHHHH
Q psy13443 80 MCYLCNYHTPTRKYMRTHIDTHNGEKPFRCALCAYSARRKTHLDDH 125 (188)
Q Consensus 80 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H 125 (188)
.|+.|++.|.....|.+|++.. .|.|.+|-+.+.+-..|..|
T Consensus 12 wcwycnrefddekiliqhqkak----hfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKAK----HFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeeecccccchhhhhhhhhhhc----cceeeeehhhhccCCCceee
Confidence 4788888888888888887653 37888888777666666665
No 66
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=92.77 E-value=0.15 Score=27.89 Aligned_cols=12 Identities=17% Similarity=0.573 Sum_probs=7.7
Q ss_pred CceeecCCCCCC
Q psy13443 76 SYTYMCYLCNYH 87 (188)
Q Consensus 76 ~~~~~C~~C~~~ 87 (188)
...|.|+.||..
T Consensus 23 ~~~F~CPnCG~~ 34 (59)
T PRK14890 23 AVKFLCPNCGEV 34 (59)
T ss_pred cCEeeCCCCCCe
Confidence 345777777765
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=91.55 E-value=0.062 Score=38.65 Aligned_cols=27 Identities=30% Similarity=0.655 Sum_probs=19.1
Q ss_pred CCCceecccCccccCCchhHHHHHHhh
Q psy13443 103 GEKPFRCALCAYSARRKTHLDDHMRRH 129 (188)
Q Consensus 103 ~~~~~~C~~C~~~~~~~~~l~~H~~~h 129 (188)
..+++.||.|+........|.--.++|
T Consensus 206 k~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 206 KGKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred cCCCCCCCCCCCcccccccceeeeecc
Confidence 446888999998877766665555554
No 68
>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=91.37 E-value=0.17 Score=24.51 Aligned_cols=11 Identities=27% Similarity=0.993 Sum_probs=6.3
Q ss_pred eecccCccccC
Q psy13443 107 FRCALCAYSAR 117 (188)
Q Consensus 107 ~~C~~C~~~~~ 117 (188)
|.|.+||..+.
T Consensus 3 ~~C~~CG~i~~ 13 (34)
T cd00729 3 WVCPVCGYIHE 13 (34)
T ss_pred EECCCCCCEeE
Confidence 56666665543
No 69
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=91.16 E-value=0.8 Score=28.74 Aligned_cols=25 Identities=36% Similarity=0.905 Sum_probs=20.2
Q ss_pred eec----ccCccccCCchhHHHHHHhhcC
Q psy13443 107 FRC----ALCAYSARRKTHLDDHMRRHTG 131 (188)
Q Consensus 107 ~~C----~~C~~~~~~~~~l~~H~~~h~~ 131 (188)
|.| ..|++...+...+..|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 788 8888888888888888877653
No 70
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.61 E-value=0.051 Score=42.37 Aligned_cols=65 Identities=26% Similarity=0.534 Sum_probs=54.7
Q ss_pred ceecccCccccCCchhHHHHHH--hhcCC--CCccCC--CCcccccCcHHHHHHHHHhcCCCCCCCCcchh
Q psy13443 106 PFRCALCAYSARRKTHLDDHMR--RHTGE--KPHACG--MCGYECAQGSQLMQHLRKVHKVDKKGGEEEEE 170 (188)
Q Consensus 106 ~~~C~~C~~~~~~~~~l~~H~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~ 170 (188)
++.|..|...|.....+..|.+ .|.++ +|+.|+ .|++.|.....+..|...+.+..+..+.....
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 359 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNS 359 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccC
Confidence 5778889999999999999999 78888 899999 79999999999999998888877766654444
No 71
>KOG2893|consensus
Probab=90.30 E-value=0.06 Score=38.21 Aligned_cols=48 Identities=25% Similarity=0.425 Sum_probs=37.7
Q ss_pred ecccCccccCCchhHHHHHHhhcCCCCccCCCCcccccCcHHHHHHHHHhcC
Q psy13443 108 RCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYECAQGSQLMQHLRKVHK 159 (188)
Q Consensus 108 ~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 159 (188)
=|..|++.|....-|..|++.. -|+|-+|.+..-+--.|..|--.+|+
T Consensus 12 wcwycnrefddekiliqhqkak----hfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKAK----HFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred eeeecccccchhhhhhhhhhhc----cceeeeehhhhccCCCceeehhhhhh
Confidence 3778999999999999887653 48999999887776677777655554
No 72
>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=89.90 E-value=0.34 Score=21.43 Aligned_cols=10 Identities=20% Similarity=0.670 Sum_probs=5.9
Q ss_pred CceeecCCCC
Q psy13443 76 SYTYMCYLCN 85 (188)
Q Consensus 76 ~~~~~C~~C~ 85 (188)
...|.|+.||
T Consensus 14 ~v~f~CPnCG 23 (24)
T PF07754_consen 14 AVPFPCPNCG 23 (24)
T ss_pred CceEeCCCCC
Confidence 3456666665
No 73
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=89.34 E-value=0.37 Score=23.81 Aligned_cols=13 Identities=23% Similarity=0.452 Sum_probs=6.4
Q ss_pred ecccCccccCCch
Q psy13443 108 RCALCAYSARRKT 120 (188)
Q Consensus 108 ~C~~C~~~~~~~~ 120 (188)
.|+.|+..|.-..
T Consensus 4 ~CP~C~~~f~v~~ 16 (37)
T PF13719_consen 4 TCPNCQTRFRVPD 16 (37)
T ss_pred ECCCCCceEEcCH
Confidence 4555555554443
No 74
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=89.19 E-value=0.093 Score=40.93 Aligned_cols=63 Identities=29% Similarity=0.504 Sum_probs=56.8
Q ss_pred ceeecCCCCCCCCCHHHHHHHHH--hcCCC--Cceecc--cCccccCCchhHHHHHHhhcCCCCccCCC
Q psy13443 77 YTYMCYLCNYHTPTRKYMRTHID--THNGE--KPFRCA--LCAYSARRKTHLDDHMRRHTGEKPHACGM 139 (188)
Q Consensus 77 ~~~~C~~C~~~f~~~~~l~~H~~--~h~~~--~~~~C~--~C~~~~~~~~~l~~H~~~h~~~~~~~C~~ 139 (188)
.++.|..|...|.....+..|.+ .|.++ +++.|+ .|+..|.+...+..|...|.+..++.+..
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 356 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKL 356 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccccc
Confidence 46889999999999999999999 89999 999999 79999999999999999998877766644
No 75
>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=88.62 E-value=0.36 Score=21.84 Aligned_cols=10 Identities=30% Similarity=0.849 Sum_probs=5.6
Q ss_pred ecCCCCCCCC
Q psy13443 80 MCYLCNYHTP 89 (188)
Q Consensus 80 ~C~~C~~~f~ 89 (188)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 4666666553
No 76
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=88.39 E-value=0.65 Score=31.51 Aligned_cols=25 Identities=40% Similarity=1.108 Sum_probs=19.1
Q ss_pred CceecccCccccCCchhHHHHHHhhcCCCCccCCCCcc
Q psy13443 105 KPFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGY 142 (188)
Q Consensus 105 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 142 (188)
+.|.|++||..+ .++.|-+||+|+.
T Consensus 133 ~~~vC~vCGy~~-------------~ge~P~~CPiCga 157 (166)
T COG1592 133 KVWVCPVCGYTH-------------EGEAPEVCPICGA 157 (166)
T ss_pred CEEEcCCCCCcc-------------cCCCCCcCCCCCC
Confidence 369999998653 3467889999984
No 77
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=88.37 E-value=0.4 Score=24.74 Aligned_cols=26 Identities=27% Similarity=0.714 Sum_probs=14.0
Q ss_pred eecccCccccCCchhHHHHHHhhcCCCCccCCCCccc
Q psy13443 107 FRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYE 143 (188)
Q Consensus 107 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~ 143 (188)
|.|..||..|... ...+.+|+.||..
T Consensus 3 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-----------SKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-----------CCCceECCCCCce
Confidence 5666666655433 1344566666643
No 78
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=88.09 E-value=1.7 Score=27.40 Aligned_cols=82 Identities=17% Similarity=0.275 Sum_probs=50.7
Q ss_pred CCccccCCCcccccCHHHHHHHHHhhhcC--CcccCCCCCCcccccccccccccccccccccccC---------CCCcee
Q psy13443 11 KQQFECDFCPYGAKQAADVHNHVQQIHMG--VNFVCVHCKQFEVVPTRKTQTLEHCATCVDMVRP---------DASYTY 79 (188)
Q Consensus 11 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~--~~~~C~~C~~~~~~~~~~~~~~~~c~~c~~~~~~---------~~~~~~ 79 (188)
+-|-.|+.|+-+......|.+.. +|.- .+|.=- ..........|-.|...|.. .....|
T Consensus 13 ~LP~~CpiCgLtLVss~HLARSy--HHLfPl~~f~ev--------~~~~~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~y 82 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARSY--HHLFPLKAFQEI--------PLEEYNGSRFCFGCQGPFPKPPVSPFDELKDSHRY 82 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHhh--hccCCCcccccc--------cccccCCCCcccCcCCCCCCcccccccccccccce
Confidence 45788999999998899998874 4421 112100 00000011234455444432 234469
Q ss_pred ecCCCCCCCCCHHHHHHHHHhcC
Q psy13443 80 MCYLCNYHTPTRKYMRTHIDTHN 102 (188)
Q Consensus 80 ~C~~C~~~f~~~~~l~~H~~~h~ 102 (188)
.|+.|...|-..-++..|...|.
T Consensus 83 ~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 83 VCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred eCCCCCCccccccchhhhhhccC
Confidence 99999999998888888887775
No 79
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=87.69 E-value=0.65 Score=22.78 Aligned_cols=13 Identities=15% Similarity=0.363 Sum_probs=6.4
Q ss_pred ecccCccccCCch
Q psy13443 108 RCALCAYSARRKT 120 (188)
Q Consensus 108 ~C~~C~~~~~~~~ 120 (188)
.|+.|+..|.-..
T Consensus 4 ~Cp~C~~~y~i~d 16 (36)
T PF13717_consen 4 TCPNCQAKYEIDD 16 (36)
T ss_pred ECCCCCCEEeCCH
Confidence 4555555554443
No 80
>KOG2186|consensus
Probab=86.99 E-value=0.49 Score=34.08 Aligned_cols=47 Identities=17% Similarity=0.463 Sum_probs=29.8
Q ss_pred eeecCCCCCCCCCHHHHHHHHHhcCCCCceecccCccccCCchhHHHHHH
Q psy13443 78 TYMCYLCNYHTPTRKYMRTHIDTHNGEKPFRCALCAYSARRKTHLDDHMR 127 (188)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~ 127 (188)
.|.|..||....-+ .+..|+..-++ ..|.|..|+..|.. ..+..|..
T Consensus 3 ~FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EEehhhhhhhcccc-chHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 36677777666543 45557666555 45777777777776 55556654
No 81
>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=86.82 E-value=0.59 Score=23.06 Aligned_cols=10 Identities=40% Similarity=0.902 Sum_probs=4.4
Q ss_pred ccCCCCcccc
Q psy13443 135 HACGMCGYEC 144 (188)
Q Consensus 135 ~~C~~C~~~f 144 (188)
..|+.|+..|
T Consensus 26 v~C~~C~~~~ 35 (38)
T TIGR02098 26 VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEE
Confidence 3444444443
No 82
>KOG2482|consensus
Probab=86.45 E-value=1.2 Score=33.60 Aligned_cols=51 Identities=25% Similarity=0.461 Sum_probs=40.1
Q ss_pred eecCCCCCCCCCHHHHHHHHHh-cCCC--------------------------CceecccCccccCCchhHHHHHHhh
Q psy13443 79 YMCYLCNYHTPTRKYMRTHIDT-HNGE--------------------------KPFRCALCAYSARRKTHLDDHMRRH 129 (188)
Q Consensus 79 ~~C~~C~~~f~~~~~l~~H~~~-h~~~--------------------------~~~~C~~C~~~~~~~~~l~~H~~~h 129 (188)
..|-.|....-....+..|+.. |.-. +...|..|.-.|-....|..|+..+
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e~ 357 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVED 357 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcccc
Confidence 5899999888889999999863 3211 2357888999999999999998754
No 83
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=86.26 E-value=1.3 Score=31.98 Aligned_cols=51 Identities=16% Similarity=0.371 Sum_probs=33.1
Q ss_pred ccCCCCCCcccccccccccccccccccccccC------CCCceeecCCCCCCCCCHH
Q psy13443 42 FVCVHCKQFEVVPTRKTQTLEHCATCVDMVRP------DASYTYMCYLCNYHTPTRK 92 (188)
Q Consensus 42 ~~C~~C~~~~~~~~~~~~~~~~c~~c~~~~~~------~~~~~~~C~~C~~~f~~~~ 92 (188)
|-|..|+......--.......|..|.+.+.+ .|-..|.|+.|+..|....
T Consensus 113 FaC~~Cd~~WwRrvp~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~~ 169 (278)
T PF15135_consen 113 FACSSCDHMWWRRVPQRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRGFA 169 (278)
T ss_pred eeccccchHHHhccCcccccccccccccccCCCccccccceeeeecccccccchhhh
Confidence 77888866433333333334467778777766 3344689999999998553
No 84
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=86.24 E-value=0.13 Score=36.53 Aligned_cols=13 Identities=31% Similarity=0.843 Sum_probs=9.8
Q ss_pred ccCCCCcccccCc
Q psy13443 135 HACGMCGYECAQG 147 (188)
Q Consensus 135 ~~C~~C~~~f~~~ 147 (188)
..|+.||.+|...
T Consensus 49 ~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 49 WVCPHCGYAAFEE 61 (214)
T ss_pred EECCCCCCccccc
Confidence 5799999887643
No 85
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=86.13 E-value=1.2 Score=33.82 Aligned_cols=24 Identities=17% Similarity=0.467 Sum_probs=13.8
Q ss_pred eecCC--CCCCCCCHHHHHHHHHhcC
Q psy13443 79 YMCYL--CNYHTPTRKYMRTHIDTHN 102 (188)
Q Consensus 79 ~~C~~--C~~~f~~~~~l~~H~~~h~ 102 (188)
|.|+. |.........|..|.++-+
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H 177 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQH 177 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhc
Confidence 55644 5555555666666666444
No 86
>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=85.93 E-value=0.53 Score=29.56 Aligned_cols=29 Identities=17% Similarity=0.400 Sum_probs=18.2
Q ss_pred ecCCCCCCCCCHHHHHHHHHhcCCCCceecccCccccCCc
Q psy13443 80 MCYLCNYHTPTRKYMRTHIDTHNGEKPFRCALCAYSARRK 119 (188)
Q Consensus 80 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~ 119 (188)
.|+.||..|.... ..|..|+.||..|...
T Consensus 11 ~Cp~CG~kFYDLn-----------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAKFYDLN-----------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcchhccCC-----------CCCccCCCCCCccCcc
Confidence 4677776665331 2566777777776665
No 87
>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=85.90 E-value=0.48 Score=24.15 Aligned_cols=11 Identities=45% Similarity=1.171 Sum_probs=6.2
Q ss_pred ccCCCCCC-ccc
Q psy13443 42 FVCVHCKQ-FEV 52 (188)
Q Consensus 42 ~~C~~C~~-~~~ 52 (188)
|.|..||. |..
T Consensus 6 y~C~~Cg~~fe~ 17 (42)
T PF09723_consen 6 YRCEECGHEFEV 17 (42)
T ss_pred EEeCCCCCEEEE
Confidence 56666665 443
No 88
>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=85.61 E-value=0.61 Score=23.95 Aligned_cols=26 Identities=38% Similarity=0.623 Sum_probs=14.0
Q ss_pred CCccCCCCcccccC----cHHHHHHHHHhc
Q psy13443 133 KPHACGMCGYECAQ----GSQLMQHLRKVH 158 (188)
Q Consensus 133 ~~~~C~~C~~~f~~----~~~l~~H~~~~h 158 (188)
....|.+|++.+.. .+.|..|++..|
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 34567777766654 367777775544
No 89
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=85.17 E-value=0.93 Score=30.20 Aligned_cols=35 Identities=17% Similarity=0.432 Sum_probs=18.1
Q ss_pred CCccccCCCcccccCHHHHHHHHHhhhcCCcccCCCCCC
Q psy13443 11 KQQFECDFCPYGAKQAADVHNHVQQIHMGVNFVCVHCKQ 49 (188)
Q Consensus 11 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~ 49 (188)
...|.|+.|+..|.....+.. ......|.|+.||.
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~----~d~~~~f~Cp~Cg~ 131 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQL----LDMDGTFTCPRCGE 131 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHh----cCCCCcEECCCCCC
Confidence 345777777777664332211 11222267777765
No 90
>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=84.78 E-value=0.63 Score=23.27 Aligned_cols=8 Identities=25% Similarity=1.028 Sum_probs=4.5
Q ss_pred ccCCCCCC
Q psy13443 42 FVCVHCKQ 49 (188)
Q Consensus 42 ~~C~~C~~ 49 (188)
|.|+.|+.
T Consensus 6 y~C~~Cg~ 13 (41)
T smart00834 6 YRCEDCGH 13 (41)
T ss_pred EEcCCCCC
Confidence 45555555
No 91
>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=84.21 E-value=1 Score=30.43 Aligned_cols=31 Identities=19% Similarity=0.351 Sum_probs=19.8
Q ss_pred CCCccccCCCcccccCHHHHHHHHHhhhcCCcccCCCCCC
Q psy13443 10 AKQQFECDFCPYGAKQAADVHNHVQQIHMGVNFVCVHCKQ 49 (188)
Q Consensus 10 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~ 49 (188)
....|.|+.|+..|+....+. ..|.|+.||.
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~ 136 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRCGA 136 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCC
Confidence 345677777777776665553 1377777765
No 92
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=84.05 E-value=0.17 Score=35.94 Aligned_cols=13 Identities=31% Similarity=0.851 Sum_probs=9.9
Q ss_pred eecccCccccCCc
Q psy13443 107 FRCALCAYSARRK 119 (188)
Q Consensus 107 ~~C~~C~~~~~~~ 119 (188)
..||.||.++...
