Query psy677
Match_columns 451
No_of_seqs 333 out of 1779
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 17:57:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy677.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/677hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.8 1.1E-20 2.4E-25 184.3 8.6 138 288-429 131-271 (279)
2 KOG2462|consensus 99.7 2.3E-18 5.1E-23 168.1 2.6 81 313-395 185-265 (279)
3 KOG3576|consensus 99.5 3.7E-15 7.9E-20 140.3 4.5 97 312-410 114-221 (267)
4 KOG3623|consensus 99.5 1.1E-14 2.4E-19 156.2 2.2 81 312-394 891-971 (1007)
5 KOG3576|consensus 99.3 7.8E-13 1.7E-17 124.7 3.7 110 290-401 120-240 (267)
6 KOG3623|consensus 99.2 3E-12 6.6E-17 137.8 1.7 80 313-394 238-330 (1007)
7 KOG1074|consensus 99.2 1.7E-11 3.6E-16 134.0 6.5 51 316-368 354-404 (958)
8 KOG1074|consensus 99.0 8.8E-11 1.9E-15 128.5 0.5 84 313-398 603-693 (958)
9 KOG3608|consensus 98.9 3.2E-10 6.9E-15 114.4 2.8 114 305-422 197-313 (467)
10 KOG3608|consensus 98.9 3.9E-10 8.5E-15 113.7 2.9 112 309-425 231-345 (467)
11 PHA00733 hypothetical protein 98.8 1.6E-09 3.5E-14 96.7 3.5 84 311-398 36-124 (128)
12 PHA02768 hypothetical protein; 98.6 6.5E-09 1.4E-13 79.5 0.7 37 323-361 11-47 (55)
13 PLN03086 PRLI-interacting fact 98.6 3.5E-08 7.7E-13 106.7 5.8 93 313-413 451-553 (567)
14 PHA02768 hypothetical protein; 98.4 2.2E-07 4.7E-12 71.2 2.8 44 345-390 5-48 (55)
15 PF13465 zf-H2C2_2: Zinc-finge 98.3 2.3E-07 5E-12 60.5 1.0 24 361-384 2-25 (26)
16 KOG3993|consensus 98.2 1.4E-07 3.1E-12 97.3 -1.2 86 316-403 268-386 (500)
17 PF13465 zf-H2C2_2: Zinc-finge 98.2 1.1E-06 2.3E-11 57.3 2.1 26 332-357 1-26 (26)
18 PHA00733 hypothetical protein 98.1 8.5E-07 1.8E-11 79.3 0.9 93 330-424 25-122 (128)
19 COG5189 SFP1 Putative transcri 98.1 2.8E-06 6E-11 85.3 4.6 73 312-394 346-419 (423)
20 PLN03086 PRLI-interacting fact 98.0 4.7E-06 1E-10 90.5 5.5 76 314-395 477-562 (567)
21 PHA00732 hypothetical protein 97.9 5.8E-06 1.3E-10 68.0 1.8 48 315-370 1-49 (79)
22 PHA00616 hypothetical protein 97.7 6.2E-06 1.3E-10 60.4 -0.2 33 316-350 2-34 (44)
23 PHA00616 hypothetical protein 97.6 2E-05 4.4E-10 57.8 1.2 34 345-378 1-34 (44)
24 PHA00732 hypothetical protein 97.5 8.5E-05 1.8E-09 61.2 3.1 47 345-397 1-48 (79)
25 PF00096 zf-C2H2: Zinc finger, 97.3 0.00015 3.2E-09 45.2 2.3 23 374-396 1-23 (23)
26 PF05605 zf-Di19: Drought indu 97.3 0.00023 5E-09 54.1 2.9 49 346-397 3-53 (54)
27 PF05605 zf-Di19: Drought indu 97.0 0.00078 1.7E-08 51.2 3.4 51 315-370 2-54 (54)
28 PF13894 zf-C2H2_4: C2H2-type 96.9 0.00078 1.7E-08 41.5 2.6 24 374-397 1-24 (24)
29 PF12756 zf-C2H2_2: C2H2 type 96.8 0.00092 2E-08 55.1 3.1 74 317-397 1-74 (100)
30 KOG3993|consensus 96.7 0.00067 1.5E-08 70.8 1.4 83 345-427 267-382 (500)
31 PF13912 zf-C2H2_6: C2H2-type 96.6 0.00087 1.9E-08 43.4 1.0 25 373-397 1-25 (27)
32 PF00096 zf-C2H2: Zinc finger, 96.2 0.0031 6.8E-08 39.2 1.8 23 316-340 1-23 (23)
33 PRK04860 hypothetical protein; 96.0 0.0022 4.8E-08 59.6 0.9 38 345-386 119-156 (160)
34 smart00355 ZnF_C2H2 zinc finge 96.0 0.0065 1.4E-07 37.6 2.5 24 374-397 1-24 (26)
35 PF09237 GAGA: GAGA factor; I 95.6 0.015 3.2E-07 44.1 3.4 40 362-401 12-52 (54)
36 PF13912 zf-C2H2_6: C2H2-type 95.5 0.0041 8.8E-08 40.2 0.3 18 323-340 7-24 (27)
37 PF13894 zf-C2H2_4: C2H2-type 95.3 0.015 3.2E-07 35.6 2.3 23 316-340 1-23 (24)
38 COG5048 FOG: Zn-finger [Genera 95.2 0.0063 1.4E-07 61.4 0.4 73 314-388 288-368 (467)
39 COG5048 FOG: Zn-finger [Genera 94.4 0.018 3.9E-07 58.1 1.4 57 345-401 289-351 (467)
40 PF12874 zf-met: Zinc-finger o 93.9 0.03 6.6E-07 35.3 1.3 23 374-396 1-23 (25)
41 KOG1146|consensus 93.9 0.063 1.4E-06 63.2 4.6 80 310-395 460-540 (1406)
42 PRK04860 hypothetical protein; 93.8 0.036 7.8E-07 51.6 2.1 40 314-359 118-157 (160)
43 PF13909 zf-H2C2_5: C2H2-type 93.7 0.071 1.5E-06 33.5 2.7 23 374-397 1-23 (24)
44 KOG4173|consensus 93.4 0.015 3.2E-07 55.9 -1.2 83 313-398 77-172 (253)
45 smart00355 ZnF_C2H2 zinc finge 92.8 0.11 2.4E-06 31.9 2.5 24 316-341 1-24 (26)
46 PF09237 GAGA: GAGA factor; I 91.7 0.23 5.1E-06 37.8 3.5 32 312-345 21-52 (54)
47 PF12171 zf-C2H2_jaz: Zinc-fin 91.0 0.055 1.2E-06 35.1 -0.4 21 374-394 2-22 (27)
48 COG5236 Uncharacterized conser 90.4 0.29 6.2E-06 50.6 3.9 106 315-423 151-273 (493)
49 PF12171 zf-C2H2_jaz: Zinc-fin 89.7 0.15 3.2E-06 33.1 0.8 22 346-367 2-23 (27)
50 PF12874 zf-met: Zinc-finger o 89.2 0.2 4.4E-06 31.5 1.2 23 316-340 1-23 (25)
51 COG5189 SFP1 Putative transcri 88.6 0.17 3.8E-06 51.6 0.9 43 370-412 346-409 (423)
52 KOG2231|consensus 88.5 0.34 7.4E-06 54.1 3.1 46 347-396 184-235 (669)
53 smart00451 ZnF_U1 U1-like zinc 86.8 0.73 1.6E-05 31.1 2.8 22 373-394 3-24 (35)
54 PF13913 zf-C2HC_2: zinc-finge 86.6 0.61 1.3E-05 30.1 2.2 21 374-395 3-23 (25)
55 PF13909 zf-H2C2_5: C2H2-type 84.4 0.9 2E-05 28.4 2.2 23 316-341 1-23 (24)
56 KOG2186|consensus 84.0 0.67 1.5E-05 46.1 2.2 49 346-397 4-52 (276)
57 KOG2231|consensus 83.4 0.83 1.8E-05 51.2 2.8 69 326-397 123-206 (669)
58 KOG2893|consensus 83.1 0.26 5.6E-06 48.6 -1.1 45 313-364 9-53 (341)
59 KOG4167|consensus 83.0 0.68 1.5E-05 51.9 2.0 25 373-397 792-816 (907)
60 KOG2893|consensus 80.6 0.94 2E-05 44.8 1.8 42 347-392 12-53 (341)
61 KOG2482|consensus 79.9 0.96 2.1E-05 46.8 1.6 23 315-339 195-217 (423)
62 PF13913 zf-C2HC_2: zinc-finge 76.4 1.1 2.3E-05 28.9 0.5 14 323-337 8-21 (25)
63 KOG4124|consensus 75.7 0.48 1E-05 49.0 -1.9 73 312-393 346-418 (442)
64 COG4049 Uncharacterized protei 75.6 2.7 5.8E-05 32.7 2.6 27 368-394 12-38 (65)
65 PF09986 DUF2225: Uncharacteri 75.2 1.4 3.1E-05 42.6 1.4 42 344-385 4-60 (214)
66 KOG1146|consensus 72.0 1.6 3.5E-05 52.0 0.9 76 316-398 1261-1353(1406)
67 cd00350 rubredoxin_like Rubred 69.3 2.8 6.1E-05 28.7 1.3 9 372-380 16-24 (33)
68 smart00451 ZnF_U1 U1-like zinc 69.3 4.1 8.9E-05 27.3 2.1 23 315-339 3-25 (35)
69 TIGR00622 ssl1 transcription f 68.2 7.5 0.00016 34.3 4.0 78 314-397 14-105 (112)
70 PF12013 DUF3505: Protein of u 67.1 6.4 0.00014 33.8 3.4 25 374-398 81-109 (109)
71 PF09538 FYDLN_acid: Protein o 66.8 3.4 7.4E-05 36.1 1.7 15 344-358 25-39 (108)
72 PF12756 zf-C2H2_2: C2H2 type 66.6 4.7 0.0001 32.8 2.4 24 315-340 50-73 (100)
73 COG1997 RPL43A Ribosomal prote 65.1 3.9 8.5E-05 34.5 1.6 32 344-385 34-65 (89)
74 PF05443 ROS_MUCR: ROS/MUCR tr 64.3 3.7 7.9E-05 37.2 1.4 27 372-401 71-97 (132)
75 smart00531 TFIIE Transcription 63.9 5.7 0.00012 36.2 2.6 39 342-384 96-134 (147)
76 PRK00464 nrdR transcriptional 63.4 3.8 8.3E-05 38.0 1.4 16 346-361 29-44 (154)
77 KOG2482|consensus 61.4 6.4 0.00014 40.9 2.7 55 345-399 144-223 (423)
78 KOG2785|consensus 61.1 4.6 9.9E-05 42.4 1.6 76 316-398 167-247 (390)
79 TIGR00373 conserved hypothetic 60.1 6.1 0.00013 36.6 2.1 34 342-384 106-139 (158)
80 COG5236 Uncharacterized conser 58.6 9.1 0.0002 39.9 3.2 73 317-396 222-305 (493)
81 PF02892 zf-BED: BED zinc fing 58.2 6.7 0.00015 28.0 1.6 25 370-394 13-41 (45)
82 TIGR02098 MJ0042_CXXC MJ0042 f 57.0 7.1 0.00015 27.1 1.5 34 346-384 3-36 (38)
83 smart00614 ZnF_BED BED zinc fi 55.6 8.5 0.00018 28.5 1.9 23 374-396 19-47 (50)
84 COG4049 Uncharacterized protei 54.9 3.1 6.6E-05 32.4 -0.7 26 312-339 14-39 (65)
85 PRK06266 transcription initiat 54.7 7.7 0.00017 36.7 1.9 34 343-385 115-148 (178)
86 KOG2186|consensus 53.3 7 0.00015 39.1 1.4 47 316-367 4-50 (276)
87 PF13719 zinc_ribbon_5: zinc-r 53.1 10 0.00022 26.7 1.8 34 346-384 3-36 (37)
88 KOG2593|consensus 52.8 11 0.00023 40.4 2.7 38 342-382 125-162 (436)
89 TIGR02300 FYDLN_acid conserved 51.0 9.3 0.0002 34.4 1.7 15 372-386 25-39 (129)
90 PF13717 zinc_ribbon_4: zinc-r 50.8 12 0.00026 26.2 1.9 33 346-383 3-35 (36)
91 PF09538 FYDLN_acid: Protein o 50.6 13 0.00029 32.5 2.5 30 346-386 10-39 (108)
92 PRK00398 rpoP DNA-directed RNA 49.3 9.4 0.0002 27.8 1.2 12 345-356 3-14 (46)
93 smart00834 CxxC_CXXC_SSSS Puta 49.0 7.9 0.00017 27.0 0.8 29 346-381 6-34 (41)
94 PRK09678 DNA-binding transcrip 48.6 9.7 0.00021 31.0 1.3 16 343-358 25-42 (72)
95 PF14353 CpXC: CpXC protein 48.3 4.9 0.00011 35.4 -0.5 19 374-392 39-57 (128)
96 cd00729 rubredoxin_SM Rubredox 48.0 11 0.00023 26.1 1.2 9 373-381 18-26 (34)
97 KOG2785|consensus 47.7 14 0.00029 39.0 2.5 24 344-367 216-242 (390)
98 PF12013 DUF3505: Protein of u 46.2 19 0.00041 30.9 2.8 25 346-370 81-109 (109)
99 TIGR02605 CxxC_CxxC_SSSS putat 46.0 9.3 0.0002 28.3 0.8 11 346-356 6-16 (52)
100 KOG0782|consensus 45.0 7.5 0.00016 42.9 0.2 53 329-387 237-290 (1004)
101 COG1592 Rubrerythrin [Energy p 44.5 13 0.00029 34.9 1.7 24 344-380 133-156 (166)
102 COG4957 Predicted transcriptio 43.8 9.7 0.00021 34.7 0.7 27 374-403 77-103 (148)
103 KOG2071|consensus 43.8 19 0.0004 40.0 2.9 27 313-341 416-442 (579)
104 PF09723 Zn-ribbon_8: Zinc rib 42.2 12 0.00027 26.9 0.9 29 346-381 6-34 (42)
105 COG1198 PriA Primosomal protei 42.0 17 0.00038 41.6 2.4 37 346-382 445-484 (730)
106 PF04959 ARS2: Arsenite-resist 41.6 23 0.0005 34.7 2.9 33 370-402 74-106 (214)
107 PF09986 DUF2225: Uncharacteri 41.1 4.6 0.0001 39.1 -2.0 44 313-358 3-61 (214)
108 smart00659 RPOLCX RNA polymera 39.5 21 0.00045 26.2 1.7 11 346-356 3-13 (44)
109 PF12760 Zn_Tnp_IS1595: Transp 38.7 57 0.0012 23.7 4.0 27 346-381 19-45 (46)
110 TIGR02300 FYDLN_acid conserved 37.4 28 0.00061 31.4 2.5 34 316-362 10-43 (129)
111 COG1996 RPC10 DNA-directed RNA 37.1 19 0.00041 27.3 1.2 11 345-355 6-16 (49)
112 COG4957 Predicted transcriptio 37.0 36 0.00079 31.1 3.2 26 313-343 74-99 (148)
113 PHA00626 hypothetical protein 36.3 25 0.00054 27.4 1.8 14 372-385 22-35 (59)
114 PF02176 zf-TRAF: TRAF-type zi 35.6 16 0.00036 27.4 0.7 42 344-386 8-55 (60)
115 PF04959 ARS2: Arsenite-resist 34.5 6.5 0.00014 38.4 -2.1 27 345-371 77-103 (214)
116 COG2888 Predicted Zn-ribbon RN 33.8 24 0.00052 27.8 1.3 32 345-381 27-58 (61)
117 PF07800 DUF1644: Protein of u 33.2 1.3E+02 0.0028 28.3 6.2 85 311-402 25-138 (162)
118 smart00440 ZnF_C2C2 C2C2 Zinc 32.5 22 0.00047 25.4 0.9 12 373-384 28-39 (40)
119 COG5151 SSL1 RNA polymerase II 31.6 47 0.001 34.4 3.3 49 347-397 364-412 (421)
120 KOG0978|consensus 31.6 29 0.00062 39.5 2.0 20 373-392 678-697 (698)
121 TIGR00373 conserved hypothetic 31.5 25 0.00054 32.5 1.3 33 313-356 107-139 (158)
122 KOG4173|consensus 30.7 17 0.00036 35.5 0.0 75 344-421 78-166 (253)
123 PRK06266 transcription initiat 30.4 27 0.00058 33.1 1.4 34 313-357 115-148 (178)
124 PTZ00255 60S ribosomal protein 29.8 29 0.00063 29.5 1.3 32 344-385 35-66 (90)
125 smart00734 ZnF_Rad18 Rad18-lik 29.7 48 0.001 21.5 2.1 20 375-395 3-22 (26)
126 PF01096 TFIIS_C: Transcriptio 28.8 14 0.0003 26.3 -0.7 12 373-384 28-39 (39)
127 COG1592 Rubrerythrin [Energy p 28.7 35 0.00075 32.2 1.8 24 315-353 134-157 (166)
128 PRK14890 putative Zn-ribbon RN 28.5 38 0.00083 26.6 1.7 31 345-381 25-56 (59)
129 TIGR00280 L37a ribosomal prote 28.5 27 0.00058 29.8 0.9 32 344-385 34-65 (91)
130 COG4530 Uncharacterized protei 28.2 31 0.00068 30.5 1.2 28 347-385 11-38 (129)
131 KOG4377|consensus 27.8 41 0.00088 36.0 2.2 68 314-384 270-360 (480)
132 KOG2461|consensus 27.8 3.1E+02 0.0067 29.4 8.8 57 325-381 339-395 (396)
133 PF01927 Mut7-C: Mut7-C RNAse 26.2 55 0.0012 29.7 2.6 48 346-393 92-144 (147)
134 COG1327 Predicted transcriptio 25.9 34 0.00073 31.8 1.1 17 344-360 27-43 (156)
135 COG3357 Predicted transcriptio 25.9 37 0.00081 29.0 1.3 28 344-381 57-84 (97)
136 PF05443 ROS_MUCR: ROS/MUCR tr 25.6 46 0.00099 30.2 1.9 29 311-344 68-96 (132)
137 smart00531 TFIIE Transcription 25.5 54 0.0012 29.8 2.4 38 313-356 97-134 (147)
138 PF01780 Ribosomal_L37ae: Ribo 25.1 25 0.00053 29.9 0.1 31 344-384 34-64 (90)
139 PRK03976 rpl37ae 50S ribosomal 24.9 34 0.00073 29.1 0.8 32 344-385 35-66 (90)
140 PF10263 SprT-like: SprT-like 24.7 30 0.00066 31.0 0.6 32 345-384 123-154 (157)
141 PF15135 UPF0515: Uncharacteri 24.6 53 0.0011 33.0 2.2 63 308-385 105-167 (278)
142 KOG2071|consensus 24.5 41 0.00089 37.5 1.6 29 371-399 416-444 (579)
143 KOG4377|consensus 24.3 32 0.0007 36.7 0.8 82 315-399 313-429 (480)
144 KOG0978|consensus 23.9 20 0.00042 40.8 -0.9 48 316-365 644-698 (698)
145 KOG4124|consensus 23.8 28 0.00061 36.5 0.2 21 373-393 349-371 (442)
146 COG1655 Uncharacterized protei 23.7 29 0.00063 34.4 0.3 39 343-381 17-70 (267)
147 TIGR00244 transcriptional regu 23.4 43 0.00092 31.0 1.3 19 344-362 27-45 (147)
148 COG3091 SprT Zn-dependent meta 23.2 41 0.00089 31.3 1.1 32 345-381 117-148 (156)
149 PRK03824 hypA hydrogenase nick 22.9 42 0.00092 30.2 1.2 13 345-357 70-82 (135)
150 COG1779 C4-type Zn-finger prot 22.8 38 0.00082 32.8 0.8 9 375-383 45-53 (201)
151 PF13878 zf-C2H2_3: zinc-finge 22.5 92 0.002 22.4 2.6 24 374-397 14-39 (41)
152 COG4888 Uncharacterized Zn rib 22.1 33 0.00072 29.8 0.3 38 343-384 20-57 (104)
153 COG3677 Transposase and inacti 21.1 99 0.0021 27.8 3.1 46 334-386 21-66 (129)
154 PF06524 NOA36: NOA36 protein; 21.0 37 0.00081 34.3 0.5 86 309-397 136-233 (314)
155 KOG3408|consensus 20.2 46 0.001 29.9 0.8 26 370-395 54-79 (129)
156 PF05191 ADK_lid: Adenylate ki 20.1 34 0.00074 24.0 -0.0 9 347-355 3-11 (36)
157 PF01363 FYVE: FYVE zinc finge 20.1 57 0.0012 25.3 1.2 14 344-357 24-37 (69)
No 1
>KOG2462|consensus
Probab=99.83 E-value=1.1e-20 Score=184.34 Aligned_cols=138 Identities=28% Similarity=0.490 Sum_probs=119.6
Q ss_pred CCCCCCcCCCCCCCCCCCCCCCCCC---CCCccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchhhhh
Q psy677 288 SPLPLKLVPVKPRKYPNRPSKTPVH---ERPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTH 364 (451)
Q Consensus 288 s~~p~~~~p~~~~~~p~~~skt~~~---eKpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H 364 (451)
..++.+...-.......++..+|.. .+-|.|++ |+|.|.+-..|+.|+|+|+ -+++|.+|||.|.+.-.|..|
T Consensus 131 ~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~--C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGH 206 (279)
T KOG2462|consen 131 YKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKY--CGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGH 206 (279)
T ss_pred eeccccccccccccccchhhcccccccccccccCCC--CCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcc
Confidence 4455555555555556666666643 56789954 9999999999999999996 689999999999999999999
Q ss_pred hhcccCCCceecCCCCCccCChHHHHHHHHHHhCcccchHHHHHHHHHHHHHHHHHHHHHhhhhc
Q psy677 365 IRTHTGEKPFSCDVCGRKFARSDEKKRHAKVHLKQRSKKESKMAVMMSQQQAQQQQQQNHVHQQQ 429 (451)
Q Consensus 365 ~rtHtGeKPfkC~~CgK~Fs~~s~Lk~HlrtH~~er~~k~~~~~~~~~qqq~qqqhQqn~~~~~~ 429 (451)
+|+|||||||.|..|+|+|+.+++|+.||.+|.+.|.|+|..|++.|+....+.+|.+.......
