Query 021063
Match_columns 318
No_of_seqs 421 out of 1891
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 07:19:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021063.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021063hhsearch_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 3.5E-22 7.7E-27 175.7 5.5 118 127-261 126-250 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.8 1.5E-20 3.3E-25 165.5 3.0 101 129-248 159-265 (279)
3 KOG1074 Transcriptional repres 99.7 1.3E-17 2.8E-22 164.6 3.7 54 128-181 350-403 (958)
4 KOG1074 Transcriptional repres 99.5 5.1E-15 1.1E-19 146.5 4.6 56 201-256 882-937 (958)
5 KOG3623 Homeobox transcription 99.5 2.8E-15 6E-20 146.1 -0.6 91 127-256 890-981 (1007)
6 KOG3576 Ovo and related transc 99.4 1.2E-14 2.6E-19 122.6 -0.6 85 127-250 113-197 (267)
7 KOG3623 Homeobox transcription 99.2 9.4E-13 2E-17 128.7 -1.1 118 131-248 210-331 (1007)
8 KOG3576 Ovo and related transc 99.2 3E-12 6.4E-17 108.2 -0.1 101 126-255 140-241 (267)
9 KOG3608 Zn finger proteins [Ge 99.1 2.9E-11 6.3E-16 109.9 0.7 120 131-250 177-316 (467)
10 KOG3608 Zn finger proteins [Ge 99.0 1.6E-10 3.4E-15 105.1 3.0 108 132-256 264-383 (467)
11 PHA00733 hypothetical protein 99.0 1.8E-10 4E-15 93.1 2.2 83 128-251 37-124 (128)
12 PHA02768 hypothetical protein; 98.8 1.3E-09 2.8E-14 73.8 1.7 40 131-172 5-44 (55)
13 PHA02768 hypothetical protein; 98.5 2E-08 4.3E-13 68.0 0.1 43 160-243 6-48 (55)
14 PLN03086 PRLI-interacting fact 98.5 1.2E-07 2.5E-12 93.6 5.0 94 129-246 451-560 (567)
15 PF13465 zf-H2C2_2: Zinc-finge 98.5 4.1E-08 8.9E-13 56.7 0.9 25 214-238 2-26 (26)
16 PF13465 zf-H2C2_2: Zinc-finge 98.3 8.3E-08 1.8E-12 55.4 -0.1 25 146-170 1-25 (26)
17 KOG3993 Transcription factor ( 98.3 2.1E-07 4.5E-12 86.9 0.2 120 131-250 295-482 (500)
18 PLN03086 PRLI-interacting fact 98.2 6.3E-07 1.4E-11 88.5 3.3 39 130-170 477-515 (567)
19 PHA00616 hypothetical protein 98.2 2.4E-07 5.2E-12 59.7 -0.3 34 131-164 1-34 (44)
20 KOG3993 Transcription factor ( 98.2 2.7E-07 5.9E-12 86.1 -0.1 104 131-251 267-381 (500)
21 PHA00733 hypothetical protein 98.2 8.4E-07 1.8E-11 71.8 2.2 44 127-172 69-112 (128)
22 PHA00616 hypothetical protein 98.1 1.3E-06 2.7E-11 56.4 1.1 31 226-256 1-31 (44)
23 PHA00732 hypothetical protein 98.0 2.3E-06 5E-11 63.1 2.0 37 131-170 1-38 (79)
24 PF00096 zf-C2H2: Zinc finger, 98.0 4.1E-06 8.8E-11 46.7 1.7 23 227-249 1-23 (23)
25 PHA00732 hypothetical protein 97.9 7.3E-06 1.6E-10 60.5 1.9 49 159-251 1-49 (79)
26 PF13912 zf-C2H2_6: C2H2-type 97.8 1.4E-05 3.1E-10 46.3 1.9 26 226-251 1-26 (27)
27 COG5189 SFP1 Putative transcri 97.7 2.4E-05 5.2E-10 70.8 2.9 25 223-247 395-419 (423)
28 PF13894 zf-C2H2_4: C2H2-type 97.6 3.5E-05 7.7E-10 42.9 2.0 24 227-250 1-24 (24)
29 PF00096 zf-C2H2: Zinc finger, 97.6 1.5E-05 3.3E-10 44.3 0.4 23 132-154 1-23 (23)
30 PF13912 zf-C2H2_6: C2H2-type 97.4 6.1E-05 1.3E-09 43.6 0.8 25 131-155 1-25 (27)
31 PF12756 zf-C2H2_2: C2H2 type 97.3 0.00014 3E-09 55.5 2.3 26 225-250 49-74 (100)
32 PF09237 GAGA: GAGA factor; I 97.2 0.00034 7.5E-09 46.2 2.9 32 223-254 21-52 (54)
33 PF05605 zf-Di19: Drought indu 97.1 0.00032 7E-09 47.8 1.9 25 224-250 29-53 (54)
34 smart00355 ZnF_C2H2 zinc finge 97.1 0.00036 7.8E-09 39.2 1.8 25 227-251 1-25 (26)
35 PF13894 zf-C2H2_4: C2H2-type 97.0 0.00028 6E-09 39.1 0.6 23 132-154 1-23 (24)
36 PRK04860 hypothetical protein; 96.6 0.0011 2.4E-08 55.7 2.2 40 129-172 117-156 (160)
37 smart00355 ZnF_C2H2 zinc finge 96.6 0.00092 2E-08 37.5 1.0 24 132-155 1-24 (26)
38 PF12874 zf-met: Zinc-finger o 96.6 0.0013 2.8E-08 37.1 1.5 23 227-249 1-23 (25)
39 PF05605 zf-Di19: Drought indu 96.6 0.001 2.2E-08 45.3 1.3 38 131-169 2-41 (54)
40 PF12874 zf-met: Zinc-finger o 95.9 0.0024 5.3E-08 36.0 0.4 23 132-154 1-23 (25)
41 PF13909 zf-H2C2_5: C2H2-type 95.9 0.0055 1.2E-07 34.2 1.8 24 227-251 1-24 (24)
42 COG5048 FOG: Zn-finger [Genera 95.7 0.01 2.3E-07 56.5 3.8 125 130-254 288-446 (467)
43 PF09237 GAGA: GAGA factor; I 95.6 0.0064 1.4E-07 40.3 1.5 33 127-159 20-52 (54)
44 PF12171 zf-C2H2_jaz: Zinc-fin 95.5 0.0064 1.4E-07 35.1 1.1 23 227-249 2-24 (27)
45 PF12171 zf-C2H2_jaz: Zinc-fin 95.1 0.008 1.7E-07 34.6 0.5 23 132-154 2-24 (27)
46 KOG1146 Homeobox protein [Gene 94.8 0.012 2.6E-07 62.9 1.5 101 133-251 438-545 (1406)
47 PRK04860 hypothetical protein; 94.5 0.01 2.3E-07 49.8 0.0 19 222-240 139-157 (160)
48 PF13913 zf-C2HC_2: zinc-finge 93.5 0.055 1.2E-06 30.6 1.8 22 227-249 3-24 (25)
49 smart00451 ZnF_U1 U1-like zinc 92.4 0.1 2.2E-06 31.7 1.9 23 226-248 3-25 (35)
50 PF13909 zf-H2C2_5: C2H2-type 91.4 0.06 1.3E-06 29.8 0.1 22 132-154 1-22 (24)
51 PF13913 zf-C2HC_2: zinc-finge 91.4 0.085 1.8E-06 29.8 0.7 21 132-153 3-23 (25)
52 COG5048 FOG: Zn-finger [Genera 90.8 0.16 3.4E-06 48.3 2.5 58 199-256 290-353 (467)
53 smart00451 ZnF_U1 U1-like zinc 90.1 0.16 3.4E-06 30.8 1.1 23 131-153 3-25 (35)
54 KOG2893 Zn finger protein [Gen 89.2 0.1 2.2E-06 46.0 -0.3 28 224-251 32-60 (341)
55 KOG1146 Homeobox protein [Gene 86.8 0.18 3.9E-06 54.4 -0.3 43 206-249 1309-1351(1406)
56 COG5189 SFP1 Putative transcri 86.8 0.24 5.3E-06 45.4 0.6 26 127-152 394-419 (423)
57 PF12756 zf-C2H2_2: C2H2 type 86.5 0.32 6.9E-06 36.5 1.1 25 131-155 50-74 (100)
58 PF02892 zf-BED: BED zinc fing 83.0 0.99 2.2E-05 29.0 2.0 27 223-249 13-44 (45)
59 cd00350 rubredoxin_like Rubred 82.2 1.1 2.4E-05 27.0 1.9 24 132-167 2-25 (33)
60 TIGR02605 CxxC_CxxC_SSSS putat 82.0 0.85 1.8E-05 30.4 1.5 31 130-167 4-34 (52)
61 smart00834 CxxC_CXXC_SSSS Puta 81.4 0.96 2.1E-05 28.3 1.5 32 130-168 4-35 (41)
62 KOG2893 Zn finger protein [Gen 80.8 0.64 1.4E-05 41.1 0.6 44 132-179 11-54 (341)
