Query psy4683
Match_columns 196
No_of_seqs 164 out of 1428
Neff 10.6
Searched_HMMs 46136
Date Fri Aug 16 23:11:34 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4683.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4683hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 100.0 4.5E-33 9.8E-38 197.3 4.7 132 54-189 129-266 (279)
2 KOG2462|consensus 99.9 3.2E-28 7E-33 172.8 6.3 136 20-163 128-266 (279)
3 KOG1074|consensus 99.9 7.4E-23 1.6E-27 163.7 1.7 79 113-191 606-693 (958)
4 KOG1074|consensus 99.8 5E-20 1.1E-24 147.8 3.7 82 54-136 604-692 (958)
5 KOG3576|consensus 99.8 1.6E-19 3.5E-24 123.0 4.6 112 53-165 115-237 (267)
6 KOG3608|consensus 99.8 1.6E-19 3.4E-24 132.4 1.0 105 85-190 264-376 (467)
7 KOG3608|consensus 99.8 1.2E-18 2.6E-23 127.9 5.5 149 39-191 191-346 (467)
8 KOG3576|consensus 99.7 9.9E-19 2.1E-23 119.2 1.6 110 82-191 115-237 (267)
9 KOG3623|consensus 99.7 3.1E-17 6.8E-22 130.3 2.8 108 56-163 211-332 (1007)
10 KOG3623|consensus 99.6 5.1E-16 1.1E-20 123.5 3.8 79 54-133 893-971 (1007)
11 PLN03086 PRLI-interacting fact 99.4 1.9E-12 4.2E-17 103.1 7.2 128 56-192 408-566 (567)
12 PHA00733 hypothetical protein 99.3 2.2E-12 4.8E-17 84.6 3.8 82 82-165 38-124 (128)
13 PLN03086 PRLI-interacting fact 99.3 8.2E-12 1.8E-16 99.6 7.4 104 54-165 452-565 (567)
14 PHA00733 hypothetical protein 99.2 6.4E-12 1.4E-16 82.5 3.7 90 47-138 32-125 (128)
15 KOG3993|consensus 99.1 1.1E-11 2.5E-16 93.5 0.9 61 48-109 260-320 (500)
16 PHA02768 hypothetical protein; 99.1 8.6E-11 1.9E-15 64.1 1.9 39 113-153 6-44 (55)
17 PHA02768 hypothetical protein; 98.9 6.2E-10 1.3E-14 60.7 2.2 40 56-98 6-45 (55)
18 PF13465 zf-H2C2_2: Zinc-finge 98.8 2.2E-09 4.8E-14 50.2 1.8 24 128-151 2-25 (26)
19 PHA00616 hypothetical protein 98.8 2.1E-09 4.6E-14 55.8 1.7 33 140-173 1-33 (44)
20 KOG3993|consensus 98.8 7.8E-10 1.7E-14 83.8 -0.3 81 85-165 268-381 (500)
21 PF13465 zf-H2C2_2: Zinc-finge 98.6 2.3E-08 4.9E-13 46.7 1.9 24 71-95 2-25 (26)
22 PHA00616 hypothetical protein 98.5 4.3E-08 9.4E-13 50.9 1.7 31 85-115 2-32 (44)
23 PHA00732 hypothetical protein 98.5 1.2E-07 2.7E-12 56.6 3.0 47 55-107 1-47 (79)
24 PHA00732 hypothetical protein 98.4 1.3E-07 2.9E-12 56.5 2.1 36 85-123 2-38 (79)
25 PF05605 zf-Di19: Drought indu 98.3 1.6E-06 3.5E-11 48.1 4.5 51 55-108 2-53 (54)
26 PF05605 zf-Di19: Drought indu 98.3 1.1E-06 2.4E-11 48.8 3.8 49 113-164 3-53 (54)
27 PF00096 zf-C2H2: Zinc finger, 98.2 6.9E-07 1.5E-11 40.4 1.5 23 141-163 1-23 (23)
28 PF13894 zf-C2H2_4: C2H2-type 98.0 4.7E-06 1E-10 37.8 1.7 24 141-164 1-24 (24)
29 PF00096 zf-C2H2: Zinc finger, 98.0 5.2E-06 1.1E-10 37.4 1.6 19 57-75 2-20 (23)
30 PF12756 zf-C2H2_2: C2H2 type 97.9 4.9E-06 1.1E-10 52.4 1.9 24 140-163 50-73 (100)
31 PF12756 zf-C2H2_2: C2H2 type 97.9 5.8E-06 1.3E-10 52.0 2.0 74 57-136 1-74 (100)
32 COG5189 SFP1 Putative transcri 97.9 4E-06 8.7E-11 61.9 0.9 70 82-161 347-419 (423)
33 PF13912 zf-C2H2_6: C2H2-type 97.8 4.9E-06 1.1E-10 39.1 0.3 25 140-164 1-25 (27)
34 PF09237 GAGA: GAGA factor; I 97.8 1.3E-05 2.9E-10 42.6 1.7 32 137-169 21-52 (54)
35 COG5189 SFP1 Putative transcri 97.7 1.6E-05 3.4E-10 58.9 1.1 70 52-133 346-419 (423)
36 PF13894 zf-C2H2_4: C2H2-type 97.7 4E-05 8.7E-10 34.6 2.1 20 56-75 1-20 (24)
37 PF13912 zf-C2H2_6: C2H2-type 97.6 4.7E-05 1E-09 35.7 1.7 21 55-75 1-21 (27)
38 KOG2231|consensus 97.5 0.00028 6E-09 58.1 6.1 126 56-189 100-262 (669)
39 smart00355 ZnF_C2H2 zinc finge 97.4 0.00011 2.5E-09 33.7 1.9 24 141-164 1-24 (26)
40 COG5236 Uncharacterized conser 97.4 0.0001 2.2E-09 55.3 2.0 133 56-195 152-310 (493)
41 PF09237 GAGA: GAGA factor; I 97.3 0.00011 2.4E-09 39.1 1.3 27 82-108 22-48 (54)
42 PF13909 zf-H2C2_5: C2H2-type 97.2 0.00026 5.5E-09 32.1 1.7 24 141-165 1-24 (24)
43 smart00355 ZnF_C2H2 zinc finge 97.0 0.00087 1.9E-08 30.5 2.4 19 57-75 2-20 (26)
44 PF12874 zf-met: Zinc-finger o 96.9 0.00035 7.5E-09 32.0 0.5 23 141-163 1-23 (25)
45 PRK04860 hypothetical protein; 96.8 0.00075 1.6E-08 46.1 1.6 29 140-173 119-147 (160)
46 PRK04860 hypothetical protein; 96.6 0.0015 3.3E-08 44.6 2.1 38 112-153 119-156 (160)
47 COG5048 FOG: Zn-finger [Genera 96.5 0.00049 1.1E-08 54.6 -0.6 131 54-185 288-464 (467)
48 PF12874 zf-met: Zinc-finger o 96.5 0.0014 3E-08 29.9 1.1 18 58-75 3-20 (25)
49 PF13909 zf-H2C2_5: C2H2-type 96.5 0.0021 4.7E-08 28.9 1.7 20 86-106 2-21 (24)
50 KOG2482|consensus 96.4 0.007 1.5E-07 45.7 4.6 130 55-187 144-355 (423)
51 KOG2482|consensus 96.2 0.022 4.7E-07 43.2 6.2 66 70-135 130-218 (423)
52 PF12171 zf-C2H2_jaz: Zinc-fin 95.9 0.0044 9.6E-08 28.8 1.2 20 56-75 2-21 (27)
53 PF12171 zf-C2H2_jaz: Zinc-fin 95.9 0.0039 8.5E-08 29.0 0.9 18 115-132 4-21 (27)
54 KOG1146|consensus 95.8 0.0034 7.3E-08 55.2 0.8 104 56-162 437-540 (1406)
55 PF13913 zf-C2HC_2: zinc-finge 95.8 0.0075 1.6E-07 27.5 1.6 20 142-162 4-23 (25)
56 KOG2231|consensus 95.7 0.013 2.9E-07 48.6 3.7 103 85-191 100-237 (669)
57 COG5236 Uncharacterized conser 95.2 0.01 2.3E-07 44.9 1.6 102 85-190 152-275 (493)
58 smart00451 ZnF_U1 U1-like zinc 94.7 0.032 6.8E-07 27.5 2.1 21 55-75 3-23 (35)
59 KOG1146|consensus 94.7 0.014 3E-07 51.6 1.2 94 55-165 1260-1353(1406)
60 KOG2893|consensus 94.6 0.009 1.9E-07 42.9 -0.1 45 56-105 11-55 (341)
61 cd00350 rubredoxin_like Rubred 94.6 0.02 4.3E-07 28.0 1.2 10 139-148 16-25 (33)
62 KOG2893|consensus 94.5 0.013 2.9E-07 42.1 0.5 41 115-159 13-53 (341)
63 smart00451 ZnF_U1 U1-like zinc 94.3 0.026 5.6E-07 27.8 1.2 23 140-162 3-25 (35)
64 KOG2785|consensus 94.0 0.21 4.6E-06 38.6 6.0 22 84-105 68-89 (390)
65 COG4049 Uncharacterized protei 93.7 0.036 7.7E-07 30.2 1.1 31 50-80 12-42 (65)
66 COG4049 Uncharacterized protei 93.7 0.035 7.6E-07 30.2 1.0 30 136-165 13-42 (65)
67 KOG4173|consensus 93.6 0.037 7.9E-07 38.9 1.3 26 137-162 141-168 (253)
68 COG5048 FOG: Zn-finger [Genera 93.1 0.022 4.9E-07 45.1 -0.4 59 112-171 289-353 (467)
69 PF12013 DUF3505: Protein of u 92.6 0.19 4.1E-06 32.1 3.5 26 140-165 80-109 (109)
70 KOG2785|consensus 92.3 0.23 4.9E-06 38.5 3.9 30 52-81 163-192 (390)
71 TIGR00622 ssl1 transcription f 92.2 0.25 5.5E-06 31.5 3.5 24 140-163 81-104 (112)
72 PF09538 FYDLN_acid: Protein o 92.1 0.084 1.8E-06 33.6 1.3 13 140-152 26-38 (108)
73 KOG2186|consensus 90.9 0.12 2.5E-06 37.7 1.2 47 55-105 3-49 (276)
74 PF09986 DUF2225: Uncharacteri 90.8 0.053 1.1E-06 39.2 -0.6 13 141-153 49-61 (214)
75 TIGR00622 ssl1 transcription f 90.0 0.52 1.1E-05 30.1 3.4 84 54-147 14-110 (112)
76 KOG2186|consensus 89.8 0.2 4.3E-06 36.6 1.5 54 85-141 4-57 (276)
77 PF12013 DUF3505: Protein of u 89.7 0.66 1.4E-05 29.6 3.9 82 55-137 11-109 (109)
78 KOG4173|consensus 89.6 0.14 3.1E-06 36.1 0.7 78 111-191 78-171 (253)
79 cd00729 rubredoxin_SM Rubredox 89.3 0.2 4.3E-06 24.7 0.9 8 140-147 18-25 (34)
80 PHA00626 hypothetical protein 88.9 0.14 3E-06 28.0 0.2 17 138-154 21-37 (59)
81 TIGR00373 conserved hypothetic 88.8 0.37 8.1E-06 33.0 2.3 33 109-150 106-138 (158)
82 PF13719 zinc_ribbon_5: zinc-r 88.3 0.3 6.4E-06 24.5 1.2 32 114-150 4-35 (37)
83 PF09538 FYDLN_acid: Protein o 88.1 0.42 9E-06 30.5 2.0 30 56-97 10-39 (108)
84 PRK00398 rpoP DNA-directed RNA 87.6 0.33 7.2E-06 25.6 1.2 10 56-65 4-13 (46)
85 PRK14890 putative Zn-ribbon RN 87.4 0.4 8.7E-06 26.7 1.4 10 139-148 47-56 (59)
86 COG2888 Predicted Zn-ribbon RN 86.7 0.53 1.2E-05 26.2 1.6 9 56-64 28-36 (61)
87 PF13717 zinc_ribbon_4: zinc-r 86.2 0.56 1.2E-05 23.4 1.5 10 85-94 26-35 (36)
88 TIGR02098 MJ0042_CXXC MJ0042 f 86.1 0.44 9.5E-06 23.9 1.1 9 57-65 4-12 (38)
89 TIGR02300 FYDLN_acid conserved 85.4 0.52 1.1E-05 30.7 1.4 15 111-125 25-39 (129)
90 PRK06266 transcription initiat 85.3 0.64 1.4E-05 32.6 1.9 34 110-152 115-148 (178)
91 smart00659 RPOLCX RNA polymera 84.9 0.54 1.2E-05 24.6 1.1 11 113-123 3-13 (44)
92 TIGR02605 CxxC_CxxC_SSSS putat 84.4 0.31 6.6E-06 26.5 0.0 11 85-95 6-16 (52)
93 TIGR00373 conserved hypothetic 83.9 1.1 2.4E-05 30.7 2.6 33 81-122 106-138 (158)
94 PF02892 zf-BED: BED zinc fing 83.3 1.2 2.5E-05 23.2 2.0 24 54-77 15-42 (45)
95 smart00834 CxxC_CXXC_SSSS Puta 83.1 0.35 7.5E-06 24.6 -0.1 11 113-123 6-16 (41)
96 PRK06266 transcription initiat 82.9 0.57 1.2E-05 32.8 0.9 32 83-123 116-147 (178)
97 PF09986 DUF2225: Uncharacteri 82.5 0.24 5.3E-06 35.8 -1.1 19 54-72 4-22 (214)
98 COG1592 Rubrerythrin [Energy p 82.2 0.79 1.7E-05 31.6 1.3 23 112-147 134-156 (166)
99 PF09723 Zn-ribbon_8: Zinc rib 81.9 0.53 1.2E-05 24.3 0.3 11 56-66 6-16 (42)
100 smart00614 ZnF_BED BED zinc fi 81.7 0.97 2.1E-05 24.3 1.3 22 140-161 18-44 (50)
101 smart00531 TFIIE Transcription 81.3 1.3 2.9E-05 29.9 2.2 36 83-122 98-133 (147)
102 smart00531 TFIIE Transcription 80.7 1.6 3.5E-05 29.5 2.4 39 109-151 96-134 (147)
103 PF05443 ROS_MUCR: ROS/MUCR tr 79.8 1 2.2E-05 29.8 1.2 27 139-169 71-97 (132)
104 smart00734 ZnF_Rad18 Rad18-lik 78.3 1.7 3.7E-05 19.8 1.4 19 142-161 3-21 (26)
105 PRK04023 DNA polymerase II lar 78.0 2.4 5.3E-05 37.4 3.2 13 140-152 663-675 (1121)
106 PRK00464 nrdR transcriptional 78.0 0.41 8.9E-06 32.6 -1.1 17 85-101 29-45 (154)
107 COG1996 RPC10 DNA-directed RNA 77.8 1.2 2.6E-05 23.9 0.8 11 55-65 6-16 (49)
108 COG1997 RPL43A Ribosomal prote 76.6 1.5 3.3E-05 26.5 1.1 11 113-123 54-64 (89)
109 PF09845 DUF2072: Zn-ribbon co 76.4 1.6 3.6E-05 28.6 1.4 28 55-93 1-28 (131)
110 COG5151 SSL1 RNA polymerase II 75.3 2.3 4.9E-05 32.3 2.0 80 83-164 321-412 (421)
111 PF03604 DNA_RNApol_7kD: DNA d 75.0 3 6.5E-05 20.2 1.8 10 84-93 17-26 (32)
112 COG3357 Predicted transcriptio 74.6 2 4.4E-05 26.1 1.3 10 56-65 59-68 (97)
113 PF10571 UPF0547: Uncharacteri 74.3 1.5 3.2E-05 20.1 0.6 10 142-151 16-25 (26)
114 PRK09678 DNA-binding transcrip 74.3 1.1 2.3E-05 26.3 0.1 8 117-124 34-41 (72)
115 PF00301 Rubredoxin: Rubredoxi 73.4 1.7 3.7E-05 23.1 0.8 9 140-148 34-42 (47)
116 PF07754 DUF1610: Domain of un 73.1 1.4 3.1E-05 19.7 0.3 10 139-148 15-24 (24)
117 PF14353 CpXC: CpXC protein 72.9 0.92 2E-05 29.8 -0.5 13 141-153 39-51 (128)
118 COG0068 HypF Hydrogenase matur 72.4 0.84 1.8E-05 38.6 -0.9 81 56-150 102-183 (750)
119 PF06524 NOA36: NOA36 protein; 72.1 1.7 3.7E-05 32.0 0.8 124 22-164 97-233 (314)
120 cd00730 rubredoxin Rubredoxin; 71.8 1.7 3.8E-05 23.4 0.5 9 140-148 34-42 (50)
121 PF15135 UPF0515: Uncharacteri 71.5 2.9 6.3E-05 30.6 1.8 11 83-93 111-121 (278)
122 COG1198 PriA Primosomal protei 70.3 2 4.3E-05 37.0 0.8 49 85-149 436-484 (730)
123 COG1198 PriA Primosomal protei 66.9 3.8 8.1E-05 35.4 1.8 46 56-121 436-484 (730)
124 KOG4124|consensus 66.5 1.3 2.8E-05 34.1 -0.9 52 110-161 347-419 (442)
125 KOG2807|consensus 66.3 9.6 0.00021 29.3 3.6 68 83-163 289-368 (378)
126 PF13451 zf-trcl: Probable zin 66.1 3.7 8E-05 22.1 1.0 11 84-94 4-14 (49)
127 PF05290 Baculo_IE-1: Baculovi 65.6 4.4 9.6E-05 26.7 1.5 11 83-93 79-89 (140)
128 PF01780 Ribosomal_L37ae: Ribo 64.2 1.9 4.1E-05 26.4 -0.3 32 83-124 34-65 (90)
129 PTZ00255 60S ribosomal protein 64.1 2.8 6E-05 25.7 0.4 32 83-124 35-66 (90)
130 PRK03824 hypA hydrogenase nick 63.7 2.6 5.7E-05 28.1 0.3 14 55-68 70-83 (135)
131 PF15269 zf-C2H2_7: Zinc-finge 63.3 4.3 9.4E-05 21.1 1.0 22 141-162 21-42 (54)
132 PF04959 ARS2: Arsenite-resist 63.3 4.9 0.00011 29.1 1.6 28 54-81 76-103 (214)
133 PF14369 zf-RING_3: zinc-finge 62.9 6.9 0.00015 19.3 1.6 9 86-94 23-31 (35)
134 KOG4167|consensus 62.5 2 4.3E-05 36.5 -0.6 26 140-165 792-817 (907)
135 TIGR00280 L37a ribosomal prote 62.3 2.7 5.8E-05 25.8 0.1 13 112-124 53-65 (91)
136 KOG3408|consensus 61.5 4 8.7E-05 26.4 0.8 24 140-163 57-80 (129)
137 KOG2593|consensus 60.7 3.7 8.1E-05 32.7 0.7 38 50-91 123-160 (436)
138 COG4896 Uncharacterized protei 60.2 6.1 0.00013 22.1 1.2 38 114-151 4-42 (68)
139 PRK14714 DNA polymerase II lar 60.2 8.4 0.00018 35.2 2.7 30 112-152 692-721 (1337)
140 PF08790 zf-LYAR: LYAR-type C2 60.0 3.2 6.8E-05 19.4 0.1 8 115-122 3-10 (28)
141 KOG4167|consensus 59.3 2 4.3E-05 36.5 -1.0 26 84-109 792-817 (907)
142 TIGR01206 lysW lysine biosynth 59.2 5.4 0.00012 21.9 1.0 6 87-92 5-10 (54)
143 PF12907 zf-met2: Zinc-binding 58.9 7 0.00015 20.0 1.3 32 56-87 2-36 (40)
144 PF13878 zf-C2H2_3: zinc-finge 57.2 12 0.00026 19.2 2.0 22 142-163 15-38 (41)
145 PRK03976 rpl37ae 50S ribosomal 56.8 3.6 7.7E-05 25.2 -0.0 32 83-124 35-66 (90)
146 COG4530 Uncharacterized protei 56.8 6.1 0.00013 25.0 1.0 12 111-122 25-36 (129)
147 PF13453 zf-TFIIB: Transcripti 56.5 4.7 0.0001 20.5 0.4 15 114-128 21-35 (41)
148 COG1655 Uncharacterized protei 56.4 2.5 5.4E-05 30.6 -0.8 9 141-149 63-71 (267)
149 TIGR00100 hypA hydrogenase nic 56.4 5 0.00011 25.9 0.6 12 113-124 71-82 (115)
150 COG1571 Predicted DNA-binding 56.0 7.1 0.00015 31.2 1.5 30 114-154 352-381 (421)
151 PF05495 zf-CHY: CHY zinc fing 55.8 1.3 2.8E-05 25.9 -2.0 30 112-149 41-70 (71)
152 PF02176 zf-TRAF: TRAF-type zi 55.2 6 0.00013 21.8 0.7 20 126-145 24-43 (60)
153 PF05191 ADK_lid: Adenylate ki 53.7 8.1 0.00018 19.2 1.0 8 58-65 4-11 (36)
154 smart00440 ZnF_C2C2 C2C2 Zinc 53.6 1.9 4E-05 22.0 -1.4 10 141-150 29-38 (40)
155 PF04959 ARS2: Arsenite-resist 53.1 7.2 0.00016 28.2 1.0 27 138-164 75-101 (214)
156 PRK00432 30S ribosomal protein 52.6 6.8 0.00015 21.1 0.7 10 140-149 37-46 (50)
157 PRK12380 hydrogenase nickel in 52.5 6.9 0.00015 25.2 0.8 11 113-123 71-81 (113)
158 PF12760 Zn_Tnp_IS1595: Transp 51.2 16 0.00035 19.1 2.0 9 139-147 36-44 (46)
159 PF07295 DUF1451: Protein of u 50.3 7.5 0.00016 26.3 0.7 31 53-94 110-140 (146)
160 PF04780 DUF629: Protein of un 50.3 12 0.00026 30.4 2.0 25 141-165 58-83 (466)
161 KOG2593|consensus 49.8 24 0.00052 28.3 3.4 39 81-122 125-163 (436)
162 PRK00564 hypA hydrogenase nick 49.4 7.7 0.00017 25.1 0.7 11 113-123 72-82 (117)
163 COG1571 Predicted DNA-binding 49.3 12 0.00027 29.9 1.8 18 80-97 363-380 (421)
164 COG2331 Uncharacterized protei 48.4 8.1 0.00018 22.7 0.6 31 55-94 12-43 (82)
165 COG3091 SprT Zn-dependent meta 48.3 7.9 0.00017 26.2 0.6 33 112-149 117-149 (156)
166 PF04810 zf-Sec23_Sec24: Sec23 47.9 5 0.00011 20.4 -0.3 13 137-149 21-33 (40)
167 PF07282 OrfB_Zn_ribbon: Putat 47.8 11 0.00024 21.6 1.1 13 139-151 45-57 (69)
168 TIGR00595 priA primosomal prot 47.8 15 0.00032 30.5 2.2 9 57-65 215-223 (505)
169 PF07503 zf-HYPF: HypF finger; 47.7 4.3 9.4E-05 20.1 -0.5 31 115-151 2-32 (35)
170 COG1675 TFA1 Transcription ini 47.1 21 0.00044 25.1 2.5 35 108-151 109-143 (176)
171 PF13824 zf-Mss51: Zinc-finger 46.9 14 0.00031 20.3 1.3 12 139-150 13-24 (55)
172 KOG2907|consensus 46.0 8.8 0.00019 24.5 0.5 11 141-151 103-113 (116)
173 KOG3408|consensus 45.8 22 0.00047 23.1 2.2 27 50-76 52-78 (129)
174 smart00154 ZnF_AN1 AN1-like Zi 45.2 11 0.00023 19.1 0.7 12 84-95 12-23 (39)
175 COG3364 Zn-ribbon containing p 45.0 16 0.00035 22.9 1.5 15 112-126 2-16 (112)
176 PRK04023 DNA polymerase II lar 44.7 18 0.0004 32.4 2.3 36 83-149 625-660 (1121)
177 smart00661 RPOL9 RNA polymeras 44.5 13 0.00028 19.8 1.0 12 140-151 20-31 (52)
178 KOG4377|consensus 44.4 12 0.00025 29.8 1.0 101 60-166 278-429 (480)
179 PF03811 Zn_Tnp_IS1: InsA N-te 44.3 6.6 0.00014 19.5 -0.2 30 113-146 6-35 (36)
180 PF01363 FYVE: FYVE zinc finge 44.0 10 0.00022 21.6 0.6 10 86-95 11-20 (69)
181 COG0068 HypF Hydrogenase matur 43.9 3.7 8E-05 34.9 -1.8 58 57-121 125-182 (750)
182 PRK14873 primosome assembly pr 43.4 17 0.00037 31.3 1.9 9 57-65 385-393 (665)
183 COG4957 Predicted transcriptio 43.0 14 0.0003 24.5 1.1 20 86-108 78-97 (148)
184 COG5151 SSL1 RNA polymerase II 43.0 14 0.0003 28.2 1.2 54 86-147 364-417 (421)
185 PRK03681 hypA hydrogenase nick 42.4 9.3 0.0002 24.6 0.2 11 113-123 71-81 (114)
186 PF07800 DUF1644: Protein of u 42.2 52 0.0011 22.6 3.7 58 113-172 81-140 (162)
187 KOG0782|consensus 42.2 3.1 6.7E-05 34.4 -2.4 51 70-126 240-290 (1004)
188 PF04423 Rad50_zn_hook: Rad50 40.9 10 0.00022 20.6 0.2 12 142-153 22-33 (54)
189 PF00081 Sod_Fe_N: Iron/mangan 40.6 7.8 0.00017 23.3 -0.3 28 169-196 8-37 (82)
190 PF07975 C1_4: TFIIH C1-like d 40.6 10 0.00022 20.6 0.1 19 113-131 22-40 (51)
191 COG3677 Transposase and inacti 40.2 13 0.00029 24.5 0.7 47 101-154 21-67 (129)
192 cd00065 FYVE FYVE domain; Zinc 40.1 20 0.00043 19.5 1.3 10 86-95 4-13 (57)
193 PF01096 TFIIS_C: Transcriptio 39.9 1.2 2.7E-05 22.6 -3.3 10 141-150 29-38 (39)
194 PRK05580 primosome assembly pr 39.7 23 0.00051 30.5 2.2 10 56-65 382-391 (679)
195 KOG1842|consensus 39.6 18 0.00039 29.1 1.4 28 55-82 15-42 (505)
196 KOG3507|consensus 39.4 13 0.00027 20.7 0.4 31 55-97 20-50 (62)
197 PF01155 HypA: Hydrogenase exp 38.8 9.4 0.0002 24.5 -0.2 13 113-125 71-83 (113)
198 PF03145 Sina: Seven in absent 38.7 27 0.00059 24.8 2.2 45 118-165 24-72 (198)
199 KOG1280|consensus 38.4 35 0.00076 26.6 2.7 23 84-106 79-101 (381)
200 PF01927 Mut7-C: Mut7-C RNAse 38.3 20 0.00043 24.2 1.3 17 84-100 124-140 (147)
201 PF04641 Rtf2: Rtf2 RING-finge 38.0 25 0.00054 26.3 2.0 13 141-153 151-163 (260)
202 PF01428 zf-AN1: AN1-like Zinc 37.5 10 0.00022 19.6 -0.1 14 139-152 12-25 (43)
203 PLN02294 cytochrome c oxidase 37.0 16 0.00035 25.3 0.7 16 138-153 139-154 (174)
204 PRK00762 hypA hydrogenase nick 36.9 15 0.00032 24.1 0.5 11 113-124 71-81 (124)
205 COG4888 Uncharacterized Zn rib 36.4 6.1 0.00013 24.6 -1.2 8 85-92 23-30 (104)
206 COG1773 Rubredoxin [Energy pro 36.1 15 0.00033 20.3 0.4 14 140-153 3-16 (55)
207 PRK12722 transcriptional activ 35.6 25 0.00053 24.9 1.5 28 85-120 135-162 (187)
208 KOG0978|consensus 35.5 16 0.00035 31.3 0.6 8 85-92 644-651 (698)
209 KOG1842|consensus 35.5 21 0.00045 28.8 1.2 27 139-165 14-40 (505)
210 KOG1280|consensus 35.3 44 0.00095 26.1 2.8 38 54-91 78-116 (381)
211 smart00064 FYVE Protein presen 34.9 22 0.00049 20.1 1.0 28 85-124 11-38 (68)
212 PF14446 Prok-RING_1: Prokaryo 34.7 25 0.00055 19.3 1.1 7 86-92 23-29 (54)
213 PF01286 XPA_N: XPA protein N- 34.0 31 0.00068 16.9 1.3 10 57-66 5-14 (34)
214 cd00924 Cyt_c_Oxidase_Vb Cytoc 33.5 22 0.00047 22.2 0.9 18 134-152 74-91 (97)
215 PF14311 DUF4379: Domain of un 33.4 30 0.00065 18.8 1.3 12 56-67 29-40 (55)
216 KOG0402|consensus 33.2 15 0.00033 22.0 0.1 31 84-124 36-66 (92)
217 KOG2636|consensus 33.0 33 0.0007 27.8 1.9 31 132-162 393-424 (497)
218 PF09963 DUF2197: Uncharacteri 32.8 23 0.0005 19.6 0.8 10 139-148 30-39 (56)
219 PF10263 SprT-like: SprT-like 32.6 13 0.00028 25.2 -0.3 10 141-150 144-153 (157)
220 smart00504 Ubox Modified RING 32.3 75 0.0016 17.4 3.0 9 142-150 37-45 (63)
221 PF04780 DUF629: Protein of un 32.2 35 0.00077 27.9 2.0 28 55-82 57-84 (466)
222 COG3809 Uncharacterized protei 31.3 23 0.00049 21.1 0.6 20 114-133 23-42 (88)
223 COG1998 RPS31 Ribosomal protei 30.5 30 0.00065 18.6 0.9 10 140-149 37-46 (51)
224 KOG2071|consensus 30.5 35 0.00075 28.7 1.7 28 138-165 416-443 (579)
225 KOG3002|consensus 30.1 27 0.0006 26.8 1.1 78 82-164 78-163 (299)
226 KOG0717|consensus 30.1 26 0.00056 28.5 1.0 22 141-162 293-314 (508)
227 PF10276 zf-CHCC: Zinc-finger 29.5 18 0.00038 18.5 -0.0 11 140-150 29-39 (40)
228 smart00731 SprT SprT homologue 29.5 27 0.00058 23.5 0.9 11 55-65 112-122 (146)
229 PRK12860 transcriptional activ 29.2 35 0.00076 24.2 1.4 11 85-95 135-145 (189)
230 PF04216 FdhE: Protein involve 29.2 5.6 0.00012 30.2 -2.8 11 139-149 237-247 (290)
231 PF06220 zf-U1: U1 zinc finger 28.9 57 0.0012 16.3 1.8 10 56-65 4-13 (38)
232 PHA02998 RNA polymerase subuni 28.6 12 0.00025 26.2 -1.0 11 141-151 172-182 (195)
233 PF10013 DUF2256: Uncharacteri 28.4 38 0.00083 17.5 1.1 17 57-73 10-26 (42)
234 PRK05978 hypothetical protein; 28.4 20 0.00043 24.4 0.1 9 86-94 54-62 (148)
235 COG4391 Uncharacterized protei 28.3 22 0.00048 20.0 0.2 46 103-152 15-60 (62)
236 PRK00420 hypothetical protein; 27.0 42 0.00091 21.6 1.4 10 85-94 41-50 (112)
237 PTZ00448 hypothetical protein; 27.0 41 0.00089 26.5 1.5 23 140-162 314-336 (373)
238 PF08792 A2L_zn_ribbon: A2L zi 26.9 28 0.0006 16.9 0.4 10 141-150 22-31 (33)
239 TIGR01384 TFS_arch transcripti 26.7 30 0.00065 21.6 0.7 13 112-124 16-28 (104)
240 PRK05452 anaerobic nitric oxid 26.7 28 0.00061 28.7 0.7 37 112-149 425-467 (479)
241 COG4306 Uncharacterized protei 26.3 23 0.00049 23.1 0.1 15 83-97 67-81 (160)
242 TIGR00143 hypF [NiFe] hydrogen 26.1 12 0.00026 32.5 -1.6 80 56-150 69-150 (711)
243 PF12773 DZR: Double zinc ribb 26.1 44 0.00096 17.5 1.2 7 114-120 31-37 (50)
244 KOG0717|consensus 26.1 36 0.00077 27.8 1.1 22 141-162 461-482 (508)
245 COG1594 RPB9 DNA-directed RNA 26.0 16 0.00034 23.6 -0.7 11 141-151 101-111 (113)
246 KOG0782|consensus 25.6 12 0.00025 31.3 -1.6 51 99-154 240-290 (1004)
247 KOG2071|consensus 25.5 54 0.0012 27.6 2.0 28 81-108 415-442 (579)
248 KOG3214|consensus 25.3 22 0.00048 22.2 -0.1 7 85-91 24-30 (109)
249 PRK04351 hypothetical protein; 25.3 26 0.00056 23.8 0.2 9 141-149 113-121 (149)
250 PF06397 Desulfoferrod_N: Desu 24.7 29 0.00063 17.3 0.3 11 55-65 6-16 (36)
251 PF02891 zf-MIZ: MIZ/SP-RING z 24.3 28 0.0006 18.7 0.1 8 141-148 42-49 (50)
252 PRK05580 primosome assembly pr 24.2 26 0.00056 30.3 0.0 24 126-149 407-430 (679)
253 PF08209 Sgf11: Sgf11 (transcr 24.0 66 0.0014 15.6 1.4 24 141-165 5-28 (33)
254 PRK14892 putative transcriptio 23.9 27 0.00058 21.9 0.1 10 142-151 44-53 (99)
255 PRK11032 hypothetical protein; 23.9 34 0.00075 23.6 0.6 32 53-95 122-153 (160)
256 TIGR00515 accD acetyl-CoA carb 22.7 63 0.0014 24.7 1.8 11 113-123 46-56 (285)
257 PF09416 UPF1_Zn_bind: RNA hel 22.3 86 0.0019 21.4 2.2 22 55-76 14-41 (152)
258 CHL00174 accD acetyl-CoA carbo 22.2 1.3E+02 0.0028 23.1 3.4 35 54-98 37-71 (296)
259 KOG1729|consensus 22.1 38 0.00083 25.8 0.6 9 142-150 216-224 (288)
260 PTZ00448 hypothetical protein; 22.0 66 0.0014 25.5 1.8 23 84-106 314-336 (373)
261 PF14205 Cys_rich_KTR: Cystein 21.8 31 0.00068 18.9 0.1 9 140-148 28-36 (55)
262 PF15616 TerY-C: TerY-C metal 21.8 15 0.00033 24.3 -1.4 8 113-120 106-113 (131)
263 PF11672 DUF3268: Protein of u 21.7 40 0.00086 21.3 0.5 9 84-92 2-10 (102)
264 COG1326 Uncharacterized archae 21.6 68 0.0015 22.9 1.6 10 113-122 31-40 (201)
265 COG5112 UFD2 U1-like Zn-finger 21.4 31 0.00068 21.8 0.0 23 140-162 55-77 (126)
266 COG5152 Uncharacterized conser 21.2 94 0.002 22.3 2.3 15 83-97 195-209 (259)
267 PF14255 Cys_rich_CPXG: Cystei 21.1 48 0.001 18.0 0.7 9 86-94 2-10 (52)
268 PF11789 zf-Nse: Zinc-finger o 21.1 79 0.0017 17.5 1.6 30 55-89 24-53 (57)
269 PTZ00043 cytochrome c oxidase 20.7 51 0.0011 24.1 0.9 17 137-153 178-194 (268)
270 PF01215 COX5B: Cytochrome c o 20.6 35 0.00075 22.8 0.1 16 138-153 110-125 (136)
271 COG1645 Uncharacterized Zn-fin 20.6 48 0.001 22.0 0.7 26 56-94 29-54 (131)
No 1
>KOG2462|consensus
Probab=99.97 E-value=4.5e-33 Score=197.33 Aligned_cols=132 Identities=24% Similarity=0.449 Sum_probs=123.7
Q ss_pred CcccccccccccCCHHHHHHHHHhhcC---CCCCccCCCCcccccCchHHHHHHHhhcCCCcccccccccccCCchHHHh
Q psy4683 54 TKFPCRLCSQEFDTKEQRKKHERKDHA---TQGLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLSKNELNV 130 (196)
Q Consensus 54 ~~~~C~~C~~~f~~~~~l~~H~~~~h~---~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~ 130 (196)
..|+|+.||+.+.+.++|.+|. .+|- ..+.+.|.+|++.|.....|.+|+++|. .+++|.+||+.|..+.-|+.