T Consensus 207 iRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES~C~~~~ 271 (279)
T KOG2462|consen 207 IRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSESACLKYL 271 (279)
T ss_pred cccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhhcccccc
Confidence 99999999999999999999999999999999999999999999999999999999887654433
No 2
>KOG2462|consensus
Probab=99.71 E-value=2.3e-18 Score=168.14 Aligned_cols=81 Identities=37% Similarity=0.774 Sum_probs=76.7
Q ss_pred CCCccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCChHHHHHH
Q psy677 313 ERPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFARSDEKKRH 392 (451)
Q Consensus 313 eKpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~~s~Lk~H 392 (451)
.-+++|.+ |||.|.+..-|+.|+|+|+|||||.|..|+|+|.++++|+.||.+|.+.|+|+|..|+|.|++++.|.+|
T Consensus 185 ~l~c~C~i--CGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH 262 (279)
T KOG2462|consen 185 TLPCECGI--CGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKH 262 (279)
T ss_pred CCCccccc--ccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHh
Confidence 35677865 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHH
Q psy677 393 AKV 395 (451)
Q Consensus 393 lrt 395 (451)
...
T Consensus 263 ~ES 265 (279)
T KOG2462|consen 263 SES 265 (279)
T ss_pred hhh
Confidence 753
No 3
>KOG3576|consensus
Probab=99.54 E-value=3.7e-15 Score=140.25 Aligned_cols=97 Identities=28% Similarity=0.624 Sum_probs=86.3
Q ss_pred CCCCccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCChHHHHH
Q psy677 312 HERPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFARSDEKKR 391 (451)
Q Consensus 312 ~eKpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~~s~Lk~ 391 (451)
....|.|.+ |+|.|.-..-|.+|++.|...|.|.|..|||.|....+|++|+|+|+|.+||+|..|+|.|.++..|..
T Consensus 114 d~d~ftCrv--CgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsles 191 (267)
T KOG3576|consen 114 DQDSFTCRV--CGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLES 191 (267)
T ss_pred CCCeeeeeh--hhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHH
Confidence 456799976 999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HH-HHHh----------CcccchHHHHHHH
Q psy677 392 HA-KVHL----------KQRSKKESKMAVM 410 (451)
Q Consensus 392 Hl-rtH~----------~er~~k~~~~~~~ 410 (451)
|+ ++|. +.|.|.|+.|+..
T Consensus 192 hl~kvhgv~~~yaykerr~kl~vcedcg~t 221 (267)
T KOG3576|consen 192 HLKKVHGVQHQYAYKERRAKLYVCEDCGYT 221 (267)
T ss_pred HHHHHcCchHHHHHHHhhhheeeecccCCC
Confidence 98 5564 3455667777543
No 4
>KOG3623|consensus
Probab=99.47 E-value=1.1e-14 Score=156.16 Aligned_cols=81 Identities=43% Similarity=0.954 Sum_probs=77.3
Q ss_pred CCCCccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCChHHHHH
Q psy677 312 HERPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFARSDEKKR 391 (451)
Q Consensus 312 ~eKpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~~s~Lk~ 391 (451)
.+..|.| +.|+|.|...+.|.||.-.|+|.|||+|.+|.|+|..+.+|..|+|.|.|||||.|+.|+|+|+....+..
T Consensus 891 e~gmyaC--DqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQ 968 (1007)
T KOG3623|consen 891 EDGMYAC--DQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQ 968 (1007)
T ss_pred ccccchH--HHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHh
Confidence 3567999 66999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHH
Q psy677 392 HAK 394 (451)
Q Consensus 392 Hlr 394 (451)
||.
T Consensus 969 HMN 971 (1007)
T KOG3623|consen 969 HMN 971 (1007)
T ss_pred hhc
Confidence 984
No 5
>KOG3576|consensus
Probab=99.32 E-value=7.8e-13 Score=124.68 Aligned_cols=110 Identities=25% Similarity=0.509 Sum_probs=96.6
Q ss_pred CCCCcCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchhhhhhhccc
Q psy677 290 LPLKLVPVKPRKYPNRPSKTPVHERPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTHIRTHT 369 (451)
Q Consensus 290 ~p~~~~p~~~~~~p~~~skt~~~eKpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H~rtHt 369 (451)
+-++...+.-.++.+++.+-|..-|.|.|.+ |||.|.+.-+|++|+|+|+|.+||+|..|+|+|..+-.|..|.+.-+
T Consensus 120 CrvCgK~F~lQRmlnrh~kch~~vkr~lct~--cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvh 197 (267)
T KOG3576|consen 120 CRVCGKKFGLQRMLNRHLKCHSDVKRHLCTF--CGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVH 197 (267)
T ss_pred eehhhhhhhHHHHHHHHhhhccHHHHHHHhh--ccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHc
Confidence 4455566666677889999999999999966 99999999999999999999999999999999999999999987544
Q ss_pred C-----------CCceecCCCCCccCChHHHHHHHHHHhCccc
Q psy677 370 G-----------EKPFSCDVCGRKFARSDEKKRHAKVHLKQRS 401 (451)
Q Consensus 370 G-----------eKPfkC~~CgK~Fs~~s~Lk~HlrtH~~er~ 401 (451)
| +|.|.|+.||..-.+...+..|++.|+...+
T Consensus 198 gv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 198 GVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred CchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 4 4679999999999999999999999976554
No 6
>KOG3623|consensus
Probab=99.21 E-value=3e-12 Score=137.76 Aligned_cols=80 Identities=34% Similarity=0.807 Sum_probs=72.8
Q ss_pred CCCccCCCCCCCCccCChHHHHHHHHHhcC-------------CCCccCcccccccCCcchhhhhhhcccCCCceecCCC
Q psy677 313 ERPYACPVENCDRRFSRSDELTRHIRIHTG-------------QKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVC 379 (451)
Q Consensus 313 eKpy~C~~e~Cgk~F~s~s~L~rH~r~Htg-------------eKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~C 379 (451)
+..|.|.. |..+|..+..|.+||.+|.. -|.|+|..|+|+|..+.+|+.|+|+|.|||||.|+.|
T Consensus 238 e~nfsC~l--CsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnC 315 (1007)
T KOG3623|consen 238 EPNFSCML--CSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNC 315 (1007)
T ss_pred CCCCcchh--hhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCCcCCccc
Confidence 44588955 99999999999999998862 3679999999999999999999999999999999999
Q ss_pred CCccCChHHHHHHHH
Q psy677 380 GRKFARSDEKKRHAK 394 (451)
Q Consensus 380 gK~Fs~~s~Lk~Hlr 394 (451)
+|+|+....+..||.
T Consensus 316 kKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 316 KKRFSHSGSYSSHMS 330 (1007)
T ss_pred ccccccCCccccccc
Confidence 999999999999983
No 7
>KOG1074|consensus
Probab=99.20 E-value=1.7e-11 Score=134.01 Aligned_cols=51 Identities=37% Similarity=0.850 Sum_probs=32.9
Q ss_pred ccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchhhhhhhcc
Q psy677 316 YACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTHIRTH 368 (451)
Q Consensus 316 y~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H~rtH 368 (451)
++|.+ |.|.|...+.|+.|.|.|+|+|||+|.+|+.+|.++.+|+.|..+|
T Consensus 354 hkCr~--CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH 404 (958)
T KOG1074|consen 354 HKCRF--CAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRH 404 (958)
T ss_pred chhhh--hHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeeeeec
Confidence 45644 6666666666666666666666666666666666666666665444
No 8
>KOG1074|consensus
Probab=98.98 E-value=8.8e-11 Score=128.49 Aligned_cols=84 Identities=36% Similarity=0.805 Sum_probs=77.2
Q ss_pred CCCccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchhhhhhhcccCC----CceecC---CCCCccCC
Q psy677 313 ERPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTHIRTHTGE----KPFSCD---VCGRKFAR 385 (451)
Q Consensus 313 eKpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H~rtHtGe----KPfkC~---~CgK~Fs~ 385 (451)
..+..|.+ |.+...-++.|+.|.|+|+|+|||+|.+|+++|.++.+|+.||.+|... -+|.|+ +|-+.|..
T Consensus 603 TdPNqCii--C~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ic~~kftn 680 (958)
T KOG1074|consen 603 TDPNQCII--CLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFICQKKFTN 680 (958)
T ss_pred CCccceee--eeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhhhcccccc
Confidence 35788976 9999999999999999999999999999999999999999999999653 358899 99999999
Q ss_pred hHHHHHHHHHHhC
Q psy677 386 SDEKKRHAKVHLK 398 (451)
Q Consensus 386 ~s~Lk~HlrtH~~ 398 (451)
.-.|..|+|+|.+
T Consensus 681 ~V~lpQhIriH~~ 693 (958)
T KOG1074|consen 681 AVTLPQHIRIHLG 693 (958)
T ss_pred cccccceEEeecC
Confidence 9999999999983
No 9
>KOG3608|consensus
Probab=98.94 E-value=3.2e-10 Score=114.39 Aligned_cols=114 Identities=23% Similarity=0.472 Sum_probs=70.0
Q ss_pred CCCCCCCCCCCccCCCCCCCCccCChHHHHHHHHHhc--CCCCccCcccccccCCcchhhhhhhcccCCCceecCCCCCc
Q psy677 305 RPSKTPVHERPYACPVENCDRRFSRSDELTRHIRIHT--GQKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRK 382 (451)
Q Consensus 305 ~~skt~~~eKpy~C~~e~Cgk~F~s~s~L~rH~r~Ht--geKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~ 382 (451)
++.++|.++|...|+. ||..|.++..|-.|++..+ ...+|.|..|-|+|.+...|+.|++.|. .-|+|+.|...
T Consensus 197 eH~r~Hs~eKvvACp~--Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHv--n~ykCplCdmt 272 (467)
T KOG3608|consen 197 EHIRTHSNEKVVACPH--CGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHV--NCYKCPLCDMT 272 (467)
T ss_pred HHHHhcCCCeEEecch--HHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhh--hcccccccccC
Confidence 3444555555555532 5555555555555554322 2345666666666666666666665553 23666666666
Q ss_pred cCChHHHHHHHH-HHhCcccchHHHHHHHHHHHHHHHHHHH
Q psy677 383 FARSDEKKRHAK-VHLKQRSKKESKMAVMMSQQQAQQQQQQ 422 (451)
Q Consensus 383 Fs~~s~Lk~Hlr-tH~~er~~k~~~~~~~~~qqq~qqqhQq 422 (451)
....+.|.+|++ .|.+.|++||..|....-....+++|.+
T Consensus 273 c~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~ 313 (467)
T KOG3608|consen 273 CSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQ 313 (467)
T ss_pred CCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHH
Confidence 666677777764 4677888888888877777777777765
No 10
>KOG3608|consensus
Probab=98.93 E-value=3.9e-10 Score=113.74 Aligned_cols=112 Identities=25% Similarity=0.525 Sum_probs=92.0
Q ss_pred CCCCCCCccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchhhhhhh-cccCCCceecCCCCCccCChH
Q psy677 309 TPVHERPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTHIR-THTGEKPFSCDVCGRKFARSD 387 (451)
Q Consensus 309 t~~~eKpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H~r-tHtGeKPfkC~~CgK~Fs~~s 387 (451)
+.....+|.| ..|.|+|.....|+.|++.|. .-|+|+.|.......+.|.+|++ .|..+|||+|+.|.+.|.+..
T Consensus 231 t~l~~n~fqC--~~C~KrFaTeklL~~Hv~rHv--n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~es 306 (467)
T KOG3608|consen 231 TELNTNSFQC--AQCFKRFATEKLLKSHVVRHV--NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRES 306 (467)
T ss_pred hhhcCCchHH--HHHHHHHhHHHHHHHHHHHhh--hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHH
Confidence 3344568999 569999999999999999984 46999999999999999999988 477889999999999999999
Q ss_pred HHHHHHHHHhCcccchHHH--HHHHHHHHHHHHHHHHHHh
Q psy677 388 EKKRHAKVHLKQRSKKESK--MAVMMSQQQAQQQQQQNHV 425 (451)
Q Consensus 388 ~Lk~HlrtH~~er~~k~~~--~~~~~~qqq~qqqhQqn~~ 425 (451)
.|.+|+.+|. +-.|.|+. |-..+...-+++.|-....
T Consensus 307 dL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evh 345 (467)
T KOG3608|consen 307 DLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVH 345 (467)
T ss_pred HHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhc
Confidence 9999999988 66788776 6666666666666655443
No 11
>PHA00733 hypothetical protein
Probab=98.85 E-value=1.6e-09 Score=96.72 Aligned_cols=84 Identities=24% Similarity=0.450 Sum_probs=70.1
Q ss_pred CCCCCccCCCCCCCCccCChHHHHHH--HH---HhcCCCCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCC
Q psy677 311 VHERPYACPVENCDRRFSRSDELTRH--IR---IHTGQKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFAR 385 (451)
Q Consensus 311 ~~eKpy~C~~e~Cgk~F~s~s~L~rH--~r---~HtgeKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~ 385 (451)
...+++.|.+ |.+.|.....|..| ++ .+.+.++|.|+.|++.|.....|..|++.| +++|.|..|++.|..
T Consensus 36 ~~~~~~~~~~--~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~ 111 (128)
T PHA00733 36 PEQKRLIRAV--VKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRN 111 (128)
T ss_pred hhhhhHHHHH--HhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCC
Confidence 3457799965 99998888877766 22 234588999999999999999999999987 467999999999999
Q ss_pred hHHHHHHHHHHhC
Q psy677 386 SDEKKRHAKVHLK 398 (451)
Q Consensus 386 ~s~Lk~HlrtH~~ 398 (451)
...|.+|+...++
T Consensus 112 ~~sL~~H~~~~h~ 124 (128)
T PHA00733 112 TDSTLDHVCKKHN 124 (128)
T ss_pred HHHHHHHHHHhcC
Confidence 9999999976654
No 12
>PHA02768 hypothetical protein; Provisional
Probab=98.65 E-value=6.5e-09 Score=79.49 Aligned_cols=37 Identities=19% Similarity=0.442 Sum_probs=18.7
Q ss_pred CCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchh
Q psy677 323 CDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHL 361 (451)
Q Consensus 323 Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~L 361 (451)
||+.|.+.++|.+|+++|+ ++|+|..|++.|.+.+.|
T Consensus 11 CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 11 CGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred hCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 5555555555555555554 345555555555444433
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.62 E-value=3.5e-08 Score=106.67 Aligned_cols=93 Identities=17% Similarity=0.456 Sum_probs=78.6
Q ss_pred CCCccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccC--------
Q psy677 313 ERPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFA-------- 384 (451)
Q Consensus 313 eKpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs-------- 384 (451)
++.+.|. .|++.|. ...|..|++.|+ ++|.|+ |++.+ .+..|..|+++|.++|++.|..|++.|.