63 smart00614 ZnF_BED BED zinc fi 80.3 1.3 2.7E-05 29.4 1.8 26 225-250 17-48 (50)
64 PF09723 Zn-ribbon_8: Zinc rib 77.1 1.5 3.3E-05 28.0 1.4 31 130-167 4-34 (42)
65 COG1997 RPL43A Ribosomal prote 76.0 2.1 4.6E-05 31.8 2.0 17 223-239 50-66 (89)
66 PF09538 FYDLN_acid: Protein o 75.8 1.9 4.2E-05 33.7 1.9 16 224-239 24-39 (108)
67 KOG2231 Predicted E3 ubiquitin 75.1 1.9 4E-05 44.1 2.1 49 181-233 187-245 (669)
68 PF09538 FYDLN_acid: Protein o 73.2 2.2 4.7E-05 33.4 1.6 30 131-171 9-38 (108)
69 COG4049 Uncharacterized protei 73.1 1.2 2.6E-05 30.2 0.1 28 126-153 12-39 (65)
70 PF09986 DUF2225: Uncharacteri 71.5 2.2 4.9E-05 37.5 1.5 43 130-172 4-61 (214)
71 KOG2785 C2H2-type Zn-finger pr 71.4 2.5 5.5E-05 40.0 1.9 28 223-250 65-94 (390)
72 PF06524 NOA36: NOA36 protein; 70.0 2.9 6.4E-05 37.5 1.9 95 127-251 138-234 (314)
73 PRK14873 primosome assembly pr 69.6 2.8 6.1E-05 43.3 2.0 40 127-167 378-418 (665)
74 PF05443 ROS_MUCR: ROS/MUCR tr 69.1 2.1 4.5E-05 34.7 0.7 28 224-254 70-97 (132)
75 cd00729 rubredoxin_SM Rubredox 67.9 4.5 9.7E-05 24.6 1.9 25 131-167 2-26 (34)
76 COG4049 Uncharacterized protei 64.9 3.1 6.7E-05 28.2 0.8 29 222-250 13-41 (65)
77 KOG4167 Predicted DNA-binding 64.2 1.4 3.1E-05 44.9 -1.3 28 224-251 790-817 (907)
78 PTZ00255 60S ribosomal protein 64.2 4.3 9.3E-05 30.6 1.5 18 223-240 51-68 (90)
79 PRK00398 rpoP DNA-directed RNA 64.2 3.6 7.8E-05 26.7 1.0 30 131-170 3-32 (46)
80 KOG2231 Predicted E3 ubiquitin 63.7 3.8 8.2E-05 41.9 1.5 83 133-230 184-275 (669)
81 smart00531 TFIIE Transcription 62.4 4.6 0.0001 33.3 1.6 37 129-169 97-133 (147)
82 TIGR00595 priA primosomal prot 62.4 4.4 9.6E-05 40.5 1.7 37 132-169 214-250 (505)
83 COG1996 RPC10 DNA-directed RNA 61.9 5.5 0.00012 26.4 1.6 30 130-169 5-34 (49)
84 TIGR02300 FYDLN_acid conserved 61.9 5.5 0.00012 31.9 1.9 20 224-243 24-43 (129)
85 PRK06266 transcription initiat 59.9 4 8.7E-05 34.9 0.8 32 130-170 116-147 (178)
86 COG1198 PriA Primosomal protei 59.8 5.8 0.00013 41.3 2.1 12 224-235 473-484 (730)
87 TIGR00622 ssl1 transcription f 59.3 20 0.00043 28.2 4.5 27 224-250 79-105 (112)
88 TIGR00373 conserved hypothetic 59.2 4.5 9.6E-05 33.9 0.9 31 130-169 108-138 (158)
89 COG1592 Rubrerythrin [Energy p 59.1 5.5 0.00012 33.6 1.5 13 222-234 145-157 (166)
90 TIGR00280 L37a ribosomal prote 58.1 5.6 0.00012 30.0 1.2 18 223-240 50-67 (91)
91 PF12013 DUF3505: Protein of u 56.7 7.9 0.00017 30.0 1.9 26 226-251 80-109 (109)
92 smart00659 RPOLCX RNA polymera 56.4 9.1 0.0002 24.7 1.8 29 131-170 2-30 (44)
93 smart00734 ZnF_Rad18 Rad18-lik 56.2 8.9 0.00019 21.7 1.6 21 227-248 2-22 (26)
94 COG1592 Rubrerythrin [Energy p 56.1 9.5 0.00021 32.2 2.4 24 131-167 134-157 (166)
95 PTZ00303 phosphatidylinositol 56.1 22 0.00048 37.0 5.3 34 132-172 461-494 (1374)
96 COG0068 HypF Hydrogenase matur 53.4 8.6 0.00019 39.5 2.0 42 130-172 121-164 (750)
97 PF01363 FYVE: FYVE zinc finge 52.8 8.7 0.00019 26.9 1.5 14 224-237 23-36 (69)
98 PRK03976 rpl37ae 50S ribosomal 52.3 7.2 0.00016 29.4 1.0 17 223-239 51-67 (90)
99 PRK00464 nrdR transcriptional 49.9 7.5 0.00016 32.4 0.8 12 160-171 29-40 (154)
100 COG4957 Predicted transcriptio 49.5 8.9 0.00019 31.0 1.2 27 225-254 75-101 (148)
101 TIGR02098 MJ0042_CXXC MJ0042 f 44.8 11 0.00023 23.2 0.7 33 132-169 3-35 (38)
102 COG2888 Predicted Zn-ribbon RN 44.6 19 0.00041 24.9 2.0 33 130-167 26-58 (61)
103 PF05443 ROS_MUCR: ROS/MUCR tr 44.1 9 0.0002 31.1 0.5 26 131-159 72-97 (132)
104 PRK05580 primosome assembly pr 44.1 14 0.0003 38.4 1.9 36 132-168 382-417 (679)
105 KOG4167 Predicted DNA-binding 44.0 7.2 0.00016 40.0 -0.1 26 130-155 791-816 (907)
106 PF01780 Ribosomal_L37ae: Ribo 43.2 5.4 0.00012 30.0 -0.9 16 224-239 51-66 (90)
107 PF13717 zinc_ribbon_4: zinc-r 42.7 19 0.00041 22.1 1.7 15 223-237 22-36 (36)
108 PF15135 UPF0515: Uncharacteri 42.6 20 0.00043 32.1 2.4 35 127-169 108-142 (278)
109 PF13878 zf-C2H2_3: zinc-finge 42.5 18 0.0004 22.8 1.6 25 226-250 13-39 (41)
110 KOG2186 Cell growth-regulating 41.8 9.8 0.00021 34.1 0.3 27 224-251 27-53 (276)
111 COG4530 Uncharacterized protei 41.4 14 0.0003 28.8 1.1 15 224-238 24-38 (129)
112 cd00065 FYVE FYVE domain; Zinc 41.3 18 0.00039 24.1 1.6 15 224-238 16-30 (57)
113 KOG4124 Putative transcription 39.6 10 0.00022 35.6 0.1 23 223-245 395-417 (442)
114 PF08790 zf-LYAR: LYAR-type C2 39.5 9.1 0.0002 22.3 -0.1 20 227-247 1-20 (28)
115 PF10571 UPF0547: Uncharacteri 39.1 15 0.00033 20.8 0.8 12 226-237 14-25 (26)
116 COG5151 SSL1 RNA polymerase II 38.8 26 0.00056 32.5 2.5 28 223-250 385-412 (421)
117 PF13719 zinc_ribbon_5: zinc-r 37.9 25 0.00053 21.7 1.6 15 223-237 22-36 (37)
118 PF10263 SprT-like: SprT-like 37.2 14 0.0003 30.4 0.5 33 129-169 121-153 (157)
119 PF09845 DUF2072: Zn-ribbon co 36.8 15 0.00033 29.6 0.7 15 226-240 1-15 (131)
120 COG1773 Rubredoxin [Energy pro 36.5 16 0.00035 24.8 0.7 13 225-237 2-14 (55)
121 smart00064 FYVE Protein presen 36.3 23 0.00049 24.7 1.5 15 224-238 24-38 (68)
122 PF03604 DNA_RNApol_7kD: DNA d 36.3 36 0.00078 20.4 2.1 27 132-169 1-27 (32)
123 PRK09678 DNA-binding transcrip 36.2 16 0.00034 26.4 0.6 38 132-171 2-41 (72)
124 PF07754 DUF1610: Domain of un 35.6 21 0.00045 20.0 0.9 9 131-139 16-24 (24)
125 KOG2482 Predicted C2H2-type Zn 35.5 20 0.00043 33.7 1.3 29 131-159 195-225 (423)
126 PF15269 zf-C2H2_7: Zinc-finge 35.0 24 0.00053 22.8 1.3 24 226-249 20-43 (54)
127 PHA00626 hypothetical protein 34.7 20 0.00044 24.4 0.9 16 224-239 21-36 (59)
128 PRK04023 DNA polymerase II lar 33.8 41 0.00088 36.3 3.4 13 225-237 662-674 (1121)
129 smart00154 ZnF_AN1 AN1-like Zi 33.1 22 0.00048 22.2 0.9 14 226-239 12-25 (39)
