Query psy7453
Match_columns 200
No_of_seqs 225 out of 2274
Neff 9.2
Searched_HMMs 46136
Date Fri Aug 16 18:43:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7453.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7453hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 2E-28 4.4E-33 188.5 5.6 116 73-196 127-264 (279)
2 KOG2462|consensus 99.9 3.1E-24 6.6E-29 165.4 5.4 100 91-200 129-240 (279)
3 KOG3608|consensus 99.7 2.3E-18 5.1E-23 136.7 2.0 133 54-197 188-343 (467)
4 KOG3576|consensus 99.7 5.6E-18 1.2E-22 125.3 1.9 85 108-200 114-198 (267)
5 KOG3623|consensus 99.7 8E-18 1.7E-22 144.0 2.2 81 108-196 891-971 (1007)
6 KOG1074|consensus 99.7 1.3E-17 2.8E-22 144.6 2.5 83 110-200 604-693 (958)
7 KOG1074|consensus 99.6 9.9E-17 2.1E-21 139.2 3.7 53 148-200 880-932 (958)
8 KOG3623|consensus 99.6 1.2E-16 2.6E-21 136.9 -0.4 114 77-196 211-330 (1007)
9 KOG3576|consensus 99.6 3.3E-16 7.2E-21 116.0 1.1 113 72-199 113-236 (267)
10 KOG3608|consensus 99.5 3E-15 6.4E-20 119.2 3.8 137 53-199 215-376 (467)
11 PHA00733 hypothetical protein 99.4 2.8E-13 6E-18 96.1 4.9 88 108-200 37-124 (128)
12 PHA02768 hypothetical protein; 99.2 1.4E-11 3E-16 73.1 2.0 42 148-191 6-47 (55)
13 PLN03086 PRLI-interacting fact 99.1 1.2E-10 2.6E-15 100.2 6.4 74 98-185 441-514 (567)
14 PLN03086 PRLI-interacting fact 99.1 1.9E-10 4.2E-15 98.9 6.2 111 75-197 432-562 (567)
15 PHA00733 hypothetical protein 99.0 1.9E-10 4.2E-15 81.6 3.6 90 71-172 35-124 (128)
16 PF13465 zf-H2C2_2: Zinc-finge 99.0 2.4E-10 5.3E-15 58.1 2.4 26 162-187 1-26 (26)
17 PHA02768 hypothetical protein; 98.9 3.4E-10 7.4E-15 67.2 0.9 43 111-163 5-47 (55)
18 KOG3993|consensus 98.7 7.8E-09 1.7E-13 84.7 1.6 82 110-199 266-380 (500)
19 PF13465 zf-H2C2_2: Zinc-finge 98.6 1.2E-08 2.6E-13 51.8 1.5 26 127-159 1-26 (26)
20 KOG3993|consensus 98.6 8.1E-09 1.8E-13 84.6 0.6 88 76-171 267-380 (500)
21 PHA00616 hypothetical protein 98.6 3E-08 6.5E-13 56.1 1.8 33 147-179 1-33 (44)
22 PHA00732 hypothetical protein 98.5 8.3E-08 1.8E-12 62.1 2.7 48 111-172 1-49 (79)
23 PHA00616 hypothetical protein 98.4 1.6E-07 3.5E-12 53.1 1.4 39 111-157 1-39 (44)
24 PHA00732 hypothetical protein 98.3 4.1E-07 8.9E-12 58.9 2.5 46 147-198 1-47 (79)
25 PF05605 zf-Di19: Drought indu 98.3 1.3E-06 2.8E-11 52.5 4.4 51 147-200 2-54 (54)
26 PF00096 zf-C2H2: Zinc finger, 98.2 1E-06 2.2E-11 43.3 2.0 23 176-198 1-23 (23)
27 PF05605 zf-Di19: Drought indu 98.1 4.5E-06 9.8E-11 50.1 3.6 51 111-171 2-53 (54)
28 PF00096 zf-C2H2: Zinc finger, 98.0 4.9E-06 1.1E-10 40.7 2.4 23 148-170 1-23 (23)
29 PF13894 zf-C2H2_4: C2H2-type 97.9 7E-06 1.5E-10 40.3 2.1 24 176-199 1-24 (24)
30 PF13912 zf-C2H2_6: C2H2-type 97.9 6.8E-06 1.5E-10 41.9 1.9 25 175-199 1-25 (27)
31 PF12756 zf-C2H2_2: C2H2 type 97.9 7.7E-06 1.7E-10 55.1 2.6 73 113-198 1-73 (100)
32 COG5189 SFP1 Putative transcri 97.8 2.3E-06 5E-11 68.1 -1.0 71 108-197 346-420 (423)
33 PF13894 zf-C2H2_4: C2H2-type 97.6 7.1E-05 1.5E-09 36.6 2.7 23 148-170 1-23 (24)
34 PF13912 zf-C2H2_6: C2H2-type 97.6 4.7E-05 1E-09 38.7 1.8 25 147-171 1-25 (27)
35 smart00355 ZnF_C2H2 zinc finge 97.5 0.00011 2.4E-09 36.4 2.3 23 176-198 1-23 (26)
36 COG5189 SFP1 Putative transcri 97.4 5.5E-05 1.2E-09 60.5 1.3 58 73-131 346-417 (423)
37 PRK04860 hypothetical protein; 97.3 0.00014 3E-09 53.5 2.5 37 147-187 119-155 (160)
38 PF09237 GAGA: GAGA factor; I 97.1 0.00065 1.4E-08 39.4 3.3 33 143-175 20-52 (54)
39 PF13909 zf-H2C2_5: C2H2-type 97.1 0.00036 7.8E-09 34.3 1.9 24 176-200 1-24 (24)
40 smart00355 ZnF_C2H2 zinc finge 97.0 0.00063 1.4E-08 33.5 2.5 24 148-171 1-24 (26)
41 PF09237 GAGA: GAGA factor; I 97.0 0.00064 1.4E-08 39.5 2.5 30 171-200 20-49 (54)
42 PF12874 zf-met: Zinc-finger o 96.8 0.001 2.2E-08 32.9 1.7 22 176-197 1-22 (25)
43 PF12874 zf-met: Zinc-finger o 96.6 0.0016 3.4E-08 32.2 1.7 23 148-170 1-23 (25)
44 PRK04860 hypothetical protein; 96.5 0.0011 2.5E-08 48.7 1.2 39 110-160 118-156 (160)
45 PF12756 zf-C2H2_2: C2H2 type 96.3 0.0043 9.4E-08 41.4 3.0 73 78-170 1-73 (100)
46 PF13909 zf-H2C2_5: C2H2-type 96.1 0.0061 1.3E-07 29.8 2.2 23 148-171 1-23 (24)
47 PF12171 zf-C2H2_jaz: Zinc-fin 96.0 0.0028 6E-08 32.1 0.8 22 176-197 2-23 (27)
48 PF12171 zf-C2H2_jaz: Zinc-fin 95.1 0.015 3.3E-07 29.3 1.6 19 112-131 2-20 (27)
49 PF13913 zf-C2HC_2: zinc-finge 95.0 0.021 4.6E-07 28.3 2.0 19 177-196 4-22 (25)
50 KOG2231|consensus 94.6 0.032 7E-07 49.6 3.2 22 77-98 100-121 (669)
51 COG5048 FOG: Zn-finger [Genera 94.2 0.012 2.5E-07 49.4 -0.2 63 110-180 288-356 (467)
52 KOG1146|consensus 94.1 0.029 6.2E-07 53.1 2.0 25 173-197 516-540 (1406)
53 PF13913 zf-C2HC_2: zinc-finge 94.0 0.056 1.2E-06 26.8 2.1 19 149-168 4-22 (25)
54 smart00451 ZnF_U1 U1-like zinc 93.8 0.052 1.1E-06 28.9 1.9 22 175-196 3-24 (35)
55 COG5048 FOG: Zn-finger [Genera 93.7 0.011 2.4E-07 49.5 -1.4 55 146-200 288-348 (467)
56 TIGR00622 ssl1 transcription f 93.5 0.078 1.7E-06 36.5 2.8 79 109-198 13-104 (112)
57 smart00451 ZnF_U1 U1-like zinc 93.1 0.08 1.7E-06 28.1 1.9 23 147-169 3-25 (35)
58 cd00350 rubredoxin_like Rubred 92.6 0.078 1.7E-06 28.1 1.4 24 148-183 2-25 (33)
59 COG4049 Uncharacterized protei 90.7 0.12 2.6E-06 30.7 0.9 29 141-169 11-39 (65)
60 PF14446 Prok-RING_1: Prokaryo 90.1 0.13 2.8E-06 30.5 0.7 28 77-104 6-33 (54)
61 PF09538 FYDLN_acid: Protein o 90.0 0.18 3.9E-06 34.6 1.5 28 94-123 11-38 (108)
62 cd00729 rubredoxin_SM Rubredox 89.3 0.2 4.4E-06 26.7 1.0 9 111-119 18-26 (34)
63 PF13719 zinc_ribbon_5: zinc-r 89.2 0.31 6.7E-06 26.5 1.7 32 149-185 4-35 (37)
64 PF10571 UPF0547: Uncharacteri 89.0 0.25 5.5E-06 24.7 1.2 22 79-102 3-24 (26)
65 KOG1146|consensus 88.7 0.083 1.8E-06 50.1 -1.2 73 112-197 1261-1350(1406)
66 TIGR02098 MJ0042_CXXC MJ0042 f 88.6 0.34 7.4E-06 26.3 1.7 33 148-185 3-35 (38)
67 KOG2231|consensus 88.5 0.78 1.7E-05 41.2 4.6 34 93-131 100-133 (669)
68 PRK14890 putative Zn-ribbon RN 88.4 0.47 1E-05 28.6 2.3 8 147-154 48-55 (59)
69 PHA00626 hypothetical protein 88.3 0.21 4.6E-06 29.6 0.7 13 111-123 23-35 (59)
70 PRK00398 rpoP DNA-directed RNA 87.6 0.27 5.8E-06 28.1 0.9 26 76-101 3-30 (46)
71 PF09845 DUF2072: Zn-ribbon co 87.4 0.27 5.9E-06 34.7 1.0 26 76-101 1-28 (131)
72 COG1198 PriA Primosomal protei 87.0 0.53 1.1E-05 42.9 2.8 48 94-184 437-484 (730)
73 PF13717 zinc_ribbon_4: zinc-r 86.8 0.6 1.3E-05 25.2 1.9 32 149-185 4-35 (36)
74 TIGR01384 TFS_arch transcripti 86.7 0.32 7E-06 33.0 1.0 35 148-186 63-101 (104)
75 PF09538 FYDLN_acid: Protein o 85.9 0.5 1.1E-05 32.4 1.6 30 148-188 10-39 (108)
76 TIGR02605 CxxC_CxxC_SSSS putat 85.6 0.37 7.9E-06 28.2 0.7 13 77-89 6-18 (52)
77 KOG2482|consensus 85.4 0.76 1.6E-05 37.7 2.7 50 148-197 280-356 (423)
78 COG2888 Predicted Zn-ribbon RN 85.3 0.93 2E-05 27.3 2.3 8 147-154 50-57 (61)
79 PF09986 DUF2225: Uncharacteri 85.2 0.24 5.3E-06 38.3 -0.2 13 148-160 49-61 (214)
80 COG4049 Uncharacterized protei 84.4 0.51 1.1E-05 28.0 0.9 24 107-131 13-36 (65)
81 PF09986 DUF2225: Uncharacteri 84.3 0.55 1.2E-05 36.3 1.4 19 74-92 3-21 (214)
82 PF09723 Zn-ribbon_8: Zinc rib 83.6 0.44 9.6E-06 26.7 0.5 12 112-123 6-17 (42)
83 KOG2893|consensus 82.9 0.3 6.4E-06 38.0 -0.6 41 114-166 13-53 (341)
84 PF02892 zf-BED: BED zinc fing 82.6 1.1 2.4E-05 25.2 1.9 22 174-195 15-40 (45)
85 COG1592 Rubrerythrin [Energy p 82.3 0.75 1.6E-05 34.0 1.4 23 147-182 134-156 (166)
86 smart00834 CxxC_CXXC_SSSS Puta 82.2 0.65 1.4E-05 25.5 0.8 12 77-88 6-17 (41)
87 smart00659 RPOLCX RNA polymera 81.4 0.74 1.6E-05 26.1 0.8 24 77-100 3-27 (44)
88 TIGR02300 FYDLN_acid conserved 81.3 0.92 2E-05 31.9 1.4 28 94-123 11-38 (129)
89 TIGR00622 ssl1 transcription f 80.6 2.1 4.5E-05 29.5 2.9 54 113-182 57-110 (112)
90 PF03604 DNA_RNApol_7kD: DNA d 80.0 1.2 2.6E-05 23.4 1.3 11 77-87 1-11 (32)
91 PRK03824 hypA hydrogenase nick 79.9 0.85 1.8E-05 32.6 0.9 16 74-89 68-83 (135)
92 PF12013 DUF3505: Protein of u 79.9 1.5 3.2E-05 30.0 2.1 25 176-200 81-109 (109)
93 COG3364 Zn-ribbon containing p 78.9 0.76 1.6E-05 30.9 0.4 26 76-101 2-29 (112)
94 PRK12380 hydrogenase nickel in 78.6 0.97 2.1E-05 31.3 0.9 28 74-101 68-95 (113)
95 PRK00464 nrdR transcriptional 78.5 0.79 1.7E-05 33.6 0.4 13 111-123 28-40 (154)
96 TIGR02300 FYDLN_acid conserved 78.2 1.5 3.3E-05 30.8 1.7 30 148-188 10-39 (129)
97 PF05443 ROS_MUCR: ROS/MUCR tr 78.0 1.3 2.8E-05 31.5 1.3 22 147-171 72-93 (132)
98 TIGR00100 hypA hydrogenase nic 77.6 1.1 2.4E-05 31.1 0.9 29 74-102 68-96 (115)
99 KOG4173|consensus 77.6 2.1 4.4E-05 32.7 2.4 48 113-167 108-166 (253)
100 smart00614 ZnF_BED BED zinc fi 77.3 1.6 3.5E-05 25.3 1.4 19 178-196 21-44 (50)
101 smart00531 TFIIE Transcription 77.3 1.6 3.6E-05 31.6 1.8 11 148-158 100-110 (147)
102 PF14445 Prok-RING_2: Prokaryo 77.3 0.22 4.7E-06 28.9 -2.2 44 76-120 7-50 (57)
103 PRK06266 transcription initiat 77.1 0.63 1.4E-05 34.9 -0.4 14 110-123 116-129 (178)
104 TIGR00373 conserved hypothetic 77.1 2.7 5.9E-05 30.9 2.9 34 142-184 104-137 (158)
105 smart00531 TFIIE Transcription 75.9 0.68 1.5E-05 33.6 -0.5 13 111-123 99-111 (147)
106 COG1996 RPC10 DNA-directed RNA 75.0 1.4 3E-05 25.6 0.7 26 75-100 5-32 (49)
107 TIGR00373 conserved hypothetic 74.7 0.74 1.6E-05 33.9 -0.6 13 111-123 109-121 (158)
108 PRK06266 transcription initiat 74.6 3.2 6.9E-05 31.2 2.8 35 142-185 112-146 (178)
109 smart00734 ZnF_Rad18 Rad18-lik 73.8 3.1 6.7E-05 20.6 1.7 19 177-196 3-21 (26)
110 PF05290 Baculo_IE-1: Baculovi 73.7 2.7 5.8E-05 29.8 2.0 33 61-93 65-97 (140)
111 PF01155 HypA: Hydrogenase exp 73.4 1 2.2E-05 31.1 -0.1 28 75-102 69-96 (113)
112 KOG2482|consensus 73.2 5.2 0.00011 33.0 3.8 23 176-198 280-302 (423)
113 KOG1280|consensus 73.0 2.4 5.2E-05 34.9 1.9 38 145-182 77-116 (381)
114 PRK12496 hypothetical protein; 72.6 2 4.3E-05 31.8 1.2 26 77-102 128-153 (164)
115 smart00661 RPOL9 RNA polymeras 71.9 2.3 5E-05 24.6 1.2 13 111-123 20-32 (52)
116 KOG2186|consensus 71.7 1.7 3.8E-05 34.2 0.8 46 112-168 4-49 (276)
117 COG3357 Predicted transcriptio 71.6 2.6 5.7E-05 27.7 1.4 14 75-88 57-70 (97)
118 KOG4167|consensus 71.4 1 2.2E-05 40.6 -0.6 24 176-199 793-816 (907)
119 COG0068 HypF Hydrogenase matur 71.3 1.3 2.9E-05 39.9 0.1 66 77-156 102-182 (750)
120 PF14353 CpXC: CpXC protein 70.7 2 4.2E-05 30.3 0.8 20 111-131 38-57 (128)
121 PRK03681 hypA hydrogenase nick 70.7 2 4.3E-05 29.8 0.8 28 74-101 68-96 (114)
122 PRK09678 DNA-binding transcrip 69.9 1 2.3E-05 28.4 -0.7 15 145-159 25-41 (72)
123 PF15135 UPF0515: Uncharacteri 69.9 3 6.6E-05 32.8 1.7 51 73-123 109-167 (278)
124 PF13240 zinc_ribbon_2: zinc-r 69.7 2.7 5.8E-05 20.2 0.9 6 114-119 16-21 (23)
125 TIGR00595 priA primosomal prot 69.5 4 8.6E-05 35.9 2.6 10 145-154 238-247 (505)
126 PRK00564 hypA hydrogenase nick 69.4 2.2 4.8E-05 29.7 0.8 29 74-102 69-98 (117)
127 PF06524 NOA36: NOA36 protein; 69.2 1.7 3.6E-05 34.4 0.2 95 94-198 127-232 (314)
128 PF05290 Baculo_IE-1: Baculovi 68.8 3.1 6.8E-05 29.5 1.5 60 84-161 73-135 (140)
129 PF12773 DZR: Double zinc ribb 68.2 4.3 9.4E-05 23.3 1.8 8 112-119 30-37 (50)
130 COG4957 Predicted transcriptio 68.0 2.4 5.3E-05 30.0 0.8 21 148-171 77-97 (148)
131 PF08271 TF_Zn_Ribbon: TFIIB z 67.4 1.9 4.2E-05 24.1 0.1 11 111-121 19-29 (43)
132 COG1592 Rubrerythrin [Energy p 67.3 3 6.4E-05 30.9 1.1 11 109-119 147-157 (166)
133 COG1997 RPL43A Ribosomal prote 67.3 2.8 6E-05 27.4 0.9 10 76-85 35-44 (89)
134 PF03107 C1_2: C1 domain; Int 67.1 3.2 7E-05 21.2 1.0 22 77-99 1-22 (30)
135 PRK14714 DNA polymerase II lar 66.1 4.8 0.0001 38.9 2.5 37 77-123 668-704 (1337)
136 COG5236 Uncharacterized conser 66.1 8.1 0.00018 32.0 3.5 71 112-198 221-304 (493)
137 PRK14873 primosome assembly pr 64.1 5.1 0.00011 36.5 2.2 14 2-15 298-311 (665)
138 PF05191 ADK_lid: Adenylate ki 64.0 3.3 7.1E-05 22.4 0.6 11 111-121 21-31 (36)
139 PF07295 DUF1451: Protein of u 63.9 4.4 9.6E-05 29.4 1.5 29 73-101 109-139 (146)
140 PF10083 DUF2321: Uncharacteri 63.6 2.1 4.6E-05 31.2 -0.2 40 79-123 31-80 (158)
141 PF01363 FYVE: FYVE zinc finge 63.4 3.2 6.9E-05 25.6 0.6 26 77-102 10-35 (69)
142 KOG2785|consensus 63.1 9.1 0.0002 32.1 3.3 51 147-197 166-242 (390)
143 PF00301 Rubredoxin: Rubredoxi 63.0 4.5 9.7E-05 23.3 1.1 9 111-119 34-42 (47)
144 COG5236 Uncharacterized conser 62.9 6.6 0.00014 32.5 2.4 48 149-197 222-273 (493)
145 TIGR01206 lysW lysine biosynth 62.6 4 8.7E-05 24.2 0.9 26 77-102 3-32 (54)
146 cd00065 FYVE FYVE domain; Zinc 62.5 4.6 0.0001 23.7 1.2 13 111-123 18-30 (57)
147 cd00730 rubredoxin Rubredoxin; 62.0 6.7 0.00015 22.9 1.8 9 111-119 34-42 (50)
148 COG1594 RPB9 DNA-directed RNA 61.6 4.3 9.3E-05 28.1 1.0 11 176-186 101-111 (113)
149 PF07754 DUF1610: Domain of un 61.6 3.4 7.4E-05 20.2 0.4 8 175-182 16-23 (24)
150 COG1198 PriA Primosomal protei 61.1 5.7 0.00012 36.5 2.0 22 93-120 463-484 (730)
151 PF05443 ROS_MUCR: ROS/MUCR tr 60.9 6.5 0.00014 28.0 1.9 25 108-143 69-93 (132)
152 PF06524 NOA36: NOA36 protein; 60.0 3.2 7E-05 32.9 0.2 26 145-170 207-232 (314)
153 COG4306 Uncharacterized protei 59.9 3.8 8.2E-05 28.7 0.5 32 92-123 39-80 (160)
154 PF07191 zinc-ribbons_6: zinc- 59.4 2 4.3E-05 27.0 -0.9 39 77-118 18-57 (70)
155 PF07649 C1_3: C1-like domain; 59.4 3.7 8.1E-05 20.9 0.3 8 79-86 3-10 (30)
156 COG0068 HypF Hydrogenase matur 58.9 1.7 3.8E-05 39.2 -1.6 80 90-184 99-182 (750)
157 smart00064 FYVE Protein presen 58.3 5.9 0.00013 24.3 1.2 24 78-101 12-35 (68)
158 PF12013 DUF3505: Protein of u 58.1 10 0.00022 25.8 2.4 24 148-171 81-108 (109)
159 PF02176 zf-TRAF: TRAF-type zi 57.8 5.5 0.00012 23.6 1.0 41 147-187 9-54 (60)
160 KOG2807|consensus 57.6 8.8 0.00019 31.5 2.3 33 93-131 277-309 (378)
161 COG5151 SSL1 RNA polymerase II 57.1 5.2 0.00011 32.6 0.9 91 93-198 309-411 (421)
162 PF08274 PhnA_Zn_Ribbon: PhnA 56.8 4.7 0.0001 20.8 0.4 25 149-184 4-28 (30)
163 PF13248 zf-ribbon_3: zinc-rib 56.0 7.5 0.00016 19.1 1.1 7 78-84 4-10 (26)
164 COG4530 Uncharacterized protei 55.3 7.1 0.00015 26.7 1.2 28 94-123 11-38 (129)
165 PRK05580 primosome assembly pr 54.8 10 0.00022 34.7 2.5 7 148-154 409-415 (679)
166 PF04959 ARS2: Arsenite-resist 54.7 11 0.00025 29.1 2.4 26 144-169 74-99 (214)
167 KOG2893|consensus 54.5 2.9 6.3E-05 32.7 -0.8 42 78-131 12-53 (341)
168 KOG4167|consensus 54.5 3.4 7.3E-05 37.5 -0.5 25 147-171 792-816 (907)
169 PF11238 DUF3039: Protein of u 54.3 8.9 0.00019 23.0 1.4 27 97-123 30-56 (58)
170 KOG4173|consensus 54.1 1.9 4.2E-05 32.9 -1.8 21 110-131 143-165 (253)
171 PF04641 Rtf2: Rtf2 RING-finge 53.4 4.1 9E-05 32.5 -0.2 51 73-123 110-162 (260)
172 TIGR00686 phnA alkylphosphonat 53.3 7 0.00015 26.7 0.9 27 78-104 4-31 (109)
173 PRK10220 hypothetical protein; 53.2 7.6 0.00017 26.5 1.1 29 77-105 4-33 (111)
174 COG3091 SprT Zn-dependent meta 52.3 7.3 0.00016 28.3 1.0 13 110-123 116-128 (156)
175 PF08792 A2L_zn_ribbon: A2L zi 51.7 8 0.00017 20.4 0.8 12 90-101 19-30 (33)
176 PF12907 zf-met2: Zinc-binding 51.0 9.5 0.00021 21.1 1.1 20 112-131 2-23 (40)
177 PF07975 C1_4: TFIIH C1-like d 50.8 3.9 8.4E-05 24.0 -0.5 16 147-162 21-36 (51)
178 PF02150 RNA_POL_M_15KD: RNA p 49.6 4.5 9.7E-05 21.6 -0.3 8 113-120 22-29 (35)
179 KOG2593|consensus 49.2 17 0.00036 31.1 2.8 36 144-182 125-160 (436)
180 smart00249 PHD PHD zinc finger 49.2 16 0.00036 19.7 2.0 9 113-121 16-24 (47)
181 PF14369 zf-RING_3: zinc-finge 49.0 12 0.00027 19.9 1.3 10 77-86 3-12 (35)
182 PRK04023 DNA polymerase II lar 48.9 13 0.00027 35.4 2.1 23 75-101 625-647 (1121)
183 PF01286 XPA_N: XPA protein N- 48.6 10 0.00022 20.2 0.9 16 77-92 4-19 (34)
184 PF07282 OrfB_Zn_ribbon: Putat 48.2 8.6 0.00019 23.6 0.7 28 94-122 30-57 (69)
185 smart00154 ZnF_AN1 AN1-like Zi 48.1 13 0.00029 20.3 1.4 18 76-93 12-29 (39)
186 PF00628 PHD: PHD-finger; Int 47.8 8.5 0.00019 22.0 0.6 24 79-103 2-25 (51)
187 PF15269 zf-C2H2_7: Zinc-finge 47.5 14 0.0003 20.9 1.4 21 176-196 21-41 (54)
188 PRK00420 hypothetical protein; 47.3 10 0.00022 26.2 1.0 27 77-103 24-51 (112)
189 PRK00432 30S ribosomal protein 46.9 11 0.00024 22.0 1.0 11 110-120 36-46 (50)
190 PRK11032 hypothetical protein; 46.2 11 0.00024 27.8 1.1 29 73-101 121-151 (160)
191 PF04959 ARS2: Arsenite-resist 46.0 11 0.00023 29.3 1.1 26 172-197 74-99 (214)
192 COG0375 HybF Zn finger protein 45.6 8.7 0.00019 26.6 0.5 27 75-101 69-95 (115)
193 PRK04023 DNA polymerase II lar 45.6 14 0.0003 35.2 1.8 34 77-120 639-672 (1121)
194 COG5151 SSL1 RNA polymerase II 45.3 12 0.00026 30.5 1.3 47 114-170 365-411 (421)
195 COG2331 Uncharacterized protei 44.7 3.8 8.3E-05 26.0 -1.2 12 77-88 13-24 (82)
196 PF12760 Zn_Tnp_IS1595: Transp 43.7 12 0.00025 21.2 0.8 8 77-84 19-26 (46)
197 KOG2593|consensus 43.6 14 0.0003 31.6 1.4 39 108-157 125-163 (436)
198 COG4888 Uncharacterized Zn rib 43.4 11 0.00024 25.4 0.7 30 74-103 20-57 (104)
199 TIGR00595 priA primosomal prot 43.0 17 0.00036 32.0 2.0 24 90-119 238-261 (505)
200 PRK05978 hypothetical protein; 41.8 16 0.00035 26.5 1.4 30 77-106 34-66 (148)
201 KOG4124|consensus 41.5 3.1 6.7E-05 34.4 -2.5 50 146-195 348-418 (442)
202 PRK14873 primosome assembly pr 40.4 17 0.00037 33.2 1.6 21 93-120 411-431 (665)
203 KOG2272|consensus 40.1 18 0.00039 28.7 1.5 15 76-90 99-113 (332)
204 TIGR00515 accD acetyl-CoA carb 40.1 13 0.00028 30.2 0.8 29 76-104 26-57 (285)
205 COG1571 Predicted DNA-binding 39.2 17 0.00036 31.1 1.3 28 94-123 352-379 (421)
206 COG1779 C4-type Zn-finger prot 38.9 14 0.00031 28.1 0.8 30 76-105 14-56 (201)
207 CHL00174 accD acetyl-CoA carbo 38.8 6.8 0.00015 31.9 -1.0 29 76-104 38-69 (296)
208 KOG4218|consensus 38.7 9.4 0.0002 31.6 -0.2 39 78-116 17-56 (475)
209 KOG2785|consensus 38.6 33 0.00071 28.9 2.9 51 111-169 166-242 (390)
210 PF14311 DUF4379: Domain of un 38.0 26 0.00057 20.5 1.7 13 148-160 29-41 (55)
211 TIGR00515 accD acetyl-CoA carb 37.9 7.2 0.00016 31.6 -1.0 33 91-123 25-57 (285)
212 COG2051 RPS27A Ribosomal prote 37.6 18 0.00039 22.4 1.0 29 77-105 20-51 (67)
213 PTZ00255 60S ribosomal protein 37.3 12 0.00026 24.8 0.1 9 76-84 36-44 (90)
214 PRK05654 acetyl-CoA carboxylas 37.0 7.4 0.00016 31.6 -1.0 28 76-103 27-57 (292)
215 PF13878 zf-C2H2_3: zinc-finge 37.0 40 0.00087 18.6 2.2 23 148-170 14-38 (41)
216 PF10263 SprT-like: SprT-like 36.8 11 0.00023 27.3 -0.2 32 147-186 123-154 (157)
217 cd00924 Cyt_c_Oxidase_Vb Cytoc 36.7 17 0.00037 24.4 0.8 17 140-157 73-89 (97)
218 KOG0782|consensus 36.6 2.1 4.6E-05 37.7 -4.3 94 82-189 189-290 (1004)
219 PF01485 IBR: IBR domain; Int 36.6 23 0.00051 20.9 1.4 12 112-123 41-52 (64)
220 KOG3408|consensus 36.4 26 0.00056 24.5 1.7 21 148-168 58-78 (129)
221 PRK14714 DNA polymerase II lar 36.1 27 0.00058 34.2 2.2 40 77-121 680-719 (1337)
222 COG1773 Rubredoxin [Energy pro 35.9 16 0.00035 21.8 0.5 12 175-186 3-14 (55)
223 KOG3507|consensus 35.6 14 0.00031 22.2 0.2 13 111-123 37-49 (62)
224 PRK00762 hypA hydrogenase nick 35.6 17 0.00037 25.5 0.7 26 74-100 68-100 (124)
225 KOG2071|consensus 35.5 24 0.00052 31.4 1.7 26 173-198 416-441 (579)
226 PF08209 Sgf11: Sgf11 (transcr 35.3 13 0.00028 19.6 0.1 19 112-132 5-23 (33)
227 COG1571 Predicted DNA-binding 35.2 22 0.00047 30.5 1.4 32 76-107 350-382 (421)
228 PRK06260 threonine synthase; V 35.2 19 0.0004 30.6 1.0 26 77-102 4-29 (397)
229 PF04810 zf-Sec23_Sec24: Sec23 35.2 13 0.00028 20.4 0.1 12 144-155 21-32 (40)
230 TIGR00280 L37a ribosomal prote 35.0 11 0.00024 24.9 -0.2 10 76-85 35-44 (91)
231 COG1327 Predicted transcriptio 35.0 17 0.00037 26.5 0.6 11 113-123 30-40 (156)
232 PF01780 Ribosomal_L37ae: Ribo 34.9 16 0.00034 24.2 0.4 28 76-103 35-64 (90)
233 COG1439 Predicted nucleic acid 34.9 18 0.00039 27.1 0.8 23 77-101 140-162 (177)
234 COG3677 Transposase and inacti 34.7 21 0.00045 25.3 1.1 15 109-123 51-65 (129)
235 smart00731 SprT SprT homologue 34.6 22 0.00048 25.5 1.2 12 111-122 112-123 (146)
236 PF13824 zf-Mss51: Zinc-finger 34.2 28 0.0006 20.8 1.3 14 109-122 12-25 (55)
237 PF05495 zf-CHY: CHY zinc fing 33.3 13 0.00029 23.2 -0.1 30 147-184 41-70 (71)
238 PRK05580 primosome assembly pr 32.7 30 0.00064 31.7 1.9 37 78-120 392-430 (679)
239 TIGR00244 transcriptional regu 32.3 20 0.00043 26.0 0.6 11 113-123 30-40 (147)
240 PF11023 DUF2614: Protein of u 31.9 20 0.00044 24.7 0.6 29 75-103 68-96 (114)
241 PF10013 DUF2256: Uncharacteri 31.9 30 0.00064 19.4 1.1 12 178-189 11-22 (42)
242 PRK14559 putative protein seri 31.7 32 0.00069 31.3 1.9 37 78-123 17-53 (645)
243 PTZ00303 phosphatidylinositol 31.6 18 0.00038 33.6 0.3 26 77-102 461-491 (1374)
244 COG1326 Uncharacterized archae 31.6 20 0.00043 27.2 0.5 7 77-83 7-13 (201)
245 COG1655 Uncharacterized protei 31.5 15 0.00032 28.7 -0.1 14 110-123 18-31 (267)
246 COG1675 TFA1 Transcription ini 31.2 12 0.00025 28.1 -0.7 13 111-123 113-125 (176)
247 PLN02294 cytochrome c oxidase 31.1 24 0.00053 26.2 0.9 13 174-186 140-152 (174)
248 PRK06450 threonine synthase; V 30.8 24 0.00052 29.3 1.0 26 77-103 4-29 (338)
249 PF04423 Rad50_zn_hook: Rad50 30.3 19 0.00042 21.0 0.2 12 177-188 22-33 (54)
250 PRK14559 putative protein seri 29.9 36 0.00078 31.0 2.0 37 78-123 3-39 (645)
251 COG4640 Predicted membrane pro 29.8 33 0.00071 29.1 1.5 21 109-130 13-33 (465)
252 KOG1280|consensus 29.6 41 0.00088 28.0 2.0 39 109-154 77-116 (381)
253 KOG3408|consensus 29.6 33 0.00072 24.0 1.3 25 173-197 55-79 (129)
254 PF09332 Mcm10: Mcm10 replicat 29.4 4.2 9.2E-05 33.8 -3.6 14 110-123 284-297 (344)
255 PF13453 zf-TFIIB: Transcripti 29.3 50 0.0011 18.0 1.8 16 148-163 20-35 (41)
256 KOG0978|consensus 29.1 21 0.00045 32.7 0.3 21 173-193 676-696 (698)
257 PF10122 Mu-like_Com: Mu-like 29.0 25 0.00055 20.5 0.6 29 76-104 4-36 (51)
258 PF01428 zf-AN1: AN1-like Zinc 28.9 31 0.00068 19.1 0.9 19 75-93 12-30 (43)
259 PRK00415 rps27e 30S ribosomal 28.3 42 0.00091 20.3 1.5 28 77-104 12-42 (59)
260 TIGR00143 hypF [NiFe] hydrogen 28.3 17 0.00038 33.4 -0.3 68 76-157 68-150 (711)
261 PF08790 zf-LYAR: LYAR-type C2 28.2 14 0.0003 18.7 -0.5 9 113-121 2-10 (28)
262 PF13451 zf-trcl: Probable zin 27.7 22 0.00048 20.6 0.2 14 174-187 3-16 (49)
263 PRK07591 threonine synthase; V 27.7 29 0.00063 29.7 1.0 27 76-103 18-44 (421)
264 PF10276 zf-CHCC: Zinc-finger 27.5 19 0.00042 19.9 -0.1 11 111-121 29-39 (40)
265 PRK04351 hypothetical protein; 27.4 27 0.00058 25.4 0.6 33 110-158 111-143 (149)
266 PF14206 Cys_rich_CPCC: Cystei 27.4 35 0.00075 21.9 1.0 26 77-102 2-30 (78)
267 COG1998 RPS31 Ribosomal protei 27.3 31 0.00067 20.0 0.7 9 111-119 37-45 (51)
268 PF01927 Mut7-C: Mut7-C RNAse 27.3 28 0.0006 25.1 0.7 12 112-123 125-136 (147)
269 PF14803 Nudix_N_2: Nudix N-te 26.4 21 0.00046 18.9 -0.1 7 148-154 23-29 (34)
270 KOG3002|consensus 26.3 36 0.00078 27.8 1.2 61 109-181 78-142 (299)
271 TIGR00627 tfb4 transcription f 26.3 37 0.00081 27.5 1.3 24 93-121 256-279 (279)
272 COG1656 Uncharacterized conser 26.2 42 0.00091 24.8 1.4 12 112-123 131-142 (165)
273 PF04780 DUF629: Protein of un 26.0 32 0.00069 29.9 0.9 28 111-145 57-84 (466)
274 PF04606 Ogr_Delta: Ogr/Delta- 25.8 16 0.00034 20.8 -0.7 6 117-122 33-38 (47)
275 PF04780 DUF629: Protein of un 25.7 57 0.0012 28.5 2.3 27 147-173 57-84 (466)
276 COG5152 Uncharacterized conser 25.5 17 0.00037 27.7 -0.7 16 75-90 195-210 (259)
277 KOG2636|consensus 25.5 50 0.0011 28.5 1.9 29 168-196 394-423 (497)
278 COG1379 PHP family phosphoeste 25.4 21 0.00045 29.5 -0.3 29 94-122 248-276 (403)
279 PF11789 zf-Nse: Zinc-finger o 25.0 48 0.001 19.7 1.3 13 110-122 23-35 (57)
280 PF11781 RRN7: RNA polymerase 24.9 42 0.00091 18.0 0.9 24 77-100 9-33 (36)
281 KOG2071|consensus 24.5 41 0.0009 30.0 1.3 28 145-172 416-443 (579)
282 PF03811 Zn_Tnp_IS1: InsA N-te 23.7 11 0.00024 20.3 -1.5 30 148-181 6-35 (36)
283 PF05129 Elf1: Transcription e 23.7 25 0.00054 22.7 -0.1 10 74-83 20-29 (81)
284 PRK03976 rpl37ae 50S ribosomal 23.6 40 0.00087 22.3 0.8 28 76-103 36-65 (90)
285 PF06397 Desulfoferrod_N: Desu 23.3 18 0.00039 19.5 -0.7 10 93-102 7-16 (36)
286 KOG2906|consensus 23.1 31 0.00068 23.1 0.3 29 95-123 4-33 (105)
287 KOG1842|consensus 23.0 46 0.00099 28.7 1.3 29 110-145 14-42 (505)
288 COG4896 Uncharacterized protei 23.0 44 0.00096 20.3 0.9 10 147-156 31-40 (68)
289 PTZ00448 hypothetical protein; 23.0 59 0.0013 27.4 1.9 23 175-197 314-336 (373)
290 KOG1842|consensus 22.5 49 0.0011 28.5 1.4 28 146-173 14-42 (505)
291 PF07227 DUF1423: Protein of u 22.3 75 0.0016 27.5 2.4 74 78-162 115-198 (446)
292 PF06220 zf-U1: U1 zinc finger 22.3 60 0.0013 17.6 1.3 11 111-121 3-13 (38)
293 KOG2636|consensus 22.1 62 0.0013 28.0 1.8 27 142-168 396-423 (497)
294 KOG2907|consensus 22.0 32 0.0007 23.7 0.2 12 176-187 103-114 (116)
295 PRK12722 transcriptional activ 21.9 65 0.0014 24.4 1.8 26 94-119 136-162 (187)
296 PRK14892 putative transcriptio 21.8 58 0.0013 21.9 1.4 7 149-155 44-50 (99)
297 KOG0717|consensus 21.8 51 0.0011 28.6 1.3 20 178-197 295-314 (508)
298 TIGR03844 cysteate_syn cysteat 21.7 45 0.00097 28.4 1.0 22 77-99 3-24 (398)
299 COG0675 Transposase and inacti 21.5 46 0.00099 26.9 1.0 25 148-187 310-334 (364)
300 COG1645 Uncharacterized Zn-fin 21.3 43 0.00093 23.8 0.7 28 77-104 29-56 (131)
301 PF11672 DUF3268: Protein of u 21.2 32 0.0007 23.3 0.0 13 110-122 1-13 (102)
302 KOG0957|consensus 20.9 42 0.00091 29.4 0.7 48 75-123 543-601 (707)
303 PF13901 DUF4206: Domain of un 20.7 80 0.0017 24.1 2.1 30 75-104 151-184 (202)
304 KOG3183|consensus 20.6 46 0.001 26.2 0.8 28 74-101 21-48 (250)
No 1
>KOG2462|consensus
Probab=99.95 E-value=2e-28 Score=188.46 Aligned_cols=116 Identities=24% Similarity=0.362 Sum_probs=107.2
Q ss_pred CCCCccccccccccccccccc---------------ccccccCcccCCCC-------CCCCcccccChhhhccCHHHHHh
Q psy7453 73 TQNHSLCKHCHSQLSHLDLLD---------------HCKTCSYMIRPNAN-------NTFSPFCIYCKAVLSTNLNELIE 130 (200)
Q Consensus 73 ~~~~~~C~~C~~~f~~~~~l~---------------~C~~C~~~f~~~~~-------~~~~~~C~~C~~~f~~~~~~l~~ 130 (200)
....|.|+.||+.+.+.++|. .|++||+.|..... ..-+++|.+|||.|+. .|-|+.
