Query psy18241
Match_columns 566
No_of_seqs 736 out of 2340
Neff 10.8
Searched_HMMs 46136
Date Fri Aug 16 17:18:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy18241.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/18241hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1074|consensus 100.0 1.8E-36 3.8E-41 296.1 6.2 57 507-563 880-936 (958)
2 KOG1074|consensus 100.0 1.1E-32 2.4E-37 269.6 4.8 387 4-478 353-936 (958)
3 KOG2462|consensus 100.0 1.2E-31 2.6E-36 231.4 6.0 135 392-554 129-263 (279)
4 KOG2462|consensus 100.0 5.6E-31 1.2E-35 227.3 5.5 135 363-500 128-265 (279)
5 KOG3608|consensus 100.0 1E-29 2.2E-34 224.4 10.5 229 311-561 140-379 (467)
6 KOG3608|consensus 99.9 4.8E-26 1E-30 201.3 9.8 214 254-499 139-373 (467)
7 KOG3623|consensus 99.9 5.9E-25 1.3E-29 211.9 12.9 106 61-166 211-331 (1007)
8 KOG3623|consensus 99.9 3.4E-24 7.3E-29 206.7 14.8 106 4-109 210-330 (1007)
9 KOG3576|consensus 99.8 5.1E-20 1.1E-24 150.5 1.6 114 418-532 114-238 (267)
10 KOG3576|consensus 99.7 4.2E-19 9.2E-24 145.1 2.9 117 361-477 113-240 (267)
11 PLN03086 PRLI-interacting fact 99.4 5.2E-13 1.1E-17 131.8 8.1 145 6-169 409-565 (567)
12 PLN03086 PRLI-interacting fact 99.4 1.6E-12 3.5E-17 128.4 9.7 143 366-527 408-561 (567)
13 PHA00733 hypothetical protein 99.3 3.5E-12 7.5E-17 102.3 4.5 81 475-559 38-124 (128)
14 PHA00733 hypothetical protein 99.2 1.8E-11 3.9E-16 98.3 4.9 55 418-474 70-124 (128)
15 PHA02768 hypothetical protein; 99.1 4E-11 8.8E-16 77.6 1.7 44 506-551 5-48 (55)
16 PHA02768 hypothetical protein; 99.0 1.7E-10 3.7E-15 74.8 1.9 42 422-465 6-47 (55)
17 KOG3993|consensus 98.9 1.7E-10 3.7E-15 106.1 0.0 141 32-172 267-486 (500)
18 PF13465 zf-H2C2_2: Zinc-finge 98.9 8.7E-10 1.9E-14 61.1 1.4 25 521-545 1-25 (26)
19 KOG3993|consensus 98.8 2.3E-09 5E-14 98.9 2.6 193 279-471 267-480 (500)
20 PF13465 zf-H2C2_2: Zinc-finge 98.7 6E-09 1.3E-13 57.7 1.8 23 465-487 2-24 (26)
21 PHA00616 hypothetical protein 98.6 1.3E-08 2.8E-13 62.6 0.7 34 506-539 1-34 (44)
22 PHA00616 hypothetical protein 98.6 3.3E-08 7.1E-13 60.9 1.8 32 534-565 1-32 (44)
23 PHA00732 hypothetical protein 98.5 6.5E-08 1.4E-12 69.9 2.8 46 477-529 1-47 (79)
24 PHA00732 hypothetical protein 98.3 3.5E-07 7.7E-12 66.1 2.8 35 450-487 2-37 (79)
25 KOG1146|consensus 98.2 1.3E-06 2.7E-11 93.0 4.9 122 423-561 1230-1355(1406)
26 PF05605 zf-Di19: Drought indu 98.2 2.4E-06 5.2E-11 57.3 3.8 51 506-559 2-54 (54)
27 PF00096 zf-C2H2: Zinc finger, 98.1 1.7E-06 3.8E-11 46.6 1.4 23 535-557 1-23 (23)
28 PF05605 zf-Di19: Drought indu 97.9 1.5E-05 3.3E-10 53.4 3.8 47 5-54 3-51 (54)
29 PF00096 zf-C2H2: Zinc finger, 97.8 1E-05 2.3E-10 43.5 1.8 23 5-27 1-23 (23)
30 PF13894 zf-C2H2_4: C2H2-type 97.7 1.6E-05 3.5E-10 43.3 1.7 24 535-558 1-24 (24)
31 PF13912 zf-C2H2_6: C2H2-type 97.7 2.1E-05 4.6E-10 44.2 1.4 26 534-559 1-26 (27)
32 PF12756 zf-C2H2_2: C2H2 type 97.5 6.4E-05 1.4E-09 58.7 2.4 23 116-138 50-72 (100)
33 PF13894 zf-C2H2_4: C2H2-type 97.5 9.2E-05 2E-09 40.2 2.1 22 118-139 2-23 (24)
34 PF12756 zf-C2H2_2: C2H2 type 97.4 7.6E-05 1.6E-09 58.2 2.3 23 88-110 50-72 (100)
35 PF09237 GAGA: GAGA factor; I 97.4 0.00011 2.5E-09 46.2 2.2 40 523-562 12-52 (54)
36 COG5189 SFP1 Putative transcri 97.4 6E-05 1.3E-09 67.5 1.3 52 504-555 347-419 (423)
37 PF13912 zf-C2H2_6: C2H2-type 97.4 0.00011 2.4E-09 41.2 1.9 24 4-27 1-24 (27)
38 COG5189 SFP1 Putative transcri 97.3 8.5E-05 1.8E-09 66.5 1.3 23 114-136 396-418 (423)
39 smart00355 ZnF_C2H2 zinc finge 97.1 0.00035 7.5E-09 38.7 2.1 24 535-558 1-24 (26)
40 COG5048 FOG: Zn-finger [Genera 97.1 0.00092 2E-08 68.5 6.2 150 392-542 288-454 (467)
41 PF13909 zf-H2C2_5: C2H2-type 97.0 0.00035 7.5E-09 37.9 1.5 24 535-559 1-24 (24)
42 PF09237 GAGA: GAGA factor; I 97.0 0.00047 1E-08 43.5 1.8 31 447-477 22-52 (54)
43 KOG2231|consensus 96.8 0.0019 4E-08 65.9 5.9 46 62-111 184-235 (669)
44 smart00355 ZnF_C2H2 zinc finge 96.7 0.0014 3E-08 36.1 2.4 22 451-472 2-23 (26)
45 PF12874 zf-met: Zinc-finger o 96.6 0.001 2.2E-08 36.4 1.2 23 535-557 1-23 (25)
46 PRK04860 hypothetical protein; 96.6 0.001 2.3E-08 55.6 1.5 38 506-547 119-156 (160)
47 PF12874 zf-met: Zinc-finger o 96.5 0.0017 3.7E-08 35.5 1.8 22 5-26 1-22 (25)
48 KOG1146|consensus 96.4 0.00055 1.2E-08 73.7 -1.1 101 366-471 1229-1350(1406)
49 KOG2231|consensus 96.4 0.0066 1.4E-07 62.1 6.3 23 146-168 184-206 (669)
50 PRK04860 hypothetical protein; 96.4 0.0015 3.3E-08 54.6 1.4 37 421-461 119-155 (160)
51 PF13909 zf-H2C2_5: C2H2-type 96.2 0.0036 7.8E-08 33.8 1.9 22 117-139 1-22 (24)
52 KOG2785|consensus 96.2 0.018 4E-07 53.9 7.5 72 252-328 167-241 (390)
53 COG5048 FOG: Zn-finger [Genera 96.2 0.0017 3.7E-08 66.5 0.8 148 4-151 289-453 (467)
54 PF12171 zf-C2H2_jaz: Zinc-fin 95.9 0.0024 5.3E-08 35.6 0.4 22 535-556 2-23 (27)
55 COG5236 Uncharacterized conser 95.6 0.014 3.1E-07 53.3 4.1 132 32-173 151-310 (493)
56 PF12171 zf-C2H2_jaz: Zinc-fin 95.6 0.0086 1.9E-07 33.4 1.7 22 394-415 2-23 (27)
57 COG5236 Uncharacterized conser 95.1 0.031 6.8E-07 51.2 4.5 86 61-152 152-252 (493)
58 PF13913 zf-C2HC_2: zinc-finge 94.5 0.027 5.9E-07 30.6 1.7 20 5-25 3-22 (25)
59 PF13913 zf-C2HC_2: zinc-finge 94.4 0.028 6.1E-07 30.5 1.5 19 536-555 4-22 (25)
60 KOG2785|consensus 94.3 0.1 2.2E-06 49.2 5.9 51 116-166 166-242 (390)
61 TIGR00622 ssl1 transcription f 93.6 0.18 3.9E-06 38.9 5.2 79 364-444 14-104 (112)
62 smart00451 ZnF_U1 U1-like zinc 92.7 0.065 1.4E-06 32.0 1.4 23 534-556 3-25 (35)
63 KOG2482|consensus 92.7 0.12 2.6E-06 47.6 3.5 134 5-139 145-357 (423)
64 cd00350 rubredoxin_like Rubred 92.5 0.078 1.7E-06 31.1 1.4 9 533-541 16-24 (33)
65 smart00451 ZnF_U1 U1-like zinc 91.6 0.16 3.4E-06 30.3 2.1 20 33-52 4-23 (35)
66 KOG4173|consensus 91.5 0.072 1.6E-06 45.1 0.7 77 59-138 78-168 (253)
67 cd00350 rubredoxin_like Rubred 91.4 0.15 3.2E-06 29.9 1.8 24 5-40 2-25 (33)
68 KOG2893|consensus 91.0 0.074 1.6E-06 46.1 0.3 41 63-107 13-53 (341)
69 KOG2893|consensus 91.0 0.076 1.7E-06 46.0 0.4 45 509-557 13-58 (341)
70 TIGR00622 ssl1 transcription f 90.0 0.54 1.2E-05 36.4 4.2 85 31-123 14-110 (112)
71 KOG2482|consensus 87.1 0.86 1.9E-05 42.2 4.2 76 252-330 280-357 (423)
72 KOG4173|consensus 85.7 0.45 9.8E-06 40.5 1.6 82 87-171 78-173 (253)
73 cd00729 rubredoxin_SM Rubredox 85.1 0.69 1.5E-05 27.3 1.7 25 4-40 2-26 (34)
74 COG4049 Uncharacterized protei 84.7 0.51 1.1E-05 30.6 1.1 25 531-555 14-38 (65)
75 PF12013 DUF3505: Protein of u 84.0 1.2 2.7E-05 34.9 3.3 25 535-559 81-109 (109)
76 COG4049 Uncharacterized protei 83.7 0.52 1.1E-05 30.5 0.8 23 114-136 15-37 (65)
77 PF09538 FYDLN_acid: Protein o 83.1 0.79 1.7E-05 35.6 1.8 30 422-462 10-39 (108)
78 PF09986 DUF2225: Uncharacteri 82.9 0.46 9.9E-06 42.6 0.5 43 505-547 4-61 (214)
79 TIGR02098 MJ0042_CXXC MJ0042 f 82.7 0.9 1.9E-05 27.6 1.6 34 4-42 2-35 (38)
80 PF13717 zinc_ribbon_4: zinc-r 80.7 1.8 3.8E-05 26.0 2.3 34 4-42 2-35 (36)
81 PF09538 FYDLN_acid: Protein o 79.3 1.3 2.9E-05 34.4 1.9 30 478-519 10-39 (108)
82 PF10571 UPF0547: Uncharacteri 79.3 1.1 2.4E-05 24.6 1.0 10 508-517 16-25 (26)
83 smart00659 RPOLCX RNA polymera 78.3 1.8 3.8E-05 27.4 1.9 12 4-15 2-13 (44)
84 PF13719 zinc_ribbon_5: zinc-r 76.8 1.5 3.3E-05 26.5 1.2 32 479-516 4-35 (37)
85 PRK00398 rpoP DNA-directed RNA 76.3 1.8 3.8E-05 27.7 1.5 12 4-15 3-14 (46)
86 smart00734 ZnF_Rad18 Rad18-lik 75.1 2.4 5.1E-05 23.3 1.6 19 6-25 3-21 (26)
87 PF12013 DUF3505: Protein of u 74.5 4.4 9.5E-05 31.8 3.7 24 89-112 81-108 (109)
88 smart00531 TFIIE Transcription 74.5 2.3 5.1E-05 35.5 2.2 39 28-70 95-133 (147)
89 COG1592 Rubrerythrin [Energy p 74.3 1.9 4.2E-05 36.3 1.7 23 506-541 134-156 (166)
90 PF02892 zf-BED: BED zinc fing 74.2 2.1 4.6E-05 27.1 1.5 25 531-555 13-41 (45)
91 smart00614 ZnF_BED BED zinc fi 73.5 2.3 4.9E-05 27.8 1.5 20 536-555 20-44 (50)
92 PRK00464 nrdR transcriptional 73.5 1.4 3E-05 36.8 0.7 12 422-433 29-40 (154)
93 KOG2186|consensus 73.1 1.5 3.3E-05 39.0 0.8 47 478-528 4-50 (276)
94 PRK06266 transcription initiat 72.7 2.4 5.3E-05 36.6 2.0 35 28-71 113-147 (178)
95 TIGR00373 conserved hypothetic 72.6 3.8 8.2E-05 34.7 3.1 35 360-403 104-138 (158)
96 TIGR02300 FYDLN_acid conserved 72.3 3 6.4E-05 33.0 2.1 30 422-462 10-39 (129)
97 COG1592 Rubrerythrin [Energy p 72.1 2.3 5.1E-05 35.8 1.6 11 418-428 146-156 (166)
98 TIGR00373 conserved hypothetic 71.7 3.5 7.7E-05 34.8 2.7 19 504-522 107-125 (158)
99 smart00834 CxxC_CXXC_SSSS Puta 71.6 1.8 3.8E-05 26.8 0.6 11 89-99 6-16 (41)
100 smart00531 TFIIE Transcription 71.6 3.5 7.6E-05 34.4 2.6 13 506-518 99-111 (147)
101 TIGR02605 CxxC_CxxC_SSSS putat 70.2 1.9 4.1E-05 28.4 0.6 9 90-98 7-15 (52)
102 KOG2186|consensus 70.0 2.1 4.5E-05 38.1 1.0 12 61-72 30-41 (276)
103 PF09986 DUF2225: Uncharacteri 69.6 2.3 5E-05 38.1 1.2 23 306-328 4-26 (214)
104 TIGR02300 FYDLN_acid conserved 67.2 4.2 9.2E-05 32.1 2.0 30 478-519 10-39 (129)
105 PRK06266 transcription initiat 67.2 5 0.00011 34.7 2.7 33 362-403 114-146 (178)
106 PF02176 zf-TRAF: TRAF-type zi 67.0 3.2 7E-05 28.2 1.3 19 464-482 25-43 (60)
107 COG2888 Predicted Zn-ribbon RN 64.2 5.7 0.00012 26.5 1.9 8 449-456 50-57 (61)
108 PF09723 Zn-ribbon_8: Zinc rib 63.3 4 8.7E-05 25.5 1.0 11 89-99 6-16 (42)
109 PRK00464 nrdR transcriptional 62.8 1.7 3.6E-05 36.3 -1.0 13 507-519 29-41 (154)
110 COG1996 RPC10 DNA-directed RNA 61.7 4.3 9.4E-05 26.1 1.0 11 4-14 6-16 (49)
111 PF03604 DNA_RNApol_7kD: DNA d 61.3 6.6 0.00014 22.8 1.6 11 89-99 1-11 (32)
112 PRK09678 DNA-binding transcrip 58.5 4.1 8.9E-05 28.9 0.5 41 478-521 2-44 (72)
113 COG1198 PriA Primosomal protei 58.3 7.7 0.00017 41.5 2.7 12 85-96 459-470 (730)
114 PRK09678 DNA-binding transcrip 58.0 3.7 8E-05 29.1 0.2 16 142-157 25-42 (72)
115 PF08274 PhnA_Zn_Ribbon: PhnA 55.3 5.1 0.00011 22.8 0.4 12 29-40 16-27 (30)
116 PF00301 Rubredoxin: Rubredoxi 54.7 9.2 0.0002 24.6 1.6 11 89-99 2-12 (47)
117 PF05443 ROS_MUCR: ROS/MUCR tr 52.9 6.6 0.00014 31.8 0.9 23 535-560 73-95 (132)
118 COG4888 Uncharacterized Zn rib 51.8 4.7 0.0001 30.2 -0.1 11 61-71 47-57 (104)
119 PF15269 zf-C2H2_7: Zinc-finge 51.0 11 0.00025 23.3 1.5 23 3-25 19-41 (54)
120 KOG2807|consensus 50.6 25 0.00053 32.9 4.2 81 421-529 276-368 (378)
121 PF06524 NOA36: NOA36 protein; 50.5 7.8 0.00017 34.7 1.1 89 29-140 139-233 (314)
122 KOG2593|consensus 50.4 16 0.00034 35.8 3.1 17 448-464 127-143 (436)
123 PF14353 CpXC: CpXC protein 50.1 3 6.6E-05 33.9 -1.4 48 479-527 3-59 (128)
124 COG1198 PriA Primosomal protei 50.0 13 0.00028 39.9 2.8 39 395-458 446-484 (730)
125 COG1997 RPL43A Ribosomal prote 49.1 9.2 0.0002 28.0 1.0 11 507-517 54-64 (89)
126 PF02176 zf-TRAF: TRAF-type zi 48.9 14 0.00031 25.0 2.0 19 103-121 25-43 (60)
127 PRK14890 putative Zn-ribbon RN 48.8 15 0.00032 24.7 1.9 9 61-69 26-34 (59)
128 KOG4167|consensus 48.3 5.4 0.00012 41.4 -0.3 25 534-558 792-816 (907)
129 PRK04023 DNA polymerase II lar 48.3 19 0.0004 39.5 3.5 10 32-41 626-635 (1121)
130 KOG2071|consensus 46.8 16 0.00034 37.4 2.7 18 113-130 510-527 (579)
131 COG4530 Uncharacterized protei 44.9 14 0.0003 28.2 1.5 13 504-516 24-36 (129)
132 cd00730 rubredoxin Rubredoxin; 44.6 15 0.00033 23.9 1.5 11 145-155 2-12 (50)
133 KOG2593|consensus 44.2 21 0.00046 34.9 3.0 16 59-74 127-142 (436)
134 PF05191 ADK_lid: Adenylate ki 42.6 9.3 0.0002 22.9 0.2 8 368-375 4-11 (36)
135 PRK04023 DNA polymerase II lar 41.9 24 0.00052 38.8 3.2 10 393-402 626-635 (1121)
136 KOG4167|consensus 41.4 7 0.00015 40.6 -0.7 23 33-55 793-815 (907)
137 PF08790 zf-LYAR: LYAR-type C2 41.0 9.8 0.00021 21.2 0.1 18 536-554 2-19 (28)
138 KOG2807|consensus 40.7 38 0.00083 31.8 3.9 87 4-123 276-374 (378)
139 PF09845 DUF2072: Zn-ribbon co 40.3 17 0.00037 29.1 1.4 12 450-461 2-13 (131)
140 PRK03824 hypA hydrogenase nick 40.0 14 0.00029 30.4 0.9 15 2-16 68-82 (135)
141 PF04959 ARS2: Arsenite-resist 39.5 10 0.00022 33.7 0.1 23 506-528 77-99 (214)
142 PF14446 Prok-RING_1: Prokaryo 39.5 19 0.00041 23.9 1.3 8 91-98 8-15 (54)
143 PF12760 Zn_Tnp_IS1595: Transp 37.9 40 0.00086 21.4 2.6 10 420-429 36-45 (46)
144 COG4957 Predicted transcriptio 37.3 19 0.0004 28.8 1.2 23 535-560 77-99 (148)
145 PF05290 Baculo_IE-1: Baculovi 36.6 31 0.00067 27.7 2.3 56 390-463 77-135 (140)
146 PF01363 FYVE: FYVE zinc finge 36.5 17 0.00037 25.5 0.9 9 479-487 11-19 (69)
147 PF08271 TF_Zn_Ribbon: TFIIB z 36.4 18 0.00039 22.6 0.8 11 31-41 18-28 (43)
148 PF05443 ROS_MUCR: ROS/MUCR tr 36.0 24 0.00053 28.6 1.7 27 30-59 70-96 (132)
149 PF13240 zinc_ribbon_2: zinc-r 35.6 18 0.00038 19.1 0.6 6 35-40 16-21 (23)
150 PF07754 DUF1610: Domain of un 35.5 21 0.00045 19.2 0.8 9 4-12 16-24 (24)
151 PF13878 zf-C2H2_3: zinc-finge 35.4 32 0.0007 21.3 1.8 23 89-111 14-38 (41)
152 PRK12380 hydrogenase nickel in 35.1 23 0.00049 28.0 1.4 12 33-44 71-82 (113)
153 COG5151 SSL1 RNA polymerase II 34.9 39 0.00085 31.3 3.0 25 420-444 387-411 (421)
154 PHA00626 hypothetical protein 34.9 17 0.00036 24.0 0.5 15 533-547 22-36 (59)
155 PF08209 Sgf11: Sgf11 (transcr 34.9 35 0.00076 20.0 1.8 23 3-26 3-25 (33)
156 cd00065 FYVE FYVE domain; Zinc 34.7 27 0.00058 23.3 1.6 12 506-517 18-29 (57)
157 TIGR01206 lysW lysine biosynth 34.5 24 0.00052 23.5 1.2 6 91-96 5-10 (54)
158 TIGR00100 hypA hydrogenase nic 34.1 22 0.00048 28.1 1.2 13 32-44 70-82 (115)
159 KOG2461|consensus 33.8 32 0.00068 34.1 2.5 77 406-482 316-392 (396)
160 PF13451 zf-trcl: Probable zin 32.8 28 0.0006 22.6 1.3 12 477-488 4-15 (49)
161 PF12907 zf-met2: Zinc-binding 32.4 18 0.00039 22.3 0.4 21 535-555 2-25 (40)
162 PRK00432 30S ribosomal protein 31.1 28 0.0006 22.7 1.1 11 534-544 37-47 (50)
163 PF14445 Prok-RING_2: Prokaryo 30.9 16 0.00034 23.4 -0.1 12 477-488 7-18 (57)
164 PF01286 XPA_N: XPA protein N- 30.6 22 0.00047 21.0 0.5 11 479-489 5-15 (34)
165 PF06524 NOA36: NOA36 protein; 30.2 31 0.00068 31.1 1.6 25 392-416 208-232 (314)
166 PRK03564 formate dehydrogenase 30.2 23 0.00051 33.5 0.9 76 32-128 187-264 (309)
167 smart00154 ZnF_AN1 AN1-like Zi 30.0 23 0.00049 21.7 0.5 13 534-546 12-24 (39)
168 COG3357 Predicted transcriptio 29.8 30 0.00066 25.5 1.2 14 392-405 57-70 (97)
169 PF01780 Ribosomal_L37ae: Ribo 29.4 21 0.00045 26.6 0.3 11 117-127 54-64 (90)
170 PTZ00255 60S ribosomal protein 29.2 21 0.00046 26.5 0.4 11 507-517 55-65 (90)
171 PF10013 DUF2256: Uncharacteri 29.0 28 0.0006 21.6 0.7 12 537-548 11-22 (42)
172 PF04216 FdhE: Protein involve 28.9 6.9 0.00015 37.1 -2.9 56 57-127 194-249 (290)
173 PF07800 DUF1644: Protein of u 28.8 1.6E+02 0.0034 24.7 5.2 38 469-506 99-137 (162)
174 PF13453 zf-TFIIB: Transcripti 28.7 27 0.00059 21.5 0.7 17 33-49 20-36 (41)
175 KOG2461|consensus 28.7 21 0.00046 35.3 0.4 78 379-456 317-394 (396)
176 PF05495 zf-CHY: CHY zinc fing 28.5 22 0.00047 25.3 0.3 10 366-375 11-20 (71)
177 PRK14714 DNA polymerase II lar 27.9 55 0.0012 37.2 3.3 11 449-459 692-702 (1337)
178 PF07649 C1_3: C1-like domain; 27.8 30 0.00066 19.5 0.8 9 534-542 15-23 (30)
179 PRK00564 hypA hydrogenase nick 27.6 33 0.00071 27.3 1.2 13 32-44 71-83 (117)
180 PF04959 ARS2: Arsenite-resist 27.0 25 0.00054 31.3 0.5 28 114-141 75-102 (214)
181 TIGR00280 L37a ribosomal prote 26.9 20 0.00043 26.7 -0.2 10 507-516 54-63 (91)
182 TIGR00595 priA primosomal prot 26.8 48 0.001 34.4 2.5 14 84-97 236-249 (505)
183 KOG0717|consensus 26.6 34 0.00074 33.9 1.3 21 5-25 293-313 (508)
184 PRK14873 primosome assembly pr 26.4 46 0.001 35.7 2.4 12 418-429 407-418 (665)
185 TIGR03826 YvyF flagellar opero 26.1 43 0.00094 27.4 1.6 12 506-517 81-92 (137)
186 smart00064 FYVE Protein presen 26.0 43 0.00093 23.4 1.5 12 506-517 26-37 (68)
187 TIGR00595 priA primosomal prot 25.9 43 0.00093 34.7 2.0 40 394-458 223-262 (505)
188 PF09963 DUF2197: Uncharacteri 25.7 30 0.00066 23.1 0.6 6 507-512 32-37 (56)
189 PF01096 TFIIS_C: Transcriptio 25.4 13 0.00028 22.7 -1.1 10 422-431 29-38 (39)
190 PF04810 zf-Sec23_Sec24: Sec23 25.3 26 0.00057 21.5 0.2 12 531-542 21-32 (40)
191 KOG0696|consensus 25.2 35 0.00076 33.5 1.1 60 417-485 69-129 (683)
192 COG1655 Uncharacterized protei 24.8 31 0.00066 30.6 0.6 28 306-333 18-45 (267)
193 KOG4124|consensus 24.3 20 0.00043 33.8 -0.7 24 114-137 396-419 (442)
194 PRK14714 DNA polymerase II lar 24.2 82 0.0018 35.9 3.7 55 366-462 668-722 (1337)
195 smart00440 ZnF_C2C2 C2C2 Zinc 23.0 29 0.00063 21.4 0.1 10 422-431 29-38 (40)
196 PRK14892 putative transcriptio 22.8 37 0.00081 26.0 0.6 12 61-72 43-54 (99)
197 PF01155 HypA: Hydrogenase exp 22.5 36 0.00078 26.9 0.5 12 33-44 71-82 (113)
198 COG1571 Predicted DNA-binding 22.2 56 0.0012 32.4 1.8 12 477-488 367-378 (421)
199 KOG3408|consensus 22.2 52 0.0011 25.9 1.3 25 532-556 55-79 (129)
200 PRK03681 hypA hydrogenase nick 22.1 39 0.00084 26.7 0.6 12 32-43 70-81 (114)
201 KOG0978|consensus 21.9 35 0.00076 36.2 0.5 17 508-524 680-696 (698)
202 KOG4377|consensus 20.8 61 0.0013 31.5 1.8 20 540-559 409-428 (480)
203 PRK03976 rpl37ae 50S ribosomal 20.8 29 0.00064 25.8 -0.2 10 507-516 55-64 (90)
204 PF09416 UPF1_Zn_bind: RNA hel 20.7 40 0.00087 28.0 0.5 14 475-488 12-25 (152)
205 KOG4377|consensus 20.6 61 0.0013 31.5 1.7 21 121-141 408-428 (480)
206 PF14311 DUF4379: Domain of un 20.5 69 0.0015 21.3 1.5 10 479-488 30-39 (55)
207 KOG2272|consensus 20.5 43 0.00094 30.0 0.7 129 2-134 97-239 (332)
208 KOG3507|consensus 20.4 53 0.0011 22.0 0.9 10 32-41 37-46 (62)
209 KOG2071|consensus 20.3 58 0.0013 33.5 1.6 24 506-529 418-441 (579)
No 1
>KOG1074|consensus
Probab=100.00 E-value=1.8e-36 Score=296.09 Aligned_cols=57 Identities=35% Similarity=0.773 Sum_probs=54.7
Q ss_pred ccCCCCCCcccCchhHHhHhhhccCCCcccCCcChhhccChhhHHHHHhhhcCCCCC
Q psy18241 507 FVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHLNIHNGTKKY 563 (566)
Q Consensus 507 ~~C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~ 563 (566)
..|.+||+.|...++|..||++|+|+|||.|.+|++.|..+.+|+.||.+|+...++
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~ 936 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPP 936 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCC
Confidence 789999999999999999999999999999999999999999999999999987665
No 2
>KOG1074|consensus
Probab=99.97 E-value=1.1e-32 Score=269.59 Aligned_cols=387 Identities=22% Similarity=0.386 Sum_probs=242.8
Q ss_pred ceeCCcccccccChhHHHHHhhhhCCCCccccCccCCccCchHHHHHHHhhcCCCCC------------ccCCccccccC
Q psy18241 4 IHECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHVGMHSGIHP------------FTCHFCNKSFT 71 (566)
Q Consensus 4 ~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~------------~~C~~C~~~f~ 71 (566)
.++|-+|.+.|.+.+.|+.|+|.|++++||+|.+||..|.++.+|+.|...|....| +.|.+|.-.|.