130 PRK12380 hydrogenase nickel in 33.0 72 0.0016 25.0 4.0 26 131-168 70-95 (113)
131 KOG2482 Predicted C2H2-type Zn 32.8 28 0.00061 32.7 1.8 31 225-255 194-226 (423)
132 KOG2071 mRNA cleavage and poly 32.6 24 0.00052 35.5 1.5 27 224-250 416-442 (579)
133 KOG0782 Predicted diacylglycer 32.6 65 0.0014 32.5 4.4 12 73-84 106-117 (1004)
134 PF12760 Zn_Tnp_IS1595: Transp 32.3 48 0.001 21.3 2.4 27 132-167 19-45 (46)
135 KOG2186 Cell growth-regulating 32.2 22 0.00049 31.9 1.1 39 131-171 3-41 (276)
136 PF09332 Mcm10: Mcm10 replicat 31.8 8.6 0.00019 36.3 -1.7 43 129-171 250-297 (344)
137 PF13451 zf-trcl: Probable zin 31.6 24 0.00053 23.4 0.9 18 224-241 2-19 (49)
138 KOG2593 Transcription initiati 30.4 24 0.00052 34.2 1.0 32 132-166 129-160 (436)
139 PRK03824 hypA hydrogenase nick 29.6 34 0.00074 27.7 1.7 39 130-168 69-116 (135)
140 COG5236 Uncharacterized conser 29.3 27 0.00059 32.8 1.1 104 131-248 151-273 (493)
141 PLN02748 tRNA dimethylallyltra 29.3 31 0.00068 34.1 1.6 28 224-251 416-446 (468)
142 PF04216 FdhE: Protein involve 29.2 9 0.00019 35.3 -2.0 36 131-169 172-207 (290)
143 COG3091 SprT Zn-dependent meta 29.2 35 0.00076 28.3 1.6 37 128-169 114-150 (156)
144 PF15325 MRI: Modulator of ret 28.6 1.4E+02 0.003 22.8 4.6 6 73-78 91-96 (106)
145 PF04959 ARS2: Arsenite-resist 28.6 26 0.00057 30.8 0.9 29 223-251 74-102 (214)
146 COG3091 SprT Zn-dependent meta 28.5 31 0.00067 28.6 1.2 13 222-235 137-149 (156)
147 PRK03681 hypA hydrogenase nick 28.4 87 0.0019 24.6 3.7 27 131-168 70-96 (114)
148 COG3364 Zn-ribbon containing p 28.0 29 0.00063 26.7 0.9 16 226-241 2-17 (112)
149 KOG4173 Alpha-SNAP protein [In 27.9 13 0.00027 32.4 -1.2 50 201-250 109-171 (253)
150 TIGR00100 hypA hydrogenase nic 27.8 38 0.00083 26.6 1.6 27 131-169 70-96 (115)
151 KOG2071 mRNA cleavage and poly 27.2 30 0.00065 34.9 1.1 27 129-155 416-442 (579)
152 COG5152 Uncharacterized conser 27.1 17 0.00037 31.4 -0.5 15 158-172 195-209 (259)
153 KOG2636 Splicing factor 3a, su 27.0 36 0.00078 33.1 1.5 26 221-246 396-422 (497)
154 KOG4124 Putative transcription 26.9 29 0.00063 32.7 0.9 44 129-172 347-411 (442)
155 PLN02294 cytochrome c oxidase 26.8 41 0.00089 28.4 1.7 15 224-238 139-153 (174)
156 PF09986 DUF2225: Uncharacteri 26.8 16 0.00034 32.2 -0.8 24 224-247 3-26 (214)
157 PF07295 DUF1451: Protein of u 26.4 20 0.00044 29.6 -0.2 10 131-140 112-121 (146)
158 PF06397 Desulfoferrod_N: Desu 26.3 33 0.00071 21.2 0.7 13 224-236 4-16 (36)
159 smart00731 SprT SprT homologue 26.2 38 0.00081 27.7 1.4 34 129-169 110-143 (146)
160 PF01428 zf-AN1: AN1-like Zinc 26.1 28 0.00061 22.1 0.5 15 225-239 12-26 (43)
161 COG1198 PriA Primosomal protei 25.9 35 0.00075 35.7 1.3 12 132-143 436-447 (730)
162 PRK00564 hypA hydrogenase nick 25.8 47 0.001 26.2 1.8 28 131-169 71-98 (117)
163 PF03811 Zn_Tnp_IS1: InsA N-te 25.6 38 0.00082 20.8 1.0 30 132-165 6-35 (36)
164 PRK14890 putative Zn-ribbon RN 25.2 45 0.00098 23.0 1.4 11 224-234 46-56 (59)
165 PF12013 DUF3505: Protein of u 24.8 36 0.00079 26.2 1.0 24 132-155 81-108 (109)
166 COG4957 Predicted transcriptio 24.2 39 0.00084 27.4 1.0 25 132-159 77-101 (148)
167 PRK04351 hypothetical protein; 24.0 41 0.0009 27.8 1.2 34 129-170 110-143 (149)
168 PF05191 ADK_lid: Adenylate ki 23.9 56 0.0012 20.1 1.5 30 132-169 2-31 (36)
169 KOG4173 Alpha-SNAP protein [In 23.7 10 0.00022 33.0 -2.5 46 133-178 108-165 (253)
170 PF10013 DUF2256: Uncharacteri 22.2 49 0.0011 21.1 1.0 16 228-243 10-25 (42)
171 PF04959 ARS2: Arsenite-resist 21.8 45 0.00098 29.4 1.1 26 128-153 74-99 (214)
172 COG5236 Uncharacterized conser 21.6 1E+02 0.0023 29.1 3.4 18 234-251 289-306 (493)
173 cd00924 Cyt_c_Oxidase_Vb Cytoc 21.5 46 0.00099 25.5 0.9 15 224-238 77-91 (97)
174 smart00440 ZnF_C2C2 C2C2 Zinc 21.4 28 0.00061 21.8 -0.2 9 160-168 29-37 (40)
175 PF00301 Rubredoxin: Rubredoxi 21.2 47 0.001 21.8 0.8 13 226-238 1-13 (47)
176 COG1571 Predicted DNA-binding 21.0 59 0.0013 31.6 1.8 19 223-241 364-382 (421)
177 PRK03564 formate dehydrogenase 20.9 66 0.0014 30.0 2.0 39 128-169 184-222 (309)
178 KOG0782 Predicted diacylglycer 20.8 32 0.00068 34.6 -0.1 15 226-240 276-290 (1004)
179 PF07975 C1_4: TFIIH C1-like d 20.4 35 0.00077 22.8 0.1 27 129-155 19-45 (51)
180 cd00730 rubredoxin Rubredoxin; 20.4 42 0.00091 22.3 0.4 12 227-238 2-13 (50)
181 PF05495 zf-CHY: CHY zinc fing 20.2 26 0.00056 25.0 -0.7 39 131-169 10-51 (71)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.85 E-value=3.5e-22 Score=175.71 Aligned_cols=118 Identities=20% Similarity=0.301 Sum_probs=107.3
Q ss_pred CCCceeecCCCCCcCCCccchhhhhhhcCC---CCCccCCCCCCCCCCCcchhhccCcccCCCCCchhhcccccccc---
Q 021063 127 GGFYVYECKTCNRSFPSFQALGGHRASHKK---PKAALAEAPEKKSSASVPALAVLPTKNEYKDSYSTLHHHDQSHM--- 200 (318)
Q Consensus 127 ~g~~~y~C~~C~K~F~s~~~L~~H~rsHt~---~kp~~C~~C~k~f~~~~~~~~h~~~~~~~f~~~~~L~~H~~~h~--- 200 (318)
.....|.|+.|||.+.+..+|.+|+.+|.. .+.+.|.+|+|.|... ..|+.|+|+|+
T Consensus 126 ~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSm-----------------pALkMHirTH~l~c 188 (279)
T KOG2462|consen 126 AKHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSM-----------------PALKMHIRTHTLPC 188 (279)
T ss_pred ccCCceeccccccccccccccchhhcccccccccccccCCCCCceeeeh-----------------HHHhhHhhccCCCc
Confidence 455679999999999999999999999964 5779999999999766 88899999987
Q ss_pred -ccchhhhhcCchhhhhhcccCCCCceeecCCCccccCChhHHHHHhhhccCCCCCCCCCcc
Q 021063 201 -QAASAAATAANNNNTANNNNKGGNKIHECSICGSEFTSGQALGGHMRRHRAAVATGNNINQ 261 (318)
Q Consensus 201 -~~~c~k~~~~~~~l~~h~~~htg~kpy~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~~~~~~ 261 (318)
|..|||.|+..+-|+.|++.|||||||.|..|+|+|+-+++|+.||++|.+.+.+.|..+.