T Consensus 451 ~~H~~C~--~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~ 523 (567)
T PLN03086 451 KNHVHCE--KCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDV 523 (567)
T ss_pred ccCccCC--CCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccch
Confidence 4567895 5999996 678999999985 889999 99765 6689999999999999999999999995
Q ss_pred --ChHHHHHHHHHHhCcccchHHHHHHHHHH
Q psy677 385 --RSDEKKRHAKVHLKQRSKKESKMAVMMSQ 413 (451)
Q Consensus 385 --~~s~Lk~HlrtH~~er~~k~~~~~~~~~q 413 (451)
+...|..|.+++ +.+.+.|..|+..+..
T Consensus 524 ~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrl 553 (567)
T PLN03086 524 RDRLRGMSEHESIC-GSRTAPCDSCGRSVML 553 (567)
T ss_pred hhhhhhHHHHHHhc-CCcceEccccCCeeee
Confidence 245899999986 8999999999765543
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.37 E-value=2.2e-07 Score=71.16 Aligned_cols=44 Identities=25% Similarity=0.532 Sum_probs=40.6
Q ss_pred CccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCChHHHH
Q psy677 345 PFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFARSDEKK 390 (451)
Q Consensus 345 Pf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~~s~Lk 390 (451)
-|.|+.|++.|.+.++|.+|+++|+ ++|+|..|+|.|.+.+.|.
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 3899999999999999999999998 7999999999999887663
No 15
>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=98.29 E-value=2.3e-07 Score=60.49 Aligned_cols=24 Identities=58% Similarity=1.286 Sum_probs=13.0
Q ss_pred hhhhhhcccCCCceecCCCCCccC
Q psy677 361 LTTHIRTHTGEKPFSCDVCGRKFA 384 (451)
Q Consensus 361 Lk~H~rtHtGeKPfkC~~CgK~Fs 384 (451)
|.+|+++|+|+|||.|+.|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 445555555555555555555554
No 16
>KOG3993|consensus
Probab=98.24 E-value=1.4e-07 Score=97.32 Aligned_cols=86 Identities=29% Similarity=0.613 Sum_probs=71.1
Q ss_pred ccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchhhhhhhccc--------CCC---------------
Q psy677 316 YACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTHIRTHT--------GEK--------------- 372 (451)
Q Consensus 316 y~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H~rtHt--------GeK--------------- 372 (451)
|+|.. |...|.+...|.+|+-...-...|+|+.|+|.|....+|..|.|.|. +..
T Consensus 268 yiCqL--CK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea 345 (500)
T KOG3993|consen 268 YICQL--CKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEA 345 (500)
T ss_pred HHHHH--HHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhc
Confidence 99955 99999999999999754333456999999999999999999999874 111
Q ss_pred ----------ceecCCCCCccCChHHHHHHHHHHhCcccch
Q psy677 373 ----------PFSCDVCGRKFARSDEKKRHAKVHLKQRSKK 403 (451)
Q Consensus 373 ----------PfkC~~CgK~Fs~~s~Lk~HlrtH~~er~~k 403 (451)
.|.|.+|+|.|.+...|++|+-+|+....-+
T Consensus 346 ~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k 386 (500)
T KOG3993|consen 346 ERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAK 386 (500)
T ss_pred cccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccch
Confidence 3899999999999999999998887654433
No 17
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.16 E-value=1.1e-06 Score=57.35 Aligned_cols=26 Identities=54% Similarity=1.133 Sum_probs=24.1
Q ss_pred HHHHHHHHhcCCCCccCcccccccCC
Q psy677 332 ELTRHIRIHTGQKPFQCRICMRSFSR 357 (451)
Q Consensus 332 ~L~rH~r~HtgeKPf~C~~C~K~F~~ 357 (451)
+|.+|+++|+++|+|.|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 58999999999999999999999963
No 18
>PHA00733 hypothetical protein
Probab=98.10 E-value=8.5e-07 Score=79.26 Aligned_cols=93 Identities=17% Similarity=0.223 Sum_probs=71.5
Q ss_pred hHHHHHHHHHhcCCCCccCcccccccCCcchhhhh--hh---cccCCCceecCCCCCccCChHHHHHHHHHHhCcccchH
Q psy677 330 SDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTH--IR---THTGEKPFSCDVCGRKFARSDEKKRHAKVHLKQRSKKE 404 (451)
Q Consensus 330 ~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H--~r---tHtGeKPfkC~~CgK~Fs~~s~Lk~HlrtH~~er~~k~ 404 (451)
...|.++-..-...+++.|.+|.+.|.....|..| ++ .+++++||.|..|++.|.....|..|++.| ++.+.|
T Consensus 25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C 102 (128)
T PHA00733 25 LEELKRYHSLTPEQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVC 102 (128)
T ss_pred HHHhhhhhcCChhhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccC
Confidence 34444433332346789999999998887777665 22 234689999999999999999999999987 456899
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q psy677 405 SKMAVMMSQQQAQQQQQQNH 424 (451)
Q Consensus 405 ~~~~~~~~qqq~qqqhQqn~ 424 (451)
..|...|.....+..|+...
T Consensus 103 ~~CgK~F~~~~sL~~H~~~~ 122 (128)
T PHA00733 103 PVCGKEFRNTDSTLDHVCKK 122 (128)
T ss_pred CCCCCccCCHHHHHHHHHHh
Confidence 99999999888888876543
No 19
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=98.10 E-value=2.8e-06 Score=85.33 Aligned_cols=73 Identities=27% Similarity=0.633 Sum_probs=51.1
Q ss_pred CCCCccCCCCCCCCccCChHHHHHHHHH-hcCCCCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCChHHHH
Q psy677 312 HERPYACPVENCDRRFSRSDELTRHIRI-HTGQKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFARSDEKK 390 (451)
Q Consensus 312 ~eKpy~C~~e~Cgk~F~s~s~L~rH~r~-HtgeKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~~s~Lk 390 (451)
.+|||+|++++|.|.|+....|+-||.. |...+...-+ .-..|.-.-...|||+|++|+|+|.....|+
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p----------~p~~~~~F~~~~KPYrCevC~KRYKNlNGLK 415 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENP----------SPEKMNIFSAKDKPYRCEVCDKRYKNLNGLK 415 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCC----------CccccccccccCCceeccccchhhccCccce
Confidence 3599999999999999999999999874 4332222211 1111111123568999999999999888888
Q ss_pred HHHH
Q psy677 391 RHAK 394 (451)
Q Consensus 391 ~Hlr 394 (451)
.|++
T Consensus 416 YHr~ 419 (423)
T COG5189 416 YHRK 419 (423)
T ss_pred eccc
Confidence 8863
No 20
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.05 E-value=4.7e-06 Score=90.50 Aligned_cols=76 Identities=21% Similarity=0.478 Sum_probs=64.8
Q ss_pred CCccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCC----------cchhhhhhhcccCCCceecCCCCCcc
Q psy677 314 RPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSR----------SDHLTTHIRTHTGEKPFSCDVCGRKF 383 (451)
Q Consensus 314 Kpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~----------~s~Lk~H~rtHtGeKPfkC~~CgK~F 383 (451)
+++.| . |++.| .+..|..|+++|...|++.|.+|++.|.. ...|..|..++ |.+++.|..||+.|
T Consensus 477 kpv~C--p-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~V 551 (567)
T PLN03086 477 EPLQC--P-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSV 551 (567)
T ss_pred CCccC--C-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCee
Confidence 78999 4 99765 66899999999999999999999999952 34799999986 99999999999998
Q ss_pred CChHHHHHHHHH
Q psy677 384 ARSDEKKRHAKV 395 (451)
Q Consensus 384 s~~s~Lk~Hlrt 395 (451)
..+ .|..|+..
T Consensus 552 rlr-dm~~H~~~ 562 (567)
T PLN03086 552 MLK-EMDIHQIA 562 (567)
T ss_pred eeh-hHHHHHHH
Confidence 877 46788743
No 21
>PHA00732 hypothetical protein
Probab=97.87 E-value=5.8e-06 Score=68.05 Aligned_cols=48 Identities=25% Similarity=0.496 Sum_probs=37.9
Q ss_pred CccCCCCCCCCccCChHHHHHHHHH-hcCCCCccCcccccccCCcchhhhhhhcccC
Q psy677 315 PYACPVENCDRRFSRSDELTRHIRI-HTGQKPFQCRICMRSFSRSDHLTTHIRTHTG 370 (451)
Q Consensus 315 py~C~~e~Cgk~F~s~s~L~rH~r~-HtgeKPf~C~~C~K~F~~~s~Lk~H~rtHtG 370 (451)
+|.| ..|++.|.+...|.+|++. |. ++.|+.|++.|. .|..|++++.+
T Consensus 1 py~C--~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKC--PICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred CccC--CCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---ChhhhhcccCC
Confidence 5788 5599999999999999985 54 368999999997 57888876643
No 22
>PHA00616 hypothetical protein
Probab=97.73 E-value=6.2e-06 Score=60.45 Aligned_cols=33 Identities=21% Similarity=0.451 Sum_probs=17.4
Q ss_pred ccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcc
Q psy677 316 YACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRI 350 (451)
Q Consensus 316 y~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~ 350 (451)
|.| ..||+.|..+..|.+|++.|+++++|.|+.
T Consensus 2 YqC--~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 2 YQC--LRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred Ccc--chhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 455 335555555555555555555555555543
No 23
>PHA00616 hypothetical protein
Probab=97.63 E-value=2e-05 Score=57.77 Aligned_cols=34 Identities=15% Similarity=0.386 Sum_probs=24.1
Q ss_pred CccCcccccccCCcchhhhhhhcccCCCceecCC
Q psy677 345 PFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDV 378 (451)
Q Consensus 345 Pf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~ 378 (451)
||+|..||+.|..+..|.+|++.|+|+++|.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 4677777777777777777777777777776654
No 24
>PHA00732 hypothetical protein
Probab=97.48 E-value=8.5e-05 Score=61.18 Aligned_cols=47 Identities=30% Similarity=0.512 Sum_probs=40.3
Q ss_pred CccCcccccccCCcchhhhhhhc-ccCCCceecCCCCCccCChHHHHHHHHHHh
Q psy677 345 PFQCRICMRSFSRSDHLTTHIRT-HTGEKPFSCDVCGRKFARSDEKKRHAKVHL 397 (451)
Q Consensus 345 Pf~C~~C~K~F~~~s~Lk~H~rt-HtGeKPfkC~~CgK~Fs~~s~Lk~HlrtH~ 397 (451)
||.|..|++.|.+...|++|++. |.+ +.|+.|++.|.+ |..|.+++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~~---l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYRR---LNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeCC---hhhhhcccC
Confidence 58999999999999999999985 653 689999999984 788886654
No 25
>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=97.34 E-value=0.00015 Score=45.22 Aligned_cols=23 Identities=35% Similarity=0.973 Sum_probs=20.0
Q ss_pred eecCCCCCccCChHHHHHHHHHH
Q psy677 374 FSCDVCGRKFARSDEKKRHAKVH 396 (451)
Q Consensus 374 fkC~~CgK~Fs~~s~Lk~HlrtH 396 (451)
|.|..|++.|.+...|.+|++.|
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 68889999999999999998875
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=97.25 E-value=0.00023 Score=54.11 Aligned_cols=49 Identities=24% Similarity=0.517 Sum_probs=23.1
Q ss_pred ccCcccccccCCcchhhhhhhc-ccC-CCceecCCCCCccCChHHHHHHHHHHh
Q psy677 346 FQCRICMRSFSRSDHLTTHIRT-HTG-EKPFSCDVCGRKFARSDEKKRHAKVHL 397 (451)
Q Consensus 346 f~C~~C~K~F~~~s~Lk~H~rt-HtG-eKPfkC~~CgK~Fs~~s~Lk~HlrtH~ 397 (451)
|.|++|++ ..+...|..|... |.. .+.+.|++|...+. .+|.+|++.++
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 45555555 3334445555443 222 23455555555433 25666665443
No 27
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=96.96 E-value=0.00078 Score=51.18 Aligned_cols=51 Identities=25% Similarity=0.597 Sum_probs=39.8
Q ss_pred CccCCCCCCCCccCChHHHHHHHHH-hcCC-CCccCcccccccCCcchhhhhhhcccC
Q psy677 315 PYACPVENCDRRFSRSDELTRHIRI-HTGQ-KPFQCRICMRSFSRSDHLTTHIRTHTG 370 (451)
Q Consensus 315 py~C~~e~Cgk~F~s~s~L~rH~r~-Htge-KPf~C~~C~K~F~~~s~Lk~H~rtHtG 370 (451)
-|.|++ |++ ..+...|..|... |..+ +.+.|++|...+. .+|.+|++.+++
T Consensus 2 ~f~CP~--C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPY--CGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQHR 54 (54)
T ss_pred CcCCCC--CCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhcC
Confidence 388977 999 5567889999876 5543 5799999998765 489999987653
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=96.93 E-value=0.00078 Score=41.54 Aligned_cols=24 Identities=33% Similarity=0.924 Sum_probs=18.7
Q ss_pred eecCCCCCccCChHHHHHHHHHHh
Q psy677 374 FSCDVCGRKFARSDEKKRHAKVHL 397 (451)
Q Consensus 374 fkC~~CgK~Fs~~s~Lk~HlrtH~ 397 (451)
|.|++|++.|.....|..|+++|+
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 678899999999999999988774
No 29
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.83 E-value=0.00092 Score=55.14 Aligned_cols=74 Identities=22% Similarity=0.518 Sum_probs=22.3
Q ss_pred cCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCChHHHHHHHHHH
Q psy677 317 ACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFARSDEKKRHAKVH 396 (451)
Q Consensus 317 ~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~~s~Lk~HlrtH 396 (451)
.|.+ |+..|.+...|..||...++-. .. ....+.....+..+.+... ...+.|..|++.|.....|..|++.+
T Consensus 1 ~C~~--C~~~f~~~~~l~~H~~~~H~~~---~~-~~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLF--CDESFSSVDDLLQHMKKKHGFD---IP-DQKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cccc--cccccccccccccccccccccc---cc-ccccccccccccccccccc-CCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 3755 9999999999999997644321 11 1122234444444444322 23799999999999999999999875
Q ss_pred h
Q psy677 397 L 397 (451)
Q Consensus 397 ~ 397 (451)
.
T Consensus 74 ~ 74 (100)
T PF12756_consen 74 H 74 (100)
T ss_dssp T
T ss_pred c
Confidence 3
No 30
>KOG3993|consensus
Probab=96.68 E-value=0.00067 Score=70.77 Aligned_cols=83 Identities=14% Similarity=0.283 Sum_probs=67.3
Q ss_pred CccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCChHHHHHHHHHHhC--------------------------
Q psy677 345 PFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFARSDEKKRHAKVHLK-------------------------- 398 (451)
Q Consensus 345 Pf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~~s~Lk~HlrtH~~-------------------------- 398 (451)
-|.|..|...|.+...|.+|..--.-..-|+|..|+|.|+-..+|..|+|.|.-
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 499999999999999999997532222449999999999999999999999851
Q ss_pred -------cccchHHHHHHHHHHHHHHHHHHHHHhhh
Q psy677 399 -------QRSKKESKMAVMMSQQQAQQQQQQNHVHQ 427 (451)
Q Consensus 399 -------er~~k~~~~~~~~~qqq~qqqhQqn~~~~ 427 (451)
+..|.|..|.+.|..|.-++.||-.....
T Consensus 347 rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~ 382 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRA 382 (500)
T ss_pred ccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhcc
Confidence 12477899999999998888886554433
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=96.60 E-value=0.00087 Score=43.37 Aligned_cols=25 Identities=36% Similarity=0.921 Sum_probs=20.1
Q ss_pred ceecCCCCCccCChHHHHHHHHHHh
Q psy677 373 PFSCDVCGRKFARSDEKKRHAKVHL 397 (451)
Q Consensus 373 PfkC~~CgK~Fs~~s~Lk~HlrtH~ 397 (451)
+|.|..|++.|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 5788888888888888888887765
No 32
>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=96.19 E-value=0.0031 Score=39.15 Aligned_cols=23 Identities=48% Similarity=1.070 Sum_probs=15.3
Q ss_pred ccCCCCCCCCccCChHHHHHHHHHh
Q psy677 316 YACPVENCDRRFSRSDELTRHIRIH 340 (451)
Q Consensus 316 y~C~~e~Cgk~F~s~s~L~rH~r~H 340 (451)
|.|. .|++.|.+...|.+|++.|
T Consensus 1 y~C~--~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCP--ICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEET--TTTEEESSHHHHHHHHHHH
T ss_pred CCCC--CCCCccCCHHHHHHHHhHC
Confidence 4563 4777777777777777654
No 33
>PRK04860 hypothetical protein; Provisional
Probab=96.04 E-value=0.0022 Score=59.59 Aligned_cols=38 Identities=26% Similarity=0.725 Sum_probs=25.8
Q ss_pred CccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCCh
Q psy677 345 PFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFARS 386 (451)
Q Consensus 345 Pf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~~ 386 (451)
+|.|. |++ ....+++|.++|+|+++|+|..|++.|...
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 46776 765 555667777777777777777777766543
No 34
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.96 E-value=0.0065 Score=37.64 Aligned_cols=24 Identities=29% Similarity=0.764 Sum_probs=20.0
Q ss_pred eecCCCCCccCChHHHHHHHHHHh
Q psy677 374 FSCDVCGRKFARSDEKKRHAKVHL 397 (451)
Q Consensus 374 fkC~~CgK~Fs~~s~Lk~HlrtH~ 397 (451)
|+|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 578888888888888888888764
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=95.57 E-value=0.015 Score=44.12 Aligned_cols=40 Identities=23% Similarity=0.555 Sum_probs=24.3
Q ss_pred hhhhhcc-cCCCceecCCCCCccCChHHHHHHHHHHhCccc
Q psy677 362 TTHIRTH-TGEKPFSCDVCGRKFARSDEKKRHAKVHLKQRS 401 (451)
Q Consensus 362 k~H~rtH-tGeKPfkC~~CgK~Fs~~s~Lk~HlrtH~~er~ 401 (451)
..+.+.| ..+.|..|++|+..+.+..+|++|+..+++.|+
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 356789999999999999999999988887664
No 36
>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=95.54 E-value=0.0041 Score=40.17 Aligned_cols=18 Identities=39% Similarity=0.713 Sum_probs=9.2
Q ss_pred CCCccCChHHHHHHHHHh
Q psy677 323 CDRRFSRSDELTRHIRIH 340 (451)
Q Consensus 323 Cgk~F~s~s~L~rH~r~H 340 (451)
|++.|.+...|..|++.|
T Consensus 7 C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 7 CGKTFSSLSALREHKRSH 24 (27)
T ss_dssp TTEEESSHHHHHHHHCTT
T ss_pred cCCccCChhHHHHHhHHh
Confidence 555555555555555443
No 37
>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=95.30 E-value=0.015 Score=35.63 Aligned_cols=23 Identities=39% Similarity=1.099 Sum_probs=14.0
Q ss_pred ccCCCCCCCCccCChHHHHHHHHHh
Q psy677 316 YACPVENCDRRFSRSDELTRHIRIH 340 (451)
Q Consensus 316 y~C~~e~Cgk~F~s~s~L~rH~r~H 340 (451)
|.|.+ |++.|.+...|..|++.|
T Consensus 1 ~~C~~--C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPI--CGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SS--TS-EESSHHHHHHHHHHH
T ss_pred CCCcC--CCCcCCcHHHHHHHHHhh
Confidence 45644 777777777777777665
No 38
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.16 E-value=0.0063 Score=61.37 Aligned_cols=73 Identities=41% Similarity=0.716 Sum_probs=58.9
Q ss_pred CCccCCCCCCCCccCChHHHHHHHH--HhcCC--CCccCc--ccccccCCcchhhhhhhcccCCCceecCC--CCCccCC
Q psy677 314 RPYACPVENCDRRFSRSDELTRHIR--IHTGQ--KPFQCR--ICMRSFSRSDHLTTHIRTHTGEKPFSCDV--CGRKFAR 385 (451)
Q Consensus 314 Kpy~C~~e~Cgk~F~s~s~L~rH~r--~Htge--KPf~C~--~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~--CgK~Fs~ 385 (451)
.++.| ..|...|.+...|.+|.+ .|.++ +++.|+ .|++.|.+...+.+|..+|++.++++|.. |.+.+..
