Query 040794
Match_columns 375
No_of_seqs 348 out of 2686
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 11:53:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040794.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040794hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462 C2H2-type Zn-finger pr 99.9 2.2E-27 4.8E-32 217.1 5.9 134 181-344 126-265 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.9 1.9E-23 4.1E-28 191.4 6.4 120 212-359 129-251 (279)
3 KOG1074 Transcriptional repres 99.8 5.5E-20 1.2E-24 188.4 2.7 77 258-347 606-692 (958)
4 KOG3576 Ovo and related transc 99.7 1.6E-18 3.5E-23 151.9 3.6 109 213-349 117-239 (267)
5 KOG1074 Transcriptional repres 99.7 2.5E-18 5.5E-23 176.3 3.3 61 178-238 598-658 (958)
6 KOG3608 Zn finger proteins [Ge 99.6 1.2E-16 2.6E-21 150.3 3.3 144 188-359 139-300 (467)
7 KOG3608 Zn finger proteins [Ge 99.6 2.9E-16 6.2E-21 147.8 2.6 160 188-361 182-362 (467)
8 KOG3576 Ovo and related transc 99.4 1.7E-14 3.6E-19 126.8 0.5 116 178-321 110-236 (267)
9 KOG3623 Homeobox transcription 99.4 4.9E-14 1.1E-18 143.0 1.3 80 253-344 890-972 (1007)
10 KOG3623 Homeobox transcription 99.3 2.7E-13 5.9E-18 137.6 1.2 66 292-358 889-957 (1007)
11 PLN03086 PRLI-interacting fact 99.1 8.2E-11 1.8E-15 120.3 8.0 64 282-346 489-564 (567)
12 PHA00733 hypothetical protein 99.1 1.1E-10 2.4E-15 98.4 3.9 81 254-347 37-124 (128)
13 PLN03086 PRLI-interacting fact 99.0 7.3E-10 1.6E-14 113.4 8.8 86 255-359 451-549 (567)
14 PHA02768 hypothetical protein; 98.9 6.6E-10 1.4E-14 78.5 1.5 44 257-314 5-48 (55)
15 PHA00733 hypothetical protein 98.8 3.8E-09 8.2E-14 89.1 3.4 83 210-319 37-121 (128)
16 PHA02768 hypothetical protein; 98.7 7E-09 1.5E-13 73.3 1.8 43 297-339 5-48 (55)
17 PF13465 zf-H2C2_2: Zinc-finge 98.6 2.6E-08 5.7E-13 60.1 2.4 26 284-309 1-26 (26)
18 KOG3993 Transcription factor ( 98.5 4E-08 8.7E-13 95.3 0.7 78 214-319 268-378 (500)
19 PHA00732 hypothetical protein 98.2 8.3E-07 1.8E-11 68.3 1.8 46 257-320 1-47 (79)
20 PHA00616 hypothetical protein 98.1 1.1E-06 2.3E-11 59.3 1.5 33 323-356 1-34 (44)
21 KOG3993 Transcription factor ( 98.1 8.3E-07 1.8E-11 86.3 0.1 81 257-349 267-383 (500)
22 PF13465 zf-H2C2_2: Zinc-finge 98.1 6.3E-07 1.4E-11 54.0 -0.5 25 201-225 2-26 (26)
23 PHA00616 hypothetical protein 97.8 1E-05 2.2E-10 54.6 1.5 40 257-308 1-40 (44)
24 PHA00732 hypothetical protein 97.6 5.3E-05 1.1E-09 58.3 3.4 46 297-345 1-47 (79)
25 PF00096 zf-C2H2: Zinc finger, 97.4 0.00012 2.5E-09 42.5 2.4 21 324-344 1-22 (23)
26 PF00096 zf-C2H2: Zinc finger, 97.4 9.9E-05 2.1E-09 42.8 1.7 22 298-319 1-22 (23)
27 PF13894 zf-C2H2_4: C2H2-type 97.3 0.00025 5.5E-09 41.0 2.6 23 324-346 1-24 (24)
28 PF05605 zf-Di19: Drought indu 97.3 0.00035 7.5E-09 49.7 3.7 46 298-346 3-53 (54)
29 COG5189 SFP1 Putative transcri 97.1 0.00011 2.4E-09 69.4 0.1 50 295-344 347-420 (423)
30 PF13912 zf-C2H2_6: C2H2-type 97.0 0.00037 8.1E-09 42.0 1.7 24 323-346 1-25 (27)
31 PF12756 zf-C2H2_2: C2H2 type 97.0 0.00058 1.3E-08 54.0 3.2 76 259-350 1-78 (100)
32 PF05605 zf-Di19: Drought indu 97.0 0.00076 1.6E-08 48.0 3.1 20 214-234 3-22 (54)
33 PF12756 zf-C2H2_2: C2H2 type 96.6 0.0011 2.4E-08 52.4 2.2 73 215-320 1-73 (100)
34 PF13894 zf-C2H2_4: C2H2-type 96.6 0.0012 2.7E-08 38.0 1.7 23 298-320 1-23 (24)
35 PF13912 zf-C2H2_6: C2H2-type 96.5 0.0013 2.9E-08 39.5 1.4 24 213-236 1-24 (27)
36 COG5189 SFP1 Putative transcri 96.4 0.0014 3.1E-08 62.1 1.4 26 209-234 345-372 (423)
37 PRK04860 hypothetical protein; 96.1 0.0025 5.5E-08 55.7 1.6 40 256-311 118-157 (160)
38 COG5048 FOG: Zn-finger [Genera 96.1 0.0028 6E-08 62.7 2.1 53 184-236 288-346 (467)
39 smart00355 ZnF_C2H2 zinc finge 95.9 0.0053 1.2E-07 35.7 1.8 20 325-344 2-22 (26)
40 smart00355 ZnF_C2H2 zinc finge 95.8 0.0068 1.5E-07 35.2 1.9 23 298-320 1-23 (26)
41 PF09237 GAGA: GAGA factor; I 95.5 0.015 3.2E-07 40.4 3.0 33 253-297 20-52 (54)
42 PF09237 GAGA: GAGA factor; I 94.8 0.015 3.3E-07 40.3 1.5 26 321-346 22-48 (54)
43 PRK04860 hypothetical protein; 94.7 0.019 4.1E-07 50.3 2.1 31 324-358 120-150 (160)
44 PF12874 zf-met: Zinc-finger o 94.5 0.019 4.2E-07 33.6 1.1 23 214-236 1-23 (25)
45 PF12874 zf-met: Zinc-finger o 94.3 0.028 6.1E-07 32.9 1.7 21 324-344 1-22 (25)
46 PF13909 zf-H2C2_5: C2H2-type 94.2 0.036 7.8E-07 32.2 1.9 22 324-346 1-23 (24)
47 KOG2231 Predicted E3 ubiquitin 93.6 0.098 2.1E-06 55.2 5.0 20 299-318 184-203 (669)
48 PF12171 zf-C2H2_jaz: Zinc-fin 93.2 0.054 1.2E-06 32.5 1.5 23 214-236 2-24 (27)
49 COG5048 FOG: Zn-finger [Genera 93.0 0.029 6.3E-07 55.4 0.1 72 212-311 288-367 (467)
50 PF12171 zf-C2H2_jaz: Zinc-fin 91.8 0.037 8E-07 33.2 -0.6 21 324-344 2-23 (27)
51 KOG1146 Homeobox protein [Gene 90.6 0.15 3.3E-06 57.0 2.3 114 216-356 439-623 (1406)
52 PF13913 zf-C2HC_2: zinc-finge 90.3 0.21 4.6E-06 29.5 1.7 20 299-319 4-23 (25)
53 PF13909 zf-H2C2_5: C2H2-type 89.8 0.22 4.8E-06 28.8 1.6 21 298-319 1-21 (24)
54 COG5236 Uncharacterized conser 89.8 0.15 3.3E-06 49.1 1.4 17 331-347 290-306 (493)
55 PF13913 zf-C2HC_2: zinc-finge 88.7 0.34 7.3E-06 28.7 1.8 20 324-344 3-23 (25)
56 smart00451 ZnF_U1 U1-like zinc 87.7 0.41 8.8E-06 30.2 1.9 22 323-344 3-25 (35)
57 KOG2231 Predicted E3 ubiquitin 87.6 0.49 1.1E-05 50.1 3.4 81 258-355 183-275 (669)
58 KOG2186 Cell growth-regulating 86.6 0.5 1.1E-05 43.8 2.5 47 257-318 3-49 (276)
59 smart00451 ZnF_U1 U1-like zinc 85.4 0.47 1E-05 29.9 1.3 22 297-318 3-24 (35)
60 KOG2482 Predicted C2H2-type Zn 84.5 0.88 1.9E-05 44.0 3.1 23 257-291 195-217 (423)
61 KOG1146 Homeobox protein [Gene 83.4 0.27 5.8E-06 55.2 -0.9 109 214-350 1229-1356(1406)
62 KOG2482 Predicted C2H2-type Zn 81.4 2.9 6.3E-05 40.6 5.3 50 297-346 195-303 (423)
63 PF01352 KRAB: KRAB box; Inte 80.5 0.45 9.8E-06 31.8 -0.3 23 128-150 19-41 (41)
64 KOG2893 Zn finger protein [Gen 78.9 0.58 1.2E-05 43.1 -0.3 41 260-316 13-53 (341)
65 COG5236 Uncharacterized conser 78.5 1.4 3E-05 42.8 2.2 64 281-346 165-244 (493)
66 KOG2186 Cell growth-regulating 78.4 1.1 2.5E-05 41.6 1.5 45 298-344 4-50 (276)
67 TIGR00622 ssl1 transcription f 77.6 2.5 5.5E-05 34.6 3.1 45 300-344 58-103 (112)
68 COG4049 Uncharacterized protei 73.9 1.5 3.3E-05 31.0 0.8 28 291-318 11-38 (65)
69 COG1198 PriA Primosomal protei 71.4 3.7 8.1E-05 44.4 3.4 14 293-306 471-484 (730)
70 PF02892 zf-BED: BED zinc fing 70.5 3.9 8.4E-05 27.3 2.2 21 324-344 17-42 (45)
71 KOG2893 Zn finger protein [Gen 70.3 1.5 3.3E-05 40.4 0.2 45 295-342 9-54 (341)
72 smart00614 ZnF_BED BED zinc fi 70.1 3.9 8.4E-05 28.2 2.2 18 327-344 23-45 (50)
73 PF09538 FYDLN_acid: Protein o 69.3 3.5 7.6E-05 33.6 2.1 16 295-310 24-39 (108)
74 KOG4173 Alpha-SNAP protein [In 68.7 3.7 8E-05 37.1 2.2 87 256-355 78-179 (253)
75 cd00350 rubredoxin_like Rubred 63.5 3.9 8.4E-05 25.7 1.0 10 296-305 16-25 (33)
76 PF05443 ROS_MUCR: ROS/MUCR tr 62.6 4.8 0.0001 34.1 1.7 23 321-346 70-93 (132)
77 PF09986 DUF2225: Uncharacteri 61.6 1.5 3.3E-05 40.2 -1.6 40 296-335 4-61 (214)
78 PF09538 FYDLN_acid: Protein o 61.2 5 0.00011 32.7 1.5 12 214-225 10-21 (108)
79 COG2888 Predicted Zn-ribbon RN 60.2 3.8 8.2E-05 29.5 0.6 8 257-264 27-34 (61)
80 PF15269 zf-C2H2_7: Zinc-finge 59.7 7.3 0.00016 26.4 1.8 21 324-344 21-42 (54)
81 PRK09678 DNA-binding transcrip 58.8 3 6.4E-05 31.5 -0.1 17 294-310 24-42 (72)
82 COG1997 RPL43A Ribosomal prote 58.7 3.4 7.4E-05 32.1 0.1 13 321-333 51-64 (89)
83 PRK00464 nrdR transcriptional 56.0 2.2 4.9E-05 37.0 -1.4 18 296-313 27-44 (154)
84 PF09723 Zn-ribbon_8: Zinc rib 55.2 5.3 0.00012 26.6 0.6 17 213-229 5-21 (42)
85 COG4049 Uncharacterized protei 55.1 5.1 0.00011 28.5 0.6 30 207-236 11-41 (65)
86 PHA00626 hypothetical protein 55.1 2.8 6E-05 29.8 -0.8 15 296-310 22-36 (59)
87 cd00729 rubredoxin_SM Rubredox 54.1 11 0.00024 23.9 1.9 12 213-224 2-13 (34)
88 smart00834 CxxC_CXXC_SSSS Puta 53.7 3.5 7.6E-05 26.8 -0.5 7 258-264 6-12 (41)
89 TIGR02300 FYDLN_acid conserved 52.1 11 0.00023 31.6 2.0 16 295-310 24-39 (129)
90 smart00531 TFIIE Transcription 51.6 11 0.00024 32.3 2.2 20 211-230 97-116 (147)
91 KOG2593 Transcription initiati 51.4 5.9 0.00013 39.8 0.5 51 280-331 111-162 (436)
92 smart00531 TFIIE Transcription 50.4 12 0.00026 32.1 2.2 37 293-332 95-133 (147)
93 PF09986 DUF2225: Uncharacteri 47.9 11 0.00025 34.4 1.8 24 212-235 4-27 (214)
94 PF09416 UPF1_Zn_bind: RNA hel 47.8 15 0.00033 31.8 2.4 27 292-318 9-41 (152)
95 PF13717 zinc_ribbon_4: zinc-r 47.8 8.2 0.00018 24.8 0.6 10 298-307 26-35 (36)
96 TIGR02098 MJ0042_CXXC MJ0042 f 47.4 13 0.00029 23.8 1.6 15 214-228 3-17 (38)
97 TIGR00373 conserved hypothetic 45.8 16 0.00034 31.8 2.3 40 285-331 97-137 (158)
98 COG1592 Rubrerythrin [Energy p 45.5 11 0.00023 33.2 1.2 14 291-304 143-156 (166)
99 TIGR02300 FYDLN_acid conserved 45.5 13 0.00028 31.1 1.6 12 214-225 10-21 (129)
100 TIGR00373 conserved hypothetic 45.1 13 0.00028 32.4 1.7 21 210-230 106-126 (158)
101 TIGR02605 CxxC_CxxC_SSSS putat 45.0 5.6 0.00012 27.5 -0.6 7 258-264 6-12 (52)
102 KOG4167 Predicted DNA-binding 44.9 6.2 0.00013 42.1 -0.5 24 297-320 792-815 (907)
103 PRK14873 primosome assembly pr 44.6 19 0.00041 38.8 3.1 11 296-306 421-431 (665)
104 PRK06266 transcription initiat 44.5 13 0.00028 33.1 1.6 20 211-230 115-134 (178)
105 KOG4167 Predicted DNA-binding 44.4 25 0.00054 37.8 3.8 24 213-236 792-815 (907)
106 PF04959 ARS2: Arsenite-resist 44.2 19 0.00041 33.1 2.6 27 321-347 75-102 (214)
107 PF12907 zf-met2: Zinc-binding 43.1 4.8 0.0001 26.7 -1.0 31 324-354 2-36 (40)
108 COG4957 Predicted transcriptio 43.1 16 0.00034 30.9 1.7 20 324-346 77-97 (148)
109 TIGR00622 ssl1 transcription f 43.1 20 0.00043 29.4 2.3 86 213-320 15-104 (112)
110 PF09845 DUF2072: Zn-ribbon co 41.7 17 0.00036 30.7 1.7 15 213-227 1-15 (131)
111 PF15269 zf-C2H2_7: Zinc-finge 41.5 16 0.00035 24.8 1.3 21 298-318 21-41 (54)
112 KOG2785 C2H2-type Zn-finger pr 41.0 69 0.0015 31.8 6.0 79 258-352 167-250 (390)
113 PF04606 Ogr_Delta: Ogr/Delta- 40.6 6.6 0.00014 26.8 -0.7 34 300-333 2-38 (47)
114 PF13719 zinc_ribbon_5: zinc-r 39.6 19 0.00041 23.2 1.4 14 295-308 23-36 (37)
115 PF04959 ARS2: Arsenite-resist 39.5 18 0.0004 33.2 1.8 24 295-318 75-98 (214)
116 PF06524 NOA36: NOA36 protein; 39.2 8 0.00017 36.3 -0.6 87 208-320 137-232 (314)
117 TIGR00595 priA primosomal prot 38.9 24 0.00052 36.7 2.8 13 181-193 209-221 (505)
118 PF12013 DUF3505: Protein of u 38.6 49 0.0011 26.6 4.0 50 256-318 10-105 (109)
119 PRK06266 transcription initiat 37.7 23 0.00049 31.6 2.0 32 294-332 114-146 (178)
120 PRK00464 nrdR transcriptional 36.4 16 0.00034 31.8 0.8 12 256-267 27-38 (154)
121 PRK00398 rpoP DNA-directed RNA 36.3 23 0.0005 23.8 1.4 14 213-226 3-16 (46)
122 TIGR01384 TFS_arch transcripti 35.9 13 0.00028 29.7 0.1 14 213-226 16-29 (104)
123 KOG3408 U1-like Zn-finger-cont 34.4 22 0.00047 29.5 1.2 24 321-344 55-79 (129)
124 PRK14890 putative Zn-ribbon RN 34.2 29 0.00063 25.0 1.7 14 213-226 25-38 (59)
125 COG5151 SSL1 RNA polymerase II 33.8 35 0.00077 32.9 2.7 78 256-345 321-411 (421)
126 PF14353 CpXC: CpXC protein 33.1 34 0.00074 28.3 2.3 21 296-316 37-57 (128)
127 PRK04023 DNA polymerase II lar 32.4 45 0.00098 37.3 3.6 9 214-222 627-635 (1121)
128 COG1592 Rubrerythrin [Energy p 32.3 32 0.00069 30.3 2.0 12 253-264 145-156 (166)
129 PF05191 ADK_lid: Adenylate ki 32.2 32 0.00069 22.2 1.5 14 214-227 2-15 (36)
130 KOG4173 Alpha-SNAP protein [In 31.9 22 0.00049 32.2 1.0 77 214-321 80-171 (253)
131 PF02176 zf-TRAF: TRAF-type zi 31.3 28 0.0006 24.5 1.3 39 296-335 8-55 (60)
132 PRK14873 primosome assembly pr 30.0 23 0.0005 38.2 0.9 26 292-331 405-431 (665)
133 PRK05580 primosome assembly pr 29.9 43 0.00092 36.2 3.0 10 296-305 420-429 (679)
134 PF01780 Ribosomal_L37ae: Ribo 29.0 19 0.00041 28.4 0.0 12 322-333 52-64 (90)
135 COG3364 Zn-ribbon containing p 28.7 31 0.00068 27.7 1.2 16 213-228 2-17 (112)
136 KOG2593 Transcription initiati 28.4 25 0.00055 35.4 0.8 40 207-265 122-161 (436)
137 PRK04023 DNA polymerase II lar 28.0 71 0.0015 35.9 4.1 15 352-366 664-678 (1121)
138 smart00734 ZnF_Rad18 Rad18-lik 28.0 42 0.00092 19.8 1.4 19 299-318 3-21 (26)
139 PRK03824 hypA hydrogenase nick 27.4 38 0.00082 28.7 1.6 15 212-226 69-83 (135)
140 smart00659 RPOLCX RNA polymera 26.8 34 0.00075 23.1 1.0 11 296-306 18-28 (44)
141 PF03604 DNA_RNApol_7kD: DNA d 25.9 48 0.001 20.8 1.5 11 214-224 1-11 (32)
142 COG3091 SprT Zn-dependent meta 25.7 33 0.00072 29.7 1.0 12 323-334 117-128 (156)
143 PTZ00255 60S ribosomal protein 25.4 28 0.0006 27.4 0.4 12 322-333 53-65 (90)
144 PF06524 NOA36: NOA36 protein; 24.7 95 0.0021 29.4 3.8 24 321-344 207-231 (314)
145 TIGR00280 L37a ribosomal prote 24.4 27 0.00058 27.6 0.1 12 322-333 52-64 (91)
146 TIGR01206 lysW lysine biosynth 24.1 32 0.0007 24.4 0.5 10 298-307 23-32 (54)
147 PF05443 ROS_MUCR: ROS/MUCR tr 23.8 38 0.00083 28.6 1.0 26 257-297 72-97 (132)
148 KOG4377 Zn-finger protein [Gen 23.5 31 0.00068 34.5 0.5 116 211-345 269-426 (480)
149 PF12760 Zn_Tnp_IS1595: Transp 23.3 34 0.00074 23.0 0.5 8 298-305 19-26 (46)
150 PRK12380 hydrogenase nickel in 23.3 51 0.0011 27.0 1.6 14 212-225 69-82 (113)
151 COG1571 Predicted DNA-binding 21.8 48 0.0011 33.5 1.4 17 294-310 364-380 (421)
152 KOG0717 Molecular chaperone (D 21.6 62 0.0013 33.1 2.1 21 324-344 293-314 (508)
153 PF07754 DUF1610: Domain of un 21.0 49 0.0011 19.4 0.8 9 213-221 16-24 (24)
154 PRK00432 30S ribosomal protein 20.9 55 0.0012 22.7 1.1 13 296-308 36-48 (50)
155 PF07975 C1_4: TFIIH C1-like d 20.9 60 0.0013 22.7 1.3 25 212-236 20-44 (51)
156 COG4896 Uncharacterized protei 20.7 46 0.00099 24.2 0.7 40 258-308 3-42 (68)
157 KOG2932 E3 ubiquitin ligase in 20.0 90 0.0019 30.3 2.7 27 320-346 141-171 (389)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.94 E-value=2.2e-27 Score=217.13 Aligned_cols=134 Identities=28% Similarity=0.464 Sum_probs=124.5
Q ss_pred CCCCCCCCCCCCCCCCCCcCCCCccccccC---CCceecCcccccccCchHHhhcccccCCCCCCCCCCcCCCCCCCCcc
Q 040794 181 GGDDSSAGYPFNRLNKGQYWIPTPSQILIG---PTQFSCPVCCKTFNRYNNMQMHMWGHGSQYRKGPESLRGTQPTGMLR 257 (375)
Q Consensus 181 ~~~~~~~~~~~~~~~~~~~~l~~h~~~h~g---~kp~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~ 257 (375)
.....+.|..|++.+.....|.+|.|+|-. .+.+.|+.|+|.|..-..|.+|+++|+ .+
T Consensus 126 ~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~------------------l~ 187 (279)
T KOG2462|consen 126 AKHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT------------------LP 187 (279)
T ss_pred ccCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC------------------CC
Confidence 344456788899999999999999999865 667999999999999999999999993 68
Q ss_pred cccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcCCCccccccccccccChhhHHHHHHhc--CCCeee-ecCcccCC
Q 040794 258 LPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHGIKPFMCRKCGKAFAVRGDWRTHEKNC--GKLWYC-ICGSDFKH 334 (375)
Q Consensus 258 ~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~gekpy~C~~Cgk~F~~~~~L~~H~k~h--~k~~~C-~Cgk~F~~ 334 (375)
++|.+|| |.|...=-|+.|+|+|||||||.|..|+|+|+.+++|+.||.|| .|+|+| .|+|+|++
T Consensus 188 c~C~iCG------------KaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl 255 (279)
T KOG2462|consen 188 CECGICG------------KAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFAL 255 (279)
T ss_pred ccccccc------------ccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHH
Confidence 9999999 99999999999999999999999999999999999999999998 699999 99999999
Q ss_pred hHHHHHHHHH
Q 040794 335 KRSLKDHIKA 344 (375)
Q Consensus 335 ~~~L~~H~r~ 344 (375)
++.|.+|...