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSR-PWLLQG 205 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSR-PWLLQG 205 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccc-hHHhhc
Confidence 344699999999999998873 79999999987654 5568999999999999 999999
Q ss_pred chhhhhhhhhcCCCCCceecCccCcccCChHHHHHHHHHcCCCCCcccccCcccccCHHHHHHHHh
Q psy7453 131 HCRTCKSMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFRSASVAGLHYHLK 196 (200)
Q Consensus 131 H~~~~~~~~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~f~~~~~L~~H~~ 196 (200)
| + |+|+|||||.|+.|+++|.+.++|+.|+++|.+.|+|+|+.|+|+|+.++-|.+|.-
T Consensus 206 H------i-RTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~E 264 (279)
T KOG2462|consen 206 H------I-RTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSE 264 (279)
T ss_pred c------c-ccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhh
Confidence 9 9 999999999999999999999999999999999999999999999999999999974
No 2
>KOG2462|consensus
Probab=99.90 E-value=3.1e-24 Score=165.43 Aligned_cols=100 Identities=28% Similarity=0.475 Sum_probs=93.0
Q ss_pred cccccccccCcccCCCC------------CCCCcccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccC
Q psy7453 91 LLDHCKTCSYMIRPNAN------------NTFSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSY 158 (200)
Q Consensus 91 ~l~~C~~C~~~f~~~~~------------~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~ 158 (200)
..++|++||+.+.+.++ ..+-+.|++|||.|.+ ...|+.| + ++|+ -+++|.+|||.|.
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvS-mpALkMH------i-rTH~--l~c~C~iCGKaFS 198 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVS-MPALKMH------I-RTHT--LPCECGICGKAFS 198 (279)
T ss_pred CceeccccccccccccccchhhcccccccccccccCCCCCceeee-hHHHhhH------h-hccC--CCccccccccccc
Confidence 44689999999988774 4678999999999999 9999999 9 9998 4799999999999
Q ss_pred ChHHHHHHHHHcCCCCCcccccCcccccCHHHHHHHHhhhcC
Q psy7453 159 NIGCMRSHIRTHTGEKPYACGQCAFRSASVAGLHYHLKKTYH 200 (200)
Q Consensus 159 ~~~~l~~H~~~H~~~k~~~C~~C~k~f~~~~~L~~H~~~h~g 200 (200)
+...|+-|+|+|+|||||.|+.|+|+|+.+++|+.||++|.+
T Consensus 199 RPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~ 240 (279)
T KOG2462|consen 199 RPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSD 240 (279)
T ss_pred chHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcC
Confidence 999999999999999999999999999999999999999975
No 3
>KOG3608|consensus
Probab=99.71 E-value=2.3e-18 Score=136.71 Aligned_cols=133 Identities=17% Similarity=0.344 Sum_probs=99.7
Q ss_pred cccchhhhhhhhhhhcCCCCCCCccccccccccccccccc--------------ccccccCcccCCCC-------CCCCc
Q psy7453 54 SLDQILNLNLSVLLVTTIPTQNHSLCKHCHSQLSHLDLLD--------------HCKTCSYMIRPNAN-------NTFSP 112 (200)
Q Consensus 54 ~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~--------------~C~~C~~~f~~~~~-------~~~~~ 112 (200)
-++.++.|+.|.+. |+++|...|+.||..|.++..|+ .|..|.+.|.+... ....|
T Consensus 188 ~~~~k~~LreH~r~---Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~y 264 (467)
T KOG3608|consen 188 HMGNKYRLREHIRT---HSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCY 264 (467)
T ss_pred hhccHHHHHHHHHh---cCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcc
Confidence 45677888888888 99999999999999999988773 68888888876543 34568
Q ss_pred ccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccCChHHHHHHHHHcCCCCCccccc--CcccccCHHH
Q psy7453 113 FCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQ--CAFRSASVAG 190 (200)
Q Consensus 113 ~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~--C~k~f~~~~~ 190 (200)
+|+.|+.+.+. .++|..| ++-.|...|||+|+.|++.|.+.+.|++|..+|+ +-.|+|+. |...|.+..+
T Consensus 265 kCplCdmtc~~-~ssL~~H------~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q 336 (467)
T KOG3608|consen 265 KCPLCDMTCSS-ASSLTTH------IRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQ 336 (467)
T ss_pred cccccccCCCC-hHHHHHH------HHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHH
Confidence 88888888888 8888888 8667888888888888888888888888887776 33344444 4444444444
Q ss_pred HHHHHhh
Q psy7453 191 LHYHLKK 197 (200)
Q Consensus 191 L~~H~~~ 197 (200)
+++|++.
T Consensus 337 ~~~H~~e 343 (467)
T KOG3608|consen 337 MRRHFLE 343 (467)
T ss_pred HHHHHHH
Confidence 4444443
No 4
>KOG3576|consensus
Probab=99.69 E-value=5.6e-18 Score=125.35 Aligned_cols=85 Identities=26% Similarity=0.391 Sum_probs=76.4
Q ss_pred CCCCcccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccCChHHHHHHHHHcCCCCCcccccCcccccC
Q psy7453 108 NTFSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFRSAS 187 (200)
Q Consensus 108 ~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~f~~ 187 (200)
+...|.|.+|+|.|.. ...|.+| + +-|...+.+.|..||+.|...-+|++|+|+|+|.+||+|..|+|+|.+
T Consensus 114 d~d~ftCrvCgK~F~l-QRmlnrh------~-kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftq 185 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGL-QRMLNRH------L-KCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQ 185 (267)
T ss_pred CCCeeeeehhhhhhhH-HHHHHHH------h-hhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHh
Confidence 5567899999999999 9999999 8 999988999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhhcC
Q psy7453 188 VAGLHYHLKKTYH 200 (200)
Q Consensus 188 ~~~L~~H~~~h~g 200 (200)
+.+|..|++..+|
T Consensus 186 rcsleshl~kvhg 198 (267)
T KOG3576|consen 186 RCSLESHLKKVHG 198 (267)
T ss_pred hccHHHHHHHHcC
Confidence 9999999886554
No 5
>KOG3623|consensus
Probab=99.68 E-value=8e-18 Score=144.02 Aligned_cols=81 Identities=21% Similarity=0.406 Sum_probs=78.1
Q ss_pred CCCCcccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccCChHHHHHHHHHcCCCCCcccccCcccccC
Q psy7453 108 NTFSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFRSAS 187 (200)
Q Consensus 108 ~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~f~~ 187 (200)
.+..|.|+.|+|.|.- .+.|.+| . -.|+|.+||+|.+|.|+|+.+..|..|+|.|.|||||+|+.|+|+|+.
T Consensus 891 e~gmyaCDqCDK~FqK-qSSLaRH------K-YEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSH 962 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQK-QSSLARH------K-YEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSH 962 (1007)
T ss_pred ccccchHHHHHHHHHh-hHHHHHh------h-hhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhccc
Confidence 5578999999999999 9999999 8 999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHh
Q psy7453 188 VAGLHYHLK 196 (200)
Q Consensus 188 ~~~L~~H~~ 196 (200)
..+...||.
T Consensus 963 SGSYSQHMN 971 (1007)
T KOG3623|consen 963 SGSYSQHMN 971 (1007)
T ss_pred ccchHhhhc
Confidence 999999984
No 6
>KOG1074|consensus
Probab=99.67 E-value=1.3e-17 Score=144.60 Aligned_cols=83 Identities=24% Similarity=0.422 Sum_probs=75.9
Q ss_pred CCcccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccCChHHHHHHHHHcCCC----CCcccc---cCc
Q psy7453 110 FSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGE----KPYACG---QCA 182 (200)
Q Consensus 110 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~H~~~----k~~~C~---~C~ 182 (200)
.|-+|.+|-++.+- ++.|+-| . |+|+||+||+|.+||++|.++++|+.|+-+|... -++.|+ +|.
T Consensus 604 dPNqCiiC~rVlSC-~saLqmH------y-rtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~ 675 (958)
T KOG1074|consen 604 DPNQCIICLRVLSC-PSALQMH------Y-RTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQ 675 (958)
T ss_pred Cccceeeeeecccc-hhhhhhh------h-hcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhc
Confidence 36789999999999 9999999 8 9999999999999999999999999999999654 348899 999
Q ss_pred ccccCHHHHHHHHhhhcC
Q psy7453 183 FRSASVAGLHYHLKKTYH 200 (200)
Q Consensus 183 k~f~~~~~L~~H~~~h~g 200 (200)
+.|...-.|..|+++|.|
T Consensus 676 ~kftn~V~lpQhIriH~~ 693 (958)
T KOG1074|consen 676 KKFTNAVTLPQHIRIHLG 693 (958)
T ss_pred ccccccccccceEEeecC
Confidence 999999999999999974
No 7
>KOG1074|consensus
Probab=99.64 E-value=9.9e-17 Score=139.22 Aligned_cols=53 Identities=28% Similarity=0.528 Sum_probs=50.9
Q ss_pred eecCccCcccCChHHHHHHHHHcCCCCCcccccCcccccCHHHHHHHHhhhcC
Q psy7453 148 FVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFRSASVAGLHYHLKKTYH 200 (200)
Q Consensus 148 ~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~f~~~~~L~~H~~~h~g 200 (200)
..|.+||+.|...++|+.|+|+|+|+|||.|..|++.|..+.+|++||.+|.+
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w 932 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMW 932 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccc
Confidence 58999999999999999999999999999999999999999999999999863
No 8
>KOG3623|consensus
Probab=99.59 E-value=1.2e-16 Score=136.91 Aligned_cols=114 Identities=23% Similarity=0.394 Sum_probs=85.7
Q ss_pred cccccccccccccccccccccccCcccCCCCCCCCcccccChhhhccCHHHHHhchhhhhhhh---hcCC---CCCceec
Q psy7453 77 SLCKHCHSQLSHLDLLDHCKTCSYMIRPNANNTFSPFCIYCKAVLSTNLNELIEHCRTCKSMI---RTDP---FRHKFVC 150 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~l~~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~---~~h~---~~k~~~C 150 (200)
..|+.|++.+.....|.++ ..+. ....+..|.|..|..+|.. +..|.+|..+|+... ..++ +-+.|+|
T Consensus 211 ltcpycdrgykrltslkeH----ikyr-hekne~nfsC~lCsytFAy-RtQLErhm~~hkpg~dqa~sltqsa~lRKFKC 284 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEH----IKYR-HEKNEPNFSCMLCSYTFAY-RTQLERHMQLHKPGGDQAISLTQSALLRKFKC 284 (1007)
T ss_pred hcchhHHHHHHHHHHHHHH----HHHH-HhhCCCCCcchhhhhhhhh-HHHHHHHHHhhcCCCcccccccchhhhccccc
Confidence 4566666666655555432 0111 1126678999999999999 999999944332220 0011 2357999
Q ss_pred CccCcccCChHHHHHHHHHcCCCCCcccccCcccccCHHHHHHHHh
Q psy7453 151 YACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFRSASVAGLHYHLK 196 (200)
Q Consensus 151 ~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~f~~~~~L~~H~~ 196 (200)
..|||+|+.+..|+.|+|+|.|||||.|+.|+|+|+...+...||-
T Consensus 285 tECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 285 TECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred cccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 9999999999999999999999999999999999999999999974
No 9
>KOG3576|consensus
Probab=99.58 E-value=3.3e-16 Score=115.99 Aligned_cols=113 Identities=21% Similarity=0.439 Sum_probs=97.3
Q ss_pred CCCCCcccccccccccccccccccccccCcccCCCCCCCCcccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecC
Q psy7453 72 PTQNHSLCKHCHSQLSHLDLLDHCKTCSYMIRPNANNTFSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCY 151 (200)
Q Consensus 72 ~~~~~~~C~~C~~~f~~~~~l~~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~ 151 (200)
.+...|.|.+|++.|.....|.++-.|. ...+.+-|..||+.|.. .-.|++| + ++|+|.+||+|.
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch-------~~vkr~lct~cgkgfnd-tfdlkrh------~-rthtgvrpykc~ 177 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCH-------SDVKRHLCTFCGKGFND-TFDLKRH------T-RTHTGVRPYKCS 177 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhc-------cHHHHHHHhhccCcccc-hhhhhhh------h-ccccCccccchh
Confidence 3456799999999999888886654443 34567899999999999 9999999 9 999999999999
Q ss_pred ccCcccCChHHHHHHHH-HcC----------CCCCcccccCcccccCHHHHHHHHhhhc
Q psy7453 152 ACDYFSYNIGCMRSHIR-THT----------GEKPYACGQCAFRSASVAGLHYHLKKTY 199 (200)
Q Consensus 152 ~C~~~f~~~~~l~~H~~-~H~----------~~k~~~C~~C~k~f~~~~~L~~H~~~h~ 199 (200)
.|+++|...-+|..|.+ +|- .+|.|.|+.||.+-.....+..|++.|+
T Consensus 178 ~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~h 236 (267)
T KOG3576|consen 178 LCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHH 236 (267)
T ss_pred hhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcC
Confidence 99999999999999976 452 2567999999999999999999998875
No 10
>KOG3608|consensus
Probab=99.55 E-value=3e-15 Score=119.21 Aligned_cols=137 Identities=22% Similarity=0.331 Sum_probs=112.6
Q ss_pred ccccchhhhhhhhhhhcCCCCCCCcccccccccccccccc----------cccccccCcccCCC----------CCCCCc
Q psy7453 53 MSLDQILNLNLSVLLVTTIPTQNHSLCKHCHSQLSHLDLL----------DHCKTCSYMIRPNA----------NNTFSP 112 (200)
Q Consensus 53 ~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l----------~~C~~C~~~f~~~~----------~~~~~~ 112 (200)
.-|.++..|..|.+..+ .-...+|.|..|.|.|.+...| |+|+.|+-.-...+ ...|||
T Consensus 215 ~~F~~~tkl~DH~rRqt-~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpf 293 (467)
T KOG3608|consen 215 ELFRTKTKLFDHLRRQT-ELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPF 293 (467)
T ss_pred HHhccccHHHHHHHhhh-hhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHHHhhhccCCCc
Confidence 34555666666766544 3456699999999999999888 58999986544332 268999
Q ss_pred ccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCc--cCcccCChHHHHHHHHH-cCCCC--CcccccCcccccC
Q psy7453 113 FCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYA--CDYFSYNIGCMRSHIRT-HTGEK--PYACGQCAFRSAS 187 (200)
Q Consensus 113 ~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~--C~~~f~~~~~l~~H~~~-H~~~k--~~~C~~C~k~f~~ 187 (200)
+|+.|++.|.+ .+.|.+| . .+|+ +--|.|+. |...|.....+++|++- |.|.. +|.|-.|++.|.+
T Consensus 294 KCd~Cd~~c~~-esdL~kH------~-~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~ 364 (467)
T KOG3608|consen 294 KCDECDTRCVR-ESDLAKH------V-QVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTS 364 (467)
T ss_pred cccchhhhhcc-HHHHHHH------H-Hhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhcc
Confidence 99999999999 9999999 8 8998 66799988 99999999999999885 55654 5999999999999
Q ss_pred HHHHHHHHhhhc
Q psy7453 188 VAGLHYHLKKTY 199 (200)
Q Consensus 188 ~~~L~~H~~~h~ 199 (200)
..+|.+|+..-+
T Consensus 365 G~~L~~HL~kkH 376 (467)
T KOG3608|consen 365 GKSLSAHLMKKH 376 (467)
T ss_pred chhHHHHHHHhh
Confidence 999999987644
No 11
>PHA00733 hypothetical protein
Probab=99.41 E-value=2.8e-13 Score=96.08 Aligned_cols=88 Identities=17% Similarity=0.164 Sum_probs=67.1
Q ss_pred CCCCcccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccCChHHHHHHHHHcCCCCCcccccCcccccC
Q psy7453 108 NTFSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFRSAS 187 (200)
Q Consensus 108 ~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~f~~ 187 (200)
.++++.|.+|++.|.. ...|..|......+ ..+ +++||.|+.||+.|.....|..|++.| +.+|.|++|++.|..
T Consensus 37 ~~~~~~~~~~~~~~~~-~~~l~~~~~l~~~~-~~~-~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~ 111 (128)
T PHA00733 37 EQKRLIRAVVKTLIYN-PQLLDESSYLYKLL-TSK-AVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRN 111 (128)
T ss_pred hhhhHHHHHHhhhccC-hhhhcchHHHHhhc-ccC-CCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCC
Confidence 4566777777766666 55554442211114 444 478999999999999999999999987 467999999999999
Q ss_pred HHHHHHHHhhhcC
Q psy7453 188 VAGLHYHLKKTYH 200 (200)
Q Consensus 188 ~~~L~~H~~~h~g 200 (200)
...|..|+...+|
T Consensus 112 ~~sL~~H~~~~h~ 124 (128)
T PHA00733 112 TDSTLDHVCKKHN 124 (128)
T ss_pred HHHHHHHHHHhcC
Confidence 9999999987664
No 12
>PHA02768 hypothetical protein; Provisional
Probab=99.16 E-value=1.4e-11 Score=73.12 Aligned_cols=42 Identities=19% Similarity=0.346 Sum_probs=34.1
Q ss_pred eecCccCcccCChHHHHHHHHHcCCCCCcccccCcccccCHHHH
Q psy7453 148 FVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFRSASVAGL 191 (200)
Q Consensus 148 ~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~f~~~~~L 191 (200)
|+|+.||+.|...++|..|+++|+ ++|+|..|++.|.+.+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 678888888888888888888887 688888888888876655
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.11 E-value=1.2e-10 Score=100.24 Aligned_cols=74 Identities=18% Similarity=0.332 Sum_probs=32.3
Q ss_pred ccCcccCCCCCCCCcccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccCChHHHHHHHHHcCCCCCcc
Q psy7453 98 CSYMIRPNANNTFSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYA 177 (200)
Q Consensus 98 C~~~f~~~~~~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~ 177 (200)
||..|... ..+..+.|+.|++.|. ...|..| + .+|+ +|+.|+ ||+.+ ....|..|+++|.+++++.
T Consensus 441 Cg~v~~r~-el~~H~~C~~Cgk~f~--~s~LekH------~-~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~ 506 (567)
T PLN03086 441 CGIVLRVE-EAKNHVHCEKCGQAFQ--QGEMEKH------M-KVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLIT 506 (567)
T ss_pred ccceeecc-ccccCccCCCCCCccc--hHHHHHH------H-HhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCcee
Confidence 44444222 2334444555554442 2334444 4 3332 344444 44322 3344444444444444444
Q ss_pred cccCcccc
Q psy7453 178 CGQCAFRS 185 (200)
Q Consensus 178 C~~C~k~f 185 (200)
|+.|++.|
T Consensus 507 C~fC~~~v 514 (567)
T PLN03086 507 CRFCGDMV 514 (567)
T ss_pred CCCCCCcc
Confidence 44444444
No 14
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.08 E-value=1.9e-10 Score=98.95 Aligned_cols=111 Identities=18% Similarity=0.349 Sum_probs=87.8
Q ss_pred CCccccc--ccccccccc--cccccccccCcccCCCC------CCCCcccccChhhhccCHHHHHhchhhhhhhhhcCCC
Q psy7453 75 NHSLCKH--CHSQLSHLD--LLDHCKTCSYMIRPNAN------NTFSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPF 144 (200)
Q Consensus 75 ~~~~C~~--C~~~f~~~~--~l~~C~~C~~~f~~~~~------~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~ 144 (200)
..-.|+. |+..|.... ....|+.|++.|..... -.+++.|+ ||+.+ . +..|..| + .+|.+
T Consensus 432 ~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~~s~LekH~~~~Hkpv~Cp-Cg~~~-~-R~~L~~H------~-~thCp 501 (567)
T PLN03086 432 HNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQQGEMEKHMKVFHEPLQCP-CGVVL-E-KEQMVQH------Q-ASTCP 501 (567)
T ss_pred cceeCCcccccceeeccccccCccCCCCCCccchHHHHHHHHhcCCCccCC-CCCCc-c-hhHHHhh------h-hccCC
Confidence 4456874 999886543 22479999998863211 23789999 99755 6 7899999 8 99999
Q ss_pred CCceecCccCcccC----------ChHHHHHHHHHcCCCCCcccccCcccccCHHHHHHHHhh
Q psy7453 145 RHKFVCYACDYFSY----------NIGCMRSHIRTHTGEKPYACGQCAFRSASVAGLHYHLKK 197 (200)
Q Consensus 145 ~k~~~C~~C~~~f~----------~~~~l~~H~~~H~~~k~~~C~~C~k~f~~~~~L~~H~~~ 197 (200)
++++.|+.|++.|. ..+.|..|..++ |.+++.|..||+.+..+ .|..|+..
T Consensus 502 ~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~~ 562 (567)
T PLN03086 502 LRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQIA 562 (567)
T ss_pred CCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHHHH
Confidence 99999999999995 245899999986 99999999999999887 56678754
No 15
>PHA00733 hypothetical protein
Probab=99.03 E-value=1.9e-10 Score=81.56 Aligned_cols=90 Identities=19% Similarity=0.237 Sum_probs=70.0
Q ss_pred CCCCCCcccccccccccccccccccccccCcccCCCCCCCCcccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceec
Q psy7453 71 IPTQNHSLCKHCHSQLSHLDLLDHCKTCSYMIRPNANNTFSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVC 150 (200)
Q Consensus 71 ~~~~~~~~C~~C~~~f~~~~~l~~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C 150 (200)
..+++++.|.+|++.|.....|..-..=-+ .....+++||.|+.|++.|.+ ...|..| + +.| +.+|.|
T Consensus 35 ~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~--~~~~~~~kPy~C~~Cgk~Fss-~s~L~~H------~-r~h--~~~~~C 102 (128)
T PHA00733 35 TPEQKRLIRAVVKTLIYNPQLLDESSYLYK--LLTSKAVSPYVCPLCLMPFSS-SVSLKQH------I-RYT--EHSKVC 102 (128)
T ss_pred ChhhhhHHHHHHhhhccChhhhcchHHHHh--hcccCCCCCccCCCCCCcCCC-HHHHHHH------H-hcC--CcCccC
Confidence 345788999999999998877743100000 012235789999999999999 9999999 8 766 457999
Q ss_pred CccCcccCChHHHHHHHHHcCC
Q psy7453 151 YACDYFSYNIGCMRSHIRTHTG 172 (200)
Q Consensus 151 ~~C~~~f~~~~~l~~H~~~H~~ 172 (200)
+.|++.|.....|..|++...+
T Consensus 103 ~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 103 PVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCCccCCHHHHHHHHHHhcC
Confidence 9999999999999999886543
No 16
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=99.00 E-value=2.4e-10 Score=58.15 Aligned_cols=26 Identities=50% Similarity=0.948 Sum_probs=20.9
Q ss_pred HHHHHHHHcCCCCCcccccCcccccC
Q psy7453 162 CMRSHIRTHTGEKPYACGQCAFRSAS 187 (200)
Q Consensus 162 ~l~~H~~~H~~~k~~~C~~C~k~f~~ 187 (200)
+|.+|+++|+|++||+|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 47788888888888888888888863
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.91 E-value=3.4e-10 Score=67.20 Aligned_cols=43 Identities=19% Similarity=0.355 Sum_probs=39.4
Q ss_pred CcccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccCChHHH
Q psy7453 111 SPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSYNIGCM 163 (200)
Q Consensus 111 ~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~~~~~l 163 (200)
-|+|+.||+.|+. .++|..| + ++|+ ++++|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~-~~~L~~H------~-r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIK-RKSMITH------L-RKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeecc-HHHHHHH------H-HhcC--CcccCCcccceeccccee
Confidence 4899999999999 9999999 9 9998 799999999999987765
No 18
>KOG3993|consensus
Probab=98.66 E-value=7.8e-09 Score=84.66 Aligned_cols=82 Identities=21% Similarity=0.267 Sum_probs=66.2
Q ss_pred CCcccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccCChHHHHHHHHHcCC--------C--------
Q psy7453 110 FSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTG--------E-------- 173 (200)
Q Consensus 110 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~H~~--------~-------- 173 (200)
..|.|..|...|.+ .-.|.+| . =.-.-.--|+|+.|+|.|+...+|..|.|.|.. .
T Consensus 266 GdyiCqLCK~kYeD-~F~LAQH------r-C~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~ 337 (500)
T KOG3993|consen 266 GDYICQLCKEKYED-AFALAQH------R-CPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVE 337 (500)
T ss_pred HHHHHHHHHHhhhh-HHHHhhc------c-CCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhh
Confidence 35899999999999 9999999 3 111112248999999999999999999998842 1
Q ss_pred -----------------CCcccccCcccccCHHHHHHHHhhhc
Q psy7453 174 -----------------KPYACGQCAFRSASVAGLHYHLKKTY 199 (200)
Q Consensus 174 -----------------k~~~C~~C~k~f~~~~~L~~H~~~h~ 199 (200)
--|.|..|+|.|.+...|+.|+-+|+
T Consensus 338 ~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 338 TRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred hhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhh
Confidence 13899999999999999999988774
No 19
>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=98.65 E-value=1.2e-08 Score=51.83 Aligned_cols=26 Identities=31% Similarity=0.405 Sum_probs=23.7
Q ss_pred HHHhchhhhhhhhhcCCCCCceecCccCcccCC
Q psy7453 127 ELIEHCRTCKSMIRTDPFRHKFVCYACDYFSYN 159 (200)
Q Consensus 127 ~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~~ 159 (200)
+|.+| + ++|++++||.|+.|++.|.+
T Consensus 1 ~l~~H------~-~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRH------M-RTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHH------H-HHHSSSSSEEESSSSEEESS
T ss_pred CHHHH------h-hhcCCCCCCCCCCCcCeeCc
Confidence 58899 9 99999999999999999974
No 20
>KOG3993|consensus
Probab=98.62 E-value=8.1e-09 Score=84.57 Aligned_cols=88 Identities=23% Similarity=0.338 Sum_probs=62.6
Q ss_pred CcccccccccccccccccccccccCcccCCCCCCCCcccccChhhhccCHHHHHhchhhhhhhh------------h---
Q psy7453 76 HSLCKHCHSQLSHLDLLDHCKTCSYMIRPNANNTFSPFCIYCKAVLSTNLNELIEHCRTCKSMI------------R--- 140 (200)
Q Consensus 76 ~~~C~~C~~~f~~~~~l~~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~------------~--- 140 (200)
-|.|..|...|.+.-.|.++ .|... --..|+|++|+|.|+- ..+|..|||-|+-.. +
T Consensus 267 dyiCqLCK~kYeD~F~LAQH-rC~RI------V~vEYrCPEC~KVFsC-PANLASHRRWHKPR~eaa~a~~~P~k~~~~~ 338 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQH-RCPRI------VHVEYRCPECDKVFSC-PANLASHRRWHKPRPEAAKAGSPPPKQAVET 338 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhc-cCCee------EEeeecCCcccccccC-chhhhhhhcccCCchhhhhcCCCChhhhhhh
Confidence 38899999988888777542 12211 2246899999999999 999999988882110 0
Q ss_pred -----------cCCCCCceecCccCcccCChHHHHHHHHHcC
Q psy7453 141 -----------TDPFRHKFVCYACDYFSYNIGCMRSHIRTHT 171 (200)
Q Consensus 141 -----------~h~~~k~~~C~~C~~~f~~~~~l~~H~~~H~ 171 (200)
....+.-|.|..|++.|.+...|+.|+.+|.