T Consensus 288 ~~~~~--~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 365 (467)
T COG5048 288 LPIKS--KQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSP 365 (467)
T ss_pred cCCCC--ccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccccc
Confidence 45677 559999999999999999 79888 899999 79999999999999999999888888754 5555554
Q ss_pred hHH
Q psy677 386 SDE 388 (451)
Q Consensus 386 ~s~ 388 (451)
...
T Consensus 366 ~~~ 368 (467)
T COG5048 366 LLN 368 (467)
T ss_pred ccC
Confidence 433
No 39
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.39 E-value=0.018 Score=58.08 Aligned_cols=57 Identities=49% Similarity=0.918 Sum_probs=28.8
Q ss_pred CccCcccccccCCcchhhhhhh--cccCC--CceecC--CCCCccCChHHHHHHHHHHhCccc
Q psy677 345 PFQCRICMRSFSRSDHLTTHIR--THTGE--KPFSCD--VCGRKFARSDEKKRHAKVHLKQRS 401 (451)
Q Consensus 345 Pf~C~~C~K~F~~~s~Lk~H~r--tHtGe--KPfkC~--~CgK~Fs~~s~Lk~HlrtH~~er~ 401 (451)
++.|..|...|.+...|.+|.+ .|.++ ++|.|. .|++.|.+...+.+|..+|.+.+.
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~ 351 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISP 351 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCc
Confidence 3445555555555555555555 45555 555555 455555555555555555544443
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=93.91 E-value=0.03 Score=35.34 Aligned_cols=23 Identities=26% Similarity=0.852 Sum_probs=18.2
Q ss_pred eecCCCCCccCChHHHHHHHHHH
Q psy677 374 FSCDVCGRKFARSDEKKRHAKVH 396 (451)
Q Consensus 374 fkC~~CgK~Fs~~s~Lk~HlrtH 396 (451)
|.|.+|++.|.....|..|++.+
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 67888888888888888887543
No 41
>KOG1146|consensus
Probab=93.85 E-value=0.063 Score=63.18 Aligned_cols=80 Identities=18% Similarity=0.375 Sum_probs=51.9
Q ss_pred CCCCCCccCCCCCCCCccCChHHHHHHHHH-hcCCCCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCChHH
Q psy677 310 PVHERPYACPVENCDRRFSRSDELTRHIRI-HTGQKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFARSDE 388 (451)
Q Consensus 310 ~~~eKpy~C~~e~Cgk~F~s~s~L~rH~r~-HtgeKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~~s~ 388 (451)
+...|-|+|+ .|+..|+....|..|||. |...+- .+|.. +..-..+.+-..--.+.++|.|..|...|..+.+
T Consensus 460 ~S~~kt~~cp--kc~~~yk~a~~L~vhmRskhp~~~~---~~c~~-gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~ 533 (1406)
T KOG1146|consen 460 HSFFKTLKCP--KCNWHYKLAQTLGVHMRSKHPESQS---AYCKA-GQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGN 533 (1406)
T ss_pred ecccccccCC--ccchhhhhHHHhhhcccccccccch---hHhHh-ccccccccccccccCCCCcccceeeeeeeecchH
Confidence 4445778895 499999999999999997 432222 33321 1111111111111235689999999999999999
Q ss_pred HHHHHHH
Q psy677 389 KKRHAKV 395 (451)
Q Consensus 389 Lk~Hlrt 395 (451)
|.+|+..
T Consensus 534 LsihlqS 540 (1406)
T KOG1146|consen 534 LSIHLQS 540 (1406)
T ss_pred HHHHHHH
Confidence 9999854
No 42
>PRK04860 hypothetical protein; Provisional
Probab=93.80 E-value=0.036 Score=51.56 Aligned_cols=40 Identities=28% Similarity=0.694 Sum_probs=33.9
Q ss_pred CCccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcc
Q psy677 314 RPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSD 359 (451)
Q Consensus 314 Kpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s 359 (451)
-+|.| . |++ ....+.+|.++|+++++|.|..|++.|....
T Consensus 118 ~~Y~C--~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRC--K-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEc--C-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 36899 4 887 6678899999999999999999999987544
No 43
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=93.73 E-value=0.071 Score=33.49 Aligned_cols=23 Identities=30% Similarity=0.587 Sum_probs=16.9
Q ss_pred eecCCCCCccCChHHHHHHHHHHh
Q psy677 374 FSCDVCGRKFARSDEKKRHAKVHL 397 (451)
Q Consensus 374 fkC~~CgK~Fs~~s~Lk~HlrtH~ 397 (451)
|+|..|..... ...|.+|+++|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 67888887777 778888888765
No 44
>KOG4173|consensus
Probab=93.44 E-value=0.015 Score=55.94 Aligned_cols=83 Identities=29% Similarity=0.606 Sum_probs=67.4
Q ss_pred CCCccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchhhhhhhcc----------cCCCceecC--CCC
Q psy677 313 ERPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTHIRTH----------TGEKPFSCD--VCG 380 (451)
Q Consensus 313 eKpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H~rtH----------tGeKPfkC~--~Cg 380 (451)
.+.|.|.+.+|-..|.....+..|..+-++ -.|.+|.+.|.+...|..|+... .|..-|.|- .|+
T Consensus 77 ~~~~~cqvagc~~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt 153 (253)
T KOG4173|consen 77 VPAFACQVAGCCQVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCT 153 (253)
T ss_pred cccccccccchHHHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhh
Confidence 345889999999999998888888765333 37999999999999999998643 355579994 599
Q ss_pred CccCChHHHHHHH-HHHhC
Q psy677 381 RKFARSDEKKRHA-KVHLK 398 (451)
Q Consensus 381 K~Fs~~s~Lk~Hl-rtH~~ 398 (451)
-.|.+....+.|+ ++|.-
T Consensus 154 ~KFkT~r~RkdH~I~~Hk~ 172 (253)
T KOG4173|consen 154 EKFKTSRDRKDHMIRMHKY 172 (253)
T ss_pred hhhhhhhhhhhHHHHhccC
Confidence 9999999999998 77753
No 45
>smart00355 ZnF_C2H2 zinc finger.
Probab=92.75 E-value=0.11 Score=31.92 Aligned_cols=24 Identities=38% Similarity=0.923 Sum_probs=15.6
Q ss_pred ccCCCCCCCCccCChHHHHHHHHHhc
Q psy677 316 YACPVENCDRRFSRSDELTRHIRIHT 341 (451)
Q Consensus 316 y~C~~e~Cgk~F~s~s~L~rH~r~Ht 341 (451)
|.|. .|++.|.....|..|++.|.
T Consensus 1 ~~C~--~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCP--ECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCC--CCcchhCCHHHHHHHHHHhc
Confidence 3563 37777777777777776653
No 46
>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=91.70 E-value=0.23 Score=37.76 Aligned_cols=32 Identities=38% Similarity=0.795 Sum_probs=17.8
Q ss_pred CCCCccCCCCCCCCccCChHHHHHHHHHhcCCCC
Q psy677 312 HERPYACPVENCDRRFSRSDELTRHIRIHTGQKP 345 (451)
Q Consensus 312 ~eKpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeKP 345 (451)
.+.|-.|++ |+..+....+|++|+..+++.||
T Consensus 21 S~~PatCP~--C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPI--CGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TT--T--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCc--chhhccchhhHHHHHHHHhcccC
Confidence 455667754 77777777777777776665554
No 47
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=90.97 E-value=0.055 Score=35.13 Aligned_cols=21 Identities=38% Similarity=0.899 Sum_probs=14.1
Q ss_pred eecCCCCCccCChHHHHHHHH
Q psy677 374 FSCDVCGRKFARSDEKKRHAK 394 (451)
Q Consensus 374 fkC~~CgK~Fs~~s~Lk~Hlr 394 (451)
|.|..|++.|.....|..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 566777777777776666653
No 48
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=90.40 E-value=0.29 Score=50.56 Aligned_cols=106 Identities=25% Similarity=0.485 Sum_probs=67.4
Q ss_pred CccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccc---cccC------CcchhhhhhhcccCCCce----ecCCCCC
Q psy677 315 PYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICM---RSFS------RSDHLTTHIRTHTGEKPF----SCDVCGR 381 (451)
Q Consensus 315 py~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~---K~F~------~~s~Lk~H~rtHtGeKPf----kC~~CgK 381 (451)
.|.|+...|..+......|+.|.+..++ .+.|..|- +.|. ++..|+.|...-..+.-| .|..|.+
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 3889988898888888999999987433 36677763 2343 445566665543222223 5999999
Q ss_pred ccCChHHHHHHHHHHhCcccchHHHHH----HHHHHHHHHHHHHHH
Q psy677 382 KFARSDEKKRHAKVHLKQRSKKESKMA----VMMSQQQAQQQQQQN 423 (451)
Q Consensus 382 ~Fs~~s~Lk~HlrtH~~er~~k~~~~~----~~~~qqq~qqqhQqn 423 (451)
.|-.-+.|.+|+|..+ ++.+-|..++ .+|.....+..|=++
T Consensus 229 ~FYdDDEL~~HcR~~H-E~ChICD~v~p~~~QYFK~Y~~Le~HF~~ 273 (493)
T COG5236 229 YFYDDDELRRHCRLRH-EACHICDMVGPIRYQYFKSYEDLEAHFRN 273 (493)
T ss_pred eecChHHHHHHHHhhh-hhhhhhhccCccchhhhhCHHHHHHHhhc
Confidence 9999999999986533 2333333332 344455555555444
No 49
>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=89.69 E-value=0.15 Score=33.08 Aligned_cols=22 Identities=32% Similarity=0.824 Sum_probs=14.5
Q ss_pred ccCcccccccCCcchhhhhhhc
Q psy677 346 FQCRICMRSFSRSDHLTTHIRT 367 (451)
Q Consensus 346 f~C~~C~K~F~~~s~Lk~H~rt 367 (451)
|.|..|++.|.+...|..|++.
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 5566666666666666666654
No 50
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=89.20 E-value=0.2 Score=31.46 Aligned_cols=23 Identities=30% Similarity=0.901 Sum_probs=14.2
Q ss_pred ccCCCCCCCCccCChHHHHHHHHHh
Q psy677 316 YACPVENCDRRFSRSDELTRHIRIH 340 (451)
Q Consensus 316 y~C~~e~Cgk~F~s~s~L~rH~r~H 340 (451)
|.|.+ |++.|.+...|..|++.+
T Consensus 1 ~~C~~--C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDI--CNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETT--TTEEESSHHHHHHHHTTH
T ss_pred CCCCC--CCCCcCCHHHHHHHHCcC
Confidence 45644 666666666666666543
No 51
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=88.64 E-value=0.17 Score=51.59 Aligned_cols=43 Identities=23% Similarity=0.449 Sum_probs=34.3
Q ss_pred CCCceecCC--CCCccCChHHHHHHHHH-H------------------hCcccchHHHHHHHHH
Q psy677 370 GEKPFSCDV--CGRKFARSDEKKRHAKV-H------------------LKQRSKKESKMAVMMS 412 (451)
Q Consensus 370 GeKPfkC~~--CgK~Fs~~s~Lk~Hlrt-H------------------~~er~~k~~~~~~~~~ 412 (451)
++|||+|++ |+|.|.....|+.|+.- | .+.|+|+|+.|.+++.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYK 409 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYK 409 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhc
Confidence 459999986 99999999999999853 3 1348899999987653
No 52
>KOG2231|consensus
Probab=88.49 E-value=0.34 Score=54.13 Aligned_cols=46 Identities=24% Similarity=0.550 Sum_probs=25.5
Q ss_pred cCcccccccCCcchhhhhhhcccCCCceecCCC------CCccCChHHHHHHHHHH
Q psy677 347 QCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVC------GRKFARSDEKKRHAKVH 396 (451)
Q Consensus 347 ~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~C------gK~Fs~~s~Lk~HlrtH 396 (451)
.|.+|...|.....|.+|++.++ |-|..| +-.|...+.|..|-|.+
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 46666666666666666666543 334444 23345555555555443
No 53
>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=86.76 E-value=0.73 Score=31.12 Aligned_cols=22 Identities=27% Similarity=0.578 Sum_probs=18.9
Q ss_pred ceecCCCCCccCChHHHHHHHH
Q psy677 373 PFSCDVCGRKFARSDEKKRHAK 394 (451)
Q Consensus 373 PfkC~~CgK~Fs~~s~Lk~Hlr 394 (451)
+|.|++|++.|.....+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 5889999999998888888874
No 54
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=86.62 E-value=0.61 Score=30.09 Aligned_cols=21 Identities=43% Similarity=1.067 Sum_probs=15.6
Q ss_pred eecCCCCCccCChHHHHHHHHH
Q psy677 374 FSCDVCGRKFARSDEKKRHAKV 395 (451)
Q Consensus 374 fkC~~CgK~Fs~~s~Lk~Hlrt 395 (451)
..|..||+.| ..+.|.+|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 3688888888 66678888765
No 55
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=84.38 E-value=0.9 Score=28.36 Aligned_cols=23 Identities=39% Similarity=0.909 Sum_probs=13.2
Q ss_pred ccCCCCCCCCccCChHHHHHHHHHhc
Q psy677 316 YACPVENCDRRFSRSDELTRHIRIHT 341 (451)
Q Consensus 316 y~C~~e~Cgk~F~s~s~L~rH~r~Ht 341 (451)
|.|. .|+.... ...|.+|++.|+
T Consensus 1 y~C~--~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCP--HCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-S--SSS-EES-HHHHHHHHHHHH
T ss_pred CCCC--CCCCcCC-HHHHHHHHHhhC
Confidence 4563 3776666 667777776653
No 56
>KOG2186|consensus
Probab=83.98 E-value=0.67 Score=46.05 Aligned_cols=49 Identities=31% Similarity=0.632 Sum_probs=36.4
Q ss_pred ccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCChHHHHHHHHHHh
Q psy677 346 FQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFARSDEKKRHAKVHL 397 (451)
Q Consensus 346 f~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~~s~Lk~HlrtH~ 397 (451)
|.|..||....- ..+.+|+.+-++ .-|.|..|++.|.+ ..++.|.+.-+
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccC-CeeEEeeccccccc-chhhhhhhhcc
Confidence 778888877653 456678887777 67888889998888 66778876544
No 57
>KOG2231|consensus
Probab=83.37 E-value=0.83 Score=51.19 Aligned_cols=69 Identities=25% Similarity=0.534 Sum_probs=45.2
Q ss_pred ccCChHHHHHHHHH-hcCCCCccCcccc---------cccCCcchhhhhhhcc-cCCCc----eecCCCCCccCChHHHH
Q psy677 326 RFSRSDELTRHIRI-HTGQKPFQCRICM---------RSFSRSDHLTTHIRTH-TGEKP----FSCDVCGRKFARSDEKK 390 (451)
Q Consensus 326 ~F~s~s~L~rH~r~-HtgeKPf~C~~C~---------K~F~~~s~Lk~H~rtH-tGeKP----fkC~~CgK~Fs~~s~Lk 390 (451)
.|.....|++|++. |. -+.|.+|- ....++..|..|+..- .+++- -.|..|...|.....|.
T Consensus 123 ~~~s~~~Lk~H~~~~H~---~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~ 199 (669)
T KOG2231|consen 123 EFKSVENLKNHMRDQHK---LHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELY 199 (669)
T ss_pred chhHHHHHHHHHHHhhh---hhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHH
Confidence 34478899999964 53 35555542 2223445666776542 12222 25899999999999999
Q ss_pred HHHHHHh
Q psy677 391 RHAKVHL 397 (451)
Q Consensus 391 ~HlrtH~ 397 (451)
+|++.++
T Consensus 200 rH~~~~h 206 (669)
T KOG2231|consen 200 RHLRFDH 206 (669)
T ss_pred Hhhccce
Confidence 9998654
No 58
>KOG2893|consensus
Probab=83.12 E-value=0.26 Score=48.59 Aligned_cols=45 Identities=31% Similarity=0.778 Sum_probs=33.1
Q ss_pred CCCccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchhhhh
Q psy677 313 ERPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTH 364 (451)
Q Consensus 313 eKpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H 364 (451)
.|+| |= .|++-|....-|..|.+. |.|+|-+|.|.+.+--.|..|
T Consensus 9 ~kpw-cw--ycnrefddekiliqhqka----khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 9 DKPW-CW--YCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred CCce-ee--ecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceee
Confidence 4555 43 388889888888888764 458899998877777777766
No 59
>KOG4167|consensus
Probab=83.00 E-value=0.68 Score=51.90 Aligned_cols=25 Identities=32% Similarity=0.729 Sum_probs=23.4
Q ss_pred ceecCCCCCccCChHHHHHHHHHHh
Q psy677 373 PFSCDVCGRKFARSDEKKRHAKVHL 397 (451)
Q Consensus 373 PfkC~~CgK~Fs~~s~Lk~HlrtH~ 397 (451)
.|.|..|+|.|.....++.|||+|.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHH
Confidence 4899999999999999999999995
No 60
>KOG2893|consensus
Probab=80.63 E-value=0.94 Score=44.78 Aligned_cols=42 Identities=29% Similarity=0.615 Sum_probs=34.0
Q ss_pred cCcccccccCCcchhhhhhhcccCCCceecCCCCCccCChHHHHHH
Q psy677 347 QCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFARSDEKKRH 392 (451)
Q Consensus 347 ~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~~s~Lk~H 392 (451)
-|-+|++-|....-|..|.+. |-|+|.+|.|....--.|..|
T Consensus 12 wcwycnrefddekiliqhqka----khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceee
Confidence 488999999999999998875 459999999876665555555
No 61
>KOG2482|consensus
Probab=79.86 E-value=0.96 Score=46.76 Aligned_cols=23 Identities=26% Similarity=0.658 Sum_probs=20.5
Q ss_pred CccCCCCCCCCccCChHHHHHHHHH
Q psy677 315 PYACPVENCDRRFSRSDELTRHIRI 339 (451)
Q Consensus 315 py~C~~e~Cgk~F~s~s~L~rH~r~ 339 (451)
.+.|-+ |.|.|+.+..|+.|||.