T Consensus 49 ~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 49 WVCPHCGYAAFEE 61 (214)
T ss_pred EECCCCCCccccc
Confidence 5799999887543
No 93
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=83.81 E-value=0.68 Score=24.44 Aligned_cols=11 Identities=27% Similarity=0.893 Sum_probs=7.2
Q ss_pred ceecccCcccc
Q psy13443 106 PFRCALCAYSA 116 (188)
Q Consensus 106 ~~~C~~C~~~~ 116 (188)
.|.|..||+.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 46666677666
No 94
>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=83.43 E-value=0.32 Score=35.13 Aligned_cols=26 Identities=35% Similarity=0.640 Sum_probs=15.6
Q ss_pred CCCccCCCCcccccCcHHHHHHHHHh
Q psy13443 132 EKPHACGMCGYECAQGSQLMQHLRKV 157 (188)
Q Consensus 132 ~~~~~C~~C~~~f~~~~~l~~H~~~~ 157 (188)
.+++.|+.|++.......|..-.|+|
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeecc
Confidence 46677777776666555555444443
No 95
>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=82.30 E-value=0.7 Score=30.12 Aligned_cols=25 Identities=32% Similarity=0.515 Sum_probs=15.0
Q ss_pred CccCCCCcccccCcHHHHHHHHHhcCCC
Q psy13443 134 PHACGMCGYECAQGSQLMQHLRKVHKVD 161 (188)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 161 (188)
...|-+||+.|.. |.+|++.||+..
T Consensus 72 ~i~clecGk~~k~---LkrHL~~~~glt 96 (132)
T PF05443_consen 72 YIICLECGKKFKT---LKRHLRTHHGLT 96 (132)
T ss_dssp -EE-TBT--EESB---HHHHHHHTT-S-
T ss_pred eeEEccCCcccch---HHHHHHHccCCC
Confidence 3678888888866 588888888754
No 96
>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=81.31 E-value=1.9 Score=29.08 Aligned_cols=32 Identities=16% Similarity=0.284 Sum_probs=21.4
Q ss_pred CCCceecccCccccCCchhHHHHHHhhcCCCCccCCCCccc
Q psy13443 103 GEKPFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYE 143 (188)
Q Consensus 103 ~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~ 143 (188)
...-|.|+.|+..|+....+. .-|.|+.||..
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCE
Confidence 344577888887777766653 24788888765
No 97
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=80.64 E-value=0.33 Score=32.55 Aligned_cols=17 Identities=12% Similarity=0.225 Sum_probs=11.8
Q ss_pred ceecccCccccCCchhH
Q psy13443 106 PFRCALCAYSARRKTHL 122 (188)
Q Consensus 106 ~~~C~~C~~~~~~~~~l 122 (188)
.+.|+.||+.|.....+
T Consensus 28 ~~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 28 RRECLACGKRFTTFERV 44 (154)
T ss_pred eeeccccCCcceEeEec
Confidence 37777888777776554
No 98
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=80.64 E-value=1.8 Score=22.85 Aligned_cols=23 Identities=39% Similarity=0.824 Sum_probs=13.2
Q ss_pred cCCCCcccccCc-----HHHHHHHHHhc
Q psy13443 136 ACGMCGYECAQG-----SQLMQHLRKVH 158 (188)
Q Consensus 136 ~C~~C~~~f~~~-----~~l~~H~~~~h 158 (188)
.|..|++.+... +.|.+|++..|
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~~~h 47 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLRRKH 47 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHHhHC
Confidence 566666555433 57777776443
No 99
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=80.52 E-value=4.1 Score=27.13 Aligned_cols=37 Identities=16% Similarity=0.284 Sum_probs=19.9
Q ss_pred CCceecccCccccCCchhHHHHHHhhcCCCCccCCCCcccc
Q psy13443 104 EKPFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYEC 144 (188)
Q Consensus 104 ~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f 144 (188)
...|.|+.|+..|.....+.. .. ....|.|+.||...
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~---~d-~~~~f~Cp~Cg~~l 133 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQL---LD-MDGTFTCPRCGEEL 133 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHh---cC-CCCcEECCCCCCEE
Confidence 345777777777665433221 01 12337777777654
No 100
>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=80.38 E-value=1.8 Score=19.45 Aligned_cols=19 Identities=26% Similarity=0.496 Sum_probs=13.2
Q ss_pred cCCCCcccccCcHHHHHHHH
Q psy13443 136 ACGMCGYECAQGSQLMQHLR 155 (188)
Q Consensus 136 ~C~~C~~~f~~~~~l~~H~~ 155 (188)
.|++|++.+ ....+..|+-
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577787777 5567777764
No 101
>PF12907 zf-met2: Zinc-binding
Probab=79.88 E-value=1.2 Score=22.46 Aligned_cols=27 Identities=22% Similarity=0.444 Sum_probs=20.2
Q ss_pred ccCCCCcccc---cCcHHHHHHHHHhcCCC
Q psy13443 135 HACGMCGYEC---AQGSQLMQHLRKVHKVD 161 (188)
Q Consensus 135 ~~C~~C~~~f---~~~~~l~~H~~~~h~~~ 161 (188)
+.|.+|..+| .....|..|....|+..
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCC
Confidence 5788888665 44577999998888765
No 102
>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=79.07 E-value=1.2 Score=23.63 Aligned_cols=11 Identities=18% Similarity=0.615 Sum_probs=6.1
Q ss_pred cccCCCccccc
Q psy13443 14 FECDFCPYGAK 24 (188)
Q Consensus 14 ~~C~~C~~~f~ 24 (188)
|.|+.|+..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 45555555554
No 103
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=78.53 E-value=1.6 Score=30.09 Aligned_cols=29 Identities=21% Similarity=0.458 Sum_probs=16.9
Q ss_pred CccccCCCcccccCHHHHHHHHHhhhcCCcccCCCCCC
Q psy13443 12 QQFECDFCPYGAKQAADVHNHVQQIHMGVNFVCVHCKQ 49 (188)
Q Consensus 12 ~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~ 49 (188)
..|.|+.|+..|+....+. ..|.|+.||.
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~ 144 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME---------YGFRCPQCGE 144 (178)
T ss_pred CEEECCCCCcEEeHHHHhh---------cCCcCCCCCC
Confidence 4567777776666554432 1366666665
No 104
>KOG2186|consensus
Probab=78.31 E-value=1.2 Score=32.18 Aligned_cols=54 Identities=22% Similarity=0.516 Sum_probs=42.8
Q ss_pred eecccCccccCCchhHHHHHHhhcCCCCccCCCCcccccCcHHHHHHHHHhcCCCCC
Q psy13443 107 FRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYECAQGSQLMQHLRKVHKVDKK 163 (188)
Q Consensus 107 ~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~ 163 (188)
|.|.+||....-. .+..|+....+ ..|.|--|+..|-. .....|.........|
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kCITEaQKY 57 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCITEAQKY 57 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC-CeeEEeeccccccc-chhhhhhhhcchHHHh
Confidence 7899999887654 56679998877 67999999999988 6778998877654443
No 105
>KOG2231|consensus
Probab=78.16 E-value=3.9 Score=34.12 Aligned_cols=69 Identities=16% Similarity=0.231 Sum_probs=38.1
Q ss_pred cCHHHHHHHHHhhhc-CCc----ccCCCCCC-cccccccccccccccccccccccCCCCceeecCCC------CCCCCCH
Q psy13443 24 KQAADVHNHVQQIHM-GVN----FVCVHCKQ-FEVVPTRKTQTLEHCATCVDMVRPDASYTYMCYLC------NYHTPTR 91 (188)
Q Consensus 24 ~~~~~l~~H~~~~~~-~~~----~~C~~C~~-~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~C~~C------~~~f~~~ 91 (188)
.+...|..|++.--. .+. -.|..|.. |.....+..|.... -|.|..| +..|...
T Consensus 160 Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~--------------h~~chfC~~~~~~neyy~~~ 225 (669)
T KOG2231|consen 160 YTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRFD--------------HEFCHFCDYKTGQNEYYNDY 225 (669)
T ss_pred ehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhccc--------------eeheeecCcccccchhcccc
Confidence 345666777632222 111 35666666 55555555555431 1334444 4566777
Q ss_pred HHHHHHHHhcCCCCceecc
Q psy13443 92 KYMRTHIDTHNGEKPFRCA 110 (188)
Q Consensus 92 ~~l~~H~~~h~~~~~~~C~ 110 (188)
..|..|.+.++ |.|.
T Consensus 226 ~dLe~HfR~~H----flCE 240 (669)
T KOG2231|consen 226 DDLEEHFRKGH----FLCE 240 (669)
T ss_pred hHHHHHhhhcC----cccc
Confidence 78888887765 6666
No 106
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=78.16 E-value=1.7 Score=30.01 Aligned_cols=30 Identities=20% Similarity=0.384 Sum_probs=16.0
Q ss_pred CceecccCccccCCchhHHHHHHhhcCCCCccCCCCccc
Q psy13443 105 KPFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYE 143 (188)
Q Consensus 105 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~ 143 (188)
.-|.|+.|+..|+....+. .-|.|+.||..
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~ 145 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME---------YGFRCPQCGEM 145 (178)
T ss_pred CEEECCCCCcEEeHHHHhh---------cCCcCCCCCCC
Confidence 3456666665555554431 23666666644
No 107
>PHA00626 hypothetical protein
Probab=77.81 E-value=1.8 Score=23.39 Aligned_cols=11 Identities=36% Similarity=1.141 Sum_probs=5.4
Q ss_pred eecCCCCCCCC
Q psy13443 79 YMCYLCNYHTP 89 (188)
Q Consensus 79 ~~C~~C~~~f~ 89 (188)
|.|+.|+..|+
T Consensus 24 YkCkdCGY~ft 34 (59)
T PHA00626 24 YVCCDCGYNDS 34 (59)
T ss_pred eEcCCCCCeec
Confidence 45555554443
No 108
>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=76.42 E-value=1.8 Score=27.88 Aligned_cols=15 Identities=7% Similarity=0.025 Sum_probs=8.3
Q ss_pred CceecccCccccCCc
Q psy13443 105 KPFRCALCAYSARRK 119 (188)
Q Consensus 105 ~~~~C~~C~~~~~~~ 119 (188)
.|..|+.||..|...
T Consensus 25 ~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 25 RPAVSPYTGEQFPPE 39 (129)
T ss_pred CCccCCCcCCccCcc
Confidence 455666666555444
No 109
>KOG2807|consensus
Probab=76.35 E-value=4.9 Score=30.32 Aligned_cols=25 Identities=12% Similarity=0.151 Sum_probs=16.6
Q ss_pred CCccCCCCcccccCcHHHHHHHHHh
Q psy13443 133 KPHACGMCGYECAQGSQLMQHLRKV 157 (188)
Q Consensus 133 ~~~~C~~C~~~f~~~~~l~~H~~~~ 157 (188)
..|.|..|...|..--+...|-..|
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred CcEEchhccceeeccchHHHHhhhh
Confidence 3477777777777766666665544
No 110
>KOG2785|consensus
Probab=75.88 E-value=4.4 Score=31.24 Aligned_cols=52 Identities=19% Similarity=0.361 Sum_probs=44.4
Q ss_pred ceeecCCCCCCCCCHHHHHHHHHhcCCC-----------------------CceecccCc---cccCCchhHHHHHHh
Q psy13443 77 YTYMCYLCNYHTPTRKYMRTHIDTHNGE-----------------------KPFRCALCA---YSARRKTHLDDHMRR 128 (188)
Q Consensus 77 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~-----------------------~~~~C~~C~---~~~~~~~~l~~H~~~ 128 (188)
.|-.|-.|++.+.+-.....||..+++- .-+.|..|. +.|.+....+.||..
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 3577999999999999999999988874 236788888 999999999999975
No 111
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=75.05 E-value=2.5 Score=23.08 Aligned_cols=41 Identities=24% Similarity=0.630 Sum_probs=20.6
Q ss_pred Cceeccc-CccccCCchhHHHHHHhhcCCCCccCCC----Cccccc
Q psy13443 105 KPFRCAL-CAYSARRKTHLDDHMRRHTGEKPHACGM----CGYECA 145 (188)
Q Consensus 105 ~~~~C~~-C~~~~~~~~~l~~H~~~h~~~~~~~C~~----C~~~f~ 145 (188)
.+..|+. |+..-.....|..|.......++..|++ |...+.
T Consensus 8 ~~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIPRKELDDHLENECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp SEEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS----S--EEE
T ss_pred CEeeCCCCCcccceeHHHHHHHHHccCCCCcEECCCCCCCCCCccc
Confidence 3456666 3333233456677777555566677777 766554
No 112
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=74.57 E-value=1.4 Score=32.84 Aligned_cols=91 Identities=15% Similarity=0.291 Sum_probs=53.1
Q ss_pred ccccccccccCCCCceeecCCCCCCCCCHHHHHHHHHh----------cCCC--CceecccCccccCCchhHHHHHHhhc
Q psy13443 63 HCATCVDMVRPDASYTYMCYLCNYHTPTRKYMRTHIDT----------HNGE--KPFRCALCAYSARRKTHLDDHMRRHT 130 (188)
Q Consensus 63 ~c~~c~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~----------h~~~--~~~~C~~C~~~~~~~~~l~~H~~~h~ 130 (188)
+|+.|...+- ..|..|+.|+........|.....- ..+. +.--|-.|...|.....-.. -.-+
T Consensus 310 ~CP~CktkVC---sLPi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~CQ~~fp~~~~~~~--~~~~ 384 (421)
T COG5151 310 ECPVCKTKVC---SLPISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQGPFPKPPVSPF--DEST 384 (421)
T ss_pred eCCcccceee---cCCccCcchhHHHHHHHHHHHHHHhhccCcccccccCCCCCCCccceeccCCCCCCCCCcc--cccc
Confidence 5666655543 3567899998776655555443321 1111 12236667777765432111 0112
Q ss_pred CCCCccCCCCcccccCcHHHHHHHHHhc
Q psy13443 131 GEKPHACGMCGYECAQGSQLMQHLRKVH 158 (188)
Q Consensus 131 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h 158 (188)
....|+|+.|...|..--+...|-..|.
T Consensus 385 ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 385 SSGRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred cccceechhhhhhhhhhhHHHHHHHHhh
Confidence 2345999999999988888888866553
No 113
>PF15269 zf-C2H2_7: Zinc-finger
Probab=74.05 E-value=3.1 Score=21.34 Aligned_cols=22 Identities=23% Similarity=0.818 Sum_probs=19.5
Q ss_pred ccccCCCcccccCHHHHHHHHH
Q psy13443 13 QFECDFCPYGAKQAADVHNHVQ 34 (188)
Q Consensus 13 ~~~C~~C~~~f~~~~~l~~H~~ 34 (188)
.|+|-.|..+...++.|.+||.
T Consensus 20 ~ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred cceeecCCcccchHHHHHHHHH
Confidence 3789999999999999999984
No 114
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=73.95 E-value=3 Score=35.38 Aligned_cols=29 Identities=34% Similarity=0.875 Sum_probs=17.0
Q ss_pred hcCCCCceecccCccccCCchhHHHHHHhhcCCCCccCCCCccc
Q psy13443 100 THNGEKPFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYE 143 (188)
Q Consensus 100 ~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~ 143 (188)
.|...+...|..||.. ...|..|+.||..
T Consensus 456 ~H~~~~~L~CH~Cg~~---------------~~~p~~Cp~Cgs~ 484 (730)
T COG1198 456 LHKATGQLRCHYCGYQ---------------EPIPQSCPECGSE 484 (730)
T ss_pred EecCCCeeEeCCCCCC---------------CCCCCCCCCCCCC
Confidence 3344455677777743 2346677777754
No 115
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=73.83 E-value=2.2 Score=22.09 Aligned_cols=8 Identities=25% Similarity=1.144 Sum_probs=4.3
Q ss_pred ccCCCCCC
Q psy13443 42 FVCVHCKQ 49 (188)
Q Consensus 42 ~~C~~C~~ 49 (188)
|.|+.||.
T Consensus 4 y~C~~CG~ 11 (46)
T PRK00398 4 YKCARCGR 11 (46)
T ss_pred EECCCCCC
Confidence 45555555
No 116
>PF14353 CpXC: CpXC protein
Probab=73.54 E-value=2.2 Score=27.60 Aligned_cols=14 Identities=14% Similarity=0.444 Sum_probs=7.4
Q ss_pred eeecCCCCCCCCCH
Q psy13443 78 TYMCYLCNYHTPTR 91 (188)
Q Consensus 78 ~~~C~~C~~~f~~~ 91 (188)
.+.|+.||..|...
T Consensus 38 ~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 38 SFTCPSCGHKFRLE 51 (128)
T ss_pred EEECCCCCCceecC
Confidence 35566666555433
No 117
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=72.86 E-value=1.9 Score=33.81 Aligned_cols=30 Identities=13% Similarity=0.412 Sum_probs=18.6
Q ss_pred ccccccccccCCCCceeecCCCCCCCCCHH
Q psy13443 63 HCATCVDMVRPDASYTYMCYLCNYHTPTRK 92 (188)
Q Consensus 63 ~c~~c~~~~~~~~~~~~~C~~C~~~f~~~~ 92 (188)
.|+.||....+.+..-|.|+.|++.++...
T Consensus 352 ~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGRMKSAGRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCchhhcCCCCcccccccccCCccc
Confidence 466666666666666666666666655443
No 118
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=71.33 E-value=3.3 Score=21.84 Aligned_cols=11 Identities=27% Similarity=1.032 Sum_probs=6.1
Q ss_pred eeecCCCCCCC
Q psy13443 78 TYMCYLCNYHT 88 (188)
Q Consensus 78 ~~~C~~C~~~f 88 (188)
.+.|+.|+..+
T Consensus 20 ~~vC~~Cg~~~ 30 (52)
T smart00661 20 RFVCRKCGYEE 30 (52)
T ss_pred EEECCcCCCeE
Confidence 45566666543
No 119
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=70.46 E-value=1.3 Score=25.62 Aligned_cols=14 Identities=21% Similarity=0.517 Sum_probs=7.1
Q ss_pred CCccCC--CCcccccC
Q psy13443 133 KPHACG--MCGYECAQ 146 (188)
Q Consensus 133 ~~~~C~--~C~~~f~~ 146 (188)
.-++|. .||.+|.+
T Consensus 26 ~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 26 RYHQCQNVNCSATFIT 41 (72)
T ss_pred eeeecCCCCCCCEEEE
Confidence 334555 55555544
No 120
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=70.40 E-value=4.3 Score=29.39 Aligned_cols=61 Identities=13% Similarity=0.181 Sum_probs=29.8
Q ss_pred CCCceeecCCCCCCCCCHHHHHHHHHhcCCCCceecccCccccCCchhHHHHHHhhcCCCCccCCCCcccccCc
Q psy13443 74 DASYTYMCYLCNYHTPTRKYMRTHIDTHNGEKPFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYECAQG 147 (188)
Q Consensus 74 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 147 (188)
...+.|.|..|+.. .-.++.....+.+|..|.+.|.-...- + -=|-.-|.|+.|+..|...