T Consensus 189 ~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~ 250 (279)
T KOG2462|consen 189 ECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCG 250 (279)
T ss_pred ccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchh
Confidence 4559999999999999999999999999999999999999999999999999999987665
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.80 E-value=1.5e-20 Score=165.47 Aligned_cols=101 Identities=25% Similarity=0.331 Sum_probs=95.9
Q ss_pred CceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCCCCcchhhccCcccCCCCCchhhccccccccccc-----
Q 021063 129 FYVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSSASVPALAVLPTKNEYKDSYSTLHHHDQSHMQAA----- 203 (318)
Q Consensus 129 ~~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~~~~~~~~h~~~~~~~f~~~~~L~~H~~~h~~~~----- 203 (318)
.+.+.|++|+|.|.+--+|..|+|+|+ -+++|.+|||.|.++ .-|+.|+|+|+|++
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRP-----------------WLLQGHiRTHTGEKPF~C~ 219 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRP-----------------WLLQGHIRTHTGEKPFSCP 219 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccch-----------------HHhhcccccccCCCCccCC
Confidence 578999999999999999999999998 679999999999888 78899999999998
Q ss_pred -hhhhhcCchhhhhhcccCCCCceeecCCCccccCChhHHHHHhhh
Q 021063 204 -SAAATAANNNNTANNNNKGGNKIHECSICGSEFTSGQALGGHMRR 248 (318)
Q Consensus 204 -c~k~~~~~~~l~~h~~~htg~kpy~C~~Cgk~F~~~~~L~~H~r~ 248 (318)
|+|.|+.+.+|+.|+.+|.+.|+|+|..|+|+|+..+.|.+|...
T Consensus 220 hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 220 HCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred cccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 999999999999999999999999999999999999999999863
No 3
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.68 E-value=1.3e-17 Score=164.57 Aligned_cols=54 Identities=20% Similarity=0.244 Sum_probs=48.7
Q ss_pred CCceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCCCCcchhhccCc
Q 021063 128 GFYVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSSASVPALAVLPT 181 (318)
Q Consensus 128 g~~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~~~~~~~~h~~~ 181 (318)
....++|.+|.|.|.+.++|+.|.|+|||++||+|.+|+.+|..+.+|..|...
T Consensus 350 ~~~khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~r 403 (958)
T KOG1074|consen 350 PFFKHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQR 403 (958)
T ss_pred ccccchhhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeeeee
Confidence 345799999999999999999999999999999999999999999888776643
No 4
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.53 E-value=5.1e-15 Score=146.46 Aligned_cols=56 Identities=18% Similarity=0.217 Sum_probs=47.1
Q ss_pred ccchhhhhcCchhhhhhcccCCCCceeecCCCccccCChhHHHHHhhhccCCCCCC
Q 021063 201 QAASAAATAANNNNTANNNNKGGNKIHECSICGSEFTSGQALGGHMRRHRAAVATG 256 (318)
Q Consensus 201 ~~~c~k~~~~~~~l~~h~~~htg~kpy~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~ 256 (318)
|..|++.|.....|..|+++|+|+|||.|.+|++.|..+.+|+.||.+|....+..
T Consensus 882 C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~s 937 (958)
T KOG1074|consen 882 CNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPS 937 (958)
T ss_pred hccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCc
Confidence 33488888888999999999999999999999999999999999999887765543
No 5
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.49 E-value=2.8e-15 Score=146.11 Aligned_cols=91 Identities=21% Similarity=0.371 Sum_probs=79.5
Q ss_pred CCCceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCCCCcchhhccCcccCCCCCchhhccccccccccchhh
Q 021063 127 GGFYVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSSASVPALAVLPTKNEYKDSYSTLHHHDQSHMQAASAA 206 (318)
Q Consensus 127 ~g~~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~~~~~~~~h~~~~~~~f~~~~~L~~H~~~h~~~~c~k 206 (318)
+.+-+|.|+.|+|+|...+.|.+|.--|+|.+||+|.+|.|.|..+ ..|..|+|.|
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHK-----------------HHLtEHkRLH------- 945 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHK-----------------HHLTEHKRLH------- 945 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhh-----------------hhhhhhhhhc-------
Confidence 4456899999999999999999999999999999999999999777 7777777777
Q ss_pred hhcCchhhhhhcccCCCCceeecCCCccccCChhHHHHHhh-hccCCCCCC
Q 021063 207 ATAANNNNTANNNNKGGNKIHECSICGSEFTSGQALGGHMR-RHRAAVATG 256 (318)
Q Consensus 207 ~~~~~~~l~~h~~~htg~kpy~C~~Cgk~F~~~~~L~~H~r-~H~~~~~~~ 256 (318)
.|||||+|+.|+|.|+..+.+..||- +-.-.+++.
T Consensus 946 ---------------SGEKPfQCdKClKRFSHSGSYSQHMNHRYSYCKpyr 981 (1007)
T KOG3623|consen 946 ---------------SGEKPFQCDKCLKRFSHSGSYSQHMNHRYSYCKPYR 981 (1007)
T ss_pred ---------------cCCCcchhhhhhhhcccccchHhhhccchhcccchh
Confidence 79999999999999999999999995 233355554
No 6
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.43 E-value=1.2e-14 Score=122.57 Aligned_cols=85 Identities=24% Similarity=0.446 Sum_probs=76.2
Q ss_pred CCCceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCCCCcchhhccCcccCCCCCchhhccccccccccchhh
Q 021063 127 GGFYVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSSASVPALAVLPTKNEYKDSYSTLHHHDQSHMQAASAA 206 (318)
Q Consensus 127 ~g~~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~~~~~~~~h~~~~~~~f~~~~~L~~H~~~h~~~~c~k 206 (318)
.+.-.|.|.+|+|.|.-..-|.+|++.|...|.|.|..|+|.|... ..|++|+|+|
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndt-----------------fdlkrh~rth------- 168 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDT-----------------FDLKRHTRTH------- 168 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccch-----------------hhhhhhhccc-------
Confidence 3445799999999999999999999999999999999999999766 7888888888
Q ss_pred hhcCchhhhhhcccCCCCceeecCCCccccCChhHHHHHhhhcc
Q 021063 207 ATAANNNNTANNNNKGGNKIHECSICGSEFTSGQALGGHMRRHR 250 (318)
Q Consensus 207 ~~~~~~~l~~h~~~htg~kpy~C~~Cgk~F~~~~~L~~H~r~H~ 250 (318)
+|.|||+|+.|+|+|++...|..|++.-+
T Consensus 169 ---------------tgvrpykc~~c~kaftqrcsleshl~kvh 197 (267)
T KOG3576|consen 169 ---------------TGVRPYKCSLCEKAFTQRCSLESHLKKVH 197 (267)
T ss_pred ---------------cCccccchhhhhHHHHhhccHHHHHHHHc
Confidence 79999999999999999999999986433
No 7
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.23 E-value=9.4e-13 Score=128.71 Aligned_cols=118 Identities=14% Similarity=0.195 Sum_probs=93.1
Q ss_pred eeecCCCCCcCCCccchhhhhhh-cC-CCCCccCCCCCCCCCCCcchhhccCcccCCCCCchhhccc--cccccccchhh
Q 021063 131 VYECKTCNRSFPSFQALGGHRAS-HK-KPKAALAEAPEKKSSASVPALAVLPTKNEYKDSYSTLHHH--DQSHMQAASAA 206 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rs-Ht-~~kp~~C~~C~k~f~~~~~~~~h~~~~~~~f~~~~~L~~H--~~~h~~~~c~k 206 (318)
...|++|.+.+.+...|+.|+.. |. .+..|.|..|..+|.+...|.+|+..|...-.....|..- .|...|..|+|
T Consensus 210 lltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgK 289 (1007)
T KOG3623|consen 210 LLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGK 289 (1007)
T ss_pred hhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccch
Confidence 47899999999999999999754 54 4555999999999998866666666554433332222111 23344566999
Q ss_pred hhcCchhhhhhcccCCCCceeecCCCccccCChhHHHHHhhh
Q 021063 207 ATAANNNNTANNNNKGGNKIHECSICGSEFTSGQALGGHMRR 248 (318)
Q Consensus 207 ~~~~~~~l~~h~~~htg~kpy~C~~Cgk~F~~~~~L~~H~r~ 248 (318)
.|....+|+.|+++|.|||||+|.-|+|.|+..+.+..||-.
T Consensus 290 AFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 290 AFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred hhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 999999999999999999999999999999999999999853
No 8
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.18 E-value=3e-12 Score=108.20 Aligned_cols=101 Identities=17% Similarity=0.206 Sum_probs=78.6
Q ss_pred CCCCceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCCCCcchhhccCcccCCCCCchhhccccc-cccccch
Q 021063 126 AGGFYVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSSASVPALAVLPTKNEYKDSYSTLHHHDQ-SHMQAAS 204 (318)
Q Consensus 126 h~g~~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~~~~~~~~h~~~~~~~f~~~~~L~~H~~-~h~~~~c 204 (318)
|...+.|-|..|||.|..-..|++|+|+|+|.+||+|..|+|.|.+. ..|..|.+ +|.