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHk-Q~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQG 205 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHK-QTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQG 205 (279)
T ss_pred Cceeccccccccccccccchhh-cccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhc
Confidence 4599999999999999999999 5563 3567999999999999999999999997 78999999999999999999
Q ss_pred hhhhhcCCCCccCcccccccCCchhHHHHHHHhhccCCccccC---ceeccCCchhhhhhhH
Q psy4683 131 HNIKQHCAQPHTCSVCKKIFVNKKNLTTHKKIHLALDRNYQCD---TYFYEGNSLAWEDTSL 189 (196)
Q Consensus 131 H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~---~~f~~~~~l~~H~~~~ 189 (196)
|+|+|+||+||.|+.|+++|..+++|+.|+++|.+ .|+|+|+ ++|+..+.|.+|..+-
T Consensus 206 HiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~-~K~~qC~~C~KsFsl~SyLnKH~ES~ 266 (279)
T KOG2462|consen 206 HIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSD-VKKHQCPRCGKSFALKSYLNKHSESA 266 (279)
T ss_pred ccccccCCCCccCCcccchhcchHHHHHHHHhhcC-CccccCcchhhHHHHHHHHHHhhhhc
Confidence 99999999999999999999999999999999999 8999999 9999999999998753
No 2
>KOG2462|consensus
Probab=99.95 E-value=3.2e-28 Score=172.76 Aligned_cols=136 Identities=21% Similarity=0.387 Sum_probs=117.8
Q ss_pred ccccccchhhhhcCCCCcccccCCCCCCCCCC---CCCcccccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccccC
Q psy4683 20 LWSFLEDENEKRNFSSEEDEESDKLDDEDNVT---SDTKFPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTSTQ 96 (196)
Q Consensus 20 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~ 96 (196)
..-+.|++|+.. .+ ..+.|..|...|- ..+.+.|..||+.|.+..+|..|+ ++|+ .+++|.+||+.|..
T Consensus 128 ~~r~~c~eCgk~-ys----T~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHi-rTH~--l~c~C~iCGKaFSR 199 (279)
T KOG2462|consen 128 HPRYKCPECGKS-YS----TSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHI-RTHT--LPCECGICGKAFSR 199 (279)
T ss_pred CCceeccccccc-cc----cccccchhhcccccccccccccCCCCCceeeehHHHhhHh-hccC--CCcccccccccccc
Confidence 345677777777 43 2444555544442 245689999999999999999999 6786 68999999999999
Q ss_pred chHHHHHHHhhcCCCcccccccccccCCchHHHhhhhhhcCCCCccCcccccccCCchhHHHHHHHh
Q psy4683 97 KYYLVKHKSRHIKDYNVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIFVNKKNLTTHKKIH 163 (196)
Q Consensus 97 ~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h 163 (196)
.+.|+-|+++|+|+|||.|+.|+++|.+.++|..|+++|.+.++|.|+.|+|+|...+.|.+|...-
T Consensus 200 PWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES~ 266 (279)
T KOG2462|consen 200 PWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSESA 266 (279)
T ss_pred hHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhhc
Confidence 9999999999999999999999999999999999999999999999999999999999999998764
No 3
>KOG1074|consensus
Probab=99.86 E-value=7.4e-23 Score=163.74 Aligned_cols=79 Identities=23% Similarity=0.391 Sum_probs=69.8
Q ss_pred ccccccccccCCchHHHhhhhhhcCCCCccCcccccccCCchhHHHHHHHhhcc---CCccccC------ceeccCCchh
Q psy4683 113 VFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIFVNKKNLTTHKKIHLAL---DRNYQCD------TYFYEGNSLA 183 (196)
Q Consensus 113 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~---~~~~~C~------~~f~~~~~l~ 183 (196)
-.|.+|.++..-.++|+.|.++|+|++||+|.+||++|.++.+|+.|+.+|--. .-+|.|+ +.|...-.|.
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V~lp 685 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAVTLP 685 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhccccccccccc
Confidence 369999999999999999999999999999999999999999999999999640 1335566 9999999999
Q ss_pred hhhhhHhh
Q psy4683 184 WEDTSLEI 191 (196)
Q Consensus 184 ~H~~~~h~ 191 (196)
.|++.|-.
T Consensus 686 QhIriH~~ 693 (958)
T KOG1074|consen 686 QHIRIHLG 693 (958)
T ss_pred ceEEeecC
Confidence 99988763
No 4
>KOG1074|consensus
Probab=99.79 E-value=5e-20 Score=147.77 Aligned_cols=82 Identities=24% Similarity=0.380 Sum_probs=63.3
Q ss_pred CcccccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccccCchHHHHHHHhhcCC----Cccccc---ccccccCCch
Q psy4683 54 TKFPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTSTQKYYLVKHKSRHIKD----YNVFCK---ICQLGFLSKN 126 (196)
Q Consensus 54 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~----~~~~C~---~C~~~f~~~~ 126 (196)
.|.+|.+|-+..+..++|+.|. ++|+|++||+|.+||+.|.++.+|+.||..|... ..+.|+ +|-+.|...-
T Consensus 604 dPNqCiiC~rVlSC~saLqmHy-rtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn~V 682 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHY-RTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTNAV 682 (958)
T ss_pred Cccceeeeeecccchhhhhhhh-hcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccccc
Confidence 4678888888888888888888 7788888888888888888888888888877543 235666 6777777666
Q ss_pred HHHhhhhhhc
Q psy4683 127 ELNVHNIKQH 136 (196)
Q Consensus 127 ~l~~H~~~~~ 136 (196)
.|..|.++|.
T Consensus 683 ~lpQhIriH~ 692 (958)
T KOG1074|consen 683 TLPQHIRIHL 692 (958)
T ss_pred cccceEEeec
Confidence 6666766665
No 5
>KOG3576|consensus
Probab=99.78 E-value=1.6e-19 Score=122.98 Aligned_cols=112 Identities=22% Similarity=0.425 Sum_probs=103.1
Q ss_pred CCcccccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccccCchHHHHHHHhhcCCCcccccccccccCCchHHHhhh
Q psy4683 53 DTKFPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLSKNELNVHN 132 (196)
Q Consensus 53 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~ 132 (196)
...|.|..|++.|.-+..|.+|+ .-|...+.+.|..||+.|.....|.+|+++|+|.+||+|..|+++|...-.|..|.
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~-kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHL-KCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHh-hhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 44599999999999999999999 78999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcCC-----------CCccCcccccccCCchhHHHHHHHhhc
Q psy4683 133 IKQHCA-----------QPHTCSVCKKIFVNKKNLTTHKKIHLA 165 (196)
Q Consensus 133 ~~~~~~-----------~~~~C~~C~~~f~~~~~l~~H~~~h~~ 165 (196)
+..+|. +.|.|..||.+-.....+..|+..|+.
T Consensus 194 ~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 194 KKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred HHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 887753 468999999999999999999999876
No 6
>KOG3608|consensus
Probab=99.75 E-value=1.6e-19 Score=132.45 Aligned_cols=105 Identities=22% Similarity=0.351 Sum_probs=45.4
Q ss_pred ccCCCCcccccCchHHHHHHH-hhcCCCcccccccccccCCchHHHhhhhhhcCCCCccCcc--cccccCCchhHHHHHH
Q psy4683 85 FSCDLCSYTSTQKYYLVKHKS-RHIKDYNVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSV--CKKIFVNKKNLTTHKK 161 (196)
Q Consensus 85 ~~C~~C~~~f~~~~~l~~H~~-~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~ 161 (196)
|+|+.|+.+....+.|.+|++ .|...+||+|+.|+..+...+.|.+|...|. +..|.|.. |..+|+....+.+|++
T Consensus 264 ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~ 342 (467)
T KOG3608|consen 264 YKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFL 342 (467)
T ss_pred ccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHH
Confidence 333344333333334444433 2333444444444444444444444444333 33444433 4444444444444444
Q ss_pred Hhhcc--CCccccC---ceeccCCchhhhhhhHh
Q psy4683 162 IHLAL--DRNYQCD---TYFYEGNSLAWEDTSLE 190 (196)
Q Consensus 162 ~h~~~--~~~~~C~---~~f~~~~~l~~H~~~~h 190 (196)
-++.+ ..+|.|. +.|++...|-.|++..|
T Consensus 343 evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH 376 (467)
T KOG3608|consen 343 EVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKH 376 (467)
T ss_pred HhccCCCCCceeeecchhhhccchhHHHHHHHhh
Confidence 43311 2234444 55555555555554444
No 7
>KOG3608|consensus
Probab=99.75 E-value=1.2e-18 Score=127.86 Aligned_cols=149 Identities=20% Similarity=0.367 Sum_probs=133.8
Q ss_pred cccCCCCCCCCCCCCCcccccccccccCCHHHHHHHHHhhc-CCCCCccCCCCcccccCchHHHHHHHhhcCCCcccccc
Q psy4683 39 EESDKLDDEDNVTSDTKFPCRLCSQEFDTKEQRKKHERKDH-ATQGLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKI 117 (196)
Q Consensus 39 ~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h-~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~ 117 (196)
+...+..|.+.|++++..-|+.||..|.+...|-.|.++.- ....+|.|..|.+.|.+...|..|++.|. ..|+|+.
T Consensus 191 ~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv--n~ykCpl 268 (467)
T KOG3608|consen 191 NKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHV--NCYKCPL 268 (467)
T ss_pred cHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhh--hcccccc
Confidence 56778899999999999999999999999999999985432 34578999999999999999999999996 6799999
Q ss_pred cccccCCchHHHhhhhhhc-CCCCccCcccccccCCchhHHHHHHHhhccCCccccC-----ceeccCCchhhhhhhHhh
Q psy4683 118 CQLGFLSKNELNVHNIKQH-CAQPHTCSVCKKIFVNKKNLTTHKKIHLALDRNYQCD-----TYFYEGNSLAWEDTSLEI 191 (196)
Q Consensus 118 C~~~f~~~~~l~~H~~~~~-~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~-----~~f~~~~~l~~H~~~~h~ 191 (196)
|+.+....+.|.+|++.-+ ..+||+|..|++.|.+.+.|.+|..+|.. ..|.|. ++|.+.-+|.+|++-||-
T Consensus 269 Cdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~--~~y~C~h~~C~~s~r~~~q~~~H~~evhE 346 (467)
T KOG3608|consen 269 CDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSK--TVYQCEHPDCHYSVRTYTQMRRHFLEVHE 346 (467)
T ss_pred cccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccc--cceecCCCCCcHHHHHHHHHHHHHHHhcc
Confidence 9999999999999998755 57899999999999999999999999874 678887 889999999999999983
No 8
>KOG3576|consensus
Probab=99.72 E-value=9.9e-19 Score=119.15 Aligned_cols=110 Identities=22% Similarity=0.358 Sum_probs=98.1
Q ss_pred CCCccCCCCcccccCchHHHHHHHhhcCCCcccccccccccCCchHHHhhhhhhcCCCCccCcccccccCCchhHHHHHH
Q psy4683 82 QGLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIFVNKKNLTTHKK 161 (196)
Q Consensus 82 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~ 161 (196)
...|.|.+|++.|.....|.+|++-|...+.+.|..||+.|.+...|.+|.++|+|.+||+|..|+++|..+-.|..|++
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~ 194 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLK 194 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHH
Confidence 45699999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred Hhhc----------cCCccccC---ceeccCCchhhhhhhHhh
Q psy4683 162 IHLA----------LDRNYQCD---TYFYEGNSLAWEDTSLEI 191 (196)
Q Consensus 162 ~h~~----------~~~~~~C~---~~f~~~~~l~~H~~~~h~ 191 (196)
.-+| ..+.|.|. ++-.....+..|+..+|-
T Consensus 195 kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp 237 (267)
T KOG3576|consen 195 KVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHP 237 (267)
T ss_pred HHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCC
Confidence 8665 24667777 555566778888888873
No 9
>KOG3623|consensus
Probab=99.66 E-value=3.1e-17 Score=130.27 Aligned_cols=108 Identities=27% Similarity=0.490 Sum_probs=90.8
Q ss_pred ccccccccccCCHHHHHHHHHhhcC-CCCCccCCCCcccccCchHHHHHHHhhcCC-------------Ccccccccccc
Q psy4683 56 FPCRLCSQEFDTKEQRKKHERKDHA-TQGLFSCDLCSYTSTQKYYLVKHKSRHIKD-------------YNVFCKICQLG 121 (196)
Q Consensus 56 ~~C~~C~~~f~~~~~l~~H~~~~h~-~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~-------------~~~~C~~C~~~ 121 (196)
..|..|++++.....|+.|+.-.|. .+..|.|..|..+|.++..|.+|+..|... +-|+|..||++
T Consensus 211 ltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKA 290 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKA 290 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchh
Confidence 6899999999999999999965563 445699999999999999999999988643 34788888888
Q ss_pred cCCchHHHhhhhhhcCCCCccCcccccccCCchhHHHHHHHh
Q psy4683 122 FLSKNELNVHNIKQHCAQPHTCSVCKKIFVNKKNLTTHKKIH 163 (196)
Q Consensus 122 f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h 163 (196)
|+.+-.|+.|+|+|.|++||.|+.|+|.|+....+..|+...
T Consensus 291 FKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSSK 332 (1007)
T KOG3623|consen 291 FKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSSK 332 (1007)
T ss_pred hhhHHHHHhhheeecCCCCcCCcccccccccCCccccccccc
Confidence 888888888888888888888888888888888888887553
No 10
>KOG3623|consensus
Probab=99.60 E-value=5.1e-16 Score=123.52 Aligned_cols=79 Identities=22% Similarity=0.453 Sum_probs=46.2
Q ss_pred CcccccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccccCchHHHHHHHhhcCCCcccccccccccCCchHHHhhhh
Q psy4683 54 TKFPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLSKNELNVHNI 133 (196)
Q Consensus 54 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 133 (196)
.+|.|+.|+++|.-.+.|.+|. -.|+|.+||+|.+|.+.|..+..|..|+|.|.|++||.|+.|++.|...+....||.
T Consensus 893 gmyaCDqCDK~FqKqSSLaRHK-YEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 893 GMYACDQCDKAFQKQSSLARHK-YEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred ccchHHHHHHHHHhhHHHHHhh-hhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhc
Confidence 4556666666666566666665 445566666666666666666566666666666666666556655555555555543
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.35 E-value=1.9e-12 Score=103.07 Aligned_cols=128 Identities=16% Similarity=0.305 Sum_probs=100.0
Q ss_pred ccccccccccCCHHHHHHHHHhhcC-------------------CCCCccCCCCcccccCchHHHHHHHhhcCCCccccc
Q psy4683 56 FPCRLCSQEFDTKEQRKKHERKDHA-------------------TQGLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCK 116 (196)
Q Consensus 56 ~~C~~C~~~f~~~~~l~~H~~~~h~-------------------~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~ 116 (196)
-.|..|..... ..+|..|. .... .+..+.|+.|++.|. ...|..|+..++ +++.|+
T Consensus 408 V~C~NC~~~i~-l~~l~lHe-~~C~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp 482 (567)
T PLN03086 408 VECRNCKHYIP-SRSIALHE-AYCSRHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP 482 (567)
T ss_pred EECCCCCCccc-hhHHHHHH-hhCCCcceeCCcccccceeeccccccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC
Confidence 46888877764 44556776 2222 124578999999996 678999999885 789999
Q ss_pred ccccccCCchHHHhhhhhhcCCCCccCcccccccCC----------chhHHHHHHHhhccCCccccC--ceeccCCchhh
Q psy4683 117 ICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIFVN----------KKNLTTHKKIHLALDRNYQCD--TYFYEGNSLAW 184 (196)
Q Consensus 117 ~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~----------~~~l~~H~~~h~~~~~~~~C~--~~f~~~~~l~~ 184 (196)
|+..+ ....|..|+..|...+++.|+.|++.|.. .+.|..|..++ | .+++.|. ......-.|..
T Consensus 483 -Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G-~rt~~C~~Cgk~Vrlrdm~~ 558 (567)
T PLN03086 483 -CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-G-SRTAPCDSCGRSVMLKEMDI 558 (567)
T ss_pred -CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-C-CcceEccccCCeeeehhHHH
Confidence 99755 67899999999999999999999999952 35899999886 6 7999988 45555678999
Q ss_pred hhhhHhhh
Q psy4683 185 EDTSLEIT 192 (196)
Q Consensus 185 H~~~~h~~ 192 (196)
|+..+|.+
T Consensus 559 H~~~~h~~ 566 (567)
T PLN03086 559 HQIAVHQK 566 (567)
T ss_pred HHHHhhcC
Confidence 99988854
No 12
>PHA00733 hypothetical protein
Probab=99.30 E-value=2.2e-12 Score=84.63 Aligned_cols=82 Identities=18% Similarity=0.184 Sum_probs=51.0
Q ss_pred CCCccCCCCcccccCchHHHHH--HH---hhcCCCcccccccccccCCchHHHhhhhhhcCCCCccCcccccccCCchhH
Q psy4683 82 QGLFSCDLCSYTSTQKYYLVKH--KS---RHIKDYNVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIFVNKKNL 156 (196)
Q Consensus 82 ~~~~~C~~C~~~f~~~~~l~~H--~~---~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l 156 (196)
.+++.|.+|...|.+...|..+ ++ .+.+.++|.|..|++.|.....|..|++.+ ..+|.|..|++.|.....|
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL 115 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDST 115 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHH
Confidence 4556666666555554444443 11 222356677777777777777777776654 3457777777777777777
Q ss_pred HHHHHHhhc
Q psy4683 157 TTHKKIHLA 165 (196)
Q Consensus 157 ~~H~~~h~~ 165 (196)
..|+...++
T Consensus 116 ~~H~~~~h~ 124 (128)
T PHA00733 116 LDHVCKKHN 124 (128)
T ss_pred HHHHHHhcC
Confidence 777776654
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.29 E-value=8.2e-12 Score=99.56 Aligned_cols=104 Identities=17% Similarity=0.361 Sum_probs=85.9
Q ss_pred CcccccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccccCchHHHHHHHhhcCCCcccccccccccCC---------
Q psy4683 54 TKFPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLS--------- 124 (196)
Q Consensus 54 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~--------- 124 (196)
..+.|+.|++.|. ...|..|+.. +. .++.|+ ||+.+ .+..|..|+..|.+.+++.|..|+..+..
T Consensus 452 ~H~~C~~Cgk~f~-~s~LekH~~~-~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d 525 (567)
T PLN03086 452 NHVHCEKCGQAFQ-QGEMEKHMKV-FH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRD 525 (567)
T ss_pred cCccCCCCCCccc-hHHHHHHHHh-cC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhh
Confidence 4578999999996 6889999954 42 789999 99755 67899999999999999999999998842
Q ss_pred -chHHHhhhhhhcCCCCccCcccccccCCchhHHHHHHHhhc
Q psy4683 125 -KNELNVHNIKQHCAQPHTCSVCKKIFVNKKNLTTHKKIHLA 165 (196)
Q Consensus 125 -~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 165 (196)
.+.|..|...+ +.+++.|..||+.+..+ .|..|+..-|.
T Consensus 526 ~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~~~h~ 565 (567)
T PLN03086 526 RLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQIAVHQ 565 (567)
T ss_pred hhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHHHHhhc
Confidence 35899998885 89999999999988765 56777766443
No 14
>PHA00733 hypothetical protein
Probab=99.24 E-value=6.4e-12 Score=82.46 Aligned_cols=90 Identities=12% Similarity=0.177 Sum_probs=72.8
Q ss_pred CCCCCCCCcccccccccccCCHHHHHHH--H--HhhcCCCCCccCCCCcccccCchHHHHHHHhhcCCCccccccccccc
Q psy4683 47 EDNVTSDTKFPCRLCSQEFDTKEQRKKH--E--RKDHATQGLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGF 122 (196)
Q Consensus 47 ~~~~~~~~~~~C~~C~~~f~~~~~l~~H--~--~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 122 (196)
-......+++.|..|.+.|.....|..+ + ...+.+.+||.|+.|++.|.....|..|++.+ ..++.|..|+++|
T Consensus 32 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F 109 (128)
T PHA00733 32 HSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEF 109 (128)
T ss_pred hcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCcc
Confidence 3333445679999999999887776665 1 12334578999999999999999999999976 3579999999999
Q ss_pred CCchHHHhhhhhhcCC
Q psy4683 123 LSKNELNVHNIKQHCA 138 (196)
Q Consensus 123 ~~~~~l~~H~~~~~~~ 138 (196)
.....|..|+...++.
T Consensus 110 ~~~~sL~~H~~~~h~~ 125 (128)
T PHA00733 110 RNTDSTLDHVCKKHNI 125 (128)
T ss_pred CCHHHHHHHHHHhcCc
Confidence 9999999999887753
No 15
>KOG3993|consensus
Probab=99.13 E-value=1.1e-11 Score=93.52 Aligned_cols=61 Identities=15% Similarity=0.296 Sum_probs=50.5
Q ss_pred CCCCCCCcccccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccccCchHHHHHHHhhcC
Q psy4683 48 DNVTSDTKFPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTSTQKYYLVKHKSRHIK 109 (196)
Q Consensus 48 ~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 109 (196)
.+.+..+.|.|..|...|.+...|.+|. -...-.-.|+|+.|++.|....+|..|.++|..
T Consensus 260 ~i~n~iGdyiCqLCK~kYeD~F~LAQHr-C~RIV~vEYrCPEC~KVFsCPANLASHRRWHKP 320 (500)
T KOG3993|consen 260 GIPNVIGDYICQLCKEKYEDAFALAQHR-CPRIVHVEYRCPECDKVFSCPANLASHRRWHKP 320 (500)
T ss_pred cCcccHHHHHHHHHHHhhhhHHHHhhcc-CCeeEEeeecCCcccccccCchhhhhhhcccCC
Confidence 3344445699999999999999999998 444444569999999999999999999999863
No 16
>PHA02768 hypothetical protein; Provisional
Probab=99.05 E-value=8.6e-11 Score=64.09 Aligned_cols=39 Identities=23% Similarity=0.408 Sum_probs=17.0
Q ss_pred ccccccccccCCchHHHhhhhhhcCCCCccCcccccccCCc
Q psy4683 113 VFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIFVNK 153 (196)
Q Consensus 113 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 153 (196)
|.|+.||+.|...++|..|+++|+ ++|+|..|++.|...