T Consensus 108 ~~drqFaC~~Cd~~--------WwRrvp~rKeVSRCr~C~~rYDPVP~d----k-mwG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 108 SVDRQFACSSCDHM--------WWRRVPQRKEVSRCRKCRKRYDPVPCD----K-MWGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred ccceeeeccccchH--------HHhccCcccccccccccccccCCCccc----c-ccceeeeecccccccchhh
Confidence 55577889998632 122333344445566666555443210 0 0122235666666655533
No 121
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=69.94 E-value=3 Score=25.04 Aligned_cols=13 Identities=38% Similarity=0.984 Sum_probs=7.6
Q ss_pred ceecccCccccCC
Q psy13443 106 PFRCALCAYSARR 118 (188)
Q Consensus 106 ~~~C~~C~~~~~~ 118 (188)
|-.|..||+.|..
T Consensus 58 Pa~CkkCGfef~~ 70 (97)
T COG3357 58 PARCKKCGFEFRD 70 (97)
T ss_pred ChhhcccCccccc
Confidence 4556666666655
No 122
>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=69.39 E-value=4.9 Score=20.77 Aligned_cols=28 Identities=21% Similarity=0.525 Sum_probs=15.8
Q ss_pred ceecccCccccCCchhHHHHHHhhcCCCCccCCCCcc
Q psy13443 106 PFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGY 142 (188)
Q Consensus 106 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~ 142 (188)
.+.|+.||.. ....+. +...|+|..|++
T Consensus 18 g~~CP~Cg~~--~~~~~~-------~~~~~~C~~C~~ 45 (46)
T PF12760_consen 18 GFVCPHCGST--KHYRLK-------TRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCe--eeEEeC-------CCCeEECCCCCC
Confidence 3678888865 111111 145578887765
No 123
>PRK04023 DNA polymerase II large subunit; Validated
Probab=68.71 E-value=5.5 Score=34.90 Aligned_cols=8 Identities=38% Similarity=1.082 Sum_probs=4.0
Q ss_pred ccCCCCcc
Q psy13443 135 HACGMCGY 142 (188)
Q Consensus 135 ~~C~~C~~ 142 (188)
+.|+.|+.
T Consensus 664 y~CPKCG~ 671 (1121)
T PRK04023 664 DECEKCGR 671 (1121)
T ss_pred CcCCCCCC
Confidence 44555553
No 124
>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=68.32 E-value=3.6 Score=29.26 Aligned_cols=29 Identities=21% Similarity=0.365 Sum_probs=22.0
Q ss_pred CCCccCCCCcccccCcHHHHHHHHHhcCC
Q psy13443 132 EKPHACGMCGYECAQGSQLMQHLRKVHKV 160 (188)
Q Consensus 132 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 160 (188)
+..|.|+.|++.|.-..-+.+|+...|.+
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 34489999999999999999999998853
No 125
>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=68.04 E-value=3.1 Score=19.80 Aligned_cols=6 Identities=33% Similarity=0.877 Sum_probs=2.5
Q ss_pred ecCCCC
Q psy13443 80 MCYLCN 85 (188)
Q Consensus 80 ~C~~C~ 85 (188)
.|+.||
T Consensus 19 rC~~CG 24 (32)
T PF03604_consen 19 RCPECG 24 (32)
T ss_dssp SBSSSS
T ss_pred ECCcCC
Confidence 344444
No 126
>KOG1280|consensus
Probab=66.44 E-value=11 Score=28.88 Aligned_cols=22 Identities=23% Similarity=0.478 Sum_probs=12.8
Q ss_pred eeecCCCCCCCCCHHHHHHHHH
Q psy13443 78 TYMCYLCNYHTPTRKYMRTHID 99 (188)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H~~ 99 (188)
.|.|+.|+.+-.+...|..|+.
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~ 100 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVL 100 (381)
T ss_pred cccCCcccccccchhHHHHHhh
Confidence 4566666665555555666654
No 127
>KOG2593|consensus
Probab=66.04 E-value=4.9 Score=31.55 Aligned_cols=37 Identities=14% Similarity=0.319 Sum_probs=23.5
Q ss_pred cCCCccccCCCcccccCHHHHHHHHHhhhc-CCcccCCCCCC
Q psy13443 9 LAKQQFECDFCPYGAKQAADVHNHVQQIHM-GVNFVCVHCKQ 49 (188)
Q Consensus 9 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~-~~~~~C~~C~~ 49 (188)
+....|.|+.|.+.|.....+. .... .-.|.|..|+.
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~----L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQ----LLDNETGEFHCENCGG 161 (436)
T ss_pred cccccccCCccccchhhhHHHH----hhcccCceEEEecCCC
Confidence 4445688888888887655442 2333 23488888864
No 128
>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=66.01 E-value=2 Score=22.86 Aligned_cols=11 Identities=36% Similarity=0.981 Sum_probs=7.0
Q ss_pred cccCCCccccc
Q psy13443 14 FECDFCPYGAK 24 (188)
Q Consensus 14 ~~C~~C~~~f~ 24 (188)
|.|..|+..|.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 56677776554
No 129
>KOG4118|consensus
Probab=65.79 E-value=3.2 Score=23.20 Aligned_cols=31 Identities=19% Similarity=0.400 Sum_probs=26.1
Q ss_pred ccCCCCcccccCcHHHHHHHHHhcCCCCCCC
Q psy13443 135 HACGMCGYECAQGSQLMQHLRKVHKVDKKGG 165 (188)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~ 165 (188)
|+|.+|.-.-..+..+..|....|+..++..
T Consensus 39 ~kCtVC~~~mpdpktfkqhfe~kHpk~~~P~ 69 (74)
T KOG4118|consen 39 HKCTVCMVQMPDPKTFKQHFENKHPKEPLPE 69 (74)
T ss_pred hhhHhhHhhCCCCchHHHHHhhcCCCCCCCH
Confidence 7899998888888888999999998887753
No 130
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=62.98 E-value=5.2 Score=17.36 Aligned_cols=6 Identities=33% Similarity=0.855 Sum_probs=3.0
Q ss_pred cCCCCC
Q psy13443 81 CYLCNY 86 (188)
Q Consensus 81 C~~C~~ 86 (188)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 555553
No 131
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=62.36 E-value=4.9 Score=21.34 Aligned_cols=10 Identities=30% Similarity=1.149 Sum_probs=5.6
Q ss_pred ceecccCccc
Q psy13443 106 PFRCALCAYS 115 (188)
Q Consensus 106 ~~~C~~C~~~ 115 (188)
.+.|..|+..
T Consensus 37 r~~C~~Cgyt 46 (50)
T PRK00432 37 RWHCGKCGYT 46 (50)
T ss_pred cEECCCcCCE
Confidence 4566666554
No 132
>KOG2593|consensus
Probab=61.96 E-value=8.1 Score=30.40 Aligned_cols=38 Identities=16% Similarity=0.316 Sum_probs=22.2
Q ss_pred cCCCCceecccCccccCCchhHHHHHHhhcCCCCccCCCCc
Q psy13443 101 HNGEKPFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCG 141 (188)
Q Consensus 101 h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~ 141 (188)
.+....|.|+.|.+.|.....++- +-.....|.|..|+
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~~L---~~~~~~~F~C~~C~ 160 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEALQL---LDNETGEFHCENCG 160 (436)
T ss_pred ccccccccCCccccchhhhHHHHh---hcccCceEEEecCC
Confidence 344456788888877777655432 11113457777776
No 133
>PF12773 DZR: Double zinc ribbon
Probab=61.89 E-value=6.4 Score=20.57 Aligned_cols=8 Identities=25% Similarity=0.646 Sum_probs=3.6
Q ss_pred eecCCCCC
Q psy13443 79 YMCYLCNY 86 (188)
Q Consensus 79 ~~C~~C~~ 86 (188)
..|+.|+.
T Consensus 30 ~~C~~Cg~ 37 (50)
T PF12773_consen 30 KICPNCGA 37 (50)
T ss_pred CCCcCCcC
Confidence 34444443
No 134
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=61.22 E-value=12 Score=33.89 Aligned_cols=34 Identities=21% Similarity=0.482 Sum_probs=18.4
Q ss_pred ccCCCCCCcccccccccccccccccccccccCCCCceeecCCCCCC
Q psy13443 42 FVCVHCKQFEVVPTRKTQTLEHCATCVDMVRPDASYTYMCYLCNYH 87 (188)
Q Consensus 42 ~~C~~C~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~C~~C~~~ 87 (188)
+.|+.||..... ..|+.||.... ..|.|+.|+..
T Consensus 668 rkCPkCG~~t~~--------~fCP~CGs~te----~vy~CPsCGae 701 (1337)
T PRK14714 668 RRCPSCGTETYE--------NRCPDCGTHTE----PVYVCPDCGAE 701 (1337)
T ss_pred EECCCCCCcccc--------ccCcccCCcCC----CceeCccCCCc
Confidence 678888762110 15666665542 24566666654
No 135
>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=61.09 E-value=6.4 Score=32.05 Aligned_cols=16 Identities=38% Similarity=0.897 Sum_probs=9.0
Q ss_pred hcCCCCceecccCccc
Q psy13443 100 THNGEKPFRCALCAYS 115 (188)
Q Consensus 100 ~h~~~~~~~C~~C~~~ 115 (188)
.|.......|..||..
T Consensus 234 ~h~~~~~l~Ch~Cg~~ 249 (505)
T TIGR00595 234 YHKKEGKLRCHYCGYQ 249 (505)
T ss_pred EecCCCeEEcCCCcCc
Confidence 3444455677777743
No 136
>KOG1280|consensus
Probab=60.36 E-value=10 Score=28.94 Aligned_cols=40 Identities=23% Similarity=0.492 Sum_probs=31.6
Q ss_pred CCCccccCCCcccccCHHHHHHHHHhhhcCCc--ccCCCCCC
Q psy13443 10 AKQQFECDFCPYGAKQAADVHNHVQQIHMGVN--FVCVHCKQ 49 (188)
Q Consensus 10 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~--~~C~~C~~ 49 (188)
.+.-|.|+.|++.-.+...|..|....|.+.+ ..|+.|..
T Consensus 76 ~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~ 117 (381)
T KOG1280|consen 76 DPQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAA 117 (381)
T ss_pred ccccccCCcccccccchhHHHHHhhhcCcccCcceeeecccc
Confidence 34469999999988888999999988887765 56777755
No 137
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=60.32 E-value=11 Score=18.90 Aligned_cols=13 Identities=23% Similarity=0.501 Sum_probs=8.6
Q ss_pred ceeecCCCCCCCC
Q psy13443 77 YTYMCYLCNYHTP 89 (188)
Q Consensus 77 ~~~~C~~C~~~f~ 89 (188)
..|.|..|+..+.
T Consensus 27 ~fy~C~~C~~~w~ 39 (40)
T smart00440 27 VFYVCTKCGHRWR 39 (40)
T ss_pred EEEEeCCCCCEeC
Confidence 3577888876543
No 138
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=60.18 E-value=7.9 Score=19.30 Aligned_cols=13 Identities=15% Similarity=0.324 Sum_probs=8.5
Q ss_pred eeecCCCCCCCCC
Q psy13443 78 TYMCYLCNYHTPT 90 (188)
Q Consensus 78 ~~~C~~C~~~f~~ 90 (188)
+|.|..|+..|-.
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 5667777766653
No 139
>PRK04023 DNA polymerase II large subunit; Validated
Probab=59.47 E-value=12 Score=32.98 Aligned_cols=8 Identities=25% Similarity=0.688 Sum_probs=4.3
Q ss_pred ccCCCCCC
Q psy13443 42 FVCVHCKQ 49 (188)
Q Consensus 42 ~~C~~C~~ 49 (188)
..|+.||.
T Consensus 627 RfCpsCG~ 634 (1121)
T PRK04023 627 RKCPSCGK 634 (1121)
T ss_pred ccCCCCCC
Confidence 45555555
No 140
>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=59.16 E-value=7.3 Score=21.09 Aligned_cols=10 Identities=40% Similarity=0.766 Sum_probs=4.8
Q ss_pred cccCCCcccc
Q psy13443 14 FECDFCPYGA 23 (188)
Q Consensus 14 ~~C~~C~~~f 23 (188)
++|+.|+..+
T Consensus 3 ~~CP~CG~~i 12 (54)
T TIGR01206 3 FECPDCGAEI 12 (54)
T ss_pred cCCCCCCCEE
Confidence 3455555443
No 141
>KOG3408|consensus
Probab=57.53 E-value=6.1 Score=25.21 Aligned_cols=25 Identities=16% Similarity=0.284 Sum_probs=19.0
Q ss_pred CCCccCCCCcccccCcHHHHHHHHH
Q psy13443 132 EKPHACGMCGYECAQGSQLMQHLRK 156 (188)
Q Consensus 132 ~~~~~C~~C~~~f~~~~~l~~H~~~ 156 (188)
...|-|-.|.+.|.+...|..|.++
T Consensus 55 ~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 55 GGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CceeehhhhhhhhcchHHHHHHHhc
Confidence 3347788888888888888888764
No 142
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=56.65 E-value=7.2 Score=25.40 Aligned_cols=25 Identities=20% Similarity=0.182 Sum_probs=19.5
Q ss_pred ccCCCCcccccCcHHHHHHHHHhcCCCC
Q psy13443 135 HACGMCGYECAQGSQLMQHLRKVHKVDK 162 (188)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 162 (188)
+.|-.+|+.|. +|.+|+.+|++..|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 67888888884 58899988887654
No 143
>PRK14873 primosome assembly protein PriA; Provisional
Probab=56.53 E-value=7.5 Score=32.84 Aligned_cols=26 Identities=23% Similarity=0.595 Sum_probs=15.6
Q ss_pred CCCCceecccCccccCCchhHHHHHHhhcCCCCccCCCCccc
Q psy13443 102 NGEKPFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYE 143 (188)
Q Consensus 102 ~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~ 143 (188)
...+...|..||.. ..|..|+.|+..
T Consensus 406 ~~~~~l~Ch~CG~~----------------~~p~~Cp~Cgs~ 431 (665)
T PRK14873 406 SAGGTPRCRWCGRA----------------APDWRCPRCGSD 431 (665)
T ss_pred cCCCeeECCCCcCC----------------CcCccCCCCcCC
Confidence 33445677777742 124578888754
No 144
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=56.22 E-value=7 Score=20.68 Aligned_cols=10 Identities=20% Similarity=0.554 Sum_probs=4.1
Q ss_pred eecccCcccc
Q psy13443 107 FRCALCAYSA 116 (188)
Q Consensus 107 ~~C~~C~~~~ 116 (188)
+.|..||..|
T Consensus 5 l~C~dCg~~F 14 (49)
T PF13451_consen 5 LTCKDCGAEF 14 (49)
T ss_pred EEcccCCCeE
Confidence 3444444443
No 145
>KOG3214|consensus
Probab=55.56 E-value=7.4 Score=23.86 Aligned_cols=13 Identities=23% Similarity=0.547 Sum_probs=6.9
Q ss_pred eecccCccccCCc
Q psy13443 107 FRCALCAYSARRK 119 (188)
Q Consensus 107 ~~C~~C~~~~~~~ 119 (188)
..|.+|+.+|...
T Consensus 48 ~sC~iC~esFqt~ 60 (109)
T KOG3214|consen 48 ASCRICEESFQTT 60 (109)
T ss_pred eeeeehhhhhccc
Confidence 4555555555543
No 146
>KOG2907|consensus
Probab=54.17 E-value=4.6 Score=25.38 Aligned_cols=38 Identities=18% Similarity=0.444 Sum_probs=21.2
Q ss_pred eecccCccccCCchhHHHHHHhhcC--CCCccCCCCcccccC
Q psy13443 107 FRCALCAYSARRKTHLDDHMRRHTG--EKPHACGMCGYECAQ 146 (188)
Q Consensus 107 ~~C~~C~~~~~~~~~l~~H~~~h~~--~~~~~C~~C~~~f~~ 146 (188)
.+|+.||..=.....++ +|..-. --.|.|+.|++.|+.
T Consensus 75 ~kCpkCghe~m~Y~T~Q--lRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQ--LRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred ccCcccCCchhhhhhhh--cccccCCceEEEEcCccceeeec
Confidence 57888886544433332 222211 123888888887764
No 147
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=53.07 E-value=17 Score=32.99 Aligned_cols=53 Identities=23% Similarity=0.449 Sum_probs=33.2
Q ss_pred cccCCCcccccCHHHHHHHHHhhhcCCcccCCCCCCcccccccccccccccccccccccCCCCceeecCCCCCCCC
Q psy13443 14 FECDFCPYGAKQAADVHNHVQQIHMGVNFVCVHCKQFEVVPTRKTQTLEHCATCVDMVRPDASYTYMCYLCNYHTP 89 (188)
Q Consensus 14 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~C~~C~~~f~ 89 (188)
+.|+.||.... ...|+.||... .....|+.|+..+.........|+.|+....
T Consensus 668 rkCPkCG~~t~----------------~~fCP~CGs~t-------e~vy~CPsCGaev~~des~a~~CP~CGtplv 720 (1337)
T PRK14714 668 RRCPSCGTETY----------------ENRCPDCGTHT-------EPVYVCPDCGAEVPPDESGRVECPRCDVELT 720 (1337)
T ss_pred EECCCCCCccc----------------cccCcccCCcC-------CCceeCccCCCccCCCccccccCCCCCCccc
Confidence 78999997411 12688887721 1123788888876654333557999985443
No 148
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=53.01 E-value=7.6 Score=23.90 Aligned_cols=8 Identities=38% Similarity=1.202 Sum_probs=7.1
Q ss_pred ccCCCCCC
Q psy13443 42 FVCVHCKQ 49 (188)
Q Consensus 42 ~~C~~C~~ 49 (188)
|.|+.|+.
T Consensus 23 FtCp~Cgh 30 (104)
T COG4888 23 FTCPRCGH 30 (104)
T ss_pred EecCccCC
Confidence 89999987
No 149
>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=52.68 E-value=6.3 Score=19.62 Aligned_cols=12 Identities=25% Similarity=0.611 Sum_probs=7.9
Q ss_pred ceeecCCCCCCC
Q psy13443 77 YTYMCYLCNYHT 88 (188)
Q Consensus 77 ~~~~C~~C~~~f 88 (188)
..|.|..|+..+
T Consensus 27 ~fy~C~~C~~~w 38 (39)
T PF01096_consen 27 LFYVCCNCGHRW 38 (39)
T ss_dssp EEEEESSSTEEE
T ss_pred EEEEeCCCCCee
Confidence 347788887644
No 150
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=52.59 E-value=9.9 Score=30.00 Aligned_cols=29 Identities=21% Similarity=0.557 Sum_probs=18.7
Q ss_pred ecccCccccCCchhHHHHHHhhcCCCCccCCCCcccccCc
Q psy13443 108 RCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYECAQG 147 (188)
Q Consensus 108 ~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~ 147 (188)
.|+.||....+. |..-|+|+.|++.+...