T Consensus 339 rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq 380 (500)
T KOG3993|consen 339 RAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQ 380 (500)
T ss_pred hhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhh
Confidence 0012235899999999999999999987763
No 21
>PHA00616 hypothetical protein
Probab=98.57 E-value=3e-08 Score=56.13 Aligned_cols=33 Identities=9% Similarity=0.163 Sum_probs=19.4
Q ss_pred ceecCccCcccCChHHHHHHHHHcCCCCCcccc
Q psy7453 147 KFVCYACDYFSYNIGCMRSHIRTHTGEKPYACG 179 (200)
Q Consensus 147 ~~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~ 179 (200)
||+|+.||+.|...+.|.+|++.|+|++++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 455666666666666666666666666555554
No 22
>PHA00732 hypothetical protein
Probab=98.50 E-value=8.3e-08 Score=62.12 Aligned_cols=48 Identities=21% Similarity=0.296 Sum_probs=33.9
Q ss_pred CcccccChhhhccCHHHHHhchhhhhhhhh-cCCCCCceecCccCcccCChHHHHHHHHHcCC
Q psy7453 111 SPFCIYCKAVLSTNLNELIEHCRTCKSMIR-TDPFRHKFVCYACDYFSYNIGCMRSHIRTHTG 172 (200)
Q Consensus 111 ~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~-~h~~~k~~~C~~C~~~f~~~~~l~~H~~~H~~ 172 (200)
||.|+.|++.|.+ ...|..| + + .|.+ +.|+.||+.|. .+..|++++.+
T Consensus 1 py~C~~Cgk~F~s-~s~Lk~H------~-r~~H~~---~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKCPICGFTTVT-LFALKQH------A-RRNHTL---TKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred CccCCCCCCccCC-HHHHHHH------h-hcccCC---CccCCCCCEeC---ChhhhhcccCC
Confidence 5778888888888 8888888 7 5 3543 46888888887 46677765543
No 23
>PHA00616 hypothetical protein
Probab=98.36 E-value=1.6e-07 Score=53.13 Aligned_cols=39 Identities=18% Similarity=0.286 Sum_probs=34.2
Q ss_pred CcccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCccc
Q psy7453 111 SPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFS 157 (200)
Q Consensus 111 ~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f 157 (200)
||+|+.||+.|.. ++.|..| + +.|++++++.|+.--..|
T Consensus 1 pYqC~~CG~~F~~-~s~l~~H------~-r~~hg~~~~~~~~~y~~f 39 (44)
T PHA00616 1 MYQCLRCGGIFRK-KKEVIEH------L-LSVHKQNKLTLEYFYIYF 39 (44)
T ss_pred CCccchhhHHHhh-HHHHHHH------H-HHhcCCCccceeEEEEEE
Confidence 6899999999999 9999999 9 999999999998643333
No 24
>PHA00732 hypothetical protein
Probab=98.31 E-value=4.1e-07 Score=58.89 Aligned_cols=46 Identities=24% Similarity=0.488 Sum_probs=39.0
Q ss_pred ceecCccCcccCChHHHHHHHHH-cCCCCCcccccCcccccCHHHHHHHHhhh
Q psy7453 147 KFVCYACDYFSYNIGCMRSHIRT-HTGEKPYACGQCAFRSASVAGLHYHLKKT 198 (200)
Q Consensus 147 ~~~C~~C~~~f~~~~~l~~H~~~-H~~~k~~~C~~C~k~f~~~~~L~~H~~~h 198 (200)
||.|+.||+.|...+.|+.|++. |. ++.|+.||+.|.+ |..|.+..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~~---l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYRR---LNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeCC---hhhhhccc
Confidence 68899999999999999999984 65 3689999999984 77787653
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=98.30 E-value=1.3e-06 Score=52.47 Aligned_cols=51 Identities=25% Similarity=0.497 Sum_probs=33.5
Q ss_pred ceecCccCcccCChHHHHHHHHH-cCCC-CCcccccCcccccCHHHHHHHHhhhcC
Q psy7453 147 KFVCYACDYFSYNIGCMRSHIRT-HTGE-KPYACGQCAFRSASVAGLHYHLKKTYH 200 (200)
Q Consensus 147 ~~~C~~C~~~f~~~~~l~~H~~~-H~~~-k~~~C~~C~k~f~~~~~L~~H~~~h~g 200 (200)
.|.|+.|++ -.+...|..|... |.++ +.+.|++|...+. .+|..|+..++|
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 367777777 4455677777654 5544 4577888877544 377778777654
No 26
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.20 E-value=1e-06 Score=43.26 Aligned_cols=23 Identities=26% Similarity=0.593 Sum_probs=14.7
Q ss_pred cccccCcccccCHHHHHHHHhhh
Q psy7453 176 YACGQCAFRSASVAGLHYHLKKT 198 (200)
Q Consensus 176 ~~C~~C~k~f~~~~~L~~H~~~h 198 (200)
|+|+.|++.|.++..|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 45666666666666666666653
No 27
>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=98.08 E-value=4.5e-06 Score=50.09 Aligned_cols=51 Identities=22% Similarity=0.340 Sum_probs=40.7
Q ss_pred CcccccChhhhccCHHHHHhchhhhhhhhhcCCCC-CceecCccCcccCChHHHHHHHHHcC
Q psy7453 111 SPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFR-HKFVCYACDYFSYNIGCMRSHIRTHT 171 (200)
Q Consensus 111 ~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~-k~~~C~~C~~~f~~~~~l~~H~~~H~ 171 (200)
.|.|++|++ ..+ ...|..| ....|..+ +.+.|++|...+. .+|..|+..+.
T Consensus 2 ~f~CP~C~~-~~~-~~~L~~H------~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFS-ESSLVEH------CEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccC-HHHHHHH------HHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 589999999 455 6889999 86777764 5799999998655 48999988754
No 28
>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=98.02 E-value=4.9e-06 Score=40.71 Aligned_cols=23 Identities=22% Similarity=0.504 Sum_probs=16.3
Q ss_pred eecCccCcccCChHHHHHHHHHc
Q psy7453 148 FVCYACDYFSYNIGCMRSHIRTH 170 (200)
Q Consensus 148 ~~C~~C~~~f~~~~~l~~H~~~H 170 (200)
|+|+.|++.|.+...|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 56777777777777777777654
No 29
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.94 E-value=7e-06 Score=40.31 Aligned_cols=24 Identities=21% Similarity=0.429 Sum_probs=14.3
Q ss_pred cccccCcccccCHHHHHHHHhhhc
Q psy7453 176 YACGQCAFRSASVAGLHYHLKKTY 199 (200)
Q Consensus 176 ~~C~~C~k~f~~~~~L~~H~~~h~ 199 (200)
|.|++|++.|.+...|..|+++|+
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 456666666666666666666653
No 30
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.92 E-value=6.8e-06 Score=41.90 Aligned_cols=25 Identities=24% Similarity=0.616 Sum_probs=17.0
Q ss_pred CcccccCcccccCHHHHHHHHhhhc
Q psy7453 175 PYACGQCAFRSASVAGLHYHLKKTY 199 (200)
Q Consensus 175 ~~~C~~C~k~f~~~~~L~~H~~~h~ 199 (200)
||.|+.|++.|.+...|..|++.|.
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 4667777777777777777776654
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.91 E-value=7.7e-06 Score=55.07 Aligned_cols=73 Identities=18% Similarity=0.457 Sum_probs=17.5
Q ss_pred ccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccCChHHHHHHHHHcCCCCCcccccCcccccCHHHHH
Q psy7453 113 FCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFRSASVAGLH 192 (200)
Q Consensus 113 ~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~f~~~~~L~ 192 (200)
+|..|+..|.+ ...|..| +...|.-.-+ ....+.....+..+.+.-. ...+.|..|++.|.+...|.
T Consensus 1 ~C~~C~~~f~~-~~~l~~H------~~~~H~~~~~-----~~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~ 67 (100)
T PF12756_consen 1 QCLFCDESFSS-VDDLLQH------MKKKHGFDIP-----DQKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQ 67 (100)
T ss_dssp -------------------------------------------------------------SSEEBSSSS-EESSHHHHH
T ss_pred Ccccccccccc-ccccccc------cccccccccc-----ccccccccccccccccccc-CCCCCCCccCCCCcCHHHHH
Confidence 48889999988 8889999 7444432221 1112223333333333211 22577777777777777777
Q ss_pred HHHhhh
Q psy7453 193 YHLKKT 198 (200)
Q Consensus 193 ~H~~~h 198 (200)
.|++.+
T Consensus 68 ~Hm~~~ 73 (100)
T PF12756_consen 68 EHMRSK 73 (100)
T ss_dssp HHHHHT
T ss_pred HHHcCc
Confidence 777753
No 32
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.84 E-value=2.3e-06 Score=68.08 Aligned_cols=71 Identities=24% Similarity=0.354 Sum_probs=45.4
Q ss_pred CCCCccccc--ChhhhccCHHHHHhchhhhhhhhhcCCCCCcee--cCccCcccCChHHHHHHHHHcCCCCCcccccCcc
Q psy7453 108 NTFSPFCIY--CKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFV--CYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAF 183 (200)
Q Consensus 108 ~~~~~~C~~--C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~--C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k 183 (200)
++|||+|++ |.|.+.. ...|+-| +..-|...+... -++=-..| -..+|||.|++|+|
T Consensus 346 d~KpykCpV~gC~K~Ykn-qnGLKYH------~lhGH~~~~~~~~p~p~~~~~F------------~~~~KPYrCevC~K 406 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKN-QNGLKYH------MLHGHQNQKLHENPSPEKMNIF------------SAKDKPYRCEVCDK 406 (423)
T ss_pred cCceecCCCCCchhhhcc-ccchhhh------hhccccCcccCCCCCccccccc------------cccCCceeccccch
Confidence 458888876 8888888 8888888 422222211111 11111122 23469999999999
Q ss_pred cccCHHHHHHHHhh
Q psy7453 184 RSASVAGLHYHLKK 197 (200)
Q Consensus 184 ~f~~~~~L~~H~~~ 197 (200)
.|+...+|+.|+.-
T Consensus 407 RYKNlNGLKYHr~H 420 (423)
T COG5189 407 RYKNLNGLKYHRKH 420 (423)
T ss_pred hhccCccceecccc
Confidence 99999999999753
No 33
>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=97.61 E-value=7.1e-05 Score=36.56 Aligned_cols=23 Identities=35% Similarity=0.592 Sum_probs=15.8
Q ss_pred eecCccCcccCChHHHHHHHHHc
Q psy7453 148 FVCYACDYFSYNIGCMRSHIRTH 170 (200)
Q Consensus 148 ~~C~~C~~~f~~~~~l~~H~~~H 170 (200)
|.|++|++.|.+...|..|+++|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 56777777777777777777765
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=97.57 E-value=4.7e-05 Score=38.67 Aligned_cols=25 Identities=28% Similarity=0.583 Sum_probs=16.3
Q ss_pred ceecCccCcccCChHHHHHHHHHcC
Q psy7453 147 KFVCYACDYFSYNIGCMRSHIRTHT 171 (200)
Q Consensus 147 ~~~C~~C~~~f~~~~~l~~H~~~H~ 171 (200)
||.|..|++.|.+...|..|++.|.
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 4666666666766666666666553
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.46 E-value=0.00011 Score=36.44 Aligned_cols=23 Identities=26% Similarity=0.546 Sum_probs=15.0
Q ss_pred cccccCcccccCHHHHHHHHhhh
Q psy7453 176 YACGQCAFRSASVAGLHYHLKKT 198 (200)
Q Consensus 176 ~~C~~C~k~f~~~~~L~~H~~~h 198 (200)
|.|+.|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 45666666666666666666654
No 36
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.43 E-value=5.5e-05 Score=60.45 Aligned_cols=58 Identities=17% Similarity=0.222 Sum_probs=40.6
Q ss_pred CCCCccccc--ccccccccccccccccccC---cccCC---------CCCCCCcccccChhhhccCHHHHHhc
Q psy7453 73 TQNHSLCKH--CHSQLSHLDLLDHCKTCSY---MIRPN---------ANNTFSPFCIYCKAVLSTNLNELIEH 131 (200)
Q Consensus 73 ~~~~~~C~~--C~~~f~~~~~l~~C~~C~~---~f~~~---------~~~~~~~~C~~C~~~f~~~~~~l~~H 131 (200)
+++||+|++ |.|.+.+...|.-+..-|. ..... ....|||+|++|+|++.. ...|+-|
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKN-lNGLKYH 417 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKN-LNGLKYH 417 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhcc-Cccceec
Confidence 469999987 9999999887752222221 11110 115689999999999998 8888888
No 37
>PRK04860 hypothetical protein; Provisional
Probab=97.34 E-value=0.00014 Score=53.51 Aligned_cols=37 Identities=27% Similarity=0.524 Sum_probs=25.0
Q ss_pred ceecCccCcccCChHHHHHHHHHcCCCCCcccccCcccccC
Q psy7453 147 KFVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFRSAS 187 (200)
Q Consensus 147 ~~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~f~~ 187 (200)
+|.|. |+. ....+++|.++|+|+++|.|..|++.|..
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 57776 765 55566677777777777777777766654
No 38
>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=97.14 E-value=0.00065 Score=39.45 Aligned_cols=33 Identities=18% Similarity=0.287 Sum_probs=18.8
Q ss_pred CCCCceecCccCcccCChHHHHHHHHHcCCCCC
Q psy7453 143 PFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKP 175 (200)
Q Consensus 143 ~~~k~~~C~~C~~~f~~~~~l~~H~~~H~~~k~ 175 (200)
..+.|-.|++|+..+....+|++|+.++.+.||
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 456677777777777777777777766655554
No 39
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.12 E-value=0.00036 Score=34.33 Aligned_cols=24 Identities=29% Similarity=0.743 Sum_probs=15.1
Q ss_pred cccccCcccccCHHHHHHHHhhhcC
Q psy7453 176 YACGQCAFRSASVAGLHYHLKKTYH 200 (200)
Q Consensus 176 ~~C~~C~k~f~~~~~L~~H~~~h~g 200 (200)
|+|+.|+.... ...|..|++.|+|
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 56777777766 6677777777654
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.05 E-value=0.00063 Score=33.54 Aligned_cols=24 Identities=25% Similarity=0.552 Sum_probs=14.7
Q ss_pred eecCccCcccCChHHHHHHHHHcC
Q psy7453 148 FVCYACDYFSYNIGCMRSHIRTHT 171 (200)
Q Consensus 148 ~~C~~C~~~f~~~~~l~~H~~~H~ 171 (200)
|.|+.|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 356666666666666666666553
No 41
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.02 E-value=0.00064 Score=39.49 Aligned_cols=30 Identities=23% Similarity=0.370 Sum_probs=22.0
Q ss_pred CCCCCcccccCcccccCHHHHHHHHhhhcC
Q psy7453 171 TGEKPYACGQCAFRSASVAGLHYHLKKTYH 200 (200)
Q Consensus 171 ~~~k~~~C~~C~k~f~~~~~L~~H~~~h~g 200 (200)
..+.|-.|++|+..+.+..+|++|+.+++|
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhc
Confidence 456889999999999999999999988764
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.75 E-value=0.001 Score=32.93 Aligned_cols=22 Identities=27% Similarity=0.526 Sum_probs=14.6
Q ss_pred cccccCcccccCHHHHHHHHhh
Q psy7453 176 YACGQCAFRSASVAGLHYHLKK 197 (200)
Q Consensus 176 ~~C~~C~k~f~~~~~L~~H~~~ 197 (200)
|.|++|++.|.+...|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 4566677777777777766654
No 43
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.58 E-value=0.0016 Score=32.24 Aligned_cols=23 Identities=26% Similarity=0.579 Sum_probs=16.8
Q ss_pred eecCccCcccCChHHHHHHHHHc
Q psy7453 148 FVCYACDYFSYNIGCMRSHIRTH 170 (200)
Q Consensus 148 ~~C~~C~~~f~~~~~l~~H~~~H 170 (200)
|.|++|++.|.+...|+.|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 56777777777777777777643
No 44
>PRK04860 hypothetical protein; Provisional
Probab=96.49 E-value=0.0011 Score=48.71 Aligned_cols=39 Identities=18% Similarity=0.226 Sum_probs=34.1
Q ss_pred CCcccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccCCh
Q psy7453 110 FSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSYNI 160 (200)
Q Consensus 110 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~~~ 160 (200)
-+|.|. |+. . ...+.+| . ++|+++++|.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~-~~~~rrH------~-ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---H-QLTVRRH------N-RVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---e-eCHHHHH------H-HHhcCCccEECCCCCceeEEe
Confidence 579998 998 5 6779999 8 999999999999999988654
No 45
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.26 E-value=0.0043 Score=41.40 Aligned_cols=73 Identities=19% Similarity=0.292 Sum_probs=21.0
Q ss_pred ccccccccccccccccccccccCcccCCCCCCCCcccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCccc
Q psy7453 78 LCKHCHSQLSHLDLLDHCKTCSYMIRPNANNTFSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFS 157 (200)
Q Consensus 78 ~C~~C~~~f~~~~~l~~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f 157 (200)
.|..|+..|.+...|..+-. ..+. +..+ ....+.. ...+..+ . +... ...+.|..|++.|
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~------~~H~----~~~~-~~~~l~~-~~~~~~~------~-~~~~-~~~~~C~~C~~~f 60 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMK------KKHG----FDIP-DQKYLVD-PNRLLNY------L-RKKV-KESFRCPYCNKTF 60 (100)
T ss_dssp --------------------------------------------------------------------SSEEBSSSS-EE
T ss_pred Cccccccccccccccccccc------cccc----cccc-ccccccc-ccccccc------c-cccc-CCCCCCCccCCCC
Confidence 48888888888877765321 1111 1111 1112223 4444444 3 3222 2368999999999
Q ss_pred CChHHHHHHHHHc
Q psy7453 158 YNIGCMRSHIRTH 170 (200)
Q Consensus 158 ~~~~~l~~H~~~H 170 (200)
.+...|..|++.+
T Consensus 61 ~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 61 RSREALQEHMRSK 73 (100)
T ss_dssp SSHHHHHHHHHHT
T ss_pred cCHHHHHHHHcCc
Confidence 9999999999874
No 46
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.08 E-value=0.0061 Score=29.78 Aligned_cols=23 Identities=22% Similarity=0.673 Sum_probs=16.8
Q ss_pred eecCccCcccCChHHHHHHHHHcC
Q psy7453 148 FVCYACDYFSYNIGCMRSHIRTHT 171 (200)
Q Consensus 148 ~~C~~C~~~f~~~~~l~~H~~~H~ 171 (200)
|+|+.|+.... ...|.+|++.|.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 67888888887 888888888753
No 47
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.03 E-value=0.0028 Score=32.07 Aligned_cols=22 Identities=27% Similarity=0.496 Sum_probs=15.6
Q ss_pred cccccCcccccCHHHHHHHHhh
Q psy7453 176 YACGQCAFRSASVAGLHYHLKK 197 (200)
Q Consensus 176 ~~C~~C~k~f~~~~~L~~H~~~ 197 (200)
|-|+.|++.|.+...|..|++.
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 5677777777777777777654
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=95.12 E-value=0.015 Score=29.28 Aligned_cols=19 Identities=32% Similarity=0.620 Sum_probs=14.1
Q ss_pred cccccChhhhccCHHHHHhc
Q psy7453 112 PFCIYCKAVLSTNLNELIEH 131 (200)
Q Consensus 112 ~~C~~C~~~f~~~~~~l~~H 131 (200)
|.|..|++.|.+ ...+..|
T Consensus 2 ~~C~~C~k~f~~-~~~~~~H 20 (27)
T PF12171_consen 2 FYCDACDKYFSS-ENQLKQH 20 (27)
T ss_dssp CBBTTTTBBBSS-HHHHHCC
T ss_pred CCcccCCCCcCC-HHHHHHH
Confidence 567777777777 7777777
No 49
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.05 E-value=0.021 Score=28.30 Aligned_cols=19 Identities=26% Similarity=0.413 Sum_probs=10.4
Q ss_pred ccccCcccccCHHHHHHHHh
Q psy7453 177 ACGQCAFRSASVAGLHYHLK 196 (200)
Q Consensus 177 ~C~~C~k~f~~~~~L~~H~~ 196 (200)
+|+.||+.| ....|.+|++
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 456666666 4445555554
No 50
>KOG2231|consensus
Probab=94.57 E-value=0.032 Score=49.64 Aligned_cols=22 Identities=23% Similarity=0.597 Sum_probs=13.3
Q ss_pred cccccccccccccccccccccc
Q psy7453 77 SLCKHCHSQLSHLDLLDHCKTC 98 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~l~~C~~C 98 (200)
+.|..|+..|.....-..|..|
T Consensus 100 ~~C~~C~~~~~~~~~~~~~~~c 121 (669)
T KOG2231|consen 100 HSCHICDRRFRALYNKKECLHC 121 (669)
T ss_pred hhcCccccchhhhcccCCCccc
Confidence 5677887777544444445555
No 51
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.24 E-value=0.012 Score=49.43 Aligned_cols=63 Identities=21% Similarity=0.292 Sum_probs=55.3
Q ss_pred CCcccccChhhhccCHHHHHhchhhhhhhhh--cCCCC--CceecC--ccCcccCChHHHHHHHHHcCCCCCccccc
Q psy7453 110 FSPFCIYCKAVLSTNLNELIEHCRTCKSMIR--TDPFR--HKFVCY--ACDYFSYNIGCMRSHIRTHTGEKPYACGQ 180 (200)
Q Consensus 110 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~--~h~~~--k~~~C~--~C~~~f~~~~~l~~H~~~H~~~k~~~C~~ 180 (200)
.++.|..|...|.. ...|..| . + .|.++ +++.|+ .|++.|.....+..|..+|.+.+++.+..
T Consensus 288 ~~~~~~~~~~~~s~-~~~l~~~------~-~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 356 (467)
T COG5048 288 LPIKSKQCNISFSR-SSPLTRH------L-RSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKL 356 (467)
T ss_pred cCCCCccccCCccc-ccccccc------c-cccccccccCCceeeeccCCCccccccccccCCcccccCCCcccccc
Confidence 47889999999999 9999999 8 7 79999 999999 79999999999999999998888777644
No 52
>KOG1146|consensus
Probab=94.11 E-value=0.029 Score=53.09 Aligned_cols=25 Identities=32% Similarity=0.820 Sum_probs=22.2
Q ss_pred CCCcccccCcccccCHHHHHHHHhh
Q psy7453 173 EKPYACGQCAFRSASVAGLHYHLKK 197 (200)
Q Consensus 173 ~k~~~C~~C~k~f~~~~~L~~H~~~ 197 (200)
.++|.|..|..++..+.+|..|++.
T Consensus 516 ~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 516 GKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred CCcccceeeeeeeecchHHHHHHHH
Confidence 3689999999999999999999874
No 53
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.02 E-value=0.056 Score=26.76 Aligned_cols=19 Identities=21% Similarity=0.315 Sum_probs=10.6
Q ss_pred ecCccCcccCChHHHHHHHH
Q psy7453 149 VCYACDYFSYNIGCMRSHIR 168 (200)
Q Consensus 149 ~C~~C~~~f~~~~~l~~H~~ 168 (200)
.|+.||+.| ....|..|+.
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 466666666 4455555543
No 54
>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=93.76 E-value=0.052 Score=28.89 Aligned_cols=22 Identities=23% Similarity=0.462 Sum_probs=15.1
Q ss_pred CcccccCcccccCHHHHHHHHh
Q psy7453 175 PYACGQCAFRSASVAGLHYHLK 196 (200)
Q Consensus 175 ~~~C~~C~k~f~~~~~L~~H~~ 196 (200)
+|-|++|++.|.....+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4667777777777777777764
No 55
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.67 E-value=0.011 Score=49.50 Aligned_cols=55 Identities=22% Similarity=0.382 Sum_probs=51.3
Q ss_pred CceecCccCcccCChHHHHHHHH--HcCCC--CCcccc--cCcccccCHHHHHHHHhhhcC
Q psy7453 146 HKFVCYACDYFSYNIGCMRSHIR--THTGE--KPYACG--QCAFRSASVAGLHYHLKKTYH 200 (200)
Q Consensus 146 k~~~C~~C~~~f~~~~~l~~H~~--~H~~~--k~~~C~--~C~k~f~~~~~L~~H~~~h~g 200 (200)
.++.|..|...|.....+..|.+ .|+++ +++.|+ .|++.|.+...+..|..+|++
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~ 348 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTS 348 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccC
Confidence 46899999999999999999999 89999 999999 799999999999999988764
No 56
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.52 E-value=0.078 Score=36.46 Aligned_cols=79 Identities=13% Similarity=0.139 Sum_probs=46.5
Q ss_pred CCCcccccChhhhccCHHHHHhchhhhhhhhhcCC-CCC------------ceecCccCcccCChHHHHHHHHHcCCCCC
Q psy7453 109 TFSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDP-FRH------------KFVCYACDYFSYNIGCMRSHIRTHTGEKP 175 (200)
Q Consensus 109 ~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~-~~k------------~~~C~~C~~~f~~~~~l~~H~~~H~~~k~ 175 (200)
+-|..|+.||-+... ...|.+- . -|. .-+ .-.|-.|+..|........- .-.....
T Consensus 13 ~LP~~CpiCgLtLVs-s~HLARS------y--HHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~--~~~~~~~ 81 (112)
T TIGR00622 13 ELPVECPICGLTLIL-STHLARS------Y--HHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFD--ELKDSHR 81 (112)
T ss_pred CCCCcCCcCCCEEec-cchHHHh------h--hccCCCcccccccccccCCCCcccCcCCCCCCccccccc--ccccccc
Confidence 346778888887777 7777653 1 111 011 12388888888754311100 0122346
Q ss_pred cccccCcccccCHHHHHHHHhhh
Q psy7453 176 YACGQCAFRSASVAGLHYHLKKT 198 (200)
Q Consensus 176 ~~C~~C~k~f~~~~~L~~H~~~h 198 (200)
|+|+.|...|--....-.|...|
T Consensus 82 y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 82 YVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred eeCCCCCCccccccchhhhhhcc
Confidence 88888888888777777776655
No 57
>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=93.10 E-value=0.08 Score=28.13 Aligned_cols=23 Identities=17% Similarity=0.397 Sum_probs=17.6
Q ss_pred ceecCccCcccCChHHHHHHHHH
Q psy7453 147 KFVCYACDYFSYNIGCMRSHIRT 169 (200)
Q Consensus 147 ~~~C~~C~~~f~~~~~l~~H~~~ 169 (200)
+|.|+.|++.|.+...+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 47788888888888888887653
No 58
>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=92.60 E-value=0.078 Score=28.11 Aligned_cols=24 Identities=29% Similarity=0.820 Sum_probs=16.4
Q ss_pred eecCccCcccCChHHHHHHHHHcCCCCCcccccCcc
Q psy7453 148 FVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAF 183 (200)
Q Consensus 148 ~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k 183 (200)
|.|..||..+.... .++.|++||.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 67888887665332 5778888874
No 59
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=90.70 E-value=0.12 Score=30.66 Aligned_cols=29 Identities=10% Similarity=0.075 Sum_probs=21.0
Q ss_pred cCCCCCceecCccCcccCChHHHHHHHHH
Q psy7453 141 TDPFRHKFVCYACDYFSYNIGCMRSHIRT 169 (200)
Q Consensus 141 ~h~~~k~~~C~~C~~~f~~~~~l~~H~~~ 169 (200)
.-.||--+.|+-||..|....++.+|...
T Consensus 11 ~RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 11 DRDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred ccCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 34566677888888888877777777654
No 60
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=90.11 E-value=0.13 Score=30.48 Aligned_cols=28 Identities=18% Similarity=0.387 Sum_probs=24.1
Q ss_pred cccccccccccccccccccccccCcccC
Q psy7453 77 SLCKHCHSQLSHLDLLDHCKTCSYMIRP 104 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~l~~C~~C~~~f~~ 104 (200)
..|+.|++.|....++..|+.|+..+.+
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR 33 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHR 33 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccH
Confidence 4699999999988999999999987764
No 61
>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=89.99 E-value=0.18 Score=34.60 Aligned_cols=28 Identities=18% Similarity=0.377 Sum_probs=16.4
Q ss_pred ccccccCcccCCCCCCCCcccccChhhhcc
Q psy7453 94 HCKTCSYMIRPNANNTFSPFCIYCKAVLST 123 (200)
Q Consensus 94 ~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~ 123 (200)
.|+.||..|... +..|..|+.||..|.-
T Consensus 11 ~Cp~CG~kFYDL--nk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 11 TCPSCGAKFYDL--NKDPIVCPKCGTEFPP 38 (108)
T ss_pred cCCCCcchhccC--CCCCccCCCCCCccCc
Confidence 455555555432 2356667777777766
No 62
>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=89.30 E-value=0.2 Score=26.73 Aligned_cols=9 Identities=33% Similarity=0.652 Sum_probs=4.8
Q ss_pred CcccccChh
Q psy7453 111 SPFCIYCKA 119 (200)
Q Consensus 111 ~~~C~~C~~ 119 (200)
|..|++|+.
T Consensus 18 p~~CP~Cg~ 26 (34)
T cd00729 18 PEKCPICGA 26 (34)
T ss_pred CCcCcCCCC
Confidence 445555554
No 63
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=89.17 E-value=0.31 Score=26.52 Aligned_cols=32 Identities=16% Similarity=0.298 Sum_probs=16.9
Q ss_pred ecCccCcccCChHHHHHHHHHcCCCCCcccccCcccc
Q psy7453 149 VCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFRS 185 (200)
Q Consensus 149 ~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~f 185 (200)
.|+.|+..|.-..+ ++-.+....+|+.|+..|
T Consensus 4 ~CP~C~~~f~v~~~-----~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDD-----KLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHH-----HcccCCcEEECCCCCcEe
Confidence 46666666654443 122333456666666555
No 64
>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=89.00 E-value=0.25 Score=24.67 Aligned_cols=22 Identities=23% Similarity=0.791 Sum_probs=10.4
Q ss_pred cccccccccccccccccccccCcc
Q psy7453 79 CKHCHSQLSHLDLLDHCKTCSYMI 102 (200)
Q Consensus 79 C~~C~~~f~~~~~l~~C~~C~~~f 102 (200)
|+.|+...... ...|+.||..|
T Consensus 3 CP~C~~~V~~~--~~~Cp~CG~~F 24 (26)
T PF10571_consen 3 CPECGAEVPES--AKFCPHCGYDF 24 (26)
T ss_pred CCCCcCCchhh--cCcCCCCCCCC
Confidence 55555544222 23455555554
No 65
>KOG1146|consensus
Probab=88.73 E-value=0.083 Score=50.15 Aligned_cols=73 Identities=15% Similarity=0.280 Sum_probs=38.5
Q ss_pred cccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccCChHHHHHHHHH-----------------cCCCC
Q psy7453 112 PFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRT-----------------HTGEK 174 (200)
Q Consensus 112 ~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~-----------------H~~~k 174 (200)
+.|..|++.|.. .-.+. | + ....+|.|..|...|...+.|..|.+. +....