T Consensus 195 r~~CLy--CekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLY--CEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeee--eccccCCcHHHHHHHHh
Confidence 477966 99999999999999986
No 62
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=76.45 E-value=1.1 Score=28.95 Aligned_cols=14 Identities=43% Similarity=0.992 Sum_probs=7.3
Q ss_pred CCCccCChHHHHHHH
Q psy677 323 CDRRFSRSDELTRHI 337 (451)
Q Consensus 323 Cgk~F~s~s~L~rH~ 337 (451)
|++.| ....|.+|+
T Consensus 8 CgR~F-~~~~l~~H~ 21 (25)
T PF13913_consen 8 CGRKF-NPDRLEKHE 21 (25)
T ss_pred CCCEE-CHHHHHHHH
Confidence 55555 444455554
No 63
>KOG4124|consensus
Probab=75.68 E-value=0.48 Score=49.01 Aligned_cols=73 Identities=26% Similarity=0.600 Sum_probs=46.8
Q ss_pred CCCCccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCChHHHHH
Q psy677 312 HERPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFARSDEKKR 391 (451)
Q Consensus 312 ~eKpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~~s~Lk~ 391 (451)
..++|.|.+..|.+.++....|+.|...-+ |.-.-.-...-.-|.......|+|+|++|.+++.....|+.
T Consensus 346 ~~~~~~~~vp~~~~~~~n~ng~~~~~~~~h---------~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~ 416 (442)
T KOG4124|consen 346 VDKPYKCPVPNCDKAYKNQNGLKYHKLHGH---------CSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKY 416 (442)
T ss_pred ecCCCCCCCCcchhhcccCcceeeccccCc---------CCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCc
Confidence 357899999999999998887776654311 11111111122234444445789999999988887777766
Q ss_pred HH
Q psy677 392 HA 393 (451)
Q Consensus 392 Hl 393 (451)
|+
T Consensus 417 ~~ 418 (442)
T KOG4124|consen 417 HR 418 (442)
T ss_pred ee
Confidence 64
No 64
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=75.58 E-value=2.7 Score=32.70 Aligned_cols=27 Identities=33% Similarity=0.679 Sum_probs=22.3
Q ss_pred ccCCCceecCCCCCccCChHHHHHHHH
Q psy677 368 HTGEKPFSCDVCGRKFARSDEKKRHAK 394 (451)
Q Consensus 368 HtGeKPfkC~~CgK~Fs~~s~Lk~Hlr 394 (451)
-.||.-++|+.|++.|.....+.+|..
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhh
Confidence 457777889999999998888888884
No 65
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=75.24 E-value=1.4 Score=42.65 Aligned_cols=42 Identities=26% Similarity=0.598 Sum_probs=26.4
Q ss_pred CCccCcccccccCCcchhhhhhhc----------ccCCCc-----eecCCCCCccCC
Q psy677 344 KPFQCRICMRSFSRSDHLTTHIRT----------HTGEKP-----FSCDVCGRKFAR 385 (451)
Q Consensus 344 KPf~C~~C~K~F~~~s~Lk~H~rt----------HtGeKP-----fkC~~CgK~Fs~ 385 (451)
|.+.|++|++.|..+.-.....|. ..+..| ..|+.||.+|..
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~ 60 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFE 60 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccc
Confidence 456777777777776655555443 123333 479999987653
No 66
>KOG1146|consensus
Probab=72.01 E-value=1.6 Score=52.01 Aligned_cols=76 Identities=18% Similarity=0.356 Sum_probs=53.9
Q ss_pred ccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchhhhhhhc-----------------ccCCCceecCC
Q psy677 316 YACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTHIRT-----------------HTGEKPFSCDV 378 (451)
Q Consensus 316 y~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H~rt-----------------HtGeKPfkC~~ 378 (451)
+.| ..|.+.|...-.+. |+.. ..+|.|..|...|.....|..|.+. |...++| |..
T Consensus 1261 ~~c--~~~~~~~~~~~~~~-~l~~---~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~ 1333 (1406)
T KOG1146|consen 1261 GEC--GAVDELLTPSFGIS-TLDV---THRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLA 1333 (1406)
T ss_pred chh--hhccccccCcccee-eccc---chhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chH
Confidence 667 44877777666555 5432 3457888888888888777777642 2334567 999
Q ss_pred CCCccCChHHHHHHHHHHhC
Q psy677 379 CGRKFARSDEKKRHAKVHLK 398 (451)
Q Consensus 379 CgK~Fs~~s~Lk~HlrtH~~ 398 (451)
|...|.....|..|||.-..
T Consensus 1334 c~~~~~~~~alqihm~~~~~ 1353 (1406)
T KOG1146|consen 1334 CEVLLSGREALQIHMRSSAH 1353 (1406)
T ss_pred HHhhcchhHHHHHHHHHhhh
Confidence 99999999999999975433
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=69.34 E-value=2.8 Score=28.66 Aligned_cols=9 Identities=56% Similarity=1.556 Sum_probs=5.0
Q ss_pred CceecCCCC
Q psy677 372 KPFSCDVCG 380 (451)
Q Consensus 372 KPfkC~~Cg 380 (451)
.++.|++|+
T Consensus 16 ~~~~CP~Cg 24 (33)
T cd00350 16 APWVCPVCG 24 (33)
T ss_pred CCCcCcCCC
Confidence 455566665
No 68
>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=69.29 E-value=4.1 Score=27.35 Aligned_cols=23 Identities=17% Similarity=0.557 Sum_probs=17.5
Q ss_pred CccCCCCCCCCccCChHHHHHHHHH
Q psy677 315 PYACPVENCDRRFSRSDELTRHIRI 339 (451)
Q Consensus 315 py~C~~e~Cgk~F~s~s~L~rH~r~ 339 (451)
+|.|.+ |++.|.+...+..|++.
T Consensus 3 ~~~C~~--C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKL--CNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccc--cCCccCCHHHHHHHHCh
Confidence 477854 88888888888888764
No 69
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=68.25 E-value=7.5 Score=34.31 Aligned_cols=78 Identities=23% Similarity=0.414 Sum_probs=50.7
Q ss_pred CCccCCCCCCCCccCChHHHHHHHHHhc--CCCC------------ccCcccccccCCcchhhhhhhcccCCCceecCCC
Q psy677 314 RPYACPVENCDRRFSRSDELTRHIRIHT--GQKP------------FQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVC 379 (451)
Q Consensus 314 Kpy~C~~e~Cgk~F~s~s~L~rH~r~Ht--geKP------------f~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~C 379 (451)
-|-.|++ |+...-....|.|.. |+ .-++ -.|--|.+.|........-. -.....|+|..|
T Consensus 14 LP~~Cpi--CgLtLVss~HLARSy--HHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~--~~~~~~y~C~~C 87 (112)
T TIGR00622 14 LPVECPI--CGLTLILSTHLARSY--HHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDE--LKDSHRYVCAVC 87 (112)
T ss_pred CCCcCCc--CCCEEeccchHHHhh--hccCCCcccccccccccCCCCcccCcCCCCCCcccccccc--cccccceeCCCC
Confidence 3556866 998888887777642 22 1111 23888988887654221100 123447999999
Q ss_pred CCccCChHHHHHHHHHHh
Q psy677 380 GRKFARSDEKKRHAKVHL 397 (451)
Q Consensus 380 gK~Fs~~s~Lk~HlrtH~ 397 (451)
...|-..-+...|...|.
T Consensus 88 ~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 88 KNVFCVDCDVFVHESLHC 105 (112)
T ss_pred CCccccccchhhhhhccC
Confidence 999998888888887775
No 70
>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=67.07 E-value=6.4 Score=33.80 Aligned_cols=25 Identities=16% Similarity=0.404 Sum_probs=22.9
Q ss_pred eec----CCCCCccCChHHHHHHHHHHhC
Q psy677 374 FSC----DVCGRKFARSDEKKRHAKVHLK 398 (451)
Q Consensus 374 fkC----~~CgK~Fs~~s~Lk~HlrtH~~ 398 (451)
|.| ..|+..+.....+.+|.+.+++
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 899 9999999999999999988764
No 71
>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=66.82 E-value=3.4 Score=36.12 Aligned_cols=15 Identities=27% Similarity=0.685 Sum_probs=6.9
Q ss_pred CCccCcccccccCCc
Q psy677 344 KPFQCRICMRSFSRS 358 (451)
Q Consensus 344 KPf~C~~C~K~F~~~ 358 (451)
.|..|+.||..|...
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 344455555444433
No 72
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=66.55 E-value=4.7 Score=32.78 Aligned_cols=24 Identities=29% Similarity=0.897 Sum_probs=19.2
Q ss_pred CccCCCCCCCCccCChHHHHHHHHHh
Q psy677 315 PYACPVENCDRRFSRSDELTRHIRIH 340 (451)
Q Consensus 315 py~C~~e~Cgk~F~s~s~L~rH~r~H 340 (451)
.+.|.+ |++.|.+...|..||+.+
T Consensus 50 ~~~C~~--C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPY--CNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSS--SS-EESSHHHHHHHHHHT
T ss_pred CCCCCc--cCCCCcCHHHHHHHHcCc
Confidence 588866 999999999999999864
No 73
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=65.11 E-value=3.9 Score=34.46 Aligned_cols=32 Identities=38% Similarity=0.688 Sum_probs=23.3
Q ss_pred CCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCC
Q psy677 344 KPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFAR 385 (451)
Q Consensus 344 KPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~ 385 (451)
..|.|+.|++. .+.|.-+ ..+.|..||..|+-
T Consensus 34 ~~~~Cp~C~~~--------~VkR~a~--GIW~C~kCg~~fAG 65 (89)
T COG1997 34 AKHVCPFCGRT--------TVKRIAT--GIWKCRKCGAKFAG 65 (89)
T ss_pred cCCcCCCCCCc--------ceeeecc--CeEEcCCCCCeecc
Confidence 46899999865 2334444 46899999999974
No 74
>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=64.31 E-value=3.7 Score=37.21 Aligned_cols=27 Identities=33% Similarity=0.587 Sum_probs=16.5
Q ss_pred CceecCCCCCccCChHHHHHHHHHHhCccc
Q psy677 372 KPFSCDVCGRKFARSDEKKRHAKVHLKQRS 401 (451)
Q Consensus 372 KPfkC~~CgK~Fs~~s~Lk~HlrtH~~er~ 401 (451)
.-..|-+|||.|.. |++|++.|+|-.+
T Consensus 71 d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 71 DYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp S-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred CeeEEccCCcccch---HHHHHHHccCCCH
Confidence 34678889998887 4899999977654
No 75
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=63.92 E-value=5.7 Score=36.16 Aligned_cols=39 Identities=15% Similarity=0.518 Sum_probs=26.6
Q ss_pred CCCCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccC
Q psy677 342 GQKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFA 384 (451)
Q Consensus 342 geKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs 384 (451)
...-|.|+.|++.|.....+.. .+. +.-|.|+.||....
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL---LDM-DGTFTCPRCGEELE 134 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh---cCC-CCcEECCCCCCEEE
Confidence 3457999999999986554432 011 23499999998654
No 76
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=63.45 E-value=3.8 Score=38.00 Aligned_cols=16 Identities=19% Similarity=0.586 Sum_probs=10.8
Q ss_pred ccCcccccccCCcchh
Q psy677 346 FQCRICMRSFSRSDHL 361 (451)
Q Consensus 346 f~C~~C~K~F~~~s~L 361 (451)
+.|+.|+++|..-..+
T Consensus 29 ~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 29 RECLACGKRFTTFERV 44 (154)
T ss_pred eeccccCCcceEeEec
Confidence 6777777777655444
No 77
>KOG2482|consensus
Probab=61.43 E-value=6.4 Score=40.92 Aligned_cols=55 Identities=24% Similarity=0.493 Sum_probs=36.9
Q ss_pred CccCcccccccC-Ccchhhhhhhc-cc---C----------------C--CceecCCCCCccCChHHHHHHHHH--HhCc
Q psy677 345 PFQCRICMRSFS-RSDHLTTHIRT-HT---G----------------E--KPFSCDVCGRKFARSDEKKRHAKV--HLKQ 399 (451)
Q Consensus 345 Pf~C~~C~K~F~-~~s~Lk~H~rt-Ht---G----------------e--KPfkC~~CgK~Fs~~s~Lk~Hlrt--H~~e 399 (451)
.-.|-+|+.-+. .++.+..|+.. |. | + ..+.|-.|.|.|..+..|+.|||. |.+-
T Consensus 144 slqClFCn~e~lgnRs~~l~Hlf~~H~lniGlpDniVyvnelLehLkekL~r~~CLyCekifrdkntLkeHMrkK~Hrri 223 (423)
T KOG2482|consen 144 SLQCLFCNNEGLGNRSEILEHLFHVHGLNIGLPDNIVYVNELLEHLKEKLERLRCLYCEKIFRDKNTLKEHMRKKRHRRI 223 (423)
T ss_pred eeEEEEecchhcccHHHHHHHHHHHhhhccCCCcceeeHHHHHHHHHHHHhhheeeeeccccCCcHHHHHHHHhccCccc
Confidence 356888977543 44555566543 31 1 0 137899999999999999999964 5443
No 78
>KOG2785|consensus
Probab=61.06 E-value=4.6 Score=42.43 Aligned_cols=76 Identities=24% Similarity=0.406 Sum_probs=46.5
Q ss_pred ccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchhhhhhhcccCCCceecCCCC---CccCChHHHHHH
Q psy677 316 YACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCG---RKFARSDEKKRH 392 (451)
Q Consensus 316 y~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~Cg---K~Fs~~s~Lk~H 392 (451)
-.|-+ |++.|+.-.....||..|++- |.-+. .-......|..-+....+ +-|.|-.|+ +.|.....-+.|
T Consensus 167 t~CLf--C~~~~k~~e~~~~HM~~~Hgf--fIPdr--eYL~D~~GLl~YLgeKV~-~~~~CL~CN~~~~~f~sleavr~H 239 (390)
T KOG2785|consen 167 TDCLF--CDKKSKSLEENLKHMFKEHGF--FIPDR--EYLTDEKGLLKYLGEKVG-IGFICLFCNELGRPFSSLEAVRAH 239 (390)
T ss_pred cceee--cCCCcccHHHHHHHHhhccCC--cCCch--HhhhchhHHHHHHHHHhc-cCceEEEeccccCcccccHHHHHH
Confidence 45865 999999999999999987762 11110 011122223222222211 347888888 889999888999
Q ss_pred H--HHHhC
Q psy677 393 A--KVHLK 398 (451)
Q Consensus 393 l--rtH~~ 398 (451)
| +.|.+
T Consensus 240 M~~K~HCk 247 (390)
T KOG2785|consen 240 MRDKGHCK 247 (390)
T ss_pred HhhccCcc
Confidence 8 44543
No 79
>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=60.08 E-value=6.1 Score=36.57 Aligned_cols=34 Identities=21% Similarity=0.468 Sum_probs=26.8
Q ss_pred CCCCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccC
Q psy677 342 GQKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFA 384 (451)
Q Consensus 342 geKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs 384 (451)
...-|.|+.|+.+|.....+. .-|.|+.||....
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAMLD 139 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCEee
Confidence 456799999999998877774 2599999997644
No 80
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=58.62 E-value=9.1 Score=39.91 Aligned_cols=73 Identities=29% Similarity=0.580 Sum_probs=48.5
Q ss_pred cCCCCCCCCccCChHHHHHHHHHhcCCCCccCccccc----ccCCcchhhhhhhcccCCCceecCC--C--C--CccCCh
Q psy677 317 ACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMR----SFSRSDHLTTHIRTHTGEKPFSCDV--C--G--RKFARS 386 (451)
Q Consensus 317 ~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K----~F~~~s~Lk~H~rtHtGeKPfkC~~--C--g--K~Fs~~ 386 (451)
.|.+ |.+.|=+...|.+|+|..+ ++-|.|+.-+. -|..-..|.+|.+.- -|.|.+ | + ..|...
T Consensus 222 ~C~F--C~~~FYdDDEL~~HcR~~H-E~ChICD~v~p~~~QYFK~Y~~Le~HF~~~----hy~ct~qtc~~~k~~vf~~~ 294 (493)
T COG5236 222 LCIF--CKIYFYDDDELRRHCRLRH-EACHICDMVGPIRYQYFKSYEDLEAHFRNA----HYCCTFQTCRVGKCYVFPYH 294 (493)
T ss_pred hhhh--ccceecChHHHHHHHHhhh-hhhhhhhccCccchhhhhCHHHHHHHhhcC----ceEEEEEEEecCcEEEeccH
Confidence 4855 9999999999999998633 33344433221 366777788887643 266643 4 2 357888
Q ss_pred HHHHHHH-HHH
Q psy677 387 DEKKRHA-KVH 396 (451)
Q Consensus 387 s~Lk~Hl-rtH 396 (451)
..|..|+ +-|
T Consensus 295 ~el~~h~~~~h 305 (493)
T COG5236 295 TELLEHLTRFH 305 (493)
T ss_pred HHHHHHHHHHh
Confidence 8899998 444
No 81
>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=58.19 E-value=6.7 Score=28.03 Aligned_cols=25 Identities=36% Similarity=0.639 Sum_probs=14.8
Q ss_pred CCCceecCCCCCccCCh----HHHHHHHH
Q psy677 370 GEKPFSCDVCGRKFARS----DEKKRHAK 394 (451)
Q Consensus 370 GeKPfkC~~CgK~Fs~~----s~Lk~Hlr 394 (451)
+..-.+|..|++.+... ..|.+|++
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 45567788888877664 67888873
No 82
>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=56.96 E-value=7.1 Score=27.09 Aligned_cols=34 Identities=26% Similarity=0.533 Sum_probs=18.6
Q ss_pred ccCcccccccCCcchhhhhhhcccCCCceecCCCCCccC
Q psy677 346 FQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFA 384 (451)
Q Consensus 346 f~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs 384 (451)
+.|+.|+..|.-..... .......+|..|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~-----~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL-----GANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHc-----CCCCCEEECCCCCCEEE
Confidence 56777777665544321 11112467777777663
No 83
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=55.60 E-value=8.5 Score=28.53 Aligned_cols=23 Identities=39% Similarity=0.886 Sum_probs=16.3
Q ss_pred eecCCCCCccCCh-----HHHHHHHH-HH
Q psy677 374 FSCDVCGRKFARS-----DEKKRHAK-VH 396 (451)
Q Consensus 374 fkC~~CgK~Fs~~-----s~Lk~Hlr-tH 396 (451)
-.|..|++.+... ++|.+|++ +|
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~h 47 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRKH 47 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhHC
Confidence 4688888777654 57888886 45
No 84
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=54.88 E-value=3.1 Score=32.39 Aligned_cols=26 Identities=31% Similarity=0.630 Sum_probs=13.2
Q ss_pred CCCCccCCCCCCCCccCChHHHHHHHHH
Q psy677 312 HERPYACPVENCDRRFSRSDELTRHIRI 339 (451)
Q Consensus 312 ~eKpy~C~~e~Cgk~F~s~s~L~rH~r~ 339 (451)
+|..+.|+- |++.|.....+.+|+..