T Consensus 256 ~SyLnKH~ES 265 (279)
T KOG2462|consen 256 KSYLNKHSES 265 (279)
T ss_pred HHHHHHhhhh
Confidence 9999999876
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.88 E-value=1.9e-23 Score=191.39 Aligned_cols=120 Identities=23% Similarity=0.479 Sum_probs=111.1
Q ss_pred CceecCcccccccCchHHhhcccccCCCCCCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHh
Q 040794 212 TQFSCPVCCKTFNRYNNMQMHMWGHGSQYRKGPESLRGTQPTGMLRLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKR 291 (375)
Q Consensus 212 kp~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~ 291 (375)
..|+|+.|||.+.+.++|.+|+.+|-.- ...+-+.|..|+ |.|.....|..|+|+
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~-------------~s~ka~~C~~C~------------K~YvSmpALkMHirT 183 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSL-------------DSKKAFSCKYCG------------KVYVSMPALKMHIRT 183 (279)
T ss_pred Cceeccccccccccccccchhhcccccc-------------cccccccCCCCC------------ceeeehHHHhhHhhc
Confidence 3599999999999999999999999321 335779999999 999999999999999
Q ss_pred hcCCCccccccccccccChhhHHHHHHhc--CCCeee-ecCcccCChHHHHHHHHHhCCCCCCCCCCCCCC
Q 040794 292 KHGIKPFMCRKCGKAFAVRGDWRTHEKNC--GKLWYC-ICGSDFKHKRSLKDHIKAFGNGHAAYGIDGFEE 359 (375)
Q Consensus 292 H~gekpy~C~~Cgk~F~~~~~L~~H~k~h--~k~~~C-~Cgk~F~~~~~L~~H~r~~H~ge~~y~C~~~~~ 359 (375)
|+ -+++|.+|||+|.+..-|+.|+|+| ||||.| .|+|+|+.+++|+.||++ |.+.|.|+|.+|.+
T Consensus 184 H~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQT-HS~~K~~qC~~C~K 251 (279)
T KOG2462|consen 184 HT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQT-HSDVKKHQCPRCGK 251 (279)
T ss_pred cC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHh-hcCCccccCcchhh
Confidence 98 7899999999999999999999976 999999 999999999999999999 89999999999964
No 3
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.78 E-value=5.5e-20 Score=188.40 Aligned_cols=77 Identities=31% Similarity=0.686 Sum_probs=70.7
Q ss_pred cccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcCCCccccccccccccChhhHHHHHHhcC------CCeee----e
Q 040794 258 LPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHGIKPFMCRKCGKAFAVRGDWRTHEKNCG------KLWYC----I 327 (375)
Q Consensus 258 ~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~gekpy~C~~Cgk~F~~~~~L~~H~k~h~------k~~~C----~ 327 (375)
-+|.+|. |+++.++.|+-|+|+|+|||||+|.+||++|+.+++|+.||.+|. -++.| +
T Consensus 606 NqCiiC~------------rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~i 673 (958)
T KOG1074|consen 606 NQCIICL------------RVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFI 673 (958)
T ss_pred cceeeee------------ecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhh
Confidence 4588888 999999999999999999999999999999999999999999983 35778 6
Q ss_pred cCcccCChHHHHHHHHHhCC
Q 040794 328 CGSDFKHKRSLKDHIKAFGN 347 (375)
Q Consensus 328 Cgk~F~~~~~L~~H~r~~H~ 347 (375)
|-+.|.....|..|+|+ |.
T Consensus 674 c~~kftn~V~lpQhIri-H~ 692 (958)
T KOG1074|consen 674 CQKKFTNAVTLPQHIRI-HL 692 (958)
T ss_pred hcccccccccccceEEe-ec
Confidence 99999999999999999 55
No 4
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.73 E-value=1.6e-18 Score=151.90 Aligned_cols=109 Identities=29% Similarity=0.546 Sum_probs=101.8
Q ss_pred ceecCcccccccCchHHhhcccccCCCCCCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhh
Q 040794 213 QFSCPVCCKTFNRYNNMQMHMWGHGSQYRKGPESLRGTQPTGMLRLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRK 292 (375)
Q Consensus 213 p~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H 292 (375)
.|.|.+|+|.|.-...|.+|++.| ...+++.|..|| |.|.+.-.|++|+|+|
T Consensus 117 ~ftCrvCgK~F~lQRmlnrh~kch----------------~~vkr~lct~cg------------kgfndtfdlkrh~rth 168 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRMLNRHLKCH----------------SDVKRHLCTFCG------------KGFNDTFDLKRHTRTH 168 (267)
T ss_pred eeeeehhhhhhhHHHHHHHHhhhc----------------cHHHHHHHhhcc------------Ccccchhhhhhhhccc
Confidence 599999999999999999999999 888999999999 9999999999999999
Q ss_pred cCCCccccccccccccChhhHHHHHH-hc------------CCCeee-ecCcccCChHHHHHHHHHhCCCC
Q 040794 293 HGIKPFMCRKCGKAFAVRGDWRTHEK-NC------------GKLWYC-ICGSDFKHKRSLKDHIKAFGNGH 349 (375)
Q Consensus 293 ~gekpy~C~~Cgk~F~~~~~L~~H~k-~h------------~k~~~C-~Cgk~F~~~~~L~~H~r~~H~ge 349 (375)
||.+||+|..|+|+|+++..|..|++ +| .|.|+| .||.+-.....+..|++.+|...
T Consensus 169 tgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~S 239 (267)
T KOG3576|consen 169 TGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFS 239 (267)
T ss_pred cCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCC
Confidence 99999999999999999999999987 34 378999 99999999999999999988764
No 5
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.71 E-value=2.5e-18 Score=176.34 Aligned_cols=61 Identities=18% Similarity=0.299 Sum_probs=54.7
Q ss_pred CCCCCCCCCCCCCCCCCCCCCcCCCCccccccCCCceecCcccccccCchHHhhcccccCC
Q 040794 178 GDHGGDDSSAGYPFNRLNKGQYWIPTPSQILIGPTQFSCPVCCKTFNRYNNMQMHMWGHGS 238 (375)
Q Consensus 178 ~~~~~~~~~~~~~~~~~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~~~~L~~H~~~H~~ 238 (375)
.+.....+..|-.|.++..-++.|+.|+|+|+|++||+|.+||++|.++.||+.||.+|..
T Consensus 598 ~~~~~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka 658 (958)
T KOG1074|consen 598 SENKRTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKA 658 (958)
T ss_pred cccccCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhccccccc
Confidence 3445556677899999999999999999999999999999999999999999999999953
No 6
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.63 E-value=1.2e-16 Score=150.27 Aligned_cols=144 Identities=17% Similarity=0.264 Sum_probs=129.7
Q ss_pred CCCCCCCCCCCcCCCCccccccC------------CCc-eecCc--ccccccCchHHhhcccccCCCCCCCCCCcCCCCC
Q 040794 188 GYPFNRLNKGQYWIPTPSQILIG------------PTQ-FSCPV--CCKTFNRYNNMQMHMWGHGSQYRKGPESLRGTQP 252 (375)
Q Consensus 188 ~~~~~~~~~~~~~l~~h~~~h~g------------~kp-~~C~~--C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~ 252 (375)
...|++.|....|+..|...|+. ++| +.|.- |.+.|..+.+|..|.++|
T Consensus 139 WedCe~~F~s~~ef~dHV~~H~l~ceyd~~~~~~D~~pv~~C~W~~Ct~~~~~k~~LreH~r~H---------------- 202 (467)
T KOG3608|consen 139 WEDCEREFVSIVEFQDHVVKHALFCEYDIQKTPEDERPVTMCNWAMCTKHMGNKYRLREHIRTH---------------- 202 (467)
T ss_pred hhhcCCcccCHHHHHHHHHHhhhhhhhhhhhCCCCCCceeeccchhhhhhhccHHHHHHHHHhc----------------
Confidence 36788999999998888766543 334 66754 999999999999999999
Q ss_pred CCCcccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcC--CCccccccccccccChhhHHHHHHhcCCCeee-ecC
Q 040794 253 TGMLRLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHG--IKPFMCRKCGKAFAVRGDWRTHEKNCGKLWYC-ICG 329 (375)
Q Consensus 253 ~~~~~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~g--ekpy~C~~Cgk~F~~~~~L~~H~k~h~k~~~C-~Cg 329 (375)
+++|...|+.|| ..|..+..|..|+|..+. ..+|+|..|-|.|+....|+.|+..|..-|+| .|+
T Consensus 203 s~eKvvACp~Cg------------~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCd 270 (467)
T KOG3608|consen 203 SNEKVVACPHCG------------ELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCD 270 (467)
T ss_pred CCCeEEecchHH------------HHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccc
Confidence 899999999999 999999999999998763 57999999999999999999999999999999 999
Q ss_pred cccCChHHHHHHHHHhCCCCCCCCCCCCCC
Q 040794 330 SDFKHKRSLKDHIKAFGNGHAAYGIDGFEE 359 (375)
Q Consensus 330 k~F~~~~~L~~H~r~~H~ge~~y~C~~~~~ 359 (375)
.+....++|.+|||..|...|||+||.||.
T Consensus 271 mtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~ 300 (467)
T KOG3608|consen 271 MTCSSASSLTTHIRYRHSKDKPFKCDECDT 300 (467)
T ss_pred cCCCChHHHHHHHHhhhccCCCccccchhh
Confidence 999999999999999999999999999974
No 7
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.60 E-value=2.9e-16 Score=147.79 Aligned_cols=160 Identities=15% Similarity=0.254 Sum_probs=114.3
Q ss_pred CCCCCCCCCCCcCCCCccccccCCCceecCcccccccCchHHhhcccccCCCCCCCCCCcCCCCCCCCcccccCCCCCCC
Q 040794 188 GYPFNRLNKGQYWIPTPSQILIGPTQFSCPVCCKTFNRYNNMQMHMWGHGSQYRKGPESLRGTQPTGMLRLPCYCCAPGC 267 (375)
Q Consensus 188 ~~~~~~~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~~ 267 (375)
...|.+.+..++.|+.|++.|+++|...|+.||..|.++..|..|.+..+. ....+|+|..|.+.|
T Consensus 182 W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~--------------l~~n~fqC~~C~KrF 247 (467)
T KOG3608|consen 182 WAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTE--------------LNTNSFQCAQCFKRF 247 (467)
T ss_pred chhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhh--------------hcCCchHHHHHHHHH
Confidence 466888888999999999999999999999999999999988888876531 112244444444111
Q ss_pred CCC--------------CCCCCCcccCCHHHHHHHHH-hhcCCCccccccccccccChhhHHHHHHhc-CCCeee-e--c
Q 040794 268 RNN--------------IDHPRAKPLKDFRTLQTHYK-RKHGIKPFMCRKCGKAFAVRGDWRTHEKNC-GKLWYC-I--C 328 (375)
Q Consensus 268 ~~~--------------~~h~~~k~f~~~~~L~~H~r-~H~gekpy~C~~Cgk~F~~~~~L~~H~k~h-~k~~~C-~--C 328 (375)
+-. .+--...+....++|.+|+| .|...|||+|..|++.|.+.+.|.+|..+| +-.|.| . |
T Consensus 248 aTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C 327 (467)
T KOG3608|consen 248 ATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEHPDC 327 (467)
T ss_pred hHHHHHHHHHHHhhhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccccceecCCCCC
Confidence 000 00000044455667777766 366788888888888888888888888888 556888 3 8
Q ss_pred CcccCChHHHHHHHHHhCCCC--CCCCCCCCCCCC
Q 040794 329 GSDFKHKRSLKDHIKAFGNGH--AAYGIDGFEEED 361 (375)
Q Consensus 329 gk~F~~~~~L~~H~r~~H~ge--~~y~C~~~~~~~ 361 (375)
..+|+....|++|++.+|.|. .+|+|-.||.--
T Consensus 328 ~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~f 362 (467)
T KOG3608|consen 328 HYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFF 362 (467)
T ss_pred cHHHHHHHHHHHHHHHhccCCCCCceeeecchhhh
Confidence 888888888888888877664 578888887644
No 8
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.44 E-value=1.7e-14 Score=126.76 Aligned_cols=116 Identities=23% Similarity=0.350 Sum_probs=104.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCcCCCCccccccCCCceecCcccccccCchHHhhcccccCCCCCCCCCCcCCCCCCCCcc
Q 040794 178 GDHGGDDSSAGYPFNRLNKGQYWIPTPSQILIGPTQFSCPVCCKTFNRYNNMQMHMWGHGSQYRKGPESLRGTQPTGMLR 257 (375)
Q Consensus 178 ~~~~~~~~~~~~~~~~~~~~~~~l~~h~~~h~g~kp~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~ 257 (375)
+...+...+.|..|+|.|..+..|.+|++.|...|.|.|..|||.|+..-.|++|+++| +|.+|
T Consensus 110 gsssd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rth----------------tgvrp 173 (267)
T KOG3576|consen 110 GSSSDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTH----------------TGVRP 173 (267)
T ss_pred cCCCCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccc----------------cCccc
Confidence 34455677889999999999999999999999999999999999999999999999999 99999
Q ss_pred cccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcC-----------CCccccccccccccChhhHHHHHHhcC
Q 040794 258 LPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHG-----------IKPFMCRKCGKAFAVRGDWRTHEKNCG 321 (375)
Q Consensus 258 ~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~g-----------ekpy~C~~Cgk~F~~~~~L~~H~k~h~ 321 (375)
|+|..|+ |.|++.-.|..|.+.-+| .|-|.|..||.+-.....+..|++.+.
T Consensus 174 ykc~~c~------------kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~h 236 (267)
T KOG3576|consen 174 YKCSLCE------------KAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHH 236 (267)
T ss_pred cchhhhh------------HHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcC
Confidence 9999999 999999999999875433 477999999999999999999998763
No 9
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.40 E-value=4.9e-14 Score=142.96 Aligned_cols=80 Identities=26% Similarity=0.492 Sum_probs=67.1
Q ss_pred CCCcccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcCCCccccccccccccChhhHHHHHHhc--CCCeee-ecC
Q 040794 253 TGMLRLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHGIKPFMCRKCGKAFAVRGDWRTHEKNC--GKLWYC-ICG 329 (375)
Q Consensus 253 ~~~~~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~gekpy~C~~Cgk~F~~~~~L~~H~k~h--~k~~~C-~Cg 329 (375)
+...+|.|..|. |.|...+.|.+|.--|+|.|||+|.+|.|+|..+-+|+.|+|.| +|||+| .|+
T Consensus 890 te~gmyaCDqCD------------K~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKCl 957 (1007)
T KOG3623|consen 890 TEDGMYACDQCD------------KAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCL 957 (1007)
T ss_pred CccccchHHHHH------------HHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhh
Confidence 445678888888 88888888888888888888888888888888888888888865 788888 888
Q ss_pred cccCChHHHHHHHHH
Q 040794 330 SDFKHKRSLKDHIKA 344 (375)
Q Consensus 330 k~F~~~~~L~~H~r~ 344 (375)
|+|+++.+.-.||..
T Consensus 958 KRFSHSGSYSQHMNH 972 (1007)
T KOG3623|consen 958 KRFSHSGSYSQHMNH 972 (1007)
T ss_pred hhcccccchHhhhcc
Confidence 888888888888874
No 10
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.33 E-value=2.7e-13 Score=137.64 Aligned_cols=66 Identities=27% Similarity=0.550 Sum_probs=61.2
Q ss_pred hcCCCccccccccccccChhhHHHHHHhc--CCCeee-ecCcccCChHHHHHHHHHhCCCCCCCCCCCCC
Q 040794 292 KHGIKPFMCRKCGKAFAVRGDWRTHEKNC--GKLWYC-ICGSDFKHKRSLKDHIKAFGNGHAAYGIDGFE 358 (375)
Q Consensus 292 H~gekpy~C~~Cgk~F~~~~~L~~H~k~h--~k~~~C-~Cgk~F~~~~~L~~H~r~~H~ge~~y~C~~~~ 358 (375)
.+.+-+|.|..|+|+|...+.|.+|+--| .|||+| +|.|+|++|..|..|+|. |.|||||+||.|.