T Consensus 1261 ~~c~~~~~~~~~-~~~~~-~------l----~~~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~ 1328 (1406)
T KOG1146|consen 1261 GECGAVDELLTP-SFGIS-T------L----DVTHRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCT 1328 (1406)
T ss_pred chhhhccccccC-cccee-e------c----ccchhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccc
Confidence 445555555555 43333 3 3 123345555555555555555555431 11123
Q ss_pred CcccccCcccccCHHHHHHHHhh
Q psy7453 175 PYACGQCAFRSASVAGLHYHLKK 197 (200)
Q Consensus 175 ~~~C~~C~k~f~~~~~L~~H~~~ 197 (200)
.| |..|...|.....|..|+++
T Consensus 1329 ~~-c~~c~~~~~~~~alqihm~~ 1350 (1406)
T KOG1146|consen 1329 YH-CLACEVLLSGREALQIHMRS 1350 (1406)
T ss_pred cc-chHHHhhcchhHHHHHHHHH
Confidence 35 77777777777777777665
No 66
>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=88.61 E-value=0.34 Score=26.32 Aligned_cols=33 Identities=15% Similarity=0.302 Sum_probs=16.1
Q ss_pred eecCccCcccCChHHHHHHHHHcCCCCCcccccCcccc
Q psy7453 148 FVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFRS 185 (200)
Q Consensus 148 ~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~f 185 (200)
+.|+.|+..|.-..... ..+.....|+.|+..|
T Consensus 3 ~~CP~C~~~~~v~~~~~-----~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL-----GANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHc-----CCCCCEEECCCCCCEE
Confidence 45666666665444321 1112235566666555
No 67
>KOG2231|consensus
Probab=88.48 E-value=0.78 Score=41.18 Aligned_cols=34 Identities=24% Similarity=0.583 Sum_probs=23.4
Q ss_pred cccccccCcccCCCCCCCCcccccChhhhccCHHHHHhc
Q psy7453 93 DHCKTCSYMIRPNANNTFSPFCIYCKAVLSTNLNELIEH 131 (200)
Q Consensus 93 ~~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~~~~~l~~H 131 (200)
..|.+|+..|.....+ -.|..| -.|.+ ...|++|
T Consensus 100 ~~C~~C~~~~~~~~~~---~~~~~c-~~~~s-~~~Lk~H 133 (669)
T KOG2231|consen 100 HSCHICDRRFRALYNK---KECLHC-TEFKS-VENLKNH 133 (669)
T ss_pred hhcCccccchhhhccc---CCCccc-cchhH-HHHHHHH
Confidence 3799999888644322 236677 67777 7778888
No 68
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=88.42 E-value=0.47 Score=28.59 Aligned_cols=8 Identities=25% Similarity=1.003 Sum_probs=4.3
Q ss_pred ceecCccC
Q psy7453 147 KFVCYACD 154 (200)
Q Consensus 147 ~~~C~~C~ 154 (200)
+|.|+.||
T Consensus 48 ~Y~CP~CG 55 (59)
T PRK14890 48 PYTCPKCG 55 (59)
T ss_pred ceECCCCC
Confidence 45555554
No 69
>PHA00626 hypothetical protein
Probab=88.25 E-value=0.21 Score=29.64 Aligned_cols=13 Identities=23% Similarity=0.243 Sum_probs=7.3
Q ss_pred CcccccChhhhcc
Q psy7453 111 SPFCIYCKAVLST 123 (200)
Q Consensus 111 ~~~C~~C~~~f~~ 123 (200)
.|.|+.||..|+.
T Consensus 23 rYkCkdCGY~ft~ 35 (59)
T PHA00626 23 DYVCCDCGYNDSK 35 (59)
T ss_pred ceEcCCCCCeech
Confidence 4556666655543
No 70
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.59 E-value=0.27 Score=28.12 Aligned_cols=26 Identities=19% Similarity=0.498 Sum_probs=12.9
Q ss_pred Cccccccccccccccc--ccccccccCc
Q psy7453 76 HSLCKHCHSQLSHLDL--LDHCKTCSYM 101 (200)
Q Consensus 76 ~~~C~~C~~~f~~~~~--l~~C~~C~~~ 101 (200)
.|.|+.||..|..... ..+|+.||..
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCe
Confidence 3566666665543322 2345555443
No 71
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=87.44 E-value=0.27 Score=34.69 Aligned_cols=26 Identities=19% Similarity=0.498 Sum_probs=21.5
Q ss_pred Ccccccccccccccc--cccccccccCc
Q psy7453 76 HSLCKHCHSQLSHLD--LLDHCKTCSYM 101 (200)
Q Consensus 76 ~~~C~~C~~~f~~~~--~l~~C~~C~~~ 101 (200)
|+.|..||+.|.+-+ .|.-|+.||-.
T Consensus 1 PH~Ct~Cg~~f~dgs~eil~GCP~CGg~ 28 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKEILSGCPECGGN 28 (131)
T ss_pred CcccCcCCCCcCCCcHHHHccCcccCCc
Confidence 678999999999865 56789999843
No 72
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=87.02 E-value=0.53 Score=42.95 Aligned_cols=48 Identities=27% Similarity=0.738 Sum_probs=29.4
Q ss_pred ccccccCcccCCCCCCCCcccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccCChHHHHHHHHHcCCC
Q psy7453 94 HCKTCSYMIRPNANNTFSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGE 173 (200)
Q Consensus 94 ~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~H~~~ 173 (200)
.|..||..+ +|+.|+..+.. | + ..+...|..||. ...
T Consensus 437 ~C~~Cg~v~----------~Cp~Cd~~lt~-------H------~-----~~~~L~CH~Cg~---------------~~~ 473 (730)
T COG1198 437 LCRDCGYIA----------ECPNCDSPLTL-------H------K-----ATGQLRCHYCGY---------------QEP 473 (730)
T ss_pred ecccCCCcc----------cCCCCCcceEE-------e------c-----CCCeeEeCCCCC---------------CCC
Confidence 576666554 47777655433 4 3 234567888863 334
Q ss_pred CCcccccCccc
Q psy7453 174 KPYACGQCAFR 184 (200)
Q Consensus 174 k~~~C~~C~k~ 184 (200)
.|..|+.||-.
T Consensus 474 ~p~~Cp~Cgs~ 484 (730)
T COG1198 474 IPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCC
Confidence 67788888754
No 73
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=86.76 E-value=0.6 Score=25.23 Aligned_cols=32 Identities=13% Similarity=0.178 Sum_probs=15.7
Q ss_pred ecCccCcccCChHHHHHHHHHcCCCCCcccccCcccc
Q psy7453 149 VCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFRS 185 (200)
Q Consensus 149 ~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~f 185 (200)
.|+.|+..|.-.... +-.+....+|+.|+..|
T Consensus 4 ~Cp~C~~~y~i~d~~-----ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEK-----IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHH-----CCCCCcEEECCCCCCEe
Confidence 456666655544432 12223345566666554
No 74
>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=86.65 E-value=0.32 Score=32.97 Aligned_cols=35 Identities=17% Similarity=0.391 Sum_probs=19.5
Q ss_pred eecCccCcccCChHHHHHHHHHcCCCC----CcccccCccccc
Q psy7453 148 FVCYACDYFSYNIGCMRSHIRTHTGEK----PYACGQCAFRSA 186 (200)
Q Consensus 148 ~~C~~C~~~f~~~~~l~~H~~~H~~~k----~~~C~~C~k~f~ 186 (200)
..|+.||..-.....++ +-..+. -|.|..|+..+.
T Consensus 63 ~~Cp~Cg~~~a~f~~~Q----~RsadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 63 VECPKCGHKEAYYWLLQ----TRRADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred CCCCCCCCCeeEEEEec----cCCCCCCcEEEEEeCCCCCeeE
Confidence 67888876544333322 122222 288888887654
No 75
>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=85.92 E-value=0.5 Score=32.42 Aligned_cols=30 Identities=20% Similarity=0.546 Sum_probs=21.6
Q ss_pred eecCccCcccCChHHHHHHHHHcCCCCCcccccCcccccCH
Q psy7453 148 FVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFRSASV 188 (200)
Q Consensus 148 ~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~f~~~ 188 (200)
..|+.||..|... +..|-.|+.||..|.-.
T Consensus 10 R~Cp~CG~kFYDL-----------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYDL-----------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhccC-----------CCCCccCCCCCCccCcc
Confidence 4688888888743 33677788888887654
No 76
>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=85.59 E-value=0.37 Score=28.20 Aligned_cols=13 Identities=23% Similarity=0.572 Sum_probs=9.0
Q ss_pred ccccccccccccc
Q psy7453 77 SLCKHCHSQLSHL 89 (200)
Q Consensus 77 ~~C~~C~~~f~~~ 89 (200)
|.|..||..|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (52)
T TIGR02605 6 YRCTACGHRFEVL 18 (52)
T ss_pred EEeCCCCCEeEEE
Confidence 6677777777654
No 77
>KOG2482|consensus
Probab=85.42 E-value=0.76 Score=37.71 Aligned_cols=50 Identities=26% Similarity=0.466 Sum_probs=37.4
Q ss_pred eecCccCcccCChHHHHHHHHH-cCC--------------------------CCCcccccCcccccCHHHHHHHHhh
Q psy7453 148 FVCYACDYFSYNIGCMRSHIRT-HTG--------------------------EKPYACGQCAFRSASVAGLHYHLKK 197 (200)
Q Consensus 148 ~~C~~C~~~f~~~~~l~~H~~~-H~~--------------------------~k~~~C~~C~k~f~~~~~L~~H~~~ 197 (200)
.+|-.|.....+...|..||.+ |.= .+.-.|-.|.-.|.....|..||-.
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e 356 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVE 356 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhccc
Confidence 4788888888888888889874 521 1234578888889999999988864
No 78
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=85.33 E-value=0.93 Score=27.33 Aligned_cols=8 Identities=25% Similarity=0.920 Sum_probs=4.4
Q ss_pred ceecCccC
Q psy7453 147 KFVCYACD 154 (200)
Q Consensus 147 ~~~C~~C~ 154 (200)
+|.|+.||
T Consensus 50 ~Y~Cp~CG 57 (61)
T COG2888 50 PYRCPKCG 57 (61)
T ss_pred ceECCCcC
Confidence 45555554
No 79
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=85.17 E-value=0.24 Score=38.30 Aligned_cols=13 Identities=31% Similarity=0.925 Sum_probs=9.7
Q ss_pred eecCccCcccCCh
Q psy7453 148 FVCYACDYFSYNI 160 (200)
Q Consensus 148 ~~C~~C~~~f~~~ 160 (200)
..|+.||.++...
T Consensus 49 ~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 49 WVCPHCGYAAFEE 61 (214)
T ss_pred EECCCCCCccccc
Confidence 5899998877543
No 80
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=84.43 E-value=0.51 Score=28.03 Aligned_cols=24 Identities=21% Similarity=0.332 Sum_probs=21.7
Q ss_pred CCCCCcccccChhhhccCHHHHHhc
Q psy7453 107 NNTFSPFCIYCKAVLSTNLNELIEH 131 (200)
Q Consensus 107 ~~~~~~~C~~C~~~f~~~~~~l~~H 131 (200)
.||--+.|+-||+.|.. ...+.+|
T Consensus 13 DGE~~lrCPRC~~~FR~-~K~Y~RH 36 (65)
T COG4049 13 DGEEFLRCPRCGMVFRR-RKDYIRH 36 (65)
T ss_pred CCceeeeCCchhHHHHH-hHHHHHH
Confidence 47788999999999999 9999999
No 81
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=84.26 E-value=0.55 Score=36.32 Aligned_cols=19 Identities=11% Similarity=0.349 Sum_probs=14.8
Q ss_pred CCCcccccccccccccccc
Q psy7453 74 QNHSLCKHCHSQLSHLDLL 92 (200)
Q Consensus 74 ~~~~~C~~C~~~f~~~~~l 92 (200)
++...|++|++.|......
T Consensus 3 ~k~~~CPvC~~~F~~~~vr 21 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVR 21 (214)
T ss_pred CCceECCCCCCeeeeeEEE
Confidence 3567899999999987544
No 82
>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=83.62 E-value=0.44 Score=26.68 Aligned_cols=12 Identities=17% Similarity=0.271 Sum_probs=5.2
Q ss_pred cccccChhhhcc
Q psy7453 112 PFCIYCKAVLST 123 (200)
Q Consensus 112 ~~C~~C~~~f~~ 123 (200)
|.|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (42)
T PF09723_consen 6 YRCEECGHEFEV 17 (42)
T ss_pred EEeCCCCCEEEE
Confidence 344444444433
No 83
>KOG2893|consensus
Probab=82.90 E-value=0.3 Score=38.05 Aligned_cols=41 Identities=24% Similarity=0.537 Sum_probs=23.1
Q ss_pred cccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccCChHHHHHH
Q psy7453 114 CIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSYNIGCMRSH 166 (200)
Q Consensus 114 C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~~~~~l~~H 166 (200)
|=+|++.|.. ..-|.+| + + .|.|+|.+|-+...+.-.|..|
T Consensus 13 cwycnrefdd-ekiliqh------q-k----akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDD-EKILIQH------Q-K----AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccch-hhhhhhh------h-h----hccceeeeehhhhccCCCceee
Confidence 5566666666 6666666 4 1 2346666666655544444444
No 84
>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=82.57 E-value=1.1 Score=25.18 Aligned_cols=22 Identities=27% Similarity=0.374 Sum_probs=9.2
Q ss_pred CCcccccCcccccCH----HHHHHHH
Q psy7453 174 KPYACGQCAFRSASV----AGLHYHL 195 (200)
Q Consensus 174 k~~~C~~C~k~f~~~----~~L~~H~ 195 (200)
....|..|++.+... +.|.+|+
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHH
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 334455555555442 4555555
No 85
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=82.33 E-value=0.75 Score=34.03 Aligned_cols=23 Identities=43% Similarity=1.038 Sum_probs=19.4
Q ss_pred ceecCccCcccCChHHHHHHHHHcCCCCCcccccCc
Q psy7453 147 KFVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCA 182 (200)
Q Consensus 147 ~~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~ 182 (200)
-|.|++||.. |.|+-|-+||+||
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCCC
Confidence 5999999854 4578899999998
No 86
>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=82.16 E-value=0.65 Score=25.50 Aligned_cols=12 Identities=17% Similarity=0.531 Sum_probs=7.7
Q ss_pred cccccccccccc
Q psy7453 77 SLCKHCHSQLSH 88 (200)
Q Consensus 77 ~~C~~C~~~f~~ 88 (200)
|.|..||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (41)
T smart00834 6 YRCEDCGHTFEV 17 (41)
T ss_pred EEcCCCCCEEEE
Confidence 567777766653
No 87
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=81.44 E-value=0.74 Score=26.14 Aligned_cols=24 Identities=21% Similarity=0.639 Sum_probs=13.5
Q ss_pred cccccccccccccc-cccccccccC
Q psy7453 77 SLCKHCHSQLSHLD-LLDHCKTCSY 100 (200)
Q Consensus 77 ~~C~~C~~~f~~~~-~l~~C~~C~~ 100 (200)
|.|..||..|.... ...+|+.||.
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~ 27 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGY 27 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCc
Confidence 66777776665542 2235555554
No 88
>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=81.32 E-value=0.92 Score=31.85 Aligned_cols=28 Identities=11% Similarity=0.088 Sum_probs=17.3
Q ss_pred ccccccCcccCCCCCCCCcccccChhhhcc
Q psy7453 94 HCKTCSYMIRPNANNTFSPFCIYCKAVLST 123 (200)
Q Consensus 94 ~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~ 123 (200)
.|+.||+.|... +..|..|+.||..|..
T Consensus 11 ~Cp~cg~kFYDL--nk~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 11 ICPNTGSKFYDL--NRRPAVSPYTGEQFPP 38 (129)
T ss_pred cCCCcCcccccc--CCCCccCCCcCCccCc
Confidence 455555555532 2357778888877765
No 89
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=80.60 E-value=2.1 Score=29.53 Aligned_cols=54 Identities=20% Similarity=0.331 Sum_probs=35.6
Q ss_pred ccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccCChHHHHHHHHHcCCCCCcccccCc
Q psy7453 113 FCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCA 182 (200)
Q Consensus 113 ~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~ 182 (200)
.|--|...|.. ...... ..-.....|.|+.|...|-..-+.-.|...|. |+-|.
T Consensus 57 ~C~~C~~~f~~-~~~~~~---------~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~------CPGC~ 110 (112)
T TIGR00622 57 FCFGCQGPFPK-PPVSPF---------DELKDSHRYVCAVCKNVFCVDCDVFVHESLHC------CPGCI 110 (112)
T ss_pred cccCcCCCCCC-cccccc---------cccccccceeCCCCCCccccccchhhhhhccC------CcCCC
Confidence 48888888876 421110 11122346899999999988888888877664 66664
No 90
>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=79.95 E-value=1.2 Score=23.42 Aligned_cols=11 Identities=18% Similarity=0.806 Sum_probs=5.1
Q ss_pred ccccccccccc
Q psy7453 77 SLCKHCHSQLS 87 (200)
Q Consensus 77 ~~C~~C~~~f~ 87 (200)
|.|..|+..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 34555555444
No 91
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=79.92 E-value=0.85 Score=32.62 Aligned_cols=16 Identities=19% Similarity=0.434 Sum_probs=12.7
Q ss_pred CCCccccccccccccc
Q psy7453 74 QNHSLCKHCHSQLSHL 89 (200)
Q Consensus 74 ~~~~~C~~C~~~f~~~ 89 (200)
...+.|..||..|...
T Consensus 68 p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 68 EAVLKCRNCGNEWSLK 83 (135)
T ss_pred ceEEECCCCCCEEecc
Confidence 3568899999888775
No 92
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=79.86 E-value=1.5 Score=29.96 Aligned_cols=25 Identities=24% Similarity=0.557 Sum_probs=23.1
Q ss_pred ccc----ccCcccccCHHHHHHHHhhhcC
Q psy7453 176 YAC----GQCAFRSASVAGLHYHLKKTYH 200 (200)
Q Consensus 176 ~~C----~~C~k~f~~~~~L~~H~~~h~g 200 (200)
|.| ..|+....+...++.|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 9999999999999999998886
No 93
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=78.89 E-value=0.76 Score=30.87 Aligned_cols=26 Identities=19% Similarity=0.554 Sum_probs=20.8
Q ss_pred Ccccccccccccccc--cccccccccCc
Q psy7453 76 HSLCKHCHSQLSHLD--LLDHCKTCSYM 101 (200)
Q Consensus 76 ~~~C~~C~~~f~~~~--~l~~C~~C~~~ 101 (200)
|+.|..||..|.+-+ .|.-|+.||-.
T Consensus 2 pH~CtrCG~vf~~g~~~il~GCp~CG~n 29 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEILSGCPKCGCN 29 (112)
T ss_pred CceecccccccccccHHHHccCccccch
Confidence 678999999999843 55789999854
No 94
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=78.63 E-value=0.97 Score=31.27 Aligned_cols=28 Identities=14% Similarity=0.349 Sum_probs=21.6
Q ss_pred CCCcccccccccccccccccccccccCc
Q psy7453 74 QNHSLCKHCHSQLSHLDLLDHCKTCSYM 101 (200)
Q Consensus 74 ~~~~~C~~C~~~f~~~~~l~~C~~C~~~ 101 (200)
.....|..|+..|........||.||..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQHDAQCPHCHGE 95 (113)
T ss_pred CcEEEcccCCCEEecCCcCccCcCCCCC
Confidence 3457899999988887666679998854
No 95
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=78.47 E-value=0.79 Score=33.56 Aligned_cols=13 Identities=23% Similarity=0.542 Sum_probs=9.6
Q ss_pred CcccccChhhhcc
Q psy7453 111 SPFCIYCKAVLST 123 (200)
Q Consensus 111 ~~~C~~C~~~f~~ 123 (200)
.++|+.||++|.+
T Consensus 28 ~~~c~~c~~~f~~ 40 (154)
T PRK00464 28 RRECLACGKRFTT 40 (154)
T ss_pred eeeccccCCcceE
Confidence 4777777777776
No 96
>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=78.21 E-value=1.5 Score=30.76 Aligned_cols=30 Identities=10% Similarity=0.133 Sum_probs=21.6
Q ss_pred eecCccCcccCChHHHHHHHHHcCCCCCcccccCcccccCH
Q psy7453 148 FVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFRSASV 188 (200)
Q Consensus 148 ~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~f~~~ 188 (200)
..|+.||+.|... +..|-.|+.||..|.-.
T Consensus 10 r~Cp~cg~kFYDL-----------nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYDL-----------NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCcccccc-----------CCCCccCCCcCCccCcc
Confidence 4688888888743 34677888888887554
No 97
>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=77.99 E-value=1.3 Score=31.54 Aligned_cols=22 Identities=27% Similarity=0.641 Sum_probs=10.0
Q ss_pred ceecCccCcccCChHHHHHHHHHcC
Q psy7453 147 KFVCYACDYFSYNIGCMRSHIRTHT 171 (200)
Q Consensus 147 ~~~C~~C~~~f~~~~~l~~H~~~H~ 171 (200)
...|-+||+.|... ++|++.|.
T Consensus 72 ~i~clecGk~~k~L---krHL~~~~ 93 (132)
T PF05443_consen 72 YIICLECGKKFKTL---KRHLRTHH 93 (132)
T ss_dssp -EE-TBT--EESBH---HHHHHHTT
T ss_pred eeEEccCCcccchH---HHHHHHcc
Confidence 35566666666533 55665553
No 98
>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=77.64 E-value=1.1 Score=31.10 Aligned_cols=29 Identities=21% Similarity=0.449 Sum_probs=22.4
Q ss_pred CCCcccccccccccccccccccccccCcc
Q psy7453 74 QNHSLCKHCHSQLSHLDLLDHCKTCSYMI 102 (200)
Q Consensus 74 ~~~~~C~~C~~~f~~~~~l~~C~~C~~~f 102 (200)
.-...|..|+..|........||.||-..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 68 PVECECEDCSEEVSPEIDLYRCPKCHGIM 96 (115)
T ss_pred CcEEEcccCCCEEecCCcCccCcCCcCCC
Confidence 33578999999988877677899988543
No 99
>KOG4173|consensus
Probab=77.62 E-value=2.1 Score=32.74 Aligned_cols=48 Identities=19% Similarity=0.323 Sum_probs=28.1
Q ss_pred ccccChhhhccCHHHHHhchhhhhhhhhcC---------CCCCceec--CccCcccCChHHHHHHH
Q psy7453 113 FCIYCKAVLSTNLNELIEHCRTCKSMIRTD---------PFRHKFVC--YACDYFSYNIGCMRSHI 167 (200)
Q Consensus 113 ~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h---------~~~k~~~C--~~C~~~f~~~~~l~~H~ 167 (200)
.|..|.+.|.+ ...|..| +.--| .|..-|+| ..|+..|.+...-+.|+
T Consensus 108 sCs~C~r~~Pt-~hLLd~H------I~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~ 166 (253)
T KOG4173|consen 108 SCSFCKRAFPT-GHLLDAH------ILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHM 166 (253)
T ss_pred hhHHHHHhCCc-hhhhhHH------HHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHH
Confidence 57777777777 6666666 52222 23334666 33666666666666664
No 100
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=77.32 E-value=1.6 Score=25.29 Aligned_cols=19 Identities=26% Similarity=0.613 Sum_probs=9.2
Q ss_pred cccCcccccCH-----HHHHHHHh
Q psy7453 178 CGQCAFRSASV-----AGLHYHLK 196 (200)
Q Consensus 178 C~~C~k~f~~~-----~~L~~H~~ 196 (200)
|..|++.++.. ++|.+|++
T Consensus 21 C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 21 CKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred ecCCCCEeeeCCCCCcHHHHHHHH
Confidence 44454444332 45555555
No 101
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=77.31 E-value=1.6 Score=31.57 Aligned_cols=11 Identities=18% Similarity=0.452 Sum_probs=4.9
Q ss_pred eecCccCcccC
Q psy7453 148 FVCYACDYFSY 158 (200)
Q Consensus 148 ~~C~~C~~~f~ 158 (200)
|.|+.|+..|.
T Consensus 100 Y~Cp~C~~~y~ 110 (147)
T smart00531 100 YKCPNCQSKYT 110 (147)
T ss_pred EECcCCCCEee
Confidence 44444444444
No 102
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=77.27 E-value=0.22 Score=28.87 Aligned_cols=44 Identities=18% Similarity=0.324 Sum_probs=31.1
Q ss_pred CcccccccccccccccccccccccCcccCCCCCCCCcccccChhh
Q psy7453 76 HSLCKHCHSQLSHLDLLDHCKTCSYMIRPNANNTFSPFCIYCKAV 120 (200)
Q Consensus 76 ~~~C~~C~~~f~~~~~l~~C~~C~~~f~~~~~~~~~~~C~~C~~~ 120 (200)
.|.|+.|...|... .|++|..||+-.-..--.++-|.|.-|+-.
T Consensus 7 ry~CDLCn~~~p~~-~LRQCvlCGRWaC~sCW~deYY~CksC~Gi 50 (57)
T PF14445_consen 7 RYSCDLCNSSHPIS-ELRQCVLCGRWACNSCWQDEYYTCKSCNGI 50 (57)
T ss_pred hHhHHhhcccCcHH-HHHHHhhhchhhhhhhhhhhHhHHHhhhch
Confidence 47899999888654 588899998764444445667777777543
No 103
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=77.15 E-value=0.63 Score=34.95 Aligned_cols=14 Identities=21% Similarity=0.479 Sum_probs=8.3
Q ss_pred CCcccccChhhhcc
Q psy7453 110 FSPFCIYCKAVLST 123 (200)
Q Consensus 110 ~~~~C~~C~~~f~~ 123 (200)
.-|.|+.|+..|+.
T Consensus 116 ~~Y~Cp~C~~rytf 129 (178)
T PRK06266 116 MFFFCPNCHIRFTF 129 (178)
T ss_pred CEEECCCCCcEEeH
Confidence 34566666666655
No 104
>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=77.05 E-value=2.7 Score=30.88 Aligned_cols=34 Identities=15% Similarity=0.208 Sum_probs=24.2
Q ss_pred CCCCCceecCccCcccCChHHHHHHHHHcCCCCCcccccCccc
Q psy7453 142 DPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFR 184 (200)
Q Consensus 142 h~~~k~~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~ 184 (200)
..+..-|.|+.|+..|....++. ..|.|+.||..
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCE
Confidence 44455688888888887777763 25888888864
No 105
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=75.85 E-value=0.68 Score=33.56 Aligned_cols=13 Identities=15% Similarity=0.281 Sum_probs=6.9
Q ss_pred CcccccChhhhcc
Q psy7453 111 SPFCIYCKAVLST 123 (200)
Q Consensus 111 ~~~C~~C~~~f~~ 123 (200)
-|.|+.|+..|..
T Consensus 99 ~Y~Cp~C~~~y~~ 111 (147)
T smart00531 99 YYKCPNCQSKYTF 111 (147)
T ss_pred EEECcCCCCEeeH
Confidence 4555555555554
No 106
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=75.01 E-value=1.4 Score=25.62 Aligned_cols=26 Identities=15% Similarity=0.305 Sum_probs=13.8
Q ss_pred CCcccccccccccccc--cccccccccC
Q psy7453 75 NHSLCKHCHSQLSHLD--LLDHCKTCSY 100 (200)
Q Consensus 75 ~~~~C~~C~~~f~~~~--~l~~C~~C~~ 100 (200)
..|.|..||+.|.... ...+|+.||.
T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 5 MEYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEEhhhcCCeeehhhccCceeCCCCCc
Confidence 3467777777774221 1235555553
No 107
>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=74.75 E-value=0.74 Score=33.85 Aligned_cols=13 Identities=8% Similarity=-0.059 Sum_probs=6.6
Q ss_pred CcccccChhhhcc
Q psy7453 111 SPFCIYCKAVLST 123 (200)
Q Consensus 111 ~~~C~~C~~~f~~ 123 (200)
-|.|+.|+..|+.
T Consensus 109 ~Y~Cp~c~~r~tf 121 (158)
T TIGR00373 109 FFICPNMCVRFTF 121 (158)
T ss_pred eEECCCCCcEeeH
Confidence 4455555555544
No 108
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=74.63 E-value=3.2 Score=31.18 Aligned_cols=35 Identities=20% Similarity=0.273 Sum_probs=27.2
Q ss_pred CCCCCceecCccCcccCChHHHHHHHHHcCCCCCcccccCcccc
Q psy7453 142 DPFRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFRS 185 (200)
Q Consensus 142 h~~~k~~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~f 185 (200)
-....-|.|+.|+..|....++. -.|.|+.||...
T Consensus 112 e~~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L 146 (178)
T PRK06266 112 EENNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEML 146 (178)
T ss_pred ccCCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCC
Confidence 33445799999999998887762 369999999654
No 109
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=73.83 E-value=3.1 Score=20.65 Aligned_cols=19 Identities=21% Similarity=0.352 Sum_probs=12.1
Q ss_pred ccccCcccccCHHHHHHHHh
Q psy7453 177 ACGQCAFRSASVAGLHYHLK 196 (200)
Q Consensus 177 ~C~~C~k~f~~~~~L~~H~~ 196 (200)
.|++|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577777776 4456666654
No 110
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=73.74 E-value=2.7 Score=29.81 Aligned_cols=33 Identities=12% Similarity=0.266 Sum_probs=23.4
Q ss_pred hhhhhhhhcCCCCCCCccccccccccccccccc
Q psy7453 61 LNLSVLLVTTIPTQNHSLCKHCHSQLSHLDLLD 93 (200)
Q Consensus 61 ~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~ 93 (200)
++....++..-.+.+.|.|..|..+...+.-|.
T Consensus 65 ~n~r~qvmnvF~d~~lYeCnIC~etS~ee~FLK 97 (140)
T PF05290_consen 65 INRRLQVMNVFLDPKLYECNICKETSAEERFLK 97 (140)
T ss_pred HHHHHHHheeecCCCceeccCcccccchhhcCC
Confidence 344444444445668999999999988888775
No 111
>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=73.40 E-value=1 Score=31.12 Aligned_cols=28 Identities=14% Similarity=0.394 Sum_probs=19.7
Q ss_pred CCcccccccccccccccccccccccCcc
Q psy7453 75 NHSLCKHCHSQLSHLDLLDHCKTCSYMI 102 (200)
Q Consensus 75 ~~~~C~~C~~~f~~~~~l~~C~~C~~~f 102 (200)
-...|..|+..|.-......||.||...
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDEFDFSCPRCGSPD 96 (113)
T ss_dssp -EEEETTTS-EEECHHCCHH-SSSSSS-
T ss_pred CcEECCCCCCEEecCCCCCCCcCCcCCC
Confidence 3478999999998887778888888653
No 112
>KOG2482|consensus
Probab=73.20 E-value=5.2 Score=33.03 Aligned_cols=23 Identities=22% Similarity=0.183 Sum_probs=18.9
Q ss_pred cccccCcccccCHHHHHHHHhhh
Q psy7453 176 YACGQCAFRSASVAGLHYHLKKT 198 (200)
Q Consensus 176 ~~C~~C~k~f~~~~~L~~H~~~h 198 (200)
.+|-.|...+-....|..||++.
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~v 302 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIV 302 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHH
Confidence 47888888888888888898864
No 113
>KOG1280|consensus
Probab=73.01 E-value=2.4 Score=34.91 Aligned_cols=38 Identities=21% Similarity=0.547 Sum_probs=21.3
Q ss_pred CCceecCccCcccCChHHHHHHHHH-cCCCCC-cccccCc
Q psy7453 145 RHKFVCYACDYFSYNIGCMRSHIRT-HTGEKP-YACGQCA 182 (200)
Q Consensus 145 ~k~~~C~~C~~~f~~~~~l~~H~~~-H~~~k~-~~C~~C~ 182 (200)
+..|.|++|+..=.+...|..|... |....+ ..|++|+
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 3457777777766666677777554 432221 2355553
No 114
>PRK12496 hypothetical protein; Provisional
Probab=72.63 E-value=2 Score=31.84 Aligned_cols=26 Identities=23% Similarity=0.540 Sum_probs=15.9
Q ss_pred cccccccccccccccccccccccCcc
Q psy7453 77 SLCKHCHSQLSHLDLLDHCKTCSYMI 102 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~l~~C~~C~~~f 102 (200)
|.|+.|++.|........|+.||...
T Consensus 128 ~~C~gC~~~~~~~~~~~~C~~CG~~~ 153 (164)
T PRK12496 128 KVCKGCKKKYPEDYPDDVCEICGSPV 153 (164)
T ss_pred EECCCCCccccCCCCCCcCCCCCChh
Confidence 66777777776544444566666543
No 115
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=71.86 E-value=2.3 Score=24.59 Aligned_cols=13 Identities=15% Similarity=0.166 Sum_probs=7.6
Q ss_pred CcccccChhhhcc
Q psy7453 111 SPFCIYCKAVLST 123 (200)
Q Consensus 111 ~~~C~~C~~~f~~ 123 (200)
.+.|+.||..+.-
T Consensus 20 ~~vC~~Cg~~~~~ 32 (52)
T smart00661 20 RFVCRKCGYEEPI 32 (52)
T ss_pred EEECCcCCCeEEC
Confidence 4566666655544
No 116
>KOG2186|consensus
Probab=71.73 E-value=1.7 Score=34.16 Aligned_cols=46 Identities=17% Similarity=0.297 Sum_probs=28.4
Q ss_pred cccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccCChHHHHHHHH
Q psy7453 112 PFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSYNIGCMRSHIR 168 (200)
Q Consensus 112 ~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~ 168 (200)
|.|..||....- ..+.+| + ..-++ .-|.|--||+.|-. .++..|..