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~ 44 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRT 44 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccc
Confidence 344444444444444444444444 344444444444433
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.93 E-value=6.2e-10 Score=60.74 Aligned_cols=40 Identities=15% Similarity=0.372 Sum_probs=23.4
Q ss_pred ccccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccccCch
Q psy4683 56 FPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTSTQKY 98 (196)
Q Consensus 56 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~ 98 (196)
|.|+.||+.|....+|..|+ +.|. ++++|..|++.|...+
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~-r~H~--k~~kc~~C~k~f~~~s 45 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHL-RKHN--TNLKLSNCKRISLRTG 45 (55)
T ss_pred cCcchhCCeeccHHHHHHHH-HhcC--CcccCCcccceecccc
Confidence 56666666666666666666 3344 4566666666655443
No 18
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.82 E-value=2.2e-09 Score=50.17 Aligned_cols=24 Identities=29% Similarity=0.533 Sum_probs=16.7
Q ss_pred HHhhhhhhcCCCCccCcccccccC
Q psy4683 128 LNVHNIKQHCAQPHTCSVCKKIFV 151 (196)
Q Consensus 128 l~~H~~~~~~~~~~~C~~C~~~f~ 151 (196)
|..|+++|++++||.|+.|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 566777777777777777777665
No 19
>PHA00616 hypothetical protein
Probab=98.81 E-value=2.1e-09 Score=55.81 Aligned_cols=33 Identities=21% Similarity=0.296 Sum_probs=30.5
Q ss_pred CccCcccccccCCchhHHHHHHHhhccCCccccC
Q psy4683 140 PHTCSVCKKIFVNKKNLTTHKKIHLALDRNYQCD 173 (196)
Q Consensus 140 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~ 173 (196)
||.|+.||+.|...+.|.+|++.|+| ++++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg-~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHK-QNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcC-CCcccee
Confidence 68999999999999999999999999 8999988
No 20
>KOG3993|consensus
Probab=98.79 E-value=7.8e-10 Score=83.80 Aligned_cols=81 Identities=22% Similarity=0.420 Sum_probs=71.1
Q ss_pred ccCCCCcccccCchHHHHHHHhhcCCCcccccccccccCCchHHHhhhhhhcCC--------------------------
Q psy4683 85 FSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLSKNELNVHNIKQHCA-------------------------- 138 (196)
Q Consensus 85 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~-------------------------- 138 (196)
|.|..|...|.....|.+|.-....-..|+|+.|+++|.-..+|..|++.|.-.
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~r 347 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAER 347 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccc
Confidence 999999999999999999987666667899999999999999999999987611
Q ss_pred -------CCccCcccccccCCchhHHHHHHHhhc
Q psy4683 139 -------QPHTCSVCKKIFVNKKNLTTHKKIHLA 165 (196)
Q Consensus 139 -------~~~~C~~C~~~f~~~~~l~~H~~~h~~ 165 (196)
..|.|..|++.|++...|+.|+-+|+.
T Consensus 348 sg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 348 SGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred cCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 138899999999999999999988874
No 21
>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=98.62 E-value=2.3e-08 Score=46.71 Aligned_cols=24 Identities=17% Similarity=0.552 Sum_probs=13.2
Q ss_pred HHHHHHhhcCCCCCccCCCCccccc
Q psy4683 71 RKKHERKDHATQGLFSCDLCSYTST 95 (196)
Q Consensus 71 l~~H~~~~h~~~~~~~C~~C~~~f~ 95 (196)
|.+|+ ..|++++||.|+.|++.|.
T Consensus 2 l~~H~-~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHM-RTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHH-HHHSSSSSEEESSSSEEES
T ss_pred HHHHh-hhcCCCCCCCCCCCcCeeC
Confidence 45555 3455555555555555553
No 22
>PHA00616 hypothetical protein
Probab=98.54 E-value=4.3e-08 Score=50.95 Aligned_cols=31 Identities=16% Similarity=0.216 Sum_probs=13.4
Q ss_pred ccCCCCcccccCchHHHHHHHhhcCCCcccc
Q psy4683 85 FSCDLCSYTSTQKYYLVKHKSRHIKDYNVFC 115 (196)
Q Consensus 85 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C 115 (196)
|+|+.||+.|.+...|..|++.|++++++.|
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 3444444444444444444444444444433
No 23
>PHA00732 hypothetical protein
Probab=98.48 E-value=1.2e-07 Score=56.63 Aligned_cols=47 Identities=28% Similarity=0.504 Sum_probs=29.0
Q ss_pred cccccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccccCchHHHHHHHhh
Q psy4683 55 KFPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTSTQKYYLVKHKSRH 107 (196)
Q Consensus 55 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h 107 (196)
||.|..|++.|.+..+|..|++..|. ++.|+.|++.|. .+..|....
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhccc
Confidence 46677777777777777777632343 346777777665 455565443
No 24
>PHA00732 hypothetical protein
Probab=98.43 E-value=1.3e-07 Score=56.48 Aligned_cols=36 Identities=28% Similarity=0.767 Sum_probs=17.0
Q ss_pred ccCCCCcccccCchHHHHHHHh-hcCCCcccccccccccC
Q psy4683 85 FSCDLCSYTSTQKYYLVKHKSR-HIKDYNVFCKICQLGFL 123 (196)
Q Consensus 85 ~~C~~C~~~f~~~~~l~~H~~~-h~~~~~~~C~~C~~~f~ 123 (196)
|.|..|++.|.....|..|++. |. ++.|+.|++.|.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~ 38 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR 38 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC
Confidence 4455555555555555555542 32 124444444444
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=98.31 E-value=1.6e-06 Score=48.14 Aligned_cols=51 Identities=22% Similarity=0.474 Sum_probs=35.0
Q ss_pred cccccccccccCCHHHHHHHHHhhcCCC-CCccCCCCcccccCchHHHHHHHhhc
Q psy4683 55 KFPCRLCSQEFDTKEQRKKHERKDHATQ-GLFSCDLCSYTSTQKYYLVKHKSRHI 108 (196)
Q Consensus 55 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~-~~~~C~~C~~~f~~~~~l~~H~~~h~ 108 (196)
.|.|+.|++. .+...|..|....|..+ +.+.||+|...+. .+|..|+..++
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 3778888884 45677888876767654 4577888887544 37777776554
No 26
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=98.30 E-value=1.1e-06 Score=48.76 Aligned_cols=49 Identities=22% Similarity=0.402 Sum_probs=25.9
Q ss_pred ccccccccccCCchHHHhhhhhhcC--CCCccCcccccccCCchhHHHHHHHhh
Q psy4683 113 VFCKICQLGFLSKNELNVHNIKQHC--AQPHTCSVCKKIFVNKKNLTTHKKIHL 164 (196)
Q Consensus 113 ~~C~~C~~~f~~~~~l~~H~~~~~~--~~~~~C~~C~~~f~~~~~l~~H~~~h~ 164 (196)
|.|+.|++ ..+...|..|....+. .+.+.||+|...+. .+|..|+..++
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 45566665 3444555555554443 23456666665433 36666666554
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.22 E-value=6.9e-07 Score=40.39 Aligned_cols=23 Identities=39% Similarity=0.775 Sum_probs=17.8
Q ss_pred ccCcccccccCCchhHHHHHHHh
Q psy4683 141 HTCSVCKKIFVNKKNLTTHKKIH 163 (196)
Q Consensus 141 ~~C~~C~~~f~~~~~l~~H~~~h 163 (196)
|.|+.|++.|.+...|..|++.|
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 56788888888888888887764
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.97 E-value=4.7e-06 Score=37.83 Aligned_cols=24 Identities=33% Similarity=0.714 Sum_probs=17.4
Q ss_pred ccCcccccccCCchhHHHHHHHhh
Q psy4683 141 HTCSVCKKIFVNKKNLTTHKKIHL 164 (196)
Q Consensus 141 ~~C~~C~~~f~~~~~l~~H~~~h~ 164 (196)
|.|++|++.|.+...|..|+.+|+
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 578888888888888888887764
No 29
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.95 E-value=5.2e-06 Score=37.43 Aligned_cols=19 Identities=32% Similarity=0.828 Sum_probs=9.2
Q ss_pred cccccccccCCHHHHHHHH
Q psy4683 57 PCRLCSQEFDTKEQRKKHE 75 (196)
Q Consensus 57 ~C~~C~~~f~~~~~l~~H~ 75 (196)
.|+.|++.|.+...|..|+
T Consensus 2 ~C~~C~~~f~~~~~l~~H~ 20 (23)
T PF00096_consen 2 KCPICGKSFSSKSNLKRHM 20 (23)
T ss_dssp EETTTTEEESSHHHHHHHH
T ss_pred CCCCCCCccCCHHHHHHHH
Confidence 4444444444444444444
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.93 E-value=4.9e-06 Score=52.37 Aligned_cols=24 Identities=25% Similarity=0.629 Sum_probs=16.4
Q ss_pred CccCcccccccCCchhHHHHHHHh
Q psy4683 140 PHTCSVCKKIFVNKKNLTTHKKIH 163 (196)
Q Consensus 140 ~~~C~~C~~~f~~~~~l~~H~~~h 163 (196)
.+.|..|++.|.+...|..|++.+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCc
Confidence 567777777777777777777764
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.92 E-value=5.8e-06 Score=52.03 Aligned_cols=74 Identities=19% Similarity=0.342 Sum_probs=22.2
Q ss_pred cccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccccCchHHHHHHHhhcCCCcccccccccccCCchHHHhhhhhhc
Q psy4683 57 PCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLSKNELNVHNIKQH 136 (196)
Q Consensus 57 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 136 (196)
+|..|+..|.+...|..|+...|.-..+ ....+.....+....+... ...+.|..|++.|.+...|..|++.+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~-----~~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIP-----DQKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp ------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred Cccccccccccccccccccccccccccc-----ccccccccccccccccccc-CCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 4899999999999999999777754333 1112223344444444332 236899999999999999999999753
No 32
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.88 E-value=4e-06 Score=61.89 Aligned_cols=70 Identities=21% Similarity=0.294 Sum_probs=47.3
Q ss_pred CCCccCCC--CcccccCchHHHHHHHhhcC-CCcccccccccccCCchHHHhhhhhhcCCCCccCcccccccCCchhHHH
Q psy4683 82 QGLFSCDL--CSYTSTQKYYLVKHKSRHIK-DYNVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIFVNKKNLTT 158 (196)
Q Consensus 82 ~~~~~C~~--C~~~f~~~~~l~~H~~~h~~-~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~ 158 (196)
.+||+|++ |.+.|.+...|..|+..-+. .+... ......+.......+||+|.+|+|.|.+..+|.-
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~----------~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKY 416 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHE----------NPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKY 416 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCC----------CCCccccccccccCCceeccccchhhccCcccee
Confidence 48888876 88888888888888764321 11110 0112223333456789999999999999999988
Q ss_pred HHH
Q psy4683 159 HKK 161 (196)
Q Consensus 159 H~~ 161 (196)
|..
T Consensus 417 Hr~ 419 (423)
T COG5189 417 HRK 419 (423)
T ss_pred ccc
Confidence 864
No 33
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.82 E-value=4.9e-06 Score=39.12 Aligned_cols=25 Identities=36% Similarity=0.712 Sum_probs=18.2
Q ss_pred CccCcccccccCCchhHHHHHHHhh
Q psy4683 140 PHTCSVCKKIFVNKKNLTTHKKIHL 164 (196)
Q Consensus 140 ~~~C~~C~~~f~~~~~l~~H~~~h~ 164 (196)
||.|..|++.|.+...|..|++.|.
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 4677777777777777777776664
No 34
>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=97.80 E-value=1.3e-05 Score=42.60 Aligned_cols=32 Identities=28% Similarity=0.604 Sum_probs=22.7
Q ss_pred CCCCccCcccccccCCchhHHHHHHHhhccCCc
Q psy4683 137 CAQPHTCSVCKKIFVNKKNLTTHKKIHLALDRN 169 (196)
Q Consensus 137 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~ 169 (196)
.++|..||+|+..++...+|++|+.+.|+ .+|
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~-~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHF-KKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTT-TS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhc-ccC
Confidence 46789999999999999999999999887 554
No 35
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.67 E-value=1.6e-05 Score=58.87 Aligned_cols=70 Identities=20% Similarity=0.364 Sum_probs=45.6
Q ss_pred CCCcccccc--cccccCCHHHHHHHHHhhcCCCCCccCC--CCcccccCchHHHHHHHhhcCCCcccccccccccCCchH
Q psy4683 52 SDTKFPCRL--CSQEFDTKEQRKKHERKDHATQGLFSCD--LCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLSKNE 127 (196)
Q Consensus 52 ~~~~~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~~C~--~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~ 127 (196)
+++||+|+. |++.|.+...|+-|+.-.|...+...-+ +--..| -...+||.|..|++.|+...+
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F------------~~~~KPYrCevC~KRYKNlNG 413 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIF------------SAKDKPYRCEVCDKRYKNLNG 413 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccc------------cccCCceeccccchhhccCcc
Confidence 358999997 9999999999999985444322211111 001111 234577888888888877777
Q ss_pred HHhhhh
Q psy4683 128 LNVHNI 133 (196)
Q Consensus 128 l~~H~~ 133 (196)
|+-|+.
T Consensus 414 LKYHr~ 419 (423)
T COG5189 414 LKYHRK 419 (423)
T ss_pred ceeccc
Confidence 777754
No 36
>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=97.66 E-value=4e-05 Score=34.61 Aligned_cols=20 Identities=30% Similarity=0.885 Sum_probs=9.8
Q ss_pred ccccccccccCCHHHHHHHH
Q psy4683 56 FPCRLCSQEFDTKEQRKKHE 75 (196)
Q Consensus 56 ~~C~~C~~~f~~~~~l~~H~ 75 (196)
|.|+.|+..|.+...|..|+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~ 20 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHM 20 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHH
Confidence 34555555555555555555
No 37
>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=97.58 E-value=4.7e-05 Score=35.67 Aligned_cols=21 Identities=24% Similarity=0.689 Sum_probs=14.5
Q ss_pred cccccccccccCCHHHHHHHH
Q psy4683 55 KFPCRLCSQEFDTKEQRKKHE 75 (196)
Q Consensus 55 ~~~C~~C~~~f~~~~~l~~H~ 75 (196)
+|.|..|++.|.+..+|..|+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~ 21 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHK 21 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHH
T ss_pred CCCCCccCCccCChhHHHHHh
Confidence 366777777777777777776
No 38
>KOG2231|consensus
Probab=97.49 E-value=0.00028 Score=58.06 Aligned_cols=126 Identities=26% Similarity=0.425 Sum_probs=86.5
Q ss_pred ccccccccccC---------------CHHHHHHHHHhhcCCCCCccCCCCcc---------cccCchHHHHHHHhhcC-C
Q psy4683 56 FPCRLCSQEFD---------------TKEQRKKHERKDHATQGLFSCDLCSY---------TSTQKYYLVKHKSRHIK-D 110 (196)
Q Consensus 56 ~~C~~C~~~f~---------------~~~~l~~H~~~~h~~~~~~~C~~C~~---------~f~~~~~l~~H~~~h~~-~ 110 (196)
+.|..|+..|. ....|+.|+...|. .+.|.+|-. ..-+...|..|+..--. +
T Consensus 100 ~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H~---~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~ 176 (669)
T KOG2231|consen 100 HSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQHK---LHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDD 176 (669)
T ss_pred hhcCccccchhhhcccCCCccccchhHHHHHHHHHHHhhh---hhccccccccceeeeeeeehehHHHHHHHHhcCCCcc
Confidence 57888877773 78889999976664 356666532 22345677777764221 2
Q ss_pred Cc----ccccccccccCCchHHHhhhhhhcCCCCccCccc------ccccCCchhHHHHHHHhhccCCc-cccC-ceecc
Q psy4683 111 YN----VFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVC------KKIFVNKKNLTTHKKIHLALDRN-YQCD-TYFYE 178 (196)
Q Consensus 111 ~~----~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C------~~~f~~~~~l~~H~~~h~~~~~~-~~C~-~~f~~ 178 (196)
+. -.|..|...|.....|.+|++.++ |.|..| +..|.....|..|.+.+|- --- -.|. +.|..
T Consensus 177 ~s~rGhp~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~Hf-lCE~~~C~~~~f~~ 251 (669)
T KOG2231|consen 177 ESCRGHPLCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGHF-LCEEEFCRTKKFYV 251 (669)
T ss_pred ccccCCccchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcCc-cccccccccceeee
Confidence 21 368999999999999999998777 556666 4668888899999998764 111 2455 77777
Q ss_pred CCchhhhhhhH
Q psy4683 179 GNSLAWEDTSL 189 (196)
Q Consensus 179 ~~~l~~H~~~~ 189 (196)
...+.+|++.|
T Consensus 252 ~~~~ei~lk~~ 262 (669)
T KOG2231|consen 252 AFELEIELKAH 262 (669)
T ss_pred hhHHHHHHHhh
Confidence 76777776633
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.42 E-value=0.00011 Score=33.66 Aligned_cols=24 Identities=33% Similarity=0.692 Sum_probs=20.5
Q ss_pred ccCcccccccCCchhHHHHHHHhh
Q psy4683 141 HTCSVCKKIFVNKKNLTTHKKIHL 164 (196)
Q Consensus 141 ~~C~~C~~~f~~~~~l~~H~~~h~ 164 (196)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 578899999999999999988764
No 40
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.37 E-value=0.0001 Score=55.35 Aligned_cols=133 Identities=21% Similarity=0.372 Sum_probs=93.0
Q ss_pred ccccc--cccccCCHHHHHHHHHhhcCCCCCccCCCCc---cccc------CchHHHHHHHhhcCCCcc----ccccccc
Q psy4683 56 FPCRL--CSQEFDTKEQRKKHERKDHATQGLFSCDLCS---YTST------QKYYLVKHKSRHIKDYNV----FCKICQL 120 (196)
Q Consensus 56 ~~C~~--C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~---~~f~------~~~~l~~H~~~h~~~~~~----~C~~C~~ 120 (196)
|.|+. |.........|..|.+..|. .+.|.+|- +.|+ ....|..|...-..+..| .|..|..
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~---~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~ 228 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHG---FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKI 228 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcC---cEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccc
Confidence 67775 77788888899999976664 36788774 3443 345566665433323233 5999999
Q ss_pred ccCCchHHHhhhhhhcCCCCccCcccccc-------cCCchhHHHHHHHhhccCCccccC----ceeccCCchhhhhhhH
Q psy4683 121 GFLSKNELNVHNIKQHCAQPHTCSVCKKI-------FVNKKNLTTHKKIHLALDRNYQCD----TYFYEGNSLAWEDTSL 189 (196)
Q Consensus 121 ~f~~~~~l~~H~~~~~~~~~~~C~~C~~~-------f~~~~~l~~H~~~h~~~~~~~~C~----~~f~~~~~l~~H~~~~ 189 (196)
.|.+...|..|.+..+. .|.+|++. |.+...|.+|.+.-+-.=..-.|. +.|.....|+.|+...
T Consensus 229 ~FYdDDEL~~HcR~~HE----~ChICD~v~p~~~QYFK~Y~~Le~HF~~~hy~ct~qtc~~~k~~vf~~~~el~~h~~~~ 304 (493)
T COG5236 229 YFYDDDELRRHCRLRHE----ACHICDMVGPIRYQYFKSYEDLEAHFRNAHYCCTFQTCRVGKCYVFPYHTELLEHLTRF 304 (493)
T ss_pred eecChHHHHHHHHhhhh----hhhhhhccCccchhhhhCHHHHHHHhhcCceEEEEEEEecCcEEEeccHHHHHHHHHHH
Confidence 99999999999887763 46666654 777778888877644211111233 7889999999999999
Q ss_pred hhhhhc
Q psy4683 190 EITLLK 195 (196)
Q Consensus 190 h~~~~~ 195 (196)
|+..+|
T Consensus 305 h~~~~~ 310 (493)
T COG5236 305 HKVNAR 310 (493)
T ss_pred hhcccc
Confidence 998775
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=97.32 E-value=0.00011 Score=39.12 Aligned_cols=27 Identities=19% Similarity=0.289 Sum_probs=10.0
Q ss_pred CCCccCCCCcccccCchHHHHHHHhhc
Q psy4683 82 QGLFSCDLCSYTSTQKYYLVKHKSRHI 108 (196)
Q Consensus 82 ~~~~~C~~C~~~f~~~~~l~~H~~~h~ 108 (196)
+.|-.|++|+..+....+|.+|+..++
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H 48 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRH 48 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHT
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHh
Confidence 334444444444444444444444333
No 42
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.21 E-value=0.00026 Score=32.09 Aligned_cols=24 Identities=33% Similarity=0.451 Sum_probs=17.2
Q ss_pred ccCcccccccCCchhHHHHHHHhhc
Q psy4683 141 HTCSVCKKIFVNKKNLTTHKKIHLA 165 (196)
Q Consensus 141 ~~C~~C~~~f~~~~~l~~H~~~h~~ 165 (196)
|.|+.|++... ...|..|++.|++
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 57888888887 7788888888653
No 43
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.98 E-value=0.00087 Score=30.53 Aligned_cols=19 Identities=32% Similarity=0.646 Sum_probs=9.3
Q ss_pred cccccccccCCHHHHHHHH
Q psy4683 57 PCRLCSQEFDTKEQRKKHE 75 (196)
Q Consensus 57 ~C~~C~~~f~~~~~l~~H~ 75 (196)
.|..|++.|.....|..|+
T Consensus 2 ~C~~C~~~f~~~~~l~~H~ 20 (26)
T smart00355 2 RCPECGKVFKSKSALKEHM 20 (26)
T ss_pred CCCCCcchhCCHHHHHHHH
Confidence 3444555555554554444
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.86 E-value=0.00035 Score=31.95 Aligned_cols=23 Identities=26% Similarity=0.664 Sum_probs=15.4
Q ss_pred ccCcccccccCCchhHHHHHHHh
Q psy4683 141 HTCSVCKKIFVNKKNLTTHKKIH 163 (196)
Q Consensus 141 ~~C~~C~~~f~~~~~l~~H~~~h 163 (196)
|.|..|++.|.+...|..|++.+
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 45677777777777777776543
No 45
>PRK04860 hypothetical protein; Provisional
Probab=96.75 E-value=0.00075 Score=46.13 Aligned_cols=29 Identities=21% Similarity=0.722 Sum_probs=14.3
Q ss_pred CccCcccccccCCchhHHHHHHHhhccCCccccC
Q psy4683 140 PHTCSVCKKIFVNKKNLTTHKKIHLALDRNYQCD 173 (196)
Q Consensus 140 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~ 173 (196)
+|.|. |+. ....+.+|.++|.+ +++|.|.
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g-~~~YrC~ 147 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRG-EAVYRCR 147 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcC-CccEECC
Confidence 45554 544 44444555555555 4555544
No 46
>PRK04860 hypothetical protein; Provisional
Probab=96.56 E-value=0.0015 Score=44.61 Aligned_cols=38 Identities=26% Similarity=0.382 Sum_probs=31.1
Q ss_pred cccccccccccCCchHHHhhhhhhcCCCCccCcccccccCCc
Q psy4683 112 NVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIFVNK 153 (196)
Q Consensus 112 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~ 153 (196)
+|.|. |+. ....+.+|.++++++++|.|..|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 58887 887 566788899999999999999999887654
No 47
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=96.52 E-value=0.00049 Score=54.62 Aligned_cols=131 Identities=24% Similarity=0.344 Sum_probs=89.2
Q ss_pred CcccccccccccCCHHHHHHHHHh-hcCCC--CCccCC--CCcccccCchHHHHHHHhhcCCCcccccc--cc-------
Q psy4683 54 TKFPCRLCSQEFDTKEQRKKHERK-DHATQ--GLFSCD--LCSYTSTQKYYLVKHKSRHIKDYNVFCKI--CQ------- 119 (196)
Q Consensus 54 ~~~~C~~C~~~f~~~~~l~~H~~~-~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h~~~~~~~C~~--C~------- 119 (196)
.++.|..|...|.....+.+|.+. .|.++ +++.|+ .|++.|.....+..|...|.+..++.+.. +.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 367 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLL 367 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccccccc
Confidence 368899999999999999999942 79998 999999 79999999999999998888766554433 22
Q ss_pred ----------------------------cccCCchHHHhhhhhhcCCC--CccCcccccccCCchhHHHHHHHhhccCCc
Q psy4683 120 ----------------------------LGFLSKNELNVHNIKQHCAQ--PHTCSVCKKIFVNKKNLTTHKKIHLALDRN 169 (196)
Q Consensus 120 ----------------------------~~f~~~~~l~~H~~~~~~~~--~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~ 169 (196)
..+.....+..|...+...+ .+.+..|...|.....+..|++.|.. ..+
T Consensus 368 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~ 446 (467)
T COG5048 368 NNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTN-HAP 446 (467)
T ss_pred CCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCccccccccccccc-CCc
Confidence 22222222222222222222 35567788888888888888888876 555
Q ss_pred cccC--ceeccCCchhhh
Q psy4683 170 YQCD--TYFYEGNSLAWE 185 (196)
Q Consensus 170 ~~C~--~~f~~~~~l~~H 185 (196)
+-|. +.|.....+..|
T Consensus 447 ~~~~~~~~~~~~~~~~~~ 464 (467)
T COG5048 447 LLCSILKSFRRDLDLSNH 464 (467)
T ss_pred eeeccccccchhhhhhcc
Confidence 5555 444444444433
No 48
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.51 E-value=0.0014 Score=29.87 Aligned_cols=18 Identities=22% Similarity=0.826 Sum_probs=8.0
Q ss_pred ccccccccCCHHHHHHHH
Q psy4683 58 CRLCSQEFDTKEQRKKHE 75 (196)
Q Consensus 58 C~~C~~~f~~~~~l~~H~ 75 (196)
|..|+..|.+...+..|+
T Consensus 3 C~~C~~~f~s~~~~~~H~ 20 (25)
T PF12874_consen 3 CDICNKSFSSENSLRQHL 20 (25)
T ss_dssp ETTTTEEESSHHHHHHHH
T ss_pred CCCCCCCcCCHHHHHHHH
Confidence 444444444444444443
No 49
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.50 E-value=0.0021 Score=28.95 Aligned_cols=20 Identities=40% Similarity=0.810 Sum_probs=7.8
Q ss_pred cCCCCcccccCchHHHHHHHh
Q psy4683 86 SCDLCSYTSTQKYYLVKHKSR 106 (196)
Q Consensus 86 ~C~~C~~~f~~~~~l~~H~~~ 106 (196)
+|+.|+.... ...|..|++.
T Consensus 2 ~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 2 KCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp E-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCcCC-HHHHHHHHHh
Confidence 3444444443 4444444443
No 50
>KOG2482|consensus
Probab=96.36 E-value=0.007 Score=45.68 Aligned_cols=130 Identities=18% Similarity=0.270 Sum_probs=80.7
Q ss_pred ccccccccccc-CCHHHHHHHHHhhcCCC---------------------CCccCCCCcccccCchHHHHHHHh--hcCC
Q psy4683 55 KFPCRLCSQEF-DTKEQRKKHERKDHATQ---------------------GLFSCDLCSYTSTQKYYLVKHKSR--HIKD 110 (196)
Q Consensus 55 ~~~C~~C~~~f-~~~~~l~~H~~~~h~~~---------------------~~~~C~~C~~~f~~~~~l~~H~~~--h~~~ 110 (196)
..+|-.|...+ +.++.+..|+-..|.-. ..+.|-.|.+.|+.+..|..||+. |...
T Consensus 144 slqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK~Hrri 223 (423)
T KOG2482|consen 144 SLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKKRHRRI 223 (423)
T ss_pred eeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhccCccc
Confidence 36799997655 67888888887666421 127999999999999999999984 3322
Q ss_pred Cc--------ccc--cccccccCCchHHHhhh--hhh---------------cCCCC--ccCcccccccCCchhHHHHHH
Q psy4683 111 YN--------VFC--KICQLGFLSKNELNVHN--IKQ---------------HCAQP--HTCSVCKKIFVNKKNLTTHKK 161 (196)
Q Consensus 111 ~~--------~~C--~~C~~~f~~~~~l~~H~--~~~---------------~~~~~--~~C~~C~~~f~~~~~l~~H~~ 161 (196)
.| |.= ..-|++.. ....+. .+- .+..+ ..|-.|.....+...|..||.
T Consensus 224 nPknreYDkfyiINY~ev~ks~t---~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v~CLfC~~~~en~~~l~eHmk 300 (423)
T KOG2482|consen 224 NPKNREYDKFYIINYLEVGKSWT---IVHSEDDRETNEDINETDDTWSDWNEDDAEALSVVCLFCTNFYENPVFLFEHMK 300 (423)
T ss_pred CCCccccceEEEEeHhhcCCccc---hhhhhhhhhhhccccccccchhhhhcCCCCccceEEEeeccchhhHHHHHHHHH
Confidence 22 100 00111110 001111 000 01112 478888888888888888888
Q ss_pred Hhhc-----------------------------cCCccccCceeccCCchhhhhh
Q psy4683 162 IHLA-----------------------------LDRNYQCDTYFYEGNSLAWEDT 187 (196)
Q Consensus 162 ~h~~-----------------------------~~~~~~C~~~f~~~~~l~~H~~ 187 (196)
+-|. ..+++.|.-.|.....|+.||.
T Consensus 301 ~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~ 355 (423)
T KOG2482|consen 301 IVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMV 355 (423)
T ss_pred HHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcc
Confidence 7552 1245567788889999999984
No 51
>KOG2482|consensus
Probab=96.15 E-value=0.022 Score=43.15 Aligned_cols=66 Identities=18% Similarity=0.283 Sum_probs=40.6
Q ss_pred HHHHHHHhhcCCCCCccCCCCccccc-CchHHHHHHHhhcC---C-------------------CcccccccccccCCch
Q psy4683 70 QRKKHERKDHATQGLFSCDLCSYTST-QKYYLVKHKSRHIK---D-------------------YNVFCKICQLGFLSKN 126 (196)
Q Consensus 70 ~l~~H~~~~h~~~~~~~C~~C~~~f~-~~~~l~~H~~~h~~---~-------------------~~~~C~~C~~~f~~~~ 126 (196)
.|.++++..-.......|-.|...+. +++.+..|+-.-++ + ..+.|-.|.+.|..+.
T Consensus 130 aLeqqQ~Eredt~fslqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkn 209 (423)
T KOG2482|consen 130 ALEQQQKEREDTIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKN 209 (423)
T ss_pred HHHHHHHHhcCCeeeeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcH
Confidence 34555533322334567989987664 45666677643221 1 1257888888888888
Q ss_pred HHHhhhhhh
Q psy4683 127 ELNVHNIKQ 135 (196)
Q Consensus 127 ~l~~H~~~~ 135 (196)
.|..||+..