T Consensus 889 kte~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRL-HSGEKPfQCdKCl 957 (1007)
T KOG3623|consen 889 KTEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRL-HSGEKPFQCDKCL 957 (1007)
T ss_pred cCccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhh-ccCCCcchhhhhh
Confidence 35567899999999999999999998855 799999 999999999999999999 9999999999884
No 11
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.14 E-value=8.2e-11 Score=120.27 Aligned_cols=64 Identities=22% Similarity=0.385 Sum_probs=31.3
Q ss_pred HHHHHHHHHhhcCCCccccccccccccC----------hhhHHHHHHhc-CCCeee-ecCcccCChHHHHHHHHHhC
Q 040794 282 FRTLQTHYKRKHGIKPFMCRKCGKAFAV----------RGDWRTHEKNC-GKLWYC-ICGSDFKHKRSLKDHIKAFG 346 (375)
Q Consensus 282 ~~~L~~H~r~H~gekpy~C~~Cgk~F~~----------~~~L~~H~k~h-~k~~~C-~Cgk~F~~~~~L~~H~r~~H 346 (375)
+..|..|+++|.+.|++.|..|++.|.. ...|..|+.++ .+++.| .||+.|..+ .|..|+...|
T Consensus 489 R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~C~~Cgk~Vrlr-dm~~H~~~~h 564 (567)
T PLN03086 489 KEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTAPCDSCGRSVMLK-EMDIHQIAVH 564 (567)
T ss_pred hhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhcCCcceEccccCCeeeeh-hHHHHHHHhh
Confidence 3455555555555555555555555521 22455555544 355555 555554444 3445544433
No 12
>PHA00733 hypothetical protein
Probab=99.06 E-value=1.1e-10 Score=98.39 Aligned_cols=81 Identities=20% Similarity=0.355 Sum_probs=67.7
Q ss_pred CCcccccCCCCCCCCCCCCCCCCcccCCHHH------HHHHHHhhcCCCccccccccccccChhhHHHHHHhcCCCeee-
Q 040794 254 GMLRLPCYCCAPGCRNNIDHPRAKPLKDFRT------LQTHYKRKHGIKPFMCRKCGKAFAVRGDWRTHEKNCGKLWYC- 326 (375)
Q Consensus 254 ~~~~~~C~~Cg~~~~~~~~h~~~k~f~~~~~------L~~H~r~H~gekpy~C~~Cgk~F~~~~~L~~H~k~h~k~~~C- 326 (375)
..+++.|.+|. +.|..... |.+|+.. .+.+||.|..||+.|.....|..|++++.++|.|
T Consensus 37 ~~~~~~~~~~~------------~~~~~~~~l~~~~~l~~~~~~-~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~ 103 (128)
T PHA00733 37 EQKRLIRAVVK------------TLIYNPQLLDESSYLYKLLTS-KAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCP 103 (128)
T ss_pred hhhhHHHHHHh------------hhccChhhhcchHHHHhhccc-CCCCCccCCCCCCcCCCHHHHHHHHhcCCcCccCC
Confidence 34788999998 55554443 4445434 4589999999999999999999999988889999
Q ss_pred ecCcccCChHHHHHHHHHhCC
Q 040794 327 ICGSDFKHKRSLKDHIKAFGN 347 (375)
Q Consensus 327 ~Cgk~F~~~~~L~~H~r~~H~ 347 (375)
.|++.|.....|++|++.+|.
T Consensus 104 ~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 104 VCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCccCCHHHHHHHHHHhcC
Confidence 999999999999999998775
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.02 E-value=7.3e-10 Score=113.37 Aligned_cols=86 Identities=21% Similarity=0.466 Sum_probs=73.9
Q ss_pred CcccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcCCCccccccccccccChhhHHHHHHhc--CCCeee-ecCcc
Q 040794 255 MLRLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHGIKPFMCRKCGKAFAVRGDWRTHEKNC--GKLWYC-ICGSD 331 (375)
Q Consensus 255 ~~~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~gekpy~C~~Cgk~F~~~~~L~~H~k~h--~k~~~C-~Cgk~ 331 (375)
...+.|..|+ +.|. ...|..|+++|+ ++|.|+ ||+.| .+..|..|+.+| .|++.| .|++.
T Consensus 451 ~~H~~C~~Cg------------k~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~ 513 (567)
T PLN03086 451 KNHVHCEKCG------------QAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDM 513 (567)
T ss_pred ccCccCCCCC------------Cccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCc
Confidence 3556899999 8885 688999999986 899999 99765 678999999876 799999 99999
Q ss_pred cC----------ChHHHHHHHHHhCCCCCCCCCCCCCC
Q 040794 332 FK----------HKRSLKDHIKAFGNGHAAYGIDGFEE 359 (375)
Q Consensus 332 F~----------~~~~L~~H~r~~H~ge~~y~C~~~~~ 359 (375)
|. ..+.|..|..+. |.+++.|+.|+.
T Consensus 514 v~~g~~~~d~~d~~s~Lt~HE~~C--G~rt~~C~~Cgk 549 (567)
T PLN03086 514 VQAGGSAMDVRDRLRGMSEHESIC--GSRTAPCDSCGR 549 (567)
T ss_pred cccCccccchhhhhhhHHHHHHhc--CCcceEccccCC
Confidence 95 246899999983 999999999974
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.87 E-value=6.6e-10 Score=78.49 Aligned_cols=44 Identities=14% Similarity=0.368 Sum_probs=28.4
Q ss_pred ccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcCCCccccccccccccChhhHH
Q 040794 257 RLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHGIKPFMCRKCGKAFAVRGDWR 314 (375)
Q Consensus 257 ~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~gekpy~C~~Cgk~F~~~~~L~ 314 (375)
.|+|+.|| |.|+..++|.+|+|+|+ ++|+|..|++.|.+.+.|+
T Consensus 5 ~y~C~~CG------------K~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICG------------EIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhC------------CeeccHHHHHHHHHhcC--CcccCCcccceecccceeE
Confidence 36666666 66666666666666666 5666666666666655543
No 15
>PHA00733 hypothetical protein
Probab=98.78 E-value=3.8e-09 Score=89.05 Aligned_cols=83 Identities=14% Similarity=0.224 Sum_probs=68.4
Q ss_pred CCCceecCcccccccCchHHhhc--ccccCCCCCCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCcccCCHHHHHH
Q 040794 210 GPTQFSCPVCCKTFNRYNNMQMH--MWGHGSQYRKGPESLRGTQPTGMLRLPCYCCAPGCRNNIDHPRAKPLKDFRTLQT 287 (375)
Q Consensus 210 g~kp~~C~~C~k~F~~~~~L~~H--~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~ 287 (375)
..+++.|.+|.+.|.....|..+ ++.|.. ..+.++|.|..|+ +.|.....|..
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~-------------~~~~kPy~C~~Cg------------k~Fss~s~L~~ 91 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLT-------------SKAVSPYVCPLCL------------MPFSSSVSLKQ 91 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcc-------------cCCCCCccCCCCC------------CcCCCHHHHHH
Confidence 35689999999999988887766 222210 0346789999999 99999999999
Q ss_pred HHHhhcCCCccccccccccccChhhHHHHHHh
Q 040794 288 HYKRKHGIKPFMCRKCGKAFAVRGDWRTHEKN 319 (375)
Q Consensus 288 H~r~H~gekpy~C~~Cgk~F~~~~~L~~H~k~ 319 (375)
|+++| .++|.|..|+++|.....|..|+..
T Consensus 92 H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~ 121 (128)
T PHA00733 92 HIRYT--EHSKVCPVCGKEFRNTDSTLDHVCK 121 (128)
T ss_pred HHhcC--CcCccCCCCCCccCCHHHHHHHHHH
Confidence 99987 4689999999999999999999874
No 16
>PHA02768 hypothetical protein; Provisional
Probab=98.69 E-value=7e-09 Score=73.32 Aligned_cols=43 Identities=16% Similarity=0.230 Sum_probs=40.6
Q ss_pred ccccccccccccChhhHHHHHHhcCCCeee-ecCcccCChHHHH
Q 040794 297 PFMCRKCGKAFAVRGDWRTHEKNCGKLWYC-ICGSDFKHKRSLK 339 (375)
Q Consensus 297 py~C~~Cgk~F~~~~~L~~H~k~h~k~~~C-~Cgk~F~~~~~L~ 339 (375)
-|.|++|||.|++..+|..|+++|.++|+| .|+|.|.+++.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcCCcccCCcccceecccceeE
Confidence 489999999999999999999999999999 9999999988774
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=98.60 E-value=2.6e-08 Score=60.10 Aligned_cols=26 Identities=38% Similarity=0.892 Sum_probs=24.2
Q ss_pred HHHHHHHhhcCCCccccccccccccC
Q 040794 284 TLQTHYKRKHGIKPFMCRKCGKAFAV 309 (375)
Q Consensus 284 ~L~~H~r~H~gekpy~C~~Cgk~F~~ 309 (375)
+|.+|+++|+|+|||.|+.|+++|.+
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 58999999999999999999999974
No 18
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.46 E-value=4e-08 Score=95.32 Aligned_cols=78 Identities=21% Similarity=0.416 Sum_probs=61.0
Q ss_pred eecCcccccccCchHHhhcccccCCCCCCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhc
Q 040794 214 FSCPVCCKTFNRYNNMQMHMWGHGSQYRKGPESLRGTQPTGMLRLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKH 293 (375)
Q Consensus 214 ~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~ 293 (375)
|.|..|...|...-.|..|.-.. .-..-|.|+.|+ |.|....+|..|.|.|.
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~R----------------IV~vEYrCPEC~------------KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPR----------------IVHVEYRCPECD------------KVFSCPANLASHRRWHK 319 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCe----------------eEEeeecCCccc------------ccccCchhhhhhhcccC
Confidence 99999999999999999998533 222669999999 99999999999999984
Q ss_pred C--------CC-------------------------ccccccccccccChhhHHHHHHh
Q 040794 294 G--------IK-------------------------PFMCRKCGKAFAVRGDWRTHEKN 319 (375)
Q Consensus 294 g--------ek-------------------------py~C~~Cgk~F~~~~~L~~H~k~ 319 (375)
- .. -|.|..|+|.|.+...|+.|+-+
T Consensus 320 PR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlt 378 (500)
T KOG3993|consen 320 PRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLT 378 (500)
T ss_pred CchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHh
Confidence 2 11 26677777777777777777543
No 19
>PHA00732 hypothetical protein
Probab=98.16 E-value=8.3e-07 Score=68.31 Aligned_cols=46 Identities=20% Similarity=0.369 Sum_probs=33.7
Q ss_pred ccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHh-hcCCCccccccccccccChhhHHHHHHhc
Q 040794 257 RLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKR-KHGIKPFMCRKCGKAFAVRGDWRTHEKNC 320 (375)
Q Consensus 257 ~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~-H~gekpy~C~~Cgk~F~~~~~L~~H~k~h 320 (375)
+|.|..|+ +.|.....|..|++. |+ ++.|..||++|. .|..|.++.
T Consensus 1 py~C~~Cg------------k~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICG------------FTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCC------------CccCCHHHHHHHhhcccC---CCccCCCCCEeC---Chhhhhccc
Confidence 47788888 888888888888874 54 357888888887 466777654
No 20
>PHA00616 hypothetical protein
Probab=98.12 E-value=1.1e-06 Score=59.32 Aligned_cols=33 Identities=18% Similarity=0.539 Sum_probs=28.2
Q ss_pred Ceee-ecCcccCChHHHHHHHHHhCCCCCCCCCCC
Q 040794 323 LWYC-ICGSDFKHKRSLKDHIKAFGNGHAAYGIDG 356 (375)
Q Consensus 323 ~~~C-~Cgk~F~~~~~L~~H~r~~H~ge~~y~C~~ 356 (375)
||+| .||+.|..++.|.+|++. |+|++++.|+-
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~-~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLS-VHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHH-hcCCCccceeE
Confidence 6888 899999999999999988 77888888863
No 21
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.06 E-value=8.3e-07 Score=86.34 Aligned_cols=81 Identities=20% Similarity=0.452 Sum_probs=68.9
Q ss_pred ccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcCCCccccccccccccChhhHHHHHHhcC----------C----
Q 040794 257 RLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHGIKPFMCRKCGKAFAVRGDWRTHEKNCG----------K---- 322 (375)
Q Consensus 257 ~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~gekpy~C~~Cgk~F~~~~~L~~H~k~h~----------k---- 322 (375)
-|.|..|. -.|.+.-.|.+|.-....---|+|++|+|.|.-..+|-.|.+.|. .
T Consensus 267 dyiCqLCK------------~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~ 334 (500)
T KOG3993|consen 267 DYICQLCK------------EKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQ 334 (500)
T ss_pred HHHHHHHH------------HhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhh
Confidence 48999998 889999999999765555556999999999999999999988551 1
Q ss_pred ---------------------Ceee-ecCcccCChHHHHHHHHHhCCCC
Q 040794 323 ---------------------LWYC-ICGSDFKHKRSLKDHIKAFGNGH 349 (375)
Q Consensus 323 ---------------------~~~C-~Cgk~F~~~~~L~~H~r~~H~ge 349 (375)
.|.| .|+|.|.+...|++|+-+||...
T Consensus 335 ~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~ 383 (500)
T KOG3993|consen 335 AVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAP 383 (500)
T ss_pred hhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccc
Confidence 3899 99999999999999999977543
No 22
>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=98.06 E-value=6.3e-07 Score=54.01 Aligned_cols=25 Identities=24% Similarity=0.656 Sum_probs=22.9
Q ss_pred CCCccccccCCCceecCcccccccC
Q 040794 201 IPTPSQILIGPTQFSCPVCCKTFNR 225 (375)
Q Consensus 201 l~~h~~~h~g~kp~~C~~C~k~F~~ 225 (375)
|..|+++|+|++||.|++|++.|.+
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEESS
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 6789999999999999999999964
No 23
>PHA00616 hypothetical protein
Probab=97.78 E-value=1e-05 Score=54.59 Aligned_cols=40 Identities=13% Similarity=0.174 Sum_probs=33.8
Q ss_pred ccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcCCCcccccccccccc
Q 040794 257 RLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHGIKPFMCRKCGKAFA 308 (375)
Q Consensus 257 ~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~gekpy~C~~Cgk~F~ 308 (375)
+|+|..|| +.|..++.|.+|++.|+|++++.|..--..|.
T Consensus 1 pYqC~~CG------------~~F~~~s~l~~H~r~~hg~~~~~~~~~y~~f~ 40 (44)
T PHA00616 1 MYQCLRCG------------GIFRKKKEVIEHLLSVHKQNKLTLEYFYIYFR 40 (44)
T ss_pred CCccchhh------------HHHhhHHHHHHHHHHhcCCCccceeEEEEEEE
Confidence 47899999 99999999999999999999998876555554
No 24
>PHA00732 hypothetical protein
Probab=97.61 E-value=5.3e-05 Score=58.34 Aligned_cols=46 Identities=22% Similarity=0.489 Sum_probs=40.5
Q ss_pred ccccccccccccChhhHHHHHHhcCCCeee-ecCcccCChHHHHHHHHHh
Q 040794 297 PFMCRKCGKAFAVRGDWRTHEKNCGKLWYC-ICGSDFKHKRSLKDHIKAF 345 (375)
Q Consensus 297 py~C~~Cgk~F~~~~~L~~H~k~h~k~~~C-~Cgk~F~~~~~L~~H~r~~ 345 (375)
||.|..||+.|.+...|+.|++.+..++.| .||++|. .|..|++++
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeC---Chhhhhccc
Confidence 689999999999999999999964446799 9999998 589999874
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=97.43 E-value=0.00012 Score=42.48 Aligned_cols=21 Identities=43% Similarity=1.023 Sum_probs=13.7
Q ss_pred eee-ecCcccCChHHHHHHHHH
Q 040794 324 WYC-ICGSDFKHKRSLKDHIKA 344 (375)
Q Consensus 324 ~~C-~Cgk~F~~~~~L~~H~r~ 344 (375)
|.| .|++.|..+..|++|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 456 666666666666666665
No 26
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.38 E-value=9.9e-05 Score=42.76 Aligned_cols=22 Identities=27% Similarity=0.845 Sum_probs=15.7
Q ss_pred cccccccccccChhhHHHHHHh
Q 040794 298 FMCRKCGKAFAVRGDWRTHEKN 319 (375)
Q Consensus 298 y~C~~Cgk~F~~~~~L~~H~k~ 319 (375)
|.|..|++.|..+..|..|+++
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 5677777777777777777764
No 27
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.26 E-value=0.00025 Score=40.99 Aligned_cols=23 Identities=35% Similarity=0.966 Sum_probs=15.5
Q ss_pred eee-ecCcccCChHHHHHHHHHhC
Q 040794 324 WYC-ICGSDFKHKRSLKDHIKAFG 346 (375)
Q Consensus 324 ~~C-~Cgk~F~~~~~L~~H~r~~H 346 (375)
|.| +|++.|..+..|++|++++|
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 567 77777777777777777755
No 28
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.25 E-value=0.00035 Score=49.73 Aligned_cols=46 Identities=28% Similarity=0.525 Sum_probs=19.7
Q ss_pred cccccccccccChhhHHHHHHh-c---CCCeee-ecCcccCChHHHHHHHHHhC
Q 040794 298 FMCRKCGKAFAVRGDWRTHEKN-C---GKLWYC-ICGSDFKHKRSLKDHIKAFG 346 (375)
Q Consensus 298 y~C~~Cgk~F~~~~~L~~H~k~-h---~k~~~C-~Cgk~F~~~~~L~~H~r~~H 346 (375)
|.|+.|++. .....|..|... | .+.+.| +|...+. .+|.+|++.+|
T Consensus 3 f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 444444442 223344444432 2 233444 4544333 25555555544
No 29
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.13 E-value=0.00011 Score=69.39 Aligned_cols=50 Identities=28% Similarity=0.586 Sum_probs=38.1
Q ss_pred CCcccccc--ccccccChhhHHHHHHh-------c--------------CCCeee-ecCcccCChHHHHHHHHH
Q 040794 295 IKPFMCRK--CGKAFAVRGDWRTHEKN-------C--------------GKLWYC-ICGSDFKHKRSLKDHIKA 344 (375)
Q Consensus 295 ekpy~C~~--Cgk~F~~~~~L~~H~k~-------h--------------~k~~~C-~Cgk~F~~~~~L~~H~r~ 344 (375)
+|||+|++ |.|+++....|+-|+.- | .|||.| .|+|+|+....|+-|++.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~H 420 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRKH 420 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecccc
Confidence 47777765 77777777777777651 1 388999 899999999999888763
No 30
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.02 E-value=0.00037 Score=41.96 Aligned_cols=24 Identities=25% Similarity=0.643 Sum_probs=16.3
Q ss_pred Ceee-ecCcccCChHHHHHHHHHhC
Q 040794 323 LWYC-ICGSDFKHKRSLKDHIKAFG 346 (375)
Q Consensus 323 ~~~C-~Cgk~F~~~~~L~~H~r~~H 346 (375)
+|.| .|++.|.....|..|++.|+
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 4667 67777777777777776643
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.00 E-value=0.00058 Score=54.03 Aligned_cols=76 Identities=18% Similarity=0.402 Sum_probs=23.0
Q ss_pred ccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcCCCccccccccccccChhhHHHHHHhc-CCCeee-ecCcccCChH
Q 040794 259 PCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHGIKPFMCRKCGKAFAVRGDWRTHEKNC-GKLWYC-ICGSDFKHKR 336 (375)
Q Consensus 259 ~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~gekpy~C~~Cgk~F~~~~~L~~H~k~h-~k~~~C-~Cgk~F~~~~ 336 (375)
+|..|+ ..|.....|..|++..++...- ....+.....+..+++.- ...+.| .|++.|....