T Consensus 4 FtCnvCgEsvKK--p~vekH------~-srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 4 FTCNVCGESVKK--PQVEKH------M-SRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eehhhhhhhccc--cchHHH------H-HhccC-CeeEEeeccccccc-chhhhhhh
Confidence 567777766554 456667 6 44444 45777777777766 45566644
No 117
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=71.55 E-value=2.6 Score=27.73 Aligned_cols=14 Identities=21% Similarity=0.586 Sum_probs=10.1
Q ss_pred CCcccccccccccc
Q psy7453 75 NHSLCKHCHSQLSH 88 (200)
Q Consensus 75 ~~~~C~~C~~~f~~ 88 (200)
.|-.|..||..|.+
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 36677778877766
No 118
>KOG4167|consensus
Probab=71.41 E-value=1 Score=40.64 Aligned_cols=24 Identities=17% Similarity=0.407 Sum_probs=21.9
Q ss_pred cccccCcccccCHHHHHHHHhhhc
Q psy7453 176 YACGQCAFRSASVAGLHYHLKKTY 199 (200)
Q Consensus 176 ~~C~~C~k~f~~~~~L~~H~~~h~ 199 (200)
|.|.+|+|.|-...++..||++|.
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHHH
Confidence 899999999999999999999884
No 119
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=71.34 E-value=1.3 Score=39.88 Aligned_cols=66 Identities=15% Similarity=0.380 Sum_probs=41.2
Q ss_pred ccccccccccccccc---cc---ccccccCcccCCCC--------CCCCc-ccccChhhhccCHHHHHhchhhhhhhhhc
Q psy7453 77 SLCKHCHSQLSHLDL---LD---HCKTCSYMIRPNAN--------NTFSP-FCIYCKAVLSTNLNELIEHCRTCKSMIRT 141 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~---l~---~C~~C~~~f~~~~~--------~~~~~-~C~~C~~~f~~~~~~l~~H~~~~~~~~~~ 141 (200)
-.|+.|-+-+.++.+ +| .|..||-+|+-... .-..| -|+.|.+.+.. ..+ . |.
T Consensus 102 a~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~d-P~n----------R-Rf 169 (750)
T COG0068 102 ATCEDCLEEIFDPNSRRYLYPFINCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKD-PLN----------R-RF 169 (750)
T ss_pred hhhHHHHHHhcCCCCcceeccccccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcC-ccc----------c-cc
Confidence 468888765555433 33 68888888775433 11123 48889888877 544 2 44
Q ss_pred CCCCCceecCccCcc
Q psy7453 142 DPFRHKFVCYACDYF 156 (200)
Q Consensus 142 h~~~k~~~C~~C~~~ 156 (200)
|. .|..|+.||-.
T Consensus 170 HA--Qp~aCp~CGP~ 182 (750)
T COG0068 170 HA--QPIACPKCGPH 182 (750)
T ss_pred cc--ccccCcccCCC
Confidence 54 36789999863
No 120
>PF14353 CpXC: CpXC protein
Probab=70.72 E-value=2 Score=30.26 Aligned_cols=20 Identities=25% Similarity=0.285 Sum_probs=11.4
Q ss_pred CcccccChhhhccCHHHHHhc
Q psy7453 111 SPFCIYCKAVLSTNLNELIEH 131 (200)
Q Consensus 111 ~~~C~~C~~~f~~~~~~l~~H 131 (200)
.|.|+.||..|.- ...+.-|
T Consensus 38 ~~~CP~Cg~~~~~-~~p~lY~ 57 (128)
T PF14353_consen 38 SFTCPSCGHKFRL-EYPLLYH 57 (128)
T ss_pred EEECCCCCCceec-CCCEEEE
Confidence 4567777776665 4443333
No 121
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=70.72 E-value=2 Score=29.77 Aligned_cols=28 Identities=18% Similarity=0.500 Sum_probs=20.7
Q ss_pred CCCcccccccccccccccc-cccccccCc
Q psy7453 74 QNHSLCKHCHSQLSHLDLL-DHCKTCSYM 101 (200)
Q Consensus 74 ~~~~~C~~C~~~f~~~~~l-~~C~~C~~~ 101 (200)
.....|..|+..|...... ..||.||..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred CcEEEcccCCCeeecCCccCCcCcCcCCC
Confidence 3457899999988876443 679888854
No 122
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=69.93 E-value=1 Score=28.44 Aligned_cols=15 Identities=13% Similarity=0.255 Sum_probs=7.9
Q ss_pred CCceecC--ccCcccCC
Q psy7453 145 RHKFVCY--ACDYFSYN 159 (200)
Q Consensus 145 ~k~~~C~--~C~~~f~~ 159 (200)
+.-++|. .||..|..
T Consensus 25 ~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 25 ERYHQCQNVNCSATFIT 41 (72)
T ss_pred eeeeecCCCCCCCEEEE
Confidence 4445555 56655543
No 123
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=69.89 E-value=3 Score=32.77 Aligned_cols=51 Identities=14% Similarity=0.346 Sum_probs=37.3
Q ss_pred CCCCcccccccccccc----cccccccccccCcccCCCC----CCCCcccccChhhhcc
Q psy7453 73 TQNHSLCKHCHSQLSH----LDLLDHCKTCSYMIRPNAN----NTFSPFCIYCKAVLST 123 (200)
Q Consensus 73 ~~~~~~C~~C~~~f~~----~~~l~~C~~C~~~f~~~~~----~~~~~~C~~C~~~f~~ 123 (200)
..+-|.|..|+...-. .....+|..|.+.|...-. |--.|.|+.|+..|.-
T Consensus 109 ~drqFaC~~Cd~~WwRrvp~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 109 VDRQFACSSCDHMWWRRVPQRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred cceeeeccccchHHHhccCcccccccccccccccCCCccccccceeeeecccccccchh
Confidence 3467999999865443 3344589999888775443 5557899999999977
No 124
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=69.70 E-value=2.7 Score=20.23 Aligned_cols=6 Identities=33% Similarity=1.027 Sum_probs=2.7
Q ss_pred cccChh
Q psy7453 114 CIYCKA 119 (200)
Q Consensus 114 C~~C~~ 119 (200)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 444443
No 125
>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=69.52 E-value=4 Score=35.88 Aligned_cols=10 Identities=30% Similarity=0.697 Sum_probs=5.7
Q ss_pred CCceecCccC
Q psy7453 145 RHKFVCYACD 154 (200)
Q Consensus 145 ~k~~~C~~C~ 154 (200)
+....|..||
T Consensus 238 ~~~l~Ch~Cg 247 (505)
T TIGR00595 238 EGKLRCHYCG 247 (505)
T ss_pred CCeEEcCCCc
Confidence 3445666665
No 126
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=69.36 E-value=2.2 Score=29.69 Aligned_cols=29 Identities=21% Similarity=0.430 Sum_probs=20.8
Q ss_pred CCCccccccccccccccc-ccccccccCcc
Q psy7453 74 QNHSLCKHCHSQLSHLDL-LDHCKTCSYMI 102 (200)
Q Consensus 74 ~~~~~C~~C~~~f~~~~~-l~~C~~C~~~f 102 (200)
.-.+.|..||..|..... ...||.||-..
T Consensus 69 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 69 KVELECKDCSHVFKPNALDYGVCEKCHSKN 98 (117)
T ss_pred CCEEEhhhCCCccccCCccCCcCcCCCCCc
Confidence 345789999988887654 34588888553
No 127
>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=69.22 E-value=1.7 Score=34.45 Aligned_cols=95 Identities=20% Similarity=0.567 Sum_probs=56.3
Q ss_pred ccccccCcccCCCCCCCCcccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccCChHHH-------HHH
Q psy7453 94 HCKTCSYMIRPNANNTFSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSYNIGCM-------RSH 166 (200)
Q Consensus 94 ~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~~~~~l-------~~H 166 (200)
.|-+|.+..+. .|.+-|+|..|....-- ..-..|+++++-. - ...|+|.-|++.= ..+.| ..|
T Consensus 127 ~C~EC~R~vw~--hGGrif~CsfC~~flCE--DDQFEHQAsCQvL-e----~E~~KC~SCNrlG-q~sCLRCK~cfCddH 196 (314)
T PF06524_consen 127 VCIECERGVWD--HGGRIFKCSFCDNFLCE--DDQFEHQASCQVL-E----SETFKCQSCNRLG-QYSCLRCKICFCDDH 196 (314)
T ss_pred Eeeeeeccccc--CCCeEEEeecCCCeeec--cchhhhhhhhhhh-h----ccccccccccccc-chhhhheeeeehhhh
Confidence 45555554432 26788999999876554 4455675555443 1 2246777765432 22222 245
Q ss_pred HHH----cCCCCCcccccCcccccCHHHHHHHHhhh
Q psy7453 167 IRT----HTGEKPYACGQCAFRSASVAGLHYHLKKT 198 (200)
Q Consensus 167 ~~~----H~~~k~~~C~~C~k~f~~~~~L~~H~~~h 198 (200)
.+. -...++++||.||........|..-.|+|
T Consensus 197 vrrKg~ky~k~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 197 VRRKGFKYEKGKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred hhhcccccccCCCCCCCCCCCcccccccceeeeecc
Confidence 443 23357899999998887777776555544
No 128
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=68.84 E-value=3.1 Score=29.48 Aligned_cols=60 Identities=18% Similarity=0.256 Sum_probs=33.4
Q ss_pred ccccccccccccccccCcccCCCCCCCCccc---ccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccCCh
Q psy7453 84 SQLSHLDLLDHCKTCSYMIRPNANNTFSPFC---IYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSYNI 160 (200)
Q Consensus 84 ~~f~~~~~l~~C~~C~~~f~~~~~~~~~~~C---~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~~~ 160 (200)
..|... .||+|.+|.......+-. ||-.| .+|+.-+.. |.+| - ..|+ +|++|.-+|++.
T Consensus 73 nvF~d~-~lYeCnIC~etS~ee~FL-KPneCCgY~iCn~Cya~----LWK~------~-~~yp-----vCPvCkTSFKss 134 (140)
T PF05290_consen 73 NVFLDP-KLYECNICKETSAEERFL-KPNECCGYSICNACYAN----LWKF------C-NLYP-----VCPVCKTSFKSS 134 (140)
T ss_pred eeecCC-CceeccCcccccchhhcC-CcccccchHHHHHHHHH----HHHH------c-ccCC-----CCCccccccccc
Confidence 345555 678888887665443321 33333 234444433 5556 4 4443 588887777765
Q ss_pred H
Q psy7453 161 G 161 (200)
Q Consensus 161 ~ 161 (200)
+
T Consensus 135 ~ 135 (140)
T PF05290_consen 135 S 135 (140)
T ss_pred c
Confidence 4
No 129
>PF12773 DZR: Double zinc ribbon
Probab=68.16 E-value=4.3 Score=23.25 Aligned_cols=8 Identities=38% Similarity=0.862 Sum_probs=3.4
Q ss_pred cccccChh
Q psy7453 112 PFCIYCKA 119 (200)
Q Consensus 112 ~~C~~C~~ 119 (200)
..|+.|+.
T Consensus 30 ~~C~~Cg~ 37 (50)
T PF12773_consen 30 KICPNCGA 37 (50)
T ss_pred CCCcCCcC
Confidence 33444443
No 130
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=67.97 E-value=2.4 Score=30.04 Aligned_cols=21 Identities=19% Similarity=0.363 Sum_probs=11.9
Q ss_pred eecCccCcccCChHHHHHHHHHcC
Q psy7453 148 FVCYACDYFSYNIGCMRSHIRTHT 171 (200)
Q Consensus 148 ~~C~~C~~~f~~~~~l~~H~~~H~ 171 (200)
..|-++|+.|. +|++|+.+|.
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~ 97 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHY 97 (148)
T ss_pred EEEeccCcchH---HHHHHHhccc
Confidence 45666666665 4556665553
No 131
>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=67.38 E-value=1.9 Score=24.09 Aligned_cols=11 Identities=36% Similarity=0.670 Sum_probs=5.1
Q ss_pred CcccccChhhh
Q psy7453 111 SPFCIYCKAVL 121 (200)
Q Consensus 111 ~~~C~~C~~~f 121 (200)
.+.|..||...
T Consensus 19 ~~vC~~CG~Vl 29 (43)
T PF08271_consen 19 ELVCPNCGLVL 29 (43)
T ss_dssp EEEETTT-BBE
T ss_pred eEECCCCCCEe
Confidence 34555555443
No 132
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=67.28 E-value=3 Score=30.94 Aligned_cols=11 Identities=27% Similarity=0.564 Sum_probs=7.1
Q ss_pred CCCcccccChh
Q psy7453 109 TFSPFCIYCKA 119 (200)
Q Consensus 109 ~~~~~C~~C~~ 119 (200)
+-|-.||+||.
T Consensus 147 e~P~~CPiCga 157 (166)
T COG1592 147 EAPEVCPICGA 157 (166)
T ss_pred CCCCcCCCCCC
Confidence 55667777763
No 133
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=67.27 E-value=2.8 Score=27.43 Aligned_cols=10 Identities=20% Similarity=0.763 Sum_probs=5.6
Q ss_pred Cccccccccc
Q psy7453 76 HSLCKHCHSQ 85 (200)
Q Consensus 76 ~~~C~~C~~~ 85 (200)
.|.|+.|++.
T Consensus 35 ~~~Cp~C~~~ 44 (89)
T COG1997 35 KHVCPFCGRT 44 (89)
T ss_pred CCcCCCCCCc
Confidence 4556666554
No 134
>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=67.07 E-value=3.2 Score=21.24 Aligned_cols=22 Identities=23% Similarity=0.747 Sum_probs=13.8
Q ss_pred ccccccccccccccccccccccc
Q psy7453 77 SLCKHCHSQLSHLDLLDHCKTCS 99 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~l~~C~~C~ 99 (200)
|.|..|++...... .|.|..|+
T Consensus 1 ~~C~~C~~~~~~~~-~Y~C~~c~ 22 (30)
T PF03107_consen 1 FWCDVCRRKIDGFY-FYHCSECC 22 (30)
T ss_pred CCCCCCCCCcCCCE-eEEeCCCC
Confidence 45677776655555 66666665
No 135
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=66.10 E-value=4.8 Score=38.87 Aligned_cols=37 Identities=19% Similarity=0.469 Sum_probs=24.6
Q ss_pred cccccccccccccccccccccccCcccCCCCCCCCcccccChhhhcc
Q psy7453 77 SLCKHCHSQLSHLDLLDHCKTCSYMIRPNANNTFSPFCIYCKAVLST 123 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~l~~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~ 123 (200)
+.|+.||..-.. ..|+.||... +..|.|+.||.....
T Consensus 668 rkCPkCG~~t~~----~fCP~CGs~t------e~vy~CPsCGaev~~ 704 (1337)
T PRK14714 668 RRCPSCGTETYE----NRCPDCGTHT------EPVYVCPDCGAEVPP 704 (1337)
T ss_pred EECCCCCCcccc----ccCcccCCcC------CCceeCccCCCccCC
Confidence 789999874322 2788888664 235688888776543
No 136
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=66.06 E-value=8.1 Score=32.01 Aligned_cols=71 Identities=27% Similarity=0.557 Sum_probs=46.7
Q ss_pred cccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCc-------ccCChHHHHHHHHHcCCCCCccccc--C-
Q psy7453 112 PFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDY-------FSYNIGCMRSHIRTHTGEKPYACGQ--C- 181 (200)
Q Consensus 112 ~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~-------~f~~~~~l~~H~~~H~~~k~~~C~~--C- 181 (200)
-.|..|...|-. -..|..| ++..| | .|.+|++ -|.+...|..|.+. --|.|.+ |
T Consensus 221 P~C~FC~~~FYd-DDEL~~H------cR~~H--E---~ChICD~v~p~~~QYFK~Y~~Le~HF~~----~hy~ct~qtc~ 284 (493)
T COG5236 221 PLCIFCKIYFYD-DDELRRH------CRLRH--E---ACHICDMVGPIRYQYFKSYEDLEAHFRN----AHYCCTFQTCR 284 (493)
T ss_pred chhhhccceecC-hHHHHHH------HHhhh--h---hhhhhhccCccchhhhhCHHHHHHHhhc----CceEEEEEEEe
Confidence 358889988888 8889999 73333 2 2555543 36777777777552 2366754 4
Q ss_pred -c--ccccCHHHHHHHHhhh
Q psy7453 182 -A--FRSASVAGLHYHLKKT 198 (200)
Q Consensus 182 -~--k~f~~~~~L~~H~~~h 198 (200)
| ..|.....|..|+-.-
T Consensus 285 ~~k~~vf~~~~el~~h~~~~ 304 (493)
T COG5236 285 VGKCYVFPYHTELLEHLTRF 304 (493)
T ss_pred cCcEEEeccHHHHHHHHHHH
Confidence 2 3677788888887553
No 137
>PRK14873 primosome assembly protein PriA; Provisional
Probab=64.09 E-value=5.1 Score=36.49 Aligned_cols=14 Identities=21% Similarity=0.012 Sum_probs=7.2
Q ss_pred ceeehhhHHHHHHH
Q psy7453 2 LVTITPTLAKVFLV 15 (200)
Q Consensus 2 ~~~~~p~~~~~~~~ 15 (200)
+.+.||++....+.
T Consensus 298 LgSaTPSles~~~~ 311 (665)
T PRK14873 298 IGGHARTAEAQALV 311 (665)
T ss_pred EECCCCCHHHHHHH
Confidence 34556665555443
No 138
>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=64.01 E-value=3.3 Score=22.36 Aligned_cols=11 Identities=27% Similarity=0.546 Sum_probs=5.8
Q ss_pred CcccccChhhh
Q psy7453 111 SPFCIYCKAVL 121 (200)
Q Consensus 111 ~~~C~~C~~~f 121 (200)
+-.|+.||-.+
T Consensus 21 ~~~Cd~cg~~L 31 (36)
T PF05191_consen 21 EGVCDNCGGEL 31 (36)
T ss_dssp TTBCTTTTEBE
T ss_pred CCccCCCCCee
Confidence 34566665544
No 139
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=63.90 E-value=4.4 Score=29.38 Aligned_cols=29 Identities=24% Similarity=0.635 Sum_probs=21.7
Q ss_pred CCCCccccccc--ccccccccccccccccCc
Q psy7453 73 TQNHSLCKHCH--SQLSHLDLLDHCKTCSYM 101 (200)
Q Consensus 73 ~~~~~~C~~C~--~~f~~~~~l~~C~~C~~~ 101 (200)
|...|.|..|| ..|.....|-.|+.||..
T Consensus 109 g~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 109 GPGTLVCENCGHEVELTHPERLPPCPKCGHT 139 (146)
T ss_pred cCceEecccCCCEEEecCCCcCCCCCCCCCC
Confidence 34569999998 456666778889888865
No 140
>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=63.64 E-value=2.1 Score=31.16 Aligned_cols=40 Identities=23% Similarity=0.610 Sum_probs=26.0
Q ss_pred cccccccccccccccccccccCcccCC----------CCCCCCcccccChhhhcc
Q psy7453 79 CKHCHSQLSHLDLLDHCKTCSYMIRPN----------ANNTFSPFCIYCKAVLST 123 (200)
Q Consensus 79 C~~C~~~f~~~~~l~~C~~C~~~f~~~----------~~~~~~~~C~~C~~~f~~ 123 (200)
|..||.. .+..|+.|+....-. ...+.|.-|..||+.|.+
T Consensus 31 C~kCG~~-----tI~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyPW 80 (158)
T PF10083_consen 31 CSKCGAK-----TITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYPW 80 (158)
T ss_pred HHHhhHH-----HHHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCch
Confidence 7777753 345677776543322 224567889999999987
No 141
>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=63.41 E-value=3.2 Score=25.62 Aligned_cols=26 Identities=27% Similarity=0.696 Sum_probs=9.7
Q ss_pred cccccccccccccccccccccccCcc
Q psy7453 77 SLCKHCHSQLSHLDLLDHCKTCSYMI 102 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~l~~C~~C~~~f 102 (200)
-.|..|++.|.....-..|..||..|
T Consensus 10 ~~C~~C~~~F~~~~rrhhCr~CG~~v 35 (69)
T PF01363_consen 10 SNCMICGKKFSLFRRRHHCRNCGRVV 35 (69)
T ss_dssp SB-TTT--B-BSSS-EEE-TTT--EE
T ss_pred CcCcCcCCcCCCceeeEccCCCCCEE
Confidence 35777777775444334565555543
No 142
>KOG2785|consensus
Probab=63.07 E-value=9.1 Score=32.05 Aligned_cols=51 Identities=20% Similarity=0.318 Sum_probs=39.1
Q ss_pred ceecCccCcccCChHHHHHHHHHcCC-----------------------CCCcccccCc---ccccCHHHHHHHHhh
Q psy7453 147 KFVCYACDYFSYNIGCMRSHIRTHTG-----------------------EKPYACGQCA---FRSASVAGLHYHLKK 197 (200)
Q Consensus 147 ~~~C~~C~~~f~~~~~l~~H~~~H~~-----------------------~k~~~C~~C~---k~f~~~~~L~~H~~~ 197 (200)
|-.|-.|++.+.+......||..++| ..-|.|-.|. +.|.+....+.||..
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 45677788888877777788776655 1357888887 899999999999863
No 143
>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=62.96 E-value=4.5 Score=23.28 Aligned_cols=9 Identities=33% Similarity=0.600 Sum_probs=4.1
Q ss_pred CcccccChh
Q psy7453 111 SPFCIYCKA 119 (200)
Q Consensus 111 ~~~C~~C~~ 119 (200)
.|.|++|+.
T Consensus 34 ~w~CP~C~a 42 (47)
T PF00301_consen 34 DWVCPVCGA 42 (47)
T ss_dssp T-B-TTTSS
T ss_pred CCcCcCCCC
Confidence 466666654
No 144
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=62.88 E-value=6.6 Score=32.50 Aligned_cols=48 Identities=23% Similarity=0.408 Sum_probs=34.1
Q ss_pred ecCccCcccCChHHHHHHHHHcCCCCCcccccCc----ccccCHHHHHHHHhh
Q psy7453 149 VCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCA----FRSASVAGLHYHLKK 197 (200)
Q Consensus 149 ~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~----k~f~~~~~L~~H~~~ 197 (200)
.|..|...|.....|..|+|... |+-|.|+.-+ +-|....+|..|.+.
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~H-E~ChICD~v~p~~~QYFK~Y~~Le~HF~~ 273 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRH-EACHICDMVGPIRYQYFKSYEDLEAHFRN 273 (493)
T ss_pred hhhhccceecChHHHHHHHHhhh-hhhhhhhccCccchhhhhCHHHHHHHhhc
Confidence 68899999999999999988532 3434443322 347888889888764
No 145
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=62.58 E-value=4 Score=24.23 Aligned_cols=26 Identities=19% Similarity=0.489 Sum_probs=13.7
Q ss_pred ccccccccccccccc----ccccccccCcc
Q psy7453 77 SLCKHCHSQLSHLDL----LDHCKTCSYMI 102 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~----l~~C~~C~~~f 102 (200)
+.|+.||..+.-... +..|+.||..+
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCEE
Confidence 567777776654332 22455555443
No 146
>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=62.52 E-value=4.6 Score=23.74 Aligned_cols=13 Identities=15% Similarity=0.585 Sum_probs=6.4
Q ss_pred CcccccChhhhcc
Q psy7453 111 SPFCIYCKAVLST 123 (200)
Q Consensus 111 ~~~C~~C~~~f~~ 123 (200)
.+.|..||+.|-.
T Consensus 18 k~~Cr~Cg~~~C~ 30 (57)
T cd00065 18 RHHCRNCGRIFCS 30 (57)
T ss_pred ccccCcCcCCcCh
Confidence 3445555555544
No 147
>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=61.97 E-value=6.7 Score=22.86 Aligned_cols=9 Identities=33% Similarity=0.600 Sum_probs=6.0
Q ss_pred CcccccChh
Q psy7453 111 SPFCIYCKA 119 (200)
Q Consensus 111 ~~~C~~C~~ 119 (200)
.|.|+.|+.
T Consensus 34 ~w~CP~C~a 42 (50)
T cd00730 34 DWVCPVCGA 42 (50)
T ss_pred CCCCCCCCC
Confidence 567777764
No 148
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=61.64 E-value=4.3 Score=28.08 Aligned_cols=11 Identities=36% Similarity=1.126 Sum_probs=7.2
Q ss_pred cccccCccccc
Q psy7453 176 YACGQCAFRSA 186 (200)
Q Consensus 176 ~~C~~C~k~f~ 186 (200)
|.|..||..|.
T Consensus 101 y~C~~Cg~~wr 111 (113)
T COG1594 101 YKCTRCGYRWR 111 (113)
T ss_pred EEecccCCEee
Confidence 66777776654
No 149
>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=61.59 E-value=3.4 Score=20.17 Aligned_cols=8 Identities=38% Similarity=1.481 Sum_probs=3.8
Q ss_pred CcccccCc
Q psy7453 175 PYACGQCA 182 (200)
Q Consensus 175 ~~~C~~C~ 182 (200)
+|.|+.||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 34455554
No 150
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=61.11 E-value=5.7 Score=36.47 Aligned_cols=22 Identities=23% Similarity=0.617 Sum_probs=12.1
Q ss_pred cccccccCcccCCCCCCCCcccccChhh
Q psy7453 93 DHCKTCSYMIRPNANNTFSPFCIYCKAV 120 (200)
Q Consensus 93 ~~C~~C~~~f~~~~~~~~~~~C~~C~~~ 120 (200)
..|..||.. ...|..|+.||-.
T Consensus 463 L~CH~Cg~~------~~~p~~Cp~Cgs~ 484 (730)
T COG1198 463 LRCHYCGYQ------EPIPQSCPECGSE 484 (730)
T ss_pred eEeCCCCCC------CCCCCCCCCCCCC
Confidence 356666543 2245667777654
No 151
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=60.90 E-value=6.5 Score=28.01 Aligned_cols=25 Identities=28% Similarity=0.464 Sum_probs=15.7
Q ss_pred CCCCcccccChhhhccCHHHHHhchhhhhhhhhcCC
Q psy7453 108 NTFSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDP 143 (200)
Q Consensus 108 ~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~ 143 (200)
.+.-..|-+||+.|.. |++| . +.|.
T Consensus 69 ~~d~i~clecGk~~k~----LkrH------L-~~~~ 93 (132)
T PF05443_consen 69 TPDYIICLECGKKFKT----LKRH------L-RTHH 93 (132)
T ss_dssp -SS-EE-TBT--EESB----HHHH------H-HHTT
T ss_pred ccCeeEEccCCcccch----HHHH------H-HHcc
Confidence 4445689999999999 7999 7 6664
No 152
>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=59.95 E-value=3.2 Score=32.87 Aligned_cols=26 Identities=19% Similarity=0.387 Sum_probs=20.0
Q ss_pred CCceecCccCcccCChHHHHHHHHHc
Q psy7453 145 RHKFVCYACDYFSYNIGCMRSHIRTH 170 (200)
Q Consensus 145 ~k~~~C~~C~~~f~~~~~l~~H~~~H 170 (200)
.+++.|+.||..-.....|..-.|+|
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeecc
Confidence 46899999998887777776666665
No 153
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=59.94 E-value=3.8 Score=28.71 Aligned_cols=32 Identities=25% Similarity=0.576 Sum_probs=20.9
Q ss_pred ccccccccCcccCC----------CCCCCCcccccChhhhcc
Q psy7453 92 LDHCKTCSYMIRPN----------ANNTFSPFCIYCKAVLST 123 (200)
Q Consensus 92 l~~C~~C~~~f~~~----------~~~~~~~~C~~C~~~f~~ 123 (200)
+.+|+.|....+-. +..+.|-.|..||.+|.+
T Consensus 39 i~qcp~csasirgd~~vegvlglg~dye~psfchncgs~fpw 80 (160)
T COG4306 39 ITQCPICSASIRGDYYVEGVLGLGGDYEPPSFCHNCGSRFPW 80 (160)
T ss_pred HhcCCccCCcccccceeeeeeccCCCCCCcchhhcCCCCCCc
Confidence 44566666543322 124567789999999987
No 154
>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=59.38 E-value=2 Score=26.97 Aligned_cols=39 Identities=18% Similarity=0.512 Sum_probs=13.4
Q ss_pred cccccccccccccccccccccccCcccCCCC-CCCCcccccCh
Q psy7453 77 SLCKHCHSQLSHLDLLDHCKTCSYMIRPNAN-NTFSPFCIYCK 118 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~l~~C~~C~~~f~~~~~-~~~~~~C~~C~ 118 (200)
|.|..|++.|... ..||.|+.....-.. |...|.|..|.
T Consensus 18 ~~C~~C~~~~~~~---a~CPdC~~~Le~LkACGAvdYFC~~c~ 57 (70)
T PF07191_consen 18 YHCEACQKDYKKE---AFCPDCGQPLEVLKACGAVDYFCNHCH 57 (70)
T ss_dssp EEETTT--EEEEE---EE-TTT-SB-EEEEETTEEEEE-TTTT
T ss_pred EECccccccceec---ccCCCcccHHHHHHHhcccceeeccCC
Confidence 4444554443222 234555443322111 34455555554
No 155
>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=59.37 E-value=3.7 Score=20.91 Aligned_cols=8 Identities=25% Similarity=0.999 Sum_probs=1.9
Q ss_pred cccccccc
Q psy7453 79 CKHCHSQL 86 (200)
Q Consensus 79 C~~C~~~f 86 (200)
|..|++..
T Consensus 3 C~~C~~~~ 10 (30)
T PF07649_consen 3 CDACGKPI 10 (30)
T ss_dssp -TTTS---
T ss_pred CCcCCCcC
Confidence 44444433
No 156
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=58.94 E-value=1.7 Score=39.20 Aligned_cols=80 Identities=21% Similarity=0.364 Sum_probs=52.4
Q ss_pred ccccccccccCcccCCCCCC--CCc-ccccChhhhccCHHHHHhchhhhhhhhhcCCCCCce-ecCccCcccCChHHHHH
Q psy7453 90 DLLDHCKTCSYMIRPNANNT--FSP-FCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKF-VCYACDYFSYNIGCMRS 165 (200)
Q Consensus 90 ~~l~~C~~C~~~f~~~~~~~--~~~-~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~-~C~~C~~~f~~~~~l~~ 165 (200)
.++..|+.|-.......... -|| .|..||=+|+- -..|--- |.++.-+.| .|+.|.+.+.+..+-+-
T Consensus 99 pD~a~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPRfTI-i~alPYD--------R~nTsM~~F~lC~~C~~EY~dP~nRRf 169 (750)
T COG0068 99 PDAATCEDCLEEIFDPNSRRYLYPFINCTNCGPRFTI-IEALPYD--------RENTSMADFPLCPFCDKEYKDPLNRRF 169 (750)
T ss_pred CchhhhHHHHHHhcCCCCcceeccccccCCCCcceee-eccCCCC--------cccCccccCcCCHHHHHHhcCcccccc
Confidence 34568999976655444322 244 39999999998 5554433 333333333 69999998888877544
Q ss_pred HHHHcCCCCCcccccCccc
Q psy7453 166 HIRTHTGEKPYACGQCAFR 184 (200)
Q Consensus 166 H~~~H~~~k~~~C~~C~k~ 184 (200)
| ..|..|+.||=.
T Consensus 170 H------AQp~aCp~CGP~ 182 (750)
T COG0068 170 H------AQPIACPKCGPH 182 (750)
T ss_pred c------cccccCcccCCC
Confidence 4 368899999853
No 157
>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 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=58.07 E-value=10 Score=25.78 Aligned_cols=24 Identities=29% Similarity=0.642 Sum_probs=17.9
Q ss_pred eec----CccCcccCChHHHHHHHHHcC
Q psy7453 148 FVC----YACDYFSYNIGCMRSHIRTHT 171 (200)
Q Consensus 148 ~~C----~~C~~~f~~~~~l~~H~~~H~ 171 (200)
|.| ..|+....+...+++|.+.+.
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 677 777777777777777777654
No 159
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=57.77 E-value=5.5 Score=23.64 Aligned_cols=41 Identities=17% Similarity=0.328 Sum_probs=16.7
Q ss_pred ceecCc-cCcccCChHHHHHHHHHcCCCCCccccc----CcccccC
Q psy7453 147 KFVCYA-CDYFSYNIGCMRSHIRTHTGEKPYACGQ----CAFRSAS 187 (200)
Q Consensus 147 ~~~C~~-C~~~f~~~~~l~~H~~~H~~~k~~~C~~----C~k~f~~ 187 (200)
+..|+. |+..-.....|..|...--..++-.|+. |+..+..
T Consensus 9 ~v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRKELDDHLENECPKRPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp EEE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS----S--EEEH
T ss_pred EeeCCCCCcccceeHHHHHHHHHccCCCCcEECCCCCCCCCCccch
Confidence 455555 2222222335556655444445555666 6555543
No 160
>KOG2807|consensus
Probab=57.59 E-value=8.8 Score=31.52 Aligned_cols=33 Identities=18% Similarity=0.391 Sum_probs=22.9
Q ss_pred cccccccCcccCCCCCCCCcccccChhhhccCHHHHHhc
Q psy7453 93 DHCKTCSYMIRPNANNTFSPFCIYCKAVLSTNLNELIEH 131 (200)
Q Consensus 93 ~~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~~~~~l~~H 131 (200)
|.|+.|+... -.-|-.|++|+-+... ...|.+-
T Consensus 277 y~CP~Ckakv-----CsLP~eCpiC~ltLVs-s~hLARS 309 (378)
T KOG2807|consen 277 YFCPQCKAKV-----CSLPIECPICSLTLVS-SPHLARS 309 (378)
T ss_pred eeCCcccCee-----ecCCccCCccceeEec-chHHHHH
Confidence 3577665443 3457789999988888 7777754
No 161
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=57.08 E-value=5.2 Score=32.59 Aligned_cols=91 Identities=15% Similarity=0.207 Sum_probs=54.3
Q ss_pred cccccccCcccCCCCCCCCcccccChhhhccCHHHHHhchhhhhhhhhcCC-----CCCc-------eecCccCcccCCh
Q psy7453 93 DHCKTCSYMIRPNANNTFSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDP-----FRHK-------FVCYACDYFSYNI 160 (200)
Q Consensus 93 ~~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~-----~~k~-------~~C~~C~~~f~~~ 160 (200)
|.|+.|.... -.-|..|+.|+-.... ...|.+- . ..-- .|+| --|-.|.-.|.-.