T Consensus 353 khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~e~~p~~~m~p~~~~e~l~~~i~st~~p 432 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHREKYPHVQMNPHPVQEHLQYVITSTGLP 432 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeeeeeccccCCccccCCCCchhhhcceeeccccC
Confidence 478999999999999999999999999999999999999999999999988865432 33444443333
Q ss_pred CchhHHHHHh-----------------------------------------------------hh---------------
Q psy18241 72 QKIGLVKHLN-----------------------------------------------------IH--------------- 83 (566)
Q Consensus 72 ~~~~L~~H~~-----------------------------------------------------~h--------------- 83 (566)
.--...-+.. ++
T Consensus 433 ~g~~vpp~k~~~~~~~~e~~~~~~sts~g~~~~~~~~~sv~~~~ts~~~~~~~s~~~~~~~~~i~~~s~e~e~~vs~g~~ 512 (958)
T KOG1074|consen 433 YGPSVPPEKAEEEAATVEPKLLVRSTSVGSATESLTPSSVSFGETSAPPLPAFSKFVLMKTVEIKSKSEEPEPAVSEGSA 512 (958)
T ss_pred CCCCCCCCCCcchhccccccccccccccCCCCCcccccccccccccCCCCCccccccccCCcccccccCCCCcccccccc
Confidence 2222111110 00
Q ss_pred --------------------------------------------------------------------------------
Q psy18241 84 -------------------------------------------------------------------------------- 83 (566)
Q Consensus 84 -------------------------------------------------------------------------------- 83 (566)
T Consensus 513 ~~~~~~gs~l~~s~~ks~~s~~~~~~~~~~~asa~m~~~~~~~~p~g~s~~~~aq~~~l~d~~~~~~~~~~tsseS~kl~ 592 (958)
T KOG1074|consen 513 ISGVLEGSPLRMSSGKSVESLPVEADLLNHAASAGMFPPSYVSRPLGPSEDTTAQALQLVDKIPEALIEISTSSESPKLT 592 (958)
T ss_pred ccccccCCccccccccCccccchhccccchhhccccCCchhhcCCCCcchhhHHHhhhhhccChhhcceeecccCCcccc
Confidence
Q ss_pred --------cCCCceeCCcCcccccchhhhHHHHhhhcCCCcccCCccccccCChhHHHHHHhhhcCCC----cccCC---
Q psy18241 84 --------NGTKKYQCHLCGKGFIHHTSYKFHQLVHSGERNVKCDICGLALTTKSHLNRHMLVHTGDR----PHECS--- 148 (566)
Q Consensus 84 --------~~~~~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~----~~~C~--- 148 (566)
....+-+|-+|-++.+-++.|+.|.++|+||+||+|.|||+.|+++.+|+.||-+|.... ++.|+
T Consensus 593 slv~~~~~~~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ 672 (958)
T KOG1074|consen 593 SLVENSENKRTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTF 672 (958)
T ss_pred ccccccccccCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchh
Confidence 001235799999999999999999999999999999999999999999999999997653 58899
Q ss_pred ccchhccchhHHHHhhhhhcccCCCCCCCccCCCCCCCCCCCcccccCCCCCCCCCchhhhhhhheeeeeeccccccccc
Q psy18241 149 VCGKRFAKKWNAQVHKKKVHGLDVPGTTHRVMPVPPIGGGEKEEDVATTDTEDDVPSIKIKFLSALIYFFVSWTFWPLVS 228 (566)
Q Consensus 149 ~C~~~f~~~~~l~~H~~~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 228 (566)
+|.+.|.....|..|++.|.+...+..... .+.
T Consensus 673 ic~~kftn~V~lpQhIriH~~~~~s~g~~a------------~e~----------------------------------- 705 (958)
T KOG1074|consen 673 ICQKKFTNAVTLPQHIRIHLGGQISNGGTA------------AEG----------------------------------- 705 (958)
T ss_pred hhcccccccccccceEEeecCCCCCCCccc------------ccc-----------------------------------
Confidence 999999999999999998775443321100 000
Q ss_pred chhhccccceeeecCCCCCCCcceecCcccccCCCHHHHHHHHhhhcCCCCcccccccccccChHHHHHHHhhhcCCC--
Q psy18241 229 QECFLTIGFFFFLTGERACMPLIHECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHVGMHNGIN-- 306 (566)
Q Consensus 229 ~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~-- 306 (566)
.-..-+|..|.+.|.....+..++..|.+... .-....+.+.+.++.
T Consensus 706 -------------------~~~adq~~~~qk~~~~a~~f~~~~se~~~~~s------------~~~~~~~~~t~t~~~~~ 754 (958)
T KOG1074|consen 706 -------------------ILAADQCSSCQKTFSDARSFSQQISEQPSPES------------EPDEQMDERTETEELDV 754 (958)
T ss_pred -------------------cchhcccchhhhcccccccchhhhhccCCccc------------CCccccccccccccccc
Confidence 00013688999999999999888877754332 112222333333333
Q ss_pred --ceecccccccccChhhHhcccccccCCCCcccccccccccccchhHHHHHHhhccCCCCc-ccccccccccchHH---
Q psy18241 307 --PFTCSFCNKSFTQKVGLQKHLPIHTGSTRFQWEQSHLNYVWRTVSELNAHIQTHSDLRPF-VCEICGQGYKMKKA--- 380 (566)
Q Consensus 307 --~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~~~l~~h~~~~~~~~~~-~C~~C~~~f~~~~~--- 380 (566)
+..+..|+..+.....+..+-..+..... ...+......-.......+++++. .+.+++..-...-.
T Consensus 755 tp~~~e~~~~~~~~~e~~i~~~g~te~asa~-------~~~vg~~s~~~~~~~~~~T~~k~~~~~~~~~~~~~~~v~~~p 827 (958)
T KOG1074|consen 755 TPPPPENSCGRELEGEMAISVRGSTEEASAN-------LDEVGTVSAAGEAGEEDDTSEKPTQASSFPGEILAPSVNMDP 827 (958)
T ss_pred CCCccccccccccCcccccccccchhhhhcC-------hhhhcCccccchhhhhcccCCCCcccccCCCcCCccccccCc
Confidence 56677777777766655554322210000 000111111111222333444554 45555433221110
Q ss_pred -HHHHHhhhcCCCCccccccccccCC---hhhhhcc--ccc------cc--CCCccccCcccccccChhhHHHHHhhccC
Q psy18241 381 -LLVHVGMHNGINPFTCSFCNKSFTQ---KVGLQKH--LPI------HT--GSTRFQCDLCGKRFIHQKSFYIHKMVHSG 446 (566)
Q Consensus 381 -l~~H~~~h~~~~~~~C~~C~k~f~~---~~~L~~H--~~~------h~--~~~~~~C~~C~k~f~~~~~l~~H~~~H~~ 446 (566)
|..-...-.++.+-. .. ..++. ...+..- +.. -. -.....|.+||+.|...+.|..|+|+|+|
T Consensus 828 vl~~~~~~~l~eg~~t-~~--n~~t~~~~~~sv~qs~~~p~l~p~l~~~~pvnn~h~C~vCgk~FsSSsALqiH~rTHtg 904 (958)
T KOG1074|consen 828 VLWNQETSMLNEGLAT-KT--NEITPEGPADSVIQSGGVPTLEPSLGRPGPVNNAHVCNVCGKQFSSSAALEIHMRTHTG 904 (958)
T ss_pred hhhccccccccccccc-cc--ccccCCCcchhhhhhccccccCCCCCCCCcccchhhhccchhcccchHHHHHhhhcCCC
Confidence 000000000000000 00 00000 0000000 000 00 11237799999999999999999999999
Q ss_pred CCCccCCcCCccCCChHHHHhHhhhhcCCCcc
Q psy18241 447 EKPIKCSACGLAVLSSSHLKRHFRVHTGEKPY 478 (566)
Q Consensus 447 ~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~ 478 (566)
+|||.|.+|+++|..+.+|+.||.+|....|+
T Consensus 905 ~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~ 936 (958)
T KOG1074|consen 905 PKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPP 936 (958)
T ss_pred CCCccchhhhhhhhhhhhhhhhhccccccCCC
Confidence 99999999999999999999999999877654
No 3
>KOG2462|consensus
Probab=99.97 E-value=1.2e-31 Score=231.37 Aligned_cols=135 Identities=35% Similarity=0.679 Sum_probs=74.6
Q ss_pred CCccccccccccCChhhhhcccccccCCCccccCcccccccChhhHHHHHhhccCCCCccCCcCCccCCChHHHHhHhhh
Q psy18241 392 NPFTCSFCNKSFTQKVGLQKHLPIHTGSTRFQCDLCGKRFIHQKSFYIHKMVHSGEKPIKCSACGLAVLSSSHLKRHFRV 471 (566)
Q Consensus 392 ~~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~ 471 (566)
..|+|+.|||.+++.++|.+|..+|-.- ...+.+.|++||+.|.+-..|+.|+|+
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~-------------------------~s~ka~~C~~C~K~YvSmpALkMHirT 183 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSL-------------------------DSKKAFSCKYCGKVYVSMPALKMHIRT 183 (279)
T ss_pred Cceeccccccccccccccchhhcccccc-------------------------cccccccCCCCCceeeehHHHhhHhhc
Confidence 3466666666666666666666665321 012344555555555555555555555
Q ss_pred hcCCCcccCcccccccccCHHHHHHHHhhcCCCCCccCCCCCCcccCchhHHhHhhhccCCCcccCCcChhhccChhhHH
Q psy18241 472 HTGEKPYQCTTCGKRLRRTVSELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLV 551 (566)
Q Consensus 472 H~~~~~~~C~~C~k~f~~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~~~f~~~~~L~ 551 (566)
|+ -+++|.+|||.|.+. ..|+-|+|+|+|||||.|+.|+|+|..+++|+.||++|++.|+|+|..|+|+|..++.|.
T Consensus 184 H~--l~c~C~iCGKaFSRP-WLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLn 260 (279)
T KOG2462|consen 184 HT--LPCECGICGKAFSRP-WLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLN 260 (279)
T ss_pred cC--CCcccccccccccch-HHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHH
Confidence 54 345555555555544 345555555555555555555555555555555555555555555555555555555555
Q ss_pred HHH
Q psy18241 552 KHL 554 (566)
Q Consensus 552 ~H~ 554 (566)
+|.
T Consensus 261 KH~ 263 (279)
T KOG2462|consen 261 KHS 263 (279)
T ss_pred Hhh
Confidence 554
No 4
>KOG2462|consensus
Probab=99.96 E-value=5.6e-31 Score=227.28 Aligned_cols=135 Identities=33% Similarity=0.664 Sum_probs=110.3
Q ss_pred CCCcccccccccccchHHHHHHHhhhcC---CCCccccccccccCChhhhhcccccccCCCccccCcccccccChhhHHH
Q psy18241 363 LRPFVCEICGQGYKMKKALLVHVGMHNG---INPFTCSFCNKSFTQKVGLQKHLPIHTGSTRFQCDLCGKRFIHQKSFYI 439 (566)
Q Consensus 363 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~---~~~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~C~~C~k~f~~~~~l~~ 439 (566)
...|+|+.||+.+.+.+.|.+|.++|-. .+.+.|++|||.+.+...|+.|+++|+ -+++|.+|||.|.+..-|+-
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQG 205 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQG 205 (279)
T ss_pred CCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhc
Confidence 4569999999999999999999999864 456788888888888888888888886 56788888888888888888
Q ss_pred HHhhccCCCCccCCcCCccCCChHHHHhHhhhhcCCCcccCcccccccccCHHHHHHHHhh
Q psy18241 440 HKMVHSGEKPIKCSACGLAVLSSSHLKRHFRVHTGEKPYQCTTCGKRLRRTVSELNAHIQT 500 (566)
Q Consensus 440 H~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~C~k~f~~~~~~l~~H~~~ 500 (566)
|+|+|+|||||.|+.|+++|..+++|+.||++|.+.|+|+|..|+|+|... +.|+.|...
T Consensus 206 HiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~-SyLnKH~ES 265 (279)
T KOG2462|consen 206 HIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALK-SYLNKHSES 265 (279)
T ss_pred ccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHH-HHHHHhhhh
Confidence 888888888888888888888888888888888888888888888888665 777777653
No 5
>KOG3608|consensus
Probab=99.96 E-value=1e-29 Score=224.35 Aligned_cols=229 Identities=30% Similarity=0.549 Sum_probs=191.8
Q ss_pred ccccccccChhhHhcccccccCCCCcccccccccccccchhHHHHHHhhccCCCC-ccc--ccccccccchHHHHHHHhh
Q psy18241 311 SFCNKSFTQKVGLQKHLPIHTGSTRFQWEQSHLNYVWRTVSELNAHIQTHSDLRP-FVC--EICGQGYKMKKALLVHVGM 387 (566)
Q Consensus 311 ~~C~~~f~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~~~l~~h~~~~~~~~~-~~C--~~C~~~f~~~~~l~~H~~~ 387 (566)
..|+..|.+...|..|+..|.---.|.. ..+..+++| +.| ..|-+.|.++..|+.|++.
T Consensus 140 edCe~~F~s~~ef~dHV~~H~l~ceyd~------------------~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~ 201 (467)
T KOG3608|consen 140 EDCEREFVSIVEFQDHVVKHALFCEYDI------------------QKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRT 201 (467)
T ss_pred hhcCCcccCHHHHHHHHHHhhhhhhhhh------------------hhCCCCCCceeeccchhhhhhhccHHHHHHHHHh
Confidence 3577777777777777765542111100 112223433 456 4688999999999999999
Q ss_pred hcCCCCccccccccccCChhhhhccccccc--CCCccccCcccccccChhhHHHHHhhccCCCCccCCcCCccCCChHHH
Q psy18241 388 HNGINPFTCSFCNKSFTQKVGLQKHLPIHT--GSTRFQCDLCGKRFIHQKSFYIHKMVHSGEKPIKCSACGLAVLSSSHL 465 (566)
Q Consensus 388 h~~~~~~~C~~C~k~f~~~~~L~~H~~~h~--~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~~l 465 (566)
|++++...|+.||..|+++..|-.|++.-+ ...+|+|..|.|.|.+...|..|++.|.. -|+|+.|+.+....++|
T Consensus 202 Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn--~ykCplCdmtc~~~ssL 279 (467)
T KOG3608|consen 202 HSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN--CYKCPLCDMTCSSASSL 279 (467)
T ss_pred cCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh--cccccccccCCCChHHH
Confidence 999999999999999999999999987654 45689999999999999999999999964 69999999999999999
Q ss_pred HhHhhh-hcCCCcccCcccccccccCHHHHHHHHhhcCCCCCccCCC--CCCcccCchhHHhHhhhcc-CC--CcccCCc
Q psy18241 466 KRHFRV-HTGEKPYQCTTCGKRLRRTVSELNAHIQTHSDLRPFVCEI--CGQGYKMKKALLVHVGMHS-GI--HPFTCHF 539 (566)
Q Consensus 466 ~~H~~~-H~~~~~~~C~~C~k~f~~~~~~l~~H~~~H~~~~~~~C~~--C~~~f~~~~~L~~H~~~H~-~~--~~~~C~~ 539 (566)
.+||+. |..++||+|+.|++.|.+. ++|+.|..+|+ +-.|+|+. |..+|++...|++|++.++ |. -+|.|..
T Consensus 280 ~~H~r~rHs~dkpfKCd~Cd~~c~~e-sdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~ 357 (467)
T KOG3608|consen 280 TTHIRYRHSKDKPFKCDECDTRCVRE-SDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHC 357 (467)
T ss_pred HHHHHhhhccCCCccccchhhhhccH-HHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeec
Confidence 999984 8899999999999999865 89999999999 56799988 9999999999999998765 43 5699999
Q ss_pred ChhhccChhhHHHHHhhhcCCC
Q psy18241 540 CNKSFTQKIGLVKHLNIHNGTK 561 (566)
Q Consensus 540 C~~~f~~~~~L~~H~~~h~~~~ 561 (566)
|++.|++..+|..|++.-+|-+
T Consensus 358 Cdr~ft~G~~L~~HL~kkH~f~ 379 (467)
T KOG3608|consen 358 CDRFFTSGKSLSAHLMKKHGFR 379 (467)
T ss_pred chhhhccchhHHHHHHHhhccc
Confidence 9999999999999987655543
No 6
>KOG3608|consensus
Probab=99.93 E-value=4.8e-26 Score=201.27 Aligned_cols=214 Identities=25% Similarity=0.536 Sum_probs=152.3
Q ss_pred cCcccccCCCHHHHHHHHhhhcC------------C-CCcccc--cccccccChHHHHHHHhhhcCCCceeccccccccc
Q psy18241 254 CPTCGKKWRTVSELNAHIQTHSD------------L-RPFVCE--ICGQGYKMKKALLVHVGMHNGINPFTCSFCNKSFT 318 (566)
Q Consensus 254 C~~C~~~f~~~~~l~~H~~~h~~------------~-~~~~C~--~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 318 (566)
...|+..|.+...+..|+..|.. + ..+.|. .|-+.|.++..|++|++.|++++...|+.|+.-|+
T Consensus 139 WedCe~~F~s~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~ 218 (467)
T KOG3608|consen 139 WEDCEREFVSIVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFR 218 (467)
T ss_pred hhhcCCcccCHHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhc
Confidence 36899999999999999987742 2 124454 37778888888888888888888888888888888
Q ss_pred ChhhHhcccccccCCCCcccccccccccccchhHHHHHHhhccCCCCcccccccccccchHHHHHHHhhhcCCCCccccc
Q psy18241 319 QKVGLQKHLPIHTGSTRFQWEQSHLNYVWRTVSELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHVGMHNGINPFTCSF 398 (566)
Q Consensus 319 ~~~~L~~H~~~h~~~~~~~~~~~~~~~~~~~~~~l~~h~~~~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~ 398 (566)
++..|..|++..+ ..+..+|.|..|.|.|.+...|..|+..|- ..|+|+.
T Consensus 219 ~~tkl~DH~rRqt----------------------------~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv--n~ykCpl 268 (467)
T KOG3608|consen 219 TKTKLFDHLRRQT----------------------------ELNTNSFQCAQCFKRFATEKLLKSHVVRHV--NCYKCPL 268 (467)
T ss_pred cccHHHHHHHhhh----------------------------hhcCCchHHHHHHHHHhHHHHHHHHHHHhh--hcccccc
Confidence 8888877765422 123456788888888888888888877774 4577777
Q ss_pred cccccCChhhhhccccc-ccCCCccccCcccccccChhhHHHHHhhccCCCCccCCc--CCccCCChHHHHhHhhhhc-C
Q psy18241 399 CNKSFTQKVGLQKHLPI-HTGSTRFQCDLCGKRFIHQKSFYIHKMVHSGEKPIKCSA--CGLAVLSSSHLKRHFRVHT-G 474 (566)
Q Consensus 399 C~k~f~~~~~L~~H~~~-h~~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~--C~~~f~~~~~l~~H~~~H~-~ 474 (566)
|+.+....+.|..|++. |..++||+|+.|++.|...+.|.+|..+|+ +-.|.|+. |..+|.+...|++|++-++ |
T Consensus 269 Cdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg 347 (467)
T KOG3608|consen 269 CDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEG 347 (467)
T ss_pred cccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccC
Confidence 77777777777777763 666777777777777777777777777776 55677766 7777777777777776443 3
Q ss_pred C--CcccCcccccccccCHHHHHHHHh
Q psy18241 475 E--KPYQCTTCGKRLRRTVSELNAHIQ 499 (566)
Q Consensus 475 ~--~~~~C~~C~k~f~~~~~~l~~H~~ 499 (566)
. -+|.|..|++.|.+- ..|..|++
T Consensus 348 ~np~~Y~CH~Cdr~ft~G-~~L~~HL~ 373 (467)
T KOG3608|consen 348 NNPILYACHCCDRFFTSG-KSLSAHLM 373 (467)
T ss_pred CCCCceeeecchhhhccc-hhHHHHHH
Confidence 2 346666666666544 44555543
No 7
>KOG3623|consensus
Probab=99.92 E-value=5.9e-25 Score=211.88 Aligned_cols=106 Identities=30% Similarity=0.699 Sum_probs=96.6
Q ss_pred ccCCccccccCCchhHHHHHhhhc--CCCceeCCcCcccccchhhhHHHHhhhcC-------------CCcccCCccccc
Q psy18241 61 FTCHFCNKSFTQKIGLVKHLNIHN--GTKKYQCHLCGKGFIHHTSYKFHQLVHSG-------------ERNVKCDICGLA 125 (566)
Q Consensus 61 ~~C~~C~~~f~~~~~L~~H~~~h~--~~~~~~C~~C~k~F~~~~~l~~H~~~h~~-------------~~~~~C~~C~~~ 125 (566)
.+|++|++.+.....|+.|++.-+ .+..|.|..|..+|..+..|.+||.+|.. .+.|+|..||+.
T Consensus 211 ltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKA 290 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKA 290 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchh
Confidence 689999999999999999987533 45679999999999999999999999853 367999999999
Q ss_pred cCChhHHHHHHhhhcCCCcccCCccchhccchhHHHHhhhh
Q psy18241 126 LTTKSHLNRHMLVHTGDRPHECSVCGKRFAKKWNAQVHKKK 166 (566)
Q Consensus 126 f~~~~~L~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 166 (566)
|..+-.|+.|+|+|.|++||.|+-|+|+|........||..