T Consensus 14 GE~~lrCPR--C~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 14 GEEFLRCPR--CGMVFRRRKDYIRHVNK 39 (65)
T ss_pred CceeeeCCc--hhHHHHHhHHHHHHhhH
Confidence 444455532 55555555555555543
No 85
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=54.69 E-value=7.7 Score=36.68 Aligned_cols=34 Identities=24% Similarity=0.565 Sum_probs=26.3
Q ss_pred CCCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCC
Q psy677 343 QKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFAR 385 (451)
Q Consensus 343 eKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~ 385 (451)
..-|.|+.|++.|.....+. .-|.|+.||.....
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLEE 148 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCee
Confidence 45799999999998777653 35999999976544
No 86
>KOG2186|consensus
Probab=53.26 E-value=7 Score=39.07 Aligned_cols=47 Identities=21% Similarity=0.595 Sum_probs=36.2
Q ss_pred ccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchhhhhhhc
Q psy677 316 YACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTHIRT 367 (451)
Q Consensus 316 y~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H~rt 367 (451)
|.|.+ ||...+.. .+.+|+..-++ .-|.|-.|++.|.+ ...+.|.+-
T Consensus 4 FtCnv--CgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 4 FTCNV--CGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred Eehhh--hhhhcccc-chHHHHHhccC-CeeEEeeccccccc-chhhhhhhh
Confidence 67855 99887654 46779987666 66999999999998 667778653
No 87
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=53.13 E-value=10 Score=26.66 Aligned_cols=34 Identities=26% Similarity=0.643 Sum_probs=19.4
Q ss_pred ccCcccccccCCcchhhhhhhcccCCCceecCCCCCccC
Q psy677 346 FQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFA 384 (451)
Q Consensus 346 f~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs 384 (451)
..|+.|+..|.-.+.- +-.+.+..+|..|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~-----l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK-----LPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHH-----cccCCcEEECCCCCcEee
Confidence 3577777777654431 112334567777777664
No 88
>KOG2593|consensus
Probab=52.78 E-value=11 Score=40.42 Aligned_cols=38 Identities=18% Similarity=0.568 Sum_probs=26.8
Q ss_pred CCCCccCcccccccCCcchhhhhhhcccCCCceecCCCCCc
Q psy677 342 GQKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRK 382 (451)
Q Consensus 342 geKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~ 382 (451)
...-|.|+.|.+.|.....+.- .-...--|.|..|+-.
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~L---~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQL---LDNETGEFHCENCGGE 162 (436)
T ss_pred ccccccCCccccchhhhHHHHh---hcccCceEEEecCCCc
Confidence 4567999999999988776642 1222345999999743
No 89
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=51.03 E-value=9.3 Score=34.44 Aligned_cols=15 Identities=20% Similarity=0.443 Sum_probs=8.4
Q ss_pred CceecCCCCCccCCh
Q psy677 372 KPFSCDVCGRKFARS 386 (451)
Q Consensus 372 KPfkC~~CgK~Fs~~ 386 (451)
.|..|++||..|...
T Consensus 25 ~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 25 RPAVSPYTGEQFPPE 39 (129)
T ss_pred CCccCCCcCCccCcc
Confidence 455666666655443
No 90
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=50.84 E-value=12 Score=26.16 Aligned_cols=33 Identities=21% Similarity=0.586 Sum_probs=19.2
Q ss_pred ccCcccccccCCcchhhhhhhcccCCCceecCCCCCcc
Q psy677 346 FQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKF 383 (451)
Q Consensus 346 f~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~F 383 (451)
..|+.|+..|.-.+... -...+..+|..|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~i-----p~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKI-----PPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHC-----CCCCcEEECCCCCCEe
Confidence 45777777776555432 1222356777777766
No 91
>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=50.60 E-value=13 Score=32.45 Aligned_cols=30 Identities=30% Similarity=0.738 Sum_probs=24.2
Q ss_pred ccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCCh
Q psy677 346 FQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFARS 386 (451)
Q Consensus 346 f~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~~ 386 (451)
..|+.||++|.. | +..|-.|++||..|.-.
T Consensus 10 R~Cp~CG~kFYD---L--------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTCPSCGAKFYD---L--------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCcchhcc---C--------CCCCccCCCCCCccCcc
Confidence 589999999964 3 23688999999999776
No 92
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=49.30 E-value=9.4 Score=27.81 Aligned_cols=12 Identities=25% Similarity=0.772 Sum_probs=6.6
Q ss_pred CccCcccccccC
Q psy677 345 PFQCRICMRSFS 356 (451)
Q Consensus 345 Pf~C~~C~K~F~ 356 (451)
.|+|..|+..|.
T Consensus 3 ~y~C~~CG~~~~ 14 (46)
T PRK00398 3 EYKCARCGREVE 14 (46)
T ss_pred EEECCCCCCEEE
Confidence 356666665543
No 93
>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=49.05 E-value=7.9 Score=26.95 Aligned_cols=29 Identities=21% Similarity=0.675 Sum_probs=14.8
Q ss_pred ccCcccccccCCcchhhhhhhcccCCCceecCCCCC
Q psy677 346 FQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGR 381 (451)
Q Consensus 346 f~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK 381 (451)
|+|..|++.|....... . ...-.|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~------~-~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKIS------D-DPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecC------C-CCCCCCCCCCC
Confidence 56666766664322211 1 23445666765
No 94
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=48.56 E-value=9.7 Score=30.99 Aligned_cols=16 Identities=25% Similarity=0.588 Sum_probs=7.6
Q ss_pred CCCccCc--ccccccCCc
Q psy677 343 QKPFQCR--ICMRSFSRS 358 (451)
Q Consensus 343 eKPf~C~--~C~K~F~~~ 358 (451)
++-+.|. .|+.+|...
T Consensus 25 ~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 25 ERYHQCQNVNCSATFITY 42 (72)
T ss_pred eeeeecCCCCCCCEEEEE
Confidence 3444554 455555443
No 95
>PF14353 CpXC: CpXC protein
Probab=48.25 E-value=4.9 Score=35.41 Aligned_cols=19 Identities=37% Similarity=0.725 Sum_probs=10.1
Q ss_pred eecCCCCCccCChHHHHHH
Q psy677 374 FSCDVCGRKFARSDEKKRH 392 (451)
Q Consensus 374 fkC~~CgK~Fs~~s~Lk~H 392 (451)
|.|+.||+.|.-...+..|
T Consensus 39 ~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 39 FTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred EECCCCCCceecCCCEEEE
Confidence 5566666665544444444
No 96
>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=48.04 E-value=11 Score=26.14 Aligned_cols=9 Identities=44% Similarity=1.302 Sum_probs=4.9
Q ss_pred ceecCCCCC
Q psy677 373 PFSCDVCGR 381 (451)
Q Consensus 373 PfkC~~CgK 381 (451)
|..|++|+.
T Consensus 18 p~~CP~Cg~ 26 (34)
T cd00729 18 PEKCPICGA 26 (34)
T ss_pred CCcCcCCCC
Confidence 445666653
No 97
>KOG2785|consensus
Probab=47.70 E-value=14 Score=39.03 Aligned_cols=24 Identities=33% Similarity=0.699 Sum_probs=19.1
Q ss_pred CCccCcccc---cccCCcchhhhhhhc
Q psy677 344 KPFQCRICM---RSFSRSDHLTTHIRT 367 (451)
Q Consensus 344 KPf~C~~C~---K~F~~~s~Lk~H~rt 367 (451)
+-|.|-+|+ +.|.+....+.||..
T Consensus 216 ~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 216 IGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred cCceEEEeccccCcccccHHHHHHHhh
Confidence 347888888 888888888888863
No 98
>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=46.16 E-value=19 Score=30.87 Aligned_cols=25 Identities=20% Similarity=0.474 Sum_probs=22.4
Q ss_pred ccC----cccccccCCcchhhhhhhcccC
Q psy677 346 FQC----RICMRSFSRSDHLTTHIRTHTG 370 (451)
Q Consensus 346 f~C----~~C~K~F~~~s~Lk~H~rtHtG 370 (451)
|.| ..|+..+.+...+.+|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 8899999999999999988765
No 99
>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=46.04 E-value=9.3 Score=28.28 Aligned_cols=11 Identities=27% Similarity=0.990 Sum_probs=5.6
Q ss_pred ccCcccccccC
Q psy677 346 FQCRICMRSFS 356 (451)
Q Consensus 346 f~C~~C~K~F~ 356 (451)
|+|..|+..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 45555555553
No 100
>KOG0782|consensus
Probab=45.04 E-value=7.5 Score=42.94 Aligned_cols=53 Identities=21% Similarity=0.469 Sum_probs=36.2
Q ss_pred ChHHHHHHHHHhcCCCCccCcccccccCCcchhhhhhhcccCC-CceecCCCCCccCChH
Q psy677 329 RSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTHIRTHTGE-KPFSCDVCGRKFARSD 387 (451)
Q Consensus 329 s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H~rtHtGe-KPfkC~~CgK~Fs~~s 387 (451)
+...|.+|-..|.....-+|..|+|.|..+..+. ..| .-..|.-|...|-.+.
T Consensus 237 rE~~fvrHHWVHrrRqeGkC~~CgKgFQQKf~Fh------sKEivAisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 237 RESGFVRHHWVHRRRQEGKCNTCGKGFQQKFFFH------SKEIVAISCSWCKQAYHLKV 290 (1004)
T ss_pred ccccchHHhHhhHhhhccccchhhhhhhhheeec------cccEEEEEehHHHHHhhcch
Confidence 4457888887777666678999999997765542 222 2356888877776554
No 101
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=44.51 E-value=13 Score=34.94 Aligned_cols=24 Identities=42% Similarity=1.045 Sum_probs=19.6
Q ss_pred CCccCcccccccCCcchhhhhhhcccCCCceecCCCC
Q psy677 344 KPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCG 380 (451)
Q Consensus 344 KPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~Cg 380 (451)
+.|.|++||.. |.|+-|-+|++||
T Consensus 133 ~~~vC~vCGy~-------------~~ge~P~~CPiCg 156 (166)
T COG1592 133 KVWVCPVCGYT-------------HEGEAPEVCPICG 156 (166)
T ss_pred CEEEcCCCCCc-------------ccCCCCCcCCCCC
Confidence 36999999754 4568899999998
No 102
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=43.82 E-value=9.7 Score=34.68 Aligned_cols=27 Identities=30% Similarity=0.450 Sum_probs=21.2
Q ss_pred eecCCCCCccCChHHHHHHHHHHhCcccch
Q psy677 374 FSCDVCGRKFARSDEKKRHAKVHLKQRSKK 403 (451)
Q Consensus 374 fkC~~CgK~Fs~~s~Lk~HlrtH~~er~~k 403 (451)
..|-+|||.|.. |++|+.+|.+-.+..
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTPd~ 103 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTPDE 103 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCHHH
Confidence 568889998864 899999998876643
No 103
>KOG2071|consensus
Probab=43.82 E-value=19 Score=40.03 Aligned_cols=27 Identities=37% Similarity=0.844 Sum_probs=21.7
Q ss_pred CCCccCCCCCCCCccCChHHHHHHHHHhc
Q psy677 313 ERPYACPVENCDRRFSRSDELTRHIRIHT 341 (451)
Q Consensus 313 eKpy~C~~e~Cgk~F~s~s~L~rH~r~Ht 341 (451)
.++..|.. ||++|.+.....+||..|.
T Consensus 416 ~~pnqC~~--CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKS--CGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcc--cccccccchhhhhHhhhhh
Confidence 45688965 9999999988888877664
No 104
>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=42.15 E-value=12 Score=26.86 Aligned_cols=29 Identities=24% Similarity=0.793 Sum_probs=16.2
Q ss_pred ccCcccccccCCcchhhhhhhcccCCCceecCCCCC
Q psy677 346 FQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGR 381 (451)
Q Consensus 346 f~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK 381 (451)
|+|..|+..|-....+ .. ...-.|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSI------SE-DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEc------CC-CCCCcCCCCCC
Confidence 6677777766433221 22 34556777765
No 105
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=42.00 E-value=17 Score=41.60 Aligned_cols=37 Identities=24% Similarity=0.510 Sum_probs=22.3
Q ss_pred ccCcccccccC---CcchhhhhhhcccCCCceecCCCCCc
Q psy677 346 FQCRICMRSFS---RSDHLTTHIRTHTGEKPFSCDVCGRK 382 (451)
Q Consensus 346 f~C~~C~K~F~---~~s~Lk~H~rtHtGeKPfkC~~CgK~ 382 (451)
++|+.|+..+. ....|.-|..-|....|+.|+.||..
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 45666654321 22344455555566788999999855
No 106
>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=41.60 E-value=23 Score=34.67 Aligned_cols=33 Identities=18% Similarity=0.498 Sum_probs=24.1
Q ss_pred CCCceecCCCCCccCChHHHHHHHHHHhCcccc
Q psy677 370 GEKPFSCDVCGRKFARSDEKKRHAKVHLKQRSK 402 (451)
Q Consensus 370 GeKPfkC~~CgK~Fs~~s~Lk~HlrtH~~er~~ 402 (451)
.+..|.|..|+|.|.-..-..+|+..-|.++..
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ve 106 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPEKVE 106 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HHHHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHHHHH
Confidence 455699999999999999999999766655543
No 107
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=41.07 E-value=4.6 Score=39.15 Aligned_cols=44 Identities=23% Similarity=0.589 Sum_probs=30.0
Q ss_pred CCCccCCCCCCCCccCChHHHHHHHHH-h--c-------CCC-----CccCcccccccCCc
Q psy677 313 ERPYACPVENCDRRFSRSDELTRHIRI-H--T-------GQK-----PFQCRICMRSFSRS 358 (451)
Q Consensus 313 eKpy~C~~e~Cgk~F~s~s~L~rH~r~-H--t-------geK-----Pf~C~~C~K~F~~~ 358 (451)
+|...|++ |++.|..+.-+....+. + . +.. ...|+.||.+|...
T Consensus 3 ~k~~~CPv--C~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPV--CGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCC--CCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 45678987 99999987665555442 1 1 122 36799999988755
No 108
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=39.54 E-value=21 Score=26.23 Aligned_cols=11 Identities=27% Similarity=0.637 Sum_probs=5.9
Q ss_pred ccCcccccccC
Q psy677 346 FQCRICMRSFS 356 (451)
Q Consensus 346 f~C~~C~K~F~ 356 (451)
|.|..|+..|.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 55555555543
No 109
>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=38.72 E-value=57 Score=23.71 Aligned_cols=27 Identities=22% Similarity=0.680 Sum_probs=17.5
Q ss_pred ccCcccccccCCcchhhhhhhcccCCCceecCCCCC
Q psy677 346 FQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGR 381 (451)
Q Consensus 346 f~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK 381 (451)
|.|+.|+.. ....|+ +...|+|..|++
T Consensus 19 ~~CP~Cg~~--~~~~~~-------~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST--KHYRLK-------TRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe--eeEEeC-------CCCeEECCCCCC
Confidence 789999864 111121 156799999976
No 110
>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=37.41 E-value=28 Score=31.44 Aligned_cols=34 Identities=18% Similarity=0.335 Sum_probs=25.0
Q ss_pred ccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchhh
Q psy677 316 YACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLT 362 (451)
Q Consensus 316 y~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk 362 (451)
..| ..||++|=. .++.|..|+.||..|.....++
T Consensus 10 r~C--p~cg~kFYD-----------Lnk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 10 RIC--PNTGSKFYD-----------LNRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred ccC--CCcCccccc-----------cCCCCccCCCcCCccCcchhhc
Confidence 568 569999832 2357899999999987664444
No 111
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=37.14 E-value=19 Score=27.28 Aligned_cols=11 Identities=27% Similarity=0.836 Sum_probs=6.2
Q ss_pred CccCccccccc
Q psy677 345 PFQCRICMRSF 355 (451)
Q Consensus 345 Pf~C~~C~K~F 355 (451)
.|+|..|++.|
T Consensus 6 ~Y~C~~Cg~~~ 16 (49)
T COG1996 6 EYKCARCGREV 16 (49)
T ss_pred EEEhhhcCCee
Confidence 35555565555
No 112
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=37.03 E-value=36 Score=31.09 Aligned_cols=26 Identities=27% Similarity=0.510 Sum_probs=18.1
Q ss_pred CCCccCCCCCCCCccCChHHHHHHHHHhcCC
Q psy677 313 ERPYACPVENCDRRFSRSDELTRHIRIHTGQ 343 (451)
Q Consensus 313 eKpy~C~~e~Cgk~F~s~s~L~rH~r~Htge 343 (451)
..--.| -+|||.|+ .|+||.++|.+-
T Consensus 74 pD~Iic--LEDGkkfK---SLKRHL~t~~gm 99 (148)
T COG4957 74 PDYIIC--LEDGKKFK---SLKRHLTTHYGL 99 (148)
T ss_pred CCeEEE--eccCcchH---HHHHHHhcccCC
Confidence 333457 56888885 488888888664
No 113
>PHA00626 hypothetical protein
Probab=36.33 E-value=25 Score=27.42 Aligned_cols=14 Identities=21% Similarity=0.612 Sum_probs=9.2
Q ss_pred CceecCCCCCccCC
Q psy677 372 KPFSCDVCGRKFAR 385 (451)
Q Consensus 372 KPfkC~~CgK~Fs~ 385 (451)
..|+|..||..|+.