T Consensus 309 y~CP~CktkV-----CsLPi~CP~Csl~Lil-sthLarS------y-hhL~PLk~f~E~p~~~~~ks~~Cf~CQ~~fp~~ 375 (421)
T COG5151 309 YECPVCKTKV-----CSLPISCPICSLQLIL-STHLARS------Y-HHLYPLKPFVEKPEGTNPKSTHCFVCQGPFPKP 375 (421)
T ss_pred eeCCccccee-----ecCCccCcchhHHHHH-HHHHHHH------H-HhhccCcccccccCCCCCCCccceeccCCCCCC
Confidence 4677775332 2347789999888777 6666653 2 1000 1222 2377777777644
Q ss_pred HHHHHHHHHcCCCCCcccccCcccccCHHHHHHHHhhh
Q psy7453 161 GCMRSHIRTHTGEKPYACGQCAFRSASVAGLHYHLKKT 198 (200)
Q Consensus 161 ~~l~~H~~~H~~~k~~~C~~C~k~f~~~~~L~~H~~~h 198 (200)
..-..-. -+..-.|+|+.|...|-...+.-.|...|
T Consensus 376 ~~~~~~~--~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 376 PVSPFDE--STSSGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred CCCcccc--cccccceechhhhhhhhhhhHHHHHHHHh
Confidence 3211000 11234699999999999888888887665
No 162
>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=56.80 E-value=4.7 Score=20.82 Aligned_cols=25 Identities=16% Similarity=0.377 Sum_probs=10.8
Q ss_pred ecCccCcccCChHHHHHHHHHcCCCCCcccccCccc
Q psy7453 149 VCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFR 184 (200)
Q Consensus 149 ~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~ 184 (200)
+|+.|+..+.. .+.-.|.|+.|+..
T Consensus 4 ~Cp~C~se~~y-----------~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 4 KCPLCGSEYTY-----------EDGELLVCPECGHE 28 (30)
T ss_dssp --TTT-----E-----------E-SSSEEETTTTEE
T ss_pred CCCCCCCccee-----------ccCCEEeCCccccc
Confidence 46777655543 34456777777753
No 163
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=55.98 E-value=7.5 Score=19.11 Aligned_cols=7 Identities=29% Similarity=1.203 Sum_probs=4.0
Q ss_pred ccccccc
Q psy7453 78 LCKHCHS 84 (200)
Q Consensus 78 ~C~~C~~ 84 (200)
.|+.||.
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 4556665
No 164
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.25 E-value=7.1 Score=26.70 Aligned_cols=28 Identities=7% Similarity=-0.172 Sum_probs=15.9
Q ss_pred ccccccCcccCCCCCCCCcccccChhhhcc
Q psy7453 94 HCKTCSYMIRPNANNTFSPFCIYCKAVLST 123 (200)
Q Consensus 94 ~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~ 123 (200)
.|+.||+.|.. .+..|..|+.||+.|..
T Consensus 11 idPetg~KFYD--LNrdPiVsPytG~s~P~ 38 (129)
T COG4530 11 IDPETGKKFYD--LNRDPIVSPYTGKSYPR 38 (129)
T ss_pred cCccccchhhc--cCCCccccCcccccchH
Confidence 34555554443 23456777777777743
No 165
>PRK05580 primosome assembly protein PriA; Validated
Probab=54.78 E-value=10 Score=34.71 Aligned_cols=7 Identities=29% Similarity=0.956 Sum_probs=3.2
Q ss_pred eecCccC
Q psy7453 148 FVCYACD 154 (200)
Q Consensus 148 ~~C~~C~ 154 (200)
..|..||
T Consensus 409 l~Ch~Cg 415 (679)
T PRK05580 409 LRCHHCG 415 (679)
T ss_pred EECCCCc
Confidence 4444444
No 166
>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=54.68 E-value=11 Score=29.10 Aligned_cols=26 Identities=23% Similarity=0.319 Sum_probs=17.2
Q ss_pred CCCceecCccCcccCChHHHHHHHHH
Q psy7453 144 FRHKFVCYACDYFSYNIGCMRSHIRT 169 (200)
Q Consensus 144 ~~k~~~C~~C~~~f~~~~~l~~H~~~ 169 (200)
++..|.|..|+|.|.-..-..+|+..
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhh
Confidence 44557777777777777777777765
No 167
>KOG2893|consensus
Probab=54.54 E-value=2.9 Score=32.69 Aligned_cols=42 Identities=19% Similarity=0.279 Sum_probs=31.1
Q ss_pred ccccccccccccccccccccccCcccCCCCCCCCcccccChhhhccCHHHHHhc
Q psy7453 78 LCKHCHSQLSHLDLLDHCKTCSYMIRPNANNTFSPFCIYCKAVLSTNLNELIEH 131 (200)
Q Consensus 78 ~C~~C~~~f~~~~~l~~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~~~~~l~~H 131 (200)
.|=.|++.|.....|.++ ...|.|+|.+|.|..-+ --.|.-|
T Consensus 12 wcwycnrefddekiliqh-----------qkakhfkchichkkl~s-gpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQH-----------QKAKHFKCHICHKKLFS-GPGLSIH 53 (341)
T ss_pred eeeecccccchhhhhhhh-----------hhhccceeeeehhhhcc-CCCceee
Confidence 377788888888777542 24578999999988766 6667777
No 168
>KOG4167|consensus
Probab=54.45 E-value=3.4 Score=37.49 Aligned_cols=25 Identities=28% Similarity=0.636 Sum_probs=22.9
Q ss_pred ceecCccCcccCChHHHHHHHHHcC
Q psy7453 147 KFVCYACDYFSYNIGCMRSHIRTHT 171 (200)
Q Consensus 147 ~~~C~~C~~~f~~~~~l~~H~~~H~ 171 (200)
-|.|..|++.|....++..||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4999999999999999999999984
No 169
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=54.32 E-value=8.9 Score=23.03 Aligned_cols=27 Identities=22% Similarity=0.519 Sum_probs=16.6
Q ss_pred cccCcccCCCCCCCCcccccChhhhcc
Q psy7453 97 TCSYMIRPNANNTFSPFCIYCKAVLST 123 (200)
Q Consensus 97 ~C~~~f~~~~~~~~~~~C~~C~~~f~~ 123 (200)
.||+.|......++.-.|+.|.+.|..
T Consensus 30 LCGk~wvp~rdp~~~PVCP~Ck~iye~ 56 (58)
T PF11238_consen 30 LCGKVWVPTRDPKPFPVCPECKEIYES 56 (58)
T ss_pred eeCceeCCCCCCCCCCCCcCHHHHHHh
Confidence 456666655555555568888776643
No 170
>KOG4173|consensus
Probab=54.12 E-value=1.9 Score=32.89 Aligned_cols=21 Identities=19% Similarity=0.208 Sum_probs=10.8
Q ss_pred CCccc--ccChhhhccCHHHHHhc
Q psy7453 110 FSPFC--IYCKAVLSTNLNELIEH 131 (200)
Q Consensus 110 ~~~~C--~~C~~~f~~~~~~l~~H 131 (200)
.-|+| +.|+..|.+ ...-..|
T Consensus 143 dMy~ClvEgCt~KFkT-~r~RkdH 165 (253)
T KOG4173|consen 143 DMYQCLVEGCTEKFKT-SRDRKDH 165 (253)
T ss_pred cHHHHHHHhhhhhhhh-hhhhhhH
Confidence 34555 335555555 5555555
No 171
>PF04641 Rtf2: Rtf2 RING-finger
Probab=53.38 E-value=4.1 Score=32.46 Aligned_cols=51 Identities=12% Similarity=0.247 Sum_probs=30.9
Q ss_pred CCCCcccccccccccccccccccccccCcccCCCCCC--CCcccccChhhhcc
Q psy7453 73 TQNHSLCKHCHSQLSHLDLLDHCKTCSYMIRPNANNT--FSPFCIYCKAVLST 123 (200)
Q Consensus 73 ~~~~~~C~~C~~~f~~~~~l~~C~~C~~~f~~~~~~~--~~~~C~~C~~~f~~ 123 (200)
...+|.|++.++.|.....+.-=..||..|......+ +...|+.|++.|..
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k~~~~Cp~c~~~f~~ 162 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELKKSKKCPVCGKPFTE 162 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhcccccccccCCcccc
Confidence 4668999999988865544432234565555433321 23457777777765
No 172
>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=53.33 E-value=7 Score=26.67 Aligned_cols=27 Identities=26% Similarity=0.549 Sum_probs=15.8
Q ss_pred ccccccccccccc-cccccccccCcccC
Q psy7453 78 LCKHCHSQLSHLD-LLDHCKTCSYMIRP 104 (200)
Q Consensus 78 ~C~~C~~~f~~~~-~l~~C~~C~~~f~~ 104 (200)
.|+.|+..|.... .++-|++|+..+..
T Consensus 4 ~CP~C~seytY~dg~~~iCpeC~~EW~~ 31 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPSCLYEWNE 31 (109)
T ss_pred cCCcCCCcceEecCCeeECccccccccc
Confidence 4777766655543 45566666665543
No 173
>PRK10220 hypothetical protein; Provisional
Probab=53.20 E-value=7.6 Score=26.52 Aligned_cols=29 Identities=21% Similarity=0.437 Sum_probs=18.2
Q ss_pred cccccccccccccc-cccccccccCcccCC
Q psy7453 77 SLCKHCHSQLSHLD-LLDHCKTCSYMIRPN 105 (200)
Q Consensus 77 ~~C~~C~~~f~~~~-~l~~C~~C~~~f~~~ 105 (200)
..|+.|+..|.... .++-|++|+..+...
T Consensus 4 P~CP~C~seytY~d~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 4 PHCPKCNSEYTYEDNGMYICPECAHEWNDA 33 (111)
T ss_pred CcCCCCCCcceEcCCCeEECCcccCcCCcc
Confidence 35777776666543 556677777665543
No 174
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=52.27 E-value=7.3 Score=28.34 Aligned_cols=13 Identities=15% Similarity=0.444 Sum_probs=7.2
Q ss_pred CCcccccChhhhcc
Q psy7453 110 FSPFCIYCKAVLST 123 (200)
Q Consensus 110 ~~~~C~~C~~~f~~ 123 (200)
.+|.|. |+..|.+
T Consensus 116 ~~Y~C~-C~q~~l~ 128 (156)
T COG3091 116 YPYRCQ-CQQHYLR 128 (156)
T ss_pred eeEEee-cCCccch
Confidence 355665 6655544
No 175
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=51.69 E-value=8 Score=20.40 Aligned_cols=12 Identities=25% Similarity=0.479 Sum_probs=5.3
Q ss_pred ccccccccccCc
Q psy7453 90 DLLDHCKTCSYM 101 (200)
Q Consensus 90 ~~l~~C~~C~~~ 101 (200)
...+.|..||..
T Consensus 19 ~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 19 DDYEVCIFCGSS 30 (33)
T ss_pred CCeEEcccCCcE
Confidence 333444444443
No 176
>PF12907 zf-met2: Zinc-binding
Probab=50.96 E-value=9.5 Score=21.13 Aligned_cols=20 Identities=30% Similarity=0.584 Sum_probs=9.7
Q ss_pred cccccChhhhcc--CHHHHHhc
Q psy7453 112 PFCIYCKAVLST--NLNELIEH 131 (200)
Q Consensus 112 ~~C~~C~~~f~~--~~~~l~~H 131 (200)
+.|.+|..+|.. +...|..|
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH 23 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEH 23 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHH
Confidence 456666644432 03456666
No 177
>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=50.78 E-value=3.9 Score=23.99 Aligned_cols=16 Identities=13% Similarity=0.193 Sum_probs=4.9
Q ss_pred ceecCccCcccCChHH
Q psy7453 147 KFVCYACDYFSYNIGC 162 (200)
Q Consensus 147 ~~~C~~C~~~f~~~~~ 162 (200)
.|.|+.|...|=-.=+
T Consensus 21 ~y~C~~C~~~FC~dCD 36 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCD 36 (51)
T ss_dssp EE--TTTT--B-HHHH
T ss_pred eEECCCCCCccccCcC
Confidence 3555555544443333
No 178
>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=49.63 E-value=4.5 Score=21.63 Aligned_cols=8 Identities=25% Similarity=0.467 Sum_probs=3.4
Q ss_pred ccccChhh
Q psy7453 113 FCIYCKAV 120 (200)
Q Consensus 113 ~C~~C~~~ 120 (200)
.|..|+..
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 45555443
No 179
>KOG2593|consensus
Probab=49.24 E-value=17 Score=31.07 Aligned_cols=36 Identities=14% Similarity=0.401 Sum_probs=18.4
Q ss_pred CCCceecCccCcccCChHHHHHHHHHcCCCCCcccccCc
Q psy7453 144 FRHKFVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCA 182 (200)
Q Consensus 144 ~~k~~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~ 182 (200)
...-|.|+.|++.|.....++- .-...-.|.|..|+
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~L---~~~~~~~F~C~~C~ 160 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQL---LDNETGEFHCENCG 160 (436)
T ss_pred ccccccCCccccchhhhHHHHh---hcccCceEEEecCC
Confidence 3445666666666665444322 22223346666665
No 180
>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 PF14369 zf-RING_3: zinc-finger
Probab=49.02 E-value=12 Score=19.93 Aligned_cols=10 Identities=20% Similarity=0.747 Sum_probs=4.3
Q ss_pred cccccccccc
Q psy7453 77 SLCKHCHSQL 86 (200)
Q Consensus 77 ~~C~~C~~~f 86 (200)
|-|-.|.+..
T Consensus 3 ywCh~C~~~V 12 (35)
T PF14369_consen 3 YWCHQCNRFV 12 (35)
T ss_pred EeCccCCCEe
Confidence 3444444433
No 182
>PRK04023 DNA polymerase II large subunit; Validated
Probab=48.89 E-value=13 Score=35.36 Aligned_cols=23 Identities=17% Similarity=0.576 Sum_probs=15.1
Q ss_pred CCcccccccccccccccccccccccCc
Q psy7453 75 NHSLCKHCHSQLSHLDLLDHCKTCSYM 101 (200)
Q Consensus 75 ~~~~C~~C~~~f~~~~~l~~C~~C~~~ 101 (200)
....|+.||... ....|+.||..
T Consensus 625 g~RfCpsCG~~t----~~frCP~CG~~ 647 (1121)
T PRK04023 625 GRRKCPSCGKET----FYRRCPFCGTH 647 (1121)
T ss_pred cCccCCCCCCcC----CcccCCCCCCC
Confidence 356788888763 33567777765
No 183
>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=48.60 E-value=10 Score=20.19 Aligned_cols=16 Identities=25% Similarity=0.517 Sum_probs=7.8
Q ss_pred cccccccccccccccc
Q psy7453 77 SLCKHCHSQLSHLDLL 92 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~l 92 (200)
-.|..|++.|.....+
T Consensus 4 ~~C~eC~~~f~dSyL~ 19 (34)
T PF01286_consen 4 PKCDECGKPFMDSYLL 19 (34)
T ss_dssp EE-TTT--EES-SSCC
T ss_pred chHhHhCCHHHHHHHH
Confidence 3577788887776544
No 184
>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=48.15 E-value=8.6 Score=23.64 Aligned_cols=28 Identities=14% Similarity=0.287 Sum_probs=14.1
Q ss_pred ccccccCcccCCCCCCCCcccccChhhhc
Q psy7453 94 HCKTCSYMIRPNANNTFSPFCIYCKAVLS 122 (200)
Q Consensus 94 ~C~~C~~~f~~~~~~~~~~~C~~C~~~f~ 122 (200)
.|+.||..... ....+.|.|+.||..+.
T Consensus 30 ~C~~CG~~~~~-~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 30 TCPRCGHRNKK-RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CccCccccccc-ccccceEEcCCCCCEEC
Confidence 35555544333 22345566666666543
No 185
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=48.10 E-value=13 Score=20.29 Aligned_cols=18 Identities=22% Similarity=0.421 Sum_probs=13.2
Q ss_pred Cccccccccccccccccc
Q psy7453 76 HSLCKHCHSQLSHLDLLD 93 (200)
Q Consensus 76 ~~~C~~C~~~f~~~~~l~ 93 (200)
|+.|..|++.|-..-.+.
T Consensus 12 ~f~C~~C~~~FC~~HR~~ 29 (39)
T smart00154 12 GFKCRHCGNLFCGEHRLP 29 (39)
T ss_pred CeECCccCCccccccCCc
Confidence 678888888887765543
No 186
>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=47.82 E-value=8.5 Score=21.97 Aligned_cols=24 Identities=17% Similarity=0.463 Sum_probs=11.4
Q ss_pred cccccccccccccccccccccCccc
Q psy7453 79 CKHCHSQLSHLDLLDHCKTCSYMIR 103 (200)
Q Consensus 79 C~~C~~~f~~~~~l~~C~~C~~~f~ 103 (200)
|..|+. ......+..|..|+..|.
T Consensus 2 C~vC~~-~~~~~~~i~C~~C~~~~H 25 (51)
T PF00628_consen 2 CPVCGQ-SDDDGDMIQCDSCNRWYH 25 (51)
T ss_dssp BTTTTS-SCTTSSEEEBSTTSCEEE
T ss_pred CcCCCC-cCCCCCeEEcCCCChhhC
Confidence 445555 233334445555555444
No 187
>PF15269 zf-C2H2_7: Zinc-finger
Probab=47.47 E-value=14 Score=20.94 Aligned_cols=21 Identities=38% Similarity=0.754 Sum_probs=10.1
Q ss_pred cccccCcccccCHHHHHHHHh
Q psy7453 176 YACGQCAFRSASVAGLHYHLK 196 (200)
Q Consensus 176 ~~C~~C~k~f~~~~~L~~H~~ 196 (200)
|+|=+|..+...++.|-.||+
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 344444444444555544443
No 188
>PRK00420 hypothetical protein; Validated
Probab=47.27 E-value=10 Score=26.18 Aligned_cols=27 Identities=19% Similarity=0.167 Sum_probs=14.6
Q ss_pred cccccccccccc-cccccccccccCccc
Q psy7453 77 SLCKHCHSQLSH-LDLLDHCKTCSYMIR 103 (200)
Q Consensus 77 ~~C~~C~~~f~~-~~~l~~C~~C~~~f~ 103 (200)
-.|+.||..+.. ...-..|+.||....
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCeee
Confidence 347777755544 344445666665433
No 189
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=46.93 E-value=11 Score=21.95 Aligned_cols=11 Identities=18% Similarity=0.102 Sum_probs=5.5
Q ss_pred CCcccccChhh
Q psy7453 110 FSPFCIYCKAV 120 (200)
Q Consensus 110 ~~~~C~~C~~~ 120 (200)
..+.|..||.+
T Consensus 36 ~r~~C~~Cgyt 46 (50)
T PRK00432 36 DRWHCGKCGYT 46 (50)
T ss_pred CcEECCCcCCE
Confidence 34555555543
No 190
>PRK11032 hypothetical protein; Provisional
Probab=46.16 E-value=11 Score=27.79 Aligned_cols=29 Identities=21% Similarity=0.555 Sum_probs=23.0
Q ss_pred CCCCccccccc--ccccccccccccccccCc
Q psy7453 73 TQNHSLCKHCH--SQLSHLDLLDHCKTCSYM 101 (200)
Q Consensus 73 ~~~~~~C~~C~--~~f~~~~~l~~C~~C~~~ 101 (200)
|...+.|..|| ..|.....|-.|+.||..
T Consensus 121 g~G~LvC~~Cg~~~~~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 121 GLGNLVCEKCHHHLAFYTPEVLPLCPKCGHD 151 (160)
T ss_pred ecceEEecCCCCEEEecCCCcCCCCCCCCCC
Confidence 45579999998 567777888899999865
No 191
>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=46.01 E-value=11 Score=29.29 Aligned_cols=26 Identities=15% Similarity=0.241 Sum_probs=20.8
Q ss_pred CCCCcccccCcccccCHHHHHHHHhh
Q psy7453 172 GEKPYACGQCAFRSASVAGLHYHLKK 197 (200)
Q Consensus 172 ~~k~~~C~~C~k~f~~~~~L~~H~~~ 197 (200)
++..|.|++|+|.|.-..-.++|+..
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhh
Confidence 44569999999999999999999875
No 192
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=45.60 E-value=8.7 Score=26.63 Aligned_cols=27 Identities=19% Similarity=0.527 Sum_probs=21.4
Q ss_pred CCcccccccccccccccccccccccCc
Q psy7453 75 NHSLCKHCHSQLSHLDLLDHCKTCSYM 101 (200)
Q Consensus 75 ~~~~C~~C~~~f~~~~~l~~C~~C~~~ 101 (200)
....|..|+..+......+.||.||-.
T Consensus 69 ~~~~C~~C~~~~~~e~~~~~CP~C~s~ 95 (115)
T COG0375 69 AECWCLDCGQEVELEELDYRCPKCGSI 95 (115)
T ss_pred cEEEeccCCCeecchhheeECCCCCCC
Confidence 357899999888888777779999844
No 193
>PRK04023 DNA polymerase II large subunit; Validated
Probab=45.55 E-value=14 Score=35.16 Aligned_cols=34 Identities=18% Similarity=0.525 Sum_probs=16.4
Q ss_pred cccccccccccccccccccccccCcccCCCCCCCCcccccChhh
Q psy7453 77 SLCKHCHSQLSHLDLLDHCKTCSYMIRPNANNTFSPFCIYCKAV 120 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~l~~C~~C~~~f~~~~~~~~~~~C~~C~~~ 120 (200)
+.|+.||.. ....+.|+.|+.... ++.|+.||..
T Consensus 639 frCP~CG~~---Te~i~fCP~CG~~~~-------~y~CPKCG~E 672 (1121)
T PRK04023 639 RRCPFCGTH---TEPVYRCPRCGIEVE-------EDECEKCGRE 672 (1121)
T ss_pred ccCCCCCCC---CCcceeCccccCcCC-------CCcCCCCCCC
Confidence 556666654 123345666643321 2446666543
No 194
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=45.27 E-value=12 Score=30.53 Aligned_cols=47 Identities=13% Similarity=0.199 Sum_probs=31.6
Q ss_pred cccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccCChHHHHHHHHHc
Q psy7453 114 CIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSYNIGCMRSHIRTH 170 (200)
Q Consensus 114 C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~~~~~l~~H~~~H 170 (200)
|-.|.-.|.- +..| .-..-+....|.|+.|-..|-..-+.-.|...|
T Consensus 365 Cf~CQ~~fp~----~~~~------~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 365 CFVCQGPFPK----PPVS------PFDESTSSGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred ceeccCCCCC----CCCC------cccccccccceechhhhhhhhhhhHHHHHHHHh
Confidence 7777777766 2333 212223345699999999998888888887766
No 195
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.70 E-value=3.8 Score=26.01 Aligned_cols=12 Identities=17% Similarity=0.564 Sum_probs=6.9
Q ss_pred cccccccccccc
Q psy7453 77 SLCKHCHSQLSH 88 (200)
Q Consensus 77 ~~C~~C~~~f~~ 88 (200)
|.|..|+..|.-
T Consensus 13 Y~c~~cg~~~dv 24 (82)
T COG2331 13 YECTECGNRFDV 24 (82)
T ss_pred EeecccchHHHH
Confidence 566666655543
No 196
>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=43.72 E-value=12 Score=21.21 Aligned_cols=8 Identities=50% Similarity=1.173 Sum_probs=4.8
Q ss_pred cccccccc
Q psy7453 77 SLCKHCHS 84 (200)
Q Consensus 77 ~~C~~C~~ 84 (200)
+.|+.||.
T Consensus 19 ~~CP~Cg~ 26 (46)
T PF12760_consen 19 FVCPHCGS 26 (46)
T ss_pred CCCCCCCC
Confidence 45666664
No 197
>KOG2593|consensus
Probab=43.61 E-value=14 Score=31.58 Aligned_cols=39 Identities=23% Similarity=0.330 Sum_probs=26.3
Q ss_pred CCCCcccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCccc
Q psy7453 108 NTFSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFS 157 (200)
Q Consensus 108 ~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f 157 (200)
....|.|+.|.+.|.. ...++ ......-.|.|..|+-..
T Consensus 125 ~~~~Y~Cp~C~kkyt~-Lea~~----------L~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTS-LEALQ----------LLDNETGEFHCENCGGEL 163 (436)
T ss_pred ccccccCCccccchhh-hHHHH----------hhcccCceEEEecCCCch
Confidence 4467999999999988 55544 223334468999987543
No 198
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=43.37 E-value=11 Score=25.39 Aligned_cols=30 Identities=13% Similarity=0.354 Sum_probs=17.9
Q ss_pred CCCcccccccccccccccc--------cccccccCccc
Q psy7453 74 QNHSLCKHCHSQLSHLDLL--------DHCKTCSYMIR 103 (200)
Q Consensus 74 ~~~~~C~~C~~~f~~~~~l--------~~C~~C~~~f~ 103 (200)
++.|.|+.|+..-...-.+ ..|..||..|.
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred CceEecCccCCeeeeEEEEEecCceeEEEcccCcceEE
Confidence 4568999998765543333 24555555543
No 199
>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=43.02 E-value=17 Score=32.04 Aligned_cols=24 Identities=21% Similarity=0.506 Sum_probs=14.6
Q ss_pred ccccccccccCcccCCCCCCCCcccccChh
Q psy7453 90 DLLDHCKTCSYMIRPNANNTFSPFCIYCKA 119 (200)
Q Consensus 90 ~~l~~C~~C~~~f~~~~~~~~~~~C~~C~~ 119 (200)
.....|..||... ..|..|+.|+.
T Consensus 238 ~~~l~Ch~Cg~~~------~~~~~Cp~C~s 261 (505)
T TIGR00595 238 EGKLRCHYCGYQE------PIPKTCPQCGS 261 (505)
T ss_pred CCeEEcCCCcCcC------CCCCCCCCCCC
Confidence 3344677777443 23667888875
No 200
>PRK05978 hypothetical protein; Provisional
Probab=41.77 E-value=16 Score=26.55 Aligned_cols=30 Identities=23% Similarity=0.508 Sum_probs=15.5
Q ss_pred cccccccccccccccc---cccccccCcccCCC
Q psy7453 77 SLCKHCHSQLSHLDLL---DHCKTCSYMIRPNA 106 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~l---~~C~~C~~~f~~~~ 106 (200)
-.|+.||+.=--...| ..|+.||..|....
T Consensus 34 grCP~CG~G~LF~g~Lkv~~~C~~CG~~~~~~~ 66 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPVDHCAACGEDFTHHR 66 (148)
T ss_pred CcCCCCCCCcccccccccCCCccccCCccccCC
Confidence 3577776432222223 25777776665543
No 201
>KOG4124|consensus
Probab=41.49 E-value=3.1 Score=34.38 Aligned_cols=50 Identities=32% Similarity=0.635 Sum_probs=33.7
Q ss_pred CceecCc--cCcccCChHHHHHHHHH-c--------------C----CCCCcccccCcccccCHHHHHHHH
Q psy7453 146 HKFVCYA--CDYFSYNIGCMRSHIRT-H--------------T----GEKPYACGQCAFRSASVAGLHYHL 195 (200)
Q Consensus 146 k~~~C~~--C~~~f~~~~~l~~H~~~-H--------------~----~~k~~~C~~C~k~f~~~~~L~~H~ 195 (200)
++|+|++ |.+...+...|+-|... | + ..|+|.|++|.+.++-...|..|+
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 4666743 77777666666555321 2 1 258999999999998877777664
No 202
>PRK14873 primosome assembly protein PriA; Provisional
Probab=40.40 E-value=17 Score=33.21 Aligned_cols=21 Identities=19% Similarity=0.395 Sum_probs=11.3
Q ss_pred cccccccCcccCCCCCCCCcccccChhh
Q psy7453 93 DHCKTCSYMIRPNANNTFSPFCIYCKAV 120 (200)
Q Consensus 93 ~~C~~C~~~f~~~~~~~~~~~C~~C~~~ 120 (200)
-.|..||.. ..|..|+.||-.
T Consensus 411 l~Ch~CG~~-------~~p~~Cp~Cgs~ 431 (665)
T PRK14873 411 PRCRWCGRA-------APDWRCPRCGSD 431 (665)
T ss_pred eECCCCcCC-------CcCccCCCCcCC
Confidence 356666642 125667777643
No 203
>KOG2272|consensus
Probab=40.11 E-value=18 Score=28.66 Aligned_cols=15 Identities=20% Similarity=0.485 Sum_probs=8.9
Q ss_pred Ccccccccccccccc
Q psy7453 76 HSLCKHCHSQLSHLD 90 (200)
Q Consensus 76 ~~~C~~C~~~f~~~~ 90 (200)
-|.|+.|.+...+..
T Consensus 99 CF~Cd~Cn~~Lad~g 113 (332)
T KOG2272|consen 99 CFRCDLCNKHLADQG 113 (332)
T ss_pred cchhHHHHHHHhhhh
Confidence 466676766655544
No 204
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=40.05 E-value=13 Score=30.16 Aligned_cols=29 Identities=24% Similarity=0.510 Sum_probs=19.7
Q ss_pred Cccccccccccccc---ccccccccccCcccC
Q psy7453 76 HSLCKHCHSQLSHL---DLLDHCKTCSYMIRP 104 (200)
Q Consensus 76 ~~~C~~C~~~f~~~---~~l~~C~~C~~~f~~ 104 (200)
-.+|+.|+.....+ .+++.|+.||..|.-
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl 57 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHMRM 57 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcCcC
Confidence 56788888776665 345677777776654
No 205
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=39.22 E-value=17 Score=31.11 Aligned_cols=28 Identities=14% Similarity=0.306 Sum_probs=18.3
Q ss_pred ccccccCcccCCCCCCCCcccccChhhhcc
Q psy7453 94 HCKTCSYMIRPNANNTFSPFCIYCKAVLST 123 (200)
Q Consensus 94 ~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~ 123 (200)
.|+.||..-.+.. ..-|+|..||..+..
T Consensus 352 ~Cp~Cg~~m~S~G--~~g~rC~kCg~~~~~ 379 (421)
T COG1571 352 VCPRCGGRMKSAG--RNGFRCKKCGTRARE 379 (421)
T ss_pred CCCccCCchhhcC--CCCcccccccccCCc
Confidence 5777776644433 337788888877766
No 206
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=38.87 E-value=14 Score=28.07 Aligned_cols=30 Identities=23% Similarity=0.417 Sum_probs=19.9
Q ss_pred Cccccccccccccccccc-------------ccccccCcccCC
Q psy7453 76 HSLCKHCHSQLSHLDLLD-------------HCKTCSYMIRPN 105 (200)
Q Consensus 76 ~~~C~~C~~~f~~~~~l~-------------~C~~C~~~f~~~ 105 (200)
...|+.||..+.....++ .|..||..+...
T Consensus 14 ~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV 56 (201)
T COG1779 14 RIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDV 56 (201)
T ss_pred eecCCcccceeeEEEeeecCCccceEEEEEEEccccCCcccce
Confidence 356999998777766664 466666655543
No 207
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=38.76 E-value=6.8 Score=31.88 Aligned_cols=29 Identities=17% Similarity=0.490 Sum_probs=17.1
Q ss_pred Ccccccccccccccc---cccccccccCcccC
Q psy7453 76 HSLCKHCHSQLSHLD---LLDHCKTCSYMIRP 104 (200)
Q Consensus 76 ~~~C~~C~~~f~~~~---~l~~C~~C~~~f~~ 104 (200)
..+|+.|+.....+. +++.|+.|+..|.-
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rl 69 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQCGYHLKM 69 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCCCCCCcCC
Confidence 456777776665543 34566666665543
No 208
>KOG4218|consensus
Probab=38.75 E-value=9.4 Score=31.63 Aligned_cols=39 Identities=21% Similarity=0.394 Sum_probs=27.1
Q ss_pred ccccccccc-cccccccccccccCcccCCCCCCCCccccc
Q psy7453 78 LCKHCHSQL-SHLDLLDHCKTCSYMIRPNANNTFSPFCIY 116 (200)
Q Consensus 78 ~C~~C~~~f-~~~~~l~~C~~C~~~f~~~~~~~~~~~C~~ 116 (200)
.|++||... .....|..|+.|.--|.+.-.+.|.|.|..