T Consensus 291 FKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 291 FKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred hhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 99999999999999999999999999999999999999854
No 8
>KOG3623|consensus
Probab=99.91 E-value=3.4e-24 Score=206.70 Aligned_cols=106 Identities=31% Similarity=0.691 Sum_probs=94.7
Q ss_pred ceeCCcccccccChhHHHHHhhhh--CCCCccccCccCCccCchHHHHHHHhhcCC-------------CCCccCCcccc
Q psy18241 4 IHECPTCGKKWRTVSELNAHIQTH--SDLRPFVCEICGQGYKMKKALLVHVGMHSG-------------IHPFTCHFCNK 68 (566)
Q Consensus 4 ~~~C~~C~~~f~~~~~L~~H~~~h--~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~-------------~~~~~C~~C~~ 68 (566)
...|+.|++.+.....|+.|++-- ..+..|.|..|..+|..+..|.+||.+|.. .+.|+|..|||
T Consensus 210 lltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgK 289 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGK 289 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccch
Confidence 568999999999999999998643 345679999999999999999999998853 35699999999
Q ss_pred ccCCchhHHHHHhhhcCCCceeCCcCcccccchhhhHHHHh
Q psy18241 69 SFTQKIGLVKHLNIHNGTKKYQCHLCGKGFIHHTSYKFHQL 109 (566)
Q Consensus 69 ~f~~~~~L~~H~~~h~~~~~~~C~~C~k~F~~~~~l~~H~~ 109 (566)
.|..+-.|+.|+|||.|+|||.|+.|+|.|+....+..||-
T Consensus 290 AFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 290 AFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred hhhhHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 99999999999999999999999999999999999999985
No 9
>KOG3576|consensus
Probab=99.77 E-value=5.1e-20 Score=150.46 Aligned_cols=114 Identities=32% Similarity=0.675 Sum_probs=81.2
Q ss_pred CCCccccCcccccccChhhHHHHHhhccCCCCccCCcCCccCCChHHHHhHhhhhcCCCcccCcccccccccCHHHHHHH
Q psy18241 418 GSTRFQCDLCGKRFIHQKSFYIHKMVHSGEKPIKCSACGLAVLSSSHLKRHFRVHTGEKPYQCTTCGKRLRRTVSELNAH 497 (566)
Q Consensus 418 ~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~C~k~f~~~~~~l~~H 497 (566)
+...|.|.+|+|.|..+..|.+|++-|...+.|-|..||+.|...-+|++|+|+|+|.+||+|..|+|.|... -.|..|
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqr-cslesh 192 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQR-CSLESH 192 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhh-ccHHHH
Confidence 4456788888888888888888888888777777888888887777777777777777777777777777655 446666
Q ss_pred Hhh-cC----------CCCCccCCCCCCcccCchhHHhHhhhccCC
Q psy18241 498 IQT-HS----------DLRPFVCEICGQGYKMKKALLVHVGMHSGI 532 (566)
Q Consensus 498 ~~~-H~----------~~~~~~C~~C~~~f~~~~~L~~H~~~H~~~ 532 (566)
.+. |. .++-|+|+.||.+-.....+..|+..|+..
T Consensus 193 l~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~ 238 (267)
T KOG3576|consen 193 LKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPF 238 (267)
T ss_pred HHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCC
Confidence 543 32 134566777776666666666666666543
No 10
>KOG3576|consensus
Probab=99.75 E-value=4.2e-19 Score=145.11 Aligned_cols=117 Identities=29% Similarity=0.640 Sum_probs=104.4
Q ss_pred cCCCCcccccccccccchHHHHHHHhhhcCCCCccccccccccCChhhhhcccccccCCCccccCcccccccChhhHHHH
Q psy18241 361 SDLRPFVCEICGQGYKMKKALLVHVGMHNGINPFTCSFCNKSFTQKVGLQKHLPIHTGSTRFQCDLCGKRFIHQKSFYIH 440 (566)
Q Consensus 361 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~C~~C~k~f~~~~~l~~H 440 (566)
++...|.|.+|+|.|.....|.+|++-|...+.|-|..|||.|....+|++|+|+|+|.+||+|..|+|.|..+-+|..|
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcslesh 192 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESH 192 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHH
Confidence 34567999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhccC-----------CCCccCCcCCccCCChHHHHhHhhhhcCCCc
Q psy18241 441 KMVHSG-----------EKPIKCSACGLAVLSSSHLKRHFRVHTGEKP 477 (566)
Q Consensus 441 ~~~H~~-----------~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~ 477 (566)
.+.-+| ++.|.|+.||.+-.....+..|++.|+...|
T Consensus 193 l~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 193 LKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred HHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 864433 4568899999988888888888888876544
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.40 E-value=5.2e-13 Score=131.81 Aligned_cols=145 Identities=23% Similarity=0.495 Sum_probs=117.0
Q ss_pred eCCcccccccChhHHHHHhhhhCCCCccccCc--cCCccCchHHHHHHHhhcCCCCCccCCccccccCCchhHHHHHhhh
Q psy18241 6 ECPTCGKKWRTVSELNAHIQTHSDLRPFVCEI--CGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHLNIH 83 (566)
Q Consensus 6 ~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L~~H~~~h 83 (566)
.|+.|.+... ...|..|.... .-..-.|+. |+..|. +..|..| +.|+.|++.|. ...|..|++++
T Consensus 409 ~C~NC~~~i~-l~~l~lHe~~C-~r~~V~Cp~~~Cg~v~~-r~el~~H---------~~C~~Cgk~f~-~s~LekH~~~~ 475 (567)
T PLN03086 409 ECRNCKHYIP-SRSIALHEAYC-SRHNVVCPHDGCGIVLR-VEEAKNH---------VHCEKCGQAFQ-QGEMEKHMKVF 475 (567)
T ss_pred ECCCCCCccc-hhHHHHHHhhC-CCcceeCCcccccceee-ccccccC---------ccCCCCCCccc-hHHHHHHHHhc
Confidence 6999987766 46677887433 334456874 999883 4444444 58999999996 68899999998
Q ss_pred cCCCceeCCcCcccccchhhhHHHHhhhcCCCcccCCccccccC----------ChhHHHHHHhhhcCCCcccCCccchh
Q psy18241 84 NGTKKYQCHLCGKGFIHHTSYKFHQLVHSGERNVKCDICGLALT----------TKSHLNRHMLVHTGDRPHECSVCGKR 153 (566)
Q Consensus 84 ~~~~~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~~C~~C~~~f~----------~~~~L~~H~~~h~~~~~~~C~~C~~~ 153 (566)
+ +++.|+ ||+.+ .+..|..|+.+|.+++++.|+.|++.|. ..+.|..|+.+. |.+++.|..||+.
T Consensus 476 H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~ 550 (567)
T PLN03086 476 H--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRS 550 (567)
T ss_pred C--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCe
Confidence 6 789999 99765 6799999999999999999999999995 245899999985 8999999999998
Q ss_pred ccchhHHHHhhhhhcc
Q psy18241 154 FAKKWNAQVHKKKVHG 169 (566)
Q Consensus 154 f~~~~~l~~H~~~~h~ 169 (566)
+..+ .+..|+..+|.
T Consensus 551 Vrlr-dm~~H~~~~h~ 565 (567)
T PLN03086 551 VMLK-EMDIHQIAVHQ 565 (567)
T ss_pred eeeh-hHHHHHHHhhc
Confidence 8765 68888887774
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.37 E-value=1.6e-12 Score=128.43 Aligned_cols=143 Identities=20% Similarity=0.484 Sum_probs=86.2
Q ss_pred cccccccccccchHHHHHHHhhhcCCCCccccc--cccccCChhhhhcccccccCCCccccCcccccccChhhHHHHHhh
Q psy18241 366 FVCEICGQGYKMKKALLVHVGMHNGINPFTCSF--CNKSFTQKVGLQKHLPIHTGSTRFQCDLCGKRFIHQKSFYIHKMV 443 (566)
Q Consensus 366 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~--C~k~f~~~~~L~~H~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~ 443 (566)
..|+.|...... ..|..|..... -..-.|+. ||..|. +..|..| +.|+.|++.|. ...|..|+++
T Consensus 408 V~C~NC~~~i~l-~~l~lHe~~C~-r~~V~Cp~~~Cg~v~~-r~el~~H---------~~C~~Cgk~f~-~s~LekH~~~ 474 (567)
T PLN03086 408 VECRNCKHYIPS-RSIALHEAYCS-RHNVVCPHDGCGIVLR-VEEAKNH---------VHCEKCGQAFQ-QGEMEKHMKV 474 (567)
T ss_pred EECCCCCCccch-hHHHHHHhhCC-CcceeCCcccccceee-ccccccC---------ccCCCCCCccc-hHHHHHHHHh
Confidence 467777776653 44556764432 23345763 777773 3344444 36777777774 5667777777
Q ss_pred ccCCCCccCCcCCccCCChHHHHhHhhhhcCCCcccCccccccccc---------CHHHHHHHHhhcCCCCCccCCCCCC
Q psy18241 444 HSGEKPIKCSACGLAVLSSSHLKRHFRVHTGEKPYQCTTCGKRLRR---------TVSELNAHIQTHSDLRPFVCEICGQ 514 (566)
Q Consensus 444 H~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~C~k~f~~---------~~~~l~~H~~~H~~~~~~~C~~C~~ 514 (566)
|+ +|+.|+ ||+.+ .+..|..|+++|.+++|+.|++|++.|.. ..+.|..|..+. |.+++.|..||+
T Consensus 475 ~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk 549 (567)
T PLN03086 475 FH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGR 549 (567)
T ss_pred cC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCC
Confidence 64 667777 77544 55677777777777777777777776631 123566666653 566666666666
Q ss_pred cccCchhHHhHhh
Q psy18241 515 GYKMKKALLVHVG 527 (566)
Q Consensus 515 ~f~~~~~L~~H~~ 527 (566)
.+..+ .|..|+.
T Consensus 550 ~Vrlr-dm~~H~~ 561 (567)
T PLN03086 550 SVMLK-EMDIHQI 561 (567)
T ss_pred eeeeh-hHHHHHH
Confidence 65433 3455543
No 13
>PHA00733 hypothetical protein
Probab=99.27 E-value=3.5e-12 Score=102.34 Aligned_cols=81 Identities=17% Similarity=0.354 Sum_probs=59.9
Q ss_pred CCcccCcccccccccCHHHH------HHHHhhcCCCCCccCCCCCCcccCchhHHhHhhhccCCCcccCCcChhhccChh
Q psy18241 475 EKPYQCTTCGKRLRRTVSEL------NAHIQTHSDLRPFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKI 548 (566)
Q Consensus 475 ~~~~~C~~C~k~f~~~~~~l------~~H~~~H~~~~~~~C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~~~f~~~~ 548 (566)
.+++.|.+|++.|... ..| ..|+.++ +.+||.|+.||+.|.+...|..|+++| +.+|.|++|+++|....
T Consensus 38 ~~~~~~~~~~~~~~~~-~~l~~~~~l~~~~~~~-~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~ 113 (128)
T PHA00733 38 QKRLIRAVVKTLIYNP-QLLDESSYLYKLLTSK-AVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTD 113 (128)
T ss_pred hhhHHHHHHhhhccCh-hhhcchHHHHhhcccC-CCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHH
Confidence 4556666666555432 333 3343333 478899999999999999999999876 45789999999999999
Q ss_pred hHHHHHhhhcC
Q psy18241 549 GLVKHLNIHNG 559 (566)
Q Consensus 549 ~L~~H~~~h~~ 559 (566)
.|.+|+...++
T Consensus 114 sL~~H~~~~h~ 124 (128)
T PHA00733 114 STLDHVCKKHN 124 (128)
T ss_pred HHHHHHHHhcC
Confidence 99999887665
No 14
>PHA00733 hypothetical protein
Probab=99.20 E-value=1.8e-11 Score=98.26 Aligned_cols=55 Identities=20% Similarity=0.343 Sum_probs=37.1
Q ss_pred CCCccccCcccccccChhhHHHHHhhccCCCCccCCcCCccCCChHHHHhHhhhhcC
Q psy18241 418 GSTRFQCDLCGKRFIHQKSFYIHKMVHSGEKPIKCSACGLAVLSSSHLKRHFRVHTG 474 (566)
Q Consensus 418 ~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~ 474 (566)
+.+||.|+.||+.|.....|..|++.| +.+|.|++|+++|.....|.+|+...++
T Consensus 70 ~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 70 AVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 356677777777777777777777665 3457777777777777777777665443
No 15
>PHA02768 hypothetical protein; Provisional
Probab=99.08 E-value=4e-11 Score=77.63 Aligned_cols=44 Identities=20% Similarity=0.498 Sum_probs=35.8
Q ss_pred CccCCCCCCcccCchhHHhHhhhccCCCcccCCcChhhccChhhHH
Q psy18241 506 PFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLV 551 (566)
Q Consensus 506 ~~~C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~~~f~~~~~L~ 551 (566)
.|.|+.||+.|....+|..||++|+ +||+|..|++.|.+++.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 4788888888888888888888887 6888888888888777664
No 16
>PHA02768 hypothetical protein; Provisional
Probab=98.99 E-value=1.7e-10 Score=74.77 Aligned_cols=42 Identities=29% Similarity=0.633 Sum_probs=23.8
Q ss_pred cccCcccccccChhhHHHHHhhccCCCCccCCcCCccCCChHHH
Q psy18241 422 FQCDLCGKRFIHQKSFYIHKMVHSGEKPIKCSACGLAVLSSSHL 465 (566)
Q Consensus 422 ~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~~l 465 (566)
|+|+.||+.|...++|..|+++|+ ++|+|..|++.|...+.|
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 555555555555555555555555 455555555555554444
No 17
>KOG3993|consensus
Probab=98.93 E-value=1.7e-10 Score=106.14 Aligned_cols=141 Identities=21% Similarity=0.367 Sum_probs=86.6
Q ss_pred ccccCccCCccCchHHHHHHHhhcCCCCCccCCccccccCCchhHHHHHhhhc---------------------------
Q psy18241 32 PFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHLNIHN--------------------------- 84 (566)
Q Consensus 32 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L~~H~~~h~--------------------------- 84 (566)
.|.|..|...|.+.-.|.+|.---.--..|+|+.|+|+|+-..+|..|.+.|.
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 35666666666666666666421111123666666666666666666666552
Q ss_pred ------CCCceeCCcCcccccchhhhHHHHhhhcCC--------------------------------------------
Q psy18241 85 ------GTKKYQCHLCGKGFIHHTSYKFHQLVHSGE-------------------------------------------- 114 (566)
Q Consensus 85 ------~~~~~~C~~C~k~F~~~~~l~~H~~~h~~~-------------------------------------------- 114 (566)
.+..|.|.+|+|.|..+..|+.|+.+|...
T Consensus 347 rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~ 426 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAG 426 (500)
T ss_pred ccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeec
Confidence 112477777777777777777776665321
Q ss_pred --CcccCCccccccCChhHHHHHHhhhcCCCcccCCccchhccchhHHHHhhhhhcccCC
Q psy18241 115 --RNVKCDICGLALTTKSHLNRHMLVHTGDRPHECSVCGKRFAKKWNAQVHKKKVHGLDV 172 (566)
Q Consensus 115 --~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~h~~~~ 172 (566)
..-.|++||-.+.++..--.+.+.-..+..|.|.+|.-.|.+...|.+|+.+.|..+.
T Consensus 427 sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~Hpse~ 486 (500)
T KOG3993|consen 427 SAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCHPSEL 486 (500)
T ss_pred cccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcChHHh
Confidence 0123555665555554444444433345568999999999999999999998885443
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=98.86 E-value=8.7e-10 Score=61.07 Aligned_cols=25 Identities=40% Similarity=0.954 Sum_probs=18.3
Q ss_pred hHHhHhhhccCCCcccCCcChhhcc
Q psy18241 521 ALLVHVGMHSGIHPFTCHFCNKSFT 545 (566)
Q Consensus 521 ~L~~H~~~H~~~~~~~C~~C~~~f~ 545 (566)
+|.+||++|+|++||+|++|+++|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 4677777777777777777777775
No 19
>KOG3993|consensus
Probab=98.79 E-value=2.3e-09 Score=98.85 Aligned_cols=193 Identities=19% Similarity=0.195 Sum_probs=117.4
Q ss_pred CcccccccccccChHHHHHHHhhhcCCCceecccccccccChhhHhcccccccCCCCcccccccccc-cccchhHHHHHH
Q psy18241 279 PFVCEICGQGYKMKKALLVHVGMHNGINPFTCSFCNKSFTQKVGLQKHLPIHTGSTRFQWEQSHLNY-VWRTVSELNAHI 357 (566)
Q Consensus 279 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~~~~~~~~~-~~~~~~~l~~h~ 357 (566)
.|.|..|...|.+.-.|..|.-.....-.|+|++|+|.|+-..+|-.|.++|.......-....-.. ...+..+.+.-.
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 4778888888888888888853222234588999999999999999998888543221100000000 000011111111
Q ss_pred hh--ccCCCCcccccccccccchHHHHHHHhhhcCCCC-----------------ccccccccccCChhhhhcccccccC
Q psy18241 358 QT--HSDLRPFVCEICGQGYKMKKALLVHVGMHNGINP-----------------FTCSFCNKSFTQKVGLQKHLPIHTG 418 (566)
Q Consensus 358 ~~--~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~-----------------~~C~~C~k~f~~~~~L~~H~~~h~~ 418 (566)
+. .+.+..|.|.+|++.|.....|+.|+.+|..... +-|..|+-.+.....--.+...+.+
T Consensus 347 rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~ 426 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAG 426 (500)
T ss_pred ccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeec
Confidence 10 1234579999999999999999999888753211 2345555444444333333333322
Q ss_pred C-CccccCcccccccChhhHHHHHhhccCCCCccCCcCCccCCChHHHHhHhhh
Q psy18241 419 S-TRFQCDLCGKRFIHQKSFYIHKMVHSGEKPIKCSACGLAVLSSSHLKRHFRV 471 (566)
Q Consensus 419 ~-~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~ 471 (566)
. ...-|++||..+.++..--.+.+.-..+.-|.|.+|..+|.+...|.+|+..
T Consensus 427 sael~~pp~~~~ppsss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~ 480 (500)
T KOG3993|consen 427 SAELELPPYDGSPPSSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINK 480 (500)
T ss_pred cccccCCCCCCCCcccCCCCCccccccchhhccccccchHhhhcCcchHhHhhh
Confidence 2 2345778887777776655555555556678888999999888888888754
No 20
>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=98.72 E-value=6e-09 Score=57.68 Aligned_cols=23 Identities=65% Similarity=1.379 Sum_probs=11.2
Q ss_pred HHhHhhhhcCCCcccCccccccc
Q psy18241 465 LKRHFRVHTGEKPYQCTTCGKRL 487 (566)
Q Consensus 465 l~~H~~~H~~~~~~~C~~C~k~f 487 (566)
|.+|+++|+|++||+|++|++.|
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F 24 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSF 24 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEE
T ss_pred HHHHhhhcCCCCCCCCCCCcCee
Confidence 44444444444444444444444
No 21
>PHA00616 hypothetical protein
Probab=98.59 E-value=1.3e-08 Score=62.64 Aligned_cols=34 Identities=21% Similarity=0.408 Sum_probs=20.8
Q ss_pred CccCCCCCCcccCchhHHhHhhhccCCCcccCCc
Q psy18241 506 PFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHF 539 (566)
Q Consensus 506 ~~~C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~ 539 (566)
||+|+.||+.|.+++.|..|++.|+|++||.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 4566666666666666666666666666666543
No 22
>PHA00616 hypothetical protein
Probab=98.55 E-value=3.3e-08 Score=60.86 Aligned_cols=32 Identities=22% Similarity=0.406 Sum_probs=30.6
Q ss_pred cccCCcChhhccChhhHHHHHhhhcCCCCCCC
Q psy18241 534 PFTCHFCNKSFTQKIGLVKHLNIHNGTKKYQA 565 (566)
Q Consensus 534 ~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~~ 565 (566)
||+|..||+.|.+++.|.+|++.|+|++++.+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 79999999999999999999999999999875
No 23
>PHA00732 hypothetical protein
Probab=98.51 E-value=6.5e-08 Score=69.87 Aligned_cols=46 Identities=24% Similarity=0.535 Sum_probs=22.7
Q ss_pred cccCcccccccccCHHHHHHHHhh-cCCCCCccCCCCCCcccCchhHHhHhhhc
Q psy18241 477 PYQCTTCGKRLRRTVSELNAHIQT-HSDLRPFVCEICGQGYKMKKALLVHVGMH 529 (566)
Q Consensus 477 ~~~C~~C~k~f~~~~~~l~~H~~~-H~~~~~~~C~~C~~~f~~~~~L~~H~~~H 529 (566)
||.|+.||+.|.+. +.|..|++. |. ++.|+.||++|. .|..|+.++
T Consensus 1 py~C~~Cgk~F~s~-s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTL-FALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCH-HHHHHHhhcccC---CCccCCCCCEeC---Chhhhhccc
Confidence 35555555555443 455555542 33 234555555554 355555443
No 24
>PHA00732 hypothetical protein
Probab=98.33 E-value=3.5e-07 Score=66.06 Aligned_cols=35 Identities=37% Similarity=0.771 Sum_probs=16.7
Q ss_pred ccCCcCCccCCChHHHHhHhhh-hcCCCcccCccccccc
Q psy18241 450 IKCSACGLAVLSSSHLKRHFRV-HTGEKPYQCTTCGKRL 487 (566)
Q Consensus 450 ~~C~~C~~~f~~~~~l~~H~~~-H~~~~~~~C~~C~k~f 487 (566)
|.|++||+.|.+.+.|..|++. |. ++.|+.||+.|
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF 37 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSY 37 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEe
Confidence 4455555555555555555442 32 23455555555
No 25
>KOG1146|consensus
Probab=98.21 E-value=1.3e-06 Score=93.03 Aligned_cols=122 Identities=12% Similarity=0.095 Sum_probs=75.4
Q ss_pred ccCcccccccChhhHHHHHhh--ccC--CCCccCCcCCccCCChHHHHhHhhhhcCCCcccCcccccccccCHHHHHHHH
Q psy18241 423 QCDLCGKRFIHQKSFYIHKMV--HSG--EKPIKCSACGLAVLSSSHLKRHFRVHTGEKPYQCTTCGKRLRRTVSELNAHI 498 (566)
Q Consensus 423 ~C~~C~k~f~~~~~l~~H~~~--H~~--~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~C~k~f~~~~~~l~~H~ 498 (566)
.|..|...|.....+..|-+- +.. ...+.|.+|++.|...-.+. |+-+ ..+|.|..|...|... +.|..|.
T Consensus 1230 ~~~~~e~~f~~~~~~~~~a~~~~~~~~~sGe~~c~~~~~~~~~~~~~~-~l~~---~~~~~~~~~~~~~~~~-~~l~~~~ 1304 (1406)
T KOG1146|consen 1230 LPNALEQPFPQEPEPTATAPPKPPELPASGEGECGAVDELLTPSFGIS-TLDV---THRYLCRQCKMAFDGE-APLTAHQ 1304 (1406)
T ss_pred cHHhhhcCccCcccccccCCCCCCcCcCCCcchhhhccccccCcccee-eccc---chhHHHHHHHhhhcch-hHHHHHH
Confidence 355555556555554444221 110 11256777777766666555 4422 3467777777777544 5555554
Q ss_pred hhcCCCCCccCCCCCCcccCchhHHhHhhhccCCCcccCCcChhhccChhhHHHHHhhhcCCC
Q psy18241 499 QTHSDLRPFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHLNIHNGTK 561 (566)
Q Consensus 499 ~~H~~~~~~~C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~ 561 (566)
..|-+.|.....+.-|+..+....+| |.+|...|.....|..||++-.+++
T Consensus 1305 -----------~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~~~~~~ 1355 (1406)
T KOG1146|consen 1305 -----------RKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRSSAHRR 1355 (1406)
T ss_pred -----------HHHHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHHhhhcc
Confidence 23445556666666667777777778 9999999999999999998755543
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=98.16 E-value=2.4e-06 Score=57.34 Aligned_cols=51 Identities=29% Similarity=0.635 Sum_probs=32.7
Q ss_pred CccCCCCCCcccCchhHHhHhhh-ccCC-CcccCCcChhhccChhhHHHHHhhhcC
Q psy18241 506 PFVCEICGQGYKMKKALLVHVGM-HSGI-HPFTCHFCNKSFTQKIGLVKHLNIHNG 559 (566)
Q Consensus 506 ~~~C~~C~~~f~~~~~L~~H~~~-H~~~-~~~~C~~C~~~f~~~~~L~~H~~~h~~ 559 (566)
.|.|++||+. .+...|..|+.. |.++ +.+.|++|...+. .+|..||+++++
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 3677777774 345667777654 4443 4577777777544 377778777654
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=98.07 E-value=1.7e-06 Score=46.58 Aligned_cols=23 Identities=39% Similarity=0.899 Sum_probs=16.3
Q ss_pred ccCCcChhhccChhhHHHHHhhh
Q psy18241 535 FTCHFCNKSFTQKIGLVKHLNIH 557 (566)
Q Consensus 535 ~~C~~C~~~f~~~~~L~~H~~~h 557 (566)
|+|++|++.|.++..|+.||++|
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 56777777777777777777664
No 28
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.89 E-value=1.5e-05 Score=53.41 Aligned_cols=47 Identities=32% Similarity=0.624 Sum_probs=19.9
Q ss_pred eeCCcccccccChhHHHHHhhh-hCC-CCccccCccCCccCchHHHHHHHhh
Q psy18241 5 HECPTCGKKWRTVSELNAHIQT-HSD-LRPFVCEICGQGYKMKKALLVHVGM 54 (566)
Q Consensus 5 ~~C~~C~~~f~~~~~L~~H~~~-h~~-~~~~~C~~C~~~f~~~~~l~~H~~~ 54 (566)
|.||.|++ ..+...|..|+.. |.+ .+.+.|++|...+. .+|..|+..