T Consensus 1 ~C~~C~------------~~f~~~~~l~~H~~~~H~~~~~----~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~ 64 (100)
T PF12756_consen 1 QCLFCD------------ESFSSVDDLLQHMKKKHGFDIP----DQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSRE 64 (100)
T ss_dssp ----------------------------------------------------------------SSEEBSSSS-EESSHH
T ss_pred Cccccc------------cccccccccccccccccccccc----cccccccccccccccccccCCCCCCCccCCCCcCHH
Confidence 488898 8899999999999766553311 122222444444454433 447999 9999999999
Q ss_pred HHHHHHHHhCCCCC
Q 040794 337 SLKDHIKAFGNGHA 350 (375)
Q Consensus 337 ~L~~H~r~~H~ge~ 350 (375)
.|..||+.++....
T Consensus 65 ~l~~Hm~~~~H~~~ 78 (100)
T PF12756_consen 65 ALQEHMRSKHHKKR 78 (100)
T ss_dssp HHHHHHHHTTTTC-
T ss_pred HHHHHHcCccCCCc
Confidence 99999998543333
No 32
>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=96.97 E-value=0.00076 Score=47.97 Aligned_cols=20 Identities=30% Similarity=0.567 Sum_probs=11.7
Q ss_pred eecCcccccccCchHHhhccc
Q 040794 214 FSCPVCCKTFNRYNNMQMHMW 234 (375)
Q Consensus 214 ~~C~~C~k~F~~~~~L~~H~~ 234 (375)
|.|+.|++. .....|..|..
T Consensus 3 f~CP~C~~~-~~~~~L~~H~~ 22 (54)
T PF05605_consen 3 FTCPYCGKG-FSESSLVEHCE 22 (54)
T ss_pred cCCCCCCCc-cCHHHHHHHHH
Confidence 566666663 33455666655
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.65 E-value=0.0011 Score=52.40 Aligned_cols=73 Identities=23% Similarity=0.389 Sum_probs=20.8
Q ss_pred ecCcccccccCchHHhhcccccCCCCCCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcC
Q 040794 215 SCPVCCKTFNRYNNMQMHMWGHGSQYRKGPESLRGTQPTGMLRLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHG 294 (375)
Q Consensus 215 ~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~g 294 (375)
+|..|+..|.....|..|+...++ +... .. +.+.....|..+++...
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~-------------------~~~~-~~------------~~l~~~~~~~~~~~~~~- 47 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHG-------------------FDIP-DQ------------KYLVDPNRLLNYLRKKV- 47 (100)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred Cccccccccccccccccccccccc-------------------cccc-cc------------ccccccccccccccccc-
Confidence 589999999999999999974321 1111 11 22333344444443322
Q ss_pred CCccccccccccccChhhHHHHHHhc
Q 040794 295 IKPFMCRKCGKAFAVRGDWRTHEKNC 320 (375)
Q Consensus 295 ekpy~C~~Cgk~F~~~~~L~~H~k~h 320 (375)
...+.|..|++.|.....|..||+.+
T Consensus 48 ~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 48 KESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 23689999999999999999999853
No 34
>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=96.61 E-value=0.0012 Score=37.95 Aligned_cols=23 Identities=35% Similarity=0.840 Sum_probs=15.9
Q ss_pred cccccccccccChhhHHHHHHhc
Q 040794 298 FMCRKCGKAFAVRGDWRTHEKNC 320 (375)
Q Consensus 298 y~C~~Cgk~F~~~~~L~~H~k~h 320 (375)
|.|..|++.|.++..|+.|++++
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 57788888888888888887653
No 35
>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=96.50 E-value=0.0013 Score=39.50 Aligned_cols=24 Identities=33% Similarity=0.710 Sum_probs=22.9
Q ss_pred ceecCcccccccCchHHhhccccc
Q 040794 213 QFSCPVCCKTFNRYNNMQMHMWGH 236 (375)
Q Consensus 213 p~~C~~C~k~F~~~~~L~~H~~~H 236 (375)
+|.|..|++.|.....|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 589999999999999999999988
No 36
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=96.37 E-value=0.0014 Score=62.05 Aligned_cols=26 Identities=31% Similarity=0.761 Sum_probs=23.2
Q ss_pred cCCCceecCc--ccccccCchHHhhccc
Q 040794 209 IGPTQFSCPV--CCKTFNRYNNMQMHMW 234 (375)
Q Consensus 209 ~g~kp~~C~~--C~k~F~~~~~L~~H~~ 234 (375)
.++|||+|++ |.|.+.....|+-|+.
T Consensus 345 ~d~KpykCpV~gC~K~YknqnGLKYH~l 372 (423)
T COG5189 345 KDGKPYKCPVEGCNKKYKNQNGLKYHML 372 (423)
T ss_pred ecCceecCCCCCchhhhccccchhhhhh
Confidence 3469999998 9999999999999985
No 37
>PRK04860 hypothetical protein; Provisional
Probab=96.14 E-value=0.0025 Score=55.72 Aligned_cols=40 Identities=25% Similarity=0.691 Sum_probs=33.5
Q ss_pred cccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcCCCccccccccccccChh
Q 040794 256 LRLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHGIKPFMCRKCGKAFAVRG 311 (375)
Q Consensus 256 ~~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~gekpy~C~~Cgk~F~~~~ 311 (375)
-+|.|. |+ + ...++.+|.++|+|+++|.|..|+..|....
T Consensus 118 ~~Y~C~-C~------------~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQ------------E---HQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CC------------C---eeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 468897 87 5 5678899999999999999999999887654
No 38
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=96.12 E-value=0.0028 Score=62.70 Aligned_cols=53 Identities=23% Similarity=0.298 Sum_probs=47.1
Q ss_pred CCCCCCCCCCCCCCCcCCCCccc--cccCC--CceecC--cccccccCchHHhhccccc
Q 040794 184 DSSAGYPFNRLNKGQYWIPTPSQ--ILIGP--TQFSCP--VCCKTFNRYNNMQMHMWGH 236 (375)
Q Consensus 184 ~~~~~~~~~~~~~~~~~l~~h~~--~h~g~--kp~~C~--~C~k~F~~~~~L~~H~~~H 236 (375)
....+..|...+....+|.+|.+ .|+++ +++.|+ .|++.|.+...+..|..+|
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~ 346 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLH 346 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccc
Confidence 46778888888899999999999 89999 999999 7999999999999999888
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.90 E-value=0.0053 Score=35.69 Aligned_cols=20 Identities=45% Similarity=0.967 Sum_probs=11.6
Q ss_pred ee-ecCcccCChHHHHHHHHH
Q 040794 325 YC-ICGSDFKHKRSLKDHIKA 344 (375)
Q Consensus 325 ~C-~Cgk~F~~~~~L~~H~r~ 344 (375)
.| .|++.|.....|..|++.
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~ 22 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMRT 22 (26)
T ss_pred CCCCCcchhCCHHHHHHHHHH
Confidence 45 556666666666666554
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.78 E-value=0.0068 Score=35.22 Aligned_cols=23 Identities=26% Similarity=0.765 Sum_probs=20.8
Q ss_pred cccccccccccChhhHHHHHHhc
Q 040794 298 FMCRKCGKAFAVRGDWRTHEKNC 320 (375)
Q Consensus 298 y~C~~Cgk~F~~~~~L~~H~k~h 320 (375)
|.|..|+++|.....|..|+++|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 68999999999999999998753
No 41
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.52 E-value=0.015 Score=40.38 Aligned_cols=33 Identities=24% Similarity=0.435 Sum_probs=20.6
Q ss_pred CCCcccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcCCCc
Q 040794 253 TGMLRLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHGIKP 297 (375)
Q Consensus 253 ~~~~~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~gekp 297 (375)
....+..|++|+ ..+.+..+|.+|+.++++.||
T Consensus 20 ~S~~PatCP~C~------------a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICG------------AVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--------------EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcch------------hhccchhhHHHHHHHHhcccC
Confidence 334667788888 778888888888887777775
No 42
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=94.83 E-value=0.015 Score=40.33 Aligned_cols=26 Identities=27% Similarity=0.594 Sum_probs=13.6
Q ss_pred CCCeee-ecCcccCChHHHHHHHHHhC
Q 040794 321 GKLWYC-ICGSDFKHKRSLKDHIKAFG 346 (375)
Q Consensus 321 ~k~~~C-~Cgk~F~~~~~L~~H~r~~H 346 (375)
+.|-.| +|+..+.+..+|++|+.+.|
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H 48 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRH 48 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHT
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHh
Confidence 456666 66666667777777766643
No 43
>PRK04860 hypothetical protein; Provisional
Probab=94.70 E-value=0.019 Score=50.28 Aligned_cols=31 Identities=23% Similarity=0.524 Sum_probs=15.7
Q ss_pred eeeecCcccCChHHHHHHHHHhCCCCCCCCCCCCC
Q 040794 324 WYCICGSDFKHKRSLKDHIKAFGNGHAAYGIDGFE 358 (375)
Q Consensus 324 ~~C~Cgk~F~~~~~L~~H~r~~H~ge~~y~C~~~~ 358 (375)
|.|.|++ ....+++|.++ |+|+++|.|..|.
T Consensus 120 Y~C~C~~---~~~~~rrH~ri-~~g~~~YrC~~C~ 150 (160)
T PRK04860 120 YRCKCQE---HQLTVRRHNRV-VRGEAVYRCRRCG 150 (160)
T ss_pred EEcCCCC---eeCHHHHHHHH-hcCCccEECCCCC
Confidence 4444444 44445555555 4555555555553
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.46 E-value=0.019 Score=33.62 Aligned_cols=23 Identities=30% Similarity=0.791 Sum_probs=21.3
Q ss_pred eecCcccccccCchHHhhccccc
Q 040794 214 FSCPVCCKTFNRYNNMQMHMWGH 236 (375)
Q Consensus 214 ~~C~~C~k~F~~~~~L~~H~~~H 236 (375)
|.|.+|++.|.....|..|++.+
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 68999999999999999999865
No 45
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.33 E-value=0.028 Score=32.88 Aligned_cols=21 Identities=38% Similarity=1.113 Sum_probs=14.0
Q ss_pred eee-ecCcccCChHHHHHHHHH
Q 040794 324 WYC-ICGSDFKHKRSLKDHIKA 344 (375)
Q Consensus 324 ~~C-~Cgk~F~~~~~L~~H~r~ 344 (375)
|.| +|++.|.....|+.|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 556 677777777777777654
No 46
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.21 E-value=0.036 Score=32.20 Aligned_cols=22 Identities=32% Similarity=0.612 Sum_probs=13.9
Q ss_pred eee-ecCcccCChHHHHHHHHHhC
Q 040794 324 WYC-ICGSDFKHKRSLKDHIKAFG 346 (375)
Q Consensus 324 ~~C-~Cgk~F~~~~~L~~H~r~~H 346 (375)
|.| .|+.... +..|.+|++.+|
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 567 6777666 677777777755
No 47
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.56 E-value=0.098 Score=55.18 Aligned_cols=20 Identities=20% Similarity=0.551 Sum_probs=12.4
Q ss_pred ccccccccccChhhHHHHHH
Q 040794 299 MCRKCGKAFAVRGDWRTHEK 318 (375)
Q Consensus 299 ~C~~Cgk~F~~~~~L~~H~k 318 (375)
.|..|...|.....|.+|++
T Consensus 184 ~C~~C~~~fld~~el~rH~~ 203 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLR 203 (669)
T ss_pred cchhhhhhhccHHHHHHhhc
Confidence 56666666666666666655
No 48
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=93.19 E-value=0.054 Score=32.52 Aligned_cols=23 Identities=35% Similarity=0.670 Sum_probs=21.1
Q ss_pred eecCcccccccCchHHhhccccc
Q 040794 214 FSCPVCCKTFNRYNNMQMHMWGH 236 (375)
Q Consensus 214 ~~C~~C~k~F~~~~~L~~H~~~H 236 (375)
|-|..|++.|.....|..|+++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCcccCCCCcCCHHHHHHHHccC
Confidence 78999999999999999999754
No 49
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.01 E-value=0.029 Score=55.40 Aligned_cols=72 Identities=19% Similarity=0.320 Sum_probs=60.8
Q ss_pred CceecCcccccccCchHHhhccc--ccCCCCCCCCCCcCCCCCCCC--cccccC--CCCCCCCCCCCCCCCcccCCHHHH
Q 040794 212 TQFSCPVCCKTFNRYNNMQMHMW--GHGSQYRKGPESLRGTQPTGM--LRLPCY--CCAPGCRNNIDHPRAKPLKDFRTL 285 (375)
Q Consensus 212 kp~~C~~C~k~F~~~~~L~~H~~--~H~~~~~~~~~~~~~~~~~~~--~~~~C~--~Cg~~~~~~~~h~~~k~f~~~~~L 285 (375)
.++.|..|...|.....|..|.+ .| +++ +++.|. .|+ +.|.+...+
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h----------------~~~~~~~~~~p~~~~~------------~~~~~~~~~ 339 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNH----------------SGESLKPFSCPYSLCG------------KLFSRNDAL 339 (467)
T ss_pred cCCCCccccCCcccccccccccccccc----------------ccccCCceeeeccCCC------------ccccccccc
Confidence 57999999999999999999999 78 777 899999 799 999999999
Q ss_pred HHHHHhhcCCCcccccc--ccccccChh
Q 040794 286 QTHYKRKHGIKPFMCRK--CGKAFAVRG 311 (375)
Q Consensus 286 ~~H~r~H~gekpy~C~~--Cgk~F~~~~ 311 (375)
..|..+|++.+++.|.. |.+.+....
T Consensus 340 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 367 (467)
T COG5048 340 KRHILLHTSISPAKEKLLNSSSKFSPLL 367 (467)
T ss_pred cCCcccccCCCccccccccCcccccccc
Confidence 99999999988877743 555554433
No 50
>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=91.77 E-value=0.037 Score=33.24 Aligned_cols=21 Identities=38% Similarity=0.960 Sum_probs=13.3
Q ss_pred eee-ecCcccCChHHHHHHHHH
Q 040794 324 WYC-ICGSDFKHKRSLKDHIKA 344 (375)
Q Consensus 324 ~~C-~Cgk~F~~~~~L~~H~r~ 344 (375)
|.| .|++.|.....|..|++.
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 556 666666666666666653
No 51
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=90.59 E-value=0.15 Score=56.99 Aligned_cols=114 Identities=21% Similarity=0.329 Sum_probs=83.0
Q ss_pred cCcccccccCchHHhhcccccCCCCCCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhc--
Q 040794 216 CPVCCKTFNRYNNMQMHMWGHGSQYRKGPESLRGTQPTGMLRLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKH-- 293 (375)
Q Consensus 216 C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~-- 293 (375)
|..|+..+.++..+..|+..-. +-.+-+.|+.|+ ..|+....|..|+|..+
T Consensus 439 ~~~~e~~~~s~r~~~~~t~~L~---------------S~~kt~~cpkc~------------~~yk~a~~L~vhmRskhp~ 491 (1406)
T KOG1146|consen 439 LTKAEPLLESKRSLEGQTVVLH---------------SFFKTLKCPKCN------------WHYKLAQTLGVHMRSKHPE 491 (1406)
T ss_pred ccchhhhhhhhcccccceeeee---------------cccccccCCccc------------hhhhhHHHhhhcccccccc
Confidence 4455666666666666665322 334779999999 99999999999999821
Q ss_pred -----------------------CCCccccccccccccChhhHHHHHHh--c-----------C----------------
Q 040794 294 -----------------------GIKPFMCRKCGKAFAVRGDWRTHEKN--C-----------G---------------- 321 (375)
Q Consensus 294 -----------------------gekpy~C~~Cgk~F~~~~~L~~H~k~--h-----------~---------------- 321 (375)
+.+||.|..|..+++.+..|.+|+.. | +
T Consensus 492 ~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~s~~P~ 571 (1406)
T KOG1146|consen 492 SQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVTSAVPE 571 (1406)
T ss_pred cchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhcccCcc
Confidence 23689999999999999999999861 0 0
Q ss_pred ----------------CCeee-ecCcccCChHHHHHHHHHhCCCCCCCCCCC
Q 040794 322 ----------------KLWYC-ICGSDFKHKRSLKDHIKAFGNGHAAYGIDG 356 (375)
Q Consensus 322 ----------------k~~~C-~Cgk~F~~~~~L~~H~r~~H~ge~~y~C~~ 356 (375)
-.|.| +|+..-+-..+|+.||..-+.-..|.-|..
T Consensus 572 ~ag~~~~ags~~pktkP~~~C~vc~yetniarnlrihmtss~~s~~p~~~Lq 623 (1406)
T KOG1146|consen 572 EAGLGPSAGSSGPKTKPSWRCEVCSYETNIARNLRIHMTASPSSSPPSLVLQ 623 (1406)
T ss_pred cccCCCCCCCCCCCCCCCcchhhhcchhhhhhccccccccCCCCCChHHHhh
Confidence 03889 899998888899999876544444444443
No 52
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=90.26 E-value=0.21 Score=29.53 Aligned_cols=20 Identities=35% Similarity=0.667 Sum_probs=10.1
Q ss_pred ccccccccccChhhHHHHHHh
Q 040794 299 MCRKCGKAFAVRGDWRTHEKN 319 (375)
Q Consensus 299 ~C~~Cgk~F~~~~~L~~H~k~ 319 (375)
.|+.||+.| ....|..|+++
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHHh
Confidence 455555555 34455555443
No 53
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=89.85 E-value=0.22 Score=28.77 Aligned_cols=21 Identities=19% Similarity=0.612 Sum_probs=14.3
Q ss_pred cccccccccccChhhHHHHHHh
Q 040794 298 FMCRKCGKAFAVRGDWRTHEKN 319 (375)
Q Consensus 298 y~C~~Cgk~F~~~~~L~~H~k~ 319 (375)
|+|..|+.+.. +..|..|+++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHh
Confidence 67888887776 7778888775
No 54
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=89.82 E-value=0.15 Score=49.13 Aligned_cols=17 Identities=24% Similarity=0.417 Sum_probs=12.6
Q ss_pred ccCChHHHHHHHHHhCC
Q 040794 331 DFKHKRSLKDHIKAFGN 347 (375)
Q Consensus 331 ~F~~~~~L~~H~r~~H~ 347 (375)
.|..-..|..|+...|.