T Consensus 140 h~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqr-----------------csleshl~kvhg---- 198 (267)
T KOG3576|consen 140 HSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQR-----------------CSLESHLKKVHG---- 198 (267)
T ss_pred ccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhh-----------------ccHHHHHHHHcC----
Confidence 45667899999999999999999999999999999999999999887 55655542 331
Q ss_pred hhhhcCchhhhhhcccCCCCceeecCCCccccCChhHHHHHhhhccCCCCC
Q 021063 205 AAATAANNNNTANNNNKGGNKIHECSICGSEFTSGQALGGHMRRHRAAVAT 255 (318)
Q Consensus 205 ~k~~~~~~~l~~h~~~htg~kpy~C~~Cgk~F~~~~~L~~H~r~H~~~~~~ 255 (318)
...+...+. ...|.|.|+.||.+-.....+..|.+.|+...|+
T Consensus 199 ---v~~~yayke-----rr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Spa 241 (267)
T KOG3576|consen 199 ---VQHQYAYKE-----RRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSPA 241 (267)
T ss_pred ---chHHHHHHH-----hhhheeeecccCCCCCChhHHHHHHHhcCCCCHH
Confidence 000000000 1378999999999999999999999999875543
No 9
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.06 E-value=2.9e-11 Score=109.86 Aligned_cols=120 Identities=15% Similarity=0.188 Sum_probs=67.2
Q ss_pred eeecCC--CCCcCCCccchhhhhhhcCCCCCccCCCCCCCCCCCcchhhccC-------------cccCCCCCchhhccc
Q 021063 131 VYECKT--CNRSFPSFQALGGHRASHKKPKAALAEAPEKKSSASVPALAVLP-------------TKNEYKDSYSTLHHH 195 (318)
Q Consensus 131 ~y~C~~--C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~~~~~~~~h~~-------------~~~~~f~~~~~L~~H 195 (318)
++.|.. |-+.|.++..|+.|.|+|+++|-..|+.|+.-|.....+--|++ .|.+.|.....|+.|
T Consensus 177 v~~C~W~~Ct~~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~H 256 (467)
T KOG3608|consen 177 VTMCNWAMCTKHMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSH 256 (467)
T ss_pred eeeccchhhhhhhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHH
Confidence 466664 88888888899999999998888888888888877644444432 133344444444444
Q ss_pred ccccc----ccchhhhhcCchhhhhhcc-cCCCCceeecCCCccccCChhHHHHHhhhcc
Q 021063 196 DQSHM----QAASAAATAANNNNTANNN-NKGGNKIHECSICGSEFTSGQALGGHMRRHR 250 (318)
Q Consensus 196 ~~~h~----~~~c~k~~~~~~~l~~h~~-~htg~kpy~C~~Cgk~F~~~~~L~~H~r~H~ 250 (318)
++.|- |.-|.-.......|..|++ .|...|||+|+.|.+.|.+.+.|.+|..+|.
T Consensus 257 v~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS 316 (467)
T KOG3608|consen 257 VVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS 316 (467)
T ss_pred HHHhhhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc
Confidence 44332 2224444444444444432 2233444444444444444444444444443
No 10
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.01 E-value=1.6e-10 Score=105.12 Aligned_cols=108 Identities=23% Similarity=0.387 Sum_probs=69.4
Q ss_pred eecCCCCCcCCCccchhhhhhh-cCCCCCccCCCCCCCCCCCcchhhccCcccCCCCCchhhcccccccccc-----c--
Q 021063 132 YECKTCNRSFPSFQALGGHRAS-HKKPKAALAEAPEKKSSASVPALAVLPTKNEYKDSYSTLHHHDQSHMQA-----A-- 203 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rs-Ht~~kp~~C~~C~k~f~~~~~~~~h~~~~~~~f~~~~~L~~H~~~h~~~-----~-- 203 (318)
|+|+.|+.+.+..+.|..|++. |.+.|||+|+.|++.|... +.|.+|..+|... .
T Consensus 264 ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~e-----------------sdL~kH~~~HS~~~y~C~h~~ 326 (467)
T KOG3608|consen 264 YKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRE-----------------SDLAKHVQVHSKTVYQCEHPD 326 (467)
T ss_pred ccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccH-----------------HHHHHHHHhccccceecCCCC
Confidence 4444444444444445555443 5555666666665555544 7777777666532 2
Q ss_pred hhhhhcCchhhhhhccc-CCC--CceeecCCCccccCChhHHHHHhhh-ccCCCCCC
Q 021063 204 SAAATAANNNNTANNNN-KGG--NKIHECSICGSEFTSGQALGGHMRR-HRAAVATG 256 (318)
Q Consensus 204 c~k~~~~~~~l~~h~~~-htg--~kpy~C~~Cgk~F~~~~~L~~H~r~-H~~~~~~~ 256 (318)
|.-.+.....+.+|++. |.| +-+|.|-.|.+.|+++-+|.+|++. |.=..|++
T Consensus 327 C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~PsG 383 (467)
T KOG3608|consen 327 CHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRLPSG 383 (467)
T ss_pred CcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcccCCCC
Confidence 66677777777777643 323 5689999999999999999999754 55445554
No 11
>PHA00733 hypothetical protein
Probab=98.98 E-value=1.8e-10 Score=93.11 Aligned_cols=83 Identities=16% Similarity=0.130 Sum_probs=67.8
Q ss_pred CCceeecCCCCCcCCCccchhhh--hh---hcCCCCCccCCCCCCCCCCCcchhhccCcccCCCCCchhhcccccccccc
Q 021063 128 GFYVYECKTCNRSFPSFQALGGH--RA---SHKKPKAALAEAPEKKSSASVPALAVLPTKNEYKDSYSTLHHHDQSHMQA 202 (318)
Q Consensus 128 g~~~y~C~~C~K~F~s~~~L~~H--~r---sHt~~kp~~C~~C~k~f~~~~~~~~h~~~~~~~f~~~~~L~~H~~~h~~~ 202 (318)
..+++.|.+|.+.|...+.|..| ++ .+.+.+||.|..|++.|... ..|..|++.|
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~-----------------s~L~~H~r~h--- 96 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSS-----------------VSLKQHIRYT--- 96 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCH-----------------HHHHHHHhcC---
Confidence 35689999999999998887765 21 23458899999999999777 7777777654
Q ss_pred chhhhhcCchhhhhhcccCCCCceeecCCCccccCChhHHHHHhhhccC
Q 021063 203 ASAAATAANNNNTANNNNKGGNKIHECSICGSEFTSGQALGGHMRRHRA 251 (318)
Q Consensus 203 ~c~k~~~~~~~l~~h~~~htg~kpy~C~~Cgk~F~~~~~L~~H~r~H~~ 251 (318)
+++|.|.+|++.|.....|..|++..++
T Consensus 97 ---------------------~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 97 ---------------------EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred ---------------------CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 4679999999999999999999987664
No 12
>PHA02768 hypothetical protein; Provisional
Probab=98.83 E-value=1.3e-09 Score=73.76 Aligned_cols=40 Identities=18% Similarity=0.277 Sum_probs=37.6
Q ss_pred eeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCCCC
Q 021063 131 VYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSSAS 172 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~~~ 172 (318)
-|+|++|||.|.+.++|..|+++|+ ++|+|..|++.|.+.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~ 44 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRT 44 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccc
Confidence 3999999999999999999999999 799999999999876
No 13
>PHA02768 hypothetical protein; Provisional
Probab=98.51 E-value=2e-08 Score=67.98 Aligned_cols=43 Identities=12% Similarity=-0.063 Sum_probs=35.8
Q ss_pred ccCCCCCCCCCCCcchhhccCcccCCCCCchhhccccccccccchhhhhcCchhhhhhcccCCCCceeecCCCccccCCh
Q 021063 160 ALAEAPEKKSSASVPALAVLPTKNEYKDSYSTLHHHDQSHMQAASAAATAANNNNTANNNNKGGNKIHECSICGSEFTSG 239 (318)
Q Consensus 160 ~~C~~C~k~f~~~~~~~~h~~~~~~~f~~~~~L~~H~~~h~~~~c~k~~~~~~~l~~h~~~htg~kpy~C~~Cgk~F~~~ 239 (318)
|.|+.|++.|... ..|..|+++| .++|+|..|++.|.+.
T Consensus 6 y~C~~CGK~Fs~~-----------------~~L~~H~r~H------------------------~k~~kc~~C~k~f~~~ 44 (55)
T PHA02768 6 YECPICGEIYIKR-----------------KSMITHLRKH------------------------NTNLKLSNCKRISLRT 44 (55)
T ss_pred cCcchhCCeeccH-----------------HHHHHHHHhc------------------------CCcccCCcccceeccc
Confidence 7888888888777 7777777777 3899999999999988
Q ss_pred hHHH
Q 021063 240 QALG 243 (318)
Q Consensus 240 ~~L~ 243 (318)
+.|.