T Consensus 352 ~Cp~Cg~~m~S~-----------G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 352 VCPRCGGRMKSA-----------GRNGFRCKKCGTRARET 380 (421)
T ss_pred CCCccCCchhhc-----------CCCCcccccccccCCcc
Confidence 677777665543 22267888888777654
No 151
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=52.56 E-value=11 Score=23.33 Aligned_cols=16 Identities=19% Similarity=0.486 Sum_probs=11.5
Q ss_pred CceecccCccccCCch
Q psy13443 105 KPFRCALCAYSARRKT 120 (188)
Q Consensus 105 ~~~~C~~C~~~~~~~~ 120 (188)
+|++|..||..|..-+
T Consensus 1 MpH~CtrCG~vf~~g~ 16 (112)
T COG3364 1 MPHQCTRCGEVFDDGS 16 (112)
T ss_pred CCceeccccccccccc
Confidence 3567888888887743
No 152
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=52.18 E-value=32 Score=26.01 Aligned_cols=25 Identities=20% Similarity=0.369 Sum_probs=17.0
Q ss_pred CceecccCccccCCchhHHHHHHhh
Q psy13443 105 KPFRCALCAYSARRKTHLDDHMRRH 129 (188)
Q Consensus 105 ~~~~C~~C~~~~~~~~~l~~H~~~h 129 (188)
..|.|+.|-..|...-+.-.|...|
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHHHh
Confidence 4577777777777766666666665
No 153
>KOG4173|consensus
Probab=52.06 E-value=9.1 Score=26.95 Aligned_cols=51 Identities=22% Similarity=0.511 Sum_probs=39.8
Q ss_pred Cceeccc--CccccCCchhHHHHHHhhcCCCCccCCCCcccccCcHHHHHHHHHhc
Q psy13443 105 KPFRCAL--CAYSARRKTHLDDHMRRHTGEKPHACGMCGYECAQGSQLMQHLRKVH 158 (188)
Q Consensus 105 ~~~~C~~--C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h 158 (188)
..+.|++ |...|.....+..|--+-++ -.|..|.+.|.+...|..|+---|
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~H 130 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWH 130 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHH
Confidence 4577887 77888888877777654333 379999999999999999986544
No 154
>PRK00420 hypothetical protein; Validated
Probab=51.86 E-value=11 Score=23.82 Aligned_cols=11 Identities=9% Similarity=0.114 Sum_probs=5.5
Q ss_pred eeecCCCCCCC
Q psy13443 78 TYMCYLCNYHT 88 (188)
Q Consensus 78 ~~~C~~C~~~f 88 (188)
...|+.|+...
T Consensus 40 ~~~Cp~Cg~~~ 50 (112)
T PRK00420 40 EVVCPVHGKVY 50 (112)
T ss_pred ceECCCCCCee
Confidence 34555555433
No 155
>KOG3408|consensus
Probab=51.41 E-value=10 Score=24.19 Aligned_cols=25 Identities=24% Similarity=0.320 Sum_probs=21.8
Q ss_pred CCCccccCCCcccccCHHHHHHHHH
Q psy13443 10 AKQQFECDFCPYGAKQAADVHNHVQ 34 (188)
Q Consensus 10 ~~~~~~C~~C~~~f~~~~~l~~H~~ 34 (188)
|-..|-|-.|.+-|.+...|..|.+
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~k 78 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFK 78 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHh
Confidence 4456899999999999999999984
No 156
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=50.98 E-value=11 Score=32.07 Aligned_cols=21 Identities=19% Similarity=0.422 Sum_probs=12.6
Q ss_pred ccccccccccCCCCceeecCCCCCC
Q psy13443 63 HCATCVDMVRPDASYTYMCYLCNYH 87 (188)
Q Consensus 63 ~c~~c~~~~~~~~~~~~~C~~C~~~ 87 (188)
.|..|+.. ...|..|+.|+..
T Consensus 464 ~CH~Cg~~----~~~p~~Cp~Cgs~ 484 (730)
T COG1198 464 RCHYCGYQ----EPIPQSCPECGSE 484 (730)
T ss_pred EeCCCCCC----CCCCCCCCCCCCC
Confidence 45555554 2456778888743
No 157
>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=50.93 E-value=9.5 Score=27.22 Aligned_cols=30 Identities=20% Similarity=0.356 Sum_probs=23.3
Q ss_pred CCCccccCCCcccccCHHHHHHHHHhhhcC
Q psy13443 10 AKQQFECDFCPYGAKQAADVHNHVQQIHMG 39 (188)
Q Consensus 10 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 39 (188)
.+.-|.|..|++.|.-..-+..|+...|.+
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 445699999999999999999999888865
No 158
>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=50.36 E-value=11 Score=17.27 Aligned_cols=10 Identities=30% Similarity=1.118 Sum_probs=3.9
Q ss_pred ceeecCCCCC
Q psy13443 77 YTYMCYLCNY 86 (188)
Q Consensus 77 ~~~~C~~C~~ 86 (188)
..|.|.+|+.
T Consensus 14 ~~Y~C~~Cdf 23 (30)
T PF07649_consen 14 WFYRCSECDF 23 (30)
T ss_dssp -EEE-TTT--
T ss_pred ceEECccCCC
Confidence 4566666654
No 159
>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=50.33 E-value=7.2 Score=18.25 Aligned_cols=8 Identities=25% Similarity=0.779 Sum_probs=3.6
Q ss_pred ceecccCc
Q psy13443 106 PFRCALCA 113 (188)
Q Consensus 106 ~~~C~~C~ 113 (188)
.+.|+.|+
T Consensus 19 ~~vCp~C~ 26 (30)
T PF08274_consen 19 LLVCPECG 26 (30)
T ss_dssp SEEETTTT
T ss_pred EEeCCccc
Confidence 34444444
No 160
>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=50.28 E-value=6 Score=21.15 Aligned_cols=20 Identities=25% Similarity=0.353 Sum_probs=6.7
Q ss_pred eeecCCCCCCCCCHHHHHHH
Q psy13443 78 TYMCYLCNYHTPTRKYMRTH 97 (188)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H 97 (188)
.|.|+.|...|-..=.+-.|
T Consensus 21 ~y~C~~C~~~FC~dCD~fiH 40 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIH 40 (51)
T ss_dssp EE--TTTT--B-HHHHHTTT
T ss_pred eEECCCCCCccccCcChhhh
Confidence 45555555555444333333
No 161
>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=49.82 E-value=16 Score=20.58 Aligned_cols=10 Identities=30% Similarity=1.036 Sum_probs=4.6
Q ss_pred ceecccCccc
Q psy13443 106 PFRCALCAYS 115 (188)
Q Consensus 106 ~~~C~~C~~~ 115 (188)
.|.|+.||..
T Consensus 46 ~~~C~~Cg~~ 55 (69)
T PF07282_consen 46 VFTCPNCGFE 55 (69)
T ss_pred eEEcCCCCCE
Confidence 3444444444
No 162
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.16 E-value=3.2 Score=29.71 Aligned_cols=39 Identities=23% Similarity=0.636 Sum_probs=21.3
Q ss_pred CceecccCccccCCchhHHHHHHhhcCC----------CC-----ccCCCCccc
Q psy13443 105 KPFRCALCAYSARRKTHLDDHMRRHTGE----------KP-----HACGMCGYE 143 (188)
Q Consensus 105 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~----------~~-----~~C~~C~~~ 143 (188)
+.+.||+|+..|.....+..-.++-.|+ -| ..||.|..+
T Consensus 18 k~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~yA 71 (267)
T COG1655 18 KTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYYA 71 (267)
T ss_pred ceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhHH
Confidence 4466777776666554443333333332 11 478888865
No 163
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=48.99 E-value=12 Score=22.62 Aligned_cols=14 Identities=14% Similarity=0.285 Sum_probs=9.0
Q ss_pred ceeecCCCCCCCCC
Q psy13443 77 YTYMCYLCNYHTPT 90 (188)
Q Consensus 77 ~~~~C~~C~~~f~~ 90 (188)
..+.|..|++.|..
T Consensus 53 GIW~C~~C~~~~AG 66 (90)
T PTZ00255 53 GIWRCKGCKKTVAG 66 (90)
T ss_pred EEEEcCCCCCEEeC
Confidence 34677777776643
No 164
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=48.35 E-value=25 Score=17.68 Aligned_cols=23 Identities=17% Similarity=0.310 Sum_probs=13.1
Q ss_pred ccCCCCcccccC--cHHHHHHHHHh
Q psy13443 135 HACGMCGYECAQ--GSQLMQHLRKV 157 (188)
Q Consensus 135 ~~C~~C~~~f~~--~~~l~~H~~~~ 157 (188)
..|+.|+..|.. +.+-..|.+-|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 467777766543 45555555443
No 165
>KOG4167|consensus
Probab=48.26 E-value=4.8 Score=33.84 Aligned_cols=27 Identities=15% Similarity=0.213 Sum_probs=22.7
Q ss_pred CCccccCCCcccccCHHHHHHHHHhhh
Q psy13443 11 KQQFECDFCPYGAKQAADVHNHVQQIH 37 (188)
Q Consensus 11 ~~~~~C~~C~~~f~~~~~l~~H~~~~~ 37 (188)
...|.|..|++.|....++..||..|-
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 457999999999999999999995443
No 166
>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=48.09 E-value=17 Score=29.21 Aligned_cols=32 Identities=19% Similarity=0.281 Sum_probs=26.5
Q ss_pred ccCCCccccCCCcccccCHHHHHHHHHhhhcC
Q psy13443 8 HLAKQQFECDFCPYGAKQAADVHNHVQQIHMG 39 (188)
Q Consensus 8 h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 39 (188)
+...+.+.|+.|.+.|.+...+..|+...|.+
T Consensus 52 n~sWrFWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 52 NKSWRFWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred cCceeEeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 33445678999999999999999999877765
No 167
>KOG2636|consensus
Probab=47.47 E-value=15 Score=29.15 Aligned_cols=27 Identities=22% Similarity=0.527 Sum_probs=21.7
Q ss_pred ccCCCccccCCCc-ccccCHHHHHHHHH
Q psy13443 8 HLAKQQFECDFCP-YGAKQAADVHNHVQ 34 (188)
Q Consensus 8 h~~~~~~~C~~C~-~~f~~~~~l~~H~~ 34 (188)
|.-...|.|.+|| +++.....+.+|+.
T Consensus 396 HGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 396 HGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred cCCCcccceeeccCccccCcHHHHHHhH
Confidence 4456679999999 78888888888874
No 168
>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=47.23 E-value=15 Score=29.57 Aligned_cols=28 Identities=14% Similarity=0.380 Sum_probs=23.3
Q ss_pred CccCCCCcccccCcHHHHHHHHHhcCCC
Q psy13443 134 PHACGMCGYECAQGSQLMQHLRKVHKVD 161 (188)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 161 (188)
.+.|+.|.+.|.....+..|+...|...
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 4789999999999999999998877544
No 169
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=46.65 E-value=12 Score=17.91 Aligned_cols=11 Identities=18% Similarity=0.528 Sum_probs=5.9
Q ss_pred eeecCCCCCCC
Q psy13443 78 TYMCYLCNYHT 88 (188)
Q Consensus 78 ~~~C~~C~~~f 88 (188)
-+.|..|+..|
T Consensus 21 ~~~C~~Cg~~~ 31 (33)
T PF08792_consen 21 YEVCIFCGSSF 31 (33)
T ss_pred eEEcccCCcEe
Confidence 34566665544
No 170
>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=45.51 E-value=7 Score=33.61 Aligned_cols=8 Identities=25% Similarity=0.708 Sum_probs=0.0
Q ss_pred ccCCCCCC
Q psy13443 42 FVCVHCKQ 49 (188)
Q Consensus 42 ~~C~~C~~ 49 (188)
+.|+.|+.
T Consensus 656 r~Cp~Cg~ 663 (900)
T PF03833_consen 656 RRCPKCGK 663 (900)
T ss_dssp --------
T ss_pred ccCcccCC
Confidence 44555544
No 171
>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=45.35 E-value=13 Score=23.58 Aligned_cols=12 Identities=17% Similarity=0.354 Sum_probs=6.5
Q ss_pred eeecCCCCCCCC
Q psy13443 78 TYMCYLCNYHTP 89 (188)
Q Consensus 78 ~~~C~~C~~~f~ 89 (188)
...|..|+..|.
T Consensus 70 ~~~C~~Cg~~~~ 81 (115)
T TIGR00100 70 ECECEDCSEEVS 81 (115)
T ss_pred EEEcccCCCEEe
Confidence 355666665544
No 172
>KOG3002|consensus
Probab=45.06 E-value=61 Score=24.57 Aligned_cols=109 Identities=19% Similarity=0.321 Sum_probs=63.0
Q ss_pred ccCCCCCCccccccccccccc-ccccccccccCCCCceeecCCCCCCCCCHHHHHHHHHhcCCCCceeccc----Ccccc
Q psy13443 42 FVCVHCKQFEVVPTRKTQTLE-HCATCVDMVRPDASYTYMCYLCNYHTPTRKYMRTHIDTHNGEKPFRCAL----CAYSA 116 (188)
Q Consensus 42 ~~C~~C~~~~~~~~~~~~~~~-~c~~c~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~----C~~~~ 116 (188)
+.|+.|-.......++...+. .|..|.. +....|+.|...+.....+..=... ......|+. |...|
T Consensus 49 leCPvC~~~l~~Pi~QC~nGHlaCssC~~------~~~~~CP~Cr~~~g~~R~~amEkV~--e~~~vpC~~~~~GC~~~~ 120 (299)
T KOG3002|consen 49 LDCPVCFNPLSPPIFQCDNGHLACSSCRT------KVSNKCPTCRLPIGNIRCRAMEKVA--EAVLVPCKNAKLGCTKSF 120 (299)
T ss_pred ccCchhhccCcccceecCCCcEehhhhhh------hhcccCCccccccccHHHHHHHHHH--HhceecccccccCCceee
Confidence 568877664444444444433 4555543 3346899999888755443332222 223355653 77787
Q ss_pred CCchhHHHHHHhhcCCCCccCCCCcccc---cCcHHHHHHHHHhcCC
Q psy13443 117 RRKTHLDDHMRRHTGEKPHACGMCGYEC---AQGSQLMQHLRKVHKV 160 (188)
Q Consensus 117 ~~~~~l~~H~~~h~~~~~~~C~~C~~~f---~~~~~l~~H~~~~h~~ 160 (188)
..... ..|.+.... .|+.|+.=+... .....|..|.+.-|+.
T Consensus 121 ~Y~~~-~~HE~~C~f-~~~~CP~p~~~C~~~G~~~~l~~H~~~~hk~ 165 (299)
T KOG3002|consen 121 PYGEK-SKHEKVCEF-RPCSCPVPGAECKYTGSYKDLYAHLNDTHKS 165 (299)
T ss_pred ccccc-ccccccccc-CCcCCCCCcccCCccCcHHHHHHHHHhhChh
Confidence 77766 566666554 677776542111 2346788888877755
No 173
>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=44.45 E-value=15 Score=22.31 Aligned_cols=12 Identities=17% Similarity=0.526 Sum_probs=8.3
Q ss_pred eeecCCCCCCCC
Q psy13443 78 TYMCYLCNYHTP 89 (188)
Q Consensus 78 ~~~C~~C~~~f~ 89 (188)
.+.|..|++.|.
T Consensus 53 IW~C~~C~~~~A 64 (91)
T TIGR00280 53 IWTCRKCGAKFA 64 (91)
T ss_pred EEEcCCCCCEEe
Confidence 467777777664
No 174
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=44.31 E-value=5.8 Score=26.41 Aligned_cols=14 Identities=14% Similarity=0.185 Sum_probs=8.1
Q ss_pred eecccCccccCCch
Q psy13443 107 FRCALCAYSARRKT 120 (188)
Q Consensus 107 ~~C~~C~~~~~~~~ 120 (188)
-.|+.|+..|.+..
T Consensus 29 ReC~~C~~RFTTfE 42 (156)
T COG1327 29 RECLECGERFTTFE 42 (156)
T ss_pred hcccccccccchhh
Confidence 35666666666543
No 175
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=44.22 E-value=8.9 Score=21.97 Aligned_cols=10 Identities=30% Similarity=0.810 Sum_probs=4.1
Q ss_pred eeecCCCCCC
Q psy13443 78 TYMCYLCNYH 87 (188)
Q Consensus 78 ~~~C~~C~~~ 87 (188)
.|.|..|...
T Consensus 17 ~~~C~~C~~~ 26 (70)
T PF07191_consen 17 HYHCEACQKD 26 (70)
T ss_dssp EEEETTT--E
T ss_pred EEECcccccc
Confidence 4555555543
No 176
>KOG2807|consensus
Probab=43.72 E-value=57 Score=24.97 Aligned_cols=31 Identities=23% Similarity=0.404 Sum_probs=21.0
Q ss_pred CceecccCccccCCchhHHHHHHhhcCCCCccCCCCc
Q psy13443 105 KPFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCG 141 (188)
Q Consensus 105 ~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~ 141 (188)
..|+|..|-..|...=+...|...| .|+.|.
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHesLh------~CpgCe 374 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHESLH------NCPGCE 374 (378)
T ss_pred CcEEchhccceeeccchHHHHhhhh------cCCCcC
Confidence 4577777777777776666676666 466665
No 177
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=43.52 E-value=22 Score=19.02 Aligned_cols=12 Identities=17% Similarity=0.681 Sum_probs=5.0
Q ss_pred eecccCccccCC
Q psy13443 107 FRCALCAYSARR 118 (188)
Q Consensus 107 ~~C~~C~~~~~~ 118 (188)
+.|+.|+..|..
T Consensus 29 W~C~~Cgh~w~~ 40 (55)
T PF14311_consen 29 WKCPKCGHEWKA 40 (55)
T ss_pred EECCCCCCeeEc
Confidence 344444444333
No 178
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=43.45 E-value=21 Score=23.95 Aligned_cols=33 Identities=36% Similarity=0.790 Sum_probs=14.5
Q ss_pred ceeecCCCCCCCCCHHHHHHHHHhcCCCCceecccCcc
Q psy13443 77 YTYMCYLCNYHTPTRKYMRTHIDTHNGEKPFRCALCAY 114 (188)
Q Consensus 77 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 114 (188)
.+|.|. |+..|.+. ..|-.+-.|+ .|.|..|+.