T Consensus 17 lCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e 56 (475)
T KOG4218|consen 17 LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSE 56 (475)
T ss_pred ccccccCccccceeeeeehhhhhhHHHHHhhcCcceeccc
Confidence 488887543 334566788888877777666777777753
No 209
>KOG2785|consensus
Probab=38.65 E-value=33 Score=28.88 Aligned_cols=51 Identities=24% Similarity=0.511 Sum_probs=40.9
Q ss_pred CcccccChhhhccCHHHHHhchhhhhhhhhcCCCC-----------------------CceecCccC---cccCChHHHH
Q psy7453 111 SPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFR-----------------------HKFVCYACD---YFSYNIGCMR 164 (200)
Q Consensus 111 ~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~-----------------------k~~~C~~C~---~~f~~~~~l~ 164 (200)
|-.|-.|++.+.+ ...-..| | ..+.|- .-|.|-.|+ +.|.+..+.+
T Consensus 166 Pt~CLfC~~~~k~-~e~~~~H------M-~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr 237 (390)
T KOG2785|consen 166 PTDCLFCDKKSKS-LEENLKH------M-FKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVR 237 (390)
T ss_pred CcceeecCCCccc-HHHHHHH------H-hhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHH
Confidence 5679999999999 8888889 8 554431 137888888 9999999999
Q ss_pred HHHHH
Q psy7453 165 SHIRT 169 (200)
Q Consensus 165 ~H~~~ 169 (200)
.||..
T Consensus 238 ~HM~~ 242 (390)
T KOG2785|consen 238 AHMRD 242 (390)
T ss_pred HHHhh
Confidence 99874
No 210
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=37.98 E-value=26 Score=20.47 Aligned_cols=13 Identities=15% Similarity=0.204 Sum_probs=7.3
Q ss_pred eecCccCcccCCh
Q psy7453 148 FVCYACDYFSYNI 160 (200)
Q Consensus 148 ~~C~~C~~~f~~~ 160 (200)
++|+.||..|...
T Consensus 29 W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 29 WKCPKCGHEWKAS 41 (55)
T ss_pred EECCCCCCeeEcc
Confidence 5666666555544
No 211
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=37.91 E-value=7.2 Score=31.59 Aligned_cols=33 Identities=12% Similarity=0.370 Sum_probs=25.2
Q ss_pred cccccccccCcccCCCCCCCCcccccChhhhcc
Q psy7453 91 LLDHCKTCSYMIRPNANNTFSPFCIYCKAVLST 123 (200)
Q Consensus 91 ~l~~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~ 123 (200)
.+.+|+.|+.....+...+..+.|+.|+..|.-
T Consensus 25 ~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl 57 (285)
T TIGR00515 25 VWTKCPKCGQVLYTKELERNLEVCPKCDHHMRM 57 (285)
T ss_pred CeeECCCCcchhhHHHHHhhCCCCCCCCCcCcC
Confidence 467899999887665545556789999988875
No 212
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=37.63 E-value=18 Score=22.37 Aligned_cols=29 Identities=21% Similarity=0.479 Sum_probs=19.0
Q ss_pred ccccccc---ccccccccccccccccCcccCC
Q psy7453 77 SLCKHCH---SQLSHLDLLDHCKTCSYMIRPN 105 (200)
Q Consensus 77 ~~C~~C~---~~f~~~~~l~~C~~C~~~f~~~ 105 (200)
.+|+.|+ -.|...+....|..||......
T Consensus 20 VkCpdC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 20 VKCPDCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred EECCCCCCEEEEeccCceEEEecccccEEEec
Confidence 4577776 4566666666777777665443
No 213
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=37.31 E-value=12 Score=24.76 Aligned_cols=9 Identities=22% Similarity=0.803 Sum_probs=5.9
Q ss_pred Ccccccccc
Q psy7453 76 HSLCKHCHS 84 (200)
Q Consensus 76 ~~~C~~C~~ 84 (200)
.|.|+.|++
T Consensus 36 ~y~CpfCgk 44 (90)
T PTZ00255 36 KYFCPFCGK 44 (90)
T ss_pred CccCCCCCC
Confidence 466777764
No 214
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=37.04 E-value=7.4 Score=31.64 Aligned_cols=28 Identities=25% Similarity=0.586 Sum_probs=15.8
Q ss_pred Ccccccccccccccc---cccccccccCccc
Q psy7453 76 HSLCKHCHSQLSHLD---LLDHCKTCSYMIR 103 (200)
Q Consensus 76 ~~~C~~C~~~f~~~~---~l~~C~~C~~~f~ 103 (200)
-.+|+.|+.....+. +++.|+.|+..|.
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 57 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHHMR 57 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCCee
Confidence 456777776555443 3445666665554
No 215
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=36.98 E-value=40 Score=18.58 Aligned_cols=23 Identities=17% Similarity=0.265 Sum_probs=12.9
Q ss_pred eecCccCcccCC--hHHHHHHHHHc
Q psy7453 148 FVCYACDYFSYN--IGCMRSHIRTH 170 (200)
Q Consensus 148 ~~C~~C~~~f~~--~~~l~~H~~~H 170 (200)
-+|+.||..+.. ..+-..|.+-|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 467777766543 34455555555
No 216
>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=36.78 E-value=11 Score=27.28 Aligned_cols=32 Identities=28% Similarity=0.570 Sum_probs=20.4
Q ss_pred ceecCccCcccCChHHHHHHHHHcCCCCCcccccCccccc
Q psy7453 147 KFVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFRSA 186 (200)
Q Consensus 147 ~~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~f~ 186 (200)
.|.|..|+..+. +|.++ ....|.|..|+..+.
T Consensus 123 ~~~C~~C~~~~~------r~~~~--~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYK------RHRRS--KRKRYRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEee------eeccc--chhhEECCCCCCEEE
Confidence 578888887764 23232 234488888886654
No 217
>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=36.66 E-value=17 Score=24.39 Aligned_cols=17 Identities=12% Similarity=0.077 Sum_probs=9.6
Q ss_pred hcCCCCCceecCccCccc
Q psy7453 140 RTDPFRHKFVCYACDYFS 157 (200)
Q Consensus 140 ~~h~~~k~~~C~~C~~~f 157 (200)
..+.+ +|..|..||..|
T Consensus 73 ~l~~g-~~~rC~eCG~~f 89 (97)
T cd00924 73 WLEKG-KPKRCPECGHVF 89 (97)
T ss_pred EEeCC-CceeCCCCCcEE
Confidence 44444 466666666555
No 218
>KOG0782|consensus
Probab=36.62 E-value=2.1 Score=37.69 Aligned_cols=94 Identities=14% Similarity=0.230 Sum_probs=52.3
Q ss_pred ccccccccccccccccccCcccCCCC---CCCCcccccC----hhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccC
Q psy7453 82 CHSQLSHLDLLDHCKTCSYMIRPNAN---NTFSPFCIYC----KAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACD 154 (200)
Q Consensus 82 C~~~f~~~~~l~~C~~C~~~f~~~~~---~~~~~~C~~C----~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~ 154 (200)
|.-.|.....-++|..|.....+.-. ..-+|.|..- |-.-.. .+.+.+| . -+|.....=+|..||
T Consensus 189 C~~r~~kS~~rRkCAaCkIVvHT~CieqLeKiNfrCKptFRe~gsr~~r-E~~fvrH------H-WVHrrRqeGkC~~Cg 260 (1004)
T KOG0782|consen 189 CRVRFAKSGERRKCAACKIVVHTNCIEQLEKINFRCKPTFREYGSRKTR-ESGFVRH------H-WVHRRRQEGKCNTCG 260 (1004)
T ss_pred HHHHHhhhhhhccceeeeEEEechHHHHHHHhccccccchhhccccCcc-cccchHH------h-HhhHhhhccccchhh
Confidence 55555555555567777654332211 2335556421 111112 3467777 6 666655555799999
Q ss_pred cccCChHHHHHHHHHcCCCC-CcccccCcccccCHH
Q psy7453 155 YFSYNIGCMRSHIRTHTGEK-PYACGQCAFRSASVA 189 (200)
Q Consensus 155 ~~f~~~~~l~~H~~~H~~~k-~~~C~~C~k~f~~~~ 189 (200)
|.|..+-.+ |..|- ...|.-|.++|..+.
T Consensus 261 KgFQQKf~F------hsKEivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 261 KGFQQKFFF------HSKEIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred hhhhhheee------ccccEEEEEehHHHHHhhcch
Confidence 988766443 43332 356888888776665
No 219
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=36.58 E-value=23 Score=20.90 Aligned_cols=12 Identities=17% Similarity=0.334 Sum_probs=6.9
Q ss_pred cccccChhhhcc
Q psy7453 112 PFCIYCKAVLST 123 (200)
Q Consensus 112 ~~C~~C~~~f~~ 123 (200)
..|+.|+..|-.
T Consensus 41 ~~C~~C~~~fC~ 52 (64)
T PF01485_consen 41 VTCPSCGTEFCF 52 (64)
T ss_dssp CCTTSCCSEECS
T ss_pred eECCCCCCcCcc
Confidence 556666655544
No 220
>KOG3408|consensus
Probab=36.37 E-value=26 Score=24.50 Aligned_cols=21 Identities=19% Similarity=0.717 Sum_probs=11.5
Q ss_pred eecCccCcccCChHHHHHHHH
Q psy7453 148 FVCYACDYFSYNIGCMRSHIR 168 (200)
Q Consensus 148 ~~C~~C~~~f~~~~~l~~H~~ 168 (200)
|-|-.|.+-|.+...|..|.+
T Consensus 58 fyCi~CaRyFi~~~~l~~H~k 78 (129)
T KOG3408|consen 58 FYCIECARYFIDAKALKTHFK 78 (129)
T ss_pred eehhhhhhhhcchHHHHHHHh
Confidence 555555555555555555544
No 221
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=36.12 E-value=27 Score=34.16 Aligned_cols=40 Identities=20% Similarity=0.541 Sum_probs=21.8
Q ss_pred cccccccccccccccccccccccCcccCCCCCCCCcccccChhhh
Q psy7453 77 SLCKHCHSQLSHLDLLDHCKTCSYMIRPNANNTFSPFCIYCKAVL 121 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~l~~C~~C~~~f~~~~~~~~~~~C~~C~~~f 121 (200)
..|+.||..... .+.|+.||........+ ...|+.|+...
T Consensus 680 ~fCP~CGs~te~---vy~CPsCGaev~~des~--a~~CP~CGtpl 719 (1337)
T PRK14714 680 NRCPDCGTHTEP---VYVCPDCGAEVPPDESG--RVECPRCDVEL 719 (1337)
T ss_pred ccCcccCCcCCC---ceeCccCCCccCCCccc--cccCCCCCCcc
Confidence 367777765432 34677777654432222 44577776443
No 222
>COG1773 Rubredoxin [Energy production and conversion]
Probab=35.86 E-value=16 Score=21.77 Aligned_cols=12 Identities=17% Similarity=0.719 Sum_probs=7.9
Q ss_pred CcccccCccccc
Q psy7453 175 PYACGQCAFRSA 186 (200)
Q Consensus 175 ~~~C~~C~k~f~ 186 (200)
.|+|.+||..|.
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 467777776664
No 223
>KOG3507|consensus
Probab=35.60 E-value=14 Score=22.22 Aligned_cols=13 Identities=15% Similarity=0.120 Sum_probs=7.7
Q ss_pred CcccccChhhhcc
Q psy7453 111 SPFCIYCKAVLST 123 (200)
Q Consensus 111 ~~~C~~C~~~f~~ 123 (200)
.++|.+||.+.-.
T Consensus 37 ~irCReCG~RIly 49 (62)
T KOG3507|consen 37 VIRCRECGYRILY 49 (62)
T ss_pred cEehhhcchHHHH
Confidence 4566666665544
No 224
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=35.59 E-value=17 Score=25.49 Aligned_cols=26 Identities=15% Similarity=0.303 Sum_probs=15.6
Q ss_pred CCCcccccccccccccc-c------ccccccccC
Q psy7453 74 QNHSLCKHCHSQLSHLD-L------LDHCKTCSY 100 (200)
Q Consensus 74 ~~~~~C~~C~~~f~~~~-~------l~~C~~C~~ 100 (200)
...+.| .|+..|.... . ...||.||-
T Consensus 68 p~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs 100 (124)
T PRK00762 68 PVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGN 100 (124)
T ss_pred CeeEEe-eCcCcccccccchhccccCCcCcCCCC
Confidence 335778 8888776431 1 145777763
No 225
>KOG2071|consensus
Probab=35.50 E-value=24 Score=31.38 Aligned_cols=26 Identities=19% Similarity=0.464 Sum_probs=21.2
Q ss_pred CCCcccccCcccccCHHHHHHHHhhh
Q psy7453 173 EKPYACGQCAFRSASVAGLHYHLKKT 198 (200)
Q Consensus 173 ~k~~~C~~C~k~f~~~~~L~~H~~~h 198 (200)
..+-+|..||.+|........||-.|
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhh
Confidence 45688999999998888888888776
No 226
>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=35.29 E-value=13 Score=19.62 Aligned_cols=19 Identities=16% Similarity=0.349 Sum_probs=10.7
Q ss_pred cccccChhhhccCHHHHHhch
Q psy7453 112 PFCIYCKAVLSTNLNELIEHC 132 (200)
Q Consensus 112 ~~C~~C~~~f~~~~~~l~~H~ 132 (200)
+.|+.|++.+.. +.+..|+
T Consensus 5 ~~C~nC~R~v~a--~RfA~HL 23 (33)
T PF08209_consen 5 VECPNCGRPVAA--SRFAPHL 23 (33)
T ss_dssp EE-TTTSSEEEG--GGHHHHH
T ss_pred EECCCCcCCcch--hhhHHHH
Confidence 567777766554 4456663
No 227
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=35.20 E-value=22 Score=30.46 Aligned_cols=32 Identities=19% Similarity=0.428 Sum_probs=26.2
Q ss_pred Cccccccccccccccc-ccccccccCcccCCCC
Q psy7453 76 HSLCKHCHSQLSHLDL-LDHCKTCSYMIRPNAN 107 (200)
Q Consensus 76 ~~~C~~C~~~f~~~~~-l~~C~~C~~~f~~~~~ 107 (200)
.-.|+.||....+... -++|+.||..+.....
T Consensus 350 ~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~~ 382 (421)
T COG1571 350 NPVCPRCGGRMKSAGRNGFRCKKCGTRARETLI 382 (421)
T ss_pred CCCCCccCCchhhcCCCCcccccccccCCcccc
Confidence 3579999999998865 7899999998876544
No 228
>PRK06260 threonine synthase; Validated
Probab=35.18 E-value=19 Score=30.59 Aligned_cols=26 Identities=15% Similarity=0.544 Sum_probs=19.3
Q ss_pred cccccccccccccccccccccccCcc
Q psy7453 77 SLCKHCHSQLSHLDLLDHCKTCSYMI 102 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~l~~C~~C~~~f 102 (200)
+.|..||..|......+.|+.|+-.+
T Consensus 4 ~~C~~cg~~~~~~~~~~~Cp~cg~~l 29 (397)
T PRK06260 4 LKCIECGKEYDPDEIIYTCPECGGLL 29 (397)
T ss_pred EEECCCCCCCCCCCccccCCCCCCeE
Confidence 67888888887666667888887543
No 229
>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=35.16 E-value=13 Score=20.38 Aligned_cols=12 Identities=17% Similarity=0.520 Sum_probs=4.9
Q ss_pred CCCceecCccCc
Q psy7453 144 FRHKFVCYACDY 155 (200)
Q Consensus 144 ~~k~~~C~~C~~ 155 (200)
+.+.+.|..|+.
T Consensus 21 ~~~~w~C~~C~~ 32 (40)
T PF04810_consen 21 GGKTWICNFCGT 32 (40)
T ss_dssp TTTEEEETTT--
T ss_pred CCCEEECcCCCC
Confidence 334455555543
No 230
>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=35.03 E-value=11 Score=24.90 Aligned_cols=10 Identities=20% Similarity=0.766 Sum_probs=6.4
Q ss_pred Cccccccccc
Q psy7453 76 HSLCKHCHSQ 85 (200)
Q Consensus 76 ~~~C~~C~~~ 85 (200)
.|.|+.|++.
T Consensus 35 ~y~CpfCgk~ 44 (91)
T TIGR00280 35 KYVCPFCGKK 44 (91)
T ss_pred CccCCCCCCC
Confidence 4677777643
No 231
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=35.02 E-value=17 Score=26.45 Aligned_cols=11 Identities=27% Similarity=0.670 Sum_probs=6.9
Q ss_pred ccccChhhhcc
Q psy7453 113 FCIYCKAVLST 123 (200)
Q Consensus 113 ~C~~C~~~f~~ 123 (200)
.|+.|+..|.+
T Consensus 30 eC~~C~~RFTT 40 (156)
T COG1327 30 ECLECGERFTT 40 (156)
T ss_pred cccccccccch
Confidence 46666666665
No 232
>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=34.92 E-value=16 Score=24.21 Aligned_cols=28 Identities=18% Similarity=0.337 Sum_probs=15.3
Q ss_pred Ccccccccccccccc--cccccccccCccc
Q psy7453 76 HSLCKHCHSQLSHLD--LLDHCKTCSYMIR 103 (200)
Q Consensus 76 ~~~C~~C~~~f~~~~--~l~~C~~C~~~f~ 103 (200)
.|.|+.|++.-.... -+-.|..|++.|.
T Consensus 35 ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 35 KYTCPFCGKTSVKRVATGIWKCKKCGKKFA 64 (90)
T ss_dssp -BEESSSSSSEEEEEETTEEEETTTTEEEE
T ss_pred CCcCCCCCCceeEEeeeEEeecCCCCCEEe
Confidence 578888887543322 1235666665554
No 233
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=34.89 E-value=18 Score=27.08 Aligned_cols=23 Identities=22% Similarity=0.574 Sum_probs=13.3
Q ss_pred cccccccccccccccccccccccCc
Q psy7453 77 SLCKHCHSQLSHLDLLDHCKTCSYM 101 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~l~~C~~C~~~ 101 (200)
+.|.-|++.|. .....|+.||..
T Consensus 140 ~rC~GC~~~f~--~~~~~Cp~CG~~ 162 (177)
T COG1439 140 LRCHGCKRIFP--EPKDFCPICGSP 162 (177)
T ss_pred EEEecCceecC--CCCCcCCCCCCc
Confidence 55666666666 333446666644
No 234
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=34.75 E-value=21 Score=25.28 Aligned_cols=15 Identities=13% Similarity=0.290 Sum_probs=9.3
Q ss_pred CCCcccccChhhhcc
Q psy7453 109 TFSPFCIYCKAVLST 123 (200)
Q Consensus 109 ~~~~~C~~C~~~f~~ 123 (200)
.-.|+|..|++.|..
T Consensus 51 ~qRyrC~~C~~tf~~ 65 (129)
T COG3677 51 HQRYKCKSCGSTFTV 65 (129)
T ss_pred ccccccCCcCcceee
Confidence 345666666666655
No 235
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=34.59 E-value=22 Score=25.54 Aligned_cols=12 Identities=17% Similarity=0.199 Sum_probs=6.3
Q ss_pred CcccccChhhhc
Q psy7453 111 SPFCIYCKAVLS 122 (200)
Q Consensus 111 ~~~C~~C~~~f~ 122 (200)
.|.|..|+..+.
T Consensus 112 ~y~C~~C~~~~~ 123 (146)
T smart00731 112 PYRCTGCGQRYL 123 (146)
T ss_pred EEECCCCCCCCc
Confidence 455655554443
No 236
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=34.16 E-value=28 Score=20.77 Aligned_cols=14 Identities=14% Similarity=0.131 Sum_probs=8.0
Q ss_pred CCCcccccChhhhc
Q psy7453 109 TFSPFCIYCKAVLS 122 (200)
Q Consensus 109 ~~~~~C~~C~~~f~ 122 (200)
...|.|+.||..+-
T Consensus 12 ~v~~~Cp~cGipth 25 (55)
T PF13824_consen 12 HVNFECPDCGIPTH 25 (55)
T ss_pred ccCCcCCCCCCcCc
Confidence 34566666665544
No 237
>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=33.35 E-value=13 Score=23.23 Aligned_cols=30 Identities=20% Similarity=0.424 Sum_probs=13.9
Q ss_pred ceecCccCcccCChHHHHHHHHHcCCCCCcccccCccc
Q psy7453 147 KFVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFR 184 (200)
Q Consensus 147 ~~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~ 184 (200)
...|..|+..+..... ..+ ..|.|+.|+..
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 5667777665544332 111 45667777644
No 238
>PRK05580 primosome assembly protein PriA; Validated
Probab=32.66 E-value=30 Score=31.73 Aligned_cols=37 Identities=24% Similarity=0.654 Sum_probs=19.7
Q ss_pred cccccccccc--ccccccccccccCcccCCCCCCCCcccccChhh
Q psy7453 78 LCKHCHSQLS--HLDLLDHCKTCSYMIRPNANNTFSPFCIYCKAV 120 (200)
Q Consensus 78 ~C~~C~~~f~--~~~~l~~C~~C~~~f~~~~~~~~~~~C~~C~~~ 120 (200)
.|+.|+-.+. .......|..||... ..|..|+.||..
T Consensus 392 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~------~~~~~Cp~Cg~~ 430 (679)
T PRK05580 392 ECPHCDASLTLHRFQRRLRCHHCGYQE------PIPKACPECGST 430 (679)
T ss_pred CCCCCCCceeEECCCCeEECCCCcCCC------CCCCCCCCCcCC
Confidence 3445543322 223334677777543 235678888654
No 239
>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=32.26 E-value=20 Score=25.98 Aligned_cols=11 Identities=27% Similarity=0.721 Sum_probs=7.3
Q ss_pred ccccChhhhcc
Q psy7453 113 FCIYCKAVLST 123 (200)
Q Consensus 113 ~C~~C~~~f~~ 123 (200)
.|..|++.|.+
T Consensus 30 eC~~C~~RFTT 40 (147)
T TIGR00244 30 ECLECHERFTT 40 (147)
T ss_pred cCCccCCccce
Confidence 46667766666
No 240
>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=31.95 E-value=20 Score=24.66 Aligned_cols=29 Identities=24% Similarity=0.509 Sum_probs=20.3
Q ss_pred CCcccccccccccccccccccccccCccc
Q psy7453 75 NHSLCKHCHSQLSHLDLLDHCKTCSYMIR 103 (200)
Q Consensus 75 ~~~~C~~C~~~f~~~~~l~~C~~C~~~f~ 103 (200)
....|+.|++...-......|..|+..-.
T Consensus 68 v~V~CP~C~K~TKmLGr~D~CM~C~~pLT 96 (114)
T PF11023_consen 68 VQVECPNCGKQTKMLGRVDACMHCKEPLT 96 (114)
T ss_pred eeeECCCCCChHhhhchhhccCcCCCcCc
Confidence 45678888887766666667877776543
No 241
>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=31.86 E-value=30 Score=19.36 Aligned_cols=12 Identities=17% Similarity=0.235 Sum_probs=7.0
Q ss_pred cccCcccccCHH
Q psy7453 178 CGQCAFRSASVA 189 (200)
Q Consensus 178 C~~C~k~f~~~~ 189 (200)
|..||+.|+.+.
T Consensus 11 C~~C~rpf~WRK 22 (42)
T PF10013_consen 11 CPVCGRPFTWRK 22 (42)
T ss_pred CcccCCcchHHH
Confidence 666666665544
No 242
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=31.73 E-value=32 Score=31.35 Aligned_cols=37 Identities=27% Similarity=0.662 Sum_probs=24.8
Q ss_pred ccccccccccccccccccccccCcccCCCCCCCCcccccChhhhcc
Q psy7453 78 LCKHCHSQLSHLDLLDHCKTCSYMIRPNANNTFSPFCIYCKAVLST 123 (200)
Q Consensus 78 ~C~~C~~~f~~~~~l~~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~ 123 (200)
-|+.||..+.. ..|+.||..... ..-.|+.||....+
T Consensus 17 FC~~CG~~l~~----~~Cp~CG~~~~~-----~~~fC~~CG~~~~~ 53 (645)
T PRK14559 17 FCQKCGTSLTH----KPCPQCGTEVPV-----DEAHCPNCGAETGT 53 (645)
T ss_pred cccccCCCCCC----CcCCCCCCCCCc-----ccccccccCCcccc
Confidence 47777776643 358888866332 22369999988887
No 243
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=31.57 E-value=18 Score=33.57 Aligned_cols=26 Identities=23% Similarity=0.696 Sum_probs=14.6
Q ss_pred ccccccccccccccc-----ccccccccCcc
Q psy7453 77 SLCKHCHSQLSHLDL-----LDHCKTCSYMI 102 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~-----l~~C~~C~~~f 102 (200)
-.|..|++.|..... -.+|..||..|
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVF 491 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRL 491 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCcccc
Confidence 457778877754321 12466666544
No 244
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=31.56 E-value=20 Score=27.24 Aligned_cols=7 Identities=29% Similarity=0.771 Sum_probs=4.7
Q ss_pred ccccccc
Q psy7453 77 SLCKHCH 83 (200)
Q Consensus 77 ~~C~~C~ 83 (200)
+.|+.||
T Consensus 7 ~~Cp~Cg 13 (201)
T COG1326 7 IECPSCG 13 (201)
T ss_pred EECCCCC
Confidence 4577777
No 245
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.51 E-value=15 Score=28.72 Aligned_cols=14 Identities=14% Similarity=0.309 Sum_probs=8.5
Q ss_pred CCcccccChhhhcc
Q psy7453 110 FSPFCIYCKAVLST 123 (200)
Q Consensus 110 ~~~~C~~C~~~f~~ 123 (200)
+.+.|++|+-.|..
T Consensus 18 k~ieCPvC~tkFkk 31 (267)
T COG1655 18 KTIECPVCNTKFKK 31 (267)
T ss_pred ceeccCcccchhhh
Confidence 44566666666655
No 246
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=31.22 E-value=12 Score=28.13 Aligned_cols=13 Identities=23% Similarity=0.337 Sum_probs=5.8
Q ss_pred CcccccChhhhcc
Q psy7453 111 SPFCIYCKAVLST 123 (200)
Q Consensus 111 ~~~C~~C~~~f~~ 123 (200)
-|.|+.|...|+.
T Consensus 113 ~y~C~~~~~r~sf 125 (176)
T COG1675 113 YYVCPNCHVKYSF 125 (176)
T ss_pred ceeCCCCCCcccH
Confidence 3445444444433
No 247
>PLN02294 cytochrome c oxidase subunit Vb
Probab=31.13 E-value=24 Score=26.21 Aligned_cols=13 Identities=23% Similarity=0.565 Sum_probs=7.1
Q ss_pred CCcccccCccccc
Q psy7453 174 KPYACGQCAFRSA 186 (200)
Q Consensus 174 k~~~C~~C~k~f~ 186 (200)
+++.|++||..|.
T Consensus 140 kp~RCpeCG~~fk 152 (174)
T PLN02294 140 KSFECPVCTQYFE 152 (174)
T ss_pred CceeCCCCCCEEE
Confidence 4555655655553
No 248
>PRK06450 threonine synthase; Validated
Probab=30.80 E-value=24 Score=29.28 Aligned_cols=26 Identities=19% Similarity=0.441 Sum_probs=17.6
Q ss_pred cccccccccccccccccccccccCccc
Q psy7453 77 SLCKHCHSQLSHLDLLDHCKTCSYMIR 103 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~l~~C~~C~~~f~ 103 (200)
+.|..||+.+.. ...+.|+.||-.+.
T Consensus 4 ~~C~~Cg~~~~~-~~~~~C~~cg~~l~ 29 (338)
T PRK06450 4 EVCMKCGKERES-IYEIRCKKCGGPFE 29 (338)
T ss_pred eEECCcCCcCCC-cccccCCcCCCEeE
Confidence 678888888755 44567887865433
No 249
>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=30.31 E-value=19 Score=21.00 Aligned_cols=12 Identities=17% Similarity=0.351 Sum_probs=6.0
Q ss_pred ccccCcccccCH
Q psy7453 177 ACGQCAFRSASV 188 (200)
Q Consensus 177 ~C~~C~k~f~~~ 188 (200)
.||+|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 788888888643
No 250
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=29.88 E-value=36 Score=31.00 Aligned_cols=37 Identities=16% Similarity=0.552 Sum_probs=23.6
Q ss_pred ccccccccccccccccccccccCcccCCCCCCCCcccccChhhhcc
Q psy7453 78 LCKHCHSQLSHLDLLDHCKTCSYMIRPNANNTFSPFCIYCKAVLST 123 (200)
Q Consensus 78 ~C~~C~~~f~~~~~l~~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~ 123 (200)
.|+.||..-.... .-|+.||..... -.|+.||.....
T Consensus 3 ~Cp~Cg~~n~~~a--kFC~~CG~~l~~-------~~Cp~CG~~~~~ 39 (645)
T PRK14559 3 ICPQCQFENPNNN--RFCQKCGTSLTH-------KPCPQCGTEVPV 39 (645)
T ss_pred cCCCCCCcCCCCC--ccccccCCCCCC-------CcCCCCCCCCCc
Confidence 5888887644333 458888877632 148888776443
No 251
>COG4640 Predicted membrane protein [Function unknown]
Probab=29.80 E-value=33 Score=29.14 Aligned_cols=21 Identities=10% Similarity=0.173 Sum_probs=13.1
Q ss_pred CCCcccccChhhhccCHHHHHh
Q psy7453 109 TFSPFCIYCKAVLSTNLNELIE 130 (200)
Q Consensus 109 ~~~~~C~~C~~~f~~~~~~l~~ 130 (200)
|..++|..||..|.. .+.+.+
T Consensus 13 Ed~~qC~qCG~~~t~-~~sqan 33 (465)
T COG4640 13 EDDVQCTQCGHKFTS-RQSQAN 33 (465)
T ss_pred cccccccccCCcCCc-hhhhhh
Confidence 334558888877777 555443
No 252
>KOG1280|consensus
Probab=29.64 E-value=41 Score=28.01 Aligned_cols=39 Identities=23% Similarity=0.417 Sum_probs=28.8
Q ss_pred CCCcccccChhhhccCHHHHHhchhhhhhhhhcCCCCCc-eecCccC
Q psy7453 109 TFSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHK-FVCYACD 154 (200)
Q Consensus 109 ~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~-~~C~~C~ 154 (200)
...|.|++|+++--+ ...|..| ....|....+ ..|++|+
T Consensus 77 ~qSftCPyC~~~Gft-e~~f~~H------v~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFT-ERQFGTH------VLSQHPEASTSVICPLCA 116 (381)
T ss_pred cccccCCcccccccc-hhHHHHH------hhhcCcccCcceeeeccc
Confidence 447999999999888 8999999 7667764332 4566664
No 253
>KOG3408|consensus
Probab=29.64 E-value=33 Score=23.96 Aligned_cols=25 Identities=24% Similarity=0.394 Sum_probs=21.9
Q ss_pred CCCcccccCcccccCHHHHHHHHhh
Q psy7453 173 EKPYACGQCAFRSASVAGLHYHLKK 197 (200)
Q Consensus 173 ~k~~~C~~C~k~f~~~~~L~~H~~~ 197 (200)
.-.|-|-.|.+-|.....|..|.++
T Consensus 55 ~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 55 GGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CceeehhhhhhhhcchHHHHHHHhc
Confidence 3458899999999999999999874
No 254
>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=29.36 E-value=4.2 Score=33.78 Aligned_cols=14 Identities=14% Similarity=0.002 Sum_probs=5.5
Q ss_pred CCcccccChhhhcc
Q psy7453 110 FSPFCIYCKAVLST 123 (200)
Q Consensus 110 ~~~~C~~C~~~f~~ 123 (200)
+-|+|..|+++..+
T Consensus 284 RFFkC~~C~~Rt~s 297 (344)
T PF09332_consen 284 RFFKCKDCGNRTIS 297 (344)
T ss_dssp EEEE-T-TS-EEEE
T ss_pred eeEECCCCCCeeee
Confidence 34555555555444
No 255
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=29.30 E-value=50 Score=17.97 Aligned_cols=16 Identities=25% Similarity=0.554 Sum_probs=7.3
Q ss_pred eecCccCcccCChHHH
Q psy7453 148 FVCYACDYFSYNIGCM 163 (200)
Q Consensus 148 ~~C~~C~~~f~~~~~l 163 (200)
..|+.|+-.+.....|
T Consensus 20 d~C~~C~G~W~d~~el 35 (41)
T PF13453_consen 20 DVCPSCGGIWFDAGEL 35 (41)
T ss_pred EECCCCCeEEccHHHH
Confidence 3444454444444443
No 256
>KOG0978|consensus
Probab=29.11 E-value=21 Score=32.65 Aligned_cols=21 Identities=10% Similarity=0.175 Sum_probs=14.1
Q ss_pred CCCcccccCcccccCHHHHHH
Q psy7453 173 EKPYACGQCAFRSASVAGLHY 193 (200)
Q Consensus 173 ~k~~~C~~C~k~f~~~~~L~~ 193 (200)
.+.-+||.|+.+|....-+..
T Consensus 676 tRqRKCP~Cn~aFganDv~~I 696 (698)
T KOG0978|consen 676 TRQRKCPKCNAAFGANDVHRI 696 (698)
T ss_pred HhcCCCCCCCCCCCccccccc
Confidence 355678888888876654443
No 257
>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=28.96 E-value=25 Score=20.53 Aligned_cols=29 Identities=21% Similarity=0.499 Sum_probs=17.6
Q ss_pred Ccccccccccccccccc----cccccccCcccC
Q psy7453 76 HSLCKHCHSQLSHLDLL----DHCKTCSYMIRP 104 (200)
Q Consensus 76 ~~~C~~C~~~f~~~~~l----~~C~~C~~~f~~ 104 (200)
.+.|..|++........ .+|+.|+....-
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~ 36 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHV 36 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccceE
Confidence 35688888776663222 367777765543
No 258
>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=28.93 E-value=31 Score=19.11 Aligned_cols=19 Identities=26% Similarity=0.382 Sum_probs=10.8
Q ss_pred CCccccccccccccccccc
Q psy7453 75 NHSLCKHCHSQLSHLDLLD 93 (200)
Q Consensus 75 ~~~~C~~C~~~f~~~~~l~ 93 (200)
.|+.|+.|++.|-..-.+.