T Consensus 45 s~l~ 48 (55)
T PHA02768 45 GEYI 48 (55)
T ss_pred ceeE
Confidence 7764
No 14
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.49 E-value=1.2e-07 Score=93.58 Aligned_cols=94 Identities=13% Similarity=0.193 Sum_probs=56.8
Q ss_pred CceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCCCCcchhhccCcccCCCCCchhhcccccccc------cc
Q 021063 129 FYVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSSASVPALAVLPTKNEYKDSYSTLHHHDQSHM------QA 202 (318)
Q Consensus 129 ~~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~~~~~~~~h~~~~~~~f~~~~~L~~H~~~h~------~~ 202 (318)
+..+.|+.|++.|. ...|..|+.+|+ +++.|+ |++.+ .. ..|..|+++|. |.
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R-----------------~~L~~H~~thCp~Kpi~C~ 508 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EK-----------------EQMVQHQASTCPLRLITCR 508 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-ch-----------------hHHHhhhhccCCCCceeCC
Confidence 34689999999996 578999999874 789998 98644 33 56666665553 22
Q ss_pred chhhhhcC----------chhhhhhcccCCCCceeecCCCccccCChhHHHHHh
Q 021063 203 ASAAATAA----------NNNNTANNNNKGGNKIHECSICGSEFTSGQALGGHM 246 (318)
Q Consensus 203 ~c~k~~~~----------~~~l~~h~~~htg~kpy~C~~Cgk~F~~~~~L~~H~ 246 (318)
.|++.+.. ...|..|.... |.+++.|..||+.|..+ .|..|+
T Consensus 509 fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~ 560 (567)
T PLN03086 509 FCGDMVQAGGSAMDVRDRLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQ 560 (567)
T ss_pred CCCCccccCccccchhhhhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHH
Confidence 24444421 12445554443 55555555555555433 334444
No 15
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.48 E-value=4.1e-08 Score=56.73 Aligned_cols=25 Identities=24% Similarity=0.555 Sum_probs=21.5
Q ss_pred hhhhcccCCCCceeecCCCccccCC
Q 021063 214 NTANNNNKGGNKIHECSICGSEFTS 238 (318)
Q Consensus 214 l~~h~~~htg~kpy~C~~Cgk~F~~ 238 (318)
|++|++.|+|+|||+|++|++.|.+
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 5667777799999999999999974
No 16
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.35 E-value=8.3e-08 Score=55.42 Aligned_cols=25 Identities=24% Similarity=0.098 Sum_probs=23.0
Q ss_pred chhhhhhhcCCCCCccCCCCCCCCC
Q 021063 146 ALGGHRASHKKPKAALAEAPEKKSS 170 (318)
Q Consensus 146 ~L~~H~rsHt~~kp~~C~~C~k~f~ 170 (318)
+|..|+++|+++|||.|++|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 4889999999999999999999885
No 17
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.25 E-value=2.1e-07 Score=86.92 Aligned_cols=120 Identities=16% Similarity=0.231 Sum_probs=73.7
Q ss_pred eeecCCCCCcCCCccchhhhhhhcCCC--------C-------------------------CccCCCCCCCCCCCcchhh
Q 021063 131 VYECKTCNRSFPSFQALGGHRASHKKP--------K-------------------------AALAEAPEKKSSASVPALA 177 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rsHt~~--------k-------------------------p~~C~~C~k~f~~~~~~~~ 177 (318)
.|+|++|+|.|+..-+|..|+|.|+.. . .|.|.+|+|+|.+..-|+.
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrK 374 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRK 374 (500)
T ss_pred eecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHH
Confidence 499999999999999999999999621 1 2678888888888766666
Q ss_pred ccCcccCCCCCc------------------hhhcccccc-----------------ccccchhhhhcCchhhhhhcccCC
Q 021063 178 VLPTKNEYKDSY------------------STLHHHDQS-----------------HMQAASAAATAANNNNTANNNNKG 222 (318)
Q Consensus 178 h~~~~~~~f~~~------------------~~L~~H~~~-----------------h~~~~c~k~~~~~~~l~~h~~~ht 222 (318)
|+..|...-... ..+..|... +....|+..++....--.+.+.-.
T Consensus 375 Hqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~sael~~pp~~~~ppsss~~sgg~~rlg~ 454 (500)
T KOG3993|consen 375 HQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGSAELELPPYDGSPPSSSGSSGGYGRLGI 454 (500)
T ss_pred hHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeeccccccCCCCCCCCcccCCCCCccccccc
Confidence 654443310000 001111100 001114434433333233322222
Q ss_pred CCceeecCCCccccCChhHHHHHhhhcc
Q 021063 223 GNKIHECSICGSEFTSGQALGGHMRRHR 250 (318)
Q Consensus 223 g~kpy~C~~Cgk~F~~~~~L~~H~r~H~ 250 (318)
.+..|.|.+|..+|.+...|.+|....+
T Consensus 455 ~~q~f~~ky~~atfyss~~ltrhin~~H 482 (500)
T KOG3993|consen 455 AEQGFTCKYCPATFYSSPGLTRHINKCH 482 (500)
T ss_pred hhhccccccchHhhhcCcchHhHhhhcC
Confidence 3567999999999999999999876543
No 18
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.24 E-value=6.3e-07 Score=88.47 Aligned_cols=39 Identities=13% Similarity=0.125 Sum_probs=35.3
Q ss_pred ceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCC
Q 021063 130 YVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSS 170 (318)
Q Consensus 130 ~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~ 170 (318)
++|.|+ |++.| .+..|..|+++|...+++.|.+|++.|.
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~ 515 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQ 515 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccc
Confidence 589999 99866 5689999999999999999999999884
No 19
>PHA00616 hypothetical protein
Probab=98.20 E-value=2.4e-07 Score=59.75 Aligned_cols=34 Identities=24% Similarity=0.343 Sum_probs=32.3
Q ss_pred eeecCCCCCcCCCccchhhhhhhcCCCCCccCCC
Q 021063 131 VYECKTCNRSFPSFQALGGHRASHKKPKAALAEA 164 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~ 164 (318)
||+|..||+.|...+.|..|++.|++++++.|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccceeE
Confidence 6999999999999999999999999999999865
No 20
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.20 E-value=2.7e-07 Score=86.13 Aligned_cols=104 Identities=21% Similarity=0.340 Sum_probs=72.9
Q ss_pred eeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCCCCcchhhccCcccCCCCCchhhccccccccccc-hhh---
Q 021063 131 VYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSSASVPALAVLPTKNEYKDSYSTLHHHDQSHMQAA-SAA--- 206 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~~~~~~~~h~~~~~~~f~~~~~L~~H~~~h~~~~-c~k--- 206 (318)
-|.|..|...|-....|.+|+-.-.-.--|+|.+|+|.|... .+|..|.|.|.-.. -.+
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCP-----------------ANLASHRRWHKPR~eaa~a~~ 329 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCP-----------------ANLASHRRWHKPRPEAAKAGS 329 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCc-----------------hhhhhhhcccCCchhhhhcCC
Confidence 499999999999999999997543333459999999999888 88889999885322 111
Q ss_pred -----hhcCchhhhhhcc--cCCCCceeecCCCccccCChhHHHHHhhhccC
Q 021063 207 -----ATAANNNNTANNN--NKGGNKIHECSICGSEFTSGQALGGHMRRHRA 251 (318)
Q Consensus 207 -----~~~~~~~l~~h~~--~htg~kpy~C~~Cgk~F~~~~~L~~H~r~H~~ 251 (318)
........+.-.+ .-..+-.|.|.+|+|.|.+...|+.|+-+|..
T Consensus 330 ~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 330 PPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred CChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 0000000111110 00124489999999999999999999988865
No 21
>PHA00733 hypothetical protein
Probab=98.17 E-value=8.4e-07 Score=71.79 Aligned_cols=44 Identities=18% Similarity=0.221 Sum_probs=39.6
Q ss_pred CCCceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCCCC
Q 021063 127 GGFYVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSSAS 172 (318)
Q Consensus 127 ~g~~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~~~ 172 (318)
.+.++|.|+.|++.|.+...|..|++.| +.+|.|.+|++.|...