T Consensus 116 ~~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~g 148 (156)
T COG3091 116 YPYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGG 148 (156)
T ss_pred eeEEee-cCCccchh---hhcccccccc-eEEeccCCc
Confidence 345555 55544322 2232333333 455555553
No 179
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=43.33 E-value=13 Score=23.65 Aligned_cols=12 Identities=17% Similarity=0.398 Sum_probs=7.2
Q ss_pred eeecCCCCCCCC
Q psy13443 78 TYMCYLCNYHTP 89 (188)
Q Consensus 78 ~~~C~~C~~~f~ 89 (188)
.+.|..|+..|.
T Consensus 70 ~~~C~~Cg~~~~ 81 (114)
T PRK03681 70 ECWCETCQQYVT 81 (114)
T ss_pred EEEcccCCCeee
Confidence 456777775444
No 180
>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=43.26 E-value=5.7 Score=26.39 Aligned_cols=16 Identities=13% Similarity=0.123 Sum_probs=10.3
Q ss_pred eecccCccccCCchhH
Q psy13443 107 FRCALCAYSARRKTHL 122 (188)
Q Consensus 107 ~~C~~C~~~~~~~~~l 122 (188)
-.|..|++.|.+...+
T Consensus 29 ReC~~C~~RFTTyErv 44 (147)
T TIGR00244 29 RECLECHERFTTFERA 44 (147)
T ss_pred ccCCccCCccceeeec
Confidence 4577777777766544
No 181
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=42.72 E-value=17 Score=23.07 Aligned_cols=11 Identities=18% Similarity=0.504 Sum_probs=5.7
Q ss_pred eecCCCCCCCC
Q psy13443 79 YMCYLCNYHTP 89 (188)
Q Consensus 79 ~~C~~C~~~f~ 89 (188)
+.|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PRK12380 71 AWCWDCSQVVE 81 (113)
T ss_pred EEcccCCCEEe
Confidence 45555554444
No 182
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=42.40 E-value=4.8 Score=33.79 Aligned_cols=74 Identities=20% Similarity=0.441 Sum_probs=42.7
Q ss_pred ccccccccccCCCCcee-----ecCCCCCCCCCHHHHHHHHHhcCCCCce-ecccCccccCCchhHHHHHHhhcCCCCcc
Q psy13443 63 HCATCVDMVRPDASYTY-----MCYLCNYHTPTRKYMRTHIDTHNGEKPF-RCALCAYSARRKTHLDDHMRRHTGEKPHA 136 (188)
Q Consensus 63 ~c~~c~~~~~~~~~~~~-----~C~~C~~~f~~~~~l~~H~~~h~~~~~~-~C~~C~~~~~~~~~l~~H~~~h~~~~~~~ 136 (188)
.|..|.+-+....++.| .|..||-.|+--..|--- +-.+.-+.| -|+.|.+.|....+-+.| ..|..
T Consensus 103 ~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPRfTIi~alPYD-R~nTsM~~F~lC~~C~~EY~dP~nRRfH------AQp~a 175 (750)
T COG0068 103 TCEDCLEEIFDPNSRRYLYPFINCTNCGPRFTIIEALPYD-RENTSMADFPLCPFCDKEYKDPLNRRFH------AQPIA 175 (750)
T ss_pred hhHHHHHHhcCCCCcceeccccccCCCCcceeeeccCCCC-cccCccccCcCCHHHHHHhcCccccccc------ccccc
Confidence 67777666665555433 388888777644332211 122222223 488888888887664443 24678
Q ss_pred CCCCccc
Q psy13443 137 CGMCGYE 143 (188)
Q Consensus 137 C~~C~~~ 143 (188)
|+.||..
T Consensus 176 Cp~CGP~ 182 (750)
T COG0068 176 CPKCGPH 182 (750)
T ss_pred CcccCCC
Confidence 8888864
No 183
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=41.81 E-value=14 Score=26.33 Aligned_cols=12 Identities=33% Similarity=0.584 Sum_probs=7.0
Q ss_pred HHHHHHHHHhcC
Q psy13443 148 SQLMQHLRKVHK 159 (188)
Q Consensus 148 ~~l~~H~~~~h~ 159 (188)
..|.+|+|.|.+
T Consensus 131 GLLLRhLRHHSN 142 (238)
T PF02084_consen 131 GLLLRHLRHHSN 142 (238)
T ss_pred HHHHHHHHHHHH
Confidence 455666665554
No 184
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=41.50 E-value=2.8 Score=35.11 Aligned_cols=33 Identities=21% Similarity=0.466 Sum_probs=22.6
Q ss_pred ecCCCCCCCCCHHHHHHHHHhcCCCCceecccCccccCC
Q psy13443 80 MCYLCNYHTPTRKYMRTHIDTHNGEKPFRCALCAYSARR 118 (188)
Q Consensus 80 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~~~~ 118 (188)
.|+.|.+.+..+.+..- |. .|..|+.||-....
T Consensus 153 lC~~C~~EY~dP~nRRf----HA--Qp~aCp~CGP~~~l 185 (750)
T COG0068 153 LCPFCDKEYKDPLNRRF----HA--QPIACPKCGPHLFL 185 (750)
T ss_pred CCHHHHHHhcCcccccc----cc--ccccCcccCCCeEE
Confidence 58999888877765333 32 36799999975433
No 185
>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=41.39 E-value=9.5 Score=19.36 Aligned_cols=15 Identities=20% Similarity=0.432 Sum_probs=9.3
Q ss_pred CccccCCCcccccCH
Q psy13443 12 QQFECDFCPYGAKQA 26 (188)
Q Consensus 12 ~~~~C~~C~~~f~~~ 26 (188)
.|+.|+.|+..|-..
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 578999999988743
No 186
>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=41.27 E-value=15 Score=20.62 Aligned_cols=6 Identities=33% Similarity=0.960 Sum_probs=1.5
Q ss_pred ecCCCC
Q psy13443 80 MCYLCN 85 (188)
Q Consensus 80 ~C~~C~ 85 (188)
.|..||
T Consensus 27 hCr~CG 32 (69)
T PF01363_consen 27 HCRNCG 32 (69)
T ss_dssp E-TTT-
T ss_pred ccCCCC
Confidence 333333
No 187
>KOG1701|consensus
Probab=41.12 E-value=24 Score=27.87 Aligned_cols=13 Identities=15% Similarity=0.526 Sum_probs=9.0
Q ss_pred ceecccCccccCC
Q psy13443 106 PFRCALCAYSARR 118 (188)
Q Consensus 106 ~~~C~~C~~~~~~ 118 (188)
=|+|..|+...+.
T Consensus 427 CY~CEDCg~~LS~ 439 (468)
T KOG1701|consen 427 CYKCEDCGLLLSS 439 (468)
T ss_pred ceehhhcCccccc
Confidence 4778888876654
No 188
>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=41.11 E-value=6.3 Score=22.62 Aligned_cols=30 Identities=20% Similarity=0.431 Sum_probs=13.3
Q ss_pred ceecccCccccCCchhHHHHHHhhcCCCCccCCCCccc
Q psy13443 106 PFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYE 143 (188)
Q Consensus 106 ~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~ 143 (188)
...|..|+........ ..+ ..+.|+.|+..
T Consensus 41 ~v~Cg~C~~~~~~~~~-------~c~-~~~~C~~C~~~ 70 (71)
T PF05495_consen 41 RVICGKCRTEQPIDEY-------SCG-ADYFCPICGLY 70 (71)
T ss_dssp EEEETTT--EEES-SB-------TT---SEEETTTTEE
T ss_pred CeECCCCCCccChhhh-------hcC-CCccCcCcCCC
Confidence 4566666655444332 111 34666666644
No 189
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=41.05 E-value=13 Score=24.16 Aligned_cols=12 Identities=25% Similarity=0.595 Sum_probs=7.0
Q ss_pred CccCCCCccccc
Q psy13443 134 PHACGMCGYECA 145 (188)
Q Consensus 134 ~~~C~~C~~~f~ 145 (188)
.|+|..|++.|.
T Consensus 53 RyrC~~C~~tf~ 64 (129)
T COG3677 53 RYKCKSCGSTFT 64 (129)
T ss_pred ccccCCcCccee
Confidence 456666666554
No 190
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.71 E-value=17 Score=22.80 Aligned_cols=12 Identities=17% Similarity=0.152 Sum_probs=7.7
Q ss_pred CceecccCcccc
Q psy13443 105 KPFRCALCAYSA 116 (188)
Q Consensus 105 ~~~~C~~C~~~~ 116 (188)
.|..|+.||++|
T Consensus 25 dPiVsPytG~s~ 36 (129)
T COG4530 25 DPIVSPYTGKSY 36 (129)
T ss_pred CccccCcccccc
Confidence 456666666666
No 191
>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=40.59 E-value=27 Score=18.60 Aligned_cols=11 Identities=27% Similarity=0.700 Sum_probs=3.9
Q ss_pred ecccCccccCC
Q psy13443 108 RCALCAYSARR 118 (188)
Q Consensus 108 ~C~~C~~~~~~ 118 (188)
.||+|++.|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 56666655543
No 192
>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=39.61 E-value=24 Score=21.48 Aligned_cols=8 Identities=63% Similarity=1.526 Sum_probs=5.0
Q ss_pred ccCCCCCC
Q psy13443 42 FVCVHCKQ 49 (188)
Q Consensus 42 ~~C~~C~~ 49 (188)
|.|..||.
T Consensus 5 F~C~~CG~ 12 (92)
T PF12647_consen 5 FTCVHCGL 12 (92)
T ss_pred cCccccCC
Confidence 56666665
No 193
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=39.59 E-value=17 Score=21.99 Aligned_cols=9 Identities=33% Similarity=0.877 Sum_probs=7.0
Q ss_pred cccCCCCCC
Q psy13443 41 NFVCVHCKQ 49 (188)
Q Consensus 41 ~~~C~~C~~ 49 (188)
.|.|+.|++
T Consensus 36 ~y~CpfCgk 44 (90)
T PRK03976 36 KHVCPVCGR 44 (90)
T ss_pred CccCCCCCC
Confidence 488888876
No 194
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=38.64 E-value=45 Score=28.26 Aligned_cols=24 Identities=29% Similarity=0.490 Sum_probs=10.7
Q ss_pred ccccccccccCCCCceeecCCCCCCCC
Q psy13443 63 HCATCVDMVRPDASYTYMCYLCNYHTP 89 (188)
Q Consensus 63 ~c~~c~~~~~~~~~~~~~C~~C~~~f~ 89 (188)
.|+.||....... --|+.||....
T Consensus 29 ~Cp~CG~~~~~~~---~fC~~CG~~~~ 52 (645)
T PRK14559 29 PCPQCGTEVPVDE---AHCPNCGAETG 52 (645)
T ss_pred cCCCCCCCCCccc---ccccccCCccc
Confidence 3555555543211 23555554443
No 195
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=38.42 E-value=16 Score=27.68 Aligned_cols=13 Identities=31% Similarity=0.682 Sum_probs=7.9
Q ss_pred CccCCCCcccccC
Q psy13443 134 PHACGMCGYECAQ 146 (188)
Q Consensus 134 ~~~C~~C~~~f~~ 146 (188)
...|..|+...+.
T Consensus 252 ~e~C~~C~~YlK~ 264 (309)
T PRK03564 252 AESCGDCGTYLKI 264 (309)
T ss_pred eeeccccccccee
Confidence 3567777765544
No 196
>KOG4377|consensus
Probab=37.79 E-value=53 Score=25.96 Aligned_cols=21 Identities=29% Similarity=0.290 Sum_probs=17.8
Q ss_pred CCcccccCcHHHHHHHHHhcC
Q psy13443 139 MCGYECAQGSQLMQHLRKVHK 159 (188)
Q Consensus 139 ~C~~~f~~~~~l~~H~~~~h~ 159 (188)
.|+.++.+.+++..|.|.|-.
T Consensus 408 Gc~~tl~s~sqm~shkrkheR 428 (480)
T KOG4377|consen 408 GCEATLYSVSQMASHKRKHER 428 (480)
T ss_pred CCceEEEehhhhhhhhhhhhh
Confidence 488999999999999887764
No 197
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=37.76 E-value=27 Score=24.09 Aligned_cols=17 Identities=12% Similarity=0.282 Sum_probs=8.2
Q ss_pred CCCceecccCccccCCc
Q psy13443 103 GEKPFRCALCAYSARRK 119 (188)
Q Consensus 103 ~~~~~~C~~C~~~~~~~ 119 (188)
...-|.|+.|...|+..
T Consensus 110 ~~~~y~C~~~~~r~sfd 126 (176)
T COG1675 110 ENNYYVCPNCHVKYSFD 126 (176)
T ss_pred cCCceeCCCCCCcccHH
Confidence 33445555555444443
No 198
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=37.45 E-value=24 Score=23.81 Aligned_cols=26 Identities=31% Similarity=0.611 Sum_probs=17.2
Q ss_pred ccccccccccCCCCceeecCCCCCCC
Q psy13443 63 HCATCVDMVRPDASYTYMCYLCNYHT 88 (188)
Q Consensus 63 ~c~~c~~~~~~~~~~~~~C~~C~~~f 88 (188)
.|+.|.+.+...+...|.|..|+..+
T Consensus 36 aC~~C~kkv~~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 36 ACPGCNKKVVEEGNGTYRCEKCNKSV 61 (166)
T ss_pred cccccCcccEeCCCCcEECCCCCCcC
Confidence 56666666655444668888888765
No 199
>PRK10220 hypothetical protein; Provisional
Probab=37.16 E-value=29 Score=21.79 Aligned_cols=15 Identities=20% Similarity=0.350 Sum_probs=8.9
Q ss_pred ceeecCCCCCCCCCH
Q psy13443 77 YTYMCYLCNYHTPTR 91 (188)
Q Consensus 77 ~~~~C~~C~~~f~~~ 91 (188)
..|.|+.|+..+...
T Consensus 19 ~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 19 GMYICPECAHEWNDA 33 (111)
T ss_pred CeEECCcccCcCCcc
Confidence 346677777655543
No 200
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=37.11 E-value=18 Score=23.08 Aligned_cols=16 Identities=13% Similarity=0.171 Sum_probs=9.9
Q ss_pred CceeecCCCCCCCCCH
Q psy13443 76 SYTYMCYLCNYHTPTR 91 (188)
Q Consensus 76 ~~~~~C~~C~~~f~~~ 91 (188)
+..+.|..|+..|...
T Consensus 69 p~~~~C~~Cg~~~~~~ 84 (117)
T PRK00564 69 KVELECKDCSHVFKPN 84 (117)
T ss_pred CCEEEhhhCCCccccC
Confidence 3346777777666543
No 201
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=36.84 E-value=17 Score=23.85 Aligned_cols=16 Identities=13% Similarity=0.262 Sum_probs=10.4
Q ss_pred CceeecCCCCCCCCCH
Q psy13443 76 SYTYMCYLCNYHTPTR 91 (188)
Q Consensus 76 ~~~~~C~~C~~~f~~~ 91 (188)
+..+.|..|+..|...
T Consensus 68 p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 68 EAVLKCRNCGNEWSLK 83 (135)
T ss_pred ceEEECCCCCCEEecc
Confidence 4557777777666543
No 202
>COG1773 Rubredoxin [Energy production and conversion]
Probab=36.76 E-value=17 Score=19.74 Aligned_cols=15 Identities=27% Similarity=0.855 Sum_probs=11.9
Q ss_pred ceecccCccccCCch
Q psy13443 106 PFRCALCAYSARRKT 120 (188)
Q Consensus 106 ~~~C~~C~~~~~~~~ 120 (188)
.|+|.+||..|.-..
T Consensus 3 ~~~C~~CG~vYd~e~ 17 (55)
T COG1773 3 RWRCSVCGYVYDPEK 17 (55)
T ss_pred ceEecCCceEecccc
Confidence 589999999886653
No 203
>KOG4124|consensus
Probab=36.60 E-value=4.6 Score=30.80 Aligned_cols=50 Identities=24% Similarity=0.517 Sum_probs=36.4
Q ss_pred Cceeccc--CccccCCchhHHHHHHhhc-------------------CCCCccCCCCcccccCcHHHHHHH
Q psy13443 105 KPFRCAL--CAYSARRKTHLDDHMRRHT-------------------GEKPHACGMCGYECAQGSQLMQHL 154 (188)
Q Consensus 105 ~~~~C~~--C~~~~~~~~~l~~H~~~h~-------------------~~~~~~C~~C~~~f~~~~~l~~H~ 154 (188)
++|.|++ |.+.+.....|..|...-+ ..|||+|++|.+.++.-..|..|.
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~ 418 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHR 418 (442)
T ss_pred CCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCcee
Confidence 5688866 8888888878777764321 257899999999888766665554
No 204
>KOG1842|consensus
Probab=36.56 E-value=21 Score=28.36 Aligned_cols=28 Identities=25% Similarity=0.343 Sum_probs=19.1
Q ss_pred CccCCCCcccccCcHHHHHHHHHhcCCC
Q psy13443 134 PHACGMCGYECAQGSQLMQHLRKVHKVD 161 (188)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 161 (188)
.|.|++|...|.+...|..|+..-|+..
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 3677777777777777777776666443
No 205
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=36.54 E-value=24 Score=17.02 Aligned_cols=9 Identities=22% Similarity=0.947 Sum_probs=4.8
Q ss_pred eeecCCCCC
Q psy13443 78 TYMCYLCNY 86 (188)
Q Consensus 78 ~~~C~~C~~ 86 (188)
.+.|+.|+.
T Consensus 22 R~vC~~Cg~ 30 (34)
T PF14803_consen 22 RLVCPACGF 30 (34)
T ss_dssp EEEETTTTE
T ss_pred ceECCCCCC
Confidence 355666653
No 206
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.47 E-value=9.4 Score=22.16 Aligned_cols=28 Identities=25% Similarity=0.510 Sum_probs=15.4
Q ss_pred cccCCCcccccCHHHHHHHHHhhhcCCc-ccCCCCCC
Q psy13443 14 FECDFCPYGAKQAADVHNHVQQIHMGVN-FVCVHCKQ 49 (188)
Q Consensus 14 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~-~~C~~C~~ 49 (188)
|.|..|+..| .+.+++ .+-| -.|+.|+.
T Consensus 13 Y~c~~cg~~~----dvvq~~----~ddplt~ce~c~a 41 (82)
T COG2331 13 YECTECGNRF----DVVQAM----TDDPLTTCEECGA 41 (82)
T ss_pred EeecccchHH----HHHHhc----ccCccccChhhCh
Confidence 6777777764 344343 2223 45666665
No 207
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=36.33 E-value=26 Score=21.01 Aligned_cols=13 Identities=15% Similarity=0.363 Sum_probs=8.2
Q ss_pred ceeecCCCCCCCC
Q psy13443 77 YTYMCYLCNYHTP 89 (188)
Q Consensus 77 ~~~~C~~C~~~f~ 89 (188)
.-+.|..|+..|.