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~ 51 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNS 51 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHH
Confidence 44555555 2334455555432 222 12344555544322 244444443
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=97.84 E-value=1e-05 Score=43.47 Aligned_cols=23 Identities=39% Similarity=0.944 Sum_probs=14.7
Q ss_pred eeCCcccccccChhHHHHHhhhh
Q psy18241 5 HECPTCGKKWRTVSELNAHIQTH 27 (566)
Q Consensus 5 ~~C~~C~~~f~~~~~L~~H~~~h 27 (566)
|+|+.|++.|.+...|..|++.|
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 56666666666666666666543
No 30
>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=97.74 E-value=1.6e-05 Score=43.30 Aligned_cols=24 Identities=42% Similarity=0.868 Sum_probs=14.6
Q ss_pred ccCCcChhhccChhhHHHHHhhhc
Q psy18241 535 FTCHFCNKSFTQKIGLVKHLNIHN 558 (566)
Q Consensus 535 ~~C~~C~~~f~~~~~L~~H~~~h~ 558 (566)
|.|++|++.|.+...|+.|+++|+
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 566677777777777777766653
No 31
>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=97.66 E-value=2.1e-05 Score=44.21 Aligned_cols=26 Identities=35% Similarity=0.700 Sum_probs=18.1
Q ss_pred cccCCcChhhccChhhHHHHHhhhcC
Q psy18241 534 PFTCHFCNKSFTQKIGLVKHLNIHNG 559 (566)
Q Consensus 534 ~~~C~~C~~~f~~~~~L~~H~~~h~~ 559 (566)
||+|++|++.|.+...|..|++.|.+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 46777777777777777777776653
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.48 E-value=6.4e-05 Score=58.67 Aligned_cols=23 Identities=22% Similarity=0.606 Sum_probs=13.5
Q ss_pred cccCCccccccCChhHHHHHHhh
Q psy18241 116 NVKCDICGLALTTKSHLNRHMLV 138 (566)
Q Consensus 116 ~~~C~~C~~~f~~~~~L~~H~~~ 138 (566)
.+.|.+|++.|.+...|..||+.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHH
T ss_pred CCCCCccCCCCcCHHHHHHHHcC
Confidence 45666666666666666666654
No 33
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.45 E-value=9.2e-05 Score=40.22 Aligned_cols=22 Identities=45% Similarity=0.945 Sum_probs=9.9
Q ss_pred cCCccccccCChhHHHHHHhhh
Q psy18241 118 KCDICGLALTTKSHLNRHMLVH 139 (566)
Q Consensus 118 ~C~~C~~~f~~~~~L~~H~~~h 139 (566)
.|++|++.|.+...|..|+++|
T Consensus 2 ~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 2 QCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp E-SSTS-EESSHHHHHHHHHHH
T ss_pred CCcCCCCcCCcHHHHHHHHHhh
Confidence 4555555555555555555443
No 34
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.44 E-value=7.6e-05 Score=58.24 Aligned_cols=23 Identities=22% Similarity=0.530 Sum_probs=12.1
Q ss_pred ceeCCcCcccccchhhhHHHHhh
Q psy18241 88 KYQCHLCGKGFIHHTSYKFHQLV 110 (566)
Q Consensus 88 ~~~C~~C~k~F~~~~~l~~H~~~ 110 (566)
.+.|.+|++.|.+...|..|++.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHH
T ss_pred CCCCCccCCCCcCHHHHHHHHcC
Confidence 35555555555555555555554
No 35
>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=97.40 E-value=0.00011 Score=46.19 Aligned_cols=40 Identities=25% Similarity=0.361 Sum_probs=23.0
Q ss_pred HhHhhhc-cCCCcccCCcChhhccChhhHHHHHhhhcCCCC
Q psy18241 523 LVHVGMH-SGIHPFTCHFCNKSFTQKIGLVKHLNIHNGTKK 562 (566)
Q Consensus 523 ~~H~~~H-~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~ 562 (566)
..+.+.+ ..+.|-.|++|+..+.+..+|++|+.++++.+|
T Consensus 12 ~~~~k~~~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 12 TKKPKSKSQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp ----CCCCTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hhHHHHhhccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 3444433 346788888888888888888888888888775
No 36
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.39 E-value=6e-05 Score=67.49 Aligned_cols=52 Identities=29% Similarity=0.682 Sum_probs=35.2
Q ss_pred CCCccCCC--CCCcccCchhHHhHhhh-c------------------cCCCcccCCcChhhccChhhHHHHHh
Q psy18241 504 LRPFVCEI--CGQGYKMKKALLVHVGM-H------------------SGIHPFTCHFCNKSFTQKIGLVKHLN 555 (566)
Q Consensus 504 ~~~~~C~~--C~~~f~~~~~L~~H~~~-H------------------~~~~~~~C~~C~~~f~~~~~L~~H~~ 555 (566)
+|||+|++ |.|.|++...|+.||.- | ...|||.|++|+|.|+....|+.|.+
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 35555544 55555555555555531 2 13589999999999999999988865
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=97.38 E-value=0.00011 Score=41.22 Aligned_cols=24 Identities=38% Similarity=0.821 Sum_probs=14.0
Q ss_pred ceeCCcccccccChhHHHHHhhhh
Q psy18241 4 IHECPTCGKKWRTVSELNAHIQTH 27 (566)
Q Consensus 4 ~~~C~~C~~~f~~~~~L~~H~~~h 27 (566)
+|+|.+|++.|.+...|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 355666666666666666665554
No 38
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.32 E-value=8.5e-05 Score=66.54 Aligned_cols=23 Identities=17% Similarity=0.546 Sum_probs=12.6
Q ss_pred CCcccCCccccccCChhHHHHHH
Q psy18241 114 ERNVKCDICGLALTTKSHLNRHM 136 (566)
Q Consensus 114 ~~~~~C~~C~~~f~~~~~L~~H~ 136 (566)
.+||+|++|++.+.+...|+-|.
T Consensus 396 ~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 396 DKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred CCceeccccchhhccCccceecc
Confidence 35555555555555555555553
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.12 E-value=0.00035 Score=38.69 Aligned_cols=24 Identities=33% Similarity=0.728 Sum_probs=14.9
Q ss_pred ccCCcChhhccChhhHHHHHhhhc
Q psy18241 535 FTCHFCNKSFTQKIGLVKHLNIHN 558 (566)
Q Consensus 535 ~~C~~C~~~f~~~~~L~~H~~~h~ 558 (566)
|+|+.|++.|.....|..|+++|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 456666666666666666666553
No 40
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=97.06 E-value=0.00092 Score=68.51 Aligned_cols=150 Identities=25% Similarity=0.441 Sum_probs=89.3
Q ss_pred CCccccccccccCChhhhhcccc--cccCC--CccccC--cccccccChhhHHHHHhhccCCCCccCCc--CCccCCChH
Q psy18241 392 NPFTCSFCNKSFTQKVGLQKHLP--IHTGS--TRFQCD--LCGKRFIHQKSFYIHKMVHSGEKPIKCSA--CGLAVLSSS 463 (566)
Q Consensus 392 ~~~~C~~C~k~f~~~~~L~~H~~--~h~~~--~~~~C~--~C~k~f~~~~~l~~H~~~H~~~~~~~C~~--C~~~f~~~~ 463 (566)
.++.|..|...|.....|..|.+ .|.++ +++.|+ .|++.|.....+..|..+|.+..++.+.. +...+....
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 367 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLL 367 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccccccc
Confidence 45667777777777777777777 67777 777777 67777777777777777777766666543 333333322
Q ss_pred HHHhHhh-----hhcCCCcccCcc--cccccccCHHHHHHHHhhcCCCC--CccCCCCCCcccCchhHHhHhhhccCCCc
Q psy18241 464 HLKRHFR-----VHTGEKPYQCTT--CGKRLRRTVSELNAHIQTHSDLR--PFVCEICGQGYKMKKALLVHVGMHSGIHP 534 (566)
Q Consensus 464 ~l~~H~~-----~H~~~~~~~C~~--C~k~f~~~~~~l~~H~~~H~~~~--~~~C~~C~~~f~~~~~L~~H~~~H~~~~~ 534 (566)
.-..+.. .-.....+.+.. |...+... ..+..|...|...+ .+.+..|++.|.....|..|++.|....+
T Consensus 368 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 446 (467)
T COG5048 368 NNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRD-SNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAP 446 (467)
T ss_pred CCCCccchhhccCccCCccccccccchhhhhccc-cccccccccccccCCcCCCCCcchhhccCcccccccccccccCCc
Confidence 2111111 111122222222 33333332 33445555555444 56678888888888888888888887777
Q ss_pred ccCCcChh
Q psy18241 535 FTCHFCNK 542 (566)
Q Consensus 535 ~~C~~C~~ 542 (566)
+-|..++.
T Consensus 447 ~~~~~~~~ 454 (467)
T COG5048 447 LLCSILKS 454 (467)
T ss_pred eeeccccc
Confidence 76655544
No 41
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=97.04 E-value=0.00035 Score=37.85 Aligned_cols=24 Identities=33% Similarity=0.668 Sum_probs=15.8
Q ss_pred ccCCcChhhccChhhHHHHHhhhcC
Q psy18241 535 FTCHFCNKSFTQKIGLVKHLNIHNG 559 (566)
Q Consensus 535 ~~C~~C~~~f~~~~~L~~H~~~h~~ 559 (566)
|+|+.|++... +..|.+|+++|+|
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 56777777776 7777777777654
No 42
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.97 E-value=0.00047 Score=43.50 Aligned_cols=31 Identities=35% Similarity=0.800 Sum_probs=14.8
Q ss_pred CCCccCCcCCccCCChHHHHhHhhhhcCCCc
Q psy18241 447 EKPIKCSACGLAVLSSSHLKRHFRVHTGEKP 477 (566)
Q Consensus 447 ~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~ 477 (566)
+.|-.|++|+..+.+..+|++|+.++++.+|
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 4455666666666666666666655555443
No 43
>KOG2231|consensus
Probab=96.85 E-value=0.0019 Score=65.93 Aligned_cols=46 Identities=24% Similarity=0.522 Sum_probs=24.1
Q ss_pred cCCccccccCCchhHHHHHhhhcCCCceeCCcCc------ccccchhhhHHHHhhh
Q psy18241 62 TCHFCNKSFTQKIGLVKHLNIHNGTKKYQCHLCG------KGFIHHTSYKFHQLVH 111 (566)
Q Consensus 62 ~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~------k~F~~~~~l~~H~~~h 111 (566)
.|.+|...|-....|.+|++.++ |.|.+|+ .-|.....|..|-+.+
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~ 235 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKG 235 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhc
Confidence 35556666666666666655443 4444442 3344555555555543
No 44
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.73 E-value=0.0014 Score=36.14 Aligned_cols=22 Identities=45% Similarity=0.883 Sum_probs=10.3
Q ss_pred cCCcCCccCCChHHHHhHhhhh
Q psy18241 451 KCSACGLAVLSSSHLKRHFRVH 472 (566)
Q Consensus 451 ~C~~C~~~f~~~~~l~~H~~~H 472 (566)
.|+.|++.|.+.+.|..|++.|
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHHh
Confidence 3444444444444444444433
No 45
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.61 E-value=0.001 Score=36.40 Aligned_cols=23 Identities=43% Similarity=0.852 Sum_probs=16.3
Q ss_pred ccCCcChhhccChhhHHHHHhhh
Q psy18241 535 FTCHFCNKSFTQKIGLVKHLNIH 557 (566)
Q Consensus 535 ~~C~~C~~~f~~~~~L~~H~~~h 557 (566)
|.|++|++.|.+...|+.|++.+
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 56777777777777777777653
No 46
>PRK04860 hypothetical protein; Provisional
Probab=96.56 E-value=0.001 Score=55.65 Aligned_cols=38 Identities=21% Similarity=0.583 Sum_probs=24.1
Q ss_pred CccCCCCCCcccCchhHHhHhhhccCCCcccCCcChhhccCh
Q psy18241 506 PFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQK 547 (566)
Q Consensus 506 ~~~C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~~~f~~~ 547 (566)
+|.|. |+. ....+.+|.++|+|+++|.|..|+..|...
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 46665 665 555666666666666666666666666543
No 47
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.52 E-value=0.0017 Score=35.51 Aligned_cols=22 Identities=23% Similarity=0.646 Sum_probs=14.6
Q ss_pred eeCCcccccccChhHHHHHhhh
Q psy18241 5 HECPTCGKKWRTVSELNAHIQT 26 (566)
Q Consensus 5 ~~C~~C~~~f~~~~~L~~H~~~ 26 (566)
|.|++|++.|.+...|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 4566677777776666666654
No 48
>KOG1146|consensus
Probab=96.42 E-value=0.00055 Score=73.73 Aligned_cols=101 Identities=16% Similarity=0.249 Sum_probs=65.0
Q ss_pred cccccccccccchHHHHHHHhhhc----CCCCccccccccccCChhhhhcccccccCCCccccCcccccccChhhHHHHH
Q psy18241 366 FVCEICGQGYKMKKALLVHVGMHN----GINPFTCSFCNKSFTQKVGLQKHLPIHTGSTRFQCDLCGKRFIHQKSFYIHK 441 (566)
Q Consensus 366 ~~C~~C~~~f~~~~~l~~H~~~h~----~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~C~~C~k~f~~~~~l~~H~ 441 (566)
..|..|...|.....+..+-+--- ....+.|..|++.|.....+. |+- ...+|.|.+|...|.....|..|.
T Consensus 1229 l~~~~~e~~f~~~~~~~~~a~~~~~~~~~sGe~~c~~~~~~~~~~~~~~-~l~---~~~~~~~~~~~~~~~~~~~l~~~~ 1304 (1406)
T KOG1146|consen 1229 LLPNALEQPFPQEPEPTATAPPKPPELPASGEGECGAVDELLTPSFGIS-TLD---VTHRYLCRQCKMAFDGEAPLTAHQ 1304 (1406)
T ss_pred ccHHhhhcCccCcccccccCCCCCCcCcCCCcchhhhccccccCcccee-ecc---cchhHHHHHHHhhhcchhHHHHHH
Confidence 456677777777766665543211 112367888888888877777 653 345788888888888888888887
Q ss_pred hh-----------------ccCCCCccCCcCCccCCChHHHHhHhhh
Q psy18241 442 MV-----------------HSGEKPIKCSACGLAVLSSSHLKRHFRV 471 (566)
Q Consensus 442 ~~-----------------H~~~~~~~C~~C~~~f~~~~~l~~H~~~ 471 (566)
+. +....+| |..|...|.....|..||++
T Consensus 1305 ~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~ 1350 (1406)
T KOG1146|consen 1305 RKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRS 1350 (1406)
T ss_pred HHHHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHH
Confidence 42 1122334 66666666666666666654
No 49
>KOG2231|consensus
Probab=96.39 E-value=0.0066 Score=62.05 Aligned_cols=23 Identities=26% Similarity=0.420 Sum_probs=11.8
Q ss_pred cCCccchhccchhHHHHhhhhhc
Q psy18241 146 ECSVCGKRFAKKWNAQVHKKKVH 168 (566)
Q Consensus 146 ~C~~C~~~f~~~~~l~~H~~~~h 168 (566)
.|..|...|.....|..|++..|
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h 206 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH 206 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce
Confidence 35555555555555555554433
No 50
>PRK04860 hypothetical protein; Provisional
Probab=96.37 E-value=0.0015 Score=54.65 Aligned_cols=37 Identities=30% Similarity=0.695 Sum_probs=21.9
Q ss_pred ccccCcccccccChhhHHHHHhhccCCCCccCCcCCccCCC
Q psy18241 421 RFQCDLCGKRFIHQKSFYIHKMVHSGEKPIKCSACGLAVLS 461 (566)
Q Consensus 421 ~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~ 461 (566)
+|.|. |++ ....+.+|.++|+|+++|.|..|+..|..
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEE
Confidence 46665 655 55555666666666666666666655543
No 51
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.22 E-value=0.0036 Score=33.79 Aligned_cols=22 Identities=41% Similarity=0.768 Sum_probs=10.8
Q ss_pred ccCCccccccCChhHHHHHHhhh
Q psy18241 117 VKCDICGLALTTKSHLNRHMLVH 139 (566)
Q Consensus 117 ~~C~~C~~~f~~~~~L~~H~~~h 139 (566)
|+|+.|+.... ...|.+|++.|
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 45555555554 55555555554
No 52
>KOG2785|consensus
Probab=96.20 E-value=0.018 Score=53.92 Aligned_cols=72 Identities=26% Similarity=0.422 Sum_probs=43.3
Q ss_pred eecCcccccCCCHHHHHHHHhhhcCCCCcccccccccccChHHHHHHHhhhcCCCceeccccc---ccccChhhHhcccc
Q psy18241 252 HECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHVGMHNGINPFTCSFCN---KSFTQKVGLQKHLP 328 (566)
Q Consensus 252 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~---~~f~~~~~L~~H~~ 328 (566)
-.|-.|++.+.+...-..||..+++--.-.=+ -......|..=+..-.+ .-|.|-.|+ +.|.+....+.||.
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~HgffIPdre----YL~D~~GLl~YLgeKV~-~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGFFIPDRE----YLTDEKGLLKYLGEKVG-IGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCCcCCchH----hhhchhHHHHHHHHHhc-cCceEEEeccccCcccccHHHHHHHh
Confidence 56999999999999999999988763210000 01122233332222111 235666676 77777777777775
No 53
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=96.16 E-value=0.0017 Score=66.51 Aligned_cols=148 Identities=24% Similarity=0.434 Sum_probs=91.3
Q ss_pred ceeCCcccccccChhHHHHHhh--hhCCC--CccccC--ccCCccCchHHHHHHHhhcCCCCCccCCc--cccccCCchh
Q psy18241 4 IHECPTCGKKWRTVSELNAHIQ--THSDL--RPFVCE--ICGQGYKMKKALLVHVGMHSGIHPFTCHF--CNKSFTQKIG 75 (566)
Q Consensus 4 ~~~C~~C~~~f~~~~~L~~H~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~h~~~~~~~C~~--C~~~f~~~~~ 75 (566)
.+.|..|...|.....|..|.+ .|.++ +++.|+ .|++.|.....+..|...|.+..++.+.. +...+.....
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 368 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLN 368 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCccccccccC
Confidence 4667777777777777777777 67777 777777 67777777777777777777776666554 3333332222
Q ss_pred HH-----HHHhhhcCCCceeCCc--CcccccchhhhHHHHhhhcCCC--cccCCccccccCChhHHHHHHhhhcCCCccc
Q psy18241 76 LV-----KHLNIHNGTKKYQCHL--CGKGFIHHTSYKFHQLVHSGER--NVKCDICGLALTTKSHLNRHMLVHTGDRPHE 146 (566)
Q Consensus 76 L~-----~H~~~h~~~~~~~C~~--C~k~F~~~~~l~~H~~~h~~~~--~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~ 146 (566)
-. .....-.....+.+.. |...+.....+..|...|...+ .+.+..|.+.|.....|..|++.|....++.
T Consensus 369 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 448 (467)
T COG5048 369 NEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAPLL 448 (467)
T ss_pred CCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccccCCcee
Confidence 11 1111112223333332 5566666666666666665544 4566778888888888888887777666655
Q ss_pred CCccc
Q psy18241 147 CSVCG 151 (566)
Q Consensus 147 C~~C~ 151 (566)
|..++
T Consensus 449 ~~~~~ 453 (467)
T COG5048 449 CSILK 453 (467)
T ss_pred ecccc
Confidence 55443
No 54
>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=95.94 E-value=0.0024 Score=35.62 Aligned_cols=22 Identities=32% Similarity=0.718 Sum_probs=12.9
Q ss_pred ccCCcChhhccChhhHHHHHhh
Q psy18241 535 FTCHFCNKSFTQKIGLVKHLNI 556 (566)
Q Consensus 535 ~~C~~C~~~f~~~~~L~~H~~~ 556 (566)
|-|.+|++.|.+...|..|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 4566666666666666666543
No 55
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.59 E-value=0.014 Score=53.32 Aligned_cols=132 Identities=21% Similarity=0.369 Sum_probs=88.9
Q ss_pred ccccCc--cCCccCchHHHHHHHhhcCCCCCccCCccc---cccC------CchhHHHHHhhhcCCCce----eCCcCcc
Q psy18241 32 PFVCEI--CGQGYKMKKALLVHVGMHSGIHPFTCHFCN---KSFT------QKIGLVKHLNIHNGTKKY----QCHLCGK 96 (566)
Q Consensus 32 ~~~C~~--C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~---~~f~------~~~~L~~H~~~h~~~~~~----~C~~C~k 96 (566)
.|.|+. |..+......|+.|.+..++ .+-|.+|- +.|. ++..|..|...-..+.-| .|..|..
T Consensus 151 ~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 151 SFKCPKSKCHRRCGSLKELKKHYKAQHG--FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKI 228 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcC--cEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccc
Confidence 467764 66666667788888876544 35677763 2343 345666776543333222 5999999
Q ss_pred cccchhhhHHHHhhhcCCCcccCCccccc-------cCChhHHHHHHhhhcCCCcccCCc--cc----hhccchhHHHHh
Q psy18241 97 GFIHHTSYKFHQLVHSGERNVKCDICGLA-------LTTKSHLNRHMLVHTGDRPHECSV--CG----KRFAKKWNAQVH 163 (566)
Q Consensus 97 ~F~~~~~l~~H~~~h~~~~~~~C~~C~~~-------f~~~~~L~~H~~~h~~~~~~~C~~--C~----~~f~~~~~l~~H 163 (566)
.|.....|.+|++.-+. +|-+|++. |.+...|.+|.+.- -|.|.+ |- ..|.....|..|
T Consensus 229 ~FYdDDEL~~HcR~~HE----~ChICD~v~p~~~QYFK~Y~~Le~HF~~~----hy~ct~qtc~~~k~~vf~~~~el~~h 300 (493)
T COG5236 229 YFYDDDELRRHCRLRHE----ACHICDMVGPIRYQYFKSYEDLEAHFRNA----HYCCTFQTCRVGKCYVFPYHTELLEH 300 (493)
T ss_pred eecChHHHHHHHHhhhh----hhhhhhccCccchhhhhCHHHHHHHhhcC----ceEEEEEEEecCcEEEeccHHHHHHH
Confidence 99999999999886442 57777764 78888899987642 244432 21 358888899999
Q ss_pred hhhhcccCCC
Q psy18241 164 KKKVHGLDVP 173 (566)
Q Consensus 164 ~~~~h~~~~~ 173 (566)
+...|+....
T Consensus 301 ~~~~h~~~~~ 310 (493)
T COG5236 301 LTRFHKVNAR 310 (493)
T ss_pred HHHHhhcccc
Confidence 9888876543
No 56
>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=95.59 E-value=0.0086 Score=33.37 Aligned_cols=22 Identities=32% Similarity=0.756 Sum_probs=14.5
Q ss_pred ccccccccccCChhhhhccccc
Q psy18241 394 FTCSFCNKSFTQKVGLQKHLPI 415 (566)
Q Consensus 394 ~~C~~C~k~f~~~~~L~~H~~~ 415 (566)
|.|+.|++.|.+...|..|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 5566677777766666666654
No 57
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.08 E-value=0.031 Score=51.23 Aligned_cols=86 Identities=22% Similarity=0.458 Sum_probs=50.6
Q ss_pred ccCCc--cccccCCchhHHHHHhhhcCCCceeCCcCcc---ccc------chhhhHHHHhhhcCCCcc----cCCccccc
Q psy18241 61 FTCHF--CNKSFTQKIGLVKHLNIHNGTKKYQCHLCGK---GFI------HHTSYKFHQLVHSGERNV----KCDICGLA 125 (566)
Q Consensus 61 ~~C~~--C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~k---~F~------~~~~l~~H~~~h~~~~~~----~C~~C~~~ 125 (566)
|.|+. |..+......|..|.+..++ .+-|.+|-. .|. ++..|..|...-..+..| .|..|...
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 FKCPKSKCHRRCGSLKELKKHYKAQHG--FVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIY 229 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcC--cEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccce
Confidence 67764 66666667788888876654 366777742 333 334555555432222222 47777777
Q ss_pred cCChhHHHHHHhhhcCCCcccCCccch
Q psy18241 126 LTTKSHLNRHMLVHTGDRPHECSVCGK 152 (566)
Q Consensus 126 f~~~~~L~~H~~~h~~~~~~~C~~C~~ 152 (566)
|-+-..|.+|++..+ -.|-+|++
T Consensus 230 FYdDDEL~~HcR~~H----E~ChICD~ 252 (493)
T COG5236 230 FYDDDELRRHCRLRH----EACHICDM 252 (493)
T ss_pred ecChHHHHHHHHhhh----hhhhhhhc
Confidence 777777777776433 23555544
No 58
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.54 E-value=0.027 Score=30.59 Aligned_cols=20 Identities=35% Similarity=0.874 Sum_probs=12.4
Q ss_pred eeCCcccccccChhHHHHHhh
Q psy18241 5 HECPTCGKKWRTVSELNAHIQ 25 (566)
Q Consensus 5 ~~C~~C~~~f~~~~~L~~H~~ 25 (566)
..|+.||+.| ....|..|+.
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3566666666 4566666654
No 59
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.36 E-value=0.028 Score=30.52 Aligned_cols=19 Identities=32% Similarity=0.663 Sum_probs=10.2
Q ss_pred cCCcChhhccChhhHHHHHh
Q psy18241 536 TCHFCNKSFTQKIGLVKHLN 555 (566)
Q Consensus 536 ~C~~C~~~f~~~~~L~~H~~ 555 (566)
+|++||+.| ....|.+|++
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHH
Confidence 455555555 4555555554
No 60
>KOG2785|consensus
Probab=94.31 E-value=0.1 Score=49.17 Aligned_cols=51 Identities=18% Similarity=0.342 Sum_probs=35.8
Q ss_pred cccCCccccccCChhHHHHHHhhhcCC-----------------------CcccCCccc---hhccchhHHHHhhhh
Q psy18241 116 NVKCDICGLALTTKSHLNRHMLVHTGD-----------------------RPHECSVCG---KRFAKKWNAQVHKKK 166 (566)
Q Consensus 116 ~~~C~~C~~~f~~~~~L~~H~~~h~~~-----------------------~~~~C~~C~---~~f~~~~~l~~H~~~ 166 (566)
|-.|-.|++.|.+...-..||..++|- .-|.|-.|. +.|.+-...+.||..