T Consensus 210 tLkeHMrkK 218 (423)
T KOG2482|consen 210 TLKEHMRKK 218 (423)
T ss_pred HHHHHHHhc
Confidence 888888753
No 52
>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=95.91 E-value=0.0044 Score=28.81 Aligned_cols=20 Identities=35% Similarity=0.750 Sum_probs=15.4
Q ss_pred ccccccccccCCHHHHHHHH
Q psy4683 56 FPCRLCSQEFDTKEQRKKHE 75 (196)
Q Consensus 56 ~~C~~C~~~f~~~~~l~~H~ 75 (196)
|-|..|++.|.+...+..|+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~ 21 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHM 21 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCT
T ss_pred CCcccCCCCcCCHHHHHHHH
Confidence 56777888888888877777
No 53
>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=95.86 E-value=0.0039 Score=29.00 Aligned_cols=18 Identities=39% Similarity=0.711 Sum_probs=7.5
Q ss_pred ccccccccCCchHHHhhh
Q psy4683 115 CKICQLGFLSKNELNVHN 132 (196)
Q Consensus 115 C~~C~~~f~~~~~l~~H~ 132 (196)
|..|++.|.+...+..|+
T Consensus 4 C~~C~k~f~~~~~~~~H~ 21 (27)
T PF12171_consen 4 CDACDKYFSSENQLKQHM 21 (27)
T ss_dssp BTTTTBBBSSHHHHHCCT
T ss_pred cccCCCCcCCHHHHHHHH
Confidence 444444444444444443
No 54
>KOG1146|consensus
Probab=95.80 E-value=0.0034 Score=55.24 Aligned_cols=104 Identities=14% Similarity=0.224 Sum_probs=71.8
Q ss_pred ccccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccccCchHHHHHHHhhcCCCcccccccccccCCchHHHhhhhhh
Q psy4683 56 FPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLSKNELNVHNIKQ 135 (196)
Q Consensus 56 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 135 (196)
-.|..|+..+.....+..|+...+...+-|.|+.|++.|.....|..||+..+.+-.- .+|-.. ...-.+.+-...-
T Consensus 437 ~e~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~--~~c~~g-q~~~~~arg~~~~ 513 (1406)
T KOG1146|consen 437 VELTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS--AYCKAG-QNHPRLARGEVYR 513 (1406)
T ss_pred ccccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccch--hHhHhc-ccccccccccccc
Confidence 3466777788888888887766677778999999999999999999999974432111 222211 1111111111223
Q ss_pred cCCCCccCcccccccCCchhHHHHHHH
Q psy4683 136 HCAQPHTCSVCKKIFVNKKNLTTHKKI 162 (196)
Q Consensus 136 ~~~~~~~C~~C~~~f~~~~~l~~H~~~ 162 (196)
.+.++|.|..|...+....+|.+|+..
T Consensus 514 ~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 514 CPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred CCCCcccceeeeeeeecchHHHHHHHH
Confidence 345789999999999999999999876
No 55
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.78 E-value=0.0075 Score=27.51 Aligned_cols=20 Identities=40% Similarity=0.924 Sum_probs=12.2
Q ss_pred cCcccccccCCchhHHHHHHH
Q psy4683 142 TCSVCKKIFVNKKNLTTHKKI 162 (196)
Q Consensus 142 ~C~~C~~~f~~~~~l~~H~~~ 162 (196)
.|+.||+.| ....|.+|+.+
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHHh
Confidence 566666666 55566666543
No 56
>KOG2231|consensus
Probab=95.68 E-value=0.013 Score=48.60 Aligned_cols=103 Identities=19% Similarity=0.361 Sum_probs=70.4
Q ss_pred ccCCCCcccc---------------cCchHHHHHHHhhcCCCcccccccc---------cccCCchHHHhhhhhhcC-CC
Q psy4683 85 FSCDLCSYTS---------------TQKYYLVKHKSRHIKDYNVFCKICQ---------LGFLSKNELNVHNIKQHC-AQ 139 (196)
Q Consensus 85 ~~C~~C~~~f---------------~~~~~l~~H~~~h~~~~~~~C~~C~---------~~f~~~~~l~~H~~~~~~-~~ 139 (196)
+.|.+|++.| .....|..|++.-+ +.+.|..|- ....+...|..|+...-. ++
T Consensus 100 ~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H--~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~ 177 (669)
T KOG2231|consen 100 HSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQH--KLHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDE 177 (669)
T ss_pred hhcCccccchhhhcccCCCccccchhHHHHHHHHHHHhh--hhhccccccccceeeeeeeehehHHHHHHHHhcCCCccc
Confidence 4576676666 36678889986433 233444432 222345677777765433 22
Q ss_pred ----CccCcccccccCCchhHHHHHHHhhccCCccccC------ceeccCCchhhhhhhHhh
Q psy4683 140 ----PHTCSVCKKIFVNKKNLTTHKKIHLALDRNYQCD------TYFYEGNSLAWEDTSLEI 191 (196)
Q Consensus 140 ----~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~~C~------~~f~~~~~l~~H~~~~h~ 191 (196)
--.|..|...|-....|++|++.++. -..-|+ ..|....+|..|.+..|.
T Consensus 178 s~rGhp~C~~C~~~fld~~el~rH~~~~h~--~chfC~~~~~~neyy~~~~dLe~HfR~~Hf 237 (669)
T KOG2231|consen 178 SCRGHPLCKFCHERFLDDDELYRHLRFDHE--FCHFCDYKTGQNEYYNDYDDLEEHFRKGHF 237 (669)
T ss_pred cccCCccchhhhhhhccHHHHHHhhcccee--heeecCcccccchhcccchHHHHHhhhcCc
Confidence 24699999999999999999998775 333442 788899999999998884
No 57
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.23 E-value=0.01 Score=44.90 Aligned_cols=102 Identities=23% Similarity=0.361 Sum_probs=73.3
Q ss_pred ccCCC--CcccccCchHHHHHHHhhcCCCcccccccc---ccc------CCchHHHhhhhhhcCCCCc----cCcccccc
Q psy4683 85 FSCDL--CSYTSTQKYYLVKHKSRHIKDYNVFCKICQ---LGF------LSKNELNVHNIKQHCAQPH----TCSVCKKI 149 (196)
Q Consensus 85 ~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~---~~f------~~~~~l~~H~~~~~~~~~~----~C~~C~~~ 149 (196)
|.|+. |.........|..|.+..++. +.|.+|- +.| .+...|..|......+..| .|..|...
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~~--~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~ 229 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHGF--VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIY 229 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcCc--EEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccce
Confidence 78875 666655667888898765532 3465552 233 3456677776554443233 59999999
Q ss_pred cCCchhHHHHHHHhhccCCccccC-------ceeccCCchhhhhhhHh
Q psy4683 150 FVNKKNLTTHKKIHLALDRNYQCD-------TYFYEGNSLAWEDTSLE 190 (196)
Q Consensus 150 f~~~~~l~~H~~~h~~~~~~~~C~-------~~f~~~~~l~~H~~~~h 190 (196)
|-....|.+|++.-+ ++.|.|+ ..|....+|..|.+.-|
T Consensus 230 FYdDDEL~~HcR~~H--E~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h 275 (493)
T COG5236 230 FYDDDELRRHCRLRH--EACHICDMVGPIRYQYFKSYEDLEAHFRNAH 275 (493)
T ss_pred ecChHHHHHHHHhhh--hhhhhhhccCccchhhhhCHHHHHHHhhcCc
Confidence 999999999999977 4899999 67888899999987654
No 58
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=94.73 E-value=0.032 Score=27.51 Aligned_cols=21 Identities=29% Similarity=0.627 Sum_probs=14.1
Q ss_pred cccccccccccCCHHHHHHHH
Q psy4683 55 KFPCRLCSQEFDTKEQRKKHE 75 (196)
Q Consensus 55 ~~~C~~C~~~f~~~~~l~~H~ 75 (196)
+|.|+.|+..|.+...+..|+
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~ 23 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHL 23 (35)
T ss_pred CeEccccCCccCCHHHHHHHH
Confidence 456777777777666666666
No 59
>KOG1146|consensus
Probab=94.69 E-value=0.014 Score=51.63 Aligned_cols=94 Identities=11% Similarity=0.160 Sum_probs=61.3
Q ss_pred cccccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccccCchHHHHHHHhhcCCCcccccccccccCCchHHHhhhhh
Q psy4683 55 KFPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLSKNELNVHNIK 134 (196)
Q Consensus 55 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 134 (196)
-+.|..|++.|.....+. |+- ...+|.|..|...|.....|..|.+. |-+.+.......-+.-.
T Consensus 1260 e~~c~~~~~~~~~~~~~~-~l~----~~~~~~~~~~~~~~~~~~~l~~~~~k-----------~~~~~~~~~~~~~~~l~ 1323 (1406)
T KOG1146|consen 1260 EGECGAVDELLTPSFGIS-TLD----VTHRYLCRQCKMAFDGEAPLTAHQRK-----------FCFAGRGSGGSMPPPLR 1323 (1406)
T ss_pred cchhhhccccccCcccee-ecc----cchhHHHHHHHhhhcchhHHHHHHHH-----------HHhccCccccCCCCccc
Confidence 367888888877666665 542 23467788888888777777777621 11233333333344444
Q ss_pred hcCCCCccCcccccccCCchhHHHHHHHhhc
Q psy4683 135 QHCAQPHTCSVCKKIFVNKKNLTTHKKIHLA 165 (196)
Q Consensus 135 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 165 (196)
+...++| |..|...|+....|..|+++-++
T Consensus 1324 ~~d~~~~-c~~c~~~~~~~~alqihm~~~~~ 1353 (1406)
T KOG1146|consen 1324 VPDCTYH-CLACEVLLSGREALQIHMRSSAH 1353 (1406)
T ss_pred Ccccccc-chHHHhhcchhHHHHHHHHHhhh
Confidence 4445566 99999999999999999988544
No 60
>KOG2893|consensus
Probab=94.62 E-value=0.009 Score=42.88 Aligned_cols=45 Identities=24% Similarity=0.431 Sum_probs=36.1
Q ss_pred ccccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccccCchHHHHHHH
Q psy4683 56 FPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTSTQKYYLVKHKS 105 (196)
Q Consensus 56 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 105 (196)
-.|-.|++.|.+..-|..|++.. -|+|.+|-+.+.+--.|..|..
T Consensus 11 pwcwycnrefddekiliqhqkak-----hfkchichkkl~sgpglsihcm 55 (341)
T KOG2893|consen 11 PWCWYCNREFDDEKILIQHQKAK-----HFKCHICHKKLFSGPGLSIHCM 55 (341)
T ss_pred ceeeecccccchhhhhhhhhhhc-----cceeeeehhhhccCCCceeehh
Confidence 36999999999999999998544 4899999988776666666643
No 61
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=94.58 E-value=0.02 Score=28.03 Aligned_cols=10 Identities=40% Similarity=1.062 Sum_probs=5.8
Q ss_pred CCccCccccc
Q psy4683 139 QPHTCSVCKK 148 (196)
Q Consensus 139 ~~~~C~~C~~ 148 (196)
.++.||.|+.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 4556666653
No 62
>KOG2893|consensus
Probab=94.48 E-value=0.013 Score=42.06 Aligned_cols=41 Identities=24% Similarity=0.519 Sum_probs=21.3
Q ss_pred ccccccccCCchHHHhhhhhhcCCCCccCcccccccCCchhHHHH
Q psy4683 115 CKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIFVNKKNLTTH 159 (196)
Q Consensus 115 C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H 159 (196)
|=.|++.|.+...|..|++.. -|+|.+|.+..-+...|..|
T Consensus 13 cwycnrefddekiliqhqkak----hfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAK----HFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhhhc----cceeeeehhhhccCCCceee
Confidence 444555555555555554432 25555555555555555554
No 63
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=94.25 E-value=0.026 Score=27.83 Aligned_cols=23 Identities=22% Similarity=0.492 Sum_probs=18.6
Q ss_pred CccCcccccccCCchhHHHHHHH
Q psy4683 140 PHTCSVCKKIFVNKKNLTTHKKI 162 (196)
Q Consensus 140 ~~~C~~C~~~f~~~~~l~~H~~~ 162 (196)
+|.|..|+..|.+...+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 57788888888888888888765
No 64
>KOG2785|consensus
Probab=93.97 E-value=0.21 Score=38.62 Aligned_cols=22 Identities=14% Similarity=0.288 Sum_probs=15.3
Q ss_pred CccCCCCcccccCchHHHHHHH
Q psy4683 84 LFSCDLCSYTSTQKYYLVKHKS 105 (196)
Q Consensus 84 ~~~C~~C~~~f~~~~~l~~H~~ 105 (196)
++.|..|.+.|........|+.
T Consensus 68 ~~~c~~c~k~~~s~~a~~~hl~ 89 (390)
T KOG2785|consen 68 VVYCEACNKSFASPKAHENHLK 89 (390)
T ss_pred ceehHHhhccccChhhHHHHHH
Confidence 4677777777777766666664
No 65
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.74 E-value=0.036 Score=30.20 Aligned_cols=31 Identities=19% Similarity=0.432 Sum_probs=23.9
Q ss_pred CCCCCcccccccccccCCHHHHHHHHHhhcC
Q psy4683 50 VTSDTKFPCRLCSQEFDTKEQRKKHERKDHA 80 (196)
Q Consensus 50 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~ 80 (196)
-.++..+.|+-||..|..+.++.+|....|.
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 3455668888888888888888888876663
No 66
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.66 E-value=0.035 Score=30.23 Aligned_cols=30 Identities=17% Similarity=0.330 Sum_probs=24.8
Q ss_pred cCCCCccCcccccccCCchhHHHHHHHhhc
Q psy4683 136 HCAQPHTCSVCKKIFVNKKNLTTHKKIHLA 165 (196)
Q Consensus 136 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 165 (196)
-|+.-+.||.|+..|.......+|....++
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 356678899999999999999999887765
No 67
>KOG4173|consensus
Probab=93.62 E-value=0.037 Score=38.91 Aligned_cols=26 Identities=19% Similarity=0.340 Sum_probs=16.0
Q ss_pred CCCCccCcc--cccccCCchhHHHHHHH
Q psy4683 137 CAQPHTCSV--CKKIFVNKKNLTTHKKI 162 (196)
Q Consensus 137 ~~~~~~C~~--C~~~f~~~~~l~~H~~~ 162 (196)
|...|.|-+ |+..|.+...-..|+-.
T Consensus 141 G~dMy~ClvEgCt~KFkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 141 GQDMYQCLVEGCTEKFKTSRDRKDHMIR 168 (253)
T ss_pred CccHHHHHHHhhhhhhhhhhhhhhHHHH
Confidence 345566643 77777776666666544
No 68
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.07 E-value=0.022 Score=45.12 Aligned_cols=59 Identities=22% Similarity=0.455 Sum_probs=31.9
Q ss_pred cccccccccccCCchHHHhhhh--hhcCC--CCccCc--ccccccCCchhHHHHHHHhhccCCccc
Q psy4683 112 NVFCKICQLGFLSKNELNVHNI--KQHCA--QPHTCS--VCKKIFVNKKNLTTHKKIHLALDRNYQ 171 (196)
Q Consensus 112 ~~~C~~C~~~f~~~~~l~~H~~--~~~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h~~~~~~~~ 171 (196)
++.|..|...|.....+..|.+ .|.++ .++.|+ .|++.|.....+..|..+|.+ ..++.
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~-~~~~~ 353 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTS-ISPAK 353 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccC-CCccc
Confidence 3445555555555555555555 45555 555555 455555555555555555555 44333
No 69
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=92.64 E-value=0.19 Score=32.10 Aligned_cols=26 Identities=23% Similarity=0.342 Sum_probs=23.0
Q ss_pred CccC----cccccccCCchhHHHHHHHhhc
Q psy4683 140 PHTC----SVCKKIFVNKKNLTTHKKIHLA 165 (196)
Q Consensus 140 ~~~C----~~C~~~f~~~~~l~~H~~~h~~ 165 (196)
.|.| ..|++.+.+...+.+|++.+||
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3889 9999999999999999998775
No 70
>KOG2785|consensus
Probab=92.27 E-value=0.23 Score=38.47 Aligned_cols=30 Identities=23% Similarity=0.367 Sum_probs=24.6
Q ss_pred CCCcccccccccccCCHHHHHHHHHhhcCC
Q psy4683 52 SDTKFPCRLCSQEFDTKEQRKKHERKDHAT 81 (196)
Q Consensus 52 ~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 81 (196)
...|-.|-.|++.+.+...-..||...|.-
T Consensus 163 e~~Pt~CLfC~~~~k~~e~~~~HM~~~Hgf 192 (390)
T KOG2785|consen 163 ELIPTDCLFCDKKSKSLEENLKHMFKEHGF 192 (390)
T ss_pred ccCCcceeecCCCcccHHHHHHHHhhccCC
Confidence 334678999999999999999999766653
No 71
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.15 E-value=0.25 Score=31.52 Aligned_cols=24 Identities=29% Similarity=0.721 Sum_probs=14.7
Q ss_pred CccCcccccccCCchhHHHHHHHh
Q psy4683 140 PHTCSVCKKIFVNKKNLTTHKKIH 163 (196)
Q Consensus 140 ~~~C~~C~~~f~~~~~l~~H~~~h 163 (196)
.|.|+.|...|=..=....|...|
T Consensus 81 ~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 81 RYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred ceeCCCCCCccccccchhhhhhcc
Confidence 466666666666655555555554
No 72
>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=92.08 E-value=0.084 Score=33.61 Aligned_cols=13 Identities=31% Similarity=0.710 Sum_probs=6.2
Q ss_pred CccCcccccccCC
Q psy4683 140 PHTCSVCKKIFVN 152 (196)
Q Consensus 140 ~~~C~~C~~~f~~ 152 (196)
|..||.||..|.-
T Consensus 26 PivCP~CG~~~~~ 38 (108)
T PF09538_consen 26 PIVCPKCGTEFPP 38 (108)
T ss_pred CccCCCCCCccCc
Confidence 4445555544443
No 73
>KOG2186|consensus
Probab=90.91 E-value=0.12 Score=37.69 Aligned_cols=47 Identities=28% Similarity=0.506 Sum_probs=27.0
Q ss_pred cccccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccccCchHHHHHHH
Q psy4683 55 KFPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTSTQKYYLVKHKS 105 (196)
Q Consensus 55 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~ 105 (196)
.|.|..||.... ...+.+|+-+ ..+ .-|.|-.|++.|.. .....|..
T Consensus 3 ~FtCnvCgEsvK-Kp~vekH~sr-Crn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 3 FFTCNVCGESVK-KPQVEKHMSR-CRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EEehhhhhhhcc-ccchHHHHHh-ccC-CeeEEeeccccccc-chhhhhhh
Confidence 366777777664 3455557633 323 45677777777765 44455544
No 74
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=90.80 E-value=0.053 Score=39.15 Aligned_cols=13 Identities=15% Similarity=0.424 Sum_probs=10.6
Q ss_pred ccCcccccccCCc
Q psy4683 141 HTCSVCKKIFVNK 153 (196)
Q Consensus 141 ~~C~~C~~~f~~~ 153 (196)
..||.||.+|...
T Consensus 49 ~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 49 WVCPHCGYAAFEE 61 (214)
T ss_pred EECCCCCCccccc
Confidence 5799999987754
No 75
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=89.98 E-value=0.52 Score=30.10 Aligned_cols=84 Identities=15% Similarity=0.247 Sum_probs=57.4
Q ss_pred CcccccccccccCCHHHHHHHHHhhcCC-CCCc------------cCCCCcccccCchHHHHHHHhhcCCCccccccccc
Q psy4683 54 TKFPCRLCSQEFDTKEQRKKHERKDHAT-QGLF------------SCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQL 120 (196)
Q Consensus 54 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~-~~~~------------~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 120 (196)
-|..|+.||-+.-....|.+.. +|.- .++| .|--|...|........ ..-.....|.|..|..
T Consensus 14 LP~~CpiCgLtLVss~HLARSy--HHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~ 89 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARSY--HHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKN 89 (112)
T ss_pred CCCcCCcCCCEEeccchHHHhh--hccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccccceeCCCCCC
Confidence 4678999999999998888875 2321 1222 38889988875431110 0022234689999999
Q ss_pred ccCCchHHHhhhhhhcCCCCccCcccc
Q psy4683 121 GFLSKNELNVHNIKQHCAQPHTCSVCK 147 (196)
Q Consensus 121 ~f~~~~~l~~H~~~~~~~~~~~C~~C~ 147 (196)
.|-..-.+..|...|. |+.|.
T Consensus 90 ~FC~dCD~fiHe~Lh~------CPGC~ 110 (112)
T TIGR00622 90 VFCVDCDVFVHESLHC------CPGCI 110 (112)
T ss_pred ccccccchhhhhhccC------CcCCC
Confidence 9998888888877664 77775
No 76
>KOG2186|consensus
Probab=89.79 E-value=0.2 Score=36.56 Aligned_cols=54 Identities=24% Similarity=0.314 Sum_probs=38.4
Q ss_pred ccCCCCcccccCchHHHHHHHhhcCCCcccccccccccCCchHHHhhhhhhcCCCCc
Q psy4683 85 FSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLSKNELNVHNIKQHCAQPH 141 (196)
Q Consensus 85 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~ 141 (196)
|.|..||.....+ .+.+|+...++ ..|.|..|+.+|-. -....|..--+..+.|
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kCITEaQKY 57 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCITEAQKY 57 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhccC-CeeEEeeccccccc-chhhhhhhhcchHHHh
Confidence 6788898877644 56668887776 67889999998887 5566776555544434
No 77
>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=89.74 E-value=0.66 Score=29.57 Aligned_cols=82 Identities=21% Similarity=0.165 Sum_probs=44.5
Q ss_pred cccccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccccCchHHHH-HHHhhc------------CCCcccc----cc
Q psy4683 55 KFPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTSTQKYYLVK-HKSRHI------------KDYNVFC----KI 117 (196)
Q Consensus 55 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~-H~~~h~------------~~~~~~C----~~ 117 (196)
-..|..|+.+... +.+..|++..|...+...-..-...+.....|.. ...... .-..|.| ..
T Consensus 11 vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gLp~~~G~~C~~~~~~ 89 (109)
T PF12013_consen 11 VLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGLPVYDGYRCQCDPPH 89 (109)
T ss_pred EEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCCCCCCCCeeeecCCCC
Confidence 3679999988865 8899999655533211100000000000000000 000000 0123789 88
Q ss_pred cccccCCchHHHhhhhhhcC
Q psy4683 118 CQLGFLSKNELNVHNIKQHC 137 (196)
Q Consensus 118 C~~~f~~~~~l~~H~~~~~~ 137 (196)
|+....+...+..|++.+||
T Consensus 90 C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 90 CGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCcEeccHHHHHHHHHHhcC
Confidence 99999999999999988775
No 78
>KOG4173|consensus
Probab=89.57 E-value=0.14 Score=36.08 Aligned_cols=78 Identities=21% Similarity=0.281 Sum_probs=55.6
Q ss_pred Ccccccc--cccccCCchHHHhhhhhhcCCCCccCcccccccCCchhHHHHHHHhh---------ccCCccccC-----c
Q psy4683 111 YNVFCKI--CQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIFVNKKNLTTHKKIHL---------ALDRNYQCD-----T 174 (196)
Q Consensus 111 ~~~~C~~--C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~---------~~~~~~~C~-----~ 174 (196)
..|.|++ |-..|.+......|-..-++. .|..|.+.|.+...|-.|+.--| .+..-|.|- .
T Consensus 78 ~~~~cqvagc~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~ 154 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTE 154 (253)
T ss_pred ccccccccchHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhh
Confidence 3466776 667777776666665444443 68889999998888888865433 124457766 8
Q ss_pred eeccCCchhhhhhhHhh
Q psy4683 175 YFYEGNSLAWEDTSLEI 191 (196)
Q Consensus 175 ~f~~~~~l~~H~~~~h~ 191 (196)
.|.+.-.-..|+...|+
T Consensus 155 KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 155 KFKTSRDRKDHMIRMHK 171 (253)
T ss_pred hhhhhhhhhhHHHHhcc
Confidence 89999999999988775
No 79
>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=89.33 E-value=0.2 Score=24.66 Aligned_cols=8 Identities=38% Similarity=1.394 Sum_probs=4.2
Q ss_pred CccCcccc
Q psy4683 140 PHTCSVCK 147 (196)
Q Consensus 140 ~~~C~~C~ 147 (196)
|..||.|+
T Consensus 18 p~~CP~Cg 25 (34)
T cd00729 18 PEKCPICG 25 (34)
T ss_pred CCcCcCCC
Confidence 34555555
No 80
>PHA00626 hypothetical protein
Probab=88.92 E-value=0.14 Score=28.00 Aligned_cols=17 Identities=12% Similarity=0.172 Sum_probs=11.4
Q ss_pred CCCccCcccccccCCch
Q psy4683 138 AQPHTCSVCKKIFVNKK 154 (196)
Q Consensus 138 ~~~~~C~~C~~~f~~~~ 154 (196)
.+.|.|+.||+.|+..+
T Consensus 21 snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 21 SDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CcceEcCCCCCeechhh
Confidence 35677888877776543
No 81
>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=88.84 E-value=0.37 Score=33.03 Aligned_cols=33 Identities=15% Similarity=0.395 Sum_probs=18.4
Q ss_pred CCCcccccccccccCCchHHHhhhhhhcCCCCccCccccccc
Q psy4683 109 KDYNVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIF 150 (196)
Q Consensus 109 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f 150 (196)
....|.|+.|+..|+...++. ..|.||.||...
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 344566666666665555543 146666666543
No 82
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=88.32 E-value=0.3 Score=24.54 Aligned_cols=32 Identities=22% Similarity=0.513 Sum_probs=14.1
Q ss_pred cccccccccCCchHHHhhhhhhcCCCCccCccccccc
Q psy4683 114 FCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIF 150 (196)
Q Consensus 114 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f 150 (196)
.|+.|+..|.....- ...+....+|+.|+..|
T Consensus 4 ~CP~C~~~f~v~~~~-----l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDK-----LPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHH-----cccCCcEEECCCCCcEe
Confidence 455555555544321 11222344555555544
No 83
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=88.14 E-value=0.42 Score=30.49 Aligned_cols=30 Identities=17% Similarity=0.413 Sum_probs=17.0
Q ss_pred ccccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccccCc
Q psy4683 56 FPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTSTQK 97 (196)
Q Consensus 56 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~ 97 (196)
..|..||+.|... +..|..|+.||..|.-.
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 4566677666422 22456677777666443
No 84
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.61 E-value=0.33 Score=25.63 Aligned_cols=10 Identities=30% Similarity=1.009 Sum_probs=5.7
Q ss_pred cccccccccc
Q psy4683 56 FPCRLCSQEF 65 (196)
Q Consensus 56 ~~C~~C~~~f 65 (196)
|.|..||..|
T Consensus 4 y~C~~CG~~~ 13 (46)
T PRK00398 4 YKCARCGREV 13 (46)
T ss_pred EECCCCCCEE
Confidence 5555565555
No 85
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=87.43 E-value=0.4 Score=26.68 Aligned_cols=10 Identities=40% Similarity=0.863 Sum_probs=6.3
Q ss_pred CCccCccccc
Q psy4683 139 QPHTCSVCKK 148 (196)
Q Consensus 139 ~~~~C~~C~~ 148 (196)
.+|.|+.||+
T Consensus 47 ~~Y~CP~CGF 56 (59)
T PRK14890 47 NPYTCPKCGF 56 (59)
T ss_pred CceECCCCCC
Confidence 4566666664
No 86
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=86.73 E-value=0.53 Score=26.17 Aligned_cols=9 Identities=44% Similarity=1.254 Sum_probs=4.3
Q ss_pred ccccccccc
Q psy4683 56 FPCRLCSQE 64 (196)
Q Consensus 56 ~~C~~C~~~ 64 (196)
|.|+.||..
T Consensus 28 F~CPnCGe~ 36 (61)
T COG2888 28 FPCPNCGEV 36 (61)
T ss_pred eeCCCCCce
Confidence 445555543
No 87
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=86.19 E-value=0.56 Score=23.36 Aligned_cols=10 Identities=20% Similarity=0.557 Sum_probs=4.8
Q ss_pred ccCCCCcccc
Q psy4683 85 FSCDLCSYTS 94 (196)
Q Consensus 85 ~~C~~C~~~f 94 (196)
.+|+.|+..|
T Consensus 26 v~C~~C~~~f 35 (36)
T PF13717_consen 26 VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEe
Confidence 4455555443
No 88
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=86.12 E-value=0.44 Score=23.92 Aligned_cols=9 Identities=33% Similarity=0.970 Sum_probs=4.3
Q ss_pred ccccccccc
Q psy4683 57 PCRLCSQEF 65 (196)
Q Consensus 57 ~C~~C~~~f 65 (196)
.|+.|+..|
T Consensus 4 ~CP~C~~~~ 12 (38)
T TIGR02098 4 QCPNCKTSF 12 (38)
T ss_pred ECCCCCCEE
Confidence 344455444
No 89
>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=85.38 E-value=0.52 Score=30.70 Aligned_cols=15 Identities=7% Similarity=-0.057 Sum_probs=7.7
Q ss_pred CcccccccccccCCc
Q psy4683 111 YNVFCKICQLGFLSK 125 (196)
Q Consensus 111 ~~~~C~~C~~~f~~~ 125 (196)
.|..|+.||..|...
T Consensus 25 ~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 25 RPAVSPYTGEQFPPE 39 (129)
T ss_pred CCccCCCcCCccCcc
Confidence 345555555555443
No 90
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=85.30 E-value=0.64 Score=32.56 Aligned_cols=34 Identities=18% Similarity=0.574 Sum_probs=19.4
Q ss_pred CCcccccccccccCCchHHHhhhhhhcCCCCccCcccccccCC
Q psy4683 110 DYNVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIFVN 152 (196)
Q Consensus 110 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~ 152 (196)
...|.|+.|+..|....++. ..|.||.||.....
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLEE 148 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCee
Confidence 34566766666666555442 24677777655433
No 91
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=84.89 E-value=0.54 Score=24.64 Aligned_cols=11 Identities=18% Similarity=0.280 Sum_probs=4.9
Q ss_pred ccccccccccC
Q psy4683 113 VFCKICQLGFL 123 (196)
Q Consensus 113 ~~C~~C~~~f~ 123 (196)
|.|..||..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 34444444433
No 92
>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=84.41 E-value=0.31 Score=26.45 Aligned_cols=11 Identities=18% Similarity=0.661 Sum_probs=5.0
Q ss_pred ccCCCCccccc
Q psy4683 85 FSCDLCSYTST 95 (196)
Q Consensus 85 ~~C~~C~~~f~ 95 (196)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 44444444443
No 93
>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=83.94 E-value=1.1 Score=30.69 Aligned_cols=33 Identities=18% Similarity=0.229 Sum_probs=23.5
Q ss_pred CCCCccCCCCcccccCchHHHHHHHhhcCCCccccccccccc
Q psy4683 81 TQGLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGF 122 (196)
Q Consensus 81 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 122 (196)
+..-|.|+.|+..|.....+. ..|.|+.||...