T Consensus 290 vf~~~~el~~h~~~~h~ 306 (493)
T COG5236 290 VFPYHTELLEHLTRFHK 306 (493)
T ss_pred EeccHHHHHHHHHHHhh
Confidence 57777788888877663
No 55
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=88.67 E-value=0.34 Score=28.66 Aligned_cols=20 Identities=40% Similarity=0.778 Sum_probs=17.1
Q ss_pred eee-ecCcccCChHHHHHHHHH
Q 040794 324 WYC-ICGSDFKHKRSLKDHIKA 344 (375)
Q Consensus 324 ~~C-~Cgk~F~~~~~L~~H~r~ 344 (375)
..| .||+.| ....|.+|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 468 999999 67789999876
No 56
>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=87.72 E-value=0.41 Score=30.19 Aligned_cols=22 Identities=32% Similarity=0.847 Sum_probs=16.1
Q ss_pred Ceee-ecCcccCChHHHHHHHHH
Q 040794 323 LWYC-ICGSDFKHKRSLKDHIKA 344 (375)
Q Consensus 323 ~~~C-~Cgk~F~~~~~L~~H~r~ 344 (375)
+|.| .|++.|.....|..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 5677 788877777777777653
No 57
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.64 E-value=0.49 Score=50.10 Aligned_cols=81 Identities=22% Similarity=0.356 Sum_probs=55.9
Q ss_pred cccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcCCCccccccc------cccccChhhHHHHHHhcCCCe---eeec
Q 040794 258 LPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHGIKPFMCRKC------GKAFAVRGDWRTHEKNCGKLW---YCIC 328 (375)
Q Consensus 258 ~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~gekpy~C~~C------gk~F~~~~~L~~H~k~h~k~~---~C~C 328 (375)
-.|..|. ..|.....|.+|++.++ |.|..| +-.|..-..|..|-+.+...- .|.|
T Consensus 183 p~C~~C~------------~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~~HflCE~~~C~~ 246 (669)
T KOG2231|consen 183 PLCKFCH------------ERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRKGHFLCEEEFCRT 246 (669)
T ss_pred ccchhhh------------hhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhhcCcccccccccc
Confidence 3599998 89999999999998776 677777 355667778888877532111 2323
Q ss_pred C---cccCChHHHHHHHHHhCCCCCCCCCC
Q 040794 329 G---SDFKHKRSLKDHIKAFGNGHAAYGID 355 (375)
Q Consensus 329 g---k~F~~~~~L~~H~r~~H~ge~~y~C~ 355 (375)
. ..|.....|++|.+ ++.-++.|.|+
T Consensus 247 ~~f~~~~~~ei~lk~~~~-~~~~e~~~~~~ 275 (669)
T KOG2231|consen 247 KKFYVAFELEIELKAHNR-FIQHEKCYICR 275 (669)
T ss_pred ceeeehhHHHHHHHhhcc-ccchheeccCC
Confidence 3 34455667777776 36677888886
No 58
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=86.57 E-value=0.5 Score=43.85 Aligned_cols=47 Identities=28% Similarity=0.600 Sum_probs=33.3
Q ss_pred ccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcCCCccccccccccccChhhHHHHHH
Q 040794 257 RLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHGIKPFMCRKCGKAFAVRGDWRTHEK 318 (375)
Q Consensus 257 ~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~gekpy~C~~Cgk~F~~~~~L~~H~k 318 (375)
-|.|..||..+ + +..|.+|+-+-++ .-|.|..||+.|.+ .+.+.|.+
T Consensus 3 ~FtCnvCgEsv------------K-Kp~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 3 FFTCNVCGESV------------K-KPQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EEehhhhhhhc------------c-ccchHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 47888888332 2 3466778777776 66888888888887 66777766
No 59
>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=85.37 E-value=0.47 Score=29.87 Aligned_cols=22 Identities=27% Similarity=0.516 Sum_probs=19.5
Q ss_pred ccccccccccccChhhHHHHHH
Q 040794 297 PFMCRKCGKAFAVRGDWRTHEK 318 (375)
Q Consensus 297 py~C~~Cgk~F~~~~~L~~H~k 318 (375)
+|.|..|++.|.....|..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 5889999999999999999976
No 60
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=84.49 E-value=0.88 Score=44.04 Aligned_cols=23 Identities=39% Similarity=0.817 Sum_probs=20.7
Q ss_pred ccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHh
Q 040794 257 RLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKR 291 (375)
Q Consensus 257 ~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~ 291 (375)
++.|-.|. |.|..+.+|+.|||.
T Consensus 195 r~~CLyCe------------kifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCE------------KIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeec------------cccCCcHHHHHHHHh
Confidence 47899999 999999999999985
No 61
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=83.44 E-value=0.27 Score=55.16 Aligned_cols=109 Identities=13% Similarity=0.222 Sum_probs=70.4
Q ss_pred eecCcccccccCchHHhhcccccCCCCCCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhc
Q 040794 214 FSCPVCCKTFNRYNNMQMHMWGHGSQYRKGPESLRGTQPTGMLRLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKH 293 (375)
Q Consensus 214 ~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~ 293 (375)
..|.+|...|.....+..|-+.-.. -.-..| -+.|..|. +.|.-...+. |+ -
T Consensus 1229 l~~~~~e~~f~~~~~~~~~a~~~~~----------~~~~sG--e~~c~~~~------------~~~~~~~~~~-~l---~ 1280 (1406)
T KOG1146|consen 1229 LLPNALEQPFPQEPEPTATAPPKPP----------ELPASG--EGECGAVD------------ELLTPSFGIS-TL---D 1280 (1406)
T ss_pred ccHHhhhcCccCcccccccCCCCCC----------cCcCCC--cchhhhcc------------ccccCcccee-ec---c
Confidence 5677788888877776655432200 000122 25677777 4444433333 22 2
Q ss_pred CCCccccccccccccChhhHHHHHHhc------------------CCCeee-ecCcccCChHHHHHHHHHhCCCCC
Q 040794 294 GIKPFMCRKCGKAFAVRGDWRTHEKNC------------------GKLWYC-ICGSDFKHKRSLKDHIKAFGNGHA 350 (375)
Q Consensus 294 gekpy~C~~Cgk~F~~~~~L~~H~k~h------------------~k~~~C-~Cgk~F~~~~~L~~H~r~~H~ge~ 350 (375)
...+|.|..|...|.....|..|.+.. ...|.| .|...|.....|..|||+-+...|
T Consensus 1281 ~~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~c~~c~~~~~~~~alqihm~~~~~~~k 1356 (1406)
T KOG1146|consen 1281 VTHRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYHCLACEVLLSGREALQIHMRSSAHRRK 1356 (1406)
T ss_pred cchhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCccccccchHHHhhcchhHHHHHHHHHhhhccc
Confidence 346788999999999888888887631 122449 999999999999999998655443
No 62
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=81.45 E-value=2.9 Score=40.60 Aligned_cols=50 Identities=20% Similarity=0.438 Sum_probs=42.5
Q ss_pred ccccccccccccChhhHHHHHHh--cCC----------------------------------------------------
Q 040794 297 PFMCRKCGKAFAVRGDWRTHEKN--CGK---------------------------------------------------- 322 (375)
Q Consensus 297 py~C~~Cgk~F~~~~~L~~H~k~--h~k---------------------------------------------------- 322 (375)
.++|-.|.|.|..+..|+.||+. |.+
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinPknreYDkfyiINY~ev~ks~t~~~~e~dret~~d~~E~D~~wsDw~ed~ 274 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINPKNREYDKFYIINYLEVGKSWTIVHSEDDRETNEDINETDDTWSDWNEDD 274 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCCCccccceEEEEeHhhcCCccchhhhhhhhhhhccccccccchhhhhcCC
Confidence 48999999999999999999983 211
Q ss_pred --C--eee-ecCcccCChHHHHHHHHHhC
Q 040794 323 --L--WYC-ICGSDFKHKRSLKDHIKAFG 346 (375)
Q Consensus 323 --~--~~C-~Cgk~F~~~~~L~~H~r~~H 346 (375)
+ -+| .|.+..-....|..||++.|
T Consensus 275 a~a~~v~CLfC~~~~en~~~l~eHmk~vH 303 (423)
T KOG2482|consen 275 AEALSVVCLFCTNFYENPVFLFEHMKIVH 303 (423)
T ss_pred CCccceEEEeeccchhhHHHHHHHHHHHH
Confidence 1 389 89999999999999999888
No 63
>PF01352 KRAB: KRAB box; InterPro: IPR001909 The Krueppel-associated box (KRAB) is a domain of around 75 amino acids that is found in the N-terminal part of about one third of eukaryotic Krueppel-type C2H2 zinc finger proteins (ZFPs) []. It is enriched in charged amino acids and can be divided into subregions A and B, which are predicted to fold into two amphipathic alpha-helices. The KRAB A and B boxes can be separated by variable spacer segments and many KRAB proteins contain only the A box []. The functions currently known for members of the KRAB-containing protein family include transcriptional repression of RNA polymerase I, II, and III promoters, binding and splicing of RNA, and control of nucleolus function. The KRAB domain functions as a transcriptional repressor when tethered to the template DNA by a DNA-binding domain. A sequence of 45 amino acids in the KRAB A subdomain has been shown to be necessary and sufficient for transcriptional repression. The B box does not repress by itself but does potentiate the repression exerted by the KRAB A subdomain [, ]. Gene silencing requires the binding of the KRAB domain to the RING-B box-coiled coil (RBCC) domain of the KAP-1/TIF1-beta corepressor. As KAP-1 binds to the heterochromatin proteins HP1, it has been proposed that the KRAB-ZFP-bound target gene could be silenced following recruitment to heterochromatin [, ]. KRAB-ZFPs probably constitute the single largest class of transcription factors within the human genome []. Although the function of KRAB-ZFPs is largely unknown, they appear to play important roles during cell differentiation and development. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B.; GO: 0003676 nucleic acid binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1V65_A.
Probab=80.49 E-value=0.45 Score=31.75 Aligned_cols=23 Identities=22% Similarity=0.041 Sum_probs=17.0
Q ss_pred cHHHHhhhccccccccceeeeec
Q 040794 128 STATAALHHEDDDETTAVTVALH 150 (375)
Q Consensus 128 ~~~q~~~~~e~~~e~~~~~v~l~ 150 (375)
+++|+.+|+++|.|++.+.++++
T Consensus 19 ~~~Qk~ly~dvm~Eny~~l~slG 41 (41)
T PF01352_consen 19 DPAQKNLYRDVMLENYRNLVSLG 41 (41)
T ss_dssp -HHHHHHHHHHHHHTTTS---S-
T ss_pred cceecccchhHHHHhhcccEecC
Confidence 57899999999999999998874
No 64
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=78.91 E-value=0.58 Score=43.07 Aligned_cols=41 Identities=29% Similarity=0.604 Sum_probs=29.4
Q ss_pred cCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcCCCccccccccccccChhhHHHH
Q 040794 260 CYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHGIKPFMCRKCGKAFAVRGDWRTH 316 (375)
Q Consensus 260 C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~gekpy~C~~Cgk~F~~~~~L~~H 316 (375)
|..|. +-|.+..-|.+|++. |-|+|.+|-|....-..|..|
T Consensus 13 cwycn------------refddekiliqhqka----khfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCN------------REFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecc------------cccchhhhhhhhhhh----ccceeeeehhhhccCCCceee
Confidence 88888 888888888888764 448888887666555555444
No 65
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=78.48 E-value=1.4 Score=42.76 Aligned_cols=64 Identities=27% Similarity=0.553 Sum_probs=38.9
Q ss_pred CHHHHHHHHHhhcCCCccccccc---ccccc------ChhhHHHHHHhc--CCC----eee-ecCcccCChHHHHHHHHH
Q 040794 281 DFRTLQTHYKRKHGIKPFMCRKC---GKAFA------VRGDWRTHEKNC--GKL----WYC-ICGSDFKHKRSLKDHIKA 344 (375)
Q Consensus 281 ~~~~L~~H~r~H~gekpy~C~~C---gk~F~------~~~~L~~H~k~h--~k~----~~C-~Cgk~F~~~~~L~~H~r~ 344 (375)
.+..|+.|.+..++. +-|..| .+.|. .+..|+.|...+ +.. -.| .|.+.|-.-..|.+|+|.
T Consensus 165 ~~k~lk~H~K~~H~~--~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~FYdDDEL~~HcR~ 242 (493)
T COG5236 165 SLKELKKHYKAQHGF--VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRL 242 (493)
T ss_pred hHHHHHHHHHhhcCc--EEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhccceecChHHHHHHHHh
Confidence 356788888876542 445554 23443 345666676644 212 247 688888888888888877
Q ss_pred hC
Q 040794 345 FG 346 (375)
Q Consensus 345 ~H 346 (375)
.|
T Consensus 243 ~H 244 (493)
T COG5236 243 RH 244 (493)
T ss_pred hh
Confidence 43
No 66
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=78.38 E-value=1.1 Score=41.57 Aligned_cols=45 Identities=31% Similarity=0.767 Sum_probs=38.5
Q ss_pred cccccccccccChhhHHHHHHhc-CCCeee-ecCcccCChHHHHHHHHH
Q 040794 298 FMCRKCGKAFAVRGDWRTHEKNC-GKLWYC-ICGSDFKHKRSLKDHIKA 344 (375)
Q Consensus 298 y~C~~Cgk~F~~~~~L~~H~k~h-~k~~~C-~Cgk~F~~~~~L~~H~r~ 344 (375)
|.|..||-+.. +..|-+|+..| ..-|.| .|++.|-+ -+.+.|.+.
T Consensus 4 FtCnvCgEsvK-Kp~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~kC 50 (276)
T KOG2186|consen 4 FTCNVCGESVK-KPQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTKC 50 (276)
T ss_pred Eehhhhhhhcc-ccchHHHHHhccCCeeEEeeccccccc-chhhhhhhh
Confidence 78999998876 66788899987 688999 89999999 678888875
No 67
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=77.58 E-value=2.5 Score=34.60 Aligned_cols=45 Identities=18% Similarity=0.252 Sum_probs=24.1
Q ss_pred cccccccccChhhHHHHHHhcCCCeee-ecCcccCChHHHHHHHHH
Q 040794 300 CRKCGKAFAVRGDWRTHEKNCGKLWYC-ICGSDFKHKRSLKDHIKA 344 (375)
Q Consensus 300 C~~Cgk~F~~~~~L~~H~k~h~k~~~C-~Cgk~F~~~~~L~~H~r~ 344 (375)
|--|.+.|........-...-...|.| .|.+.|-..=..-.|...
T Consensus 58 C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~L 103 (112)
T TIGR00622 58 CFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESL 103 (112)
T ss_pred ccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhc
Confidence 667777776443111000011345777 777777666666666655
No 68
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=73.91 E-value=1.5 Score=31.05 Aligned_cols=28 Identities=29% Similarity=0.638 Sum_probs=23.9
Q ss_pred hhcCCCccccccccccccChhhHHHHHH
Q 040794 291 RKHGIKPFMCRKCGKAFAVRGDWRTHEK 318 (375)
Q Consensus 291 ~H~gekpy~C~~Cgk~F~~~~~L~~H~k 318 (375)
..-|+--++|+.||+.|....+..+|..
T Consensus 11 ~RDGE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 11 DRDGEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred ccCCceeeeCCchhHHHHHhHHHHHHhh
Confidence 3457778999999999999999999986
No 69
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=71.36 E-value=3.7 Score=44.42 Aligned_cols=14 Identities=29% Similarity=0.698 Sum_probs=10.4
Q ss_pred cCCCcccccccccc
Q 040794 293 HGIKPFMCRKCGKA 306 (375)
Q Consensus 293 ~gekpy~C~~Cgk~ 306 (375)
....|..|+.||..
T Consensus 471 ~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 471 QEPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCCC
Confidence 45678888888855
No 70
>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=70.49 E-value=3.9 Score=27.30 Aligned_cols=21 Identities=38% Similarity=0.662 Sum_probs=9.3
Q ss_pred eee-ecCcccCCh----HHHHHHHHH
Q 040794 324 WYC-ICGSDFKHK----RSLKDHIKA 344 (375)
Q Consensus 324 ~~C-~Cgk~F~~~----~~L~~H~r~ 344 (375)
..| .|++.++.. +.|++|++.
T Consensus 17 a~C~~C~~~~~~~~~~ts~l~~HL~~ 42 (45)
T PF02892_consen 17 AKCKYCGKVIKYSSGGTSNLKRHLKK 42 (45)
T ss_dssp EEETTTTEE-----SSTHHHHHHHHH
T ss_pred EEeCCCCeEEeeCCCcHHHHHHhhhh
Confidence 445 455554442 566666644
No 71
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=70.30 E-value=1.5 Score=40.39 Aligned_cols=45 Identities=29% Similarity=0.532 Sum_probs=36.3
Q ss_pred CCccccccccccccChhhHHHHHHhcCCCeee-ecCcccCChHHHHHHH
Q 040794 295 IKPFMCRKCGKAFAVRGDWRTHEKNCGKLWYC-ICGSDFKHKRSLKDHI 342 (375)
Q Consensus 295 ekpy~C~~Cgk~F~~~~~L~~H~k~h~k~~~C-~Cgk~F~~~~~L~~H~ 342 (375)
.||+ |-.|.+-|-...-|+.|++ .|-|+| +|.|..-.--.|..|-
T Consensus 9 ~kpw-cwycnrefddekiliqhqk--akhfkchichkkl~sgpglsihc 54 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQK--AKHFKCHICHKKLFSGPGLSIHC 54 (341)
T ss_pred CCce-eeecccccchhhhhhhhhh--hccceeeeehhhhccCCCceeeh
Confidence 4554 8999999999999999988 577999 9999876666666663
No 72
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=70.07 E-value=3.9 Score=28.24 Aligned_cols=18 Identities=22% Similarity=0.719 Sum_probs=10.1
Q ss_pred ecCcccCCh-----HHHHHHHHH
Q 040794 327 ICGSDFKHK-----RSLKDHIKA 344 (375)
Q Consensus 327 ~Cgk~F~~~-----~~L~~H~r~ 344 (375)
.|++.++.. ++|.+|++.
T Consensus 23 ~C~~~l~~~~~~gTs~L~rHl~~ 45 (50)
T smart00614 23 YCGKKLSRSSKGGTSNLRRHLRR 45 (50)
T ss_pred CCCCEeeeCCCCCcHHHHHHHHh
Confidence 455555443 567777663
No 73
>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=69.32 E-value=3.5 Score=33.63 Aligned_cols=16 Identities=38% Similarity=0.968 Sum_probs=11.0
Q ss_pred CCccccccccccccCh
Q 040794 295 IKPFMCRKCGKAFAVR 310 (375)
Q Consensus 295 ekpy~C~~Cgk~F~~~ 310 (375)
..|..|++||..|.-.
T Consensus 24 k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 24 KDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCCccCCCCCCccCcc
Confidence 4677777777777654
No 74
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=68.69 E-value=3.7 Score=37.13 Aligned_cols=87 Identities=23% Similarity=0.415 Sum_probs=64.5
Q ss_pred cccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcCCCccccccccccccChhhHHHHHH-hc-----------CCC
Q 040794 256 LRLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHGIKPFMCRKCGKAFAVRGDWRTHEK-NC-----------GKL 323 (375)
Q Consensus 256 ~~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~gekpy~C~~Cgk~F~~~~~L~~H~k-~h-----------~k~ 323 (375)
..|.|.+-|+. ..|........|+.+-+| -.|..|.+.|...--|..|+. .| .-.