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 35777777776654
No 114
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=35.60 E-value=16 Score=27.41 Aligned_cols=42 Identities=21% Similarity=0.642 Sum_probs=20.3
Q ss_pred CCccCcc--cccccCCcchhhhhhhcccCCCceecCC----CCCccCCh
Q psy677 344 KPFQCRI--CMRSFSRSDHLTTHIRTHTGEKPFSCDV----CGRKFARS 386 (451)
Q Consensus 344 KPf~C~~--C~K~F~~~s~Lk~H~rtHtGeKPfkC~~----CgK~Fs~~ 386 (451)
++..|+. |...+. +..|..|....-..++..|.. |+..|.+.
T Consensus 8 ~~v~C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~~~ 55 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERVPRE 55 (60)
T ss_dssp SEEE-TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EEEHH
T ss_pred CEeeCCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCccchh
Confidence 3455655 333343 445666666555556666776 76665543
No 115
>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=34.45 E-value=6.5 Score=38.40 Aligned_cols=27 Identities=22% Similarity=0.579 Sum_probs=16.3
Q ss_pred CccCcccccccCCcchhhhhhhcccCC
Q psy677 345 PFQCRICMRSFSRSDHLTTHIRTHTGE 371 (451)
Q Consensus 345 Pf~C~~C~K~F~~~s~Lk~H~rtHtGe 371 (451)
.|.|..|+|.|.-...+++|+...|.+
T Consensus 77 K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 77 KWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp EEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred EECCCCCCcccCChHHHHHHHhhcCHH
Confidence 477777777777777777777655443
No 116
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=33.85 E-value=24 Score=27.81 Aligned_cols=32 Identities=22% Similarity=0.396 Sum_probs=16.7
Q ss_pred CccCcccccccCCcchhhhhhhcccCCCceecCCCCC
Q psy677 345 PFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGR 381 (451)
Q Consensus 345 Pf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK 381 (451)
.|.|+.||+.--.+.. .-.. -..+|+|+.||.
T Consensus 27 ~F~CPnCGe~~I~Rc~----~CRk-~g~~Y~Cp~CGF 58 (61)
T COG2888 27 KFPCPNCGEVEIYRCA----KCRK-LGNPYRCPKCGF 58 (61)
T ss_pred EeeCCCCCceeeehhh----hHHH-cCCceECCCcCc
Confidence 4777777754322111 1111 135788888873
No 117
>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=33.22 E-value=1.3e+02 Score=28.33 Aligned_cols=85 Identities=22% Similarity=0.405 Sum_probs=51.9
Q ss_pred CCCCCccCCCCCCCCccCChHHHHHHHHHhcCC--------------------------CCccCcccccccCCcchhhhh
Q psy677 311 VHERPYACPVENCDRRFSRSDELTRHIRIHTGQ--------------------------KPFQCRICMRSFSRSDHLTTH 364 (451)
Q Consensus 311 ~~eKpy~C~~e~Cgk~F~s~s~L~rH~r~Htge--------------------------KPf~C~~C~K~F~~~s~Lk~H 364 (451)
.|-+||.| +-.|....-|.+-.+.+... ....|+.|.....-..-.. -
T Consensus 25 kgcRpymc-----~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~CPLCRG~V~GWtvve-~ 98 (162)
T PF07800_consen 25 KGCRPYMC-----DTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPELACPLCRGEVKGWTVVE-P 98 (162)
T ss_pred CCcccccc-----CCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccccccccCccccCceeceEEch-H
Confidence 45678886 44666677777666554321 1467888865544443332 3
Q ss_pred hhcccCCCceecCC--CCCccCChHHHHHHHHH-HhCcccc
Q psy677 365 IRTHTGEKPFSCDV--CGRKFARSDEKKRHAKV-HLKQRSK 402 (451)
Q Consensus 365 ~rtHtGeKPfkC~~--CgK~Fs~~s~Lk~Hlrt-H~~er~~ 402 (451)
.|.+...|+-.|.. |... .....|++|.|. |-..++-
T Consensus 99 AR~~LN~K~RsC~~e~C~F~-GtY~eLrKHar~~HP~~rP~ 138 (162)
T PF07800_consen 99 ARRFLNAKKRSCSQESCSFS-GTYSELRKHARSEHPSARPS 138 (162)
T ss_pred HHHHhccCCccCcccccccc-cCHHHHHHHHHhhCCCCCCc
Confidence 56677778877754 6533 345679999864 5455543
No 118
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=32.50 E-value=22 Score=25.44 Aligned_cols=12 Identities=25% Similarity=0.958 Sum_probs=9.2
Q ss_pred ceecCCCCCccC
Q psy677 373 PFSCDVCGRKFA 384 (451)
Q Consensus 373 PfkC~~CgK~Fs 384 (451)
-|.|..|++.|.
T Consensus 28 fy~C~~C~~~w~ 39 (40)
T smart00440 28 FYVCTKCGHRWR 39 (40)
T ss_pred EEEeCCCCCEeC
Confidence 488988988764
No 119
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=31.62 E-value=47 Score=34.41 Aligned_cols=49 Identities=18% Similarity=0.491 Sum_probs=32.2
Q ss_pred cCcccccccCCcchhhhhhhcccCCCceecCCCCCccCChHHHHHHHHHHh
Q psy677 347 QCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFARSDEKKRHAKVHL 397 (451)
Q Consensus 347 ~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~~s~Lk~HlrtH~ 397 (451)
.|-.|...|.....-..-. -+..-.|.|+.|...|-.-.+...|...|.
T Consensus 364 ~Cf~CQ~~fp~~~~~~~~~--~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 364 HCFVCQGPFPKPPVSPFDE--STSSGRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred cceeccCCCCCCCCCcccc--cccccceechhhhhhhhhhhHHHHHHHHhh
Confidence 3777777776533221111 122346999999999998888888887775
No 120
>KOG0978|consensus
Probab=31.62 E-value=29 Score=39.52 Aligned_cols=20 Identities=25% Similarity=0.571 Sum_probs=12.0
Q ss_pred ceecCCCCCccCChHHHHHH
Q psy677 373 PFSCDVCGRKFARSDEKKRH 392 (451)
Q Consensus 373 PfkC~~CgK~Fs~~s~Lk~H 392 (451)
.-+|+.|+..|.-.+-+..|
T Consensus 678 qRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 678 QRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred cCCCCCCCCCCCcccccccC
Confidence 34677777777665554433
No 121
>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=31.49 E-value=25 Score=32.51 Aligned_cols=33 Identities=21% Similarity=0.459 Sum_probs=25.7
Q ss_pred CCCccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccC
Q psy677 313 ERPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFS 356 (451)
Q Consensus 313 eKpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~ 356 (451)
..-|.| +.|+.+|+...++. .-|.|+.||....
T Consensus 107 ~~~Y~C--p~c~~r~tf~eA~~---------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 107 NMFFIC--PNMCVRFTFNEAME---------LNFTCPRCGAMLD 139 (158)
T ss_pred CCeEEC--CCCCcEeeHHHHHH---------cCCcCCCCCCEee
Confidence 456899 55999998888775 2599999998653
No 122
>KOG4173|consensus
Probab=30.66 E-value=17 Score=35.49 Aligned_cols=75 Identities=21% Similarity=0.392 Sum_probs=51.7
Q ss_pred CCccCcc--cccccCCcchhhhhhhcccCCCceecCCCCCccCChHHHHHHHH-HHh---------CcccchHH--HHHH
Q psy677 344 KPFQCRI--CMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFARSDEKKRHAK-VHL---------KQRSKKES--KMAV 409 (451)
Q Consensus 344 KPf~C~~--C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~~s~Lk~Hlr-tH~---------~er~~k~~--~~~~ 409 (451)
+.|.|.+ |-..|...++...|..+-+|. .|..|.+.|....-|..|+. .|- |..-|.|- .|..
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 4588987 888999988888888665553 79999999999999999973 442 23334442 3445
Q ss_pred HHHHHHHHHHHH
Q psy677 410 MMSQQQAQQQQQ 421 (451)
Q Consensus 410 ~~~qqq~qqqhQ 421 (451)
.|........|.
T Consensus 155 KFkT~r~RkdH~ 166 (253)
T KOG4173|consen 155 KFKTSRDRKDHM 166 (253)
T ss_pred hhhhhhhhhhHH
Confidence 555555444443
No 123
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=30.44 E-value=27 Score=33.05 Aligned_cols=34 Identities=24% Similarity=0.603 Sum_probs=25.7
Q ss_pred CCCccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCC
Q psy677 313 ERPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSR 357 (451)
Q Consensus 313 eKpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~ 357 (451)
..-|.| +.|+++|+...++. .-|.|+.||.....
T Consensus 115 ~~~Y~C--p~C~~rytf~eA~~---------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 115 NMFFFC--PNCHIRFTFDEAME---------YGFRCPQCGEMLEE 148 (178)
T ss_pred CCEEEC--CCCCcEEeHHHHhh---------cCCcCCCCCCCCee
Confidence 345899 45999998877653 25999999986544
No 124
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=29.80 E-value=29 Score=29.52 Aligned_cols=32 Identities=19% Similarity=0.517 Sum_probs=22.2
Q ss_pred CCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCC
Q psy677 344 KPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFAR 385 (451)
Q Consensus 344 KPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~ 385 (451)
..|.|++|++.- ++ |. +.-.+.|..|++.|+-
T Consensus 35 a~y~CpfCgk~~-----vk---R~--a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 35 AKYFCPFCGKHA-----VK---RQ--AVGIWRCKGCKKTVAG 66 (90)
T ss_pred CCccCCCCCCCc-----ee---ee--eeEEEEcCCCCCEEeC
Confidence 469999998542 22 11 2346899999999874
No 125
>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=29.74 E-value=48 Score=21.53 Aligned_cols=20 Identities=25% Similarity=0.471 Sum_probs=14.5
Q ss_pred ecCCCCCccCChHHHHHHHHH
Q psy677 375 SCDVCGRKFARSDEKKRHAKV 395 (451)
Q Consensus 375 kC~~CgK~Fs~~s~Lk~Hlrt 395 (451)
.|++|++.+ ....+++|+..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD~ 22 (26)
T smart00734 3 QCPVCFREV-PENLINSHLDS 22 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHHH
Confidence 588888887 55677777753
No 126
>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=28.81 E-value=14 Score=26.30 Aligned_cols=12 Identities=25% Similarity=0.855 Sum_probs=9.2
Q ss_pred ceecCCCCCccC
Q psy677 373 PFSCDVCGRKFA 384 (451)
Q Consensus 373 PfkC~~CgK~Fs 384 (451)
-|.|..|++.|.
T Consensus 28 fy~C~~C~~~wr 39 (39)
T PF01096_consen 28 FYVCCNCGHRWR 39 (39)
T ss_dssp EEEESSSTEEEE
T ss_pred EEEeCCCCCeeC
Confidence 388999988763
No 127
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=28.71 E-value=35 Score=32.16 Aligned_cols=24 Identities=42% Similarity=1.006 Sum_probs=19.4
Q ss_pred CccCCCCCCCCccCChHHHHHHHHHhcCCCCccCccccc
Q psy677 315 PYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMR 353 (451)
Q Consensus 315 py~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K 353 (451)
.|+|++ ||.. |.++-|-+|++|+.
T Consensus 134 ~~vC~v--CGy~-------------~~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPV--CGYT-------------HEGEAPEVCPICGA 157 (166)
T ss_pred EEEcCC--CCCc-------------ccCCCCCcCCCCCC
Confidence 699977 9965 35678999999984
No 128
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=28.53 E-value=38 Score=26.62 Aligned_cols=31 Identities=26% Similarity=0.686 Sum_probs=16.7
Q ss_pred CccCcccccc-cCCcchhhhhhhcccCCCceecCCCCC
Q psy677 345 PFQCRICMRS-FSRSDHLTTHIRTHTGEKPFSCDVCGR 381 (451)
Q Consensus 345 Pf~C~~C~K~-F~~~s~Lk~H~rtHtGeKPfkC~~CgK 381 (451)
.|.|+.||+. -.+-...+ .-..+|+|+.||.
T Consensus 25 ~F~CPnCG~~~I~RC~~CR------k~~~~Y~CP~CGF 56 (59)
T PRK14890 25 KFLCPNCGEVIIYRCEKCR------KQSNPYTCPKCGF 56 (59)
T ss_pred EeeCCCCCCeeEeechhHH------hcCCceECCCCCC
Confidence 4777777765 22211111 1125788888874
No 129
>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=28.49 E-value=27 Score=29.79 Aligned_cols=32 Identities=28% Similarity=0.715 Sum_probs=22.0
Q ss_pred CCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCC
Q psy677 344 KPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFAR 385 (451)
Q Consensus 344 KPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~ 385 (451)
..|.|++|++.- ++ |. +.-.++|..|++.|+-
T Consensus 34 a~y~CpfCgk~~-----vk---R~--a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 34 AKYVCPFCGKKT-----VK---RG--STGIWTCRKCGAKFAG 65 (91)
T ss_pred cCccCCCCCCCc-----eE---EE--eeEEEEcCCCCCEEeC
Confidence 469999998642 11 22 2346899999999864
No 130
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.17 E-value=31 Score=30.46 Aligned_cols=28 Identities=18% Similarity=0.300 Sum_probs=19.3
Q ss_pred cCcccccccCCcchhhhhhhcccCCCceecCCCCCccCC
Q psy677 347 QCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFAR 385 (451)
Q Consensus 347 ~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~ 385 (451)
.|+.|++.|.. | ...|..|++||+.|.+
T Consensus 11 idPetg~KFYD---L--------NrdPiVsPytG~s~P~ 38 (129)
T COG4530 11 IDPETGKKFYD---L--------NRDPIVSPYTGKSYPR 38 (129)
T ss_pred cCccccchhhc---c--------CCCccccCcccccchH
Confidence 57778877753 2 2367788888888844
No 131
>KOG4377|consensus
Probab=27.79 E-value=41 Score=36.00 Aligned_cols=68 Identities=26% Similarity=0.637 Sum_probs=45.0
Q ss_pred CCccCCCCCCCCccCChHHHHHHHHHhcCCC------------CccCc--ccccccCCcchhhhhhhcccCC-----C--
Q psy677 314 RPYACPVENCDRRFSRSDELTRHIRIHTGQK------------PFQCR--ICMRSFSRSDHLTTHIRTHTGE-----K-- 372 (451)
Q Consensus 314 Kpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeK------------Pf~C~--~C~K~F~~~s~Lk~H~rtHtGe-----K-- 372 (451)
.-|.|--+.|+..+..+.+..+|...|...+ -|.|. .|.| ..++...|...|+.. +
T Consensus 270 Ehyhcl~e~C~ykr~~k~DvirH~~~hkkrdnsL~dgf~rfs~syhC~~~~C~k---sTsdV~~h~nFht~~~n~Gfrrt 346 (480)
T KOG4377|consen 270 EHYHCLNEYCFYKRGQKNDVIRHVEIHKKRDNSLIDGFHRFSNSYHCTGQICEK---STSDVLLHDNFHTDKRNNGFRRT 346 (480)
T ss_pred hhhcccCccccccccchhhhHHHHHHHhhcccccccchhhcCccchhhhcccCc---ccccccccCccccccccCceecc
Confidence 4577877789877777999999998886432 25674 4888 445556677666432 1
Q ss_pred ceecCCCC--CccC
Q psy677 373 PFSCDVCG--RKFA 384 (451)
Q Consensus 373 PfkC~~Cg--K~Fs 384 (451)
-|.|..|+ ..|.
T Consensus 347 hfhC~r~gCTdtfK 360 (480)
T KOG4377|consen 347 HFHCQRIGCTDTFK 360 (480)
T ss_pred eeEEeccCCccccc
Confidence 36787776 4444
No 132
>KOG2461|consensus
Probab=27.75 E-value=3.1e+02 Score=29.37 Aligned_cols=57 Identities=9% Similarity=-0.069 Sum_probs=27.5
Q ss_pred CccCChHHHHHHHHHhcCCCCccCcccccccCCcchhhhhhhcccCCCceecCCCCC
Q psy677 325 RRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGR 381 (451)
Q Consensus 325 k~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK 381 (451)
+.+.....+..|...|.++..+.+..+...+.....+..+..+|+..+.+.+..|++
T Consensus 339 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 395 (396)
T KOG2461|consen 339 RTPAGQLIYTQSHSMEVAEPTDMAPNQIWKIYHTGVLGFLIITTDESECNNMSFVCK 395 (396)
T ss_pred cccccccchhhhhhcccCCCCcccccccccceeccccceeeeeccccccccccccCC
Confidence 333333444444455555555555444444444444445555555555555555443
No 133
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=26.19 E-value=55 Score=29.67 Aligned_cols=48 Identities=17% Similarity=0.338 Sum_probs=27.4
Q ss_pred ccCcccccccCCcchhhhhhhcc-----cCCCceecCCCCCccCChHHHHHHH
Q psy677 346 FQCRICMRSFSRSDHLTTHIRTH-----TGEKPFSCDVCGRKFARSDEKKRHA 393 (451)
Q Consensus 346 f~C~~C~K~F~~~s~Lk~H~rtH-----tGeKPfkC~~CgK~Fs~~s~Lk~Hl 393 (451)
-.|..|+..+..-..-..-.++. ..+.-+.|..|||.|-.-+++.+-.
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~~~~ 144 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHWRRME 144 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccHHHHH
Confidence 46999988654322111101111 1234578999999998776665543
No 134
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=25.93 E-value=34 Score=31.83 Aligned_cols=17 Identities=18% Similarity=0.469 Sum_probs=11.9
Q ss_pred CCccCcccccccCCcch
Q psy677 344 KPFQCRICMRSFSRSDH 360 (451)
Q Consensus 344 KPf~C~~C~K~F~~~s~ 360 (451)
+.-.|..|+++|.+...
T Consensus 27 RRReC~~C~~RFTTfE~ 43 (156)
T COG1327 27 RRRECLECGERFTTFER 43 (156)
T ss_pred hhhcccccccccchhhe
Confidence 34578888888876543
No 135
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=25.89 E-value=37 Score=28.99 Aligned_cols=28 Identities=32% Similarity=0.827 Sum_probs=19.5
Q ss_pred CCccCcccccccCCcchhhhhhhcccCCCceecCCCCC
Q psy677 344 KPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGR 381 (451)
Q Consensus 344 KPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK 381 (451)
+|-.|..||..|.+ ..+ .+|-+|+.|..