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 345588888888887666653 368888888754
No 94
>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=83.32 E-value=1.2 Score=23.23 Aligned_cols=24 Identities=25% Similarity=0.549 Sum_probs=14.0
Q ss_pred CcccccccccccCCH----HHHHHHHHh
Q psy4683 54 TKFPCRLCSQEFDTK----EQRKKHERK 77 (196)
Q Consensus 54 ~~~~C~~C~~~f~~~----~~l~~H~~~ 77 (196)
....|..|++.+... ++|.+|++.
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHHHH
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhhhh
Confidence 456788888888654 677777744
No 95
>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=83.05 E-value=0.35 Score=24.65 Aligned_cols=11 Identities=27% Similarity=0.495 Sum_probs=5.2
Q ss_pred ccccccccccC
Q psy4683 113 VFCKICQLGFL 123 (196)
Q Consensus 113 ~~C~~C~~~f~ 123 (196)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 34555555443
No 96
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=82.89 E-value=0.57 Score=32.82 Aligned_cols=32 Identities=22% Similarity=0.335 Sum_probs=21.1
Q ss_pred CCccCCCCcccccCchHHHHHHHhhcCCCcccccccccccC
Q psy4683 83 GLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFL 123 (196)
Q Consensus 83 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 123 (196)
.-|.|+.|+..|.....+. ..|.|+.||....
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLE 147 (178)
T ss_pred CEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCe
Confidence 4477888887776555432 3678888876543
No 97
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=82.47 E-value=0.24 Score=35.76 Aligned_cols=19 Identities=42% Similarity=0.903 Sum_probs=13.0
Q ss_pred CcccccccccccCCHHHHH
Q psy4683 54 TKFPCRLCSQEFDTKEQRK 72 (196)
Q Consensus 54 ~~~~C~~C~~~f~~~~~l~ 72 (196)
+.+.|+.|++.|....-..
T Consensus 4 k~~~CPvC~~~F~~~~vrs 22 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRS 22 (214)
T ss_pred CceECCCCCCeeeeeEEEc
Confidence 3567888888887664433
No 98
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=82.24 E-value=0.79 Score=31.60 Aligned_cols=23 Identities=22% Similarity=0.728 Sum_probs=14.9
Q ss_pred cccccccccccCCchHHHhhhhhhcCCCCccCcccc
Q psy4683 112 NVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCK 147 (196)
Q Consensus 112 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~ 147 (196)
-|.|++||..+ -++.|..||+||
T Consensus 134 ~~vC~vCGy~~-------------~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTH-------------EGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCcc-------------cCCCCCcCCCCC
Confidence 57777776542 235677777777
No 99
>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=81.95 E-value=0.53 Score=24.34 Aligned_cols=11 Identities=36% Similarity=1.201 Sum_probs=7.0
Q ss_pred ccccccccccC
Q psy4683 56 FPCRLCSQEFD 66 (196)
Q Consensus 56 ~~C~~C~~~f~ 66 (196)
|.|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (42)
T PF09723_consen 6 YRCEECGHEFE 16 (42)
T ss_pred EEeCCCCCEEE
Confidence 56666666663
No 100
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=81.69 E-value=0.97 Score=24.30 Aligned_cols=22 Identities=27% Similarity=0.545 Sum_probs=15.2
Q ss_pred CccCcccccccCCc-----hhHHHHHH
Q psy4683 140 PHTCSVCKKIFVNK-----KNLTTHKK 161 (196)
Q Consensus 140 ~~~C~~C~~~f~~~-----~~l~~H~~ 161 (196)
.-.|..|++.++.. +.|.+|+.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 34677787777655 47777777
No 101
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=81.31 E-value=1.3 Score=29.89 Aligned_cols=36 Identities=17% Similarity=0.233 Sum_probs=20.2
Q ss_pred CCccCCCCcccccCchHHHHHHHhhcCCCccccccccccc
Q psy4683 83 GLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGF 122 (196)
Q Consensus 83 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 122 (196)
.-|.|+.|+..|.....+.. ... ...|.|+.||...
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQL---LDM-DGTFTCPRCGEEL 133 (147)
T ss_pred cEEECcCCCCEeeHHHHHHh---cCC-CCcEECCCCCCEE
Confidence 45778888877764332211 011 2337788887654
No 102
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=80.69 E-value=1.6 Score=29.50 Aligned_cols=39 Identities=15% Similarity=0.268 Sum_probs=26.8
Q ss_pred CCCcccccccccccCCchHHHhhhhhhcCCCCccCcccccccC
Q psy4683 109 KDYNVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIFV 151 (196)
Q Consensus 109 ~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 151 (196)
....|.|+.|+..|....++..- .. ...|.||.||....
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~---d~-~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLL---DM-DGTFTCPRCGEELE 134 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhc---CC-CCcEECCCCCCEEE
Confidence 45578999999999876554331 11 33499999997754
No 103
>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=79.75 E-value=1 Score=29.79 Aligned_cols=27 Identities=26% Similarity=0.362 Sum_probs=16.8
Q ss_pred CCccCcccccccCCchhHHHHHHHhhccCCc
Q psy4683 139 QPHTCSVCKKIFVNKKNLTTHKKIHLALDRN 169 (196)
Q Consensus 139 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~ 169 (196)
....|-+||+.|.. |.+|++.|+| -.|
T Consensus 71 d~i~clecGk~~k~---LkrHL~~~~g-ltp 97 (132)
T PF05443_consen 71 DYIICLECGKKFKT---LKRHLRTHHG-LTP 97 (132)
T ss_dssp S-EE-TBT--EESB---HHHHHHHTT--S-H
T ss_pred CeeEEccCCcccch---HHHHHHHccC-CCH
Confidence 44689999999875 4899999987 444
No 104
>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=78.33 E-value=1.7 Score=19.84 Aligned_cols=19 Identities=21% Similarity=0.543 Sum_probs=13.0
Q ss_pred cCcccccccCCchhHHHHHH
Q psy4683 142 TCSVCKKIFVNKKNLTTHKK 161 (196)
Q Consensus 142 ~C~~C~~~f~~~~~l~~H~~ 161 (196)
.||+|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 578888777 5556666665
No 105
>PRK04023 DNA polymerase II large subunit; Validated
Probab=78.03 E-value=2.4 Score=37.43 Aligned_cols=13 Identities=15% Similarity=0.399 Sum_probs=8.9
Q ss_pred CccCcccccccCC
Q psy4683 140 PHTCSVCKKIFVN 152 (196)
Q Consensus 140 ~~~C~~C~~~f~~ 152 (196)
++.|+.||..-..
T Consensus 663 ~y~CPKCG~El~~ 675 (1121)
T PRK04023 663 EDECEKCGREPTP 675 (1121)
T ss_pred CCcCCCCCCCCCc
Confidence 4778888866443
No 106
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=77.95 E-value=0.41 Score=32.61 Aligned_cols=17 Identities=18% Similarity=0.094 Sum_probs=11.6
Q ss_pred ccCCCCcccccCchHHH
Q psy4683 85 FSCDLCSYTSTQKYYLV 101 (196)
Q Consensus 85 ~~C~~C~~~f~~~~~l~ 101 (196)
++|+.||++|.+...+.
T Consensus 29 ~~c~~c~~~f~~~e~~~ 45 (154)
T PRK00464 29 RECLACGKRFTTFERVE 45 (154)
T ss_pred eeccccCCcceEeEecc
Confidence 67888888877654443
No 107
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=77.75 E-value=1.2 Score=23.90 Aligned_cols=11 Identities=27% Similarity=0.954 Sum_probs=7.3
Q ss_pred ccccccccccc
Q psy4683 55 KFPCRLCSQEF 65 (196)
Q Consensus 55 ~~~C~~C~~~f 65 (196)
.|.|..||+.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 36677777766
No 108
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=76.58 E-value=1.5 Score=26.52 Aligned_cols=11 Identities=27% Similarity=0.612 Sum_probs=5.5
Q ss_pred ccccccccccC
Q psy4683 113 VFCKICQLGFL 123 (196)
Q Consensus 113 ~~C~~C~~~f~ 123 (196)
+.|..|+..|.
T Consensus 54 W~C~kCg~~fA 64 (89)
T COG1997 54 WKCRKCGAKFA 64 (89)
T ss_pred EEcCCCCCeec
Confidence 44555555544
No 109
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=76.36 E-value=1.6 Score=28.63 Aligned_cols=28 Identities=18% Similarity=0.476 Sum_probs=19.2
Q ss_pred cccccccccccCCHHHHHHHHHhhcCCCCCccCCCCccc
Q psy4683 55 KFPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYT 93 (196)
Q Consensus 55 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~ 93 (196)
|++|..||+.|.+.+.- + . --|+.||..
T Consensus 1 PH~Ct~Cg~~f~dgs~e---i---l-----~GCP~CGg~ 28 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGSKE---I---L-----SGCPECGGN 28 (131)
T ss_pred CcccCcCCCCcCCCcHH---H---H-----ccCcccCCc
Confidence 57899999999766531 2 1 249999854
No 110
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=75.28 E-value=2.3 Score=32.28 Aligned_cols=80 Identities=19% Similarity=0.330 Sum_probs=46.1
Q ss_pred CCccCCCCcccccCchHHHHHHHhhcCCCc------------ccccccccccCCchHHHhhhhhhcCCCCccCccccccc
Q psy4683 83 GLFSCDLCSYTSTQKYYLVKHKSRHIKDYN------------VFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIF 150 (196)
Q Consensus 83 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~------------~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f 150 (196)
.|..|+.|+-..-....|.+....-..-++ -.|-.|...|.-...-..-. -+..-.|.|+.|...|
T Consensus 321 LPi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~CQ~~fp~~~~~~~~~--~~ss~rY~Ce~CK~~F 398 (421)
T COG5151 321 LPISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQGPFPKPPVSPFDE--STSSGRYQCELCKSTF 398 (421)
T ss_pred CCccCcchhHHHHHHHHHHHHHHhhccCcccccccCCCCCCCccceeccCCCCCCCCCcccc--cccccceechhhhhhh
Confidence 366788887655444444443222222222 23777777776543211111 1223469999999999
Q ss_pred CCchhHHHHHHHhh
Q psy4683 151 VNKKNLTTHKKIHL 164 (196)
Q Consensus 151 ~~~~~l~~H~~~h~ 164 (196)
-..-....|...|.
T Consensus 399 C~dCdvfiHe~Lh~ 412 (421)
T COG5151 399 CSDCDVFIHETLHF 412 (421)
T ss_pred hhhhHHHHHHHHhh
Confidence 88888888877764
No 111
>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=75.02 E-value=3 Score=20.16 Aligned_cols=10 Identities=20% Similarity=0.534 Sum_probs=5.5
Q ss_pred CccCCCCccc
Q psy4683 84 LFSCDLCSYT 93 (196)
Q Consensus 84 ~~~C~~C~~~ 93 (196)
+..|+.||..
T Consensus 17 ~irC~~CG~R 26 (32)
T PF03604_consen 17 PIRCPECGHR 26 (32)
T ss_dssp TSSBSSSS-S
T ss_pred cEECCcCCCe
Confidence 4566666654
No 112
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=74.60 E-value=2 Score=26.14 Aligned_cols=10 Identities=40% Similarity=0.959 Sum_probs=4.8
Q ss_pred cccccccccc
Q psy4683 56 FPCRLCSQEF 65 (196)
Q Consensus 56 ~~C~~C~~~f 65 (196)
-.|..||..|
T Consensus 59 a~CkkCGfef 68 (97)
T COG3357 59 ARCKKCGFEF 68 (97)
T ss_pred hhhcccCccc
Confidence 3444455444
No 113
>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=74.28 E-value=1.5 Score=20.09 Aligned_cols=10 Identities=30% Similarity=0.577 Sum_probs=6.7
Q ss_pred cCcccccccC
Q psy4683 142 TCSVCKKIFV 151 (196)
Q Consensus 142 ~C~~C~~~f~ 151 (196)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 5777777664
No 114
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=74.26 E-value=1.1 Score=26.29 Aligned_cols=8 Identities=25% Similarity=0.746 Sum_probs=3.5
Q ss_pred ccccccCC
Q psy4683 117 ICQLGFLS 124 (196)
Q Consensus 117 ~C~~~f~~ 124 (196)
.||.+|..
T Consensus 34 eCg~tF~t 41 (72)
T PRK09678 34 NCSATFIT 41 (72)
T ss_pred CCCCEEEE
Confidence 44444443
No 115
>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=73.36 E-value=1.7 Score=23.11 Aligned_cols=9 Identities=33% Similarity=0.881 Sum_probs=4.5
Q ss_pred CccCccccc
Q psy4683 140 PHTCSVCKK 148 (196)
Q Consensus 140 ~~~C~~C~~ 148 (196)
-|.|+.|+.
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 467777764
No 116
>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=73.14 E-value=1.4 Score=19.74 Aligned_cols=10 Identities=30% Similarity=0.763 Sum_probs=6.5
Q ss_pred CCccCccccc
Q psy4683 139 QPHTCSVCKK 148 (196)
Q Consensus 139 ~~~~C~~C~~ 148 (196)
.+|.||.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4577777763
No 117
>PF14353 CpXC: CpXC protein
Probab=72.86 E-value=0.92 Score=29.83 Aligned_cols=13 Identities=31% Similarity=0.651 Sum_probs=7.0
Q ss_pred ccCcccccccCCc
Q psy4683 141 HTCSVCKKIFVNK 153 (196)
Q Consensus 141 ~~C~~C~~~f~~~ 153 (196)
|.||.||..|.-.
T Consensus 39 ~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 39 FTCPSCGHKFRLE 51 (128)
T ss_pred EECCCCCCceecC
Confidence 5555555555443
No 118
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=72.44 E-value=0.84 Score=38.55 Aligned_cols=81 Identities=20% Similarity=0.310 Sum_probs=49.6
Q ss_pred ccccccccccCCHHHHHHHHHhhcCCCCCc-cCCCCcccccCchHHHHHHHhhcCCCcccccccccccCCchHHHhhhhh
Q psy4683 56 FPCRLCSQEFDTKEQRKKHERKDHATQGLF-SCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLSKNELNVHNIK 134 (196)
Q Consensus 56 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~-~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 134 (196)
-.|+.|-+.+-+..+-.-+. || .|..||-.|+-...|---...-+-..--.|+.|.+.|.++.+-. .
T Consensus 102 a~C~~Cl~Ei~dp~~rrY~Y--------PF~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRR----f 169 (750)
T COG0068 102 ATCEDCLEEIFDPNSRRYLY--------PFINCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNRR----F 169 (750)
T ss_pred hhhHHHHHHhcCCCCcceec--------cccccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccccc----c
Confidence 46888876664444322222 33 59999998876554433322222222236999999998886633 3
Q ss_pred hcCCCCccCccccccc
Q psy4683 135 QHCAQPHTCSVCKKIF 150 (196)
Q Consensus 135 ~~~~~~~~C~~C~~~f 150 (196)
| .+|.-||.||-..
T Consensus 170 H--AQp~aCp~CGP~~ 183 (750)
T COG0068 170 H--AQPIACPKCGPHL 183 (750)
T ss_pred c--cccccCcccCCCe
Confidence 3 4678899999743
No 119
>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=72.11 E-value=1.7 Score=32.01 Aligned_cols=124 Identities=16% Similarity=0.213 Sum_probs=64.1
Q ss_pred ccccchhhhhcCCCCcccccCCCCCCCCCCCCCcccccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccccCchHHH
Q psy4683 22 SFLEDENEKRNFSSEEDEESDKLDDEDNVTSDTKFPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTSTQKYYLV 101 (196)
Q Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~ 101 (196)
-.+|+-|+-+.-- ...-|..|.-.-+- ....|..|.+.. ..|. -+.|+|..|.. |.-...--
T Consensus 97 GaiCDfCEawvCH----grkCl~~HaC~Cpl-~da~C~EC~R~v-----------w~hG-Grif~CsfC~~-flCEDDQF 158 (314)
T PF06524_consen 97 GAICDFCEAWVCH----GRKCLSTHACTCPL-QDAVCIECERGV-----------WDHG-GRIFKCSFCDN-FLCEDDQF 158 (314)
T ss_pred hhhhccchhheec----cccccccccccCcC-CCcEeeeeeccc-----------ccCC-CeEEEeecCCC-eeeccchh
Confidence 3455666555333 22333333322221 123577777654 4453 36788888875 33333344
Q ss_pred HHHHhh--cCCCcccccccccccCCchHH-------Hhhhhh----hcCCCCccCcccccccCCchhHHHHHHHhh
Q psy4683 102 KHKSRH--IKDYNVFCKICQLGFLSKNEL-------NVHNIK----QHCAQPHTCSVCKKIFVNKKNLTTHKKIHL 164 (196)
Q Consensus 102 ~H~~~h--~~~~~~~C~~C~~~f~~~~~l-------~~H~~~----~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 164 (196)
.|+.+- .....|+|..|++.-. .+-| ..|.+. ....++++||.|+........|..-.++|.
T Consensus 159 EHQAsCQvLe~E~~KC~SCNrlGq-~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKCg~et~eTkdLSmStR~hk 233 (314)
T PF06524_consen 159 EHQASCQVLESETFKCQSCNRLGQ-YSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKCGYETQETKDLSMSTRSHK 233 (314)
T ss_pred hhhhhhhhhhcccccccccccccc-hhhhheeeeehhhhhhhcccccccCCCCCCCCCCCcccccccceeeeecch
Confidence 455432 2234566666654311 1111 123322 123578999999988887777776666664
No 120
>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=71.76 E-value=1.7 Score=23.43 Aligned_cols=9 Identities=33% Similarity=0.881 Sum_probs=5.6
Q ss_pred CccCccccc
Q psy4683 140 PHTCSVCKK 148 (196)
Q Consensus 140 ~~~C~~C~~ 148 (196)
.|.|+.|+.
T Consensus 34 ~w~CP~C~a 42 (50)
T cd00730 34 DWVCPVCGA 42 (50)
T ss_pred CCCCCCCCC
Confidence 366777763
No 121
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=71.55 E-value=2.9 Score=30.64 Aligned_cols=11 Identities=27% Similarity=0.745 Sum_probs=6.1
Q ss_pred CCccCCCCccc
Q psy4683 83 GLFSCDLCSYT 93 (196)
Q Consensus 83 ~~~~C~~C~~~ 93 (196)
+.|.|..|+..
T Consensus 111 rqFaC~~Cd~~ 121 (278)
T PF15135_consen 111 RQFACSSCDHM 121 (278)
T ss_pred eeeeccccchH
Confidence 44666666543
No 122
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=70.35 E-value=2 Score=36.98 Aligned_cols=49 Identities=18% Similarity=0.416 Sum_probs=25.5
Q ss_pred ccCCCCcccccCchHHHHHHHhhcCCCcccccccccccCCchHHHhhhhhhcCCCCccCcccccc
Q psy4683 85 FSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKI 149 (196)
Q Consensus 85 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~ 149 (196)
..|..||..+..... ..-+..|.......|..||. ....|..|+.||..
T Consensus 436 l~C~~Cg~v~~Cp~C-d~~lt~H~~~~~L~CH~Cg~---------------~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 436 LLCRDCGYIAECPNC-DSPLTLHKATGQLRCHYCGY---------------QEPIPQSCPECGSE 484 (730)
T ss_pred eecccCCCcccCCCC-CcceEEecCCCeeEeCCCCC---------------CCCCCCCCCCCCCC
Confidence 356667665533211 00022233334455666653 34567889999966
No 123
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=66.94 E-value=3.8 Score=35.35 Aligned_cols=46 Identities=22% Similarity=0.496 Sum_probs=24.6
Q ss_pred ccccccccccCCHH---HHHHHHHhhcCCCCCccCCCCcccccCchHHHHHHHhhcCCCcccccccccc
Q psy4683 56 FPCRLCSQEFDTKE---QRKKHERKDHATQGLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLG 121 (196)
Q Consensus 56 ~~C~~C~~~f~~~~---~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 121 (196)
..|..||..+.... .|.- |...+...|..||. ....|..|+.||..
T Consensus 436 l~C~~Cg~v~~Cp~Cd~~lt~-----H~~~~~L~CH~Cg~---------------~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 436 LLCRDCGYIAECPNCDSPLTL-----HKATGQLRCHYCGY---------------QEPIPQSCPECGSE 484 (730)
T ss_pred eecccCCCcccCCCCCcceEE-----ecCCCeeEeCCCCC---------------CCCCCCCCCCCCCC
Confidence 34777776653221 2322 33334566666664 23456677777754
No 124
>KOG4124|consensus
Probab=66.53 E-value=1.3 Score=34.11 Aligned_cols=52 Identities=29% Similarity=0.626 Sum_probs=35.8
Q ss_pred CCcccccc--cccccCCchHHHhhhhhhc-------------------CCCCccCcccccccCCchhHHHHHH
Q psy4683 110 DYNVFCKI--CQLGFLSKNELNVHNIKQH-------------------CAQPHTCSVCKKIFVNKKNLTTHKK 161 (196)
Q Consensus 110 ~~~~~C~~--C~~~f~~~~~l~~H~~~~~-------------------~~~~~~C~~C~~~f~~~~~l~~H~~ 161 (196)
.++++|.+ |.+.+....+|..|.-..+ ..++|+|++|.+.+.....|.-|..
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~~ 419 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHRT 419 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCceee
Confidence 34567765 8888888777777754333 2467888888888888777665543
No 125
>KOG2807|consensus
Probab=66.29 E-value=9.6 Score=29.29 Aligned_cols=68 Identities=21% Similarity=0.354 Sum_probs=39.5
Q ss_pred CCccCCCCcccccCchHHHHHHHhhcCCCccc------------ccccccccCCchHHHhhhhhhcCCCCccCccccccc
Q psy4683 83 GLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVF------------CKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIF 150 (196)
Q Consensus 83 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~------------C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f 150 (196)
.|..|+.|+-..-....|.+-...-.+-++|. |-.|+.. -.+.-.|.|..|.-.|
T Consensus 289 LP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~-------------~~~~~~y~C~~Ck~~F 355 (378)
T KOG2807|consen 289 LPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGE-------------LLSSGRYRCESCKNVF 355 (378)
T ss_pred CCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccc-------------cCCCCcEEchhcccee
Confidence 46778888877777767766554433333321 3333111 1123357888888877
Q ss_pred CCchhHHHHHHHh
Q psy4683 151 VNKKNLTTHKKIH 163 (196)
Q Consensus 151 ~~~~~l~~H~~~h 163 (196)
=..=....|-..|
T Consensus 356 CldCDv~iHesLh 368 (378)
T KOG2807|consen 356 CLDCDVFIHESLH 368 (378)
T ss_pred eccchHHHHhhhh
Confidence 7766666676665
No 126
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=66.08 E-value=3.7 Score=22.05 Aligned_cols=11 Identities=18% Similarity=0.516 Sum_probs=5.3
Q ss_pred CccCCCCcccc
Q psy4683 84 LFSCDLCSYTS 94 (196)
Q Consensus 84 ~~~C~~C~~~f 94 (196)
.+.|..||..|
T Consensus 4 ~l~C~dCg~~F 14 (49)
T PF13451_consen 4 TLTCKDCGAEF 14 (49)
T ss_pred eEEcccCCCeE
Confidence 34455555444
No 127
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=65.62 E-value=4.4 Score=26.73 Aligned_cols=11 Identities=36% Similarity=1.093 Sum_probs=5.5
Q ss_pred CCccCCCCccc
Q psy4683 83 GLFSCDLCSYT 93 (196)
Q Consensus 83 ~~~~C~~C~~~ 93 (196)
+.|.|.+|..+
T Consensus 79 ~lYeCnIC~et 89 (140)
T PF05290_consen 79 KLYECNICKET 89 (140)
T ss_pred CceeccCcccc
Confidence 44555555543
No 128
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=64.24 E-value=1.9 Score=26.41 Aligned_cols=32 Identities=25% Similarity=0.548 Sum_probs=16.8
Q ss_pred CCccCCCCcccccCchHHHHHHHhhcCCCcccccccccccCC
Q psy4683 83 GLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLS 124 (196)
Q Consensus 83 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 124 (196)
..|.|+.|++.-... ...--+.|..|++.|..
T Consensus 34 ~ky~Cp~Cgk~~vkR----------~a~GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKR----------VATGIWKCKKCGKKFAG 65 (90)
T ss_dssp S-BEESSSSSSEEEE----------EETTEEEETTTTEEEE-
T ss_pred CCCcCCCCCCceeEE----------eeeEEeecCCCCCEEeC
Confidence 347777777654221 11223677777766643
No 129
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=64.12 E-value=2.8 Score=25.71 Aligned_cols=32 Identities=16% Similarity=0.312 Sum_probs=16.8
Q ss_pred CCccCCCCcccccCchHHHHHHHhhcCCCcccccccccccCC
Q psy4683 83 GLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLS 124 (196)
Q Consensus 83 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 124 (196)
..|.|+.|++.-... ...-.+.|..|++.|..
T Consensus 35 a~y~CpfCgk~~vkR----------~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 35 AKYFCPFCGKHAVKR----------QAVGIWRCKGCKKTVAG 66 (90)
T ss_pred CCccCCCCCCCceee----------eeeEEEEcCCCCCEEeC
Confidence 356777776542211 11234567777766654
No 130
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=63.75 E-value=2.6 Score=28.07 Aligned_cols=14 Identities=36% Similarity=0.835 Sum_probs=10.7
Q ss_pred cccccccccccCCH
Q psy4683 55 KFPCRLCSQEFDTK 68 (196)
Q Consensus 55 ~~~C~~C~~~f~~~ 68 (196)
.+.|..||..|...
T Consensus 70 ~~~C~~CG~~~~~~ 83 (135)
T PRK03824 70 VLKCRNCGNEWSLK 83 (135)
T ss_pred EEECCCCCCEEecc
Confidence 47899999888653
No 131
>PF15269 zf-C2H2_7: Zinc-finger
Probab=63.33 E-value=4.3 Score=21.12 Aligned_cols=22 Identities=27% Similarity=0.363 Sum_probs=15.4
Q ss_pred ccCcccccccCCchhHHHHHHH
Q psy4683 141 HTCSVCKKIFVNKKNLTTHKKI 162 (196)
Q Consensus 141 ~~C~~C~~~f~~~~~l~~H~~~ 162 (196)
|+|-.|..+..-.+.|..||+-
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 5677777777777777777654
No 132
>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=63.25 E-value=4.9 Score=29.06 Aligned_cols=28 Identities=32% Similarity=0.589 Sum_probs=21.8
Q ss_pred CcccccccccccCCHHHHHHHHHhhcCC
Q psy4683 54 TKFPCRLCSQEFDTKEQRKKHERKDHAT 81 (196)
Q Consensus 54 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~ 81 (196)
..|.|..|++.|....-+..|+...|..
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred CEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 3599999999999999999999877753
No 133
>PF14369 zf-RING_3: zinc-finger
Probab=62.86 E-value=6.9 Score=19.30 Aligned_cols=9 Identities=22% Similarity=0.486 Sum_probs=5.8
Q ss_pred cCCCCcccc
Q psy4683 86 SCDLCSYTS 94 (196)
Q Consensus 86 ~C~~C~~~f 94 (196)
.|+.|+-.|
T Consensus 23 ~CP~C~~gF 31 (35)
T PF14369_consen 23 ACPRCHGGF 31 (35)
T ss_pred CCcCCCCcE
Confidence 477776665
No 134
>KOG4167|consensus
Probab=62.53 E-value=2 Score=36.49 Aligned_cols=26 Identities=31% Similarity=0.553 Sum_probs=23.7
Q ss_pred CccCcccccccCCchhHHHHHHHhhc
Q psy4683 140 PHTCSVCKKIFVNKKNLTTHKKIHLA 165 (196)
Q Consensus 140 ~~~C~~C~~~f~~~~~l~~H~~~h~~ 165 (196)
.|.|.+|++.|-.-.++..||++|.-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 48999999999999999999999964
No 135
>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=62.34 E-value=2.7 Score=25.80 Aligned_cols=13 Identities=23% Similarity=0.485 Sum_probs=7.6
Q ss_pred cccccccccccCC
Q psy4683 112 NVFCKICQLGFLS 124 (196)
Q Consensus 112 ~~~C~~C~~~f~~ 124 (196)
.+.|..|++.|..
T Consensus 53 IW~C~~C~~~~AG 65 (91)
T TIGR00280 53 IWTCRKCGAKFAG 65 (91)
T ss_pred EEEcCCCCCEEeC
Confidence 3566666666543
No 136
>KOG3408|consensus
Probab=61.46 E-value=4 Score=26.37 Aligned_cols=24 Identities=33% Similarity=0.639 Sum_probs=21.4
Q ss_pred CccCcccccccCCchhHHHHHHHh
Q psy4683 140 PHTCSVCKKIFVNKKNLTTHKKIH 163 (196)
Q Consensus 140 ~~~C~~C~~~f~~~~~l~~H~~~h 163 (196)
.|.|..|.+-|.+...|..|.++.