T Consensus 78 ~~~~cqvagc~----------~~~d~lD~~E~hY~~~h~---~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dM 144 (253)
T KOG4173|consen 78 PAFACQVAGCC----------QVFDALDDYEHHYHTLHG---NSCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDM 144 (253)
T ss_pred ccccccccchH----------HHHhhhhhHHHhhhhccc---chhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccH
Confidence 56789885532 777777777777755443 379999999999988888875 22 245
Q ss_pred eee---ecCcccCChHHHHHHHHHhCCCCCCCCCC
Q 040794 324 WYC---ICGSDFKHKRSLKDHIKAFGNGHAAYGID 355 (375)
Q Consensus 324 ~~C---~Cgk~F~~~~~L~~H~r~~H~ge~~y~C~ 355 (375)
|.| -|+-.|+....-++|+-..|.=-.-|..+
T Consensus 145 y~ClvEgCt~KFkT~r~RkdH~I~~Hk~Pa~frFd 179 (253)
T KOG4173|consen 145 YQCLVEGCTEKFKTSRDRKDHMIRMHKYPADFRFD 179 (253)
T ss_pred HHHHHHhhhhhhhhhhhhhhHHHHhccCCcceeec
Confidence 999 49999999999999987767544444443
No 75
>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=63.53 E-value=3.9 Score=25.75 Aligned_cols=10 Identities=40% Similarity=1.298 Sum_probs=6.1
Q ss_pred Cccccccccc
Q 040794 296 KPFMCRKCGK 305 (375)
Q Consensus 296 kpy~C~~Cgk 305 (375)
.++.|+.||.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 5666666653
No 76
>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=62.56 E-value=4.8 Score=34.08 Aligned_cols=23 Identities=30% Similarity=0.655 Sum_probs=14.2
Q ss_pred CCCeee-ecCcccCChHHHHHHHHHhC
Q 040794 321 GKLWYC-ICGSDFKHKRSLKDHIKAFG 346 (375)
Q Consensus 321 ~k~~~C-~Cgk~F~~~~~L~~H~r~~H 346 (375)
+..-.| +|||.|+.. ++|++.||
T Consensus 70 ~d~i~clecGk~~k~L---krHL~~~~ 93 (132)
T PF05443_consen 70 PDYIICLECGKKFKTL---KRHLRTHH 93 (132)
T ss_dssp SS-EE-TBT--EESBH---HHHHHHTT
T ss_pred cCeeEEccCCcccchH---HHHHHHcc
Confidence 455678 899988764 89999854
No 77
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=61.62 E-value=1.5 Score=40.19 Aligned_cols=40 Identities=25% Similarity=0.546 Sum_probs=22.9
Q ss_pred CccccccccccccChhhHHHHHHh---------c---CC-----Ceee-ecCcccCCh
Q 040794 296 KPFMCRKCGKAFAVRGDWRTHEKN---------C---GK-----LWYC-ICGSDFKHK 335 (375)
Q Consensus 296 kpy~C~~Cgk~F~~~~~L~~H~k~---------h---~k-----~~~C-~Cgk~F~~~ 335 (375)
|.+.|++|++.|..+.-.....+. + .. .++| .||.+|...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 456777777777665444433331 0 11 2568 888876654
No 78
>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=61.16 E-value=5 Score=32.74 Aligned_cols=12 Identities=33% Similarity=0.858 Sum_probs=7.4
Q ss_pred eecCcccccccC
Q 040794 214 FSCPVCCKTFNR 225 (375)
Q Consensus 214 ~~C~~C~k~F~~ 225 (375)
..|+.||+.|.-
T Consensus 10 R~Cp~CG~kFYD 21 (108)
T PF09538_consen 10 RTCPSCGAKFYD 21 (108)
T ss_pred ccCCCCcchhcc
Confidence 456666666653
No 79
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=60.19 E-value=3.8 Score=29.52 Aligned_cols=8 Identities=38% Similarity=1.285 Sum_probs=5.6
Q ss_pred ccccCCCC
Q 040794 257 RLPCYCCA 264 (375)
Q Consensus 257 ~~~C~~Cg 264 (375)
.|.|+.||
T Consensus 27 ~F~CPnCG 34 (61)
T COG2888 27 KFPCPNCG 34 (61)
T ss_pred EeeCCCCC
Confidence 46777777
No 80
>PF15269 zf-C2H2_7: Zinc-finger
Probab=59.66 E-value=7.3 Score=26.40 Aligned_cols=21 Identities=29% Similarity=0.545 Sum_probs=15.9
Q ss_pred eee-ecCcccCChHHHHHHHHH
Q 040794 324 WYC-ICGSDFKHKRSLKDHIKA 344 (375)
Q Consensus 324 ~~C-~Cgk~F~~~~~L~~H~r~ 344 (375)
|+| +|.-+...++.|-.||+-
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 567 787777788888888764
No 81
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=58.84 E-value=3 Score=31.46 Aligned_cols=17 Identities=18% Similarity=0.491 Sum_probs=10.8
Q ss_pred CCCccccc--cccccccCh
Q 040794 294 GIKPFMCR--KCGKAFAVR 310 (375)
Q Consensus 294 gekpy~C~--~Cgk~F~~~ 310 (375)
.++.++|. .||.+|...
T Consensus 24 ~~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 24 KERYHQCQNVNCSATFITY 42 (72)
T ss_pred heeeeecCCCCCCCEEEEE
Confidence 35566776 677777643
No 82
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=58.65 E-value=3.4 Score=32.14 Aligned_cols=13 Identities=38% Similarity=1.239 Sum_probs=6.9
Q ss_pred CCCeee-ecCcccC
Q 040794 321 GKLWYC-ICGSDFK 333 (375)
Q Consensus 321 ~k~~~C-~Cgk~F~ 333 (375)
-.-|.| .||..|+
T Consensus 51 ~GIW~C~kCg~~fA 64 (89)
T COG1997 51 TGIWKCRKCGAKFA 64 (89)
T ss_pred cCeEEcCCCCCeec
Confidence 445555 5555554
No 83
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=55.99 E-value=2.2 Score=37.04 Aligned_cols=18 Identities=28% Similarity=0.499 Sum_probs=13.3
Q ss_pred CccccccccccccChhhH
Q 040794 296 KPFMCRKCGKAFAVRGDW 313 (375)
Q Consensus 296 kpy~C~~Cgk~F~~~~~L 313 (375)
+.++|+.||++|.....+
T Consensus 27 ~~~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 27 RRRECLACGKRFTTFERV 44 (154)
T ss_pred eeeeccccCCcceEeEec
Confidence 348899999999865544
No 84
>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=55.19 E-value=5.3 Score=26.59 Aligned_cols=17 Identities=18% Similarity=0.700 Sum_probs=13.0
Q ss_pred ceecCcccccccCchHH
Q 040794 213 QFSCPVCCKTFNRYNNM 229 (375)
Q Consensus 213 p~~C~~C~k~F~~~~~L 229 (375)
-|.|..||..|.....+
T Consensus 5 ey~C~~Cg~~fe~~~~~ 21 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSI 21 (42)
T ss_pred EEEeCCCCCEEEEEEEc
Confidence 48999999988865543
No 85
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=55.09 E-value=5.1 Score=28.45 Aligned_cols=30 Identities=27% Similarity=0.451 Sum_probs=25.6
Q ss_pred cccCCCceecCcccccccCchHHhhccc-cc
Q 040794 207 ILIGPTQFSCPVCCKTFNRYNNMQMHMW-GH 236 (375)
Q Consensus 207 ~h~g~kp~~C~~C~k~F~~~~~L~~H~~-~H 236 (375)
...|+.-+.|+-|++.|...-.+.+|.. .|
T Consensus 11 ~RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 11 DRDGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred ccCCceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 4567778999999999999999999986 45
No 86
>PHA00626 hypothetical protein
Probab=55.08 E-value=2.8 Score=29.82 Aligned_cols=15 Identities=20% Similarity=0.592 Sum_probs=10.0
Q ss_pred CccccccccccccCh
Q 040794 296 KPFMCRKCGKAFAVR 310 (375)
Q Consensus 296 kpy~C~~Cgk~F~~~ 310 (375)
..|.|+.||..|+..
T Consensus 22 nrYkCkdCGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCDCGYNDSKD 36 (59)
T ss_pred cceEcCCCCCeechh
Confidence 457777777777643
No 87
>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=54.09 E-value=11 Score=23.92 Aligned_cols=12 Identities=33% Similarity=0.866 Sum_probs=9.1
Q ss_pred ceecCccccccc
Q 040794 213 QFSCPVCCKTFN 224 (375)
Q Consensus 213 p~~C~~C~k~F~ 224 (375)
.|+|..||..+.
T Consensus 2 ~~~C~~CG~i~~ 13 (34)
T cd00729 2 VWVCPVCGYIHE 13 (34)
T ss_pred eEECCCCCCEeE
Confidence 488999997543
No 88
>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=53.65 E-value=3.5 Score=26.84 Aligned_cols=7 Identities=29% Similarity=0.795 Sum_probs=4.0
Q ss_pred cccCCCC
Q 040794 258 LPCYCCA 264 (375)
Q Consensus 258 ~~C~~Cg 264 (375)
|.|..||
T Consensus 6 y~C~~Cg 12 (41)
T smart00834 6 YRCEDCG 12 (41)
T ss_pred EEcCCCC
Confidence 5555555
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=52.05 E-value=11 Score=31.62 Aligned_cols=16 Identities=19% Similarity=0.362 Sum_probs=11.0
Q ss_pred CCccccccccccccCh
Q 040794 295 IKPFMCRKCGKAFAVR 310 (375)
Q Consensus 295 ekpy~C~~Cgk~F~~~ 310 (375)
..|..|++||..|.-.
T Consensus 24 k~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 24 RRPAVSPYTGEQFPPE 39 (129)
T ss_pred CCCccCCCcCCccCcc
Confidence 4677777777776544
No 90
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=51.59 E-value=11 Score=32.31 Aligned_cols=20 Identities=20% Similarity=0.549 Sum_probs=15.0
Q ss_pred CCceecCcccccccCchHHh
Q 040794 211 PTQFSCPVCCKTFNRYNNMQ 230 (375)
Q Consensus 211 ~kp~~C~~C~k~F~~~~~L~ 230 (375)
..-|.|+.|+..|.....+.
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~ 116 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQ 116 (147)
T ss_pred CcEEECcCCCCEeeHHHHHH
Confidence 34699999999998655443
No 91
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=51.40 E-value=5.9 Score=39.79 Aligned_cols=51 Identities=16% Similarity=0.434 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHhhcCCCccccccccccccChhhHHHHHHhcCCCeee-ecCcc
Q 040794 280 KDFRTLQTHYKRKHGIKPFMCRKCGKAFAVRGDWRTHEKNCGKLWYC-ICGSD 331 (375)
Q Consensus 280 ~~~~~L~~H~r~H~gekpy~C~~Cgk~F~~~~~L~~H~k~h~k~~~C-~Cgk~ 331 (375)
.....|..-++--+...-|.|+.|.+.|+....++-= -.-...|.| .|+-.
T Consensus 111 ~m~krled~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~-~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 111 QMRKRLEDRLRDDTNVAGYVCPNCQKKYTSLEALQLL-DNETGEFHCENCGGE 162 (436)
T ss_pred HHHHHHHHHhhhccccccccCCccccchhhhHHHHhh-cccCceEEEecCCCc
Confidence 3334444444445666779999999999988776531 112457888 78754
No 92
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=50.39 E-value=12 Score=32.09 Aligned_cols=37 Identities=14% Similarity=0.433 Sum_probs=20.9
Q ss_pred cCCCccccccccccccChhhHHH-HHHhcCCCeee-ecCccc
Q 040794 293 HGIKPFMCRKCGKAFAVRGDWRT-HEKNCGKLWYC-ICGSDF 332 (375)
Q Consensus 293 ~gekpy~C~~Cgk~F~~~~~L~~-H~k~h~k~~~C-~Cgk~F 332 (375)
....-|.|+.|++.|.....+.. + . ...|.| .||...
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~~d--~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQLLD--M-DGTFTCPRCGEEL 133 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHhcC--C-CCcEECCCCCCEE
Confidence 34456777777777775444332 1 1 233777 777654
No 93
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=47.86 E-value=11 Score=34.44 Aligned_cols=24 Identities=25% Similarity=0.508 Sum_probs=19.2
Q ss_pred CceecCcccccccCchHHhhcccc
Q 040794 212 TQFSCPVCCKTFNRYNNMQMHMWG 235 (375)
Q Consensus 212 kp~~C~~C~k~F~~~~~L~~H~~~ 235 (375)
|.+.|++|++.|..+.-.....++
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~ 27 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRV 27 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceE
Confidence 568999999999998776666553
No 94
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=47.81 E-value=15 Score=31.75 Aligned_cols=27 Identities=19% Similarity=0.244 Sum_probs=15.7
Q ss_pred hcCCCcccccccccccc------ChhhHHHHHH
Q 040794 292 KHGIKPFMCRKCGKAFA------VRGDWRTHEK 318 (375)
Q Consensus 292 H~gekpy~C~~Cgk~F~------~~~~L~~H~k 318 (375)
|...--.+|..|+|-|- ..+++..|+.
T Consensus 9 ~~p~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv 41 (152)
T PF09416_consen 9 HDPSCVVKCNTCNKWFCNGRGNTSGSHIVNHLV 41 (152)
T ss_dssp --CCCEEEETTTTEEEES--TTSSS-HHHHHHH
T ss_pred CCcccEeEcCCCCcEeecCCCCCcccHHHHHHH
Confidence 44455567888887773 4455666655
No 95
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=47.78 E-value=8.2 Score=24.83 Aligned_cols=10 Identities=50% Similarity=1.288 Sum_probs=4.7
Q ss_pred cccccccccc
Q 040794 298 FMCRKCGKAF 307 (375)
Q Consensus 298 y~C~~Cgk~F 307 (375)
.+|..|+..|
T Consensus 26 v~C~~C~~~f 35 (36)
T PF13717_consen 26 VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEe
Confidence 4444444443
No 96
>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=47.44 E-value=13 Score=23.76 Aligned_cols=15 Identities=27% Similarity=0.793 Sum_probs=10.7
Q ss_pred eecCcccccccCchH
Q 040794 214 FSCPVCCKTFNRYNN 228 (375)
Q Consensus 214 ~~C~~C~k~F~~~~~ 228 (375)
+.|+.|+..|.-...
T Consensus 3 ~~CP~C~~~~~v~~~ 17 (38)
T TIGR02098 3 IQCPNCKTSFRVVDS 17 (38)
T ss_pred EECCCCCCEEEeCHH
Confidence 578888887775554
No 97
>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=45.83 E-value=16 Score=31.85 Aligned_cols=40 Identities=18% Similarity=0.345 Sum_probs=23.7
Q ss_pred HHHHHHhhcCCCccccccccccccChhhHHHHHHhcCCCeee-ecCcc
Q 040794 285 LQTHYKRKHGIKPFMCRKCGKAFAVRGDWRTHEKNCGKLWYC-ICGSD 331 (375)
Q Consensus 285 L~~H~r~H~gekpy~C~~Cgk~F~~~~~L~~H~k~h~k~~~C-~Cgk~ 331 (375)
|..-+...+...-|.|+.|+..|+....+. --|.| .||..
T Consensus 97 lk~~l~~e~~~~~Y~Cp~c~~r~tf~eA~~-------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 97 LREKLEFETNNMFFICPNMCVRFTFNEAME-------LNFTCPRCGAM 137 (158)
T ss_pred HHHHHhhccCCCeEECCCCCcEeeHHHHHH-------cCCcCCCCCCE
Confidence 333334444555677777777777666654 25777 67764
No 98
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=45.47 E-value=11 Score=33.23 Aligned_cols=14 Identities=36% Similarity=0.861 Sum_probs=11.2
Q ss_pred hhcCCCcccccccc
Q 040794 291 RKHGIKPFMCRKCG 304 (375)
Q Consensus 291 ~H~gekpy~C~~Cg 304 (375)
++.|+-|-+|+.||
T Consensus 143 ~~~ge~P~~CPiCg 156 (166)
T COG1592 143 THEGEAPEVCPICG 156 (166)
T ss_pred cccCCCCCcCCCCC
Confidence 35678889999998
No 99
>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=45.45 E-value=13 Score=31.10 Aligned_cols=12 Identities=25% Similarity=0.415 Sum_probs=9.0
Q ss_pred eecCcccccccC
Q 040794 214 FSCPVCCKTFNR 225 (375)
Q Consensus 214 ~~C~~C~k~F~~ 225 (375)
..|+.||+.|..
T Consensus 10 r~Cp~cg~kFYD 21 (129)
T TIGR02300 10 RICPNTGSKFYD 21 (129)
T ss_pred ccCCCcCccccc
Confidence 568888887764
No 100
>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=45.15 E-value=13 Score=32.37 Aligned_cols=21 Identities=29% Similarity=0.581 Sum_probs=17.2
Q ss_pred CCCceecCcccccccCchHHh
Q 040794 210 GPTQFSCPVCCKTFNRYNNMQ 230 (375)
Q Consensus 210 g~kp~~C~~C~k~F~~~~~L~ 230 (375)
...-|.|+.|+..|+....+.
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~ 126 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME 126 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH
Confidence 345699999999999888775
No 101
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=45.01 E-value=5.6 Score=27.50 Aligned_cols=7 Identities=29% Similarity=1.008 Sum_probs=4.5
Q ss_pred cccCCCC
Q 040794 258 LPCYCCA 264 (375)
Q Consensus 258 ~~C~~Cg 264 (375)
|.|..||
T Consensus 6 y~C~~Cg 12 (52)
T TIGR02605 6 YRCTACG 12 (52)
T ss_pred EEeCCCC
Confidence 6666666
No 102
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=44.86 E-value=6.2 Score=42.10 Aligned_cols=24 Identities=38% Similarity=0.646 Sum_probs=22.0
Q ss_pred ccccccccccccChhhHHHHHHhc
Q 040794 297 PFMCRKCGKAFAVRGDWRTHEKNC 320 (375)
Q Consensus 297 py~C~~Cgk~F~~~~~L~~H~k~h 320 (375)
-|.|++|+|.|.....+..|||+|
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHH
Confidence 489999999999999999999987
No 103
>PRK14873 primosome assembly protein PriA; Provisional
Probab=44.62 E-value=19 Score=38.83 Aligned_cols=11 Identities=27% Similarity=0.963 Sum_probs=7.3
Q ss_pred Ccccccccccc
Q 040794 296 KPFMCRKCGKA 306 (375)
Q Consensus 296 kpy~C~~Cgk~ 306 (375)
.|+.|+.||..
T Consensus 421 ~p~~Cp~Cgs~ 431 (665)
T PRK14873 421 PDWRCPRCGSD 431 (665)
T ss_pred cCccCCCCcCC
Confidence 46777777754
No 104
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=44.55 E-value=13 Score=33.09 Aligned_cols=20 Identities=30% Similarity=0.551 Sum_probs=16.1
Q ss_pred CCceecCcccccccCchHHh
Q 040794 211 PTQFSCPVCCKTFNRYNNMQ 230 (375)
Q Consensus 211 ~kp~~C~~C~k~F~~~~~L~ 230 (375)
..-|.|+.|+..|+....+.
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~ 134 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAME 134 (178)
T ss_pred CCEEECCCCCcEEeHHHHhh
Confidence 34699999999999887653
No 105
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=44.42 E-value=25 Score=37.75 Aligned_cols=24 Identities=33% Similarity=0.619 Sum_probs=23.0
Q ss_pred ceecCcccccccCchHHhhccccc
Q 040794 213 QFSCPVCCKTFNRYNNMQMHMWGH 236 (375)
Q Consensus 213 p~~C~~C~k~F~~~~~L~~H~~~H 236 (375)
-|.|..|+|.|...-.+..||++|
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHH
Confidence 599999999999999999999999
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=44.21 E-value=19 Score=33.08 Aligned_cols=27 Identities=30% Similarity=0.619 Sum_probs=20.3
Q ss_pred CCCeee-ecCcccCChHHHHHHHHHhCC
Q 040794 321 GKLWYC-ICGSDFKHKRSLKDHIKAFGN 347 (375)
Q Consensus 321 ~k~~~C-~Cgk~F~~~~~L~~H~r~~H~ 347 (375)
+..|.| .|+|.|+-..-.++||...|.