T Consensus 52 GIW~C~kCg~~fA 64 (89)
T COG1997 52 GIWKCRKCGAKFA 64 (89)
T ss_pred CeEEcCCCCCeec
Confidence 3466777776664
No 208
>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=35.33 E-value=12 Score=26.19 Aligned_cols=24 Identities=21% Similarity=0.513 Sum_probs=0.0
Q ss_pred CCccccCCCccc-ccCHHHHHHHHH
Q psy13443 11 KQQFECDFCPYG-AKQAADVHNHVQ 34 (188)
Q Consensus 11 ~~~~~C~~C~~~-f~~~~~l~~H~~ 34 (188)
...|.|.+||.. |.-+..+..|+.
T Consensus 99 ~~ey~CEICGN~~Y~GrkaFekHF~ 123 (196)
T PF11931_consen 99 GVEYKCEICGNQSYKGRKAFEKHFQ 123 (196)
T ss_dssp -------------------------
T ss_pred CCeeeeEeCCCcceecHHHHHHhcC
Confidence 456888888853 556777777763
No 209
>KOG4167|consensus
Probab=34.95 E-value=9.1 Score=32.33 Aligned_cols=25 Identities=24% Similarity=0.452 Sum_probs=22.8
Q ss_pred ceecccCccccCCchhHHHHHHhhc
Q psy13443 106 PFRCALCAYSARRKTHLDDHMRRHT 130 (188)
Q Consensus 106 ~~~C~~C~~~~~~~~~l~~H~~~h~ 130 (188)
-|.|..|++.|....++..||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 3899999999999999999999985
No 210
>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=34.62 E-value=11 Score=22.86 Aligned_cols=9 Identities=22% Similarity=1.014 Sum_probs=6.9
Q ss_pred cccCCCCCC
Q psy13443 41 NFVCVHCKQ 49 (188)
Q Consensus 41 ~~~C~~C~~ 49 (188)
+|.|+.|++
T Consensus 35 ky~Cp~Cgk 43 (90)
T PF01780_consen 35 KYTCPFCGK 43 (90)
T ss_dssp -BEESSSSS
T ss_pred CCcCCCCCC
Confidence 488888887
No 211
>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=34.60 E-value=24 Score=22.08 Aligned_cols=13 Identities=23% Similarity=0.539 Sum_probs=7.9
Q ss_pred eeecCCCCCCCCC
Q psy13443 78 TYMCYLCNYHTPT 90 (188)
Q Consensus 78 ~~~C~~C~~~f~~ 90 (188)
.|.|+.|+.....
T Consensus 19 ~~iCpeC~~EW~~ 31 (109)
T TIGR00686 19 QLICPSCLYEWNE 31 (109)
T ss_pred eeECccccccccc
Confidence 4667777665543
No 212
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=33.82 E-value=40 Score=18.36 Aligned_cols=11 Identities=27% Similarity=0.640 Sum_probs=5.8
Q ss_pred CCccCCCCccc
Q psy13443 133 KPHACGMCGYE 143 (188)
Q Consensus 133 ~~~~C~~C~~~ 143 (188)
..|.|+.||..
T Consensus 13 v~~~Cp~cGip 23 (55)
T PF13824_consen 13 VNFECPDCGIP 23 (55)
T ss_pred cCCcCCCCCCc
Confidence 34556666544
No 213
>KOG2272|consensus
Probab=33.38 E-value=6.1 Score=28.72 Aligned_cols=43 Identities=21% Similarity=0.498 Sum_probs=19.1
Q ss_pred ccCCCCCC-cccccccccccccccccccccccCCCCceeecCCC
Q psy13443 42 FVCVHCKQ-FEVVPTRKTQTLEHCATCVDMVRPDASYTYMCYLC 84 (188)
Q Consensus 42 ~~C~~C~~-~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~~C~~C 84 (188)
|.|..|++ ..+..-++......|..|.......+...|.|..|
T Consensus 100 F~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KC 143 (332)
T KOG2272|consen 100 FRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKC 143 (332)
T ss_pred chhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhh
Confidence 66666655 44433334444444444444433333333333333
No 214
>PF14369 zf-RING_3: zinc-finger
Probab=33.33 E-value=27 Score=16.93 Aligned_cols=8 Identities=25% Similarity=0.471 Sum_probs=3.4
Q ss_pred cCCCCCCC
Q psy13443 81 CYLCNYHT 88 (188)
Q Consensus 81 C~~C~~~f 88 (188)
|+.|+-+|
T Consensus 24 CP~C~~gF 31 (35)
T PF14369_consen 24 CPRCHGGF 31 (35)
T ss_pred CcCCCCcE
Confidence 44444333
No 215
>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=33.32 E-value=4 Score=19.88 Aligned_cols=12 Identities=25% Similarity=0.537 Sum_probs=5.6
Q ss_pred CccCCCCccccc
Q psy13443 134 PHACGMCGYECA 145 (188)
Q Consensus 134 ~~~C~~C~~~f~ 145 (188)
+..|..||-.+.
T Consensus 21 ~isC~~CGPr~~ 32 (35)
T PF07503_consen 21 FISCTNCGPRYS 32 (35)
T ss_dssp T--BTTCC-SCC
T ss_pred CccCCCCCCCEE
Confidence 456777776553
No 216
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=33.31 E-value=29 Score=16.76 Aligned_cols=6 Identities=33% Similarity=1.160 Sum_probs=1.4
Q ss_pred CCCCCC
Q psy13443 44 CVHCKQ 49 (188)
Q Consensus 44 C~~C~~ 49 (188)
|..|++
T Consensus 6 C~eC~~ 11 (34)
T PF01286_consen 6 CDECGK 11 (34)
T ss_dssp -TTT--
T ss_pred HhHhCC
Confidence 444444
No 217
>PRK05978 hypothetical protein; Provisional
Probab=33.26 E-value=31 Score=23.08 Aligned_cols=8 Identities=25% Similarity=0.575 Sum_probs=5.9
Q ss_pred ccCCCCCC
Q psy13443 42 FVCVHCKQ 49 (188)
Q Consensus 42 ~~C~~C~~ 49 (188)
-+|+.|++
T Consensus 34 grCP~CG~ 41 (148)
T PRK05978 34 GRCPACGE 41 (148)
T ss_pred CcCCCCCC
Confidence 47888876
No 218
>KOG0717|consensus
Probab=33.11 E-value=27 Score=27.98 Aligned_cols=34 Identities=18% Similarity=0.316 Sum_probs=25.6
Q ss_pred ccCCCCcccccCcHHHHHHHH-HhcCCCCCCCCcc
Q psy13443 135 HACGMCGYECAQGSQLMQHLR-KVHKVDKKGGEEE 168 (188)
Q Consensus 135 ~~C~~C~~~f~~~~~l~~H~~-~~h~~~~~~~~~~ 168 (188)
..|.-|+..|.+..-|..|+. +.|+.-+......
T Consensus 461 ~~C~tCr~~FdSRnkLF~Hlk~tgHa~~~~~sk~~ 495 (508)
T KOG0717|consen 461 ISCTTCRESFDSRNKLFAHLKKTGHARLPSKSKPN 495 (508)
T ss_pred HhhhhhhhhccchhHHHHHhhhcCCeeccccCCcc
Confidence 579999999999999999985 4666555544433
No 219
>KOG0717|consensus
Probab=33.01 E-value=31 Score=27.66 Aligned_cols=22 Identities=23% Similarity=0.585 Sum_probs=20.2
Q ss_pred eecCCCCCCCCCHHHHHHHHHh
Q psy13443 79 YMCYLCNYHTPTRKYMRTHIDT 100 (188)
Q Consensus 79 ~~C~~C~~~f~~~~~l~~H~~~ 100 (188)
+.|..|+++|.+-..+.+|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7899999999999999999864
No 220
>PRK12496 hypothetical protein; Provisional
Probab=32.98 E-value=23 Score=24.08 Aligned_cols=11 Identities=27% Similarity=0.637 Sum_probs=7.8
Q ss_pred eecCCCCCCCC
Q psy13443 79 YMCYLCNYHTP 89 (188)
Q Consensus 79 ~~C~~C~~~f~ 89 (188)
|.|..|++.|.
T Consensus 128 ~~C~gC~~~~~ 138 (164)
T PRK12496 128 KVCKGCKKKYP 138 (164)
T ss_pred EECCCCCcccc
Confidence 66777777765
No 221
>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=32.84 E-value=33 Score=17.93 Aligned_cols=11 Identities=27% Similarity=0.733 Sum_probs=5.7
Q ss_pred CceeecCCCCC
Q psy13443 76 SYTYMCYLCNY 86 (188)
Q Consensus 76 ~~~~~C~~C~~ 86 (188)
...|.|..|+.
T Consensus 26 ~~g~~C~~C~~ 36 (53)
T PF00130_consen 26 KQGYRCSWCGL 36 (53)
T ss_dssp SCEEEETTTT-
T ss_pred CCeEEECCCCC
Confidence 34466666653
No 222
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=32.57 E-value=45 Score=23.41 Aligned_cols=11 Identities=27% Similarity=0.510 Sum_probs=6.6
Q ss_pred CccCCCCcccc
Q psy13443 134 PHACGMCGYEC 144 (188)
Q Consensus 134 ~~~C~~C~~~f 144 (188)
.+.|..||..+
T Consensus 30 lvrC~eCG~V~ 40 (201)
T COG1326 30 LVRCEECGTVH 40 (201)
T ss_pred EEEccCCCcEe
Confidence 35666666655
No 223
>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=32.27 E-value=32 Score=18.27 Aligned_cols=9 Identities=22% Similarity=0.501 Sum_probs=3.7
Q ss_pred cCCCCCCCC
Q psy13443 81 CYLCNYHTP 89 (188)
Q Consensus 81 C~~C~~~f~ 89 (188)
|..|++.|.
T Consensus 5 C~~C~~~F~ 13 (57)
T cd00065 5 CMGCGKPFT 13 (57)
T ss_pred CcccCcccc
Confidence 344444443
No 224
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=32.09 E-value=34 Score=22.63 Aligned_cols=11 Identities=27% Similarity=0.615 Sum_probs=5.5
Q ss_pred eeecCCCCCCC
Q psy13443 78 TYMCYLCNYHT 88 (188)
Q Consensus 78 ~~~C~~C~~~f 88 (188)
.|.|..|+..+
T Consensus 112 ~y~C~~C~~~~ 122 (146)
T smart00731 112 PYRCTGCGQRY 122 (146)
T ss_pred EEECCCCCCCC
Confidence 45555555443
No 225
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=32.07 E-value=16 Score=24.08 Aligned_cols=26 Identities=27% Similarity=0.623 Sum_probs=14.0
Q ss_pred ccc--cccccccCCCCceeecCCCCCCC
Q psy13443 63 HCA--TCVDMVRPDASYTYMCYLCNYHT 88 (188)
Q Consensus 63 ~c~--~c~~~~~~~~~~~~~C~~C~~~f 88 (188)
.|+ .|.+.+...+...|.|+.|++..
T Consensus 20 aC~~~~C~kKv~~~~~~~y~C~~C~~~~ 47 (146)
T PF08646_consen 20 ACPNEKCNKKVTENGDGSYRCEKCNKTV 47 (146)
T ss_dssp E-TSTTTS-B-EEETTTEEEETTTTEEE
T ss_pred CCCCccCCCEeecCCCcEEECCCCCCcC
Confidence 455 55555554545567777777654
No 226
>KOG4727|consensus
Probab=31.88 E-value=33 Score=23.48 Aligned_cols=24 Identities=25% Similarity=0.609 Sum_probs=21.1
Q ss_pred CCccccCCCcccccCHHHHHHHHH
Q psy13443 11 KQQFECDFCPYGAKQAADVHNHVQ 34 (188)
Q Consensus 11 ~~~~~C~~C~~~f~~~~~l~~H~~ 34 (188)
...|-|.+|.-.|.+..++..|+.
T Consensus 73 ~~GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 73 KGGYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred cCceeeeecceeehhhHHHHHHhc
Confidence 346999999999999999999983
No 227
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=31.68 E-value=33 Score=26.42 Aligned_cols=27 Identities=26% Similarity=0.495 Sum_probs=18.8
Q ss_pred hccCCCccccCCCc-ccccCHHHHHHHH
Q psy13443 7 THLAKQQFECDFCP-YGAKQAADVHNHV 33 (188)
Q Consensus 7 ~h~~~~~~~C~~C~-~~f~~~~~l~~H~ 33 (188)
.|.-++.|.|.+|| +.+..+..+.+|+
T Consensus 368 lhgLd~ef~CEICgNyvy~GR~~FdrHF 395 (470)
T COG5188 368 LHGLDIEFECEICGNYVYYGRDRFDRHF 395 (470)
T ss_pred hcCCCcceeeeecccccccchHHHHhhh
Confidence 34446678888888 6667777777776
No 228
>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=31.45 E-value=40 Score=15.46 Aligned_cols=8 Identities=38% Similarity=0.866 Sum_probs=5.2
Q ss_pred eeecCCCC
Q psy13443 78 TYMCYLCN 85 (188)
Q Consensus 78 ~~~C~~C~ 85 (188)
.|.|..|.
T Consensus 15 ~Y~C~~c~ 22 (30)
T PF03107_consen 15 FYHCSECC 22 (30)
T ss_pred eEEeCCCC
Confidence 56676666
No 229
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=31.45 E-value=41 Score=21.36 Aligned_cols=16 Identities=19% Similarity=0.551 Sum_probs=11.3
Q ss_pred CCccccCCCcccccCH
Q psy13443 11 KQQFECDFCPYGAKQA 26 (188)
Q Consensus 11 ~~~~~C~~C~~~f~~~ 26 (188)
...+.|..||..+...
T Consensus 20 ~~~l~C~kCgye~~~~ 35 (113)
T COG1594 20 GGKLVCRKCGYEEEAS 35 (113)
T ss_pred CcEEECCCCCcchhcc
Confidence 3468899999775544
No 230
>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=31.40 E-value=8.5 Score=24.35 Aligned_cols=14 Identities=14% Similarity=0.211 Sum_probs=8.0
Q ss_pred eeecCCCCCCCCCH
Q psy13443 78 TYMCYLCNYHTPTR 91 (188)
Q Consensus 78 ~~~C~~C~~~f~~~ 91 (188)
.+.|..|+..|...
T Consensus 70 ~~~C~~Cg~~~~~~ 83 (113)
T PF01155_consen 70 RARCRDCGHEFEPD 83 (113)
T ss_dssp EEEETTTS-EEECH
T ss_pred cEECCCCCCEEecC
Confidence 35677777666544
No 231
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=31.35 E-value=49 Score=24.82 Aligned_cols=26 Identities=27% Similarity=0.401 Sum_probs=19.2
Q ss_pred CCccCCCCcccccCcHHHHHHHHHhc
Q psy13443 133 KPHACGMCGYECAQGSQLMQHLRKVH 158 (188)
Q Consensus 133 ~~~~C~~C~~~f~~~~~l~~H~~~~h 158 (188)
.-|.|..|-+.|.+...|.+|+....
T Consensus 47 ~lyiCe~Clky~~~~~~l~~H~~~C~ 72 (290)
T PLN03238 47 KLYICEYCLKYMRKKKSLLRHLAKCD 72 (290)
T ss_pred eEEEcCCCcchhCCHHHHHHHHHhCC
Confidence 44778888888888888888876544
No 232
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=31.32 E-value=64 Score=17.48 Aligned_cols=8 Identities=25% Similarity=0.658 Sum_probs=4.4
Q ss_pred eecCCCCC
Q psy13443 79 YMCYLCNY 86 (188)
Q Consensus 79 ~~C~~C~~ 86 (188)
..|+.|+.
T Consensus 22 VvCp~Cga 29 (54)
T PF14446_consen 22 VVCPECGA 29 (54)
T ss_pred EECCCCCC
Confidence 45666653
No 233
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.00 E-value=41 Score=25.15 Aligned_cols=11 Identities=27% Similarity=0.709 Sum_probs=5.4
Q ss_pred eecccCccccC
Q psy13443 107 FRCALCAYSAR 117 (188)
Q Consensus 107 ~~C~~C~~~~~ 117 (188)
|.|++|...|.
T Consensus 256 yvCs~Clsi~C 266 (279)
T TIGR00627 256 FVCSVCLSVLC 266 (279)
T ss_pred EECCCccCCcC
Confidence 45555554443
No 234
>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=30.82 E-value=44 Score=20.57 Aligned_cols=36 Identities=28% Similarity=0.518 Sum_probs=18.7
Q ss_pred eecccCccccCCchhHHHHHHhhcCC---CCccCCCCccccc
Q psy13443 107 FRCALCAYSARRKTHLDDHMRRHTGE---KPHACGMCGYECA 145 (188)
Q Consensus 107 ~~C~~C~~~~~~~~~l~~H~~~h~~~---~~~~C~~C~~~f~ 145 (188)
..|+.||..-.....++ ++. ..+ ..|.|..|++.++
T Consensus 63 ~~Cp~Cg~~~a~f~~~Q--~Rs-adE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 63 VECPKCGHKEAYYWLLQ--TRR-ADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred CCCCCCCCCeeEEEEec--cCC-CCCCcEEEEEeCCCCCeeE
Confidence 57888875543333221 111 111 1278888887654
No 235
>KOG2636|consensus
Probab=30.81 E-value=48 Score=26.49 Aligned_cols=23 Identities=22% Similarity=0.749 Sum_probs=14.2
Q ss_pred CceecccCc-cccCCchhHHHHHH
Q psy13443 105 KPFRCALCA-YSARRKTHLDDHMR 127 (188)
Q Consensus 105 ~~~~C~~C~-~~~~~~~~l~~H~~ 127 (188)
..|.|.+|| +++.....+.+|..
T Consensus 400 ~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 400 IEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred cccceeeccCccccCcHHHHHHhH
Confidence 346666666 66666666666654
No 236
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=30.43 E-value=36 Score=18.54 Aligned_cols=13 Identities=8% Similarity=-0.064 Sum_probs=5.2
Q ss_pred ceeecCCCCCCCC
Q psy13443 77 YTYMCYLCNYHTP 89 (188)
Q Consensus 77 ~~~~C~~C~~~f~ 89 (188)
.|.....|+..|.