T Consensus 57 qfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 57 QFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred eeehhhhhhhhcchHHHHHHHhcc
Confidence 488999999999999999998873
No 137
>KOG2593|consensus
Probab=60.73 E-value=3.7 Score=32.66 Aligned_cols=38 Identities=21% Similarity=0.541 Sum_probs=22.2
Q ss_pred CCCCCcccccccccccCCHHHHHHHHHhhcCCCCCccCCCCc
Q psy4683 50 VTSDTKFPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCS 91 (196)
Q Consensus 50 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~ 91 (196)
.+....|.|+.|.+.|.....++.=- .....|.|..|+
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea~~L~~----~~~~~F~C~~C~ 160 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEALQLLD----NETGEFHCENCG 160 (436)
T ss_pred ccccccccCCccccchhhhHHHHhhc----ccCceEEEecCC
Confidence 33444577777777776655543322 123457777776
No 138
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.24 E-value=6.1 Score=22.14 Aligned_cols=38 Identities=13% Similarity=0.386 Sum_probs=17.0
Q ss_pred cccccccc-cCCchHHHhhhhhhcCCCCccCcccccccC
Q psy4683 114 FCKICQLG-FLSKNELNVHNIKQHCAQPHTCSVCKKIFV 151 (196)
Q Consensus 114 ~C~~C~~~-f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 151 (196)
+|.+|++. +.+...+..-+-.....+.|.|++|.-...
T Consensus 4 kCiiCd~v~~iD~rt~~tKrLrN~PIrtymC~eC~~Rva 42 (68)
T COG4896 4 KCIICDRVDEIDNRTFKTKRLRNKPIRTYMCPECEHRVA 42 (68)
T ss_pred eEEEecceeeecchhHHHHHhhCCCceeEechhhHhhhc
Confidence 45556542 233333333322233344566776664433
No 139
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=60.18 E-value=8.4 Score=35.21 Aligned_cols=30 Identities=13% Similarity=0.284 Sum_probs=17.2
Q ss_pred cccccccccccCCchHHHhhhhhhcCCCCccCcccccccCC
Q psy4683 112 NVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIFVN 152 (196)
Q Consensus 112 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~ 152 (196)
.+.|+.||....... ++ ...|+.|+.-...
T Consensus 692 vy~CPsCGaev~~de---------s~--a~~CP~CGtplv~ 721 (1337)
T PRK14714 692 VYVCPDCGAEVPPDE---------SG--RVECPRCDVELTP 721 (1337)
T ss_pred ceeCccCCCccCCCc---------cc--cccCCCCCCcccc
Confidence 567888887543311 11 3468999854433
No 140
>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=60.01 E-value=3.2 Score=19.40 Aligned_cols=8 Identities=38% Similarity=0.928 Sum_probs=3.7
Q ss_pred cccccccc
Q psy4683 115 CKICQLGF 122 (196)
Q Consensus 115 C~~C~~~f 122 (196)
|..|++.|
T Consensus 3 CiDC~~~F 10 (28)
T PF08790_consen 3 CIDCSKDF 10 (28)
T ss_dssp ETTTTEEE
T ss_pred eecCCCCc
Confidence 44444444
No 141
>KOG4167|consensus
Probab=59.25 E-value=2 Score=36.45 Aligned_cols=26 Identities=19% Similarity=0.304 Sum_probs=23.5
Q ss_pred CccCCCCcccccCchHHHHHHHhhcC
Q psy4683 84 LFSCDLCSYTSTQKYYLVKHKSRHIK 109 (196)
Q Consensus 84 ~~~C~~C~~~f~~~~~l~~H~~~h~~ 109 (196)
.|.|..|++.|.....+..||+.|.-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 49999999999999999999998863
No 142
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=59.18 E-value=5.4 Score=21.92 Aligned_cols=6 Identities=33% Similarity=0.916 Sum_probs=2.3
Q ss_pred CCCCcc
Q psy4683 87 CDLCSY 92 (196)
Q Consensus 87 C~~C~~ 92 (196)
|+.||.
T Consensus 5 CP~CG~ 10 (54)
T TIGR01206 5 CPDCGA 10 (54)
T ss_pred CCCCCC
Confidence 333333
No 143
>PF12907 zf-met2: Zinc-binding
Probab=58.92 E-value=7 Score=20.00 Aligned_cols=32 Identities=28% Similarity=0.687 Sum_probs=18.4
Q ss_pred cccccccccc---CCHHHHHHHHHhhcCCCCCccC
Q psy4683 56 FPCRLCSQEF---DTKEQRKKHERKDHATQGLFSC 87 (196)
Q Consensus 56 ~~C~~C~~~f---~~~~~l~~H~~~~h~~~~~~~C 87 (196)
+.|.+|-.+| .+...|..|....|....+-.|
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~~~C 36 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKNTFEEC 36 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCCCHHHc
Confidence 4577777544 4455677777656655433333
No 144
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=57.20 E-value=12 Score=19.16 Aligned_cols=22 Identities=32% Similarity=0.688 Sum_probs=10.9
Q ss_pred cCcccccccCCc--hhHHHHHHHh
Q psy4683 142 TCSVCKKIFVNK--KNLTTHKKIH 163 (196)
Q Consensus 142 ~C~~C~~~f~~~--~~l~~H~~~h 163 (196)
.|+.||..|... ..-..|.+-|
T Consensus 15 ~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 15 TCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred CCCCCCCEECCCCHHHHHHHHHHH
Confidence 566666555543 2334444444
No 145
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=56.80 E-value=3.6 Score=25.23 Aligned_cols=32 Identities=16% Similarity=0.414 Sum_probs=16.4
Q ss_pred CCccCCCCcccccCchHHHHHHHhhcCCCcccccccccccCC
Q psy4683 83 GLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLS 124 (196)
Q Consensus 83 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 124 (196)
..|.|+.|++.-... ...-.+.|..|++.|..
T Consensus 35 a~y~CpfCgk~~vkR----------~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 35 AKHVCPVCGRPKVKR----------VGTGIWECRKCGAKFAG 66 (90)
T ss_pred cCccCCCCCCCceEE----------EEEEEEEcCCCCCEEeC
Confidence 346777776542211 12234566667666653
No 146
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.76 E-value=6.1 Score=25.04 Aligned_cols=12 Identities=0% Similarity=0.008 Sum_probs=6.1
Q ss_pred Cccccccccccc
Q psy4683 111 YNVFCKICQLGF 122 (196)
Q Consensus 111 ~~~~C~~C~~~f 122 (196)
.|..|+.||++|
T Consensus 25 dPiVsPytG~s~ 36 (129)
T COG4530 25 DPIVSPYTGKSY 36 (129)
T ss_pred CccccCcccccc
Confidence 344555555555
No 147
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=56.46 E-value=4.7 Score=20.55 Aligned_cols=15 Identities=27% Similarity=0.545 Sum_probs=6.6
Q ss_pred cccccccccCCchHH
Q psy4683 114 FCKICQLGFLSKNEL 128 (196)
Q Consensus 114 ~C~~C~~~f~~~~~l 128 (196)
.|+.|+..+.+...|
T Consensus 21 ~C~~C~G~W~d~~el 35 (41)
T PF13453_consen 21 VCPSCGGIWFDAGEL 35 (41)
T ss_pred ECCCCCeEEccHHHH
Confidence 344444444444333
No 148
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.39 E-value=2.5 Score=30.63 Aligned_cols=9 Identities=22% Similarity=0.722 Sum_probs=6.8
Q ss_pred ccCcccccc
Q psy4683 141 HTCSVCKKI 149 (196)
Q Consensus 141 ~~C~~C~~~ 149 (196)
..||.|+.+
T Consensus 63 vvCP~C~yA 71 (267)
T COG1655 63 VVCPICYYA 71 (267)
T ss_pred EEcchhhHH
Confidence 569999865
No 149
>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=56.37 E-value=5 Score=25.89 Aligned_cols=12 Identities=17% Similarity=0.321 Sum_probs=5.9
Q ss_pred ccccccccccCC
Q psy4683 113 VFCKICQLGFLS 124 (196)
Q Consensus 113 ~~C~~C~~~f~~ 124 (196)
+.|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (115)
T TIGR00100 71 CECEDCSEEVSP 82 (115)
T ss_pred EEcccCCCEEec
Confidence 345555554443
No 150
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=56.00 E-value=7.1 Score=31.23 Aligned_cols=30 Identities=17% Similarity=0.266 Sum_probs=19.4
Q ss_pred cccccccccCCchHHHhhhhhhcCCCCccCcccccccCCch
Q psy4683 114 FCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIFVNKK 154 (196)
Q Consensus 114 ~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~ 154 (196)
.|+.||.+..+. |..-|+|+.||+.+....
T Consensus 352 ~Cp~Cg~~m~S~-----------G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGRMKSA-----------GRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCchhhc-----------CCCCcccccccccCCccc
Confidence 577787765443 223688888887776553
No 151
>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=55.84 E-value=1.3 Score=25.90 Aligned_cols=30 Identities=17% Similarity=0.336 Sum_probs=12.9
Q ss_pred cccccccccccCCchHHHhhhhhhcCCCCccCcccccc
Q psy4683 112 NVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKI 149 (196)
Q Consensus 112 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~ 149 (196)
...|..|+..+..... ..+ ..|.|+.|+..
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 4556666655444322 011 34666666644
No 152
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=55.18 E-value=6 Score=21.84 Aligned_cols=20 Identities=25% Similarity=0.396 Sum_probs=9.0
Q ss_pred hHHHhhhhhhcCCCCccCcc
Q psy4683 126 NELNVHNIKQHCAQPHTCSV 145 (196)
Q Consensus 126 ~~l~~H~~~~~~~~~~~C~~ 145 (196)
..|..|.......++..|+.
T Consensus 24 ~~l~~H~~~~C~~~~v~C~~ 43 (60)
T PF02176_consen 24 KELDDHLENECPKRPVPCPY 43 (60)
T ss_dssp CCHHHHHHTTSTTSEEE-SS
T ss_pred HHHHHHHHccCCCCcEECCC
Confidence 34555555444444445555
No 153
>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=53.70 E-value=8.1 Score=19.19 Aligned_cols=8 Identities=25% Similarity=1.012 Sum_probs=3.7
Q ss_pred cccccccc
Q psy4683 58 CRLCSQEF 65 (196)
Q Consensus 58 C~~C~~~f 65 (196)
|..||..|
T Consensus 4 C~~Cg~~Y 11 (36)
T PF05191_consen 4 CPKCGRIY 11 (36)
T ss_dssp ETTTTEEE
T ss_pred cCCCCCcc
Confidence 44444444
No 154
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=53.57 E-value=1.9 Score=22.04 Aligned_cols=10 Identities=20% Similarity=0.710 Sum_probs=5.3
Q ss_pred ccCccccccc
Q psy4683 141 HTCSVCKKIF 150 (196)
Q Consensus 141 ~~C~~C~~~f 150 (196)
|.|..|+..+
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 5555555443
No 155
>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=53.15 E-value=7.2 Score=28.22 Aligned_cols=27 Identities=19% Similarity=0.381 Sum_probs=17.8
Q ss_pred CCCccCcccccccCCchhHHHHHHHhh
Q psy4683 138 AQPHTCSVCKKIFVNKKNLTTHKKIHL 164 (196)
Q Consensus 138 ~~~~~C~~C~~~f~~~~~l~~H~~~h~ 164 (196)
+..|.|+.|+|.|.-..-..+|+..-|
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcC
Confidence 345778888888887777777777744
No 156
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=52.64 E-value=6.8 Score=21.12 Aligned_cols=10 Identities=20% Similarity=0.531 Sum_probs=4.8
Q ss_pred CccCcccccc
Q psy4683 140 PHTCSVCKKI 149 (196)
Q Consensus 140 ~~~C~~C~~~ 149 (196)
.+.|..||..
T Consensus 37 r~~C~~Cgyt 46 (50)
T PRK00432 37 RWHCGKCGYT 46 (50)
T ss_pred cEECCCcCCE
Confidence 3455555543
No 157
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=52.53 E-value=6.9 Score=25.16 Aligned_cols=11 Identities=18% Similarity=0.365 Sum_probs=5.4
Q ss_pred ccccccccccC
Q psy4683 113 VFCKICQLGFL 123 (196)
Q Consensus 113 ~~C~~C~~~f~ 123 (196)
+.|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (113)
T PRK12380 71 AWCWDCSQVVE 81 (113)
T ss_pred EEcccCCCEEe
Confidence 34555554443
No 158
>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=51.18 E-value=16 Score=19.08 Aligned_cols=9 Identities=22% Similarity=0.800 Sum_probs=4.5
Q ss_pred CCccCcccc
Q psy4683 139 QPHTCSVCK 147 (196)
Q Consensus 139 ~~~~C~~C~ 147 (196)
..|.|..|+
T Consensus 36 ~~~~C~~C~ 44 (46)
T PF12760_consen 36 GRYRCKACR 44 (46)
T ss_pred CeEECCCCC
Confidence 345555554
No 159
>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=50.34 E-value=7.5 Score=26.30 Aligned_cols=31 Identities=26% Similarity=0.583 Sum_probs=17.6
Q ss_pred CCcccccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccc
Q psy4683 53 DTKFPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTS 94 (196)
Q Consensus 53 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f 94 (196)
-+-|.|..||.... ..+.+. .-.|+.|+...
T Consensus 110 ~G~l~C~~Cg~~~~----------~~~~~~-l~~Cp~C~~~~ 140 (146)
T PF07295_consen 110 PGTLVCENCGHEVE----------LTHPER-LPPCPKCGHTE 140 (146)
T ss_pred CceEecccCCCEEE----------ecCCCc-CCCCCCCCCCe
Confidence 34578888877542 223333 23688887653
No 160
>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=50.29 E-value=12 Score=30.45 Aligned_cols=25 Identities=28% Similarity=0.531 Sum_probs=19.2
Q ss_pred ccCcccccccCCchhHHHHHHH-hhc
Q psy4683 141 HTCSVCKKIFVNKKNLTTHKKI-HLA 165 (196)
Q Consensus 141 ~~C~~C~~~f~~~~~l~~H~~~-h~~ 165 (196)
+.|+.|.+.|.....+..|+.. |.+
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhh
Confidence 6788888888888888888776 444
No 161
>KOG2593|consensus
Probab=49.79 E-value=24 Score=28.34 Aligned_cols=39 Identities=15% Similarity=0.186 Sum_probs=24.3
Q ss_pred CCCCccCCCCcccccCchHHHHHHHhhcCCCccccccccccc
Q psy4683 81 TQGLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGF 122 (196)
Q Consensus 81 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 122 (196)
....|.|+.|.+.|.....++ ..-...-.|.|..|+...
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGGEL 163 (436)
T ss_pred ccccccCCccccchhhhHHHH---hhcccCceEEEecCCCch
Confidence 345699999999887554332 222223468888887543
No 162
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=49.43 E-value=7.7 Score=25.13 Aligned_cols=11 Identities=36% Similarity=0.612 Sum_probs=5.5
Q ss_pred ccccccccccC
Q psy4683 113 VFCKICQLGFL 123 (196)
Q Consensus 113 ~~C~~C~~~f~ 123 (196)
+.|..|+..|.
T Consensus 72 ~~C~~Cg~~~~ 82 (117)
T PRK00564 72 LECKDCSHVFK 82 (117)
T ss_pred EEhhhCCCccc
Confidence 34555554443
No 163
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=49.34 E-value=12 Score=29.94 Aligned_cols=18 Identities=22% Similarity=0.519 Sum_probs=9.8
Q ss_pred CCCCCccCCCCcccccCc
Q psy4683 80 ATQGLFSCDLCSYTSTQK 97 (196)
Q Consensus 80 ~~~~~~~C~~C~~~f~~~ 97 (196)
.|.+-|+|+-||..+...
T Consensus 363 ~G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 363 AGRNGFRCKKCGTRARET 380 (421)
T ss_pred cCCCCcccccccccCCcc
Confidence 344456666666655443
No 164
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.41 E-value=8.1 Score=22.74 Aligned_cols=31 Identities=19% Similarity=0.521 Sum_probs=19.2
Q ss_pred cccccccccccCCHHHHHHHHHhhcCCCCC-ccCCCCcccc
Q psy4683 55 KFPCRLCSQEFDTKEQRKKHERKDHATQGL-FSCDLCSYTS 94 (196)
Q Consensus 55 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~-~~C~~C~~~f 94 (196)
.|.|..|+..| .+..++ .+-| -.|+.|+..+
T Consensus 12 ~Y~c~~cg~~~----dvvq~~-----~ddplt~ce~c~a~~ 43 (82)
T COG2331 12 SYECTECGNRF----DVVQAM-----TDDPLTTCEECGARL 43 (82)
T ss_pred EEeecccchHH----HHHHhc-----ccCccccChhhChHH
Confidence 37888888866 444444 2223 3588888644
No 165
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=48.27 E-value=7.9 Score=26.23 Aligned_cols=33 Identities=24% Similarity=0.454 Sum_probs=18.7
Q ss_pred cccccccccccCCchHHHhhhhhhcCCCCccCcccccc
Q psy4683 112 NVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKI 149 (196)
Q Consensus 112 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~ 149 (196)
+|.|. |+..|.+. .+|-..-.|+ .|.|..|+-.
T Consensus 117 ~Y~C~-C~q~~l~~---RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 117 PYRCQ-CQQHYLRI---RRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred eEEee-cCCccchh---hhcccccccc-eEEeccCCce
Confidence 46677 77665543 3344444445 6777777643
No 166
>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=47.87 E-value=5 Score=20.39 Aligned_cols=13 Identities=15% Similarity=0.503 Sum_probs=6.9
Q ss_pred CCCCccCcccccc
Q psy4683 137 CAQPHTCSVCKKI 149 (196)
Q Consensus 137 ~~~~~~C~~C~~~ 149 (196)
+.+.|.|+.|+..
T Consensus 21 ~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 21 GGKTWICNFCGTK 33 (40)
T ss_dssp TTTEEEETTT--E
T ss_pred CCCEEECcCCCCc
Confidence 4456777777654
No 167
>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=47.84 E-value=11 Score=21.56 Aligned_cols=13 Identities=23% Similarity=0.383 Sum_probs=6.6
Q ss_pred CCccCcccccccC
Q psy4683 139 QPHTCSVCKKIFV 151 (196)
Q Consensus 139 ~~~~C~~C~~~f~ 151 (196)
+.|.|+.||..+.
T Consensus 45 r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 45 RVFTCPNCGFEMD 57 (69)
T ss_pred ceEEcCCCCCEEC
Confidence 3455555555433
No 168
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=47.81 E-value=15 Score=30.47 Aligned_cols=9 Identities=33% Similarity=0.789 Sum_probs=4.9
Q ss_pred ccccccccc
Q psy4683 57 PCRLCSQEF 65 (196)
Q Consensus 57 ~C~~C~~~f 65 (196)
.|..||...
T Consensus 215 ~C~~Cg~~~ 223 (505)
T TIGR00595 215 LCRSCGYIL 223 (505)
T ss_pred EhhhCcCcc
Confidence 455555544
No 169
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=47.66 E-value=4.3 Score=20.07 Aligned_cols=31 Identities=16% Similarity=0.411 Sum_probs=14.0
Q ss_pred ccccccccCCchHHHhhhhhhcCCCCccCcccccccC
Q psy4683 115 CKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIFV 151 (196)
Q Consensus 115 C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 151 (196)
|+.|.+.+.+..+ ++.| -++..|..||-.++
T Consensus 2 C~~C~~Ey~~p~~----RR~~--~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 2 CDDCLKEYFDPSN----RRFH--YQFISCTNCGPRYS 32 (35)
T ss_dssp -HHHHHHHCSTTS----TTTT---TT--BTTCC-SCC
T ss_pred CHHHHHHHcCCCC----Cccc--CcCccCCCCCCCEE
Confidence 5566666555543 2222 23456777776654
No 170
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=47.08 E-value=21 Score=25.07 Aligned_cols=35 Identities=14% Similarity=0.409 Sum_probs=20.1
Q ss_pred cCCCcccccccccccCCchHHHhhhhhhcCCCCccCcccccccC
Q psy4683 108 IKDYNVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIFV 151 (196)
Q Consensus 108 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~ 151 (196)
.....|.|+.|.-.|+...++. . .|.||.||....
T Consensus 109 ~~~~~y~C~~~~~r~sfdeA~~------~---~F~Cp~Cg~~L~ 143 (176)
T COG1675 109 TENNYYVCPNCHVKYSFDEAME------L---GFTCPKCGEDLE 143 (176)
T ss_pred ccCCceeCCCCCCcccHHHHHH------h---CCCCCCCCchhh
Confidence 3455677877665555443321 1 178888886543
No 171
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=46.92 E-value=14 Score=20.35 Aligned_cols=12 Identities=17% Similarity=0.276 Sum_probs=6.1
Q ss_pred CCccCccccccc
Q psy4683 139 QPHTCSVCKKIF 150 (196)
Q Consensus 139 ~~~~C~~C~~~f 150 (196)
..|.|+.||-.+
T Consensus 13 v~~~Cp~cGipt 24 (55)
T PF13824_consen 13 VNFECPDCGIPT 24 (55)
T ss_pred cCCcCCCCCCcC
Confidence 345555555443
No 172
>KOG2907|consensus
Probab=46.01 E-value=8.8 Score=24.50 Aligned_cols=11 Identities=45% Similarity=0.848 Sum_probs=7.5
Q ss_pred ccCcccccccC
Q psy4683 141 HTCSVCKKIFV 151 (196)
Q Consensus 141 ~~C~~C~~~f~ 151 (196)
|.|+.|++.|+
T Consensus 103 YTC~kC~~k~~ 113 (116)
T KOG2907|consen 103 YTCPKCKYKFT 113 (116)
T ss_pred EEcCccceeee
Confidence 66777776665
No 173
>KOG3408|consensus
Probab=45.77 E-value=22 Score=23.14 Aligned_cols=27 Identities=22% Similarity=0.422 Sum_probs=22.0
Q ss_pred CCCCCcccccccccccCCHHHHHHHHH
Q psy4683 50 VTSDTKFPCRLCSQEFDTKEQRKKHER 76 (196)
Q Consensus 50 ~~~~~~~~C~~C~~~f~~~~~l~~H~~ 76 (196)
-+|...|-|-.|.+-|.+...|..|.+
T Consensus 52 lPG~GqfyCi~CaRyFi~~~~l~~H~k 78 (129)
T KOG3408|consen 52 LPGGGQFYCIECARYFIDAKALKTHFK 78 (129)
T ss_pred CCCCceeehhhhhhhhcchHHHHHHHh
Confidence 345566889999999999999999984
No 174
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=45.20 E-value=11 Score=19.11 Aligned_cols=12 Identities=25% Similarity=0.498 Sum_probs=9.5
Q ss_pred CccCCCCccccc
Q psy4683 84 LFSCDLCSYTST 95 (196)
Q Consensus 84 ~~~C~~C~~~f~ 95 (196)
||.|..|+..|-
T Consensus 12 ~f~C~~C~~~FC 23 (39)
T smart00154 12 GFKCRHCGNLFC 23 (39)
T ss_pred CeECCccCCccc
Confidence 788888888774
No 175
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=45.01 E-value=16 Score=22.90 Aligned_cols=15 Identities=20% Similarity=0.255 Sum_probs=10.5
Q ss_pred cccccccccccCCch
Q psy4683 112 NVFCKICQLGFLSKN 126 (196)
Q Consensus 112 ~~~C~~C~~~f~~~~ 126 (196)
|..|..||..|.+-+
T Consensus 2 pH~CtrCG~vf~~g~ 16 (112)
T COG3364 2 PHQCTRCGEVFDDGS 16 (112)
T ss_pred Cceeccccccccccc
Confidence 456777888877643
No 176
>PRK04023 DNA polymerase II large subunit; Validated
Probab=44.70 E-value=18 Score=32.39 Aligned_cols=36 Identities=19% Similarity=0.464 Sum_probs=23.0
Q ss_pred CCccCCCCcccccCchHHHHHHHhhcCCCcccccccccccCCchHHHhhhhhhcCCCCccCcccccc
Q psy4683 83 GLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKI 149 (196)
Q Consensus 83 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~ 149 (196)
....|+.||... ..+.|+.||.. ....+.|+.|+..
T Consensus 625 g~RfCpsCG~~t----------------~~frCP~CG~~---------------Te~i~fCP~CG~~ 660 (1121)
T PRK04023 625 GRRKCPSCGKET----------------FYRRCPFCGTH---------------TEPVYRCPRCGIE 660 (1121)
T ss_pred cCccCCCCCCcC----------------CcccCCCCCCC---------------CCcceeCccccCc
Confidence 446788888752 23578888765 2345778888543
No 177
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=44.55 E-value=13 Score=19.77 Aligned_cols=12 Identities=17% Similarity=0.238 Sum_probs=6.0
Q ss_pred CccCcccccccC
Q psy4683 140 PHTCSVCKKIFV 151 (196)
Q Consensus 140 ~~~C~~C~~~f~ 151 (196)
.|.|+.||..+.
T Consensus 20 ~~vC~~Cg~~~~ 31 (52)
T smart00661 20 RFVCRKCGYEEP 31 (52)
T ss_pred EEECCcCCCeEE
Confidence 355555554443
No 178
>KOG4377|consensus
Probab=44.45 E-value=12 Score=29.80 Aligned_cols=101 Identities=16% Similarity=0.254 Sum_probs=56.6
Q ss_pred ccccccCCHHHHHHHHHhhcCCC------------CCccCC--CCcccccCchHHHHHHHhhcCC-------Cccccccc
Q psy4683 60 LCSQEFDTKEQRKKHERKDHATQ------------GLFSCD--LCSYTSTQKYYLVKHKSRHIKD-------YNVFCKIC 118 (196)
Q Consensus 60 ~C~~~f~~~~~l~~H~~~~h~~~------------~~~~C~--~C~~~f~~~~~l~~H~~~h~~~-------~~~~C~~C 118 (196)
.|+..+..+..+.+|. ..|... ..|.|. .|.+ +......|..-|+.. ..|.|..|
T Consensus 278 ~C~ykr~~k~DvirH~-~~hkkrdnsL~dgf~rfs~syhC~~~~C~k---sTsdV~~h~nFht~~~n~GfrrthfhC~r~ 353 (480)
T KOG4377|consen 278 YCFYKRGQKNDVIRHV-EIHKKRDNSLIDGFHRFSNSYHCTGQICEK---STSDVLLHDNFHTDKRNNGFRRTHFHCQRI 353 (480)
T ss_pred cccccccchhhhHHHH-HHHhhcccccccchhhcCccchhhhcccCc---ccccccccCccccccccCceecceeEEecc
Confidence 4877777788888998 445322 125663 4776 344555555555321 23568777
Q ss_pred ccccCCchHHHhhhhhhcC----CC------------------------CccC--cccccccCCchhHHHHHHHhhcc
Q psy4683 119 QLGFLSKNELNVHNIKQHC----AQ------------------------PHTC--SVCKKIFVNKKNLTTHKKIHLAL 166 (196)
Q Consensus 119 ~~~f~~~~~l~~H~~~~~~----~~------------------------~~~C--~~C~~~f~~~~~l~~H~~~h~~~ 166 (196)
+-++..+ ...|...|-. +. -+.| .-|+.++.+.+.+..|.+.|.++
T Consensus 354 gCTdtfK--~~khk~yh~kdda~~~dGfkkf~k~e~cay~gCkys~~cnhfhc~r~Gc~~tl~s~sqm~shkrkheRq 429 (480)
T KOG4377|consen 354 GCTDTFK--DSKHKPYHYKDDAGEIDGFKKFFKDENCAYTGCKYSGICNHFHCDRLGCEATLYSVSQMASHKRKHERQ 429 (480)
T ss_pred CCccccc--cccccccccCcchhhhhhhhhhhccccCCccCcccccceeeeeecccCCceEEEehhhhhhhhhhhhhh
Confidence 6333322 3334332221 10 1234 23888888888888888888653
No 179
>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=44.28 E-value=6.6 Score=19.54 Aligned_cols=30 Identities=23% Similarity=0.390 Sum_probs=15.2
Q ss_pred ccccccccccCCchHHHhhhhhhcCCCCccCccc
Q psy4683 113 VFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVC 146 (196)
Q Consensus 113 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C 146 (196)
..|+.|+..- .+.+|=+...|.+.|.|..|
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 3466655321 13344444455566777666
No 180
>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=43.96 E-value=10 Score=21.64 Aligned_cols=10 Identities=20% Similarity=0.693 Sum_probs=3.6
Q ss_pred cCCCCccccc
Q psy4683 86 SCDLCSYTST 95 (196)
Q Consensus 86 ~C~~C~~~f~ 95 (196)
.|..|++.|.
T Consensus 11 ~C~~C~~~F~ 20 (69)
T PF01363_consen 11 NCMICGKKFS 20 (69)
T ss_dssp B-TTT--B-B
T ss_pred cCcCcCCcCC
Confidence 4666777663
No 181
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=43.92 E-value=3.7 Score=34.94 Aligned_cols=58 Identities=16% Similarity=0.263 Sum_probs=38.3
Q ss_pred cccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccccCchHHHHHHHhhcCCCcccccccccc
Q psy4683 57 PCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLG 121 (196)
Q Consensus 57 ~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~ 121 (196)
.|..||-.|.-..+|=--+..+...+- -.|+.|.+.|.+..+.+.| -++..|+.||-.
T Consensus 125 ~CT~CGPRfTIi~alPYDR~nTsM~~F-~lC~~C~~EY~dP~nRRfH------AQp~aCp~CGP~ 182 (750)
T COG0068 125 NCTNCGPRFTIIEALPYDRENTSMADF-PLCPFCDKEYKDPLNRRFH------AQPIACPKCGPH 182 (750)
T ss_pred ccCCCCcceeeeccCCCCcccCccccC-cCCHHHHHHhcCccccccc------cccccCcccCCC
Confidence 499999999766655333322222221 2599999999888874444 257789999853
No 182
>PRK14873 primosome assembly protein PriA; Provisional
Probab=43.44 E-value=17 Score=31.28 Aligned_cols=9 Identities=22% Similarity=0.648 Sum_probs=5.4
Q ss_pred ccccccccc
Q psy4683 57 PCRLCSQEF 65 (196)
Q Consensus 57 ~C~~C~~~f 65 (196)
.|..||..+
T Consensus 385 ~C~~Cg~~~ 393 (665)
T PRK14873 385 ACARCRTPA 393 (665)
T ss_pred EhhhCcCee
Confidence 566666643
No 183
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=43.00 E-value=14 Score=24.50 Aligned_cols=20 Identities=20% Similarity=0.152 Sum_probs=8.8
Q ss_pred cCCCCcccccCchHHHHHHHhhc
Q psy4683 86 SCDLCSYTSTQKYYLVKHKSRHI 108 (196)
Q Consensus 86 ~C~~C~~~f~~~~~l~~H~~~h~ 108 (196)
.|-++|+.|. .|.+|+..|.