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 346888 888888888888888888775
No 107
>PF12907 zf-met2: Zinc-binding
Probab=43.13 E-value=4.8 Score=26.70 Aligned_cols=31 Identities=23% Similarity=0.380 Sum_probs=19.2
Q ss_pred eee-ecCcccCC---hHHHHHHHHHhCCCCCCCCC
Q 040794 324 WYC-ICGSDFKH---KRSLKDHIKAFGNGHAAYGI 354 (375)
Q Consensus 324 ~~C-~Cgk~F~~---~~~L~~H~r~~H~ge~~y~C 354 (375)
+.| +|-..|.. ...|+.|....|++..+-.|
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~~~C 36 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKNTFEEC 36 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCCCHHHc
Confidence 456 67755543 35688888777777544443
No 108
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=43.12 E-value=16 Score=30.91 Aligned_cols=20 Identities=40% Similarity=0.584 Sum_probs=14.9
Q ss_pred eee-ecCcccCChHHHHHHHHHhC
Q 040794 324 WYC-ICGSDFKHKRSLKDHIKAFG 346 (375)
Q Consensus 324 ~~C-~Cgk~F~~~~~L~~H~r~~H 346 (375)
..| .|||.|+ +|+||+.+||
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~ 97 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHY 97 (148)
T ss_pred EEEeccCcchH---HHHHHHhccc
Confidence 568 7888885 5788888843
No 109
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=43.07 E-value=20 Score=29.43 Aligned_cols=86 Identities=19% Similarity=0.342 Sum_probs=49.9
Q ss_pred ceecCcccccccCchHHhhcccccC----CCCCCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCcccCCHHHHHHH
Q 040794 213 QFSCPVCCKTFNRYNNMQMHMWGHG----SQYRKGPESLRGTQPTGMLRLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTH 288 (375)
Q Consensus 213 p~~C~~C~k~F~~~~~L~~H~~~H~----~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H 288 (375)
|-.|+.||-+......|.+.- |+ ..+...++. .....-.|.-|. +.|.......+
T Consensus 15 P~~CpiCgLtLVss~HLARSy--HHLfPl~~f~ev~~~------~~~~~~~C~~C~------------~~f~~~~~~~~- 73 (112)
T TIGR00622 15 PVECPICGLTLILSTHLARSY--HHLFPLKAFQEIPLE------EYNGSRFCFGCQ------------GPFPKPPVSPF- 73 (112)
T ss_pred CCcCCcCCCEEeccchHHHhh--hccCCCccccccccc------ccCCCCcccCcC------------CCCCCcccccc-
Confidence 788999999988888887632 21 001101000 000112488888 66654321110
Q ss_pred HHhhcCCCccccccccccccChhhHHHHHHhc
Q 040794 289 YKRKHGIKPFMCRKCGKAFAVRGDWRTHEKNC 320 (375)
Q Consensus 289 ~r~H~gekpy~C~~Cgk~F~~~~~L~~H~k~h 320 (375)
..-.....|+|..|...|-..-++..|...|
T Consensus 74 -~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 74 -DELKDSHRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred -cccccccceeCCCCCCccccccchhhhhhcc
Confidence 0012345799999999999988888775544
No 110
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=41.73 E-value=17 Score=30.68 Aligned_cols=15 Identities=20% Similarity=0.589 Sum_probs=12.2
Q ss_pred ceecCcccccccCch
Q 040794 213 QFSCPVCCKTFNRYN 227 (375)
Q Consensus 213 p~~C~~C~k~F~~~~ 227 (375)
|++|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 578999999998665
No 111
>PF15269 zf-C2H2_7: Zinc-finger
Probab=41.48 E-value=16 Score=24.76 Aligned_cols=21 Identities=19% Similarity=0.398 Sum_probs=15.9
Q ss_pred cccccccccccChhhHHHHHH
Q 040794 298 FMCRKCGKAFAVRGDWRTHEK 318 (375)
Q Consensus 298 y~C~~Cgk~F~~~~~L~~H~k 318 (375)
|+|-.|.-+..-++.|..||+
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 567777777777888888877
No 112
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=41.02 E-value=69 Score=31.83 Aligned_cols=79 Identities=18% Similarity=0.336 Sum_probs=50.3
Q ss_pred cccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcCCCccccccccccccChhhHHHHHH-hcCCCeee-ecC---ccc
Q 040794 258 LPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHGIKPFMCRKCGKAFAVRGDWRTHEK-NCGKLWYC-ICG---SDF 332 (375)
Q Consensus 258 ~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~gekpy~C~~Cgk~F~~~~~L~~H~k-~h~k~~~C-~Cg---k~F 332 (375)
-.|-.|+ +.+++.-.-.+||..++|-.- +.=. ..+....|..-+. .-+.-+.| .|. +.|
T Consensus 167 t~CLfC~------------~~~k~~e~~~~HM~~~HgffI---Pdre-YL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f 230 (390)
T KOG2785|consen 167 TDCLFCD------------KKSKSLEENLKHMFKEHGFFI---PDRE-YLTDEKGLLKYLGEKVGIGFICLFCNELGRPF 230 (390)
T ss_pred cceeecC------------CCcccHHHHHHHHhhccCCcC---CchH-hhhchhHHHHHHHHHhccCceEEEeccccCcc
Confidence 5688888 888888888888888876321 0000 0011222222222 23567889 899 999
Q ss_pred CChHHHHHHHHHhCCCCCCC
Q 040794 333 KHKRSLKDHIKAFGNGHAAY 352 (375)
Q Consensus 333 ~~~~~L~~H~r~~H~ge~~y 352 (375)
...-+-+.||.....-.-+|
T Consensus 231 ~sleavr~HM~~K~HCkl~y 250 (390)
T KOG2785|consen 231 SSLEAVRAHMRDKGHCKLPY 250 (390)
T ss_pred cccHHHHHHHhhccCcccCC
Confidence 99999999998764444555
No 113
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=40.64 E-value=6.6 Score=26.83 Aligned_cols=34 Identities=24% Similarity=0.528 Sum_probs=15.4
Q ss_pred cccccccccChhhHHHHHHhcCCCeee---ecCcccC
Q 040794 300 CRKCGKAFAVRGDWRTHEKNCGKLWYC---ICGSDFK 333 (375)
Q Consensus 300 C~~Cgk~F~~~~~L~~H~k~h~k~~~C---~Cgk~F~ 333 (375)
|+.||..-.-+.....+...-+.-|+| .||..|.
T Consensus 2 CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 2 CPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFV 38 (47)
T ss_pred cCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEE
Confidence 555554443333333222223344555 3666664
No 114
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=39.61 E-value=19 Score=23.20 Aligned_cols=14 Identities=36% Similarity=0.833 Sum_probs=7.8
Q ss_pred CCcccccccccccc
Q 040794 295 IKPFMCRKCGKAFA 308 (375)
Q Consensus 295 ekpy~C~~Cgk~F~ 308 (375)
.+..+|..|+..|.
T Consensus 23 ~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 23 GRKVRCPKCGHVFR 36 (37)
T ss_pred CcEEECCCCCcEee
Confidence 34456666665553
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=39.54 E-value=18 Score=33.16 Aligned_cols=24 Identities=29% Similarity=0.376 Sum_probs=19.5
Q ss_pred CCccccccccccccChhhHHHHHH
Q 040794 295 IKPFMCRKCGKAFAVRGDWRTHEK 318 (375)
Q Consensus 295 ekpy~C~~Cgk~F~~~~~L~~H~k 318 (375)
+..|.|..|+|.|.-...++.|+.
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~ 98 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIF 98 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHH
T ss_pred CCEECCCCCCcccCChHHHHHHHh
Confidence 445999999999999999999987
No 116
>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=39.20 E-value=8 Score=36.28 Aligned_cols=87 Identities=23% Similarity=0.289 Sum_probs=46.1
Q ss_pred ccCCCceecCcccccccCchHHhhcccccCCCCCCCCCCcCCCCCCCCcccccCCCCCC----C-----CCCCCCCCCcc
Q 040794 208 LIGPTQFSCPVCCKTFNRYNNMQMHMWGHGSQYRKGPESLRGTQPTGMLRLPCYCCAPG----C-----RNNIDHPRAKP 278 (375)
Q Consensus 208 h~g~kp~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~----~-----~~~~~h~~~k~ 278 (375)
..|.+.|+|..|....- ...--.|+..-.. ...-.|+|.-|..- | ....+|.+.|.
T Consensus 137 ~hGGrif~CsfC~~flC-EDDQFEHQAsCQv--------------Le~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg 201 (314)
T PF06524_consen 137 DHGGRIFKCSFCDNFLC-EDDQFEHQASCQV--------------LESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKG 201 (314)
T ss_pred cCCCeEEEeecCCCeee-ccchhhhhhhhhh--------------hhcccccccccccccchhhhheeeeehhhhhhhcc
Confidence 34677899999986443 4433456543210 11123555555411 0 01124444454
Q ss_pred cCCHHHHHHHHHhhcCCCccccccccccccChhhHHHHHHhc
Q 040794 279 LKDFRTLQTHYKRKHGIKPFMCRKCGKAFAVRGDWRTHEKNC 320 (375)
Q Consensus 279 f~~~~~L~~H~r~H~gekpy~C~~Cgk~F~~~~~L~~H~k~h 320 (375)
|++. ..+++.|++||.--..-..|..-.++|
T Consensus 202 ~ky~-----------k~k~~PCPKCg~et~eTkdLSmStR~h 232 (314)
T PF06524_consen 202 FKYE-----------KGKPIPCPKCGYETQETKDLSMSTRSH 232 (314)
T ss_pred cccc-----------cCCCCCCCCCCCcccccccceeeeecc
Confidence 4432 348899999997766666665444444
No 117
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.90 E-value=24 Score=36.69 Aligned_cols=13 Identities=8% Similarity=-0.110 Sum_probs=6.2
Q ss_pred CCCCCCCCCCCCC
Q 040794 181 GGDDSSAGYPFNR 193 (375)
Q Consensus 181 ~~~~~~~~~~~~~ 193 (375)
.+.....|..|+.
T Consensus 209 Gya~~~~C~~Cg~ 221 (505)
T TIGR00595 209 GYSKNLLCRSCGY 221 (505)
T ss_pred cCCCeeEhhhCcC
Confidence 3344445555643
No 118
>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=38.63 E-value=49 Score=26.56 Aligned_cols=50 Identities=22% Similarity=0.515 Sum_probs=0.0
Q ss_pred cccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcCCCc--------------------------------------
Q 040794 256 LRLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHGIKP-------------------------------------- 297 (375)
Q Consensus 256 ~~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~gekp-------------------------------------- 297 (375)
+-..|..|+ ....- +.+..|++..+...+
T Consensus 10 ~vlIC~~C~------------~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gLp 76 (109)
T PF12013_consen 10 RVLICRQCQ------------YAVQP-SEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGLP 76 (109)
T ss_pred CEEEeCCCC------------cccCc-hHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCCCC
Q ss_pred ----ccc----ccccccccChhhHHHHHH
Q 040794 298 ----FMC----RKCGKAFAVRGDWRTHEK 318 (375)
Q Consensus 298 ----y~C----~~Cgk~F~~~~~L~~H~k 318 (375)
|.| ..|+..+.....+++|.+
T Consensus 77 ~~~G~~C~~~~~~C~y~~~~~~~m~~H~~ 105 (109)
T PF12013_consen 77 VYDGYRCQCDPPHCGYITRSKKTMRKHWR 105 (109)
T ss_pred CCCCeeeecCCCCCCcEeccHHHHHHHHH
No 119
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=37.67 E-value=23 Score=31.56 Aligned_cols=32 Identities=22% Similarity=0.498 Sum_probs=17.6
Q ss_pred CCCccccccccccccChhhHHHHHHhcCCCeee-ecCccc
Q 040794 294 GIKPFMCRKCGKAFAVRGDWRTHEKNCGKLWYC-ICGSDF 332 (375)
Q Consensus 294 gekpy~C~~Cgk~F~~~~~L~~H~k~h~k~~~C-~Cgk~F 332 (375)
...-|.|+.|++.|+....+. .-|.| .||...
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~-------~~F~Cp~Cg~~L 146 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME-------YGFRCPQCGEML 146 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh-------cCCcCCCCCCCC
Confidence 334566666666666555442 24666 666543
No 120
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=36.39 E-value=16 Score=31.84 Aligned_cols=12 Identities=25% Similarity=0.595 Sum_probs=8.6
Q ss_pred cccccCCCCCCC
Q 040794 256 LRLPCYCCAPGC 267 (375)
Q Consensus 256 ~~~~C~~Cg~~~ 267 (375)
+.++|+.||+.|
T Consensus 27 ~~~~c~~c~~~f 38 (154)
T PRK00464 27 RRRECLACGKRF 38 (154)
T ss_pred eeeeccccCCcc
Confidence 348899999444
No 121
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=36.31 E-value=23 Score=23.85 Aligned_cols=14 Identities=14% Similarity=0.591 Sum_probs=10.9
Q ss_pred ceecCcccccccCc
Q 040794 213 QFSCPVCCKTFNRY 226 (375)
Q Consensus 213 p~~C~~C~k~F~~~ 226 (375)
.|.|+.||..|...
T Consensus 3 ~y~C~~CG~~~~~~ 16 (46)
T PRK00398 3 EYKCARCGREVELD 16 (46)
T ss_pred EEECCCCCCEEEEC
Confidence 58999999877643
No 122
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=35.93 E-value=13 Score=29.74 Aligned_cols=14 Identities=21% Similarity=0.624 Sum_probs=11.1
Q ss_pred ceecCcccccccCc
Q 040794 213 QFSCPVCCKTFNRY 226 (375)
Q Consensus 213 p~~C~~C~k~F~~~ 226 (375)
.+.|+.|+..+...
T Consensus 16 ~~~C~~C~~~~~~~ 29 (104)
T TIGR01384 16 VYVCPSCGYEKEKK 29 (104)
T ss_pred eEECcCCCCccccc
Confidence 58899999877653
No 123
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=34.44 E-value=22 Score=29.51 Aligned_cols=24 Identities=38% Similarity=0.830 Sum_probs=16.4
Q ss_pred CCCeee-ecCcccCChHHHHHHHHH
Q 040794 321 GKLWYC-ICGSDFKHKRSLKDHIKA 344 (375)
Q Consensus 321 ~k~~~C-~Cgk~F~~~~~L~~H~r~ 344 (375)
...|.| .|.+-|.....|..|.|+
T Consensus 55 ~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 55 GGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CceeehhhhhhhhcchHHHHHHHhc
Confidence 345677 677777777777777654
No 124
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=34.16 E-value=29 Score=25.03 Aligned_cols=14 Identities=29% Similarity=0.681 Sum_probs=10.2
Q ss_pred ceecCcccccccCc
Q 040794 213 QFSCPVCCKTFNRY 226 (375)
Q Consensus 213 p~~C~~C~k~F~~~ 226 (375)
.|.|+.||+....+
T Consensus 25 ~F~CPnCG~~~I~R 38 (59)
T PRK14890 25 KFLCPNCGEVIIYR 38 (59)
T ss_pred EeeCCCCCCeeEee
Confidence 59999999873333
No 125
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=33.75 E-value=35 Score=32.91 Aligned_cols=78 Identities=22% Similarity=0.326 Sum_probs=44.5
Q ss_pred cccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcCCCc------------cccccccccccChhhHHHHHHhcCCC
Q 040794 256 LRLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHGIKP------------FMCRKCGKAFAVRGDWRTHEKNCGKL 323 (375)
Q Consensus 256 ~~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~gekp------------y~C~~Cgk~F~~~~~L~~H~k~h~k~ 323 (375)
.|..|+.|. -.+....+|.+-+..----|+ -.|..|.-.|.-...-..-..+-...
T Consensus 321 LPi~CP~Cs------------l~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~CQ~~fp~~~~~~~~~~~ss~r 388 (421)
T COG5151 321 LPISCPICS------------LQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQGPFPKPPVSPFDESTSSGR 388 (421)
T ss_pred CCccCcchh------------HHHHHHHHHHHHHHhhccCcccccccCCCCCCCccceeccCCCCCCCCCcccccccccc
Confidence 567788887 555444555443322111222 24778877776443221111123457
Q ss_pred eee-ecCcccCChHHHHHHHHHh
Q 040794 324 WYC-ICGSDFKHKRSLKDHIKAF 345 (375)
Q Consensus 324 ~~C-~Cgk~F~~~~~L~~H~r~~ 345 (375)
|.| .|...|-.--..-.|...|
T Consensus 389 Y~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 389 YQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred eechhhhhhhhhhhHHHHHHHHh
Confidence 899 8998888777766776663
No 126
>PF14353 CpXC: CpXC protein
Probab=33.06 E-value=34 Score=28.35 Aligned_cols=21 Identities=29% Similarity=0.597 Sum_probs=13.9
Q ss_pred CccccccccccccChhhHHHH
Q 040794 296 KPFMCRKCGKAFAVRGDWRTH 316 (375)
Q Consensus 296 kpy~C~~Cgk~F~~~~~L~~H 316 (375)
--|.|+.||..|.-...+.-|
T Consensus 37 ~~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred CEEECCCCCCceecCCCEEEE
Confidence 357888888888765554443
No 127
>PRK04023 DNA polymerase II large subunit; Validated
Probab=32.44 E-value=45 Score=37.34 Aligned_cols=9 Identities=44% Similarity=1.021 Sum_probs=5.2
Q ss_pred eecCccccc
Q 040794 214 FSCPVCCKT 222 (375)
Q Consensus 214 ~~C~~C~k~ 222 (375)
..|+.||..
T Consensus 627 RfCpsCG~~ 635 (1121)
T PRK04023 627 RKCPSCGKE 635 (1121)
T ss_pred ccCCCCCCc
Confidence 456666654
No 128
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=32.29 E-value=32 Score=30.32 Aligned_cols=12 Identities=25% Similarity=0.476 Sum_probs=9.4
Q ss_pred CCCcccccCCCC
Q 040794 253 TGMLRLPCYCCA 264 (375)
Q Consensus 253 ~~~~~~~C~~Cg 264 (375)
.++-|-+|++||
T Consensus 145 ~ge~P~~CPiCg 156 (166)
T COG1592 145 EGEAPEVCPICG 156 (166)
T ss_pred cCCCCCcCCCCC
Confidence 345778999999
No 129
>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=32.20 E-value=32 Score=22.17 Aligned_cols=14 Identities=21% Similarity=0.527 Sum_probs=10.9
Q ss_pred eecCcccccccCch
Q 040794 214 FSCPVCCKTFNRYN 227 (375)
Q Consensus 214 ~~C~~C~k~F~~~~ 227 (375)
..|+.||+.|+...
T Consensus 2 r~C~~Cg~~Yh~~~ 15 (36)
T PF05191_consen 2 RICPKCGRIYHIEF 15 (36)
T ss_dssp EEETTTTEEEETTT
T ss_pred cCcCCCCCcccccc
Confidence 57999999987544
No 130
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=31.93 E-value=22 Score=32.22 Aligned_cols=77 Identities=22% Similarity=0.527 Sum_probs=48.2
Q ss_pred eecCc--ccccccCchHHhhcccccCCCCCCCCCCcCCCCCCCCcccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHh
Q 040794 214 FSCPV--CCKTFNRYNNMQMHMWGHGSQYRKGPESLRGTQPTGMLRLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKR 291 (375)
Q Consensus 214 ~~C~~--C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~ 291 (375)
|.|++ |-..|.....+..|-.+-+ .-.|..|. +.|-+..-|..|+.-
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h-------------------~~sCs~C~------------r~~Pt~hLLd~HI~E 128 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLH-------------------GNSCSFCK------------RAFPTGHLLDAHILE 128 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhcc-------------------cchhHHHH------------HhCCchhhhhHHHHH
Confidence 56665 5566666665555553221 12477777 777776666666642
Q ss_pred ----------hcCCCccccc--cccccccChhhHHHHHH-hcC
Q 040794 292 ----------KHGIKPFMCR--KCGKAFAVRGDWRTHEK-NCG 321 (375)
Q Consensus 292 ----------H~gekpy~C~--~Cgk~F~~~~~L~~H~k-~h~ 321 (375)
-.|.--|+|- .|+..|...-.-+.|+- +|.