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 356777777777777777777766541 235677777 778888888888763
No 61
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=93.61 E-value=0.18 Score=38.92 Aligned_cols=79 Identities=20% Similarity=0.367 Sum_probs=38.7
Q ss_pred CCcccccccccccchHHHHHHHhhhcCCCC------------ccccccccccCChhhhhcccccccCCCccccCcccccc
Q psy18241 364 RPFVCEICGQGYKMKKALLVHVGMHNGINP------------FTCSFCNKSFTQKVGLQKHLPIHTGSTRFQCDLCGKRF 431 (566)
Q Consensus 364 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~------------~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~C~~C~k~f 431 (566)
-|..|++||-+..+...|.+-..-=-...+ -.|--|++.|........ ..-....+|+|+.|...|
T Consensus 14 LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~F 91 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKNVF 91 (112)
T ss_pred CCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccccceeCCCCCCcc
Confidence 466788888777777666653210001111 136666666654321110 001223356666666666
Q ss_pred cChhhHHHHHhhc
Q psy18241 432 IHQKSFYIHKMVH 444 (566)
Q Consensus 432 ~~~~~l~~H~~~H 444 (566)
-..-....|...|
T Consensus 92 C~dCD~fiHe~Lh 104 (112)
T TIGR00622 92 CVDCDVFVHESLH 104 (112)
T ss_pred ccccchhhhhhcc
Confidence 5555555555444
No 62
>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=92.75 E-value=0.065 Score=31.98 Aligned_cols=23 Identities=39% Similarity=0.790 Sum_probs=17.5
Q ss_pred cccCCcChhhccChhhHHHHHhh
Q psy18241 534 PFTCHFCNKSFTQKIGLVKHLNI 556 (566)
Q Consensus 534 ~~~C~~C~~~f~~~~~L~~H~~~ 556 (566)
+|.|++|++.|.....+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 57788888888888888888753
No 63
>KOG2482|consensus
Probab=92.67 E-value=0.12 Score=47.57 Aligned_cols=134 Identities=19% Similarity=0.319 Sum_probs=80.2
Q ss_pred eeCCccccccc-ChhHHHHHhh-hhC---------------------CCCccccCccCCccCchHHHHHHHhh--cCCCC
Q psy18241 5 HECPTCGKKWR-TVSELNAHIQ-THS---------------------DLRPFVCEICGQGYKMKKALLVHVGM--HSGIH 59 (566)
Q Consensus 5 ~~C~~C~~~f~-~~~~L~~H~~-~h~---------------------~~~~~~C~~C~~~f~~~~~l~~H~~~--h~~~~ 59 (566)
-+|-+|...+. +.+....|+- +|. ....+.|-.|.+.|..+..|+.||+. |....
T Consensus 145 lqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK~Hrrin 224 (423)
T KOG2482|consen 145 LQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKKRHRRIN 224 (423)
T ss_pred eEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhccCcccC
Confidence 36778876654 5566666753 231 12357899999999999999999864 44333
Q ss_pred CccCCcccccc--------CCchhHHHHH--hhh---------------cCCCc--eeCCcCcccccchhhhHHHHhhhc
Q psy18241 60 PFTCHFCNKSF--------TQKIGLVKHL--NIH---------------NGTKK--YQCHLCGKGFIHHTSYKFHQLVHS 112 (566)
Q Consensus 60 ~~~C~~C~~~f--------~~~~~L~~H~--~~h---------------~~~~~--~~C~~C~k~F~~~~~l~~H~~~h~ 112 (566)
|-. ..-++-| ++......+. .+- .+..+ .+|-.|.....+...|..||.+-+
T Consensus 225 Pkn-reYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~a~a~~v~CLfC~~~~en~~~l~eHmk~vH 303 (423)
T KOG2482|consen 225 PKN-REYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDDAEALSVVCLFCTNFYENPVFLFEHMKIVH 303 (423)
T ss_pred CCc-cccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCCCCccceEEEeeccchhhHHHHHHHHHHHH
Confidence 310 0001100 0001111111 000 01122 589999998888999999987432
Q ss_pred C---------------------------CCcccCCccccccCChhHHHHHHhhh
Q psy18241 113 G---------------------------ERNVKCDICGLALTTKSHLNRHMLVH 139 (566)
Q Consensus 113 ~---------------------------~~~~~C~~C~~~f~~~~~L~~H~~~h 139 (566)
. ...-.|-.|...|.....|..||.-+
T Consensus 304 e~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e~ 357 (423)
T KOG2482|consen 304 EFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVED 357 (423)
T ss_pred HhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcccc
Confidence 1 01235889999999999999999754
No 64
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=92.47 E-value=0.078 Score=31.11 Aligned_cols=9 Identities=33% Similarity=1.213 Sum_probs=4.7
Q ss_pred CcccCCcCh
Q psy18241 533 HPFTCHFCN 541 (566)
Q Consensus 533 ~~~~C~~C~ 541 (566)
.++.|++||
T Consensus 16 ~~~~CP~Cg 24 (33)
T cd00350 16 APWVCPVCG 24 (33)
T ss_pred CCCcCcCCC
Confidence 445555554
No 65
>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=91.60 E-value=0.16 Score=30.29 Aligned_cols=20 Identities=20% Similarity=0.667 Sum_probs=9.3
Q ss_pred cccCccCCccCchHHHHHHH
Q psy18241 33 FVCEICGQGYKMKKALLVHV 52 (566)
Q Consensus 33 ~~C~~C~~~f~~~~~l~~H~ 52 (566)
|.|++|+..|.+...+..|+
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~ 23 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHL 23 (35)
T ss_pred eEccccCCccCCHHHHHHHH
Confidence 44444444444444444444
No 66
>KOG4173|consensus
Probab=91.51 E-value=0.072 Score=45.11 Aligned_cols=77 Identities=23% Similarity=0.481 Sum_probs=58.0
Q ss_pred CCccCCc--cccccCCchhHHHHHhhhcCCCceeCCcCcccccchhhhHHHHhh-h---------cCCCcccCC--cccc
Q psy18241 59 HPFTCHF--CNKSFTQKIGLVKHLNIHNGTKKYQCHLCGKGFIHHTSYKFHQLV-H---------SGERNVKCD--ICGL 124 (566)
Q Consensus 59 ~~~~C~~--C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~k~F~~~~~l~~H~~~-h---------~~~~~~~C~--~C~~ 124 (566)
..|.|++ |...|........|...-++. .|.+|.+.|.+...|..|+.. | .|...|+|- .|+.
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 3477876 778888888888887655543 689999999998888888742 2 355678884 4888
Q ss_pred ccCChhHHHHHHhh
Q psy18241 125 ALTTKSHLNRHMLV 138 (566)
Q Consensus 125 ~f~~~~~L~~H~~~ 138 (566)
.|.+...-+.||..
T Consensus 155 KFkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 155 KFKTSRDRKDHMIR 168 (253)
T ss_pred hhhhhhhhhhHHHH
Confidence 88888888888753
No 67
>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=91.42 E-value=0.15 Score=29.94 Aligned_cols=24 Identities=38% Similarity=1.053 Sum_probs=14.3
Q ss_pred eeCCcccccccChhHHHHHhhhhCCCCccccCccCC
Q psy18241 5 HECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQ 40 (566)
Q Consensus 5 ~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~ 40 (566)
|+|.+||..+.... .++.|++|+.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 56777776655332 4566666665
No 68
>KOG2893|consensus
Probab=90.99 E-value=0.074 Score=46.09 Aligned_cols=41 Identities=27% Similarity=0.803 Sum_probs=22.3
Q ss_pred CCccccccCCchhHHHHHhhhcCCCceeCCcCcccccchhhhHHH
Q psy18241 63 CHFCNKSFTQKIGLVKHLNIHNGTKKYQCHLCGKGFIHHTSYKFH 107 (566)
Q Consensus 63 C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~k~F~~~~~l~~H 107 (566)
|-+|++.|.....|.+|++.. -|+|.+|.|...+-..|..|
T Consensus 13 cwycnrefddekiliqhqkak----hfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKAK----HFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhhhc----cceeeeehhhhccCCCceee
Confidence 555666666666665555432 25566665555544445444
No 69
>KOG2893|consensus
Probab=90.97 E-value=0.076 Score=46.01 Aligned_cols=45 Identities=31% Similarity=0.717 Sum_probs=31.8
Q ss_pred CCCCCCcccCchhHHhHhhhccCCCcccCCcChhhccChhhHHHH-Hhhh
Q psy18241 509 CEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKH-LNIH 557 (566)
Q Consensus 509 C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~~~f~~~~~L~~H-~~~h 557 (566)
|-+|++.|.....|..|++. |-|+|.+|-|...+--.|..| |.+|
T Consensus 13 cwycnrefddekiliqhqka----khfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred eeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceeehhhhh
Confidence 77777777777777777653 447777777777777777777 5555
No 70
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.03 E-value=0.54 Score=36.37 Aligned_cols=85 Identities=20% Similarity=0.345 Sum_probs=51.3
Q ss_pred CccccCccCCccCchHHHHHHHhh------------cCCCCCccCCccccccCCchhHHHHHhhhcCCCceeCCcCcccc
Q psy18241 31 RPFVCEICGQGYKMKKALLVHVGM------------HSGIHPFTCHFCNKSFTQKIGLVKHLNIHNGTKKYQCHLCGKGF 98 (566)
Q Consensus 31 ~~~~C~~C~~~f~~~~~l~~H~~~------------h~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~k~F 98 (566)
-|-.|++||........|.+-..- -.....-.|--|...|........ ..-.....|+|+.|...|
T Consensus 14 LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~--~~~~~~~~y~C~~C~~~F 91 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPF--DELKDSHRYVCAVCKNVF 91 (112)
T ss_pred CCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccc--cccccccceeCCCCCCcc
Confidence 456677777777666666543210 001111248888888876432110 002234578999999999
Q ss_pred cchhhhHHHHhhhcCCCcccCCccc
Q psy18241 99 IHHTSYKFHQLVHSGERNVKCDICG 123 (566)
Q Consensus 99 ~~~~~l~~H~~~h~~~~~~~C~~C~ 123 (566)
-..-+.-.|...|. |+-|.
T Consensus 92 C~dCD~fiHe~Lh~------CPGC~ 110 (112)
T TIGR00622 92 CVDCDVFVHESLHC------CPGCI 110 (112)
T ss_pred ccccchhhhhhccC------CcCCC
Confidence 88888888887773 77665
No 71
>KOG2482|consensus
Probab=87.10 E-value=0.86 Score=42.24 Aligned_cols=76 Identities=14% Similarity=0.253 Sum_probs=44.5
Q ss_pred eecCcccccCCCHHHHHHHHhhhcCCCCc--ccccccccccChHHHHHHHhhhcCCCceecccccccccChhhHhccccc
Q psy18241 252 HECPTCGKKWRTVSELNAHIQTHSDLRPF--VCEICGQGYKMKKALLVHVGMHNGINPFTCSFCNKSFTQKVGLQKHLPI 329 (566)
Q Consensus 252 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~--~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L~~H~~~ 329 (566)
..|-.|.....+...|..||.+-+.-.-. +=+ =+-.|..+-.+..=.|. ....-.|-.|.-.|.....|..||..
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd-~~Ln~YqrvrviNyiRk--q~~~~~c~~cd~~F~~e~~l~~hm~e 356 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSD-YSLNFYQRVRVINYIRK--QKKKSRCAECDLSFWKEPGLLIHMVE 356 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhhccc-cccchhhhhhHHHHHHH--HhhccccccccccccCcchhhhhccc
Confidence 57999999999999999999865431100 000 00111111112111111 11234677888899999999999865
Q ss_pred c
Q psy18241 330 H 330 (566)
Q Consensus 330 h 330 (566)
+
T Consensus 357 ~ 357 (423)
T KOG2482|consen 357 D 357 (423)
T ss_pred c
Confidence 4
No 72
>KOG4173|consensus
Probab=85.73 E-value=0.45 Score=40.51 Aligned_cols=82 Identities=24% Similarity=0.534 Sum_probs=65.9
Q ss_pred CceeCCc--CcccccchhhhHHHHhhhcCCCcccCCccccccCChhHHHHHHh-hh---------cCCCcccCC--ccch
Q psy18241 87 KKYQCHL--CGKGFIHHTSYKFHQLVHSGERNVKCDICGLALTTKSHLNRHML-VH---------TGDRPHECS--VCGK 152 (566)
Q Consensus 87 ~~~~C~~--C~k~F~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L~~H~~-~h---------~~~~~~~C~--~C~~ 152 (566)
..|.|++ |...|.....+..|..+-++. .|.+|.+.|.+...|..|+. .| .|..-|+|- -|+.
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 4578987 889999998888887554443 79999999999999999974 23 355679995 5999
Q ss_pred hccchhHHHHhhhhhcccC
Q psy18241 153 RFAKKWNAQVHKKKVHGLD 171 (566)
Q Consensus 153 ~f~~~~~l~~H~~~~h~~~ 171 (566)
.|.+......|+...|...
T Consensus 155 KFkT~r~RkdH~I~~Hk~P 173 (253)
T KOG4173|consen 155 KFKTSRDRKDHMIRMHKYP 173 (253)
T ss_pred hhhhhhhhhhHHHHhccCC
Confidence 9999999999998777543
No 73
>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=85.11 E-value=0.69 Score=27.31 Aligned_cols=25 Identities=36% Similarity=0.860 Sum_probs=14.3
Q ss_pred ceeCCcccccccChhHHHHHhhhhCCCCccccCccCC
Q psy18241 4 IHECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQ 40 (566)
Q Consensus 4 ~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~ 40 (566)
.|+|.+||..+.... .|-.|++|+.
T Consensus 2 ~~~C~~CG~i~~g~~------------~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGEE------------APEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECCc------------CCCcCcCCCC
Confidence 466777776654321 3456666665
No 74
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=84.69 E-value=0.51 Score=30.60 Aligned_cols=25 Identities=24% Similarity=0.606 Sum_probs=12.9
Q ss_pred CCCcccCCcChhhccChhhHHHHHh
Q psy18241 531 GIHPFTCHFCNKSFTQKIGLVKHLN 555 (566)
Q Consensus 531 ~~~~~~C~~C~~~f~~~~~L~~H~~ 555 (566)
||--+.|+-||..|..+.+..+|+.
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhh
Confidence 4444555555555555555555543
No 75
>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=84.03 E-value=1.2 Score=34.94 Aligned_cols=25 Identities=24% Similarity=0.490 Sum_probs=23.5
Q ss_pred ccC----CcChhhccChhhHHHHHhhhcC
Q psy18241 535 FTC----HFCNKSFTQKIGLVKHLNIHNG 559 (566)
Q Consensus 535 ~~C----~~C~~~f~~~~~L~~H~~~h~~ 559 (566)
|.| ..|++.+.+...|++|++.+||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 899 9999999999999999998876
No 76
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=83.74 E-value=0.52 Score=30.55 Aligned_cols=23 Identities=26% Similarity=0.712 Sum_probs=9.8
Q ss_pred CCcccCCccccccCChhHHHHHH
Q psy18241 114 ERNVKCDICGLALTTKSHLNRHM 136 (566)
Q Consensus 114 ~~~~~C~~C~~~f~~~~~L~~H~ 136 (566)
|.-++|+-||+.|....++.+|+
T Consensus 15 E~~lrCPRC~~~FR~~K~Y~RHV 37 (65)
T COG4049 15 EEFLRCPRCGMVFRRRKDYIRHV 37 (65)
T ss_pred ceeeeCCchhHHHHHhHHHHHHh
Confidence 33344444444444444444444
No 77
>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=83.07 E-value=0.79 Score=35.58 Aligned_cols=30 Identities=30% Similarity=0.774 Sum_probs=17.4
Q ss_pred cccCcccccccChhhHHHHHhhccCCCCccCCcCCccCCCh
Q psy18241 422 FQCDLCGKRFIHQKSFYIHKMVHSGEKPIKCSACGLAVLSS 462 (566)
Q Consensus 422 ~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~ 462 (566)
..|+.||++|... +..|..|+.||..|.-.
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 3566666666542 23566666666666544
No 78
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=82.94 E-value=0.46 Score=42.56 Aligned_cols=43 Identities=26% Similarity=0.707 Sum_probs=26.1
Q ss_pred CCccCCCCCCcccCchhHHhHhhh---cc-------CCCc-----ccCCcChhhccCh
Q psy18241 505 RPFVCEICGQGYKMKKALLVHVGM---HS-------GIHP-----FTCHFCNKSFTQK 547 (566)
Q Consensus 505 ~~~~C~~C~~~f~~~~~L~~H~~~---H~-------~~~~-----~~C~~C~~~f~~~ 547 (566)
+...|++|++.|.++..+....++ .+ |..| ..|+.||.+|...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 445677777777666555555432 11 2233 4799999888765
No 79
>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=82.70 E-value=0.9 Score=27.63 Aligned_cols=34 Identities=24% Similarity=0.586 Sum_probs=18.4
Q ss_pred ceeCCcccccccChhHHHHHhhhhCCCCccccCccCCcc
Q psy18241 4 IHECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGY 42 (566)
Q Consensus 4 ~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f 42 (566)
.+.|+.|+..|.-..+... .+.....|+.|+..|
T Consensus 2 ~~~CP~C~~~~~v~~~~~~-----~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLG-----ANGGKVRCGKCGHVW 35 (38)
T ss_pred EEECCCCCCEEEeCHHHcC-----CCCCEEECCCCCCEE
Confidence 4567777776665443321 122245677776665
No 80
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=80.65 E-value=1.8 Score=25.98 Aligned_cols=34 Identities=29% Similarity=0.619 Sum_probs=19.0
Q ss_pred ceeCCcccccccChhHHHHHhhhhCCCCccccCccCCcc
Q psy18241 4 IHECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGY 42 (566)
Q Consensus 4 ~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f 42 (566)
...|+.|+..|.-..+.. -......+|+.|+..|
T Consensus 2 ~i~Cp~C~~~y~i~d~~i-----p~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKI-----PPKGRKVRCSKCGHVF 35 (36)
T ss_pred EEECCCCCCEEeCCHHHC-----CCCCcEEECCCCCCEe
Confidence 346777777766555431 1233456666666655
No 81
>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=79.31 E-value=1.3 Score=34.36 Aligned_cols=30 Identities=33% Similarity=0.872 Sum_probs=17.8
Q ss_pred ccCcccccccccCHHHHHHHHhhcCCCCCccCCCCCCcccCc
Q psy18241 478 YQCTTCGKRLRRTVSELNAHIQTHSDLRPFVCEICGQGYKMK 519 (566)
Q Consensus 478 ~~C~~C~k~f~~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~ 519 (566)
..|+.||++|.. |+ ..|-.|+.||..|.-.
T Consensus 10 R~Cp~CG~kFYD----Ln--------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYD----LN--------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhcc----CC--------CCCccCCCCCCccCcc
Confidence 357777776632 22 3566677777766544
No 82
>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=79.26 E-value=1.1 Score=24.57 Aligned_cols=10 Identities=30% Similarity=1.056 Sum_probs=7.1
Q ss_pred cCCCCCCccc
Q psy18241 508 VCEICGQGYK 517 (566)
Q Consensus 508 ~C~~C~~~f~ 517 (566)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 5777777774
No 83
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=78.30 E-value=1.8 Score=27.37 Aligned_cols=12 Identities=33% Similarity=0.769 Sum_probs=7.0
Q ss_pred ceeCCccccccc
Q psy18241 4 IHECPTCGKKWR 15 (566)
Q Consensus 4 ~~~C~~C~~~f~ 15 (566)
.|.|..||..|.
T Consensus 2 ~Y~C~~Cg~~~~ 13 (44)
T smart00659 2 IYICGECGRENE 13 (44)
T ss_pred EEECCCCCCEee
Confidence 456666666555
No 84
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=76.85 E-value=1.5 Score=26.47 Aligned_cols=32 Identities=28% Similarity=0.658 Sum_probs=14.7
Q ss_pred cCcccccccccCHHHHHHHHhhcCCCCCccCCCCCCcc
Q psy18241 479 QCTTCGKRLRRTVSELNAHIQTHSDLRPFVCEICGQGY 516 (566)
Q Consensus 479 ~C~~C~k~f~~~~~~l~~H~~~H~~~~~~~C~~C~~~f 516 (566)
.|+.|+..|.-..+.|. .+.+..+|+.|+..|
T Consensus 4 ~CP~C~~~f~v~~~~l~------~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLP------AGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHHcc------cCCcEEECCCCCcEe
Confidence 45556655543322111 123345566665555
No 85
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=76.32 E-value=1.8 Score=27.70 Aligned_cols=12 Identities=25% Similarity=0.769 Sum_probs=6.2
Q ss_pred ceeCCccccccc
Q psy18241 4 IHECPTCGKKWR 15 (566)
Q Consensus 4 ~~~C~~C~~~f~ 15 (566)
.|+|+.||..|.
T Consensus 3 ~y~C~~CG~~~~ 14 (46)
T PRK00398 3 EYKCARCGREVE 14 (46)
T ss_pred EEECCCCCCEEE
Confidence 455555555544
No 86
>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=75.11 E-value=2.4 Score=23.26 Aligned_cols=19 Identities=26% Similarity=0.739 Sum_probs=12.7
Q ss_pred eCCcccccccChhHHHHHhh
Q psy18241 6 ECPTCGKKWRTVSELNAHIQ 25 (566)
Q Consensus 6 ~C~~C~~~f~~~~~L~~H~~ 25 (566)
.||+|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 577777777 5566666654
No 87
>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=74.53 E-value=4.4 Score=31.80 Aligned_cols=24 Identities=21% Similarity=0.355 Sum_probs=15.1
Q ss_pred eeC----CcCcccccchhhhHHHHhhhc
Q psy18241 89 YQC----HLCGKGFIHHTSYKFHQLVHS 112 (566)
Q Consensus 89 ~~C----~~C~k~F~~~~~l~~H~~~h~ 112 (566)
|.| ..|+..+.+...+.+|.+.++
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 566 666666666666666665544
No 88
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=74.48 E-value=2.3 Score=35.48 Aligned_cols=39 Identities=21% Similarity=0.445 Sum_probs=24.3
Q ss_pred CCCCccccCccCCccCchHHHHHHHhhcCCCCCccCCcccccc
Q psy18241 28 SDLRPFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSF 70 (566)
Q Consensus 28 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f 70 (566)
.+..-|.|+.|+..|.....+.. . . ....|.|+.||...
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~-~--d-~~~~f~Cp~Cg~~l 133 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQL-L--D-MDGTFTCPRCGEEL 133 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHh-c--C-CCCcEECCCCCCEE
Confidence 34456888888888876554432 0 1 12348888888765
No 89
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=74.34 E-value=1.9 Score=36.26 Aligned_cols=23 Identities=35% Similarity=0.908 Sum_probs=15.7
Q ss_pred CccCCCCCCcccCchhHHhHhhhccCCCcccCCcCh
Q psy18241 506 PFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCN 541 (566)
Q Consensus 506 ~~~C~~C~~~f~~~~~L~~H~~~H~~~~~~~C~~C~ 541 (566)
-|.|++||..+ -|+-|-+||+||
T Consensus 134 ~~vC~vCGy~~-------------~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTH-------------EGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCcc-------------cCCCCCcCCCCC
Confidence 47777777653 356677777777
No 90
>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=74.21 E-value=2.1 Score=27.13 Aligned_cols=25 Identities=24% Similarity=0.547 Sum_probs=13.0
Q ss_pred CCCcccCCcChhhccCh----hhHHHHHh
Q psy18241 531 GIHPFTCHFCNKSFTQK----IGLVKHLN 555 (566)
Q Consensus 531 ~~~~~~C~~C~~~f~~~----~~L~~H~~ 555 (566)
+....+|.+|++.+... ++|.+|++
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 34456677777766653 67777773
No 91
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=73.49 E-value=2.3 Score=27.81 Aligned_cols=20 Identities=30% Similarity=0.853 Sum_probs=11.0
Q ss_pred cCCcChhhccCh-----hhHHHHHh
Q psy18241 536 TCHFCNKSFTQK-----IGLVKHLN 555 (566)
Q Consensus 536 ~C~~C~~~f~~~-----~~L~~H~~ 555 (566)
.|..|++.++.. ++|.+|++
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHH
Confidence 455555555443 46666665
No 92
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=73.48 E-value=1.4 Score=36.78 Aligned_cols=12 Identities=50% Similarity=1.024 Sum_probs=6.7
Q ss_pred cccCcccccccC
Q psy18241 422 FQCDLCGKRFIH 433 (566)
Q Consensus 422 ~~C~~C~k~f~~ 433 (566)
++|+.||++|..
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 555555555544
No 93
>KOG2186|consensus
Probab=73.06 E-value=1.5 Score=38.97 Aligned_cols=47 Identities=19% Similarity=0.614 Sum_probs=29.2
Q ss_pred ccCcccccccccCHHHHHHHHhhcCCCCCccCCCCCCcccCchhHHhHhhh
Q psy18241 478 YQCTTCGKRLRRTVSELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHVGM 528 (566)
Q Consensus 478 ~~C~~C~k~f~~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~~L~~H~~~ 528 (566)
|.|.+||..... ..+..|+..-.+ .-|.|--||+.|.. .+...|..-
T Consensus 4 FtCnvCgEsvKK--p~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 4 FTCNVCGESVKK--PQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred Eehhhhhhhccc--cchHHHHHhccC-CeeEEeeccccccc-chhhhhhhh
Confidence 667777776643 346666666555 45677777777766 556666543
No 94
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=72.73 E-value=2.4 Score=36.58 Aligned_cols=35 Identities=20% Similarity=0.493 Sum_probs=24.4
Q ss_pred CCCCccccCccCCccCchHHHHHHHhhcCCCCCccCCccccccC
Q psy18241 28 SDLRPFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFT 71 (566)
Q Consensus 28 ~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 71 (566)
.+..-|.|+.|+..|+....+. ..|.|+.||....
T Consensus 113 ~~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLE 147 (178)
T ss_pred cCCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCe
Confidence 3445688888888887776653 2588888887643
No 95
>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=72.57 E-value=3.8 Score=34.66 Aligned_cols=35 Identities=20% Similarity=0.440 Sum_probs=20.7
Q ss_pred ccCCCCcccccccccccchHHHHHHHhhhcCCCCcccccccccc
Q psy18241 360 HSDLRPFVCEICGQGYKMKKALLVHVGMHNGINPFTCSFCNKSF 403 (566)
Q Consensus 360 ~~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~k~f 403 (566)
..+..-|.|+.|+..|+...++. ..|.|+.||...