T Consensus 78 icLEDGkkfK---SLKRHL~t~~ 97 (148)
T COG4957 78 ICLEDGKKFK---SLKRHLTTHY 97 (148)
T ss_pred EEeccCcchH---HHHHHHhccc
Confidence 3444444443 3444444443
No 184
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=42.99 E-value=14 Score=28.22 Aligned_cols=54 Identities=17% Similarity=0.340 Sum_probs=34.7
Q ss_pred cCCCCcccccCchHHHHHHHhhcCCCcccccccccccCCchHHHhhhhhhcCCCCccCcccc
Q psy4683 86 SCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCK 147 (196)
Q Consensus 86 ~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~ 147 (196)
.|-.|.-.|.....-..- .-+....|.|..|...|...-....|...| .|..|.
T Consensus 364 ~Cf~CQ~~fp~~~~~~~~--~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh------~C~gCe 417 (421)
T COG5151 364 HCFVCQGPFPKPPVSPFD--ESTSSGRYQCELCKSTFCSDCDVFIHETLH------FCIGCE 417 (421)
T ss_pred cceeccCCCCCCCCCccc--ccccccceechhhhhhhhhhhHHHHHHHHh------hCCCCc
Confidence 477777777654321111 112245689999999999988888887665 366554
No 185
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=42.42 E-value=9.3 Score=24.62 Aligned_cols=11 Identities=27% Similarity=0.700 Sum_probs=5.5
Q ss_pred ccccccccccC
Q psy4683 113 VFCKICQLGFL 123 (196)
Q Consensus 113 ~~C~~C~~~f~ 123 (196)
+.|..|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (114)
T PRK03681 71 CWCETCQQYVT 81 (114)
T ss_pred EEcccCCCeee
Confidence 34555554443
No 186
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=42.25 E-value=52 Score=22.62 Aligned_cols=58 Identities=16% Similarity=0.218 Sum_probs=29.7
Q ss_pred ccccccccccCCchHHHhhhhhhcCCCCccCcc--cccccCCchhHHHHHHHhhccCCcccc
Q psy4683 113 VFCKICQLGFLSKNELNVHNIKQHCAQPHTCSV--CKKIFVNKKNLTTHKKIHLALDRNYQC 172 (196)
Q Consensus 113 ~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~~C 172 (196)
..|+.|......+... .--+.+-..++-.|.. |.+. .+...|++|.+.-|...+|-.-
T Consensus 81 L~CPLCRG~V~GWtvv-e~AR~~LN~K~RsC~~e~C~F~-GtY~eLrKHar~~HP~~rP~~v 140 (162)
T PF07800_consen 81 LACPLCRGEVKGWTVV-EPARRFLNAKKRSCSQESCSFS-GTYSELRKHARSEHPSARPSEV 140 (162)
T ss_pred ccCccccCceeceEEc-hHHHHHhccCCccCcccccccc-cCHHHHHHHHHhhCCCCCCccC
Confidence 4577775443333222 2234444455555654 4433 3456777787774433555443
No 187
>KOG0782|consensus
Probab=42.20 E-value=3.1 Score=34.42 Aligned_cols=51 Identities=20% Similarity=0.371 Sum_probs=24.9
Q ss_pred HHHHHHHhhcCCCCCccCCCCcccccCchHHHHHHHhhcCCCcccccccccccCCch
Q psy4683 70 QRKKHERKDHATQGLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLSKN 126 (196)
Q Consensus 70 ~l~~H~~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~ 126 (196)
.+.+|. ..|.....=+|..|++.|..+..+ |-+. .....|.+|..+|-.+-
T Consensus 240 ~fvrHH-WVHrrRqeGkC~~CgKgFQQKf~F--hsKE---ivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 240 GFVRHH-WVHRRRQEGKCNTCGKGFQQKFFF--HSKE---IVAISCSWCKQAYHLKV 290 (1004)
T ss_pred cchHHh-HhhHhhhccccchhhhhhhhheee--cccc---EEEEEehHHHHHhhcch
Confidence 455554 445444444666777666544221 1110 12345666666665543
No 188
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=40.93 E-value=10 Score=20.64 Aligned_cols=12 Identities=17% Similarity=0.692 Sum_probs=6.4
Q ss_pred cCcccccccCCc
Q psy4683 142 TCSVCKKIFVNK 153 (196)
Q Consensus 142 ~C~~C~~~f~~~ 153 (196)
.||.|++.|...
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 899999888764
No 189
>PF00081 Sod_Fe_N: Iron/manganese superoxide dismutases, alpha-hairpin domain Note: SCOP classifies the two domains separately.; InterPro: IPR019831 Superoxide dismutases (SODs) (1.15.1.1 from EC) catalyse the conversion of superoxide radicals to molecular oxygen. Their function is to destroy the radicals that are normally produced within cells and are toxic to biological systems. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one [, , ]. This family includes both single metal-binding SODs and cambialistic SOD, which can bind either Mn or Fe. Fe/MnSODs are ubiquitous enzymes that are responsible for the majority of SOD activity in prokaryotes, fungi, blue-green algae and mitochondria. Fe/MnSODs are found as homodimers or homotetramers. The structure of Fe/MnSODs can be divided into two domains, an alpha N-terminal domain and an alpha/beta C-terminal domain, connected by a loop. The structure of the N-terminal domain consists of a two helices in an antiparallel hairpin, with a left-handed twist []. The structure of the C-terminal domain is of the alpha/beta type, and consists of a three-stranded antiparallel beta-sheet in the order 213, along with four helices in the arrangement alpha/beta(2)/alpha/beta/alpha(2) []. This entry represents the N-terminal domain of Manganese/iron superoxide dismutase. ; GO: 0004784 superoxide dismutase activity, 0046872 metal ion binding, 0006801 superoxide metabolic process, 0055114 oxidation-reduction process; PDB: 3TQJ_A 1MY6_A 1BT8_A 1BSM_B 1AR5_A 1BS3_A 1AR4_A 1AVM_A 3DC6_C 1ZSP_B ....
Probab=40.59 E-value=7.8 Score=23.29 Aligned_cols=28 Identities=7% Similarity=0.190 Sum_probs=21.0
Q ss_pred ccccC--ceeccCCchhhhhhhHhhhhhcC
Q psy4683 169 NYQCD--TYFYEGNSLAWEDTSLEITLLKK 196 (196)
Q Consensus 169 ~~~C~--~~f~~~~~l~~H~~~~h~~~~~~ 196 (196)
||..+ ..|-....|..|...||.+|+++
T Consensus 8 pY~y~aLeP~is~~t~~~H~~kHh~~YV~~ 37 (82)
T PF00081_consen 8 PYAYDALEPYISEETMELHHDKHHQGYVNN 37 (82)
T ss_dssp SSSTTTTTTTS-HHHHHHHHHTHHHHHHHH
T ss_pred CCChhhhhhhhhhHHHHHHHHHHHHHHHHH
Confidence 45555 66777888999999999998863
No 190
>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=40.55 E-value=10 Score=20.60 Aligned_cols=19 Identities=21% Similarity=0.457 Sum_probs=6.2
Q ss_pred ccccccccccCCchHHHhh
Q psy4683 113 VFCKICQLGFLSKNELNVH 131 (196)
Q Consensus 113 ~~C~~C~~~f~~~~~l~~H 131 (196)
|.|+.|...|-..=.+..|
T Consensus 22 y~C~~C~~~FC~dCD~fiH 40 (51)
T PF07975_consen 22 YRCPKCKNHFCIDCDVFIH 40 (51)
T ss_dssp E--TTTT--B-HHHHHTTT
T ss_pred EECCCCCCccccCcChhhh
Confidence 4444444444444444444
No 191
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=40.20 E-value=13 Score=24.53 Aligned_cols=47 Identities=19% Similarity=0.268 Sum_probs=26.2
Q ss_pred HHHHHhhcCCCcccccccccccCCchHHHhhhhhhcCCCCccCcccccccCCch
Q psy4683 101 VKHKSRHIKDYNVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIFVNKK 154 (196)
Q Consensus 101 ~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~ 154 (196)
..+++...+ ...|+.|+...... +-..-.+.+.|.|+.|++.|....
T Consensus 21 ~~~~~~~~~--~~~cP~C~s~~~~k-----~g~~~~~~qRyrC~~C~~tf~~~~ 67 (129)
T COG3677 21 AYAIRMQIT--KVNCPRCKSSNVVK-----IGGIRRGHQRYKCKSCGSTFTVET 67 (129)
T ss_pred HHHHhhhcc--cCcCCCCCccceee-----ECCccccccccccCCcCcceeeec
Confidence 334444432 23678887544111 111223356799999999988654
No 192
>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=40.06 E-value=20 Score=19.46 Aligned_cols=10 Identities=40% Similarity=0.531 Sum_probs=6.1
Q ss_pred cCCCCccccc
Q psy4683 86 SCDLCSYTST 95 (196)
Q Consensus 86 ~C~~C~~~f~ 95 (196)
.|..|++.|.
T Consensus 4 ~C~~C~~~F~ 13 (57)
T cd00065 4 SCMGCGKPFT 13 (57)
T ss_pred cCcccCcccc
Confidence 4666666664
No 193
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=39.92 E-value=1.2 Score=22.57 Aligned_cols=10 Identities=20% Similarity=0.647 Sum_probs=5.3
Q ss_pred ccCccccccc
Q psy4683 141 HTCSVCKKIF 150 (196)
Q Consensus 141 ~~C~~C~~~f 150 (196)
|.|..|+..|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 5555555543
No 194
>PRK05580 primosome assembly protein PriA; Validated
Probab=39.70 E-value=23 Score=30.54 Aligned_cols=10 Identities=30% Similarity=0.564 Sum_probs=5.1
Q ss_pred cccccccccc
Q psy4683 56 FPCRLCSQEF 65 (196)
Q Consensus 56 ~~C~~C~~~f 65 (196)
..|..||..+
T Consensus 382 ~~C~~Cg~~~ 391 (679)
T PRK05580 382 LLCRDCGWVA 391 (679)
T ss_pred eEhhhCcCcc
Confidence 3455555543
No 195
>KOG1842|consensus
Probab=39.56 E-value=18 Score=29.11 Aligned_cols=28 Identities=18% Similarity=0.424 Sum_probs=25.5
Q ss_pred cccccccccccCCHHHHHHHHHhhcCCC
Q psy4683 55 KFPCRLCSQEFDTKEQRKKHERKDHATQ 82 (196)
Q Consensus 55 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 82 (196)
.|.|+.|...|.+...|..|....|.++
T Consensus 15 gflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 15 GFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred cccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 5899999999999999999998888764
No 196
>KOG3507|consensus
Probab=39.41 E-value=13 Score=20.74 Aligned_cols=31 Identities=26% Similarity=0.512 Sum_probs=19.4
Q ss_pred cccccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccccCc
Q psy4683 55 KFPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTSTQK 97 (196)
Q Consensus 55 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~ 97 (196)
-|.|..|+..- .-...-.+.|..||.....+
T Consensus 20 iYiCgdC~~en------------~lk~~D~irCReCG~RIlyK 50 (62)
T KOG3507|consen 20 IYICGDCGQEN------------TLKRGDVIRCRECGYRILYK 50 (62)
T ss_pred EEEeccccccc------------cccCCCcEehhhcchHHHHH
Confidence 38888887643 22233467888888765433
No 197
>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=38.81 E-value=9.4 Score=24.53 Aligned_cols=13 Identities=23% Similarity=0.519 Sum_probs=6.7
Q ss_pred ccccccccccCCc
Q psy4683 113 VFCKICQLGFLSK 125 (196)
Q Consensus 113 ~~C~~C~~~f~~~ 125 (196)
+.|..|+..|...
T Consensus 71 ~~C~~Cg~~~~~~ 83 (113)
T PF01155_consen 71 ARCRDCGHEFEPD 83 (113)
T ss_dssp EEETTTS-EEECH
T ss_pred EECCCCCCEEecC
Confidence 4566666665543
No 198
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=38.74 E-value=27 Score=24.81 Aligned_cols=45 Identities=22% Similarity=0.294 Sum_probs=25.2
Q ss_pred cccccCCchHHHhhhhhhcCCCCccCcc----cccccCCchhHHHHHHHhhc
Q psy4683 118 CQLGFLSKNELNVHNIKQHCAQPHTCSV----CKKIFVNKKNLTTHKKIHLA 165 (196)
Q Consensus 118 C~~~f~~~~~l~~H~~~~~~~~~~~C~~----C~~~f~~~~~l~~H~~~h~~ 165 (196)
|...+. ......|.... .-+|+.||. |+..= ....|..|....|.
T Consensus 24 C~~~~~-~~~~~~HE~~C-~~~p~~CP~~~~~C~~~G-~~~~l~~Hl~~~H~ 72 (198)
T PF03145_consen 24 CTETFP-YSEKREHEEEC-PFRPCSCPFPGSGCDWQG-SYKELLDHLRDKHS 72 (198)
T ss_dssp ---EE--GGGHHHHHHT--TTSEEE-SSSSTT---EE-ECCCHHHHHHHHTT
T ss_pred Cccccc-ccChhhHhccC-CCcCCcCCCCCCCccccC-CHHHHHHHHHHHCC
Confidence 766644 45667777644 467899987 66443 34589999998776
No 199
>KOG1280|consensus
Probab=38.37 E-value=35 Score=26.62 Aligned_cols=23 Identities=17% Similarity=0.356 Sum_probs=11.5
Q ss_pred CccCCCCcccccCchHHHHHHHh
Q psy4683 84 LFSCDLCSYTSTQKYYLVKHKSR 106 (196)
Q Consensus 84 ~~~C~~C~~~f~~~~~l~~H~~~ 106 (196)
.|.|++|+..-.+...+..|...
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s 101 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLS 101 (381)
T ss_pred cccCCcccccccchhHHHHHhhh
Confidence 35555555544445555555443
No 200
>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=38.33 E-value=20 Score=24.22 Aligned_cols=17 Identities=12% Similarity=0.225 Sum_probs=11.3
Q ss_pred CccCCCCcccccCchHH
Q psy4683 84 LFSCDLCSYTSTQKYYL 100 (196)
Q Consensus 84 ~~~C~~C~~~f~~~~~l 100 (196)
-+.|+.|++.|+.=+..
T Consensus 124 f~~C~~C~kiyW~GsH~ 140 (147)
T PF01927_consen 124 FWRCPGCGKIYWEGSHW 140 (147)
T ss_pred EEECCCCCCEecccccH
Confidence 46788888887654433
No 201
>PF04641 Rtf2: Rtf2 RING-finger
Probab=37.95 E-value=25 Score=26.29 Aligned_cols=13 Identities=38% Similarity=0.925 Sum_probs=9.9
Q ss_pred ccCcccccccCCc
Q psy4683 141 HTCSVCKKIFVNK 153 (196)
Q Consensus 141 ~~C~~C~~~f~~~ 153 (196)
..|+.|+..|...
T Consensus 151 ~~Cp~c~~~f~~~ 163 (260)
T PF04641_consen 151 KKCPVCGKPFTEE 163 (260)
T ss_pred ccccccCCccccC
Confidence 4599999888754
No 202
>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=37.48 E-value=10 Score=19.57 Aligned_cols=14 Identities=36% Similarity=0.747 Sum_probs=7.9
Q ss_pred CCccCcccccccCC
Q psy4683 139 QPHTCSVCKKIFVN 152 (196)
Q Consensus 139 ~~~~C~~C~~~f~~ 152 (196)
-|+.|..|+..|=.
T Consensus 12 ~~~~C~~C~~~FC~ 25 (43)
T PF01428_consen 12 LPFKCKHCGKSFCL 25 (43)
T ss_dssp SHEE-TTTS-EE-T
T ss_pred CCeECCCCCcccCc
Confidence 36788888877743
No 203
>PLN02294 cytochrome c oxidase subunit Vb
Probab=36.98 E-value=16 Score=25.27 Aligned_cols=16 Identities=25% Similarity=0.692 Sum_probs=12.9
Q ss_pred CCCccCcccccccCCc
Q psy4683 138 AQPHTCSVCKKIFVNK 153 (196)
Q Consensus 138 ~~~~~C~~C~~~f~~~ 153 (196)
.+|++|++||..|...
T Consensus 139 Gkp~RCpeCG~~fkL~ 154 (174)
T PLN02294 139 GKSFECPVCTQYFELE 154 (174)
T ss_pred CCceeCCCCCCEEEEE
Confidence 4689999999988643
No 204
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=36.93 E-value=15 Score=24.10 Aligned_cols=11 Identities=18% Similarity=0.404 Sum_probs=6.0
Q ss_pred ccccccccccCC
Q psy4683 113 VFCKICQLGFLS 124 (196)
Q Consensus 113 ~~C~~C~~~f~~ 124 (196)
+.| .|+..|..
T Consensus 71 ~~C-~Cg~~~~~ 81 (124)
T PRK00762 71 IEC-ECGYEGVV 81 (124)
T ss_pred EEe-eCcCcccc
Confidence 456 66655543
No 205
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=36.39 E-value=6.1 Score=24.65 Aligned_cols=8 Identities=38% Similarity=1.115 Sum_probs=3.9
Q ss_pred ccCCCCcc
Q psy4683 85 FSCDLCSY 92 (196)
Q Consensus 85 ~~C~~C~~ 92 (196)
|.|+.|+.
T Consensus 23 FtCp~Cgh 30 (104)
T COG4888 23 FTCPRCGH 30 (104)
T ss_pred EecCccCC
Confidence 45555543
No 206
>COG1773 Rubredoxin [Energy production and conversion]
Probab=36.06 E-value=15 Score=20.25 Aligned_cols=14 Identities=29% Similarity=0.693 Sum_probs=10.1
Q ss_pred CccCcccccccCCc
Q psy4683 140 PHTCSVCKKIFVNK 153 (196)
Q Consensus 140 ~~~C~~C~~~f~~~ 153 (196)
.|+|..||..|.-.
T Consensus 3 ~~~C~~CG~vYd~e 16 (55)
T COG1773 3 RWRCSVCGYVYDPE 16 (55)
T ss_pred ceEecCCceEeccc
Confidence 47888888877643
No 207
>PRK12722 transcriptional activator FlhC; Provisional
Probab=35.63 E-value=25 Score=24.94 Aligned_cols=28 Identities=21% Similarity=0.329 Sum_probs=13.8
Q ss_pred ccCCCCcccccCchHHHHHHHhhcCCCccccccccc
Q psy4683 85 FSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQL 120 (196)
Q Consensus 85 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~ 120 (196)
..|..||-.|-.... .....|.|+.|.-
T Consensus 135 ~~C~~Cgg~fv~~~~--------e~~~~f~CplC~~ 162 (187)
T PRK12722 135 SSCNCCGGHFVTHAH--------DPVGSFVCGLCQP 162 (187)
T ss_pred ccCCCCCCCeecccc--------ccCCCCcCCCCCC
Confidence 446666665542221 2234566666653
No 208
>KOG0978|consensus
Probab=35.46 E-value=16 Score=31.35 Aligned_cols=8 Identities=25% Similarity=1.099 Sum_probs=4.1
Q ss_pred ccCCCCcc
Q psy4683 85 FSCDLCSY 92 (196)
Q Consensus 85 ~~C~~C~~ 92 (196)
.+|+.|..
T Consensus 644 LkCs~Cn~ 651 (698)
T KOG0978|consen 644 LKCSVCNT 651 (698)
T ss_pred eeCCCccC
Confidence 45555553
No 209
>KOG1842|consensus
Probab=35.46 E-value=21 Score=28.83 Aligned_cols=27 Identities=19% Similarity=0.336 Sum_probs=19.7
Q ss_pred CCccCcccccccCCchhHHHHHHHhhc
Q psy4683 139 QPHTCSVCKKIFVNKKNLTTHKKIHLA 165 (196)
Q Consensus 139 ~~~~C~~C~~~f~~~~~l~~H~~~h~~ 165 (196)
..|.||+|...|.+...|..|...-|.
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~ 40 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHF 40 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhcc
Confidence 357788888888888888888776443
No 210
>KOG1280|consensus
Probab=35.31 E-value=44 Score=26.11 Aligned_cols=38 Identities=26% Similarity=0.454 Sum_probs=28.9
Q ss_pred CcccccccccccCCHHHHHHHHHhhcCCCC-CccCCCCc
Q psy4683 54 TKFPCRLCSQEFDTKEQRKKHERKDHATQG-LFSCDLCS 91 (196)
Q Consensus 54 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~-~~~C~~C~ 91 (196)
..|.|+.|+..=-+...+..|....|.... ...|+.|+
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~ 116 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCA 116 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccc
Confidence 359999999988889999999977775432 24566665
No 211
>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 PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=34.72 E-value=25 Score=19.30 Aligned_cols=7 Identities=29% Similarity=0.795 Sum_probs=3.0
Q ss_pred cCCCCcc
Q psy4683 86 SCDLCSY 92 (196)
Q Consensus 86 ~C~~C~~ 92 (196)
.|+.|+.
T Consensus 23 vCp~Cga 29 (54)
T PF14446_consen 23 VCPECGA 29 (54)
T ss_pred ECCCCCC
Confidence 3444443
No 213
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=33.96 E-value=31 Score=16.92 Aligned_cols=10 Identities=30% Similarity=0.823 Sum_probs=3.7
Q ss_pred cccccccccC
Q psy4683 57 PCRLCSQEFD 66 (196)
Q Consensus 57 ~C~~C~~~f~ 66 (196)
.|..|++.|.
T Consensus 5 ~C~eC~~~f~ 14 (34)
T PF01286_consen 5 KCDECGKPFM 14 (34)
T ss_dssp E-TTT--EES
T ss_pred hHhHhCCHHH
Confidence 4555555553
No 214
>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=33.52 E-value=22 Score=22.24 Aligned_cols=18 Identities=22% Similarity=0.632 Sum_probs=12.9
Q ss_pred hhcCCCCccCcccccccCC
Q psy4683 134 KQHCAQPHTCSVCKKIFVN 152 (196)
Q Consensus 134 ~~~~~~~~~C~~C~~~f~~ 152 (196)
.+.+ +|++|+.||..|..
T Consensus 74 l~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 74 LEKG-KPKRCPECGHVFKL 91 (97)
T ss_pred EeCC-CceeCCCCCcEEEE
Confidence 3444 68889999888763
No 215
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=33.44 E-value=30 Score=18.80 Aligned_cols=12 Identities=25% Similarity=0.913 Sum_probs=7.4
Q ss_pred ccccccccccCC
Q psy4683 56 FPCRLCSQEFDT 67 (196)
Q Consensus 56 ~~C~~C~~~f~~ 67 (196)
++|..||..|..
T Consensus 29 W~C~~Cgh~w~~ 40 (55)
T PF14311_consen 29 WKCPKCGHEWKA 40 (55)
T ss_pred EECCCCCCeeEc
Confidence 567777666643
No 216
>KOG0402|consensus
Probab=33.16 E-value=15 Score=22.03 Aligned_cols=31 Identities=13% Similarity=0.340 Sum_probs=16.9
Q ss_pred CccCCCCcccccCchHHHHHHHhhcCCCcccccccccccCC
Q psy4683 84 LFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKICQLGFLS 124 (196)
Q Consensus 84 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~ 124 (196)
.|.|+.||+.-... ...--+.|..|.+++..
T Consensus 36 ky~CsfCGK~~vKR----------~AvGiW~C~~C~kv~ag 66 (92)
T KOG0402|consen 36 KYTCSFCGKKTVKR----------KAVGIWKCGSCKKVVAG 66 (92)
T ss_pred hhhhhhcchhhhhh----------hceeEEecCCccceecc
Confidence 47788888643211 11223567777766653
No 217
>KOG2636|consensus
Probab=33.03 E-value=33 Score=27.77 Aligned_cols=31 Identities=13% Similarity=0.286 Sum_probs=25.2
Q ss_pred hhhhcCCCCccCcccc-cccCCchhHHHHHHH
Q psy4683 132 NIKQHCAQPHTCSVCK-KIFVNKKNLTTHKKI 162 (196)
Q Consensus 132 ~~~~~~~~~~~C~~C~-~~f~~~~~l~~H~~~ 162 (196)
-+.|.....|.|.+|| +++.-+..+.+|..-
T Consensus 393 yKLHGL~~ey~CEICGNy~Y~GrkaF~RHF~E 424 (497)
T KOG2636|consen 393 YKLHGLDIEYNCEICGNYVYKGRKAFDRHFNE 424 (497)
T ss_pred HhhcCCCcccceeeccCccccCcHHHHHHhHH
Confidence 3456667789999999 999999999999643
No 218
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=32.82 E-value=23 Score=19.62 Aligned_cols=10 Identities=30% Similarity=0.816 Sum_probs=5.2
Q ss_pred CCccCccccc
Q psy4683 139 QPHTCSVCKK 148 (196)
Q Consensus 139 ~~~~C~~C~~ 148 (196)
..|.|..|..
T Consensus 30 ~tYmC~eC~~ 39 (56)
T PF09963_consen 30 HTYMCDECKE 39 (56)
T ss_pred cceeChhHHH
Confidence 3455665553
No 219
>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=32.61 E-value=13 Score=25.19 Aligned_cols=10 Identities=20% Similarity=0.541 Sum_probs=5.8
Q ss_pred ccCccccccc
Q psy4683 141 HTCSVCKKIF 150 (196)
Q Consensus 141 ~~C~~C~~~f 150 (196)
|.|+.|+..+
T Consensus 144 ~~C~~C~~~l 153 (157)
T PF10263_consen 144 YRCGRCGGPL 153 (157)
T ss_pred EECCCCCCEE
Confidence 5666666443
No 220
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=32.30 E-value=75 Score=17.35 Aligned_cols=9 Identities=22% Similarity=0.091 Sum_probs=5.3
Q ss_pred cCccccccc
Q psy4683 142 TCSVCKKIF 150 (196)
Q Consensus 142 ~C~~C~~~f 150 (196)
.||.|+..+
T Consensus 37 ~cP~~~~~~ 45 (63)
T smart00504 37 TDPVTGQPL 45 (63)
T ss_pred CCCCCcCCC
Confidence 466666555
No 221
>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=32.18 E-value=35 Score=27.92 Aligned_cols=28 Identities=25% Similarity=0.521 Sum_probs=24.5
Q ss_pred cccccccccccCCHHHHHHHHHhhcCCC
Q psy4683 55 KFPCRLCSQEFDTKEQRKKHERKDHATQ 82 (196)
Q Consensus 55 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~ 82 (196)
.+.|+.|.+.|.+...+..|+...|.+.
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~~~ 84 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHPAG 84 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhhhh
Confidence 3679999999999999999998788764
No 222
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.29 E-value=23 Score=21.05 Aligned_cols=20 Identities=25% Similarity=0.514 Sum_probs=11.9
Q ss_pred cccccccccCCchHHHhhhh
Q psy4683 114 FCKICQLGFLSKNELNVHNI 133 (196)
Q Consensus 114 ~C~~C~~~f~~~~~l~~H~~ 133 (196)
.|+.|+.+....+.|..-+.
T Consensus 23 ~CPrCrGVWLDrGELdKli~ 42 (88)
T COG3809 23 YCPRCRGVWLDRGELDKLIE 42 (88)
T ss_pred eCCccccEeecchhHHHHHH
Confidence 46666666666666555443
No 223
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=30.52 E-value=30 Score=18.58 Aligned_cols=10 Identities=20% Similarity=0.561 Sum_probs=5.4
Q ss_pred CccCcccccc
Q psy4683 140 PHTCSVCKKI 149 (196)
Q Consensus 140 ~~~C~~C~~~ 149 (196)
.|.|..||.+
T Consensus 37 R~~CGkCgyT 46 (51)
T COG1998 37 RWACGKCGYT 46 (51)
T ss_pred eeEeccccce
Confidence 3556666543
No 224
>KOG2071|consensus
Probab=30.49 E-value=35 Score=28.66 Aligned_cols=28 Identities=25% Similarity=0.523 Sum_probs=24.2
Q ss_pred CCCccCcccccccCCchhHHHHHHHhhc
Q psy4683 138 AQPHTCSVCKKIFVNKKNLTTHKKIHLA 165 (196)
Q Consensus 138 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~ 165 (196)
..|-.|..||..|........||.+|..
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 4567899999999999999999988864
No 225
>KOG3002|consensus
Probab=30.12 E-value=27 Score=26.76 Aligned_cols=78 Identities=22% Similarity=0.284 Sum_probs=46.7
Q ss_pred CCCccCCCCcccccCchHHHHHHHhhcCCCcccccc----cccccCCchHHHhhhhhhcCCCCccCcc----cccccCCc
Q psy4683 82 QGLFSCDLCSYTSTQKYYLVKHKSRHIKDYNVFCKI----CQLGFLSKNELNVHNIKQHCAQPHTCSV----CKKIFVNK 153 (196)
Q Consensus 82 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~----C~~~f~~~~~l~~H~~~~~~~~~~~C~~----C~~~f~~~ 153 (196)
..+.+|+.|...+.....+..-.. .....+.|+. |.+.|..... ..|.+.... .||.||. |... ...