T Consensus 129 ~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 129 WHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred HHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhcc
Confidence 2355568884 48888888888888875 453
No 131
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=31.28 E-value=28 Score=24.46 Aligned_cols=39 Identities=21% Similarity=0.609 Sum_probs=21.2
Q ss_pred Ccccccc--ccccccChhhHHHHHH-hc-CCCeee-e----cCcccCCh
Q 040794 296 KPFMCRK--CGKAFAVRGDWRTHEK-NC-GKLWYC-I----CGSDFKHK 335 (375)
Q Consensus 296 kpy~C~~--Cgk~F~~~~~L~~H~k-~h-~k~~~C-~----Cgk~F~~~ 335 (375)
.+..|+. |...+. +..|..|+. .+ .++-.| . |+..+...
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 4567766 434444 567888888 55 466677 6 77776554
No 132
>PRK14873 primosome assembly protein PriA; Provisional
Probab=30.01 E-value=23 Score=38.17 Aligned_cols=26 Identities=42% Similarity=0.859 Sum_probs=17.7
Q ss_pred hcCCCccccccccccccChhhHHHHHHhcCCCeee-ecCcc
Q 040794 292 KHGIKPFMCRKCGKAFAVRGDWRTHEKNCGKLWYC-ICGSD 331 (375)
Q Consensus 292 H~gekpy~C~~Cgk~F~~~~~L~~H~k~h~k~~~C-~Cgk~ 331 (375)
|...+...|..||.. ..++.| .||..
T Consensus 405 h~~~~~l~Ch~CG~~--------------~~p~~Cp~Cgs~ 431 (665)
T PRK14873 405 PSAGGTPRCRWCGRA--------------APDWRCPRCGSD 431 (665)
T ss_pred ecCCCeeECCCCcCC--------------CcCccCCCCcCC
Confidence 444566788888842 247789 89875
No 133
>PRK05580 primosome assembly protein PriA; Validated
Probab=29.93 E-value=43 Score=36.25 Aligned_cols=10 Identities=40% Similarity=1.049 Sum_probs=4.8
Q ss_pred Cccccccccc
Q 040794 296 KPFMCRKCGK 305 (375)
Q Consensus 296 kpy~C~~Cgk 305 (375)
.|..|+.||.
T Consensus 420 ~~~~Cp~Cg~ 429 (679)
T PRK05580 420 IPKACPECGS 429 (679)
T ss_pred CCCCCCCCcC
Confidence 3445555543
No 134
>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=28.99 E-value=19 Score=28.38 Aligned_cols=12 Identities=42% Similarity=1.345 Sum_probs=6.1
Q ss_pred CCeee-ecCcccC
Q 040794 322 KLWYC-ICGSDFK 333 (375)
Q Consensus 322 k~~~C-~Cgk~F~ 333 (375)
.-|.| .|++.|+
T Consensus 52 GIW~C~~C~~~~A 64 (90)
T PF01780_consen 52 GIWKCKKCGKKFA 64 (90)
T ss_dssp TEEEETTTTEEEE
T ss_pred EEeecCCCCCEEe
Confidence 34555 5555543
No 135
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=28.72 E-value=31 Score=27.69 Aligned_cols=16 Identities=19% Similarity=0.561 Sum_probs=13.1
Q ss_pred ceecCcccccccCchH
Q 040794 213 QFSCPVCCKTFNRYNN 228 (375)
Q Consensus 213 p~~C~~C~k~F~~~~~ 228 (375)
|+.|..||..|...+.
T Consensus 2 pH~CtrCG~vf~~g~~ 17 (112)
T COG3364 2 PHQCTRCGEVFDDGSE 17 (112)
T ss_pred CceecccccccccccH
Confidence 6789999999998643
No 136
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=28.38 E-value=25 Score=35.41 Aligned_cols=40 Identities=18% Similarity=0.385 Sum_probs=27.9
Q ss_pred cccCCCceecCcccccccCchHHhhcccccCCCCCCCCCCcCCCCCCCCcccccCCCCC
Q 040794 207 ILIGPTQFSCPVCCKTFNRYNNMQMHMWGHGSQYRKGPESLRGTQPTGMLRLPCYCCAP 265 (375)
Q Consensus 207 ~h~g~kp~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~Cg~ 265 (375)
.-+....|.|+.|.+.|+....++.-- .....|.|..|+.
T Consensus 122 d~t~~~~Y~Cp~C~kkyt~Lea~~L~~-------------------~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 122 DDTNVAGYVCPNCQKKYTSLEALQLLD-------------------NETGEFHCENCGG 161 (436)
T ss_pred hccccccccCCccccchhhhHHHHhhc-------------------ccCceEEEecCCC
Confidence 344566799999999999877665322 1124588999983
No 137
>PRK04023 DNA polymerase II large subunit; Validated
Probab=28.00 E-value=71 Score=35.90 Aligned_cols=15 Identities=20% Similarity=0.164 Sum_probs=9.0
Q ss_pred CCCCCCCCCCCCCcc
Q 040794 352 YGIDGFEEEDEPASE 366 (375)
Q Consensus 352 y~C~~~~~~~~~~~~ 366 (375)
|.|..|+.+-.+.+.
T Consensus 664 y~CPKCG~El~~~s~ 678 (1121)
T PRK04023 664 DECEKCGREPTPYSK 678 (1121)
T ss_pred CcCCCCCCCCCccce
Confidence 567777666554443
No 138
>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=27.96 E-value=42 Score=19.85 Aligned_cols=19 Identities=16% Similarity=0.277 Sum_probs=9.8
Q ss_pred ccccccccccChhhHHHHHH
Q 040794 299 MCRKCGKAFAVRGDWRTHEK 318 (375)
Q Consensus 299 ~C~~Cgk~F~~~~~L~~H~k 318 (375)
.|+.|++.+ ....+..|+.
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 455666555 3345555543
No 139
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=27.40 E-value=38 Score=28.66 Aligned_cols=15 Identities=13% Similarity=0.445 Sum_probs=11.4
Q ss_pred CceecCcccccccCc
Q 040794 212 TQFSCPVCCKTFNRY 226 (375)
Q Consensus 212 kp~~C~~C~k~F~~~ 226 (375)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 358899999887654
No 140
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=26.82 E-value=34 Score=23.06 Aligned_cols=11 Identities=36% Similarity=0.906 Sum_probs=6.8
Q ss_pred Ccccccccccc
Q 040794 296 KPFMCRKCGKA 306 (375)
Q Consensus 296 kpy~C~~Cgk~ 306 (375)
.+.+|+.||..
T Consensus 18 ~~irC~~CG~r 28 (44)
T smart00659 18 DVVRCRECGYR 28 (44)
T ss_pred CceECCCCCce
Confidence 45677777643
No 141
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=25.90 E-value=48 Score=20.78 Aligned_cols=11 Identities=18% Similarity=0.646 Sum_probs=7.9
Q ss_pred eecCccccccc
Q 040794 214 FSCPVCCKTFN 224 (375)
Q Consensus 214 ~~C~~C~k~F~ 224 (375)
|.|..||..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 67888888766
No 142
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=25.72 E-value=33 Score=29.67 Aligned_cols=12 Identities=17% Similarity=0.675 Sum_probs=5.5
Q ss_pred CeeeecCcccCC
Q 040794 323 LWYCICGSDFKH 334 (375)
Q Consensus 323 ~~~C~Cgk~F~~ 334 (375)
+|.|.|+..|.+
T Consensus 117 ~Y~C~C~q~~l~ 128 (156)
T COG3091 117 PYRCQCQQHYLR 128 (156)
T ss_pred eEEeecCCccch
Confidence 344455544433
No 143
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=25.42 E-value=28 Score=27.43 Aligned_cols=12 Identities=25% Similarity=0.869 Sum_probs=6.2
Q ss_pred CCeee-ecCcccC
Q 040794 322 KLWYC-ICGSDFK 333 (375)
Q Consensus 322 k~~~C-~Cgk~F~ 333 (375)
..|.| .|++.|+
T Consensus 53 GIW~C~~C~~~~A 65 (90)
T PTZ00255 53 GIWRCKGCKKTVA 65 (90)
T ss_pred EEEEcCCCCCEEe
Confidence 44555 5555554
No 144
>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=24.75 E-value=95 Score=29.35 Aligned_cols=24 Identities=25% Similarity=0.528 Sum_probs=14.7
Q ss_pred CCCeee-ecCcccCChHHHHHHHHH
Q 040794 321 GKLWYC-ICGSDFKHKRSLKDHIKA 344 (375)
Q Consensus 321 ~k~~~C-~Cgk~F~~~~~L~~H~r~ 344 (375)
.+++.| .||........|-.-.|+
T Consensus 207 ~k~~PCPKCg~et~eTkdLSmStR~ 231 (314)
T PF06524_consen 207 GKPIPCPKCGYETQETKDLSMSTRS 231 (314)
T ss_pred CCCCCCCCCCCcccccccceeeeec
Confidence 356666 666666666666655555
No 145
>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=24.38 E-value=27 Score=27.57 Aligned_cols=12 Identities=42% Similarity=1.378 Sum_probs=6.0
Q ss_pred CCeee-ecCcccC
Q 040794 322 KLWYC-ICGSDFK 333 (375)
Q Consensus 322 k~~~C-~Cgk~F~ 333 (375)
..|.| .|++.|+
T Consensus 52 GIW~C~~C~~~~A 64 (91)
T TIGR00280 52 GIWTCRKCGAKFA 64 (91)
T ss_pred EEEEcCCCCCEEe
Confidence 44555 5555543
No 146
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=24.10 E-value=32 Score=24.37 Aligned_cols=10 Identities=30% Similarity=1.155 Sum_probs=5.4
Q ss_pred cccccccccc
Q 040794 298 FMCRKCGKAF 307 (375)
Q Consensus 298 y~C~~Cgk~F 307 (375)
..|+.||..|
T Consensus 23 V~Cp~CGael 32 (54)
T TIGR01206 23 VICDECGAEL 32 (54)
T ss_pred EeCCCCCCEE
Confidence 4555555544
No 147
>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=23.84 E-value=38 Score=28.65 Aligned_cols=26 Identities=35% Similarity=0.823 Sum_probs=16.6
Q ss_pred ccccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcCCCc
Q 040794 257 RLPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHGIKP 297 (375)
Q Consensus 257 ~~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~gekp 297 (375)
...|-+|| |.|+. |.+|++.|+|..|
T Consensus 72 ~i~clecG------------k~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 72 YIICLECG------------KKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp -EE-TBT--------------EESB---HHHHHHHTT-S-H
T ss_pred eeEEccCC------------cccch---HHHHHHHccCCCH
Confidence 46799999 88865 5899999988765
No 148
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=23.47 E-value=31 Score=34.52 Aligned_cols=116 Identities=17% Similarity=0.273 Sum_probs=64.3
Q ss_pred CCceec--CcccccccCchHHhhcccccCCCCCCCCCCcCCCCCCCCcccccCC--CCCCCCCCCCCCCCcccCCHHHHH
Q 040794 211 PTQFSC--PVCCKTFNRYNNMQMHMWGHGSQYRKGPESLRGTQPTGMLRLPCYC--CAPGCRNNIDHPRAKPLKDFRTLQ 286 (375)
Q Consensus 211 ~kp~~C--~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~C~~--Cg~~~~~~~~h~~~k~f~~~~~L~ 286 (375)
...|.| +.|+..+.++..+.+|...|.. ...++...+..-.-.|.|.. |. | ..+.+.
T Consensus 269 rEhyhcl~e~C~ykr~~k~DvirH~~~hkk----rdnsL~dgf~rfs~syhC~~~~C~------------k---sTsdV~ 329 (480)
T KOG4377|consen 269 REHYHCLNEYCFYKRGQKNDVIRHVEIHKK----RDNSLIDGFHRFSNSYHCTGQICE------------K---STSDVL 329 (480)
T ss_pred chhhcccCccccccccchhhhHHHHHHHhh----cccccccchhhcCccchhhhcccC------------c---cccccc
Confidence 345777 4498777778999999988832 11222221110011134432 43 3 345566
Q ss_pred HHHHhhcCC-------CccccccccccccCh--hhHHHHHHh----------------c-----C-----CCeee---ec
Q 040794 287 THYKRKHGI-------KPFMCRKCGKAFAVR--GDWRTHEKN----------------C-----G-----KLWYC---IC 328 (375)
Q Consensus 287 ~H~r~H~ge-------kpy~C~~Cgk~F~~~--~~L~~H~k~----------------h-----~-----k~~~C---~C 328 (375)
.|-..|+.. .-|.|..||=+++.+ ..-.-|.+- + . .-+.| -|
T Consensus 330 ~h~nFht~~~n~GfrrthfhC~r~gCTdtfK~~khk~yh~kdda~~~dGfkkf~k~e~cay~gCkys~~cnhfhc~r~Gc 409 (480)
T KOG4377|consen 330 LHDNFHTDKRNNGFRRTHFHCQRIGCTDTFKDSKHKPYHYKDDAGEIDGFKKFFKDENCAYTGCKYSGICNHFHCDRLGC 409 (480)
T ss_pred ccCccccccccCceecceeEEeccCCccccccccccccccCcchhhhhhhhhhhccccCCccCcccccceeeeeecccCC
Confidence 666666532 237888888444333 211222220 0 0 12567 39
Q ss_pred CcccCChHHHHHHHHHh
Q 040794 329 GSDFKHKRSLKDHIKAF 345 (375)
Q Consensus 329 gk~F~~~~~L~~H~r~~ 345 (375)
+..|...+....|.|.|
T Consensus 410 ~~tl~s~sqm~shkrkh 426 (480)
T KOG4377|consen 410 EATLYSVSQMASHKRKH 426 (480)
T ss_pred ceEEEehhhhhhhhhhh
Confidence 99999999999999884
No 149
>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=23.35 E-value=34 Score=23.05 Aligned_cols=8 Identities=50% Similarity=1.580 Sum_probs=4.3
Q ss_pred cccccccc
Q 040794 298 FMCRKCGK 305 (375)
Q Consensus 298 y~C~~Cgk 305 (375)
+.|+.||.
T Consensus 19 ~~CP~Cg~ 26 (46)
T PF12760_consen 19 FVCPHCGS 26 (46)
T ss_pred CCCCCCCC
Confidence 44666653
No 150
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=23.28 E-value=51 Score=26.97 Aligned_cols=14 Identities=21% Similarity=0.311 Sum_probs=10.9
Q ss_pred CceecCcccccccC
Q 040794 212 TQFSCPVCCKTFNR 225 (375)
Q Consensus 212 kp~~C~~C~k~F~~ 225 (375)
-.+.|..|+..|..
T Consensus 69 ~~~~C~~Cg~~~~~ 82 (113)
T PRK12380 69 AQAWCWDCSQVVEI 82 (113)
T ss_pred cEEEcccCCCEEec
Confidence 35889999987763
No 151
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=21.78 E-value=48 Score=33.51 Aligned_cols=17 Identities=35% Similarity=0.759 Sum_probs=11.2
Q ss_pred CCCccccccccccccCh
Q 040794 294 GIKPFMCRKCGKAFAVR 310 (375)
Q Consensus 294 gekpy~C~~Cgk~F~~~ 310 (375)
|.+-|+|+.||..+...
T Consensus 364 G~~g~rC~kCg~~~~~~ 380 (421)
T COG1571 364 GRNGFRCKKCGTRARET 380 (421)
T ss_pred CCCCcccccccccCCcc
Confidence 44467777777776644
No 152
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=21.60 E-value=62 Score=33.07 Aligned_cols=21 Identities=38% Similarity=0.998 Sum_probs=18.9
Q ss_pred eee-ecCcccCChHHHHHHHHH
Q 040794 324 WYC-ICGSDFKHKRSLKDHIKA 344 (375)
Q Consensus 324 ~~C-~Cgk~F~~~~~L~~H~r~ 344 (375)
+.| +|.|+|+.-..|+.|...
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 899 999999999999999765
No 153
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=20.96 E-value=49 Score=19.39 Aligned_cols=9 Identities=44% Similarity=1.121 Sum_probs=7.7
Q ss_pred ceecCcccc
Q 040794 213 QFSCPVCCK 221 (375)
Q Consensus 213 p~~C~~C~k 221 (375)
.|.|+.||+
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 699999985
No 154
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.93 E-value=55 Score=22.72 Aligned_cols=13 Identities=31% Similarity=0.667 Sum_probs=8.8
Q ss_pred Ccccccccccccc
Q 040794 296 KPFMCRKCGKAFA 308 (375)
Q Consensus 296 kpy~C~~Cgk~F~ 308 (375)
..+.|..||..+-
T Consensus 36 ~r~~C~~Cgyt~~ 48 (50)
T PRK00432 36 DRWHCGKCGYTEF 48 (50)
T ss_pred CcEECCCcCCEEe
Confidence 5677888876553
No 155
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=20.86 E-value=60 Score=22.74 Aligned_cols=25 Identities=24% Similarity=0.514 Sum_probs=17.0
Q ss_pred CceecCcccccccCchHHhhccccc
Q 040794 212 TQFSCPVCCKTFNRYNNMQMHMWGH 236 (375)
Q Consensus 212 kp~~C~~C~k~F~~~~~L~~H~~~H 236 (375)
..|.|+.|.+.|-..-.+-.|...|
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CeEECCCCCCccccCcChhhhcccc
Confidence 4699999999999999999998887
No 156
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.75 E-value=46 Score=24.19 Aligned_cols=40 Identities=30% Similarity=0.593 Sum_probs=25.7
Q ss_pred cccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHhhcCCCcccccccccccc
Q 040794 258 LPCYCCAPGCRNNIDHPRAKPLKDFRTLQTHYKRKHGIKPFMCRKCGKAFA 308 (375)
Q Consensus 258 ~~C~~Cg~~~~~~~~h~~~k~f~~~~~L~~H~r~H~gekpy~C~~Cgk~F~ 308 (375)
.+|..|.. ..+.+..++..-+..-.-.+.|.|++|.-...
T Consensus 3 vkCiiCd~-----------v~~iD~rt~~tKrLrN~PIrtymC~eC~~Rva 42 (68)
T COG4896 3 VKCIICDR-----------VDEIDNRTFKTKRLRNKPIRTYMCPECEHRVA 42 (68)
T ss_pred ceEEEecc-----------eeeecchhHHHHHhhCCCceeEechhhHhhhc
Confidence 35777762 44556666665555555667799999965544
No 157
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=20.04 E-value=90 Score=30.26 Aligned_cols=27 Identities=26% Similarity=0.582 Sum_probs=22.4
Q ss_pred cCCCeee---e-cCcccCChHHHHHHHHHhC
Q 040794 320 CGKLWYC---I-CGSDFKHKRSLKDHIKAFG 346 (375)
Q Consensus 320 h~k~~~C---~-Cgk~F~~~~~L~~H~r~~H 346 (375)
-+..|.| . |-++|..+..|..|+..-|
T Consensus 141 ~g~iFmC~~~~GC~RTyLsqrDlqAHInhrH 171 (389)
T KOG2932|consen 141 MGGIFMCAAPHGCLRTYLSQRDLQAHINHRH 171 (389)
T ss_pred ccceEEeecchhHHHHHhhHHHHHHHhhhhh
Confidence 3778999 3 9999999999999997544
Done!