T Consensus 23 ~PV~s~~C~H~fe 35 (57)
T PF11789_consen 23 DPVKSKKCGHTFE 35 (57)
T ss_dssp SEEEESSS--EEE
T ss_pred CCcCcCCCCCeec
Confidence 3444455554444
No 237
>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=30.32 E-value=7.7 Score=17.84 Aligned_cols=9 Identities=22% Similarity=0.563 Sum_probs=5.0
Q ss_pred ecccCcccc
Q psy13443 108 RCALCAYSA 116 (188)
Q Consensus 108 ~C~~C~~~~ 116 (188)
.|..|+..|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 455555555
No 238
>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=30.12 E-value=18 Score=18.22 Aligned_cols=11 Identities=36% Similarity=0.954 Sum_probs=7.4
Q ss_pred CccCCCCcccc
Q psy13443 134 PHACGMCGYEC 144 (188)
Q Consensus 134 ~~~C~~C~~~f 144 (188)
+..|++|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 45777777665
No 239
>PHA02998 RNA polymerase subunit; Provisional
Probab=30.11 E-value=58 Score=22.55 Aligned_cols=14 Identities=21% Similarity=0.363 Sum_probs=9.0
Q ss_pred eeecCCCCCCCCCH
Q psy13443 78 TYMCYLCNYHTPTR 91 (188)
Q Consensus 78 ~~~C~~C~~~f~~~ 91 (188)
.|.|..|+..|.-+
T Consensus 171 FYkC~~CG~~wkpp 184 (195)
T PHA02998 171 RHACRDCKKHFKPP 184 (195)
T ss_pred EEEcCCCCCccCCc
Confidence 46777777766543
No 240
>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=29.91 E-value=22 Score=17.47 Aligned_cols=11 Identities=18% Similarity=0.664 Sum_probs=5.3
Q ss_pred ccccCCCcccc
Q psy13443 13 QFECDFCPYGA 23 (188)
Q Consensus 13 ~~~C~~C~~~f 23 (188)
.|+|+.||...
T Consensus 6 ~YkC~~CGniV 16 (36)
T PF06397_consen 6 FYKCEHCGNIV 16 (36)
T ss_dssp EEE-TTT--EE
T ss_pred EEEccCCCCEE
Confidence 57777777653
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=29.80 E-value=18 Score=17.72 Aligned_cols=13 Identities=31% Similarity=0.956 Sum_probs=5.5
Q ss_pred hcCCCCceecccC
Q psy13443 100 THNGEKPFRCALC 112 (188)
Q Consensus 100 ~h~~~~~~~C~~C 112 (188)
...|...|+|..|
T Consensus 23 ~~~G~qryrC~~C 35 (36)
T PF03811_consen 23 SPSGHQRYRCKDC 35 (36)
T ss_pred CCCCCEeEecCcC
Confidence 3333334454444
No 242
>PLN02294 cytochrome c oxidase subunit Vb
Probab=29.79 E-value=28 Score=23.84 Aligned_cols=16 Identities=19% Similarity=0.355 Sum_probs=13.0
Q ss_pred CCCccCCCCcccccCc
Q psy13443 132 EKPHACGMCGYECAQG 147 (188)
Q Consensus 132 ~~~~~C~~C~~~f~~~ 147 (188)
.+|.+|+.||..|.-.
T Consensus 139 Gkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 139 GKSFECPVCTQYFELE 154 (174)
T ss_pred CCceeCCCCCCEEEEE
Confidence 4789999999988643
No 243
>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=29.59 E-value=39 Score=17.00 Aligned_cols=7 Identities=29% Similarity=0.942 Sum_probs=3.9
Q ss_pred cCCCCCC
Q psy13443 43 VCVHCKQ 49 (188)
Q Consensus 43 ~C~~C~~ 49 (188)
.|+.|+.
T Consensus 2 ~Cp~Cg~ 8 (43)
T PF08271_consen 2 KCPNCGS 8 (43)
T ss_dssp SBTTTSS
T ss_pred CCcCCcC
Confidence 4555554
No 244
>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=29.28 E-value=29 Score=21.40 Aligned_cols=13 Identities=38% Similarity=0.807 Sum_probs=8.1
Q ss_pred CCccCCCCccccc
Q psy13443 133 KPHACGMCGYECA 145 (188)
Q Consensus 133 ~~~~C~~C~~~f~ 145 (188)
+|.+|..||..|.
T Consensus 78 ~~~rC~eCG~~fk 90 (97)
T cd00924 78 KPKRCPECGHVFK 90 (97)
T ss_pred CceeCCCCCcEEE
Confidence 5666666666654
No 245
>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=28.98 E-value=36 Score=22.63 Aligned_cols=11 Identities=18% Similarity=0.301 Sum_probs=5.3
Q ss_pred eeecCCCCCCC
Q psy13443 78 TYMCYLCNYHT 88 (188)
Q Consensus 78 ~~~C~~C~~~f 88 (188)
.+.|+.|++.|
T Consensus 124 f~~C~~C~kiy 134 (147)
T PF01927_consen 124 FWRCPGCGKIY 134 (147)
T ss_pred EEECCCCCCEe
Confidence 34555555443
No 246
>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=28.96 E-value=21 Score=23.76 Aligned_cols=11 Identities=27% Similarity=0.637 Sum_probs=5.5
Q ss_pred eeecCCCCCCC
Q psy13443 78 TYMCYLCNYHT 88 (188)
Q Consensus 78 ~~~C~~C~~~f 88 (188)
.|.|..|+..+
T Consensus 123 ~~~C~~C~~~~ 133 (157)
T PF10263_consen 123 VYRCPSCGREY 133 (157)
T ss_pred EEEcCCCCCEe
Confidence 35555555443
No 247
>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=28.82 E-value=23 Score=26.82 Aligned_cols=12 Identities=25% Similarity=0.451 Sum_probs=7.3
Q ss_pred CCceeecCCCCC
Q psy13443 75 ASYTYMCYLCNY 86 (188)
Q Consensus 75 ~~~~~~C~~C~~ 86 (188)
+.+-..|+.|+.
T Consensus 207 G~RyL~CslC~t 218 (305)
T TIGR01562 207 GLRYLSCSLCAT 218 (305)
T ss_pred CceEEEcCCCCC
Confidence 345566777764
No 248
>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=28.80 E-value=39 Score=16.20 Aligned_cols=21 Identities=14% Similarity=0.319 Sum_probs=11.0
Q ss_pred eeecCCCCCCCCCHHHHHHHHH
Q psy13443 78 TYMCYLCNYHTPTRKYMRTHID 99 (188)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H~~ 99 (188)
.+.|+.|++.+. .+.+..|+.
T Consensus 4 ~~~C~nC~R~v~-a~RfA~HLe 24 (33)
T PF08209_consen 4 YVECPNCGRPVA-ASRFAPHLE 24 (33)
T ss_dssp EEE-TTTSSEEE-GGGHHHHHH
T ss_pred eEECCCCcCCcc-hhhhHHHHH
Confidence 356777776544 334555654
No 249
>KOG3507|consensus
Probab=28.68 E-value=34 Score=18.80 Aligned_cols=10 Identities=40% Similarity=1.052 Sum_probs=5.0
Q ss_pred ceecccCccc
Q psy13443 106 PFRCALCAYS 115 (188)
Q Consensus 106 ~~~C~~C~~~ 115 (188)
+++|..||..
T Consensus 37 ~irCReCG~R 46 (62)
T KOG3507|consen 37 VIRCRECGYR 46 (62)
T ss_pred cEehhhcchH
Confidence 4555555543
No 250
>PRK04351 hypothetical protein; Provisional
Probab=28.63 E-value=33 Score=23.00 Aligned_cols=11 Identities=27% Similarity=0.745 Sum_probs=5.3
Q ss_pred ceecccCcccc
Q psy13443 106 PFRCALCAYSA 116 (188)
Q Consensus 106 ~~~C~~C~~~~ 116 (188)
.|.|..|+..+
T Consensus 132 ~yrCg~C~g~L 142 (149)
T PRK04351 132 RYRCGKCRGKL 142 (149)
T ss_pred cEEeCCCCcEe
Confidence 35555555443
No 251
>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=28.35 E-value=45 Score=16.97 Aligned_cols=16 Identities=13% Similarity=0.125 Sum_probs=12.9
Q ss_pred ccCCCcccccCHHHHH
Q psy13443 15 ECDFCPYGAKQAADVH 30 (188)
Q Consensus 15 ~C~~C~~~f~~~~~l~ 30 (188)
.|..|+..|.-+....
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 6999999998776654
No 252
>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=28.34 E-value=33 Score=16.72 Aligned_cols=9 Identities=22% Similarity=0.231 Sum_probs=4.3
Q ss_pred ccCCCcccc
Q psy13443 15 ECDFCPYGA 23 (188)
Q Consensus 15 ~C~~C~~~f 23 (188)
.|+.||..|
T Consensus 3 ~C~~Cg~~Y 11 (36)
T PF05191_consen 3 ICPKCGRIY 11 (36)
T ss_dssp EETTTTEEE
T ss_pred CcCCCCCcc
Confidence 344555544
No 253
>KOG0320|consensus
Probab=28.22 E-value=11 Score=26.02 Aligned_cols=7 Identities=29% Similarity=0.966 Sum_probs=3.8
Q ss_pred ccCCCCC
Q psy13443 42 FVCVHCK 48 (188)
Q Consensus 42 ~~C~~C~ 48 (188)
|.|++|-
T Consensus 132 ~~CPiCl 138 (187)
T KOG0320|consen 132 YKCPICL 138 (187)
T ss_pred cCCCcee
Confidence 5555553
No 254
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.13 E-value=14 Score=23.74 Aligned_cols=13 Identities=23% Similarity=0.470 Sum_probs=6.0
Q ss_pred eecCCCCCCCCCH
Q psy13443 79 YMCYLCNYHTPTR 91 (188)
Q Consensus 79 ~~C~~C~~~f~~~ 91 (188)
--|..||..|++.
T Consensus 69 sfchncgs~fpwt 81 (160)
T COG4306 69 SFCHNCGSRFPWT 81 (160)
T ss_pred chhhcCCCCCCcH
Confidence 3344555544443
No 255
>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=28.07 E-value=28 Score=18.20 Aligned_cols=36 Identities=19% Similarity=0.547 Sum_probs=18.7
Q ss_pred eecccCccccCCchhHHHHHHhhcC------CCCccCCCCccc
Q psy13443 107 FRCALCAYSARRKTHLDDHMRRHTG------EKPHACGMCGYE 143 (188)
Q Consensus 107 ~~C~~C~~~~~~~~~l~~H~~~h~~------~~~~~C~~C~~~ 143 (188)
|.|.+|+..|.-...-.. ..+-.| ..-|.|+.|+..
T Consensus 2 y~C~~CgyvYd~~~Gd~~-~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPE-NGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EEETTTSBEEETTTBBGG-GTB-TT--GGGS-TT-B-TTTSSB
T ss_pred cCCCCCCEEEcCCcCCcc-cCcCCCCCHHHCCCCCcCcCCCCc
Confidence 789999988866543111 001111 123899999854
No 256
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=27.95 E-value=30 Score=22.54 Aligned_cols=12 Identities=33% Similarity=0.814 Sum_probs=6.2
Q ss_pred ccCCCCcccccC
Q psy13443 135 HACGMCGYECAQ 146 (188)
Q Consensus 135 ~~C~~C~~~f~~ 146 (188)
.+|..|++.|..
T Consensus 2 H~Ct~Cg~~f~d 13 (131)
T PF09845_consen 2 HQCTKCGRVFED 13 (131)
T ss_pred cccCcCCCCcCC
Confidence 445555555544
No 257
>COG2879 Uncharacterized small protein [Function unknown]
Probab=27.86 E-value=73 Score=17.83 Aligned_cols=19 Identities=21% Similarity=0.259 Sum_probs=14.2
Q ss_pred CcHHHHHHHHHhcCCCCCC
Q psy13443 146 QGSQLMQHLRKVHKVDKKG 164 (188)
Q Consensus 146 ~~~~l~~H~~~~h~~~~~~ 164 (188)
.-.....|++.+|+++|+.
T Consensus 24 dYdnYVehmr~~hPd~p~m 42 (65)
T COG2879 24 DYDNYVEHMRKKHPDKPPM 42 (65)
T ss_pred cHHHHHHHHHHhCcCCCcc
Confidence 3456778999998888763
No 258
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=27.49 E-value=90 Score=15.44 Aligned_cols=15 Identities=13% Similarity=0.107 Sum_probs=6.6
Q ss_pred ecCCCCCCCCCHHHH
Q psy13443 80 MCYLCNYHTPTRKYM 94 (188)
Q Consensus 80 ~C~~C~~~f~~~~~l 94 (188)
.|+.|+-.+.....|
T Consensus 21 ~C~~C~G~W~d~~el 35 (41)
T PF13453_consen 21 VCPSCGGIWFDAGEL 35 (41)
T ss_pred ECCCCCeEEccHHHH
Confidence 444444444444333
No 259
>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=27.44 E-value=30 Score=23.13 Aligned_cols=7 Identities=29% Similarity=0.975 Sum_probs=3.2
Q ss_pred eecccCc
Q psy13443 107 FRCALCA 113 (188)
Q Consensus 107 ~~C~~C~ 113 (188)
|.|..||
T Consensus 113 l~C~~Cg 119 (146)
T PF07295_consen 113 LVCENCG 119 (146)
T ss_pred EecccCC
Confidence 4444444
No 260
>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=27.28 E-value=39 Score=16.49 Aligned_cols=11 Identities=27% Similarity=0.606 Sum_probs=5.5
Q ss_pred CCceeecCCCC
Q psy13443 75 ASYTYMCYLCN 85 (188)
Q Consensus 75 ~~~~~~C~~C~ 85 (188)
.+..|.|..|+
T Consensus 22 ~dG~~yC~~cG 32 (36)
T PF11781_consen 22 DDGFYYCDRCG 32 (36)
T ss_pred cCCEEEhhhCc
Confidence 34445555555
No 261
>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=27.16 E-value=55 Score=16.86 Aligned_cols=14 Identities=21% Similarity=0.297 Sum_probs=7.5
Q ss_pred CCceeecCCCCCCC
Q psy13443 75 ASYTYMCYLCNYHT 88 (188)
Q Consensus 75 ~~~~~~C~~C~~~f 88 (188)
......|..|+..|
T Consensus 11 ~~~~i~C~~C~~~~ 24 (51)
T PF00628_consen 11 DGDMIQCDSCNRWY 24 (51)
T ss_dssp TSSEEEBSTTSCEE
T ss_pred CCCeEEcCCCChhh
Confidence 34445666666544
No 262
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=26.69 E-value=41 Score=17.38 Aligned_cols=6 Identities=50% Similarity=1.459 Sum_probs=3.1
Q ss_pred CCCCCC
Q psy13443 44 CVHCKQ 49 (188)
Q Consensus 44 C~~C~~ 49 (188)
||.||.
T Consensus 2 CP~Cg~ 7 (47)
T PF04606_consen 2 CPHCGS 7 (47)
T ss_pred cCCCCC
Confidence 555554
No 263
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.49 E-value=34 Score=18.97 Aligned_cols=18 Identities=11% Similarity=0.285 Sum_probs=7.7
Q ss_pred ccCCCccc-ccCHHHHHHH
Q psy13443 15 ECDFCPYG-AKQAADVHNH 32 (188)
Q Consensus 15 ~C~~C~~~-f~~~~~l~~H 32 (188)
+|.+|.+. +.+...+..-
T Consensus 4 kCiiCd~v~~iD~rt~~tK 22 (68)
T COG4896 4 KCIICDRVDEIDNRTFKTK 22 (68)
T ss_pred eEEEecceeeecchhHHHH
Confidence 45555532 3344444433
No 264
>KOG1842|consensus
Probab=26.32 E-value=40 Score=26.92 Aligned_cols=28 Identities=18% Similarity=0.446 Sum_probs=25.5
Q ss_pred ccccCCCcccccCHHHHHHHHHhhhcCC
Q psy13443 13 QFECDFCPYGAKQAADVHNHVQQIHMGV 40 (188)
Q Consensus 13 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~ 40 (188)
.|-|++|...|.....|..|+...|++.
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 5899999999999999999998888754
No 265
>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=26.11 E-value=16 Score=28.12 Aligned_cols=37 Identities=30% Similarity=0.606 Sum_probs=14.4
Q ss_pred ccccCCCcccccCHHHHH---HHHHhhhcCCc--ccCCCCCC
Q psy13443 13 QFECDFCPYGAKQAADVH---NHVQQIHMGVN--FVCVHCKQ 49 (188)
Q Consensus 13 ~~~C~~C~~~f~~~~~l~---~H~~~~~~~~~--~~C~~C~~ 49 (188)
-+.|..|.++.......= .|....+.... |+|..|+.
T Consensus 252 av~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~ 293 (344)
T PF09332_consen 252 AVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGN 293 (344)
T ss_dssp EEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-
T ss_pred EEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCC
Confidence 367888887655443332 33222222222 78888887
No 266
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=25.93 E-value=33 Score=21.21 Aligned_cols=12 Identities=17% Similarity=0.492 Sum_probs=6.6
Q ss_pred eecccCccccCC
Q psy13443 107 FRCALCAYSARR 118 (188)
Q Consensus 107 ~~C~~C~~~~~~ 118 (188)
..|+.||..+..
T Consensus 43 ~~C~~CG~y~~~ 54 (99)
T PRK14892 43 ITCGNCGLYTEF 54 (99)
T ss_pred EECCCCCCccCE
Confidence 456666655444
No 267
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=25.53 E-value=48 Score=17.55 Aligned_cols=10 Identities=30% Similarity=1.109 Sum_probs=5.0
Q ss_pred ceecccCccc
Q psy13443 106 PFRCALCAYS 115 (188)
Q Consensus 106 ~~~C~~C~~~ 115 (188)
.+.|..||..
T Consensus 37 R~~CGkCgyT 46 (51)
T COG1998 37 RWACGKCGYT 46 (51)
T ss_pred eeEeccccce
Confidence 3555555543
No 268
>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=25.49 E-value=49 Score=25.14 Aligned_cols=11 Identities=18% Similarity=0.265 Sum_probs=6.3
Q ss_pred eecCCCCCCCC
Q psy13443 79 YMCYLCNYHTP 89 (188)
Q Consensus 79 ~~C~~C~~~f~ 89 (188)
..|+.|+..+.