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEe
Confidence 34445566777776666666553 246666666543
No 96
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=72.26 E-value=3 Score=32.98 Aligned_cols=30 Identities=17% Similarity=0.280 Sum_probs=17.6
Q ss_pred cccCcccccccChhhHHHHHhhccCCCCccCCcCCccCCCh
Q psy18241 422 FQCDLCGKRFIHQKSFYIHKMVHSGEKPIKCSACGLAVLSS 462 (566)
Q Consensus 422 ~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~ 462 (566)
..|+.||++|... +..|..|+.||..|.-.
T Consensus 10 r~Cp~cg~kFYDL-----------nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYDL-----------NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCcccccc-----------CCCCccCCCcCCccCcc
Confidence 4566666666542 33566666666666544
No 97
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=72.06 E-value=2.3 Score=35.79 Aligned_cols=11 Identities=36% Similarity=0.993 Sum_probs=5.2
Q ss_pred CCCccccCccc
Q psy18241 418 GSTRFQCDLCG 428 (566)
Q Consensus 418 ~~~~~~C~~C~ 428 (566)
|+.|-+||+||
T Consensus 146 ge~P~~CPiCg 156 (166)
T COG1592 146 GEAPEVCPICG 156 (166)
T ss_pred CCCCCcCCCCC
Confidence 34444444444
No 98
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=71.74 E-value=3.5 Score=34.85 Aligned_cols=19 Identities=16% Similarity=0.324 Sum_probs=9.6
Q ss_pred CCCccCCCCCCcccCchhH
Q psy18241 504 LRPFVCEICGQGYKMKKAL 522 (566)
Q Consensus 504 ~~~~~C~~C~~~f~~~~~L 522 (566)
..-|.|+.|+..|+.-.++
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAM 125 (158)
T ss_pred CCeEECCCCCcEeeHHHHH
Confidence 3345555555555554444
No 99
>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=71.60 E-value=1.8 Score=26.79 Aligned_cols=11 Identities=45% Similarity=1.183 Sum_probs=5.5
Q ss_pred eeCCcCccccc
Q psy18241 89 YQCHLCGKGFI 99 (566)
Q Consensus 89 ~~C~~C~k~F~ 99 (566)
|+|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 44555555444
No 100
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=71.57 E-value=3.5 Score=34.42 Aligned_cols=13 Identities=23% Similarity=0.708 Sum_probs=6.8
Q ss_pred CccCCCCCCcccC
Q psy18241 506 PFVCEICGQGYKM 518 (566)
Q Consensus 506 ~~~C~~C~~~f~~ 518 (566)
-|.|+.|+..|..
T Consensus 99 ~Y~Cp~C~~~y~~ 111 (147)
T smart00531 99 YYKCPNCQSKYTF 111 (147)
T ss_pred EEECcCCCCEeeH
Confidence 3555555555553
No 101
>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=70.19 E-value=1.9 Score=28.41 Aligned_cols=9 Identities=44% Similarity=1.339 Sum_probs=3.4
Q ss_pred eCCcCcccc
Q psy18241 90 QCHLCGKGF 98 (566)
Q Consensus 90 ~C~~C~k~F 98 (566)
+|..||..|
T Consensus 7 ~C~~Cg~~f 15 (52)
T TIGR02605 7 RCTACGHRF 15 (52)
T ss_pred EeCCCCCEe
Confidence 333333333
No 102
>KOG2186|consensus
Probab=70.00 E-value=2.1 Score=38.10 Aligned_cols=12 Identities=42% Similarity=1.063 Sum_probs=4.9
Q ss_pred ccCCccccccCC
Q psy18241 61 FTCHFCNKSFTQ 72 (566)
Q Consensus 61 ~~C~~C~~~f~~ 72 (566)
|.|-.|+++|..
T Consensus 30 fSCIDC~k~F~~ 41 (276)
T KOG2186|consen 30 FSCIDCGKTFER 41 (276)
T ss_pred eEEeeccccccc
Confidence 344444444433
No 103
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=69.57 E-value=2.3 Score=38.10 Aligned_cols=23 Identities=26% Similarity=0.518 Sum_probs=16.0
Q ss_pred CceecccccccccChhhHhcccc
Q psy18241 306 NPFTCSFCNKSFTQKVGLQKHLP 328 (566)
Q Consensus 306 ~~~~C~~C~~~f~~~~~L~~H~~ 328 (566)
+.++|++|+..|.++.-.....+
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r 26 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIR 26 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCce
Confidence 45788888888887765554444
No 104
>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=67.24 E-value=4.2 Score=32.13 Aligned_cols=30 Identities=23% Similarity=0.485 Sum_probs=17.4
Q ss_pred ccCcccccccccCHHHHHHHHhhcCCCCCccCCCCCCcccCc
Q psy18241 478 YQCTTCGKRLRRTVSELNAHIQTHSDLRPFVCEICGQGYKMK 519 (566)
Q Consensus 478 ~~C~~C~k~f~~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~ 519 (566)
..|+.||++|.. | +..|-.|+.||..|.-.
T Consensus 10 r~Cp~cg~kFYD----L--------nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 10 RICPNTGSKFYD----L--------NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccCCCcCccccc----c--------CCCCccCCCcCCccCcc
Confidence 456667766632 2 23566677777666544
No 105
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=67.17 E-value=5 Score=34.67 Aligned_cols=33 Identities=21% Similarity=0.545 Sum_probs=19.0
Q ss_pred CCCCcccccccccccchHHHHHHHhhhcCCCCcccccccccc
Q psy18241 362 DLRPFVCEICGQGYKMKKALLVHVGMHNGINPFTCSFCNKSF 403 (566)
Q Consensus 362 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~k~f 403 (566)
+..-|.|+.|+..|+...++. ..|.|+.||...
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L 146 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEML 146 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCC
Confidence 344566777776666655542 246666666544
No 106
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=66.96 E-value=3.2 Score=28.24 Aligned_cols=19 Identities=21% Similarity=0.510 Sum_probs=7.5
Q ss_pred HHHhHhhhhcCCCcccCcc
Q psy18241 464 HLKRHFRVHTGEKPYQCTT 482 (566)
Q Consensus 464 ~l~~H~~~H~~~~~~~C~~ 482 (566)
.|..|+..--..++..|++
T Consensus 25 ~l~~H~~~~C~~~~v~C~~ 43 (60)
T PF02176_consen 25 ELDDHLENECPKRPVPCPY 43 (60)
T ss_dssp CHHHHHHTTSTTSEEE-SS
T ss_pred HHHHHHHccCCCCcEECCC
Confidence 4444444333333444444
No 107
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=64.15 E-value=5.7 Score=26.54 Aligned_cols=8 Identities=50% Similarity=1.630 Sum_probs=3.7
Q ss_pred CccCCcCC
Q psy18241 449 PIKCSACG 456 (566)
Q Consensus 449 ~~~C~~C~ 456 (566)
+|+|+.||
T Consensus 50 ~Y~Cp~CG 57 (61)
T COG2888 50 PYRCPKCG 57 (61)
T ss_pred ceECCCcC
Confidence 44444444
No 108
>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=63.28 E-value=4 Score=25.46 Aligned_cols=11 Identities=45% Similarity=1.229 Sum_probs=5.1
Q ss_pred eeCCcCccccc
Q psy18241 89 YQCHLCGKGFI 99 (566)
Q Consensus 89 ~~C~~C~k~F~ 99 (566)
|+|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (42)
T PF09723_consen 6 YRCEECGHEFE 16 (42)
T ss_pred EEeCCCCCEEE
Confidence 44444444444
No 109
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=62.77 E-value=1.7 Score=36.33 Aligned_cols=13 Identities=23% Similarity=0.582 Sum_probs=7.0
Q ss_pred ccCCCCCCcccCc
Q psy18241 507 FVCEICGQGYKMK 519 (566)
Q Consensus 507 ~~C~~C~~~f~~~ 519 (566)
++|+.||++|.+-
T Consensus 29 ~~c~~c~~~f~~~ 41 (154)
T PRK00464 29 RECLACGKRFTTF 41 (154)
T ss_pred eeccccCCcceEe
Confidence 5555555555543
No 110
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=61.69 E-value=4.3 Score=26.13 Aligned_cols=11 Identities=27% Similarity=0.827 Sum_probs=5.8
Q ss_pred ceeCCcccccc
Q psy18241 4 IHECPTCGKKW 14 (566)
Q Consensus 4 ~~~C~~C~~~f 14 (566)
.|.|..|++.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 45555555555
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=61.34 E-value=6.6 Score=22.79 Aligned_cols=11 Identities=36% Similarity=0.833 Sum_probs=5.2
Q ss_pred eeCCcCccccc
Q psy18241 89 YQCHLCGKGFI 99 (566)
Q Consensus 89 ~~C~~C~k~F~ 99 (566)
|.|..||..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 44555555544
No 112
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=58.50 E-value=4.1 Score=28.89 Aligned_cols=41 Identities=15% Similarity=0.389 Sum_probs=21.0
Q ss_pred ccCcccccccccCHHHHHHHHhhcCCCCCccCC--CCCCcccCchh
Q psy18241 478 YQCTTCGKRLRRTVSELNAHIQTHSDLRPFVCE--ICGQGYKMKKA 521 (566)
Q Consensus 478 ~~C~~C~k~f~~~~~~l~~H~~~H~~~~~~~C~--~C~~~f~~~~~ 521 (566)
+.|+.||.......+... . .-..++-++|. .||.+|.....
T Consensus 2 m~CP~Cg~~a~irtSr~~-s--~~~~~~Y~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYI-T--DTTKERYHQCQNVNCSATFITYES 44 (72)
T ss_pred ccCCCCCCccEEEEChhc-C--hhhheeeeecCCCCCCCEEEEEEE
Confidence 467778765532211110 0 11334556776 77777765544
No 113
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=58.31 E-value=7.7 Score=41.53 Aligned_cols=12 Identities=42% Similarity=1.066 Sum_probs=6.4
Q ss_pred CCCceeCCcCcc
Q psy18241 85 GTKKYQCHLCGK 96 (566)
Q Consensus 85 ~~~~~~C~~C~k 96 (566)
......|..||.
T Consensus 459 ~~~~L~CH~Cg~ 470 (730)
T COG1198 459 ATGQLRCHYCGY 470 (730)
T ss_pred CCCeeEeCCCCC
Confidence 334455666655
No 114
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=58.01 E-value=3.7 Score=29.12 Aligned_cols=16 Identities=31% Similarity=0.771 Sum_probs=9.3
Q ss_pred CCcccCC--ccchhccch
Q psy18241 142 DRPHECS--VCGKRFAKK 157 (566)
Q Consensus 142 ~~~~~C~--~C~~~f~~~ 157 (566)
+.-++|. .||.+|...
T Consensus 25 ~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 25 ERYHQCQNVNCSATFITY 42 (72)
T ss_pred eeeeecCCCCCCCEEEEE
Confidence 4455665 666666554
No 115
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=55.33 E-value=5.1 Score=22.84 Aligned_cols=12 Identities=42% Similarity=0.872 Sum_probs=6.0
Q ss_pred CCCccccCccCC
Q psy18241 29 DLRPFVCEICGQ 40 (566)
Q Consensus 29 ~~~~~~C~~C~~ 40 (566)
+...|.|+.|+.
T Consensus 16 D~~~~vCp~C~~ 27 (30)
T PF08274_consen 16 DGELLVCPECGH 27 (30)
T ss_dssp -SSSEEETTTTE
T ss_pred cCCEEeCCcccc
Confidence 344556666653
No 116
>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=54.69 E-value=9.2 Score=24.56 Aligned_cols=11 Identities=45% Similarity=1.111 Sum_probs=5.1
Q ss_pred eeCCcCccccc
Q psy18241 89 YQCHLCGKGFI 99 (566)
Q Consensus 89 ~~C~~C~k~F~ 99 (566)
|+|.+|+..|.
T Consensus 2 y~C~~CgyvYd 12 (47)
T PF00301_consen 2 YQCPVCGYVYD 12 (47)
T ss_dssp EEETTTSBEEE
T ss_pred cCCCCCCEEEc
Confidence 44555554443
No 117
>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=52.89 E-value=6.6 Score=31.80 Aligned_cols=23 Identities=39% Similarity=0.806 Sum_probs=10.5
Q ss_pred ccCCcChhhccChhhHHHHHhhhcCC
Q psy18241 535 FTCHFCNKSFTQKIGLVKHLNIHNGT 560 (566)
Q Consensus 535 ~~C~~C~~~f~~~~~L~~H~~~h~~~ 560 (566)
-.|-+||+.|.. |++|++.|+|-
T Consensus 73 i~clecGk~~k~---LkrHL~~~~gl 95 (132)
T PF05443_consen 73 IICLECGKKFKT---LKRHLRTHHGL 95 (132)
T ss_dssp EE-TBT--EESB---HHHHHHHTT-S
T ss_pred eEEccCCcccch---HHHHHHHccCC
Confidence 456666665542 46666666554
No 118
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=51.79 E-value=4.7 Score=30.22 Aligned_cols=11 Identities=36% Similarity=0.715 Sum_probs=5.3
Q ss_pred ccCCccccccC
Q psy18241 61 FTCHFCNKSFT 71 (566)
Q Consensus 61 ~~C~~C~~~f~ 71 (566)
..|..||..|.
T Consensus 47 ~~Cg~CGls~e 57 (104)
T COG4888 47 AVCGNCGLSFE 57 (104)
T ss_pred EEcccCcceEE
Confidence 34555555443
No 119
>PF15269 zf-C2H2_7: Zinc-finger
Probab=51.01 E-value=11 Score=23.28 Aligned_cols=23 Identities=22% Similarity=0.349 Sum_probs=13.7
Q ss_pred CceeCCcccccccChhHHHHHhh
Q psy18241 3 LIHECPTCGKKWRTVSELNAHIQ 25 (566)
Q Consensus 3 ~~~~C~~C~~~f~~~~~L~~H~~ 25 (566)
..|+|..|..+...++.|-+||+
T Consensus 19 ~~ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 19 FKYKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ccceeecCCcccchHHHHHHHHH
Confidence 34566666666666666666654
No 120
>KOG2807|consensus
Probab=50.63 E-value=25 Score=32.94 Aligned_cols=81 Identities=26% Similarity=0.606 Sum_probs=48.3
Q ss_pred ccccCcccccccChhhHHHHHhhccCCCCccCCcCCccCCChHHHHhHhhh----------hcCCC--cccCcccccccc
Q psy18241 421 RFQCDLCGKRFIHQKSFYIHKMVHSGEKPIKCSACGLAVLSSSHLKRHFRV----------HTGEK--PYQCTTCGKRLR 488 (566)
Q Consensus 421 ~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~----------H~~~~--~~~C~~C~k~f~ 488 (566)
-|.|+.|....- .-|..|++|+....+..+|.+=.+- -.++. .-.|-.|+-...
T Consensus 276 Gy~CP~CkakvC--------------sLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~ 341 (378)
T KOG2807|consen 276 GYFCPQCKAKVC--------------SLPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELL 341 (378)
T ss_pred ceeCCcccCeee--------------cCCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccC
Confidence 478888865432 3577888888888888877764321 11111 111555521111
Q ss_pred cCHHHHHHHHhhcCCCCCccCCCCCCcccCchhHHhHhhhc
Q psy18241 489 RTVSELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHVGMH 529 (566)
Q Consensus 489 ~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~~L~~H~~~H 529 (566)
+...|+|+.|...|----+.-.|...|
T Consensus 342 --------------~~~~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 342 --------------SSGRYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred --------------CCCcEEchhccceeeccchHHHHhhhh
Confidence 224588888888887777777776665
No 121
>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=50.53 E-value=7.8 Score=34.73 Aligned_cols=89 Identities=21% Similarity=0.401 Sum_probs=49.4
Q ss_pred CCCccccCccCCccCchHHHHHHHhhc--CCCCCccCCccccccCCchhHHHHHhhhcCCCceeCCcCcccccchhhhHH
Q psy18241 29 DLRPFVCEICGQGYKMKKALLVHVGMH--SGIHPFTCHFCNKSFTQKIGLVKHLNIHNGTKKYQCHLCGKGFIHHTSYKF 106 (566)
Q Consensus 29 ~~~~~~C~~C~~~f~~~~~l~~H~~~h--~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~k~F~~~~~l~~ 106 (566)
+.+.|+|.+|+.- .-...--.|+..- .....|+|.-|++. ..|.|-.|.-.|-. .
T Consensus 139 GGrif~CsfC~~f-lCEDDQFEHQAsCQvLe~E~~KC~SCNrl-----------------Gq~sCLRCK~cfCd-----d 195 (314)
T PF06524_consen 139 GGRIFKCSFCDNF-LCEDDQFEHQASCQVLESETFKCQSCNRL-----------------GQYSCLRCKICFCD-----D 195 (314)
T ss_pred CCeEEEeecCCCe-eeccchhhhhhhhhhhhcccccccccccc-----------------cchhhhheeeeehh-----h
Confidence 6678888888753 2333333454332 22345777777652 12344444443432 2
Q ss_pred HHhh----hcCCCcccCCccccccCChhHHHHHHhhhc
Q psy18241 107 HQLV----HSGERNVKCDICGLALTTKSHLNRHMLVHT 140 (566)
Q Consensus 107 H~~~----h~~~~~~~C~~C~~~f~~~~~L~~H~~~h~ 140 (566)
|.+. -...+++.|+.||........|..-.|+|.
T Consensus 196 HvrrKg~ky~k~k~~PCPKCg~et~eTkdLSmStR~hk 233 (314)
T PF06524_consen 196 HVRRKGFKYEKGKPIPCPKCGYETQETKDLSMSTRSHK 233 (314)
T ss_pred hhhhcccccccCCCCCCCCCCCcccccccceeeeecch
Confidence 3322 123467888989888777777776666653
No 122
>KOG2593|consensus
Probab=50.38 E-value=16 Score=35.81 Aligned_cols=17 Identities=18% Similarity=0.243 Sum_probs=8.8
Q ss_pred CCccCCcCCccCCChHH
Q psy18241 448 KPIKCSACGLAVLSSSH 464 (566)
Q Consensus 448 ~~~~C~~C~~~f~~~~~ 464 (566)
.-|.|+.|++.|.....
T Consensus 127 ~~Y~Cp~C~kkyt~Lea 143 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEA 143 (436)
T ss_pred ccccCCccccchhhhHH
Confidence 34555555555554443
No 123
>PF14353 CpXC: CpXC protein
Probab=50.07 E-value=3 Score=33.86 Aligned_cols=48 Identities=31% Similarity=0.695 Sum_probs=25.6
Q ss_pred cCcccccccccCH---------HHHHHHHhhcCCCCCccCCCCCCcccCchhHHhHhh
Q psy18241 479 QCTTCGKRLRRTV---------SELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHVG 527 (566)
Q Consensus 479 ~C~~C~k~f~~~~---------~~l~~H~~~H~~~~~~~C~~C~~~f~~~~~L~~H~~ 527 (566)
.|+.||..|...+ ..|+.-+. -...-.|.|+.||..|.-...+.-|-.
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il-~g~l~~~~CP~Cg~~~~~~~p~lY~D~ 59 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKIL-DGSLFSFTCPSCGHKFRLEYPLLYHDP 59 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHH-cCCcCEEECCCCCCceecCCCEEEEcC
Confidence 5888888875331 11222111 111224778888888776665555443
No 124
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=50.04 E-value=13 Score=39.87 Aligned_cols=39 Identities=28% Similarity=0.825 Sum_probs=23.4
Q ss_pred cccccccccCChhhhhcccccccCCCccccCcccccccChhhHHHHHhhccCCCCccCCcCCcc
Q psy18241 395 TCSFCNKSFTQKVGLQKHLPIHTGSTRFQCDLCGKRFIHQKSFYIHKMVHSGEKPIKCSACGLA 458 (566)
Q Consensus 395 ~C~~C~k~f~~~~~L~~H~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~~~ 458 (566)
+|+.|+.. |..| .......|..||.. ...|..|+.||-.
T Consensus 446 ~Cp~Cd~~------lt~H----~~~~~L~CH~Cg~~---------------~~~p~~Cp~Cgs~ 484 (730)
T COG1198 446 ECPNCDSP------LTLH----KATGQLRCHYCGYQ---------------EPIPQSCPECGSE 484 (730)
T ss_pred cCCCCCcc------eEEe----cCCCeeEeCCCCCC---------------CCCCCCCCCCCCC
Confidence 57777655 2233 33455677777753 3457777777754
No 125
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=49.13 E-value=9.2 Score=27.96 Aligned_cols=11 Identities=27% Similarity=1.005 Sum_probs=5.2
Q ss_pred ccCCCCCCccc
Q psy18241 507 FVCEICGQGYK 517 (566)
Q Consensus 507 ~~C~~C~~~f~ 517 (566)
+.|..||..|.
T Consensus 54 W~C~kCg~~fA 64 (89)
T COG1997 54 WKCRKCGAKFA 64 (89)
T ss_pred EEcCCCCCeec
Confidence 44444544443
No 126
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=48.91 E-value=14 Score=24.97 Aligned_cols=19 Identities=21% Similarity=0.219 Sum_probs=6.9
Q ss_pred hhHHHHhhhcCCCcccCCc
Q psy18241 103 SYKFHQLVHSGERNVKCDI 121 (566)
Q Consensus 103 ~l~~H~~~h~~~~~~~C~~ 121 (566)
.|..|+...-..++..|+.
T Consensus 25 ~l~~H~~~~C~~~~v~C~~ 43 (60)
T PF02176_consen 25 ELDDHLENECPKRPVPCPY 43 (60)
T ss_dssp CHHHHHHTTSTTSEEE-SS
T ss_pred HHHHHHHccCCCCcEECCC
Confidence 3444443333333334444
No 127
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=48.77 E-value=15 Score=24.75 Aligned_cols=9 Identities=33% Similarity=0.929 Sum_probs=4.7
Q ss_pred ccCCccccc
Q psy18241 61 FTCHFCNKS 69 (566)
Q Consensus 61 ~~C~~C~~~ 69 (566)
|.|+.||+.
T Consensus 26 F~CPnCG~~ 34 (59)
T PRK14890 26 FLCPNCGEV 34 (59)
T ss_pred eeCCCCCCe
Confidence 555555543
No 128
>KOG4167|consensus
Probab=48.34 E-value=5.4 Score=41.39 Aligned_cols=25 Identities=28% Similarity=0.531 Sum_probs=23.0
Q ss_pred cccCCcChhhccChhhHHHHHhhhc
Q psy18241 534 PFTCHFCNKSFTQKIGLVKHLNIHN 558 (566)
Q Consensus 534 ~~~C~~C~~~f~~~~~L~~H~~~h~ 558 (566)
-|.|..|||.|..-.++..||++|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4999999999999999999999985
No 129
>PRK04023 DNA polymerase II large subunit; Validated
Probab=48.25 E-value=19 Score=39.52 Aligned_cols=10 Identities=30% Similarity=0.740 Sum_probs=6.0
Q ss_pred ccccCccCCc
Q psy18241 32 PFVCEICGQG 41 (566)
Q Consensus 32 ~~~C~~C~~~ 41 (566)
...|+.||..
T Consensus 626 ~RfCpsCG~~ 635 (1121)
T PRK04023 626 RRKCPSCGKE 635 (1121)
T ss_pred CccCCCCCCc
Confidence 4456666665
No 130
>KOG2071|consensus
Probab=46.81 E-value=16 Score=37.41 Aligned_cols=18 Identities=28% Similarity=0.540 Sum_probs=14.1
Q ss_pred CCCcccCCccccccCChh
Q psy18241 113 GERNVKCDICGLALTTKS 130 (566)
Q Consensus 113 ~~~~~~C~~C~~~f~~~~ 130 (566)
+++...|++|+..|....
T Consensus 510 ~e~~~~C~IC~EkFe~v~ 527 (579)
T KOG2071|consen 510 SERQASCPICQEKFEVVF 527 (579)
T ss_pred cccccCCcccccccceee
Confidence 367789999999987643
No 131
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.91 E-value=14 Score=28.15 Aligned_cols=13 Identities=31% Similarity=0.621 Sum_probs=8.2
Q ss_pred CCCccCCCCCCcc
Q psy18241 504 LRPFVCEICGQGY 516 (566)
Q Consensus 504 ~~~~~C~~C~~~f 516 (566)
..|-.|+.||++|
T Consensus 24 rdPiVsPytG~s~ 36 (129)
T COG4530 24 RDPIVSPYTGKSY 36 (129)
T ss_pred CCccccCcccccc
Confidence 3566666666666
No 132
>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=44.63 E-value=15 Score=23.94 Aligned_cols=11 Identities=36% Similarity=1.035 Sum_probs=7.9
Q ss_pred ccCCccchhcc
Q psy18241 145 HECSVCGKRFA 155 (566)
Q Consensus 145 ~~C~~C~~~f~ 155 (566)
|+|.+||..+.
T Consensus 2 y~C~~CgyiYd 12 (50)
T cd00730 2 YECRICGYIYD 12 (50)
T ss_pred cCCCCCCeEEC
Confidence 67888887664
No 133
>KOG2593|consensus
Probab=44.24 E-value=21 Score=34.95 Aligned_cols=16 Identities=25% Similarity=0.594 Sum_probs=7.5
Q ss_pred CCccCCccccccCCch
Q psy18241 59 HPFTCHFCNKSFTQKI 74 (566)
Q Consensus 59 ~~~~C~~C~~~f~~~~ 74 (566)
..|.|+.|++.|+...