T Consensus 78 ~~~~~CP~Cr~~~g~~R~~amEkV--~e~~~vpC~~~~~GC~~~~~Y~~~-~~HE~~C~f-~~~~CP~p~~~C~~~-G~~ 152 (299)
T KOG3002|consen 78 KVSNKCPTCRLPIGNIRCRAMEKV--AEAVLVPCKNAKLGCTKSFPYGEK-SKHEKVCEF-RPCSCPVPGAECKYT-GSY 152 (299)
T ss_pred hhcccCCccccccccHHHHHHHHH--HHhceecccccccCCceeeccccc-ccccccccc-CCcCCCCCcccCCcc-CcH
Confidence 456789999888875544443332 3334556653 7777766554 567666655 6777764 4432 334
Q ss_pred hhHHHHHHHhh
Q psy4683 154 KNLTTHKKIHL 164 (196)
Q Consensus 154 ~~l~~H~~~h~ 164 (196)
..|..|...-+
T Consensus 153 ~~l~~H~~~~h 163 (299)
T KOG3002|consen 153 KDLYAHLNDTH 163 (299)
T ss_pred HHHHHHHHhhC
Confidence 56777776643
No 226
>KOG0717|consensus
Probab=30.11 E-value=26 Score=28.49 Aligned_cols=22 Identities=36% Similarity=0.696 Sum_probs=20.3
Q ss_pred ccCcccccccCCchhHHHHHHH
Q psy4683 141 HTCSVCKKIFVNKKNLTTHKKI 162 (196)
Q Consensus 141 ~~C~~C~~~f~~~~~l~~H~~~ 162 (196)
+.|..|.++|.+...|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7899999999999999999876
No 227
>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=29.50 E-value=18 Score=18.52 Aligned_cols=11 Identities=27% Similarity=0.896 Sum_probs=7.9
Q ss_pred CccCccccccc
Q psy4683 140 PHTCSVCKKIF 150 (196)
Q Consensus 140 ~~~C~~C~~~f 150 (196)
+-.|+.|+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 56788887766
No 228
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=29.47 E-value=27 Score=23.49 Aligned_cols=11 Identities=27% Similarity=0.927 Sum_probs=5.4
Q ss_pred ccccccccccc
Q psy4683 55 KFPCRLCSQEF 65 (196)
Q Consensus 55 ~~~C~~C~~~f 65 (196)
.|.|..|+..+
T Consensus 112 ~y~C~~C~~~~ 122 (146)
T smart00731 112 PYRCTGCGQRY 122 (146)
T ss_pred EEECCCCCCCC
Confidence 34555555444
No 229
>PRK12860 transcriptional activator FlhC; Provisional
Probab=29.24 E-value=35 Score=24.23 Aligned_cols=11 Identities=18% Similarity=0.268 Sum_probs=6.0
Q ss_pred ccCCCCccccc
Q psy4683 85 FSCDLCSYTST 95 (196)
Q Consensus 85 ~~C~~C~~~f~ 95 (196)
..|..||-.|.
T Consensus 135 ~~C~~Cgg~fv 145 (189)
T PRK12860 135 ARCCRCGGKFV 145 (189)
T ss_pred ccCCCCCCCee
Confidence 44566665554
No 230
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=29.18 E-value=5.6 Score=30.23 Aligned_cols=11 Identities=18% Similarity=0.625 Sum_probs=5.6
Q ss_pred CCccCcccccc
Q psy4683 139 QPHTCSVCKKI 149 (196)
Q Consensus 139 ~~~~C~~C~~~ 149 (196)
+.+.|..|+..
T Consensus 237 rve~C~~C~~Y 247 (290)
T PF04216_consen 237 RVEVCESCGSY 247 (290)
T ss_dssp EEEEETTTTEE
T ss_pred EEEECCcccch
Confidence 34556666543
No 231
>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=28.93 E-value=57 Score=16.32 Aligned_cols=10 Identities=20% Similarity=0.853 Sum_probs=3.1
Q ss_pred cccccccccc
Q psy4683 56 FPCRLCSQEF 65 (196)
Q Consensus 56 ~~C~~C~~~f 65 (196)
|-|+.|+..|
T Consensus 4 yyCdyC~~~~ 13 (38)
T PF06220_consen 4 YYCDYCKKYL 13 (38)
T ss_dssp -B-TTT--B-
T ss_pred eeccccccee
Confidence 5566666666
No 232
>PHA02998 RNA polymerase subunit; Provisional
Probab=28.65 E-value=12 Score=26.16 Aligned_cols=11 Identities=55% Similarity=1.090 Sum_probs=8.1
Q ss_pred ccCcccccccC
Q psy4683 141 HTCSVCKKIFV 151 (196)
Q Consensus 141 ~~C~~C~~~f~ 151 (196)
|.|..||..|.
T Consensus 172 YkC~~CG~~wk 182 (195)
T PHA02998 172 HACRDCKKHFK 182 (195)
T ss_pred EEcCCCCCccC
Confidence 67888887665
No 233
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=28.42 E-value=38 Score=17.49 Aligned_cols=17 Identities=18% Similarity=0.634 Sum_probs=12.2
Q ss_pred cccccccccCCHHHHHH
Q psy4683 57 PCRLCSQEFDTKEQRKK 73 (196)
Q Consensus 57 ~C~~C~~~f~~~~~l~~ 73 (196)
.|..|+..|..+.....
T Consensus 10 ~C~~C~rpf~WRKKW~~ 26 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWAR 26 (42)
T ss_pred cCcccCCcchHHHHHHH
Confidence 58888888877665543
No 234
>PRK05978 hypothetical protein; Provisional
Probab=28.40 E-value=20 Score=24.35 Aligned_cols=9 Identities=22% Similarity=0.600 Sum_probs=5.8
Q ss_pred cCCCCcccc
Q psy4683 86 SCDLCSYTS 94 (196)
Q Consensus 86 ~C~~C~~~f 94 (196)
.|+.||..|
T Consensus 54 ~C~~CG~~~ 62 (148)
T PRK05978 54 HCAACGEDF 62 (148)
T ss_pred CccccCCcc
Confidence 477777655
No 235
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.25 E-value=22 Score=20.01 Aligned_cols=46 Identities=13% Similarity=0.106 Sum_probs=21.4
Q ss_pred HHHhhcCCCcccccccccccCCchHHHhhhhhhcCCCCccCcccccccCC
Q psy4683 103 HKSRHIKDYNVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIFVN 152 (196)
Q Consensus 103 H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~ 152 (196)
|...+.+..++.|+--+-.|.....+. -. ..+..-.|+.|+..|+.
T Consensus 15 ~~~I~~~~~~l~C~g~~~p~~HPrV~L---~m-g~~gev~CPYC~t~y~l 60 (62)
T COG4391 15 HETIEIGDLPLMCPGPEPPNDHPRVFL---DM-GDEGEVVCPYCSTRYRL 60 (62)
T ss_pred ceEEEeCCeeEEcCCCCCCCCCCEEEE---Ec-CCCCcEecCccccEEEe
Confidence 334455566666654333322211100 00 12333578888877763
No 236
>PRK00420 hypothetical protein; Validated
Probab=27.05 E-value=42 Score=21.62 Aligned_cols=10 Identities=10% Similarity=0.228 Sum_probs=5.2
Q ss_pred ccCCCCcccc
Q psy4683 85 FSCDLCSYTS 94 (196)
Q Consensus 85 ~~C~~C~~~f 94 (196)
..|+.||...
T Consensus 41 ~~Cp~Cg~~~ 50 (112)
T PRK00420 41 VVCPVHGKVY 50 (112)
T ss_pred eECCCCCCee
Confidence 4455555533
No 237
>PTZ00448 hypothetical protein; Provisional
Probab=26.98 E-value=41 Score=26.53 Aligned_cols=23 Identities=13% Similarity=0.379 Sum_probs=21.1
Q ss_pred CccCcccccccCCchhHHHHHHH
Q psy4683 140 PHTCSVCKKIFVNKKNLTTHKKI 162 (196)
Q Consensus 140 ~~~C~~C~~~f~~~~~l~~H~~~ 162 (196)
.|.|..|+-.|.+....+.|+++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 68899999999999999999987
No 238
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=26.87 E-value=28 Score=16.88 Aligned_cols=10 Identities=30% Similarity=0.863 Sum_probs=5.7
Q ss_pred ccCccccccc
Q psy4683 141 HTCSVCKKIF 150 (196)
Q Consensus 141 ~~C~~C~~~f 150 (196)
+.|+.|+.+|
T Consensus 22 ~~C~~Cg~~~ 31 (33)
T PF08792_consen 22 EVCIFCGSSF 31 (33)
T ss_pred EEcccCCcEe
Confidence 4566666554
No 239
>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=26.72 E-value=30 Score=21.63 Aligned_cols=13 Identities=15% Similarity=0.248 Sum_probs=8.3
Q ss_pred cccccccccccCC
Q psy4683 112 NVFCKICQLGFLS 124 (196)
Q Consensus 112 ~~~C~~C~~~f~~ 124 (196)
.+.|+.|+..+..
T Consensus 16 ~~~C~~C~~~~~~ 28 (104)
T TIGR01384 16 VYVCPSCGYEKEK 28 (104)
T ss_pred eEECcCCCCcccc
Confidence 4677777766543
No 240
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=26.69 E-value=28 Score=28.66 Aligned_cols=37 Identities=14% Similarity=0.257 Sum_probs=20.2
Q ss_pred cccccccccccCCchHHHhhhhhhcC------CCCccCcccccc
Q psy4683 112 NVFCKICQLGFLSKNELNVHNIKQHC------AQPHTCSVCKKI 149 (196)
Q Consensus 112 ~~~C~~C~~~f~~~~~l~~H~~~~~~------~~~~~C~~C~~~ 149 (196)
.|.|..|+..|.....-... .+..| ...|.||.|+-.
T Consensus 425 ~~~c~~c~~~yd~~~g~~~~-~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 425 RMQCSVCQWIYDPAKGEPMQ-DVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred eEEECCCCeEECCCCCCccc-CCCCCCChhhCCCCCcCcCCCCc
Confidence 47788888888764322111 11111 224788888843
No 241
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.27 E-value=23 Score=23.15 Aligned_cols=15 Identities=13% Similarity=0.089 Sum_probs=8.1
Q ss_pred CCccCCCCcccccCc
Q psy4683 83 GLFSCDLCSYTSTQK 97 (196)
Q Consensus 83 ~~~~C~~C~~~f~~~ 97 (196)
.|--|..||..|...
T Consensus 67 ~psfchncgs~fpwt 81 (160)
T COG4306 67 PPSFCHNCGSRFPWT 81 (160)
T ss_pred CcchhhcCCCCCCcH
Confidence 444566666666543
No 242
>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=26.15 E-value=12 Score=32.46 Aligned_cols=80 Identities=23% Similarity=0.340 Sum_probs=46.3
Q ss_pred ccccccccccCCHHHHHHHHHhhcCCCCCc-cCCCCcccccCchHHHHHHHhhcCCCc-ccccccccccCCchHHHhhhh
Q psy4683 56 FPCRLCSQEFDTKEQRKKHERKDHATQGLF-SCDLCSYTSTQKYYLVKHKSRHIKDYN-VFCKICQLGFLSKNELNVHNI 133 (196)
Q Consensus 56 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~-~C~~C~~~f~~~~~l~~H~~~h~~~~~-~~C~~C~~~f~~~~~l~~H~~ 133 (196)
..|+.|-+.+.+..+.+-+ -|| .|..||-.|.-...|-.-.. .+.-.. -.|+.|.+.|.++.+- +
T Consensus 69 a~C~~Cl~E~~dp~~Rry~--------YpF~nCt~CGPr~~i~~~lpydr~-~t~m~~f~~C~~C~~ey~~p~~r----r 135 (711)
T TIGR00143 69 ATCSDCLEEMLDKNDRRYL--------YPFISCTHCGPRFTIIEALPYDRE-NTSMADFPLCPDCAKEYKDPLDR----R 135 (711)
T ss_pred hhHHHHHHHhcCCCccccc--------CCcccccCCCCCeEEeecCCCCCC-CcCCCCCcCCHHHHHHhcCCccc----c
Confidence 5688887766544432211 233 49999987764444332221 111122 3699999888877543 3
Q ss_pred hhcCCCCccCccccccc
Q psy4683 134 KQHCAQPHTCSVCKKIF 150 (196)
Q Consensus 134 ~~~~~~~~~C~~C~~~f 150 (196)
.| -++-.|+.||-..
T Consensus 136 ~h--~~~~~C~~Cgp~l 150 (711)
T TIGR00143 136 FH--AQPIACPRCGPQL 150 (711)
T ss_pred CC--CCCccCCCCCcEE
Confidence 33 3567899998655
No 243
>PF12773 DZR: Double zinc ribbon
Probab=26.14 E-value=44 Score=17.53 Aligned_cols=7 Identities=29% Similarity=0.876 Sum_probs=3.3
Q ss_pred ccccccc
Q psy4683 114 FCKICQL 120 (196)
Q Consensus 114 ~C~~C~~ 120 (196)
.|+.|+.
T Consensus 31 ~C~~Cg~ 37 (50)
T PF12773_consen 31 ICPNCGA 37 (50)
T ss_pred CCcCCcC
Confidence 4444444
No 244
>KOG0717|consensus
Probab=26.13 E-value=36 Score=27.75 Aligned_cols=22 Identities=27% Similarity=0.646 Sum_probs=19.6
Q ss_pred ccCcccccccCCchhHHHHHHH
Q psy4683 141 HTCSVCKKIFVNKKNLTTHKKI 162 (196)
Q Consensus 141 ~~C~~C~~~f~~~~~l~~H~~~ 162 (196)
..|.-|+..|.++..|..|+..
T Consensus 461 ~~C~tCr~~FdSRnkLF~Hlk~ 482 (508)
T KOG0717|consen 461 ISCTTCRESFDSRNKLFAHLKK 482 (508)
T ss_pred HhhhhhhhhccchhHHHHHhhh
Confidence 5688999999999999999876
No 245
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=26.01 E-value=16 Score=23.56 Aligned_cols=11 Identities=18% Similarity=0.498 Sum_probs=6.7
Q ss_pred ccCcccccccC
Q psy4683 141 HTCSVCKKIFV 151 (196)
Q Consensus 141 ~~C~~C~~~f~ 151 (196)
|.|..||..++
T Consensus 101 y~C~~Cg~~wr 111 (113)
T COG1594 101 YKCTRCGYRWR 111 (113)
T ss_pred EEecccCCEee
Confidence 66666666553
No 246
>KOG0782|consensus
Probab=25.65 E-value=12 Score=31.25 Aligned_cols=51 Identities=25% Similarity=0.404 Sum_probs=28.1
Q ss_pred HHHHHHHhhcCCCcccccccccccCCchHHHhhhhhhcCCCCccCcccccccCCch
Q psy4683 99 YLVKHKSRHIKDYNVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKIFVNKK 154 (196)
Q Consensus 99 ~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~C~~C~~~f~~~~ 154 (196)
.+.+|-..|.....-+|..|++.|..+..+..-. .....|..|..+|-.+.
T Consensus 240 ~fvrHHWVHrrRqeGkC~~CgKgFQQKf~FhsKE-----ivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 240 GFVRHHWVHRRRQEGKCNTCGKGFQQKFFFHSKE-----IVAISCSWCKQAYHLKV 290 (1004)
T ss_pred cchHHhHhhHhhhccccchhhhhhhhheeecccc-----EEEEEehHHHHHhhcch
Confidence 5555555554444456777777766554331111 22356777777776654
No 247
>KOG2071|consensus
Probab=25.50 E-value=54 Score=27.60 Aligned_cols=28 Identities=18% Similarity=0.186 Sum_probs=21.8
Q ss_pred CCCCccCCCCcccccCchHHHHHHHhhc
Q psy4683 81 TQGLFSCDLCSYTSTQKYYLVKHKSRHI 108 (196)
Q Consensus 81 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~ 108 (196)
...|..|..||..|.+......||-.|.
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 4567889999999998887777776553
No 248
>KOG3214|consensus
Probab=25.29 E-value=22 Score=22.17 Aligned_cols=7 Identities=43% Similarity=1.416 Sum_probs=3.8
Q ss_pred ccCCCCc
Q psy4683 85 FSCDLCS 91 (196)
Q Consensus 85 ~~C~~C~ 91 (196)
|.|+.|.
T Consensus 24 FnClfcn 30 (109)
T KOG3214|consen 24 FNCLFCN 30 (109)
T ss_pred eccCccc
Confidence 5555554
No 249
>PRK04351 hypothetical protein; Provisional
Probab=25.29 E-value=26 Score=23.84 Aligned_cols=9 Identities=22% Similarity=0.682 Sum_probs=4.0
Q ss_pred ccCcccccc
Q psy4683 141 HTCSVCKKI 149 (196)
Q Consensus 141 ~~C~~C~~~ 149 (196)
|.|..|+..
T Consensus 113 Y~C~~Cg~~ 121 (149)
T PRK04351 113 YECQSCGQQ 121 (149)
T ss_pred EECCCCCCE
Confidence 444444433
No 250
>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=24.73 E-value=29 Score=17.27 Aligned_cols=11 Identities=18% Similarity=0.643 Sum_probs=5.7
Q ss_pred ccccccccccc
Q psy4683 55 KFPCRLCSQEF 65 (196)
Q Consensus 55 ~~~C~~C~~~f 65 (196)
-|+|..||...
T Consensus 6 ~YkC~~CGniV 16 (36)
T PF06397_consen 6 FYKCEHCGNIV 16 (36)
T ss_dssp EEE-TTT--EE
T ss_pred EEEccCCCCEE
Confidence 47888888765
No 251
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=24.28 E-value=28 Score=18.67 Aligned_cols=8 Identities=38% Similarity=1.240 Sum_probs=3.2
Q ss_pred ccCccccc
Q psy4683 141 HTCSVCKK 148 (196)
Q Consensus 141 ~~C~~C~~ 148 (196)
|.||+|++
T Consensus 42 W~CPiC~~ 49 (50)
T PF02891_consen 42 WKCPICNK 49 (50)
T ss_dssp -B-TTT--
T ss_pred eECcCCcC
Confidence 77888764
No 252
>PRK05580 primosome assembly protein PriA; Validated
Probab=24.23 E-value=26 Score=30.31 Aligned_cols=24 Identities=21% Similarity=0.468 Sum_probs=14.5
Q ss_pred hHHHhhhhhhcCCCCccCcccccc
Q psy4683 126 NELNVHNIKQHCAQPHTCSVCKKI 149 (196)
Q Consensus 126 ~~l~~H~~~~~~~~~~~C~~C~~~ 149 (196)
..|.-|........|..|+.||..
T Consensus 407 ~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 407 RRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CeEECCCCcCCCCCCCCCCCCcCC
Confidence 334444444445567789999765
No 253
>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=24.04 E-value=66 Score=15.64 Aligned_cols=24 Identities=13% Similarity=0.362 Sum_probs=13.9
Q ss_pred ccCcccccccCCchhHHHHHHHhhc
Q psy4683 141 HTCSVCKKIFVNKKNLTTHKKIHLA 165 (196)
Q Consensus 141 ~~C~~C~~~f~~~~~l~~H~~~h~~ 165 (196)
+.|+.|++.+. .+.+..|+..-.|
T Consensus 5 ~~C~nC~R~v~-a~RfA~HLekCmg 28 (33)
T PF08209_consen 5 VECPNCGRPVA-ASRFAPHLEKCMG 28 (33)
T ss_dssp EE-TTTSSEEE-GGGHHHHHHHHTC
T ss_pred EECCCCcCCcc-hhhhHHHHHHHHc
Confidence 56777776543 4556667665544
No 254
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=23.95 E-value=27 Score=21.94 Aligned_cols=10 Identities=30% Similarity=0.524 Sum_probs=4.6
Q ss_pred cCcccccccC
Q psy4683 142 TCSVCKKIFV 151 (196)
Q Consensus 142 ~C~~C~~~f~ 151 (196)
.|+.||..+.
T Consensus 44 ~C~~CG~y~~ 53 (99)
T PRK14892 44 TCGNCGLYTE 53 (99)
T ss_pred ECCCCCCccC
Confidence 4455544433
No 255
>PRK11032 hypothetical protein; Provisional
Probab=23.93 E-value=34 Score=23.57 Aligned_cols=32 Identities=13% Similarity=0.207 Sum_probs=18.7
Q ss_pred CCcccccccccccCCHHHHHHHHHhhcCCCCCccCCCCccccc
Q psy4683 53 DTKFPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTST 95 (196)
Q Consensus 53 ~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~ 95 (196)
-+-+.|..||... + ..|.+..| .|+.||....
T Consensus 122 ~G~LvC~~Cg~~~--------~--~~~p~~i~-pCp~C~~~~F 153 (160)
T PRK11032 122 LGNLVCEKCHHHL--------A--FYTPEVLP-LCPKCGHDQF 153 (160)
T ss_pred cceEEecCCCCEE--------E--ecCCCcCC-CCCCCCCCee
Confidence 3457888888754 2 22333333 5888886543
No 256
>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=22.68 E-value=63 Score=24.66 Aligned_cols=11 Identities=18% Similarity=0.471 Sum_probs=5.5
Q ss_pred ccccccccccC
Q psy4683 113 VFCKICQLGFL 123 (196)
Q Consensus 113 ~~C~~C~~~f~ 123 (196)
+.|+.|+.-|.
T Consensus 46 ~vc~~c~~h~r 56 (285)
T TIGR00515 46 EVCPKCDHHMR 56 (285)
T ss_pred CCCCCCCCcCc
Confidence 34555555443
No 257
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=22.29 E-value=86 Score=21.45 Aligned_cols=22 Identities=18% Similarity=0.374 Sum_probs=11.7
Q ss_pred ccccccccccc------CCHHHHHHHHH
Q psy4683 55 KFPCRLCSQEF------DTKEQRKKHER 76 (196)
Q Consensus 55 ~~~C~~C~~~f------~~~~~l~~H~~ 76 (196)
-.+|..|++-| ...+.+..|+.
T Consensus 14 vv~C~~c~kWFCNg~~~~s~SHIv~HLv 41 (152)
T PF09416_consen 14 VVKCNTCNKWFCNGRGNTSGSHIVNHLV 41 (152)
T ss_dssp EEEETTTTEEEES--TTSSS-HHHHHHH
T ss_pred EeEcCCCCcEeecCCCCCcccHHHHHHH
Confidence 35566666655 24445666653
No 258
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=22.22 E-value=1.3e+02 Score=23.14 Aligned_cols=35 Identities=20% Similarity=0.284 Sum_probs=23.2
Q ss_pred CcccccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccccCch
Q psy4683 54 TKFPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTSTQKY 98 (196)
Q Consensus 54 ~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f~~~~ 98 (196)
-..+|+.|+.....+ .|.. .-+.|+.|+..|.-..
T Consensus 37 lw~kc~~C~~~~~~~-~l~~---------~~~vcp~c~~h~rltA 71 (296)
T CHL00174 37 LWVQCENCYGLNYKK-FLKS---------KMNICEQCGYHLKMSS 71 (296)
T ss_pred CeeECCCccchhhHH-HHHH---------cCCCCCCCCCCcCCCH
Confidence 457899999876432 2222 2368999998886443
No 259
>KOG1729|consensus
Probab=22.11 E-value=38 Score=25.83 Aligned_cols=9 Identities=22% Similarity=0.881 Sum_probs=4.9
Q ss_pred cCccccccc
Q psy4683 142 TCSVCKKIF 150 (196)
Q Consensus 142 ~C~~C~~~f 150 (196)
.|..|-..+
T Consensus 216 vC~~CF~el 224 (288)
T KOG1729|consen 216 VCDICFEEL 224 (288)
T ss_pred ecHHHHHHH
Confidence 555555444
No 260
>PTZ00448 hypothetical protein; Provisional
Probab=22.05 E-value=66 Score=25.47 Aligned_cols=23 Identities=13% Similarity=0.349 Sum_probs=18.0
Q ss_pred CccCCCCcccccCchHHHHHHHh
Q psy4683 84 LFSCDLCSYTSTQKYYLVKHKSR 106 (196)
Q Consensus 84 ~~~C~~C~~~f~~~~~l~~H~~~ 106 (196)
.|.|..|+..|.+....+.|+++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 57888888888777777777763
No 261
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=21.81 E-value=31 Score=18.92 Aligned_cols=9 Identities=44% Similarity=1.117 Sum_probs=4.6
Q ss_pred CccCccccc
Q psy4683 140 PHTCSVCKK 148 (196)
Q Consensus 140 ~~~C~~C~~ 148 (196)
|.-|+.|..
T Consensus 28 PlyCpKCK~ 36 (55)
T PF14205_consen 28 PLYCPKCKQ 36 (55)
T ss_pred cccCCCCCc
Confidence 445555543
No 262
>PF15616 TerY-C: TerY-C metal binding domain
Probab=21.76 E-value=15 Score=24.32 Aligned_cols=8 Identities=38% Similarity=0.741 Sum_probs=3.8
Q ss_pred cccccccc
Q psy4683 113 VFCKICQL 120 (196)
Q Consensus 113 ~~C~~C~~ 120 (196)
..|++|++
T Consensus 106 ~~CPwCg~ 113 (131)
T PF15616_consen 106 VTCPWCGN 113 (131)
T ss_pred EECCCCCC
Confidence 44555544
No 263
>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=21.69 E-value=40 Score=21.31 Aligned_cols=9 Identities=22% Similarity=0.578 Sum_probs=5.1
Q ss_pred CccCCCCcc
Q psy4683 84 LFSCDLCSY 92 (196)
Q Consensus 84 ~~~C~~C~~ 92 (196)
|-.|+.||.
T Consensus 2 p~~CpYCg~ 10 (102)
T PF11672_consen 2 PIICPYCGG 10 (102)
T ss_pred CcccCCCCC
Confidence 445666664
No 264
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=21.63 E-value=68 Score=22.88 Aligned_cols=10 Identities=30% Similarity=0.534 Sum_probs=4.9
Q ss_pred cccccccccc
Q psy4683 113 VFCKICQLGF 122 (196)
Q Consensus 113 ~~C~~C~~~f 122 (196)
+.|..||..+
T Consensus 31 vrC~eCG~V~ 40 (201)
T COG1326 31 VRCEECGTVH 40 (201)
T ss_pred EEccCCCcEe
Confidence 4455555444
No 265
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=21.36 E-value=31 Score=21.78 Aligned_cols=23 Identities=39% Similarity=0.735 Sum_probs=19.6
Q ss_pred CccCcccccccCCchhHHHHHHH
Q psy4683 140 PHTCSVCKKIFVNKKNLTTHKKI 162 (196)
Q Consensus 140 ~~~C~~C~~~f~~~~~l~~H~~~ 162 (196)
.+.|..|.+-|.+...|..|.+.
T Consensus 55 qhYCieCaryf~t~~aL~~Hkkg 77 (126)
T COG5112 55 QHYCIECARYFITEKALMEHKKG 77 (126)
T ss_pred eeeeehhHHHHHHHHHHHHHhcc
Confidence 36799999999999999988765
No 266
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=21.18 E-value=94 Score=22.27 Aligned_cols=15 Identities=20% Similarity=0.436 Sum_probs=9.3
Q ss_pred CCccCCCCcccccCc
Q psy4683 83 GLFSCDLCSYTSTQK 97 (196)
Q Consensus 83 ~~~~C~~C~~~f~~~ 97 (196)
.||.|.+|-+.|..+
T Consensus 195 IPF~C~iCKkdy~sp 209 (259)
T COG5152 195 IPFLCGICKKDYESP 209 (259)
T ss_pred Cceeehhchhhccch
Confidence 467777777666443
No 267
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=21.14 E-value=48 Score=18.04 Aligned_cols=9 Identities=22% Similarity=0.685 Sum_probs=5.1
Q ss_pred cCCCCcccc
Q psy4683 86 SCDLCSYTS 94 (196)
Q Consensus 86 ~C~~C~~~f 94 (196)
.||.||..+
T Consensus 2 ~CPyCge~~ 10 (52)
T PF14255_consen 2 QCPYCGEPI 10 (52)
T ss_pred CCCCCCCee
Confidence 466666554
No 268
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=21.10 E-value=79 Score=17.47 Aligned_cols=30 Identities=20% Similarity=0.389 Sum_probs=11.6
Q ss_pred cccccccccccCCHHHHHHHHHhhcCCCCCccCCC
Q psy4683 55 KFPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDL 89 (196)
Q Consensus 55 ~~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~ 89 (196)
|+....|+-.|. +.++...+ ...+...|+.
T Consensus 24 PV~s~~C~H~fe-k~aI~~~i----~~~~~~~CPv 53 (57)
T PF11789_consen 24 PVKSKKCGHTFE-KEAILQYI----QRNGSKRCPV 53 (57)
T ss_dssp EEEESSS--EEE-HHHHHHHC----TTTS-EE-SC
T ss_pred CcCcCCCCCeec-HHHHHHHH----HhcCCCCCCC
Confidence 455555666663 33333333 1233455655
No 269
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=20.65 E-value=51 Score=24.08 Aligned_cols=17 Identities=24% Similarity=0.425 Sum_probs=13.9
Q ss_pred CCCCccCcccccccCCc
Q psy4683 137 CAQPHTCSVCKKIFVNK 153 (196)
Q Consensus 137 ~~~~~~C~~C~~~f~~~ 153 (196)
..++.+|+.||..|...
T Consensus 178 EGkpqRCpECGqVFKLV 194 (268)
T PTZ00043 178 EGFLYRCGECDQIFMLV 194 (268)
T ss_pred CCCCccCCCCCcEEEEE
Confidence 45689999999999854
No 270
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=20.62 E-value=35 Score=22.83 Aligned_cols=16 Identities=31% Similarity=0.856 Sum_probs=12.8
Q ss_pred CCCccCcccccccCCc
Q psy4683 138 AQPHTCSVCKKIFVNK 153 (196)
Q Consensus 138 ~~~~~C~~C~~~f~~~ 153 (196)
.+|.+|+.||..|...
T Consensus 110 g~~~RCpeCG~~fkL~ 125 (136)
T PF01215_consen 110 GKPQRCPECGQVFKLK 125 (136)
T ss_dssp TSEEEETTTEEEEEEE
T ss_pred CCccCCCCCCeEEEEE
Confidence 3589999999988753
No 271
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=20.57 E-value=48 Score=21.99 Aligned_cols=26 Identities=19% Similarity=0.570 Sum_probs=14.3
Q ss_pred ccccccccccCCHHHHHHHHHhhcCCCCCccCCCCcccc
Q psy4683 56 FPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLCSYTS 94 (196)
Q Consensus 56 ~~C~~C~~~f~~~~~l~~H~~~~h~~~~~~~C~~C~~~f 94 (196)
+.|+.||... ..+.|. ..|+.|+..+
T Consensus 29 ~hCp~Cg~PL-----------F~KdG~--v~CPvC~~~~ 54 (131)
T COG1645 29 KHCPKCGTPL-----------FRKDGE--VFCPVCGYRE 54 (131)
T ss_pred hhCcccCCcc-----------eeeCCe--EECCCCCceE
Confidence 4577777653 123332 5577777443
Done!