T Consensus 57 ~Pa~CkkCGfef~~-~~i---------k~pSRCP~CKS 84 (97)
T COG3357 57 RPARCKKCGFEFRD-DKI---------KKPSRCPKCKS 84 (97)
T ss_pred cChhhcccCccccc-ccc---------CCcccCCcchh
Confidence 57788899888865 211 35778888853
No 136
>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=25.61 E-value=46 Score=30.21 Aligned_cols=29 Identities=31% Similarity=0.729 Sum_probs=15.9
Q ss_pred CCCCCccCCCCCCCCccCChHHHHHHHHHhcCCC
Q psy677 311 VHERPYACPVENCDRRFSRSDELTRHIRIHTGQK 344 (451)
Q Consensus 311 ~~eKpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeK 344 (451)
..+.--.| -.||+.|+. |++|++.|+|-.
T Consensus 68 I~~d~i~c--lecGk~~k~---LkrHL~~~~glt 96 (132)
T PF05443_consen 68 ITPDYIIC--LECGKKFKT---LKRHLRTHHGLT 96 (132)
T ss_dssp B-SS-EE---TBT--EESB---HHHHHHHTT-S-
T ss_pred cccCeeEE--ccCCcccch---HHHHHHHccCCC
Confidence 34444668 459999976 689999987643
No 137
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=25.46 E-value=54 Score=29.75 Aligned_cols=38 Identities=18% Similarity=0.541 Sum_probs=25.1
Q ss_pred CCCccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccC
Q psy677 313 ERPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFS 356 (451)
Q Consensus 313 eKpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~ 356 (451)
..-|.| +.|+..|.....+.. .+. ...|.|+.|+....
T Consensus 97 ~~~Y~C--p~C~~~y~~~ea~~~---~d~-~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 97 NAYYKC--PNCQSKYTFLEANQL---LDM-DGTFTCPRCGEELE 134 (147)
T ss_pred CcEEEC--cCCCCEeeHHHHHHh---cCC-CCcEECCCCCCEEE
Confidence 446999 559999986544332 111 34499999998653
No 138
>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=25.14 E-value=25 Score=29.93 Aligned_cols=31 Identities=35% Similarity=0.911 Sum_probs=21.6
Q ss_pred CCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccC
Q psy677 344 KPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFA 384 (451)
Q Consensus 344 KPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs 384 (451)
..|.|++|++.- ++ |.-.| .++|..|++.|+
T Consensus 34 ~ky~Cp~Cgk~~-----vk---R~a~G--IW~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTS-----VK---RVATG--IWKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSE-----EE---EEETT--EEEETTTTEEEE
T ss_pred CCCcCCCCCCce-----eE---EeeeE--EeecCCCCCEEe
Confidence 469999998753 21 23344 499999999886
No 139
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=24.86 E-value=34 Score=29.14 Aligned_cols=32 Identities=31% Similarity=0.645 Sum_probs=21.9
Q ss_pred CCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCC
Q psy677 344 KPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFAR 385 (451)
Q Consensus 344 KPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~ 385 (451)
..|.|++|++.-. + |.- .-.+.|..|++.|+-
T Consensus 35 a~y~CpfCgk~~v-----k---R~a--~GIW~C~~C~~~~AG 66 (90)
T PRK03976 35 AKHVCPVCGRPKV-----K---RVG--TGIWECRKCGAKFAG 66 (90)
T ss_pred cCccCCCCCCCce-----E---EEE--EEEEEcCCCCCEEeC
Confidence 4699999975421 1 222 246899999999864
No 140
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=24.66 E-value=30 Score=31.02 Aligned_cols=32 Identities=28% Similarity=0.791 Sum_probs=16.4
Q ss_pred CccCcccccccCCcchhhhhhhcccCCCceecCCCCCccC
Q psy677 345 PFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFA 384 (451)
Q Consensus 345 Pf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs 384 (451)
.|.|..|+..+. +|.+. ..+.|.|..|+..|.
T Consensus 123 ~~~C~~C~~~~~------r~~~~--~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 123 VYRCPSCGREYK------RHRRS--KRKRYRCGRCGGPLV 154 (157)
T ss_pred EEEcCCCCCEee------eeccc--chhhEECCCCCCEEE
Confidence 366666665542 23332 223367777765543
No 141
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=24.60 E-value=53 Score=32.99 Aligned_cols=63 Identities=24% Similarity=0.579 Sum_probs=36.3
Q ss_pred CCCCCCCCccCCCCCCCCccCChHHHHHHHHHhcCCCCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCC
Q psy677 308 KTPVHERPYACPVENCDRRFSRSDELTRHIRIHTGQKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFAR 385 (451)
Q Consensus 308 kt~~~eKpy~C~~e~Cgk~F~s~s~L~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~ 385 (451)
..+...+.|.| ..|...+ .++.-.....-.|..|.+.|---.. ...-|.--|.|..|++.|.-
T Consensus 105 ~ip~~drqFaC--~~Cd~~W--------wRrvp~rKeVSRCr~C~~rYDPVP~-----dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 105 LIPSVDRQFAC--SSCDHMW--------WRRVPQRKEVSRCRKCRKRYDPVPC-----DKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred cccccceeeec--cccchHH--------HhccCcccccccccccccccCCCcc-----ccccceeeeecccccccchh
Confidence 34555688999 5597543 1222223334568888877743321 11224455888888888764
No 142
>KOG2071|consensus
Probab=24.52 E-value=41 Score=37.46 Aligned_cols=29 Identities=31% Similarity=0.761 Sum_probs=22.6
Q ss_pred CCceecCCCCCccCChHHHHHHHHHHhCc
Q psy677 371 EKPFSCDVCGRKFARSDEKKRHAKVHLKQ 399 (451)
Q Consensus 371 eKPfkC~~CgK~Fs~~s~Lk~HlrtH~~e 399 (451)
.++..|..||++|.......+||..|.+.
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~dw 444 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHDDW 444 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhhhh
Confidence 45678999999998888888887777543
No 143
>KOG4377|consensus
Probab=24.27 E-value=32 Score=36.73 Aligned_cols=82 Identities=27% Similarity=0.568 Sum_probs=49.6
Q ss_pred CccCCCCCCCCccCChHHHHHHHHHhcCC-------CCccCcccc--cccCCcchhhhhhhcccCC----Cc--------
Q psy677 315 PYACPVENCDRRFSRSDELTRHIRIHTGQ-------KPFQCRICM--RSFSRSDHLTTHIRTHTGE----KP-------- 373 (451)
Q Consensus 315 py~C~~e~Cgk~F~s~s~L~rH~r~Htge-------KPf~C~~C~--K~F~~~s~Lk~H~rtHtGe----KP-------- 373 (451)
-|.|....|.| +.++...|-..|+.. .-|.|..|+ -.|....+-..|.+-+.++ +.
T Consensus 313 syhC~~~~C~k---sTsdV~~h~nFht~~~n~GfrrthfhC~r~gCTdtfK~~khk~yh~kdda~~~dGfkkf~k~e~ca 389 (480)
T KOG4377|consen 313 SYHCTGQICEK---STSDVLLHDNFHTDKRNNGFRRTHFHCQRIGCTDTFKDSKHKPYHYKDDAGEIDGFKKFFKDENCA 389 (480)
T ss_pred cchhhhcccCc---ccccccccCccccccccCceecceeEEeccCCccccccccccccccCcchhhhhhhhhhhccccCC
Confidence 37898889988 345566676666532 247888776 5555333333344333221 11
Q ss_pred ------------eecC--CCCCccCChHHHHHHHHHHhCc
Q psy677 374 ------------FSCD--VCGRKFARSDEKKRHAKVHLKQ 399 (451)
Q Consensus 374 ------------fkC~--~CgK~Fs~~s~Lk~HlrtH~~e 399 (451)
|.|. -|+..|...+.+..|.|.|.++
T Consensus 390 y~gCkys~~cnhfhc~r~Gc~~tl~s~sqm~shkrkheRq 429 (480)
T KOG4377|consen 390 YTGCKYSGICNHFHCDRLGCEATLYSVSQMASHKRKHERQ 429 (480)
T ss_pred ccCcccccceeeeeecccCCceEEEehhhhhhhhhhhhhh
Confidence 2333 2788888888899998888643
No 144
>KOG0978|consensus
Probab=23.94 E-value=20 Score=40.82 Aligned_cols=48 Identities=21% Similarity=0.477 Sum_probs=30.5
Q ss_pred ccCCCCCCCCccCChHHHH-HHHH------HhcCCCCccCcccccccCCcchhhhhh
Q psy677 316 YACPVENCDRRFSRSDELT-RHIR------IHTGQKPFQCRICMRSFSRSDHLTTHI 365 (451)
Q Consensus 316 y~C~~e~Cgk~F~s~s~L~-rH~r------~HtgeKPf~C~~C~K~F~~~s~Lk~H~ 365 (451)
..|++ |+.+|+...-.+ .|.. .-...|--+||.|+.+|...+.+..|+
T Consensus 644 LkCs~--Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~I~l 698 (698)
T KOG0978|consen 644 LKCSV--CNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHRIHL 698 (698)
T ss_pred eeCCC--ccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccccccCC
Confidence 56866 887776544322 2432 222334458999999999888776663
No 145
>KOG4124|consensus
Probab=23.82 E-value=28 Score=36.47 Aligned_cols=21 Identities=29% Similarity=0.831 Sum_probs=10.6
Q ss_pred ceecCC--CCCccCChHHHHHHH
Q psy677 373 PFSCDV--CGRKFARSDEKKRHA 393 (451)
Q Consensus 373 PfkC~~--CgK~Fs~~s~Lk~Hl 393 (451)
+|+|.+ |.+.+.....|+.|.
T Consensus 349 ~~~~~vp~~~~~~~n~ng~~~~~ 371 (442)
T KOG4124|consen 349 PYKCPVPNCDKAYKNQNGLKYHK 371 (442)
T ss_pred CCCCCCCcchhhcccCcceeecc
Confidence 345543 555555555555543
No 146
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.67 E-value=29 Score=34.44 Aligned_cols=39 Identities=28% Similarity=0.686 Sum_probs=24.5
Q ss_pred CCCccCcccccccCCcchhhhhhhcccCCC----------c-----eecCCCCC
Q psy677 343 QKPFQCRICMRSFSRSDHLTTHIRTHTGEK----------P-----FSCDVCGR 381 (451)
Q Consensus 343 eKPf~C~~C~K~F~~~s~Lk~H~rtHtGeK----------P-----fkC~~CgK 381 (451)
++.+.|++|+-.|....-+..-.|+-.|+- | ..|+.|+.
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~y 70 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYY 70 (267)
T ss_pred hceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhH
Confidence 455778888877776665555555544331 2 36999974
No 147
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=23.40 E-value=43 Score=30.99 Aligned_cols=19 Identities=16% Similarity=0.436 Sum_probs=12.8
Q ss_pred CCccCcccccccCCcchhh
Q psy677 344 KPFQCRICMRSFSRSDHLT 362 (451)
Q Consensus 344 KPf~C~~C~K~F~~~s~Lk 362 (451)
+.-.|..|+++|.+--.+.
T Consensus 27 RRReC~~C~~RFTTyErve 45 (147)
T TIGR00244 27 RRRECLECHERFTTFERAE 45 (147)
T ss_pred ecccCCccCCccceeeecc
Confidence 3457888888887655443
No 148
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=23.20 E-value=41 Score=31.29 Aligned_cols=32 Identities=31% Similarity=0.966 Sum_probs=16.1
Q ss_pred CccCcccccccCCcchhhhhhhcccCCCceecCCCCC
Q psy677 345 PFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGR 381 (451)
Q Consensus 345 Pf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK 381 (451)
+|.|. |+..|.+ .++|-.+-.|+ .|.|..|+-
T Consensus 117 ~Y~C~-C~q~~l~---~RRhn~~~~g~-~YrC~~C~g 148 (156)
T COG3091 117 PYRCQ-CQQHYLR---IRRHNTVRRGE-VYRCGKCGG 148 (156)
T ss_pred eEEee-cCCccch---hhhcccccccc-eEEeccCCc
Confidence 46666 6655543 22333333444 566666653
No 149
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.89 E-value=42 Score=30.24 Aligned_cols=13 Identities=31% Similarity=0.697 Sum_probs=6.6
Q ss_pred CccCcccccccCC
Q psy677 345 PFQCRICMRSFSR 357 (451)
Q Consensus 345 Pf~C~~C~K~F~~ 357 (451)
.+.|..|+..|..
T Consensus 70 ~~~C~~CG~~~~~ 82 (135)
T PRK03824 70 VLKCRNCGNEWSL 82 (135)
T ss_pred EEECCCCCCEEec
Confidence 3555555555443
No 150
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=22.82 E-value=38 Score=32.83 Aligned_cols=9 Identities=33% Similarity=1.014 Sum_probs=4.5
Q ss_pred ecCCCCCcc
Q psy677 375 SCDVCGRKF 383 (451)
Q Consensus 375 kC~~CgK~F 383 (451)
.|..||.++
T Consensus 45 ~C~~CgYR~ 53 (201)
T COG1779 45 VCERCGYRS 53 (201)
T ss_pred EccccCCcc
Confidence 455555444
No 151
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=22.54 E-value=92 Score=22.35 Aligned_cols=24 Identities=29% Similarity=0.659 Sum_probs=17.0
Q ss_pred eecCCCCCccCC--hHHHHHHHHHHh
Q psy677 374 FSCDVCGRKFAR--SDEKKRHAKVHL 397 (451)
Q Consensus 374 fkC~~CgK~Fs~--~s~Lk~HlrtH~ 397 (451)
-.|..||..|.. ...-+.|.+-|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 478888887764 556677777764
No 152
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=22.15 E-value=33 Score=29.76 Aligned_cols=38 Identities=24% Similarity=0.429 Sum_probs=18.6
Q ss_pred CCCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccC
Q psy677 343 QKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFA 384 (451)
Q Consensus 343 eKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs 384 (451)
.+.|.|+.|+.--.....++.- .+.---.|..||..|.
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~----~~~g~~~Cg~CGls~e 57 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKT----VNIGTAVCGNCGLSFE 57 (104)
T ss_pred CceEecCccCCeeeeEEEEEec----CceeEEEcccCcceEE
Confidence 3456677776544333332211 1112246777777664
No 153
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.14 E-value=99 Score=27.77 Aligned_cols=46 Identities=22% Similarity=0.491 Sum_probs=25.9
Q ss_pred HHHHHHhcCCCCccCcccccccCCcchhhhhhhcccCCCceecCCCCCccCCh
Q psy677 334 TRHIRIHTGQKPFQCRICMRSFSRSDHLTTHIRTHTGEKPFSCDVCGRKFARS 386 (451)
Q Consensus 334 ~rH~r~HtgeKPf~C~~C~K~F~~~s~Lk~H~rtHtGeKPfkC~~CgK~Fs~~ 386 (451)
..+++.+.. .-.|+.|+... ..++-..-.|...|+|..|++.|...
T Consensus 21 ~~~~~~~~~--~~~cP~C~s~~-----~~k~g~~~~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 21 AYAIRMQIT--KVNCPRCKSSN-----VVKIGGIRRGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred HHHHhhhcc--cCcCCCCCccc-----eeeECCccccccccccCCcCcceeee
Confidence 345555433 24688886443 11111122235569999999998754
No 154
>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=21.04 E-value=37 Score=34.26 Aligned_cols=86 Identities=22% Similarity=0.397 Sum_probs=47.8
Q ss_pred CCCCCCCccCCCCCCCCccCChHHHHHHHHH--hcCCCCccCcccccccCCc------chhhhhhhc----ccCCCceec
Q psy677 309 TPVHERPYACPVENCDRRFSRSDELTRHIRI--HTGQKPFQCRICMRSFSRS------DHLTTHIRT----HTGEKPFSC 376 (451)
Q Consensus 309 t~~~eKpy~C~~e~Cgk~F~s~s~L~rH~r~--HtgeKPf~C~~C~K~F~~~------s~Lk~H~rt----HtGeKPfkC 376 (451)
...+.+.|.|.+ |..-. -...--.|... -.....|+|..|++.-... -....|.|. ....+++.|
T Consensus 136 w~hGGrif~Csf--C~~fl-CEDDQFEHQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~k~k~~PC 212 (314)
T PF06524_consen 136 WDHGGRIFKCSF--CDNFL-CEDDQFEHQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYEKGKPIPC 212 (314)
T ss_pred ccCCCeEEEeec--CCCee-eccchhhhhhhhhhhhcccccccccccccchhhhheeeeehhhhhhhcccccccCCCCCC
Confidence 345678899966 87543 33333345433 1123457777776531110 112234443 233478899
Q ss_pred CCCCCccCChHHHHHHHHHHh
Q psy677 377 DVCGRKFARSDEKKRHAKVHL 397 (451)
Q Consensus 377 ~~CgK~Fs~~s~Lk~HlrtH~ 397 (451)
+.|+..-.....|..-.|+|.
T Consensus 213 PKCg~et~eTkdLSmStR~hk 233 (314)
T PF06524_consen 213 PKCGYETQETKDLSMSTRSHK 233 (314)
T ss_pred CCCCCcccccccceeeeecch
Confidence 999977766666666556664
No 155
>KOG3408|consensus
Probab=20.23 E-value=46 Score=29.89 Aligned_cols=26 Identities=35% Similarity=0.581 Sum_probs=22.2
Q ss_pred CCCceecCCCCCccCChHHHHHHHHH
Q psy677 370 GEKPFSCDVCGRKFARSDEKKRHAKV 395 (451)
Q Consensus 370 GeKPfkC~~CgK~Fs~~s~Lk~Hlrt 395 (451)
|.-.|.|-.|.+-|.....|..|.|+
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 44459999999999999999999854
No 156
>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=20.08 E-value=34 Score=24.02 Aligned_cols=9 Identities=33% Similarity=0.837 Sum_probs=5.5
Q ss_pred cCccccccc
Q psy677 347 QCRICMRSF 355 (451)
Q Consensus 347 ~C~~C~K~F 355 (451)
.|+.|++.|
T Consensus 3 ~C~~Cg~~Y 11 (36)
T PF05191_consen 3 ICPKCGRIY 11 (36)
T ss_dssp EETTTTEEE
T ss_pred CcCCCCCcc
Confidence 466666665
No 157
>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=20.06 E-value=57 Score=25.29 Aligned_cols=14 Identities=29% Similarity=0.667 Sum_probs=5.7
Q ss_pred CCccCcccccccCC
Q psy677 344 KPFQCRICMRSFSR 357 (451)
Q Consensus 344 KPf~C~~C~K~F~~ 357 (451)
+.+.|..||+.|-.
T Consensus 24 rrhhCr~CG~~vC~ 37 (69)
T PF01363_consen 24 RRHHCRNCGRVVCS 37 (69)
T ss_dssp -EEE-TTT--EEEC
T ss_pred eeEccCCCCCEECC
Confidence 34566666665543
Done!