T Consensus 127 ~~Y~Cp~C~kkyt~Le 142 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLE 142 (436)
T ss_pred ccccCCccccchhhhH
Confidence 3455555555554433
No 134
>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=42.64 E-value=9.3 Score=22.91 Aligned_cols=8 Identities=50% Similarity=1.323 Sum_probs=3.9
Q ss_pred cccccccc
Q psy18241 368 CEICGQGY 375 (566)
Q Consensus 368 C~~C~~~f 375 (566)
|+.||+.|
T Consensus 4 C~~Cg~~Y 11 (36)
T PF05191_consen 4 CPKCGRIY 11 (36)
T ss_dssp ETTTTEEE
T ss_pred cCCCCCcc
Confidence 44455544
No 135
>PRK04023 DNA polymerase II large subunit; Validated
Probab=41.92 E-value=24 Score=38.77 Aligned_cols=10 Identities=30% Similarity=0.680 Sum_probs=6.4
Q ss_pred Cccccccccc
Q psy18241 393 PFTCSFCNKS 402 (566)
Q Consensus 393 ~~~C~~C~k~ 402 (566)
...|+.||..
T Consensus 626 ~RfCpsCG~~ 635 (1121)
T PRK04023 626 RRKCPSCGKE 635 (1121)
T ss_pred CccCCCCCCc
Confidence 4567777765
No 136
>KOG4167|consensus
Probab=41.42 E-value=7 Score=40.63 Aligned_cols=23 Identities=30% Similarity=0.582 Sum_probs=11.6
Q ss_pred cccCccCCccCchHHHHHHHhhc
Q psy18241 33 FVCEICGQGYKMKKALLVHVGMH 55 (566)
Q Consensus 33 ~~C~~C~~~f~~~~~l~~H~~~h 55 (566)
|.|.+|++.|.....++.||+.|
T Consensus 793 FpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 793 FPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eehHHHHHHHHHHhhhhHHHHHH
Confidence 34555555555555555555544
No 137
>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=40.98 E-value=9.8 Score=21.24 Aligned_cols=18 Identities=28% Similarity=0.536 Sum_probs=7.3
Q ss_pred cCCcChhhccChhhHHHHH
Q psy18241 536 TCHFCNKSFTQKIGLVKHL 554 (566)
Q Consensus 536 ~C~~C~~~f~~~~~L~~H~ 554 (566)
.|-.|++.| .....+.|.
T Consensus 2 sCiDC~~~F-~~~~y~~Ht 19 (28)
T PF08790_consen 2 SCIDCSKDF-DGDSYKSHT 19 (28)
T ss_dssp EETTTTEEE-EGGGTTT--
T ss_pred eeecCCCCc-CcCCcCCCC
Confidence 344555555 333444443
No 138
>KOG2807|consensus
Probab=40.66 E-value=38 Score=31.76 Aligned_cols=87 Identities=22% Similarity=0.396 Sum_probs=53.3
Q ss_pred ceeCCcccccccChhHHHHHhhhhCCCCccccCccCCccCchHHHHHHHhh----------cCCC--CCccCCccccccC
Q psy18241 4 IHECPTCGKKWRTVSELNAHIQTHSDLRPFVCEICGQGYKMKKALLVHVGM----------HSGI--HPFTCHFCNKSFT 71 (566)
Q Consensus 4 ~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~----------h~~~--~~~~C~~C~~~f~ 71 (566)
.|.||.|....- .-|-.|++|+........|.+=..- -.+. +.-.|-.|+..
T Consensus 276 Gy~CP~CkakvC--------------sLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~-- 339 (378)
T KOG2807|consen 276 GYFCPQCKAKVC--------------SLPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGE-- 339 (378)
T ss_pred ceeCCcccCeee--------------cCCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccc--
Confidence 577888765432 3467899998888777766543210 0111 11126566111
Q ss_pred CchhHHHHHhhhcCCCceeCCcCcccccchhhhHHHHhhhcCCCcccCCccc
Q psy18241 72 QKIGLVKHLNIHNGTKKYQCHLCGKGFIHHTSYKFHQLVHSGERNVKCDICG 123 (566)
Q Consensus 72 ~~~~L~~H~~~h~~~~~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~~C~~C~ 123 (566)
-.+...|+|..|...|-..-+.-.|...| .|+-|.
T Consensus 340 -----------~~~~~~y~C~~Ck~~FCldCDv~iHesLh------~CpgCe 374 (378)
T KOG2807|consen 340 -----------LLSSGRYRCESCKNVFCLDCDVFIHESLH------NCPGCE 374 (378)
T ss_pred -----------cCCCCcEEchhccceeeccchHHHHhhhh------cCCCcC
Confidence 12344688999999988888888887776 477665
No 139
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=40.28 E-value=17 Score=29.14 Aligned_cols=12 Identities=25% Similarity=0.714 Sum_probs=5.5
Q ss_pred ccCCcCCccCCC
Q psy18241 450 IKCSACGLAVLS 461 (566)
Q Consensus 450 ~~C~~C~~~f~~ 461 (566)
++|..||+.|..
T Consensus 2 H~Ct~Cg~~f~d 13 (131)
T PF09845_consen 2 HQCTKCGRVFED 13 (131)
T ss_pred cccCcCCCCcCC
Confidence 344444444443
No 140
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=40.03 E-value=14 Score=30.35 Aligned_cols=15 Identities=27% Similarity=0.990 Sum_probs=8.0
Q ss_pred CCceeCCcccccccC
Q psy18241 2 PLIHECPTCGKKWRT 16 (566)
Q Consensus 2 ~~~~~C~~C~~~f~~ 16 (566)
|..+.|..||..|..
T Consensus 68 p~~~~C~~CG~~~~~ 82 (135)
T PRK03824 68 EAVLKCRNCGNEWSL 82 (135)
T ss_pred ceEEECCCCCCEEec
Confidence 345555666555543
No 141
>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=39.54 E-value=10 Score=33.69 Aligned_cols=23 Identities=22% Similarity=0.475 Sum_probs=11.8
Q ss_pred CccCCCCCCcccCchhHHhHhhh
Q psy18241 506 PFVCEICGQGYKMKKALLVHVGM 528 (566)
Q Consensus 506 ~~~C~~C~~~f~~~~~L~~H~~~ 528 (566)
.|.|.+|+|.|.-..-...|+..
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHH
T ss_pred EECCCCCCcccCChHHHHHHHhh
Confidence 35555555555555555555544
No 142
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=39.52 E-value=19 Score=23.86 Aligned_cols=8 Identities=63% Similarity=1.639 Sum_probs=3.5
Q ss_pred CCcCcccc
Q psy18241 91 CHLCGKGF 98 (566)
Q Consensus 91 C~~C~k~F 98 (566)
|+.||+.|
T Consensus 8 C~~Cg~~~ 15 (54)
T PF14446_consen 8 CPVCGKKF 15 (54)
T ss_pred ChhhCCcc
Confidence 44444444
No 143
>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=37.85 E-value=40 Score=21.45 Aligned_cols=10 Identities=40% Similarity=1.155 Sum_probs=5.1
Q ss_pred CccccCcccc
Q psy18241 420 TRFQCDLCGK 429 (566)
Q Consensus 420 ~~~~C~~C~k 429 (566)
..|+|..|++
T Consensus 36 ~~~~C~~C~~ 45 (46)
T PF12760_consen 36 GRYRCKACRK 45 (46)
T ss_pred CeEECCCCCC
Confidence 4455555543
No 144
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=37.31 E-value=19 Score=28.82 Aligned_cols=23 Identities=35% Similarity=0.564 Sum_probs=12.6
Q ss_pred ccCCcChhhccChhhHHHHHhhhcCC
Q psy18241 535 FTCHFCNKSFTQKIGLVKHLNIHNGT 560 (566)
Q Consensus 535 ~~C~~C~~~f~~~~~L~~H~~~h~~~ 560 (566)
..|-.+|+.|+ +|++|+.+|.|-
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gm 99 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGL 99 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCC
Confidence 34555555553 456666665554
No 145
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=36.56 E-value=31 Score=27.68 Aligned_cols=56 Identities=18% Similarity=0.418 Sum_probs=29.0
Q ss_pred CCCCccccccccccCChhhhhcccccccCCCcccc---CcccccccChhhHHHHHhhccCCCCccCCcCCccCCChH
Q psy18241 390 GINPFTCSFCNKSFTQKVGLQKHLPIHTGSTRFQC---DLCGKRFIHQKSFYIHKMVHSGEKPIKCSACGLAVLSSS 463 (566)
Q Consensus 390 ~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~C---~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~ 463 (566)
..+-|+|.+|..+...+.-|+ |-.| .+|+.- -..|+.|-..| -+|++|..+|.+++
T Consensus 77 d~~lYeCnIC~etS~ee~FLK----------PneCCgY~iCn~C---ya~LWK~~~~y-----pvCPvCkTSFKss~ 135 (140)
T PF05290_consen 77 DPKLYECNICKETSAEERFLK----------PNECCGYSICNAC---YANLWKFCNLY-----PVCPVCKTSFKSSS 135 (140)
T ss_pred CCCceeccCcccccchhhcCC----------cccccchHHHHHH---HHHHHHHcccC-----CCCCcccccccccc
Confidence 346677888777665543322 2222 122222 24455555444 25777777776654
No 146
>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=36.45 E-value=17 Score=25.52 Aligned_cols=9 Identities=44% Similarity=1.368 Sum_probs=2.6
Q ss_pred cCccccccc
Q psy18241 479 QCTTCGKRL 487 (566)
Q Consensus 479 ~C~~C~k~f 487 (566)
.|.+|++.|
T Consensus 11 ~C~~C~~~F 19 (69)
T PF01363_consen 11 NCMICGKKF 19 (69)
T ss_dssp B-TTT--B-
T ss_pred cCcCcCCcC
Confidence 355555555
No 147
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=36.36 E-value=18 Score=22.63 Aligned_cols=11 Identities=36% Similarity=0.767 Sum_probs=5.7
Q ss_pred CccccCccCCc
Q psy18241 31 RPFVCEICGQG 41 (566)
Q Consensus 31 ~~~~C~~C~~~ 41 (566)
..+.|..||..
T Consensus 18 g~~vC~~CG~V 28 (43)
T PF08271_consen 18 GELVCPNCGLV 28 (43)
T ss_dssp TEEEETTT-BB
T ss_pred CeEECCCCCCE
Confidence 34566666654
No 148
>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=35.97 E-value=24 Score=28.59 Aligned_cols=27 Identities=30% Similarity=0.637 Sum_probs=15.2
Q ss_pred CCccccCccCCccCchHHHHHHHhhcCCCC
Q psy18241 30 LRPFVCEICGQGYKMKKALLVHVGMHSGIH 59 (566)
Q Consensus 30 ~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~ 59 (566)
+....|-+||+.|+. |.+|++.|+|..
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~glt 96 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLT 96 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCC
Confidence 344678888888866 478888887654
No 149
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=35.58 E-value=18 Score=19.14 Aligned_cols=6 Identities=50% Similarity=1.459 Sum_probs=3.2
Q ss_pred cCccCC
Q psy18241 35 CEICGQ 40 (566)
Q Consensus 35 C~~C~~ 40 (566)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 555554
No 150
>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=35.46 E-value=21 Score=19.18 Aligned_cols=9 Identities=44% Similarity=1.154 Sum_probs=5.9
Q ss_pred ceeCCcccc
Q psy18241 4 IHECPTCGK 12 (566)
Q Consensus 4 ~~~C~~C~~ 12 (566)
.|.||.||+
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 567777763
No 151
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=35.42 E-value=32 Score=21.30 Aligned_cols=23 Identities=26% Similarity=0.491 Sum_probs=13.3
Q ss_pred eeCCcCcccccc--hhhhHHHHhhh
Q psy18241 89 YQCHLCGKGFIH--HTSYKFHQLVH 111 (566)
Q Consensus 89 ~~C~~C~k~F~~--~~~l~~H~~~h 111 (566)
-.|+.||..|.. ...-+.|.+.|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 467777776643 34455565555
No 152
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=35.12 E-value=23 Score=28.00 Aligned_cols=12 Identities=25% Similarity=0.346 Sum_probs=6.9
Q ss_pred cccCccCCccCc
Q psy18241 33 FVCEICGQGYKM 44 (566)
Q Consensus 33 ~~C~~C~~~f~~ 44 (566)
+.|..|+..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PRK12380 71 AWCWDCSQVVEI 82 (113)
T ss_pred EEcccCCCEEec
Confidence 556666665543
No 153
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=34.94 E-value=39 Score=31.28 Aligned_cols=25 Identities=36% Similarity=0.903 Sum_probs=13.0
Q ss_pred CccccCcccccccChhhHHHHHhhc
Q psy18241 420 TRFQCDLCGKRFIHQKSFYIHKMVH 444 (566)
Q Consensus 420 ~~~~C~~C~k~f~~~~~l~~H~~~H 444 (566)
.+|+|+.|...|-..-....|...|
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHHHh
Confidence 3455555555555555555554443
No 154
>PHA00626 hypothetical protein
Probab=34.93 E-value=17 Score=24.04 Aligned_cols=15 Identities=13% Similarity=0.450 Sum_probs=11.1
Q ss_pred CcccCCcChhhccCh
Q psy18241 533 HPFTCHFCNKSFTQK 547 (566)
Q Consensus 533 ~~~~C~~C~~~f~~~ 547 (566)
..|+|+.||+.|+.-
T Consensus 22 nrYkCkdCGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCDCGYNDSKD 36 (59)
T ss_pred cceEcCCCCCeechh
Confidence 468888888888653
No 155
>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=34.86 E-value=35 Score=20.01 Aligned_cols=23 Identities=30% Similarity=0.732 Sum_probs=14.9
Q ss_pred CceeCCcccccccChhHHHHHhhh
Q psy18241 3 LIHECPTCGKKWRTVSELNAHIQT 26 (566)
Q Consensus 3 ~~~~C~~C~~~f~~~~~L~~H~~~ 26 (566)
..+.|+.|++... .+.+..|+..
T Consensus 3 ~~~~C~nC~R~v~-a~RfA~HLek 25 (33)
T PF08209_consen 3 PYVECPNCGRPVA-ASRFAPHLEK 25 (33)
T ss_dssp -EEE-TTTSSEEE-GGGHHHHHHH
T ss_pred CeEECCCCcCCcc-hhhhHHHHHH
Confidence 4678888888766 4667777654
No 156
>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=34.66 E-value=27 Score=23.30 Aligned_cols=12 Identities=25% Similarity=0.653 Sum_probs=5.9
Q ss_pred CccCCCCCCccc
Q psy18241 506 PFVCEICGQGYK 517 (566)
Q Consensus 506 ~~~C~~C~~~f~ 517 (566)
.+.|..||+.|-
T Consensus 18 k~~Cr~Cg~~~C 29 (57)
T cd00065 18 RHHCRNCGRIFC 29 (57)
T ss_pred ccccCcCcCCcC
Confidence 344555555543
No 157
>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=34.55 E-value=24 Score=23.46 Aligned_cols=6 Identities=50% Similarity=1.337 Sum_probs=2.2
Q ss_pred CCcCcc
Q psy18241 91 CHLCGK 96 (566)
Q Consensus 91 C~~C~k 96 (566)
|+.||.
T Consensus 5 CP~CG~ 10 (54)
T TIGR01206 5 CPDCGA 10 (54)
T ss_pred CCCCCC
Confidence 333333
No 158
>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=34.08 E-value=22 Score=28.14 Aligned_cols=13 Identities=23% Similarity=0.450 Sum_probs=7.7
Q ss_pred ccccCccCCccCc
Q psy18241 32 PFVCEICGQGYKM 44 (566)
Q Consensus 32 ~~~C~~C~~~f~~ 44 (566)
.+.|..|+..|..
T Consensus 70 ~~~C~~Cg~~~~~ 82 (115)
T TIGR00100 70 ECECEDCSEEVSP 82 (115)
T ss_pred EEEcccCCCEEec
Confidence 3556666666644
No 159
>KOG2461|consensus
Probab=33.82 E-value=32 Score=34.10 Aligned_cols=77 Identities=8% Similarity=-0.127 Sum_probs=38.0
Q ss_pred hhhhhcccccccCCCccccCcccccccChhhHHHHHhhccCCCCccCCcCCccCCChHHHHhHhhhhcCCCcccCcc
Q psy18241 406 KVGLQKHLPIHTGSTRFQCDLCGKRFIHQKSFYIHKMVHSGEKPIKCSACGLAVLSSSHLKRHFRVHTGEKPYQCTT 482 (566)
Q Consensus 406 ~~~L~~H~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~~l~~H~~~H~~~~~~~C~~ 482 (566)
...+..+...+++..+.-++++.+.+.....+..+...+.++.++.+..+...+.....+..+..+|.....+.+..
T Consensus 316 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 392 (396)
T KOG2461|consen 316 QLVLDQSEVPATVSVWTGETIPVRTPAGQLIYTQSHSMEVAEPTDMAPNQIWKIYHTGVLGFLIITTDESECNNMSF 392 (396)
T ss_pred ccccccccccccccccCcCcccccccccccchhhhhhcccCCCCcccccccccceeccccceeeeeccccccccccc
Confidence 33444445555555555555555555555555555555555555554444444444444444444444444443333
No 160
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=32.80 E-value=28 Score=22.58 Aligned_cols=12 Identities=25% Similarity=0.827 Sum_probs=5.1
Q ss_pred cccCcccccccc
Q psy18241 477 PYQCTTCGKRLR 488 (566)
Q Consensus 477 ~~~C~~C~k~f~ 488 (566)
.+.|..||..|.
T Consensus 4 ~l~C~dCg~~Fv 15 (49)
T PF13451_consen 4 TLTCKDCGAEFV 15 (49)
T ss_pred eEEcccCCCeEE
Confidence 334444444443
No 161
>PF12907 zf-met2: Zinc-binding
Probab=32.38 E-value=18 Score=22.26 Aligned_cols=21 Identities=29% Similarity=0.702 Sum_probs=9.4
Q ss_pred ccCCcChhhccC---hhhHHHHHh
Q psy18241 535 FTCHFCNKSFTQ---KIGLVKHLN 555 (566)
Q Consensus 535 ~~C~~C~~~f~~---~~~L~~H~~ 555 (566)
+.|.+|-..|.. ...|+.|..
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~e 25 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAE 25 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHH
Confidence 345555533322 233555543
No 162
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=31.12 E-value=28 Score=22.74 Aligned_cols=11 Identities=18% Similarity=0.504 Sum_probs=5.8
Q ss_pred cccCCcChhhc
Q psy18241 534 PFTCHFCNKSF 544 (566)
Q Consensus 534 ~~~C~~C~~~f 544 (566)
.+.|..||..+
T Consensus 37 r~~C~~Cgyt~ 47 (50)
T PRK00432 37 RWHCGKCGYTE 47 (50)
T ss_pred cEECCCcCCEE
Confidence 45555555543
No 163
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=30.88 E-value=16 Score=23.41 Aligned_cols=12 Identities=25% Similarity=0.731 Sum_probs=7.1
Q ss_pred cccCcccccccc
Q psy18241 477 PYQCTTCGKRLR 488 (566)
Q Consensus 477 ~~~C~~C~k~f~ 488 (566)
.|.|+.|+-+|.
T Consensus 7 ry~CDLCn~~~p 18 (57)
T PF14445_consen 7 RYSCDLCNSSHP 18 (57)
T ss_pred hHhHHhhcccCc
Confidence 356666666653
No 164
>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=30.58 E-value=22 Score=21.02 Aligned_cols=11 Identities=36% Similarity=1.008 Sum_probs=3.9
Q ss_pred cCccccccccc
Q psy18241 479 QCTTCGKRLRR 489 (566)
Q Consensus 479 ~C~~C~k~f~~ 489 (566)
.|..||+.|..
T Consensus 5 ~C~eC~~~f~d 15 (34)
T PF01286_consen 5 KCDECGKPFMD 15 (34)
T ss_dssp E-TTT--EES-
T ss_pred hHhHhCCHHHH
Confidence 45566666643
No 165
>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=30.24 E-value=31 Score=31.08 Aligned_cols=25 Identities=20% Similarity=0.410 Sum_probs=14.5
Q ss_pred CCccccccccccCChhhhhcccccc
Q psy18241 392 NPFTCSFCNKSFTQKVGLQKHLPIH 416 (566)
Q Consensus 392 ~~~~C~~C~k~f~~~~~L~~H~~~h 416 (566)
+++.|+.||........|..-.|+|
T Consensus 208 k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 208 KPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred CCCCCCCCCCcccccccceeeeecc
Confidence 5566666666665555555555544
No 166
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=30.19 E-value=23 Score=33.52 Aligned_cols=76 Identities=20% Similarity=0.571 Sum_probs=39.7
Q ss_pred ccccCccCCccCchHHHHHHHhhcCCCCCccCCccccccCCchhHHHHHhhhcCCCceeCCcCcccccchhhhHHHHh-h
Q psy18241 32 PFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFTQKIGLVKHLNIHNGTKKYQCHLCGKGFIHHTSYKFHQL-V 110 (566)
Q Consensus 32 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~k~F~~~~~l~~H~~-~ 110 (566)
.-.|++||..=. .+ + .+.....|.+-..|..|+-.... ...+|+.||.. ..|..... .
T Consensus 187 ~~~CPvCGs~P~-~s-~-v~~~~~~G~RyL~CslC~teW~~--------------~R~~C~~Cg~~----~~l~y~~~~~ 245 (309)
T PRK03564 187 RQFCPVCGSMPV-SS-V-VQIGTTQGLRYLHCNLCESEWHV--------------VRVKCSNCEQS----GKLHYWSLDS 245 (309)
T ss_pred CCCCCCCCCcch-hh-e-eeccCCCCceEEEcCCCCCcccc--------------cCccCCCCCCC----CceeeeeecC
Confidence 346888886422 11 1 12233456666778888764421 23578888852 22222111 0
Q ss_pred h-cCCCcccCCccccccCC
Q psy18241 111 H-SGERNVKCDICGLALTT 128 (566)
Q Consensus 111 h-~~~~~~~C~~C~~~f~~ 128 (566)
- .+.+...|+.|+.-.+.
T Consensus 246 ~~~~~r~e~C~~C~~YlK~ 264 (309)
T PRK03564 246 EQAAVKAESCGDCGTYLKI 264 (309)
T ss_pred CCcceEeeeccccccccee
Confidence 0 12345678888865544
No 167
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=29.96 E-value=23 Score=21.70 Aligned_cols=13 Identities=31% Similarity=0.861 Sum_probs=9.2
Q ss_pred cccCCcChhhccC
Q psy18241 534 PFTCHFCNKSFTQ 546 (566)
Q Consensus 534 ~~~C~~C~~~f~~ 546 (566)
||+|..|++.|=.
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 7777777777743
No 168
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=29.83 E-value=30 Score=25.50 Aligned_cols=14 Identities=29% Similarity=0.719 Sum_probs=8.1
Q ss_pred CCccccccccccCC
Q psy18241 392 NPFTCSFCNKSFTQ 405 (566)
Q Consensus 392 ~~~~C~~C~k~f~~ 405 (566)
.|-.|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 35556666666654
No 169
>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=29.37 E-value=21 Score=26.58 Aligned_cols=11 Identities=36% Similarity=0.869 Sum_probs=5.9
Q ss_pred ccCCccccccC
Q psy18241 117 VKCDICGLALT 127 (566)
Q Consensus 117 ~~C~~C~~~f~ 127 (566)
++|..|++.|.
T Consensus 54 W~C~~C~~~~A 64 (90)
T PF01780_consen 54 WKCKKCGKKFA 64 (90)
T ss_dssp EEETTTTEEEE
T ss_pred eecCCCCCEEe
Confidence 55555555553
No 170
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=29.17 E-value=21 Score=26.53 Aligned_cols=11 Identities=18% Similarity=0.579 Sum_probs=5.1
Q ss_pred ccCCCCCCccc
Q psy18241 507 FVCEICGQGYK 517 (566)
Q Consensus 507 ~~C~~C~~~f~ 517 (566)
..|..|++.|.
T Consensus 55 W~C~~C~~~~A 65 (90)
T PTZ00255 55 WRCKGCKKTVA 65 (90)
T ss_pred EEcCCCCCEEe
Confidence 44444444443
No 171
>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=29.04 E-value=28 Score=21.60 Aligned_cols=12 Identities=33% Similarity=0.913 Sum_probs=5.8
Q ss_pred CCcChhhccChh
Q psy18241 537 CHFCNKSFTQKI 548 (566)
Q Consensus 537 C~~C~~~f~~~~ 548 (566)
|.+||+.|+.+.
T Consensus 11 C~~C~rpf~WRK 22 (42)
T PF10013_consen 11 CPVCGRPFTWRK 22 (42)
T ss_pred CcccCCcchHHH
Confidence 555555554443
No 172
>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=28.89 E-value=6.9 Score=37.11 Aligned_cols=56 Identities=21% Similarity=0.452 Sum_probs=21.4
Q ss_pred CCCCccCCccccccCCchhHHHHHhhhcCCCceeCCcCcccccchhhhHHHHhhhcCCCcccCCccccccC
Q psy18241 57 GIHPFTCHFCNKSFTQKIGLVKHLNIHNGTKKYQCHLCGKGFIHHTSYKFHQLVHSGERNVKCDICGLALT 127 (566)
Q Consensus 57 ~~~~~~C~~C~~~f~~~~~L~~H~~~h~~~~~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 127 (566)
|.+-..|..|+..... ....|+.||..-...-.+.. ...-.+.+.+.|+.|+.-++
T Consensus 194 G~R~L~Cs~C~t~W~~--------------~R~~Cp~Cg~~~~~~l~~~~-~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 194 GKRYLHCSLCGTEWRF--------------VRIKCPYCGNTDHEKLEYFT-VEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp -EEEEEETTT--EEE----------------TTS-TTT---SS-EEE---------SEEEEEETTTTEEEE
T ss_pred ccEEEEcCCCCCeeee--------------cCCCCcCCCCCCCcceeeEe-cCCCCcEEEEECCcccchHH
Confidence 4455667777765421 12468888765332221110 11112344567888875544
No 173
>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=28.77 E-value=1.6e+02 Score=24.72 Aligned_cols=38 Identities=29% Similarity=0.404 Sum_probs=20.9
Q ss_pred hhhhcCCCcccCcccccccccCHHHHHHHHhh-cCCCCC
Q psy18241 469 FRVHTGEKPYQCTTCGKRLRRTVSELNAHIQT-HSDLRP 506 (566)
Q Consensus 469 ~~~H~~~~~~~C~~C~k~f~~~~~~l~~H~~~-H~~~~~ 506 (566)
.|.+.+.|+-.|..=+=.|..+...|+.|.+. |...+|
T Consensus 99 AR~~LN~K~RsC~~e~C~F~GtY~eLrKHar~~HP~~rP 137 (162)
T PF07800_consen 99 ARRFLNAKKRSCSQESCSFSGTYSELRKHARSEHPSARP 137 (162)
T ss_pred HHHHhccCCccCcccccccccCHHHHHHHHHhhCCCCCC
Confidence 34455556655555444566666666666653 444443
No 174
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=28.68 E-value=27 Score=21.52 Aligned_cols=17 Identities=29% Similarity=0.358 Sum_probs=8.3
Q ss_pred cccCccCCccCchHHHH
Q psy18241 33 FVCEICGQGYKMKKALL 49 (566)
Q Consensus 33 ~~C~~C~~~f~~~~~l~ 49 (566)
+.|+.|+-.+-....|.