T Consensus 12 ~~~~C~~C~~~FC~~Hr~~ 30 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKHRLP 30 (43)
T ss_dssp SHEE-TTTS-EE-TTTHST
T ss_pred CCeECCCCCcccCccccCc
Confidence 4678888888887665443
No 259
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=28.34 E-value=42 Score=20.30 Aligned_cols=28 Identities=21% Similarity=0.522 Sum_probs=16.8
Q ss_pred ccccccc---ccccccccccccccccCcccC
Q psy7453 77 SLCKHCH---SQLSHLDLLDHCKTCSYMIRP 104 (200)
Q Consensus 77 ~~C~~C~---~~f~~~~~l~~C~~C~~~f~~ 104 (200)
.+|+.|+ -.|+..+..-.|..||....+
T Consensus 12 VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 12 VKCPDCGNEQVVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred EECCCCCCeEEEEecCCcEEECcccCCCccc
Confidence 3566665 345666666667777665543
No 260
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=28.32 E-value=17 Score=33.40 Aligned_cols=68 Identities=13% Similarity=0.239 Sum_probs=39.9
Q ss_pred Ccccccccccccccccc---c---ccccccCcccCCCC--CC------CCc-ccccChhhhccCHHHHHhchhhhhhhhh
Q psy7453 76 HSLCKHCHSQLSHLDLL---D---HCKTCSYMIRPNAN--NT------FSP-FCIYCKAVLSTNLNELIEHCRTCKSMIR 140 (200)
Q Consensus 76 ~~~C~~C~~~f~~~~~l---~---~C~~C~~~f~~~~~--~~------~~~-~C~~C~~~f~~~~~~l~~H~~~~~~~~~ 140 (200)
.-.|+.|-+-+.+..+- | -|..||-.|.-... .. ..| .|+.|.+-+.. ..+- |
T Consensus 68 ~a~C~~Cl~E~~dp~~Rry~YpF~nCt~CGPr~~i~~~lpydr~~t~m~~f~~C~~C~~ey~~-p~~r-----------r 135 (711)
T TIGR00143 68 VATCSDCLEEMLDKNDRRYLYPFISCTHCGPRFTIIEALPYDRENTSMADFPLCPDCAKEYKD-PLDR-----------R 135 (711)
T ss_pred hhhHHHHHHHhcCCCcccccCCcccccCCCCCeEEeecCCCCCCCcCCCCCcCCHHHHHHhcC-Cccc-----------c
Confidence 35688887666554332 2 68888877664332 11 122 48888877766 4332 4
Q ss_pred cCCCCCceecCccCccc
Q psy7453 141 TDPFRHKFVCYACDYFS 157 (200)
Q Consensus 141 ~h~~~k~~~C~~C~~~f 157 (200)
.|. .+-.|..||-..
T Consensus 136 ~h~--~~~~C~~Cgp~l 150 (711)
T TIGR00143 136 FHA--QPIACPRCGPQL 150 (711)
T ss_pred CCC--CCccCCCCCcEE
Confidence 443 256788888654
No 261
>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=28.17 E-value=14 Score=18.74 Aligned_cols=9 Identities=33% Similarity=0.748 Sum_probs=4.5
Q ss_pred ccccChhhh
Q psy7453 113 FCIYCKAVL 121 (200)
Q Consensus 113 ~C~~C~~~f 121 (200)
.|-.|++.|
T Consensus 2 sCiDC~~~F 10 (28)
T PF08790_consen 2 SCIDCSKDF 10 (28)
T ss_dssp EETTTTEEE
T ss_pred eeecCCCCc
Confidence 344555555
No 262
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=27.69 E-value=22 Score=20.62 Aligned_cols=14 Identities=21% Similarity=0.472 Sum_probs=8.0
Q ss_pred CCcccccCcccccC
Q psy7453 174 KPYACGQCAFRSAS 187 (200)
Q Consensus 174 k~~~C~~C~k~f~~ 187 (200)
+.+.|..||..|..
T Consensus 3 k~l~C~dCg~~Fvf 16 (49)
T PF13451_consen 3 KTLTCKDCGAEFVF 16 (49)
T ss_pred eeEEcccCCCeEEE
Confidence 45566666665543
No 263
>PRK07591 threonine synthase; Validated
Probab=27.68 E-value=29 Score=29.71 Aligned_cols=27 Identities=15% Similarity=0.436 Sum_probs=19.4
Q ss_pred CcccccccccccccccccccccccCccc
Q psy7453 76 HSLCKHCHSQLSHLDLLDHCKTCSYMIR 103 (200)
Q Consensus 76 ~~~C~~C~~~f~~~~~l~~C~~C~~~f~ 103 (200)
-+.|..||+.|..... +.|+.||-.+.
T Consensus 18 ~l~C~~Cg~~~~~~~~-~~C~~cg~~l~ 44 (421)
T PRK07591 18 ALKCRECGAEYPLGPI-HVCEECFGPLE 44 (421)
T ss_pred EEEeCCCCCcCCCCCC-ccCCCCCCeEE
Confidence 3778888888876544 78888875443
No 264
>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=27.47 E-value=19 Score=19.88 Aligned_cols=11 Identities=27% Similarity=0.739 Sum_probs=5.8
Q ss_pred CcccccChhhh
Q psy7453 111 SPFCIYCKAVL 121 (200)
Q Consensus 111 ~~~C~~C~~~f 121 (200)
+-.|+.|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 44555555544
No 265
>PRK04351 hypothetical protein; Provisional
Probab=27.40 E-value=27 Score=25.40 Aligned_cols=33 Identities=15% Similarity=0.219 Sum_probs=18.0
Q ss_pred CCcccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecCccCcccC
Q psy7453 110 FSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCYACDYFSY 158 (200)
Q Consensus 110 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~~C~~~f~ 158 (200)
-.|.|..||..+.+ . +.+. ...|.|..|+-.+.
T Consensus 111 y~Y~C~~Cg~~~~r--------------~-Rr~n-~~~yrCg~C~g~L~ 143 (149)
T PRK04351 111 YLYECQSCGQQYLR--------------K-RRIN-TKRYRCGKCRGKLK 143 (149)
T ss_pred EEEECCCCCCEeee--------------e-eecC-CCcEEeCCCCcEee
Confidence 35667777755544 2 2221 24577777765543
No 266
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=27.38 E-value=35 Score=21.93 Aligned_cols=26 Identities=23% Similarity=0.433 Sum_probs=15.6
Q ss_pred ccccccc-cccccccc--ccccccccCcc
Q psy7453 77 SLCKHCH-SQLSHLDL--LDHCKTCSYMI 102 (200)
Q Consensus 77 ~~C~~C~-~~f~~~~~--l~~C~~C~~~f 102 (200)
|.|+-|| .+|..... ...|++|.-..
T Consensus 2 ~~CPCCg~~Tl~~~~~~~ydIC~VC~WEd 30 (78)
T PF14206_consen 2 YPCPCCGYYTLEERGEGTYDICPVCFWED 30 (78)
T ss_pred ccCCCCCcEEeccCCCcCceECCCCCccc
Confidence 5688887 44444443 55677776443
No 267
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=27.30 E-value=31 Score=20.05 Aligned_cols=9 Identities=22% Similarity=0.209 Sum_probs=4.0
Q ss_pred CcccccChh
Q psy7453 111 SPFCIYCKA 119 (200)
Q Consensus 111 ~~~C~~C~~ 119 (200)
.+.|.-||.
T Consensus 37 R~~CGkCgy 45 (51)
T COG1998 37 RWACGKCGY 45 (51)
T ss_pred eeEeccccc
Confidence 344444443
No 268
>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=27.25 E-value=28 Score=25.08 Aligned_cols=12 Identities=17% Similarity=0.179 Sum_probs=5.8
Q ss_pred cccccChhhhcc
Q psy7453 112 PFCIYCKAVLST 123 (200)
Q Consensus 112 ~~C~~C~~~f~~ 123 (200)
+.|+.||+.|-.
T Consensus 125 ~~C~~C~kiyW~ 136 (147)
T PF01927_consen 125 WRCPGCGKIYWE 136 (147)
T ss_pred EECCCCCCEecc
Confidence 445555555443
No 269
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=26.39 E-value=21 Score=18.93 Aligned_cols=7 Identities=57% Similarity=1.322 Sum_probs=2.9
Q ss_pred eecCccC
Q psy7453 148 FVCYACD 154 (200)
Q Consensus 148 ~~C~~C~ 154 (200)
+.|+.||
T Consensus 23 ~vC~~Cg 29 (34)
T PF14803_consen 23 LVCPACG 29 (34)
T ss_dssp EEETTTT
T ss_pred eECCCCC
Confidence 3344443
No 270
>KOG3002|consensus
Probab=26.32 E-value=36 Score=27.84 Aligned_cols=61 Identities=13% Similarity=0.138 Sum_probs=36.1
Q ss_pred CCCcccccChhhhccCHHHHHhchhhhhhhhhcCCCCCceecC----ccCcccCChHHHHHHHHHcCCCCCcccccC
Q psy7453 109 TFSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFRHKFVCY----ACDYFSYNIGCMRSHIRTHTGEKPYACGQC 181 (200)
Q Consensus 109 ~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~k~~~C~----~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C 181 (200)
+++.+|+.|...+.. ...+.-- ++ ...-.+.|+ -|.+.|..... ..|.+.-.. .||.|+.-
T Consensus 78 ~~~~~CP~Cr~~~g~-~R~~amE--------kV-~e~~~vpC~~~~~GC~~~~~Y~~~-~~HE~~C~f-~~~~CP~p 142 (299)
T KOG3002|consen 78 KVSNKCPTCRLPIGN-IRCRAME--------KV-AEAVLVPCKNAKLGCTKSFPYGEK-SKHEKVCEF-RPCSCPVP 142 (299)
T ss_pred hhcccCCcccccccc-HHHHHHH--------HH-HHhceecccccccCCceeeccccc-ccccccccc-CCcCCCCC
Confidence 567788888888876 5444422 22 222345565 37777776655 456554443 67777654
No 271
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.32 E-value=37 Score=27.46 Aligned_cols=24 Identities=25% Similarity=0.759 Sum_probs=13.9
Q ss_pred cccccccCcccCCCCCCCCcccccChhhh
Q psy7453 93 DHCKTCSYMIRPNANNTFSPFCIYCKAVL 121 (200)
Q Consensus 93 ~~C~~C~~~f~~~~~~~~~~~C~~C~~~f 121 (200)
|.|+.|--.|-. .|-.|+.||-.|
T Consensus 256 yvCs~Clsi~C~-----~p~~C~~Cgt~f 279 (279)
T TIGR00627 256 FVCSVCLSVLCQ-----YTPICKTCKTAF 279 (279)
T ss_pred EECCCccCCcCC-----CCCCCCCCCCCC
Confidence 456666655532 234777777654
No 272
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=26.19 E-value=42 Score=24.83 Aligned_cols=12 Identities=17% Similarity=0.290 Sum_probs=5.8
Q ss_pred cccccChhhhcc
Q psy7453 112 PFCIYCKAVLST 123 (200)
Q Consensus 112 ~~C~~C~~~f~~ 123 (200)
+.|+.||+.|--
T Consensus 131 ~~C~~CgkiYW~ 142 (165)
T COG1656 131 YRCPKCGKIYWK 142 (165)
T ss_pred eECCCCcccccC
Confidence 345555555443
No 273
>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=25.96 E-value=32 Score=29.94 Aligned_cols=28 Identities=21% Similarity=0.348 Sum_probs=22.9
Q ss_pred CcccccChhhhccCHHHHHhchhhhhhhhhcCCCC
Q psy7453 111 SPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFR 145 (200)
Q Consensus 111 ~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~ 145 (200)
-+.|+.|.+.|.. ...+..| +...|.+.
T Consensus 57 FWiCp~CskkF~d-~~~~~~H------~~~eH~~~ 84 (466)
T PF04780_consen 57 FWICPRCSKKFSD-AESCLSH------MEQEHPAG 84 (466)
T ss_pred EeeCCcccceeCC-HHHHHHH------HHHhhhhh
Confidence 3579999999999 9999999 86677653
No 274
>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=25.81 E-value=16 Score=20.85 Aligned_cols=6 Identities=17% Similarity=0.589 Sum_probs=3.1
Q ss_pred Chhhhc
Q psy7453 117 CKAVLS 122 (200)
Q Consensus 117 C~~~f~ 122 (200)
||..|.
T Consensus 33 Cg~tfv 38 (47)
T PF04606_consen 33 CGHTFV 38 (47)
T ss_pred CCCEEE
Confidence 555554
No 275
>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=25.70 E-value=57 Score=28.46 Aligned_cols=27 Identities=19% Similarity=0.342 Sum_probs=23.4
Q ss_pred ceecCccCcccCChHHHHHHHHH-cCCC
Q psy7453 147 KFVCYACDYFSYNIGCMRSHIRT-HTGE 173 (200)
Q Consensus 147 ~~~C~~C~~~f~~~~~l~~H~~~-H~~~ 173 (200)
-+.|+.|.+.|.....+..|+.. |.+.
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 47999999999999999999874 7654
No 276
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=25.53 E-value=17 Score=27.70 Aligned_cols=16 Identities=19% Similarity=0.281 Sum_probs=11.1
Q ss_pred CCcccccccccccccc
Q psy7453 75 NHSLCKHCHSQLSHLD 90 (200)
Q Consensus 75 ~~~~C~~C~~~f~~~~ 90 (200)
-||.|.+|.+.|.++-
T Consensus 195 IPF~C~iCKkdy~spv 210 (259)
T COG5152 195 IPFLCGICKKDYESPV 210 (259)
T ss_pred Cceeehhchhhccchh
Confidence 3778888877776653
No 277
>KOG2636|consensus
Probab=25.49 E-value=50 Score=28.49 Aligned_cols=29 Identities=17% Similarity=0.449 Sum_probs=23.2
Q ss_pred HHcCCCCCcccccCc-ccccCHHHHHHHHh
Q psy7453 168 RTHTGEKPYACGQCA-FRSASVAGLHYHLK 196 (200)
Q Consensus 168 ~~H~~~k~~~C~~C~-k~f~~~~~L~~H~~ 196 (200)
+.|-=...|.|.+|| ++|.-+..+.+|..
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 345556789999999 89998889988854
No 278
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=25.40 E-value=21 Score=29.52 Aligned_cols=29 Identities=14% Similarity=0.332 Sum_probs=19.9
Q ss_pred ccccccCcccCCCCCCCCcccccChhhhc
Q psy7453 94 HCKTCSYMIRPNANNTFSPFCIYCKAVLS 122 (200)
Q Consensus 94 ~C~~C~~~f~~~~~~~~~~~C~~C~~~f~ 122 (200)
.|..|...|.-.......+.|+.||..+.
T Consensus 248 AC~rC~t~y~le~A~~~~wrCpkCGg~ik 276 (403)
T COG1379 248 ACSRCYTRYSLEEAKSLRWRCPKCGGKIK 276 (403)
T ss_pred HHHHhhhccCcchhhhhcccCcccccchh
Confidence 57777777766555556677888877654
No 279
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=24.97 E-value=48 Score=19.75 Aligned_cols=13 Identities=8% Similarity=-0.036 Sum_probs=4.8
Q ss_pred CCcccccChhhhc
Q psy7453 110 FSPFCIYCKAVLS 122 (200)
Q Consensus 110 ~~~~C~~C~~~f~ 122 (200)
.|++...|+..|.
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 3444444444443
No 280
>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=24.88 E-value=42 Score=17.98 Aligned_cols=24 Identities=25% Similarity=0.413 Sum_probs=12.3
Q ss_pred cccccccccccc-cccccccccccC
Q psy7453 77 SLCKHCHSQLSH-LDLLDHCKTCSY 100 (200)
Q Consensus 77 ~~C~~C~~~f~~-~~~l~~C~~C~~ 100 (200)
..|++|+..+.. ..-++-|..||.
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCce
Confidence 457777654332 233445555553
No 281
>KOG2071|consensus
Probab=24.53 E-value=41 Score=29.99 Aligned_cols=28 Identities=14% Similarity=0.194 Sum_probs=22.1
Q ss_pred CCceecCccCcccCChHHHHHHHHHcCC
Q psy7453 145 RHKFVCYACDYFSYNIGCMRSHIRTHTG 172 (200)
Q Consensus 145 ~k~~~C~~C~~~f~~~~~l~~H~~~H~~ 172 (200)
..|-.|..||..|.+......|+..|..
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhhh
Confidence 4567899999999888888888777754
No 282
>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=23.73 E-value=11 Score=20.32 Aligned_cols=30 Identities=20% Similarity=0.619 Sum_probs=15.1
Q ss_pred eecCccCcccCChHHHHHHHHHcCCCCCcccccC
Q psy7453 148 FVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQC 181 (200)
Q Consensus 148 ~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C 181 (200)
..|+.|+..= .+.+|=....|...|.|..|
T Consensus 6 v~CP~C~s~~----~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 6 VHCPRCQSTE----GVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeCCCCCCCC----cceeCCCCCCCCEeEecCcC
Confidence 3466664321 13344444455566777666
No 283
>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=23.67 E-value=25 Score=22.71 Aligned_cols=10 Identities=20% Similarity=0.511 Sum_probs=3.3
Q ss_pred CCCccccccc
Q psy7453 74 QNHSLCKHCH 83 (200)
Q Consensus 74 ~~~~~C~~C~ 83 (200)
.+.|.|+.|+
T Consensus 20 ~~~F~CPfC~ 29 (81)
T PF05129_consen 20 PKVFDCPFCN 29 (81)
T ss_dssp SS----TTT-
T ss_pred CceEcCCcCC
Confidence 3457788877
No 284
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=23.62 E-value=40 Score=22.28 Aligned_cols=28 Identities=14% Similarity=0.356 Sum_probs=15.4
Q ss_pred Ccccccccccccccc--cccccccccCccc
Q psy7453 76 HSLCKHCHSQLSHLD--LLDHCKTCSYMIR 103 (200)
Q Consensus 76 ~~~C~~C~~~f~~~~--~l~~C~~C~~~f~ 103 (200)
.|.|+.|++.-.... -+-.|..|++.|.
T Consensus 36 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 36 KHVCPVCGRPKVKRVGTGIWECRKCGAKFA 65 (90)
T ss_pred CccCCCCCCCceEEEEEEEEEcCCCCCEEe
Confidence 578888865422221 2335666665554
No 285
>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=23.28 E-value=18 Score=19.52 Aligned_cols=10 Identities=20% Similarity=0.876 Sum_probs=3.1
Q ss_pred cccccccCcc
Q psy7453 93 DHCKTCSYMI 102 (200)
Q Consensus 93 ~~C~~C~~~f 102 (200)
|+|..||...
T Consensus 7 YkC~~CGniV 16 (36)
T PF06397_consen 7 YKCEHCGNIV 16 (36)
T ss_dssp EE-TTT--EE
T ss_pred EEccCCCCEE
Confidence 4444444443
No 286
>KOG2906|consensus
Probab=23.11 E-value=31 Score=23.13 Aligned_cols=29 Identities=24% Similarity=0.493 Sum_probs=16.9
Q ss_pred cccccCcccCCCCCC-CCcccccChhhhcc
Q psy7453 95 CKTCSYMIRPNANNT-FSPFCIYCKAVLST 123 (200)
Q Consensus 95 C~~C~~~f~~~~~~~-~~~~C~~C~~~f~~ 123 (200)
||.||-...-...+. ..|.|..|+..|.-
T Consensus 4 CP~Cgn~Live~g~~~~rf~C~tCpY~~~I 33 (105)
T KOG2906|consen 4 CPTCGNMLIVESGESCNRFSCRTCPYVFPI 33 (105)
T ss_pred cCCCCCEEEEecCCeEeeEEcCCCCceeeE
Confidence 555555544333333 45778888877765
No 287
>KOG1842|consensus
Probab=23.04 E-value=46 Score=28.72 Aligned_cols=29 Identities=21% Similarity=0.208 Sum_probs=23.6
Q ss_pred CCcccccChhhhccCHHHHHhchhhhhhhhhcCCCC
Q psy7453 110 FSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTDPFR 145 (200)
Q Consensus 110 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h~~~ 145 (200)
..|.|++|.+-|.. .+.|..| ....|.++
T Consensus 14 egflCPiC~~dl~~-~~~L~~H------~d~eH~~e 42 (505)
T KOG1842|consen 14 EGFLCPICLLDLPN-LSALNDH------LDVEHFEE 42 (505)
T ss_pred hcccCchHhhhhhh-HHHHHHH------Hhhhcccc
Confidence 46889999999999 9999999 65666654
No 288
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.03 E-value=44 Score=20.32 Aligned_cols=10 Identities=20% Similarity=0.800 Sum_probs=5.1
Q ss_pred ceecCccCcc
Q psy7453 147 KFVCYACDYF 156 (200)
Q Consensus 147 ~~~C~~C~~~ 156 (200)
.|-|+.|...
T Consensus 31 tymC~eC~~R 40 (68)
T COG4896 31 TYMCPECEHR 40 (68)
T ss_pred eEechhhHhh
Confidence 3556655433
No 289
>PTZ00448 hypothetical protein; Provisional
Probab=22.95 E-value=59 Score=27.35 Aligned_cols=23 Identities=13% Similarity=0.402 Sum_probs=19.0
Q ss_pred CcccccCcccccCHHHHHHHHhh
Q psy7453 175 PYACGQCAFRSASVAGLHYHLKK 197 (200)
Q Consensus 175 ~~~C~~C~k~f~~~~~L~~H~~~ 197 (200)
.|.|..|+-.|......+.|+++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 57888888888888888888875
No 290
>KOG1842|consensus
Probab=22.53 E-value=49 Score=28.53 Aligned_cols=28 Identities=25% Similarity=0.473 Sum_probs=23.7
Q ss_pred CceecCccCcccCChHHHHHHHHH-cCCC
Q psy7453 146 HKFVCYACDYFSYNIGCMRSHIRT-HTGE 173 (200)
Q Consensus 146 k~~~C~~C~~~f~~~~~l~~H~~~-H~~~ 173 (200)
.-|.|++|...|.+...|..|.-. |.++
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 358999999999999999999865 6543
No 291
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=22.31 E-value=75 Score=27.47 Aligned_cols=74 Identities=26% Similarity=0.335 Sum_probs=46.6
Q ss_pred cccccc--ccccccccccccccccCcccCCCCCCCCcccccChhhhccCHHHHHhchhhhhhhhhcC--------CCCCc
Q psy7453 78 LCKHCH--SQLSHLDLLDHCKTCSYMIRPNANNTFSPFCIYCKAVLSTNLNELIEHCRTCKSMIRTD--------PFRHK 147 (200)
Q Consensus 78 ~C~~C~--~~f~~~~~l~~C~~C~~~f~~~~~~~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~h--------~~~k~ 147 (200)
.|.+|. .+|-+. --|.+|.+ |....++-.-..|+.||.+... .-.|+.. +.++- +.+..
T Consensus 115 ~C~iC~~~~gFC~~---C~C~iC~k-fD~~~n~~~Wi~Cd~CgH~cH~-dCALr~~------~i~~G~s~~g~~g~~d~~ 183 (446)
T PF07227_consen 115 DCKICCSEPGFCRR---CMCCICSK-FDDNKNTCSWIGCDVCGHWCHL-DCALRHE------LIGTGPSVKGSIGTLDMQ 183 (446)
T ss_pred CcchhcCCCCcccc---CCccccCC-cccCCCCeeEEeccCCCceehh-hhhcccc------cccCCccCCCCCccCceE
Confidence 355553 344332 36888877 6665555555679999998888 7777766 42211 12557
Q ss_pred eecCccCcccCChHH
Q psy7453 148 FVCYACDYFSYNIGC 162 (200)
Q Consensus 148 ~~C~~C~~~f~~~~~ 162 (200)
|.|.-||+.-.-.+.
T Consensus 184 f~C~~C~~~seLlG~ 198 (446)
T PF07227_consen 184 FHCRACGKTSELLGF 198 (446)
T ss_pred EEccCCCChhhHHHH
Confidence 999999876544333
No 292
>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=22.27 E-value=60 Score=17.57 Aligned_cols=11 Identities=45% Similarity=1.044 Sum_probs=3.7
Q ss_pred CcccccChhhh
Q psy7453 111 SPFCIYCKAVL 121 (200)
Q Consensus 111 ~~~C~~C~~~f 121 (200)
.|-|+.|+..|
T Consensus 3 ryyCdyC~~~~ 13 (38)
T PF06220_consen 3 RYYCDYCKKYL 13 (38)
T ss_dssp S-B-TTT--B-
T ss_pred Ceeccccccee
Confidence 45666666666
No 293
>KOG2636|consensus
Probab=22.06 E-value=62 Score=27.97 Aligned_cols=27 Identities=15% Similarity=0.392 Sum_probs=21.4
Q ss_pred CCCCCceecCccC-cccCChHHHHHHHH
Q psy7453 142 DPFRHKFVCYACD-YFSYNIGCMRSHIR 168 (200)
Q Consensus 142 h~~~k~~~C~~C~-~~f~~~~~l~~H~~ 168 (200)
|.-...|.|.+|| +++.....+.+|-.
T Consensus 396 HGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 396 HGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred cCCCcccceeeccCccccCcHHHHHHhH
Confidence 3344569999999 88888899999954
No 294
>KOG2907|consensus
Probab=22.00 E-value=32 Score=23.69 Aligned_cols=12 Identities=25% Similarity=1.018 Sum_probs=8.6
Q ss_pred cccccCcccccC
Q psy7453 176 YACGQCAFRSAS 187 (200)
Q Consensus 176 ~~C~~C~k~f~~ 187 (200)
|.|+.|++.|..
T Consensus 103 YTC~kC~~k~~e 114 (116)
T KOG2907|consen 103 YTCPKCKYKFTE 114 (116)
T ss_pred EEcCccceeeec
Confidence 778777777654
No 295
>PRK12722 transcriptional activator FlhC; Provisional
Probab=21.90 E-value=65 Score=24.41 Aligned_cols=26 Identities=23% Similarity=0.447 Sum_probs=15.0
Q ss_pred ccccccCcccCCCC-CCCCcccccChh
Q psy7453 94 HCKTCSYMIRPNAN-NTFSPFCIYCKA 119 (200)
Q Consensus 94 ~C~~C~~~f~~~~~-~~~~~~C~~C~~ 119 (200)
.|..||-.|..... ....|.|+.|.-
T Consensus 136 ~C~~Cgg~fv~~~~e~~~~f~CplC~~ 162 (187)
T PRK12722 136 SCNCCGGHFVTHAHDPVGSFVCGLCQP 162 (187)
T ss_pred cCCCCCCCeeccccccCCCCcCCCCCC
Confidence 56666666664332 234677777754
No 296
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=21.80 E-value=58 Score=21.94 Aligned_cols=7 Identities=29% Similarity=0.895 Sum_probs=2.8
Q ss_pred ecCccCc
Q psy7453 149 VCYACDY 155 (200)
Q Consensus 149 ~C~~C~~ 155 (200)
.|..||.
T Consensus 44 ~C~~CG~ 50 (99)
T PRK14892 44 TCGNCGL 50 (99)
T ss_pred ECCCCCC
Confidence 3444443
No 297
>KOG0717|consensus
Probab=21.79 E-value=51 Score=28.63 Aligned_cols=20 Identities=25% Similarity=0.292 Sum_probs=0.0
Q ss_pred cccCcccccCHHHHHHHHhh
Q psy7453 178 CGQCAFRSASVAGLHYHLKK 197 (200)
Q Consensus 178 C~~C~k~f~~~~~L~~H~~~ 197 (200)
|.+|.|+|.+...|.-|...
T Consensus 295 C~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 295 CVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred EeeccccccchHHHHhhHHH
No 298
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=21.73 E-value=45 Score=28.41 Aligned_cols=22 Identities=18% Similarity=0.241 Sum_probs=16.1
Q ss_pred ccccccccccccccccccccccc
Q psy7453 77 SLCKHCHSQLSHLDLLDHCKTCS 99 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~l~~C~~C~ 99 (200)
+.|..||+.|. ....+.|+.|+
T Consensus 3 l~C~~Cg~~~~-~~~~~~C~~c~ 24 (398)
T TIGR03844 3 LRCPGCGEVLP-DHYTLSCPLDC 24 (398)
T ss_pred EEeCCCCCccC-CccccCCCCCC
Confidence 57888888887 44457787776
No 299
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.47 E-value=46 Score=26.91 Aligned_cols=25 Identities=20% Similarity=0.615 Sum_probs=18.2
Q ss_pred eecCccCcccCChHHHHHHHHHcCCCCCcccccCcccccC
Q psy7453 148 FVCYACDYFSYNIGCMRSHIRTHTGEKPYACGQCAFRSAS 187 (200)
Q Consensus 148 ~~C~~C~~~f~~~~~l~~H~~~H~~~k~~~C~~C~k~f~~ 187 (200)
-.|+.||. ...+.|.|+.||..+..
T Consensus 310 ~~C~~cg~---------------~~~r~~~C~~cg~~~~r 334 (364)
T COG0675 310 KTCPCCGH---------------LSGRLFKCPRCGFVHDR 334 (364)
T ss_pred ccccccCC---------------ccceeEECCCCCCeehh
Confidence 36888987 22467999999987644
No 300
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=21.34 E-value=43 Score=23.81 Aligned_cols=28 Identities=25% Similarity=0.450 Sum_probs=16.0
Q ss_pred cccccccccccccccccccccccCcccC
Q psy7453 77 SLCKHCHSQLSHLDLLDHCKTCSYMIRP 104 (200)
Q Consensus 77 ~~C~~C~~~f~~~~~l~~C~~C~~~f~~ 104 (200)
..|+.||.....+..-.-||+||+.+..
T Consensus 29 ~hCp~Cg~PLF~KdG~v~CPvC~~~~~~ 56 (131)
T COG1645 29 KHCPKCGTPLFRKDGEVFCPVCGYREVV 56 (131)
T ss_pred hhCcccCCcceeeCCeEECCCCCceEEE
Confidence 4577777654444444457777754443
No 301
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.18 E-value=32 Score=23.30 Aligned_cols=13 Identities=23% Similarity=0.521 Sum_probs=7.5
Q ss_pred CCcccccChhhhc
Q psy7453 110 FSPFCIYCKAVLS 122 (200)
Q Consensus 110 ~~~~C~~C~~~f~ 122 (200)
||-.|+.||..-.
T Consensus 1 ~p~~CpYCg~~~~ 13 (102)
T PF11672_consen 1 KPIICPYCGGPAE 13 (102)
T ss_pred CCcccCCCCCeeE
Confidence 3556777765443
No 302
>KOG0957|consensus
Probab=20.85 E-value=42 Score=29.44 Aligned_cols=48 Identities=23% Similarity=0.445 Sum_probs=32.1
Q ss_pred CCcccccccccccccccccccccccCcccCCCC-----------CCCCcccccChhhhcc
Q psy7453 75 NHSLCKHCHSQLSHLDLLDHCKTCSYMIRPNAN-----------NTFSPFCIYCKAVLST 123 (200)
Q Consensus 75 ~~~~C~~C~~~f~~~~~l~~C~~C~~~f~~~~~-----------~~~~~~C~~C~~~f~~ 123 (200)
..|.|.+|.+.-.. ..|.+|++|...|.-.-. ...-|+|.+|++.-++
T Consensus 543 ~~ysCgiCkks~dQ-Hll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECdk~esS 601 (707)
T KOG0957|consen 543 MNYSCGICKKSTDQ-HLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECDKNESS 601 (707)
T ss_pred cceeeeeeccchhh-HHHhhcchhhceeeccccCCccccCcccccCcceeecccccccCc
Confidence 36999999886443 456789999877653211 2334789999766544
No 303
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=20.74 E-value=80 Score=24.10 Aligned_cols=30 Identities=17% Similarity=0.425 Sum_probs=14.8
Q ss_pred CCcccccccc---cccccc-cccccccccCcccC
Q psy7453 75 NHSLCKHCHS---QLSHLD-LLDHCKTCSYMIRP 104 (200)
Q Consensus 75 ~~~~C~~C~~---~f~~~~-~l~~C~~C~~~f~~ 104 (200)
+-|.|+.|+. .|.... ...+|+.|+..|..
T Consensus 151 kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~ 184 (202)
T PF13901_consen 151 KGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHK 184 (202)
T ss_pred CCCCCccCCCCCCCCCCCCCCeeeCCcCccccch
Confidence 4466766653 222222 33456666655554
No 304
>KOG3183|consensus
Probab=20.65 E-value=46 Score=26.17 Aligned_cols=28 Identities=11% Similarity=0.081 Sum_probs=18.7
Q ss_pred CCCcccccccccccccccccccccccCc
Q psy7453 74 QNHSLCKHCHSQLSHLDLLDHCKTCSYM 101 (200)
Q Consensus 74 ~~~~~C~~C~~~f~~~~~l~~C~~C~~~ 101 (200)
--||.|+.|+..|-...-.|.=..|...
T Consensus 21 FLPf~Cd~C~~~FC~eHrsye~H~Cp~~ 48 (250)
T KOG3183|consen 21 FLPFKCDGCSGIFCLEHRSYESHHCPKG 48 (250)
T ss_pred ccceeeCCccchhhhccchHhhcCCCcc
Confidence 3589999999888877666543333333
Done!