T Consensus 69 ~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~ 112 (128)
T PHA00733 69 KAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNT 112 (128)
T ss_pred CCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCH
Confidence 4467999999999999999999999987 4579999999999877
No 22
>PHA00616 hypothetical protein
Probab=98.07 E-value=1.3e-06 Score=56.43 Aligned_cols=31 Identities=16% Similarity=0.303 Sum_probs=28.8
Q ss_pred eeecCCCccccCChhHHHHHhhhccCCCCCC
Q 021063 226 IHECSICGSEFTSGQALGGHMRRHRAAVATG 256 (318)
Q Consensus 226 py~C~~Cgk~F~~~~~L~~H~r~H~~~~~~~ 256 (318)
||+|..||+.|...+.|..|++.|+|+++..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~ 31 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLT 31 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccc
Confidence 6999999999999999999999999987654
No 23
>PHA00732 hypothetical protein
Probab=98.04 E-value=2.3e-06 Score=63.13 Aligned_cols=37 Identities=19% Similarity=0.324 Sum_probs=33.0
Q ss_pred eeecCCCCCcCCCccchhhhhhh-cCCCCCccCCCCCCCCC
Q 021063 131 VYECKTCNRSFPSFQALGGHRAS-HKKPKAALAEAPEKKSS 170 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rs-Ht~~kp~~C~~C~k~f~ 170 (318)
||.|..|++.|.+...|..|++. |.+ +.|+.|++.|.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~ 38 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYR 38 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeC
Confidence 58999999999999999999984 764 68999999994
No 24
>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=97.96 E-value=4.1e-06 Score=46.68 Aligned_cols=23 Identities=52% Similarity=1.019 Sum_probs=21.9
Q ss_pred eecCCCccccCChhHHHHHhhhc
Q 021063 227 HECSICGSEFTSGQALGGHMRRH 249 (318)
Q Consensus 227 y~C~~Cgk~F~~~~~L~~H~r~H 249 (318)
|+|.+|++.|.+...|..||+.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 79999999999999999999986
No 25
>PHA00732 hypothetical protein
Probab=97.86 E-value=7.3e-06 Score=60.47 Aligned_cols=49 Identities=12% Similarity=0.286 Sum_probs=36.5
Q ss_pred CccCCCCCCCCCCCcchhhccCcccCCCCCchhhccccccccccchhhhhcCchhhhhhcccCCCCceeecCCCccccCC
Q 021063 159 AALAEAPEKKSSASVPALAVLPTKNEYKDSYSTLHHHDQSHMQAASAAATAANNNNTANNNNKGGNKIHECSICGSEFTS 238 (318)
Q Consensus 159 p~~C~~C~k~f~~~~~~~~h~~~~~~~f~~~~~L~~H~~~h~~~~c~k~~~~~~~l~~h~~~htg~kpy~C~~Cgk~F~~ 238 (318)
||.|..|++.|... ..|..|++.+ | .++.|++||+.|.
T Consensus 1 py~C~~Cgk~F~s~-----------------s~Lk~H~r~~---------------------H---~~~~C~~CgKsF~- 38 (79)
T PHA00732 1 MFKCPICGFTTVTL-----------------FALKQHARRN---------------------H---TLTKCPVCNKSYR- 38 (79)
T ss_pred CccCCCCCCccCCH-----------------HHHHHHhhcc---------------------c---CCCccCCCCCEeC-
Confidence 57899999888766 7777777642 1 2468999999998
Q ss_pred hhHHHHHhhhccC
Q 021063 239 GQALGGHMRRHRA 251 (318)
Q Consensus 239 ~~~L~~H~r~H~~ 251 (318)
.|..|.+++..
T Consensus 39 --~l~~H~~~~~~ 49 (79)
T PHA00732 39 --RLNQHFYSQYD 49 (79)
T ss_pred --ChhhhhcccCC
Confidence 57888866543
No 26
>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=97.77 E-value=1.4e-05 Score=46.30 Aligned_cols=26 Identities=42% Similarity=0.685 Sum_probs=24.4
Q ss_pred eeecCCCccccCChhHHHHHhhhccC
Q 021063 226 IHECSICGSEFTSGQALGGHMRRHRA 251 (318)
Q Consensus 226 py~C~~Cgk~F~~~~~L~~H~r~H~~ 251 (318)
||+|.+|++.|....+|..|++.|..
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 69999999999999999999999864
No 27
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.69 E-value=2.4e-05 Score=70.84 Aligned_cols=25 Identities=20% Similarity=0.476 Sum_probs=21.8
Q ss_pred CCceeecCCCccccCChhHHHHHhh
Q 021063 223 GNKIHECSICGSEFTSGQALGGHMR 247 (318)
Q Consensus 223 g~kpy~C~~Cgk~F~~~~~L~~H~r 247 (318)
..|||.|++|+|.|...-.|+-|..
T Consensus 395 ~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 395 KDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCCceeccccchhhccCccceeccc
Confidence 4799999999999999988887753
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.63 E-value=3.5e-05 Score=42.87 Aligned_cols=24 Identities=46% Similarity=0.935 Sum_probs=20.5
Q ss_pred eecCCCccccCChhHHHHHhhhcc
Q 021063 227 HECSICGSEFTSGQALGGHMRRHR 250 (318)
Q Consensus 227 y~C~~Cgk~F~~~~~L~~H~r~H~ 250 (318)
|.|.+|++.|.+...|..|+++|+
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 789999999999999999999874
No 29
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.63 E-value=1.5e-05 Score=44.32 Aligned_cols=23 Identities=39% Similarity=0.778 Sum_probs=21.7
Q ss_pred eecCCCCCcCCCccchhhhhhhc
Q 021063 132 YECKTCNRSFPSFQALGGHRASH 154 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rsH 154 (318)
|+|+.|++.|.+...|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 79999999999999999999875
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=97.38 E-value=6.1e-05 Score=43.57 Aligned_cols=25 Identities=40% Similarity=0.864 Sum_probs=23.5
Q ss_pred eeecCCCCCcCCCccchhhhhhhcC
Q 021063 131 VYECKTCNRSFPSFQALGGHRASHK 155 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rsHt 155 (318)
||+|..|++.|.+..+|..|++.|.
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 6999999999999999999999885
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.31 E-value=0.00014 Score=55.51 Aligned_cols=26 Identities=35% Similarity=0.681 Sum_probs=22.6
Q ss_pred ceeecCCCccccCChhHHHHHhhhcc
Q 021063 225 KIHECSICGSEFTSGQALGGHMRRHR 250 (318)
Q Consensus 225 kpy~C~~Cgk~F~~~~~L~~H~r~H~ 250 (318)
..+.|.+|++.|.+...|..||+.+.
T Consensus 49 ~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 49 ESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 47999999999999999999999753
No 32
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.20 E-value=0.00034 Score=46.25 Aligned_cols=32 Identities=19% Similarity=0.428 Sum_probs=23.9
Q ss_pred CCceeecCCCccccCChhHHHHHhhhccCCCC
Q 021063 223 GNKIHECSICGSEFTSGQALGGHMRRHRAAVA 254 (318)
Q Consensus 223 g~kpy~C~~Cgk~F~~~~~L~~H~r~H~~~~~ 254 (318)
.+.|..|++|+..+.+..+|.+||.++++.+|
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 48999999999999999999999998887765
No 33
>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=97.06 E-value=0.00032 Score=47.82 Aligned_cols=25 Identities=32% Similarity=0.537 Sum_probs=20.6
Q ss_pred CceeecCCCccccCChhHHHHHhhhcc
Q 021063 224 NKIHECSICGSEFTSGQALGGHMRRHR 250 (318)
Q Consensus 224 ~kpy~C~~Cgk~F~~~~~L~~H~r~H~ 250 (318)
.+.+.|++|...+. .+|.+||+.++
T Consensus 29 ~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 29 SKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CCCccCCCchhhhh--hHHHHHHHHhc
Confidence 46799999999766 49999998765
No 34
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.06 E-value=0.00036 Score=39.22 Aligned_cols=25 Identities=44% Similarity=0.753 Sum_probs=22.8
Q ss_pred eecCCCccccCChhHHHHHhhhccC
Q 021063 227 HECSICGSEFTSGQALGGHMRRHRA 251 (318)
Q Consensus 227 y~C~~Cgk~F~~~~~L~~H~r~H~~ 251 (318)
|+|..|++.|.....|..|++.|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~~ 25 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHXX 25 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhcc
Confidence 6899999999999999999998753
No 35
>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=96.95 E-value=0.00028 Score=39.10 Aligned_cols=23 Identities=35% Similarity=0.758 Sum_probs=19.7
Q ss_pred eecCCCCCcCCCccchhhhhhhc
Q 021063 132 YECKTCNRSFPSFQALGGHRASH 154 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rsH 154 (318)
|.|++|++.|.+...|..|++.|
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 78999999999999999999876
No 36
>PRK04860 hypothetical protein; Provisional
Probab=96.65 E-value=0.0011 Score=55.67 Aligned_cols=40 Identities=13% Similarity=0.203 Sum_probs=35.3
Q ss_pred CceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCCCC
Q 021063 129 FYVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSSAS 172 (318)
Q Consensus 129 ~~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~~~ 172 (318)
.++|.|. |++ ....+.+|.++|+++++|.|..|+..|...