T Consensus 20 d~C~~C~G~W~d~~el~ 36 (41)
T PF13453_consen 20 DVCPSCGGIWFDAGELE 36 (41)
T ss_pred EECCCCCeEEccHHHHH
Confidence 44555555554444443
No 175
>KOG2461|consensus
Probab=28.67 E-value=21 Score=35.27 Aligned_cols=78 Identities=4% Similarity=-0.223 Sum_probs=45.2
Q ss_pred HHHHHHHhhhcCCCCccccccccccCChhhhhcccccccCCCccccCcccccccChhhHHHHHhhccCCCCccCCcCC
Q psy18241 379 KALLVHVGMHNGINPFTCSFCNKSFTQKVGLQKHLPIHTGSTRFQCDLCGKRFIHQKSFYIHKMVHSGEKPIKCSACG 456 (566)
Q Consensus 379 ~~l~~H~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~ 456 (566)
..+..+...+.+..+..++++.+.+.....+..|...+.++.++.+..+...+.....+..+..+|.....+.+..|+
T Consensus 317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 394 (396)
T KOG2461|consen 317 LVLDQSEVPATVSVWTGETIPVRTPAGQLIYTQSHSMEVAEPTDMAPNQIWKIYHTGVLGFLIITTDESECNNMSFVC 394 (396)
T ss_pred cccccccccccccccCcCcccccccccccchhhhhhcccCCCCcccccccccceeccccceeeeeccccccccccccC
Confidence 334444455555555666666666666666666666666666665555555555555555555556555555555544
No 176
>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=28.50 E-value=22 Score=25.31 Aligned_cols=10 Identities=30% Similarity=0.667 Sum_probs=4.6
Q ss_pred cccccccccc
Q psy18241 366 FVCEICGQGY 375 (566)
Q Consensus 366 ~~C~~C~~~f 375 (566)
++++-|++.|
T Consensus 11 ~~~~cC~~~y 20 (71)
T PF05495_consen 11 IRFPCCGKYY 20 (71)
T ss_dssp EEETTTTEEE
T ss_pred EECCcccCee
Confidence 3444454444
No 177
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=27.93 E-value=55 Score=37.20 Aligned_cols=11 Identities=36% Similarity=0.839 Sum_probs=6.6
Q ss_pred CccCCcCCccC
Q psy18241 449 PIKCSACGLAV 459 (566)
Q Consensus 449 ~~~C~~C~~~f 459 (566)
+|.|+.||...
T Consensus 692 vy~CPsCGaev 702 (1337)
T PRK14714 692 VYVCPDCGAEV 702 (1337)
T ss_pred ceeCccCCCcc
Confidence 45666666653
No 178
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=27.78 E-value=30 Score=19.52 Aligned_cols=9 Identities=22% Similarity=0.700 Sum_probs=3.1
Q ss_pred cccCCcChh
Q psy18241 534 PFTCHFCNK 542 (566)
Q Consensus 534 ~~~C~~C~~ 542 (566)
.|.|.+|+.
T Consensus 15 ~Y~C~~Cdf 23 (30)
T PF07649_consen 15 FYRCSECDF 23 (30)
T ss_dssp EEE-TTT--
T ss_pred eEECccCCC
Confidence 455555543
No 179
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=27.60 E-value=33 Score=27.30 Aligned_cols=13 Identities=23% Similarity=0.621 Sum_probs=7.7
Q ss_pred ccccCccCCccCc
Q psy18241 32 PFVCEICGQGYKM 44 (566)
Q Consensus 32 ~~~C~~C~~~f~~ 44 (566)
.+.|..||..|..
T Consensus 71 ~~~C~~Cg~~~~~ 83 (117)
T PRK00564 71 ELECKDCSHVFKP 83 (117)
T ss_pred EEEhhhCCCcccc
Confidence 3556666666644
No 180
>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=27.01 E-value=25 Score=31.31 Aligned_cols=28 Identities=18% Similarity=0.535 Sum_probs=17.9
Q ss_pred CCcccCCccccccCChhHHHHHHhhhcC
Q psy18241 114 ERNVKCDICGLALTTKSHLNRHMLVHTG 141 (566)
Q Consensus 114 ~~~~~C~~C~~~f~~~~~L~~H~~~h~~ 141 (566)
+..|.|.+|+|.|.-.....+|+..-+.
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 4457788888888888888888765443
No 181
>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=26.86 E-value=20 Score=26.75 Aligned_cols=10 Identities=30% Similarity=1.175 Sum_probs=4.6
Q ss_pred ccCCCCCCcc
Q psy18241 507 FVCEICGQGY 516 (566)
Q Consensus 507 ~~C~~C~~~f 516 (566)
+.|..|++.|
T Consensus 54 W~C~~C~~~~ 63 (91)
T TIGR00280 54 WTCRKCGAKF 63 (91)
T ss_pred EEcCCCCCEE
Confidence 4444444444
No 182
>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=26.82 E-value=48 Score=34.38 Aligned_cols=14 Identities=36% Similarity=0.850 Sum_probs=7.7
Q ss_pred cCCCceeCCcCccc
Q psy18241 84 NGTKKYQCHLCGKG 97 (566)
Q Consensus 84 ~~~~~~~C~~C~k~ 97 (566)
.......|..||..
T Consensus 236 ~~~~~l~Ch~Cg~~ 249 (505)
T TIGR00595 236 KKEGKLRCHYCGYQ 249 (505)
T ss_pred cCCCeEEcCCCcCc
Confidence 33445566666654
No 183
>KOG0717|consensus
Probab=26.56 E-value=34 Score=33.90 Aligned_cols=21 Identities=24% Similarity=0.580 Sum_probs=12.9
Q ss_pred eeCCcccccccChhHHHHHhh
Q psy18241 5 HECPTCGKKWRTVSELNAHIQ 25 (566)
Q Consensus 5 ~~C~~C~~~f~~~~~L~~H~~ 25 (566)
+-|.+|+++|.+...|.+|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 456666666666666666653
No 184
>PRK14873 primosome assembly protein PriA; Provisional
Probab=26.36 E-value=46 Score=35.73 Aligned_cols=12 Identities=25% Similarity=0.794 Sum_probs=7.3
Q ss_pred CCCccccCcccc
Q psy18241 418 GSTRFQCDLCGK 429 (566)
Q Consensus 418 ~~~~~~C~~C~k 429 (566)
......|..||.
T Consensus 407 ~~~~l~Ch~CG~ 418 (665)
T PRK14873 407 AGGTPRCRWCGR 418 (665)
T ss_pred CCCeeECCCCcC
Confidence 344566777774
No 185
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=26.12 E-value=43 Score=27.40 Aligned_cols=12 Identities=33% Similarity=0.969 Sum_probs=8.5
Q ss_pred CccCCCCCCccc
Q psy18241 506 PFVCEICGQGYK 517 (566)
Q Consensus 506 ~~~C~~C~~~f~ 517 (566)
-|.|+.||..-.
T Consensus 81 ~~~CE~CG~~I~ 92 (137)
T TIGR03826 81 GYPCERCGTSIR 92 (137)
T ss_pred cCcccccCCcCC
Confidence 377888887643
No 186
>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 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=25.92 E-value=43 Score=34.72 Aligned_cols=40 Identities=30% Similarity=0.786 Sum_probs=25.0
Q ss_pred ccccccccccCChhhhhcccccccCCCccccCcccccccChhhHHHHHhhccCCCCccCCcCCcc
Q psy18241 394 FTCSFCNKSFTQKVGLQKHLPIHTGSTRFQCDLCGKRFIHQKSFYIHKMVHSGEKPIKCSACGLA 458 (566)
Q Consensus 394 ~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~~~ 458 (566)
..|+.|+-. |. .|.......|..||... .-|..|+.||..
T Consensus 223 ~~C~~C~~~------l~----~h~~~~~l~Ch~Cg~~~---------------~~~~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVS------LT----YHKKEGKLRCHYCGYQE---------------PIPKTCPQCGSE 262 (505)
T ss_pred cCCCCCCCc------eE----EecCCCeEEcCCCcCcC---------------CCCCCCCCCCCC
Confidence 567777543 22 33445567888888653 346778888764
No 188
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=25.72 E-value=30 Score=23.09 Aligned_cols=6 Identities=33% Similarity=1.647 Sum_probs=2.5
Q ss_pred ccCCCC
Q psy18241 507 FVCEIC 512 (566)
Q Consensus 507 ~~C~~C 512 (566)
|.|+.|
T Consensus 32 YmC~eC 37 (56)
T PF09963_consen 32 YMCDEC 37 (56)
T ss_pred eeChhH
Confidence 444444
No 189
>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=25.44 E-value=13 Score=22.73 Aligned_cols=10 Identities=40% Similarity=1.195 Sum_probs=5.3
Q ss_pred cccCcccccc
Q psy18241 422 FQCDLCGKRF 431 (566)
Q Consensus 422 ~~C~~C~k~f 431 (566)
|.|..||..|
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 5555555544
No 190
>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=25.32 E-value=26 Score=21.53 Aligned_cols=12 Identities=33% Similarity=1.041 Sum_probs=5.5
Q ss_pred CCCcccCCcChh
Q psy18241 531 GIHPFTCHFCNK 542 (566)
Q Consensus 531 ~~~~~~C~~C~~ 542 (566)
+.+.+.|.+|+.
T Consensus 21 ~~~~w~C~~C~~ 32 (40)
T PF04810_consen 21 GGKTWICNFCGT 32 (40)
T ss_dssp TTTEEEETTT--
T ss_pred CCCEEECcCCCC
Confidence 444555666554
No 191
>KOG0696|consensus
Probab=25.19 E-value=35 Score=33.47 Aligned_cols=60 Identities=28% Similarity=0.597 Sum_probs=41.8
Q ss_pred cCCCccccCcccccccChhhHHHHHhhccCCCCccCCcCCccCCChHHHHhHh-hhhcCCCcccCccccc
Q psy18241 417 TGSTRFQCDLCGKRFIHQKSFYIHKMVHSGEKPIKCSACGLAVLSSSHLKRHF-RVHTGEKPYQCTTCGK 485 (566)
Q Consensus 417 ~~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~~~f~~~~~l~~H~-~~H~~~~~~~C~~C~k 485 (566)
-|..-|+|.+|. +..|+|-|.- -.|.|+-=++.+.+-..-..|. ++|+-..|--|+.||-
T Consensus 69 fgKQGfQCqvC~--------fvvHkrChef-VtF~CPGadkg~dtDdpr~kHkf~~~tYssPTFCDhCGs 129 (683)
T KOG0696|consen 69 FGKQGFQCQVCC--------FVVHKRCHEF-VTFSCPGADKGPDTDDPRSKHKFKIHTYSSPTFCDHCGS 129 (683)
T ss_pred cccCceeeeEEe--------ehhhhhhcce-EEEECCCCCCCCCCCCcccccceeeeecCCCchhhhHHH
Confidence 355668888885 3567776642 2577888888888777777774 5677677777888874
No 192
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.77 E-value=31 Score=30.59 Aligned_cols=28 Identities=21% Similarity=0.500 Sum_probs=17.4
Q ss_pred CceecccccccccChhhHhcccccccCC
Q psy18241 306 NPFTCSFCNKSFTQKVGLQKHLPIHTGS 333 (566)
Q Consensus 306 ~~~~C~~C~~~f~~~~~L~~H~~~h~~~ 333 (566)
+.+.|++|+..|..+..+..-.++-.++
T Consensus 18 k~ieCPvC~tkFkkeev~tgsiRiiagD 45 (267)
T COG1655 18 KTIECPVCNTKFKKEEVKTGSIRIIAGD 45 (267)
T ss_pred ceeccCcccchhhhhheeccceeEeccc
Confidence 4567888888887665554444444443
No 193
>KOG4124|consensus
Probab=24.30 E-value=20 Score=33.79 Aligned_cols=24 Identities=17% Similarity=0.484 Sum_probs=16.9
Q ss_pred CCcccCCccccccCChhHHHHHHh
Q psy18241 114 ERNVKCDICGLALTTKSHLNRHML 137 (566)
Q Consensus 114 ~~~~~C~~C~~~f~~~~~L~~H~~ 137 (566)
.++|+|++|.+.++....|+-|..
T Consensus 396 nk~~r~~i~~~~~k~~~~l~~~~~ 419 (442)
T KOG4124|consen 396 NKPYRCEVCSKRYKNLNGLKYHRT 419 (442)
T ss_pred cCcccChhhhhhhccCCCCCceee
Confidence 567888888887777666665543
No 194
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=24.17 E-value=82 Score=35.92 Aligned_cols=55 Identities=22% Similarity=0.556 Sum_probs=35.7
Q ss_pred cccccccccccchHHHHHHHhhhcCCCCccccccccccCChhhhhcccccccCCCccccCcccccccChhhHHHHHhhcc
Q psy18241 366 FVCEICGQGYKMKKALLVHVGMHNGINPFTCSFCNKSFTQKVGLQKHLPIHTGSTRFQCDLCGKRFIHQKSFYIHKMVHS 445 (566)
Q Consensus 366 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~C~~C~k~f~~~~~l~~H~~~H~ 445 (566)
+.|+.||..-. ...|+.||... +.+|.|+.||....... +
T Consensus 668 rkCPkCG~~t~----------------~~fCP~CGs~t---------------e~vy~CPsCGaev~~de---------s 707 (1337)
T PRK14714 668 RRCPSCGTETY----------------ENRCPDCGTHT---------------EPVYVCPDCGAEVPPDE---------S 707 (1337)
T ss_pred EECCCCCCccc----------------cccCcccCCcC---------------CCceeCccCCCccCCCc---------c
Confidence 78999986421 13688898764 23578999998754321 1
Q ss_pred CCCCccCCcCCccCCCh
Q psy18241 446 GEKPIKCSACGLAVLSS 462 (566)
Q Consensus 446 ~~~~~~C~~C~~~f~~~ 462 (566)
+ ...|+.||......
T Consensus 708 ~--a~~CP~CGtplv~~ 722 (1337)
T PRK14714 708 G--RVECPRCDVELTPY 722 (1337)
T ss_pred c--cccCCCCCCccccc
Confidence 2 45699999655443
No 195
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=23.04 E-value=29 Score=21.36 Aligned_cols=10 Identities=40% Similarity=1.331 Sum_probs=4.8
Q ss_pred cccCcccccc
Q psy18241 422 FQCDLCGKRF 431 (566)
Q Consensus 422 ~~C~~C~k~f 431 (566)
|.|..|+..|
T Consensus 29 y~C~~C~~~w 38 (40)
T smart00440 29 YVCTKCGHRW 38 (40)
T ss_pred EEeCCCCCEe
Confidence 4455555443
No 196
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=22.83 E-value=37 Score=25.96 Aligned_cols=12 Identities=25% Similarity=0.376 Sum_probs=7.4
Q ss_pred ccCCccccccCC
Q psy18241 61 FTCHFCNKSFTQ 72 (566)
Q Consensus 61 ~~C~~C~~~f~~ 72 (566)
..|..||..+..
T Consensus 43 ~~C~~CG~y~~~ 54 (99)
T PRK14892 43 ITCGNCGLYTEF 54 (99)
T ss_pred EECCCCCCccCE
Confidence 457777666544
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=22.47 E-value=36 Score=26.88 Aligned_cols=12 Identities=25% Similarity=0.728 Sum_probs=6.1
Q ss_pred cccCccCCccCc
Q psy18241 33 FVCEICGQGYKM 44 (566)
Q Consensus 33 ~~C~~C~~~f~~ 44 (566)
+.|..||..|..
T Consensus 71 ~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 71 ARCRDCGHEFEP 82 (113)
T ss_dssp EEETTTS-EEEC
T ss_pred EECCCCCCEEec
Confidence 456666666543
No 198
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=22.25 E-value=56 Score=32.38 Aligned_cols=12 Identities=42% Similarity=1.196 Sum_probs=6.6
Q ss_pred cccCcccccccc
Q psy18241 477 PYQCTTCGKRLR 488 (566)
Q Consensus 477 ~~~C~~C~k~f~ 488 (566)
-|+|+.||..++
T Consensus 367 g~rC~kCg~~~~ 378 (421)
T COG1571 367 GFRCKKCGTRAR 378 (421)
T ss_pred CcccccccccCC
Confidence 455555555554
No 199
>KOG3408|consensus
Probab=22.24 E-value=52 Score=25.87 Aligned_cols=25 Identities=24% Similarity=0.432 Sum_probs=17.7
Q ss_pred CCcccCCcChhhccChhhHHHHHhh
Q psy18241 532 IHPFTCHFCNKSFTQKIGLVKHLNI 556 (566)
Q Consensus 532 ~~~~~C~~C~~~f~~~~~L~~H~~~ 556 (566)
...|-|-.|.+-|.+...|..|.++
T Consensus 55 ~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 55 GGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CceeehhhhhhhhcchHHHHHHHhc
Confidence 3457777777777777777777654
No 200
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=22.07 E-value=39 Score=26.75 Aligned_cols=12 Identities=33% Similarity=0.523 Sum_probs=7.0
Q ss_pred ccccCccCCccC
Q psy18241 32 PFVCEICGQGYK 43 (566)
Q Consensus 32 ~~~C~~C~~~f~ 43 (566)
.+.|..|+..|.
T Consensus 70 ~~~C~~Cg~~~~ 81 (114)
T PRK03681 70 ECWCETCQQYVT 81 (114)
T ss_pred EEEcccCCCeee
Confidence 355666666554
No 201
>KOG0978|consensus
Probab=21.89 E-value=35 Score=36.16 Aligned_cols=17 Identities=12% Similarity=0.454 Sum_probs=9.0
Q ss_pred cCCCCCCcccCchhHHh
Q psy18241 508 VCEICGQGYKMKKALLV 524 (566)
Q Consensus 508 ~C~~C~~~f~~~~~L~~ 524 (566)
+||.|+.+|.....+..
T Consensus 680 KCP~Cn~aFganDv~~I 696 (698)
T KOG0978|consen 680 KCPKCNAAFGANDVHRI 696 (698)
T ss_pred CCCCCCCCCCccccccc
Confidence 46666666655444433
No 202
>KOG4377|consensus
Probab=20.84 E-value=61 Score=31.52 Aligned_cols=20 Identities=15% Similarity=0.340 Sum_probs=17.5
Q ss_pred ChhhccChhhHHHHHhhhcC
Q psy18241 540 CNKSFTQKIGLVKHLNIHNG 559 (566)
Q Consensus 540 C~~~f~~~~~L~~H~~~h~~ 559 (566)
|+..|...+.+..|-+.|..
T Consensus 409 c~~tl~s~sqm~shkrkheR 428 (480)
T KOG4377|consen 409 CEATLYSVSQMASHKRKHER 428 (480)
T ss_pred CceEEEehhhhhhhhhhhhh
Confidence 89999999999999888864
No 203
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=20.82 E-value=29 Score=25.82 Aligned_cols=10 Identities=30% Similarity=1.112 Sum_probs=4.6
Q ss_pred ccCCCCCCcc
Q psy18241 507 FVCEICGQGY 516 (566)
Q Consensus 507 ~~C~~C~~~f 516 (566)
..|..|++.|
T Consensus 55 W~C~~C~~~~ 64 (90)
T PRK03976 55 WECRKCGAKF 64 (90)
T ss_pred EEcCCCCCEE
Confidence 4444444444
No 204
>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=20.69 E-value=40 Score=27.99 Aligned_cols=14 Identities=29% Similarity=0.567 Sum_probs=7.9
Q ss_pred CCcccCcccccccc
Q psy18241 475 EKPYQCTTCGKRLR 488 (566)
Q Consensus 475 ~~~~~C~~C~k~f~ 488 (566)
.-..+|..|+|-|-
T Consensus 12 ~~vv~C~~c~kWFC 25 (152)
T PF09416_consen 12 SCVVKCNTCNKWFC 25 (152)
T ss_dssp CCEEEETTTTEEEE
T ss_pred ccEeEcCCCCcEee
Confidence 34455666666664
No 205
>KOG4377|consensus
Probab=20.62 E-value=61 Score=31.52 Aligned_cols=21 Identities=24% Similarity=0.300 Sum_probs=17.7
Q ss_pred ccccccCChhHHHHHHhhhcC
Q psy18241 121 ICGLALTTKSHLNRHMLVHTG 141 (566)
Q Consensus 121 ~C~~~f~~~~~L~~H~~~h~~ 141 (566)
-|+.++.+.+.+..|.+.|..
T Consensus 408 Gc~~tl~s~sqm~shkrkheR 428 (480)
T KOG4377|consen 408 GCEATLYSVSQMASHKRKHER 428 (480)
T ss_pred CCceEEEehhhhhhhhhhhhh
Confidence 488899999999999988853
No 206
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=20.51 E-value=69 Score=21.25 Aligned_cols=10 Identities=30% Similarity=1.142 Sum_probs=4.5
Q ss_pred cCcccccccc
Q psy18241 479 QCTTCGKRLR 488 (566)
Q Consensus 479 ~C~~C~k~f~ 488 (566)
+|+.||-.+.
T Consensus 30 ~C~~Cgh~w~ 39 (55)
T PF14311_consen 30 KCPKCGHEWK 39 (55)
T ss_pred ECCCCCCeeE
Confidence 4444444443
No 207
>KOG2272|consensus
Probab=20.50 E-value=43 Score=30.00 Aligned_cols=129 Identities=19% Similarity=0.346 Sum_probs=0.0
Q ss_pred CCceeCCcccccccChhHHHHHhhhh----------CCCCccccCccCCccCchHHHHHHHhhcCCCCCccCCccccccC
Q psy18241 2 PLIHECPTCGKKWRTVSELNAHIQTH----------SDLRPFVCEICGQGYKMKKALLVHVGMHSGIHPFTCHFCNKSFT 71 (566)
Q Consensus 2 ~~~~~C~~C~~~f~~~~~L~~H~~~h----------~~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f~ 71 (566)
|.-|.|++|++...+...++.--+.- .+...|.|..|...... ..|.---..-++.. |+|..|++...
T Consensus 97 p~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~-~~l~fr~d~yH~yH-FkCt~C~keL~ 174 (332)
T KOG2272|consen 97 PACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDE-QPLTFRGDPYHPYH-FKCTTCGKELT 174 (332)
T ss_pred cccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhccc-ccccccCCCCCccc-eeccccccccc
Q ss_pred CchhHHHH----HhhhcCCCceeCCcCcccccchhhhHHHHhhhcCCCcccCCccccccCChhHHHH
Q psy18241 72 QKIGLVKH----LNIHNGTKKYQCHLCGKGFIHHTSYKFHQLVHSGERNVKCDICGLALTTKSHLNR 134 (566)
Q Consensus 72 ~~~~L~~H----~~~h~~~~~~~C~~C~k~F~~~~~l~~H~~~h~~~~~~~C~~C~~~f~~~~~L~~ 134 (566)
+-+.-.+= ++-|..-+--.|-.|.+.-..+.....=..+|..- |.|..|.+.|.--..+.+
T Consensus 175 sdaRevk~eLyClrChD~mgipiCgaC~rpIeervi~amgKhWHveH--FvCa~CekPFlGHrHYEk 239 (332)
T KOG2272|consen 175 SDAREVKGELYCLRCHDKMGIPICGACRRPIEERVIFAMGKHWHVEH--FVCAKCEKPFLGHRHYEK 239 (332)
T ss_pred chhhhhccceeccccccccCCcccccccCchHHHHHHHhccccchhh--eeehhcCCcccchhhhhh
No 208
>KOG3507|consensus
Probab=20.42 E-value=53 Score=22.00 Aligned_cols=10 Identities=30% Similarity=0.727 Sum_probs=4.8
Q ss_pred ccccCccCCc
Q psy18241 32 PFVCEICGQG 41 (566)
Q Consensus 32 ~~~C~~C~~~ 41 (566)
.+.|..||..
T Consensus 37 ~irCReCG~R 46 (62)
T KOG3507|consen 37 VIRCRECGYR 46 (62)
T ss_pred cEehhhcchH
Confidence 4455555543
No 209
>KOG2071|consensus
Probab=20.31 E-value=58 Score=33.54 Aligned_cols=24 Identities=25% Similarity=0.605 Sum_probs=12.0
Q ss_pred CccCCCCCCcccCchhHHhHhhhc
Q psy18241 506 PFVCEICGQGYKMKKALLVHVGMH 529 (566)
Q Consensus 506 ~~~C~~C~~~f~~~~~L~~H~~~H 529 (566)
|.+|..||..|........||-.|
T Consensus 418 pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 418 PNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred cchhcccccccccchhhhhHhhhh
Confidence 344555555555555555555444
Done!