T Consensus 44 ~~CP~C~~~lr 54 (309)
T TIGR00570 44 GSCPECDTPLR 54 (309)
T ss_pred CCCCCCCCccc
Confidence 35666665544
No 269
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=25.42 E-value=49 Score=16.77 Aligned_cols=7 Identities=29% Similarity=0.928 Sum_probs=3.3
Q ss_pred eecCCCC
Q psy13443 79 YMCYLCN 85 (188)
Q Consensus 79 ~~C~~C~ 85 (188)
+.|..|+
T Consensus 29 ~~C~~C~ 35 (50)
T cd00029 29 LRCSWCK 35 (50)
T ss_pred eEcCCCC
Confidence 4444443
No 270
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=25.23 E-value=43 Score=21.88 Aligned_cols=8 Identities=25% Similarity=0.642 Sum_probs=4.5
Q ss_pred ccCCCCCC
Q psy13443 42 FVCVHCKQ 49 (188)
Q Consensus 42 ~~C~~C~~ 49 (188)
..|+.||.
T Consensus 29 ~hCp~Cg~ 36 (131)
T COG1645 29 KHCPKCGT 36 (131)
T ss_pred hhCcccCC
Confidence 45666655
No 271
>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=25.17 E-value=88 Score=19.76 Aligned_cols=22 Identities=9% Similarity=0.169 Sum_probs=14.8
Q ss_pred ceeecCCCCCCCCCHHHHHHHH
Q psy13443 77 YTYMCYLCNYHTPTRKYMRTHI 98 (188)
Q Consensus 77 ~~~~C~~C~~~f~~~~~l~~H~ 98 (188)
..+.|+.||..+.+......-.
T Consensus 30 ~~~~C~~CGe~~~~~e~~~~~~ 51 (127)
T TIGR03830 30 PGWYCPACGEELLDPEESKRNS 51 (127)
T ss_pred eeeECCCCCCEEEcHHHHHHHH
Confidence 4467888888887776544443
No 272
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=24.65 E-value=51 Score=16.66 Aligned_cols=7 Identities=29% Similarity=0.880 Sum_probs=3.3
Q ss_pred cCCCCCC
Q psy13443 43 VCVHCKQ 49 (188)
Q Consensus 43 ~C~~C~~ 49 (188)
.|+.|+.
T Consensus 19 ~Cp~C~~ 25 (41)
T PF06677_consen 19 HCPDCGT 25 (41)
T ss_pred ccCCCCC
Confidence 4555543
No 273
>PRK05580 primosome assembly protein PriA; Validated
Probab=24.63 E-value=55 Score=27.96 Aligned_cols=21 Identities=19% Similarity=0.410 Sum_probs=11.2
Q ss_pred ccccccccccCCCCceeecCCCCCC
Q psy13443 63 HCATCVDMVRPDASYTYMCYLCNYH 87 (188)
Q Consensus 63 ~c~~c~~~~~~~~~~~~~C~~C~~~ 87 (188)
.|..|+... ..+..|+.|+..
T Consensus 410 ~Ch~Cg~~~----~~~~~Cp~Cg~~ 430 (679)
T PRK05580 410 RCHHCGYQE----PIPKACPECGST 430 (679)
T ss_pred ECCCCcCCC----CCCCCCCCCcCC
Confidence 455555443 234567777643
No 274
>PF15616 TerY-C: TerY-C metal binding domain
Probab=24.61 E-value=51 Score=21.58 Aligned_cols=10 Identities=20% Similarity=0.710 Sum_probs=5.9
Q ss_pred ceecccCccc
Q psy13443 106 PFRCALCAYS 115 (188)
Q Consensus 106 ~~~C~~C~~~ 115 (188)
...||.|+..
T Consensus 105 ~~~CPwCg~~ 114 (131)
T PF15616_consen 105 EVTCPWCGNE 114 (131)
T ss_pred CEECCCCCCe
Confidence 4566666654
No 275
>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=24.25 E-value=62 Score=15.95 Aligned_cols=21 Identities=19% Similarity=0.638 Sum_probs=8.6
Q ss_pred ccccCCCccccc-CHHHH-HHHH
Q psy13443 13 QFECDFCPYGAK-QAADV-HNHV 33 (188)
Q Consensus 13 ~~~C~~C~~~f~-~~~~l-~~H~ 33 (188)
.|-|+.|...|. +.... ..|.
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~ 25 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHE 25 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT
T ss_pred CeecccccceecCCChHHHHHhh
Confidence 478999998883 44333 4453
No 276
>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=24.17 E-value=30 Score=20.47 Aligned_cols=8 Identities=38% Similarity=1.132 Sum_probs=2.8
Q ss_pred ccCCCCCC
Q psy13443 42 FVCVHCKQ 49 (188)
Q Consensus 42 ~~C~~C~~ 49 (188)
|.|+.|+-
T Consensus 23 F~CPfC~~ 30 (81)
T PF05129_consen 23 FDCPFCNH 30 (81)
T ss_dssp ---TTT--
T ss_pred EcCCcCCC
Confidence 89999983
No 277
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=24.16 E-value=38 Score=18.52 Aligned_cols=9 Identities=22% Similarity=0.538 Sum_probs=4.8
Q ss_pred CccCCCCcc
Q psy13443 134 PHACGMCGY 142 (188)
Q Consensus 134 ~~~C~~C~~ 142 (188)
+|.|..|..
T Consensus 31 tYmC~eC~~ 39 (56)
T PF09963_consen 31 TYMCDECKE 39 (56)
T ss_pred ceeChhHHH
Confidence 355555543
No 278
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=24.07 E-value=39 Score=18.11 Aligned_cols=11 Identities=27% Similarity=0.640 Sum_probs=7.4
Q ss_pred ccCCCCccccc
Q psy13443 135 HACGMCGYECA 145 (188)
Q Consensus 135 ~~C~~C~~~f~ 145 (188)
+.|++||..+.
T Consensus 1 i~CPyCge~~~ 11 (52)
T PF14255_consen 1 IQCPYCGEPIE 11 (52)
T ss_pred CCCCCCCCeeE
Confidence 35788887654
No 279
>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=23.84 E-value=27 Score=18.64 Aligned_cols=7 Identities=43% Similarity=1.236 Sum_probs=2.8
Q ss_pred cCCCCCC
Q psy13443 43 VCVHCKQ 49 (188)
Q Consensus 43 ~C~~C~~ 49 (188)
.|..|++
T Consensus 6 RC~~Cnk 12 (51)
T PF10122_consen 6 RCGHCNK 12 (51)
T ss_pred eccchhH
Confidence 3444433
No 280
>KOG1940|consensus
Probab=23.81 E-value=1.4e+02 Score=22.47 Aligned_cols=19 Identities=11% Similarity=0.510 Sum_probs=11.0
Q ss_pred cccCCCcccccCHHHHHHHH
Q psy13443 14 FECDFCPYGAKQAADVHNHV 33 (188)
Q Consensus 14 ~~C~~C~~~f~~~~~l~~H~ 33 (188)
|.|++|.+ ..+...+.++.
T Consensus 197 y~CP~C~~-~~d~~~~~~~~ 215 (276)
T KOG1940|consen 197 YTCPICSK-PGDMSHYFRKL 215 (276)
T ss_pred CCCCcccc-hHHHHHHHHHH
Confidence 66777666 55555544444
No 281
>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 TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=22.96 E-value=37 Score=16.07 Aligned_cols=11 Identities=18% Similarity=0.703 Sum_probs=7.1
Q ss_pred ccccCCCcccc
Q psy13443 13 QFECDFCPYGA 23 (188)
Q Consensus 13 ~~~C~~C~~~f 23 (188)
.|+|..|+..+
T Consensus 7 ~ykC~~Cgniv 17 (34)
T TIGR00319 7 VYKCEVCGNIV 17 (34)
T ss_pred EEEcCCCCcEE
Confidence 56777777654
No 283
>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=22.93 E-value=38 Score=16.02 Aligned_cols=10 Identities=20% Similarity=0.800 Sum_probs=5.3
Q ss_pred ccccCCCccc
Q psy13443 13 QFECDFCPYG 22 (188)
Q Consensus 13 ~~~C~~C~~~ 22 (188)
.|+|..|+..
T Consensus 4 ~ykC~~CGni 13 (34)
T cd00974 4 VYKCEICGNI 13 (34)
T ss_pred EEEcCCCCcE
Confidence 3555555544
No 284
>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 PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=22.68 E-value=75 Score=21.46 Aligned_cols=15 Identities=20% Similarity=0.286 Sum_probs=7.5
Q ss_pred ceeecCCCCCCCCCH
Q psy13443 77 YTYMCYLCNYHTPTR 91 (188)
Q Consensus 77 ~~~~C~~C~~~f~~~ 91 (188)
.|.-|..||+.|++.
T Consensus 67 ~PsYC~~CGkpyPWt 81 (158)
T PF10083_consen 67 APSYCHNCGKPYPWT 81 (158)
T ss_pred CChhHHhCCCCCchH
Confidence 344455555555544
No 286
>KOG0978|consensus
Probab=22.68 E-value=13 Score=31.49 Aligned_cols=13 Identities=15% Similarity=0.416 Sum_probs=6.9
Q ss_pred eecccCccccCCc
Q psy13443 107 FRCALCAYSARRK 119 (188)
Q Consensus 107 ~~C~~C~~~~~~~ 119 (188)
-+||.|+.+|...
T Consensus 679 RKCP~Cn~aFgan 691 (698)
T KOG0978|consen 679 RKCPKCNAAFGAN 691 (698)
T ss_pred CCCCCCCCCCCcc
Confidence 3555555555543
No 287
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=22.60 E-value=76 Score=16.99 Aligned_cols=11 Identities=18% Similarity=0.522 Sum_probs=6.1
Q ss_pred CCceecccCcc
Q psy13443 104 EKPFRCALCAY 114 (188)
Q Consensus 104 ~~~~~C~~C~~ 114 (188)
.....|+.||+
T Consensus 44 ~~i~~Cp~CgR 54 (56)
T PF02591_consen 44 DEIVFCPNCGR 54 (56)
T ss_pred CCeEECcCCCc
Confidence 34456666654
No 288
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=22.49 E-value=27 Score=16.88 Aligned_cols=8 Identities=38% Similarity=1.157 Sum_probs=3.8
Q ss_pred ecCCCCCC
Q psy13443 80 MCYLCNYH 87 (188)
Q Consensus 80 ~C~~C~~~ 87 (188)
.|..|++.
T Consensus 22 ~C~~C~Y~ 29 (35)
T PF02150_consen 22 ACRTCGYE 29 (35)
T ss_dssp EESSSS-E
T ss_pred CCCCCCCc
Confidence 45555544
No 289
>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=22.46 E-value=81 Score=15.60 Aligned_cols=10 Identities=30% Similarity=0.969 Sum_probs=4.3
Q ss_pred ceeecCCCCC
Q psy13443 77 YTYMCYLCNY 86 (188)
Q Consensus 77 ~~~~C~~C~~ 86 (188)
+.+.|.+|+.
T Consensus 23 ~~w~C~~C~~ 32 (40)
T PF04810_consen 23 KTWICNFCGT 32 (40)
T ss_dssp TEEEETTT--
T ss_pred CEEECcCCCC
Confidence 3455555554
No 290
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=22.26 E-value=63 Score=20.49 Aligned_cols=15 Identities=13% Similarity=0.211 Sum_probs=8.1
Q ss_pred eecccCccccCCchh
Q psy13443 107 FRCALCAYSARRKTH 121 (188)
Q Consensus 107 ~~C~~C~~~~~~~~~ 121 (188)
..|..|+.......+
T Consensus 86 D~CM~C~~pLTLd~~ 100 (114)
T PF11023_consen 86 DACMHCKEPLTLDPS 100 (114)
T ss_pred hccCcCCCcCccCch
Confidence 466666655544443
No 291
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=21.99 E-value=1.8e+02 Score=17.10 Aligned_cols=6 Identities=33% Similarity=0.944 Sum_probs=1.9
Q ss_pred ecCCCC
Q psy13443 80 MCYLCN 85 (188)
Q Consensus 80 ~C~~C~ 85 (188)
.|..|+
T Consensus 30 AC~eC~ 35 (80)
T PF14569_consen 30 ACHECA 35 (80)
T ss_dssp S-SSS-
T ss_pred EEcccC
Confidence 355553
No 292
>PHA02942 putative transposase; Provisional
Probab=21.94 E-value=74 Score=25.05 Aligned_cols=14 Identities=36% Similarity=0.975 Sum_probs=9.2
Q ss_pred CceecccCccccCC
Q psy13443 105 KPFRCALCAYSARR 118 (188)
Q Consensus 105 ~~~~C~~C~~~~~~ 118 (188)
+.|.|+.||.....
T Consensus 341 r~f~C~~CG~~~dr 354 (383)
T PHA02942 341 RYFHCPSCGYENDR 354 (383)
T ss_pred CEEECCCCCCEeCc
Confidence 46777777766544
No 293
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=21.09 E-value=38 Score=21.09 Aligned_cols=23 Identities=26% Similarity=0.423 Sum_probs=17.9
Q ss_pred CccCCCCcccccCcHHHHHHHHH
Q psy13443 134 PHACGMCGYECAQGSQLMQHLRK 156 (188)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~ 156 (188)
.+-|-.|.+.|.+...|..|.+.
T Consensus 55 qhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 55 QHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred eeeeehhHHHHHHHHHHHHHhcc
Confidence 35677888888888888888753
No 294
>PTZ00448 hypothetical protein; Provisional
Probab=21.02 E-value=74 Score=24.83 Aligned_cols=24 Identities=17% Similarity=0.449 Sum_probs=18.6
Q ss_pred eeecCCCCCCCCCHHHHHHHHHhc
Q psy13443 78 TYMCYLCNYHTPTRKYMRTHIDTH 101 (188)
Q Consensus 78 ~~~C~~C~~~f~~~~~l~~H~~~h 101 (188)
.|.|..|+-.|.+......|+++.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSD 337 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSE 337 (373)
T ss_pred CccccccccccCCHHHHHHHhhhh
Confidence 477888888888778888887653
No 295
>KOG0782|consensus
Probab=20.84 E-value=12 Score=30.75 Aligned_cols=51 Identities=14% Similarity=0.204 Sum_probs=34.0
Q ss_pred HHHHHHHhcCCCCceecccCccccCCchhHHHHHHhhcCCCCccCCCCcccccCcH
Q psy13443 93 YMRTHIDTHNGEKPFRCALCAYSARRKTHLDDHMRRHTGEKPHACGMCGYECAQGS 148 (188)
Q Consensus 93 ~l~~H~~~h~~~~~~~C~~C~~~~~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~ 148 (188)
.|..|-=+|....-=+|..|++.|..+..+..-. --...|.+|..+|..+.
T Consensus 240 ~fvrHHWVHrrRqeGkC~~CgKgFQQKf~FhsKE-----ivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQEGKCNTCGKGFQQKFFFHSKE-----IVAISCSWCKQAYHLKV 290 (1004)
T ss_pred cchHHhHhhHhhhccccchhhhhhhhheeecccc-----EEEEEehHHHHHhhcch
Confidence 5667766666555568999999998876552211 12367899988887654
No 296
>KOG2906|consensus
Probab=20.83 E-value=51 Score=20.28 Aligned_cols=15 Identities=27% Similarity=0.700 Sum_probs=11.0
Q ss_pred ceeecCCCCCCCCCH
Q psy13443 77 YTYMCYLCNYHTPTR 91 (188)
Q Consensus 77 ~~~~C~~C~~~f~~~ 91 (188)
..|.|..|++.|+-.
T Consensus 20 ~rf~C~tCpY~~~I~ 34 (105)
T KOG2906|consen 20 NRFSCRTCPYVFPIS 34 (105)
T ss_pred eeEEcCCCCceeeEe
Confidence 357889998877644
No 297
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=20.71 E-value=81 Score=27.50 Aligned_cols=9 Identities=22% Similarity=0.453 Sum_probs=4.5
Q ss_pred cCCCccccc
Q psy13443 16 CDFCPYGAK 24 (188)
Q Consensus 16 C~~C~~~f~ 24 (188)
|..|++.|.
T Consensus 463 C~~C~kkFf 471 (1374)
T PTZ00303 463 CPSCGRAFI 471 (1374)
T ss_pred ccCcCCccc
Confidence 555555543
No 298
>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=20.54 E-value=1.9e+02 Score=22.02 Aligned_cols=13 Identities=15% Similarity=0.187 Sum_probs=8.9
Q ss_pred ceeecCCCCCCCC
Q psy13443 77 YTYMCYLCNYHTP 89 (188)
Q Consensus 77 ~~~~C~~C~~~f~ 89 (188)
..|.|..|+..+.
T Consensus 285 ~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 285 TFVTCEECGNRWK 297 (299)
T ss_pred EEEEcCCCCCeee
Confidence 3478888886543
No 299
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=20.33 E-value=73 Score=21.75 Aligned_cols=13 Identities=23% Similarity=0.652 Sum_probs=7.3
Q ss_pred eecccCccccCCc
Q psy13443 107 FRCALCAYSARRK 119 (188)
Q Consensus 107 ~~C~~C~~~~~~~ 119 (188)
+.|+.||+.|=--
T Consensus 131 ~~C~~CgkiYW~G 143 (165)
T COG1656 131 YRCPKCGKIYWKG 143 (165)
T ss_pred eECCCCcccccCc
Confidence 5566666665333
No 300
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=20.22 E-value=70 Score=25.77 Aligned_cols=30 Identities=23% Similarity=0.306 Sum_probs=23.7
Q ss_pred CCccCCCCcccccCcHHHHHHHHHhcCCCC
Q psy13443 133 KPHACGMCGYECAQGSQLMQHLRKVHKVDK 162 (188)
Q Consensus 133 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 162 (188)
.-|.|..|-+.|.+...|.+|+.......|
T Consensus 197 ~lyiCe~Cl~y~~~~~~~~~H~~~C~~~~P 226 (450)
T PLN00104 197 KLYFCEFCLKFMKRKEQLQRHMKKCDLKHP 226 (450)
T ss_pred eEEEchhhhhhhcCHHHHHHHHhcCCCCCC
Confidence 348999999999999999999875543333
No 301
>PTZ00064 histone acetyltransferase; Provisional
Probab=20.17 E-value=80 Score=25.85 Aligned_cols=29 Identities=21% Similarity=0.325 Sum_probs=23.5
Q ss_pred CccCCCCcccccCcHHHHHHHHHhcCCCC
Q psy13443 134 PHACGMCGYECAQGSQLMQHLRKVHKVDK 162 (188)
Q Consensus 134 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 162 (188)
-|.|..|-+.|.+...|.+|+....-..|
T Consensus 280 LYICEfCLkY~~s~~~l~rH~~~C~~rhP 308 (552)
T PTZ00064 280 LHFCEYCLDFFCFEDELIRHLSRCQLRHP 308 (552)
T ss_pred EEEccchhhhhCCHHHHHHHHhcCCCCCC
Confidence 48999999999999999999875543333
Done!