T Consensus 117 ~~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 117 TFPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 4789998 998 678899999999999999999999988543
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.59 E-value=0.00092 Score=37.48 Aligned_cols=24 Identities=38% Similarity=0.737 Sum_probs=22.3
Q ss_pred eecCCCCCcCCCccchhhhhhhcC
Q 021063 132 YECKTCNRSFPSFQALGGHRASHK 155 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rsHt 155 (318)
|+|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 689999999999999999999875
No 38
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.57 E-value=0.0013 Score=37.13 Aligned_cols=23 Identities=35% Similarity=0.768 Sum_probs=21.4
Q ss_pred eecCCCccccCChhHHHHHhhhc
Q 021063 227 HECSICGSEFTSGQALGGHMRRH 249 (318)
Q Consensus 227 y~C~~Cgk~F~~~~~L~~H~r~H 249 (318)
|.|.+|++.|.+...|..|++.+
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 78999999999999999999865
No 39
>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=96.56 E-value=0.001 Score=45.30 Aligned_cols=38 Identities=18% Similarity=0.294 Sum_probs=30.0
Q ss_pred eeecCCCCCcCCCccchhhhhh-hcCCC-CCccCCCCCCCC
Q 021063 131 VYECKTCNRSFPSFQALGGHRA-SHKKP-KAALAEAPEKKS 169 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~r-sHt~~-kp~~C~~C~k~f 169 (318)
.|.|++|++ .-+...|..|.. .|..+ +.+.|++|...+
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~ 41 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRV 41 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhh
Confidence 499999999 455789999955 47765 569999998754
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.95 E-value=0.0024 Score=35.95 Aligned_cols=23 Identities=39% Similarity=0.717 Sum_probs=21.5
Q ss_pred eecCCCCCcCCCccchhhhhhhc
Q 021063 132 YECKTCNRSFPSFQALGGHRASH 154 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rsH 154 (318)
|.|.+|++.|.+...|..|++++
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 78999999999999999999875
No 41
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.91 E-value=0.0055 Score=34.20 Aligned_cols=24 Identities=25% Similarity=0.584 Sum_probs=19.6
Q ss_pred eecCCCccccCChhHHHHHhhhccC
Q 021063 227 HECSICGSEFTSGQALGGHMRRHRA 251 (318)
Q Consensus 227 y~C~~Cgk~F~~~~~L~~H~r~H~~ 251 (318)
|+|+.|..... ...|..|+++|++
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 79999999988 9999999998753
No 42
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.67 E-value=0.01 Score=56.50 Aligned_cols=125 Identities=14% Similarity=0.080 Sum_probs=83.2
Q ss_pred ceeecCCCCCcCCCccchhhhhh--hcCCC--CCccCC--CCCCCCCCCcchhhccCcccCCCC-------------Cch
Q 021063 130 YVYECKTCNRSFPSFQALGGHRA--SHKKP--KAALAE--APEKKSSASVPALAVLPTKNEYKD-------------SYS 190 (318)
Q Consensus 130 ~~y~C~~C~K~F~s~~~L~~H~r--sHt~~--kp~~C~--~C~k~f~~~~~~~~h~~~~~~~f~-------------~~~ 190 (318)
.++.|..|.+.|.....|..|.+ .|+++ +|+.|. .|++.|.+...+..|...+...-. ...
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 367 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLL 367 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccccccCcccccccc
Confidence 57999999999999999999999 89999 999999 799999998777776665544110 000
Q ss_pred h------hccccccccc-------cchhhhhcCchhhhhhcccCCCCc--eeecCCCccccCChhHHHHHhhhccCCCC
Q 021063 191 T------LHHHDQSHMQ-------AASAAATAANNNNTANNNNKGGNK--IHECSICGSEFTSGQALGGHMRRHRAAVA 254 (318)
Q Consensus 191 ~------L~~H~~~h~~-------~~c~k~~~~~~~l~~h~~~htg~k--py~C~~Cgk~F~~~~~L~~H~r~H~~~~~ 254 (318)
. +..+...+.. ..|-..+.....+..|...+...+ .+.|..|.+.|...-.|..|++.|....+
T Consensus 368 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 446 (467)
T COG5048 368 NNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAP 446 (467)
T ss_pred CCCCccchhhccCccCCccccccccchhhhhccccccccccccccccCCcCCCCCcchhhccCcccccccccccccCCc
Confidence 0 0000000100 014455555555555555554444 45567788888888888888888775443
No 43
>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=95.62 E-value=0.0064 Score=40.32 Aligned_cols=33 Identities=15% Similarity=0.141 Sum_probs=23.6
Q ss_pred CCCceeecCCCCCcCCCccchhhhhhhcCCCCC
Q 021063 127 GGFYVYECKTCNRSFPSFQALGGHRASHKKPKA 159 (318)
Q Consensus 127 ~g~~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp 159 (318)
..+.|..|++|+..+++..+|++|+.++.+.||
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 456799999999999999999999988776665
No 44
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=95.53 E-value=0.0064 Score=35.06 Aligned_cols=23 Identities=30% Similarity=0.625 Sum_probs=21.0
Q ss_pred eecCCCccccCChhHHHHHhhhc
Q 021063 227 HECSICGSEFTSGQALGGHMRRH 249 (318)
Q Consensus 227 y~C~~Cgk~F~~~~~L~~H~r~H 249 (318)
|-|.+|++.|.....|..|++..
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 78999999999999999999753
No 45
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=95.05 E-value=0.008 Score=34.62 Aligned_cols=23 Identities=30% Similarity=0.642 Sum_probs=21.1
Q ss_pred eecCCCCCcCCCccchhhhhhhc
Q 021063 132 YECKTCNRSFPSFQALGGHRASH 154 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rsH 154 (318)
|-|..|++.|.+...|..|+++.
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 78999999999999999998763
No 46
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=94.85 E-value=0.012 Score=62.88 Aligned_cols=101 Identities=20% Similarity=0.184 Sum_probs=57.0
Q ss_pred ecCCCCCcCCCccchhhhhhh-cCCCCCccCCCCCCCCCCCcchhhccCcccCCCCCchhhcccccc-ccccc---hhhh
Q 021063 133 ECKTCNRSFPSFQALGGHRAS-HKKPKAALAEAPEKKSSASVPALAVLPTKNEYKDSYSTLHHHDQS-HMQAA---SAAA 207 (318)
Q Consensus 133 ~C~~C~K~F~s~~~L~~H~rs-Ht~~kp~~C~~C~k~f~~~~~~~~h~~~~~~~f~~~~~L~~H~~~-h~~~~---c~k~ 207 (318)
.|..|+..|.+...|..|+.. |...|-|.|+.|+..|... ..|..|+|. |.... |. .
T Consensus 438 e~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a-----------------~~L~vhmRskhp~~~~~~c~-~ 499 (1406)
T KOG1146|consen 438 ELTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLA-----------------QTLGVHMRSKHPESQSAYCK-A 499 (1406)
T ss_pred cccchhhhhhhhcccccceeeeecccccccCCccchhhhhH-----------------HHhhhcccccccccchhHhH-h
Confidence 344555566666666666543 6666677777777666555 444555444 11000 00 0
Q ss_pred hcCchhhhhhcccCCCCceeecCCCccccCChhHHHHHhh--hccC
Q 021063 208 TAANNNNTANNNNKGGNKIHECSICGSEFTSGQALGGHMR--RHRA 251 (318)
Q Consensus 208 ~~~~~~l~~h~~~htg~kpy~C~~Cgk~F~~~~~L~~H~r--~H~~ 251 (318)
+.....+.+....-.+.++|.|..|..+|+..++|..||. .|+.
T Consensus 500 gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS~~h~~ 545 (1406)
T KOG1146|consen 500 GQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQSDLHRN 545 (1406)
T ss_pred ccccccccccccccCCCCcccceeeeeeeecchHHHHHHHHHhhHH
Confidence 0000001110111135789999999999999999999987 3543
No 47
>PRK04860 hypothetical protein; Provisional
Probab=94.49 E-value=0.01 Score=49.76 Aligned_cols=19 Identities=21% Similarity=0.555 Sum_probs=16.4
Q ss_pred CCCceeecCCCccccCChh
Q 021063 222 GGNKIHECSICGSEFTSGQ 240 (318)
Q Consensus 222 tg~kpy~C~~Cgk~F~~~~ 240 (318)
+|+++|.|..|+..|....
T Consensus 139 ~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 139 RGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred cCCccEECCCCCceeEEec
Confidence 7899999999999987543
No 48
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=93.52 E-value=0.055 Score=30.62 Aligned_cols=22 Identities=32% Similarity=0.670 Sum_probs=18.6
Q ss_pred eecCCCccccCChhHHHHHhhhc
Q 021063 227 HECSICGSEFTSGQALGGHMRRH 249 (318)
Q Consensus 227 y~C~~Cgk~F~~~~~L~~H~r~H 249 (318)
.+|.+||+.| ....|..|++..
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~C 24 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKIC 24 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHhc
Confidence 4799999999 778899998753
No 49
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=92.36 E-value=0.1 Score=31.67 Aligned_cols=23 Identities=22% Similarity=0.556 Sum_probs=20.8
Q ss_pred eeecCCCccccCChhHHHHHhhh
Q 021063 226 IHECSICGSEFTSGQALGGHMRR 248 (318)
Q Consensus 226 py~C~~Cgk~F~~~~~L~~H~r~ 248 (318)
+|.|.+|++.|.....|..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999999999863
No 50
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=91.39 E-value=0.06 Score=29.85 Aligned_cols=22 Identities=32% Similarity=0.581 Sum_probs=17.7
Q ss_pred eecCCCCCcCCCccchhhhhhhc
Q 021063 132 YECKTCNRSFPSFQALGGHRASH 154 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rsH 154 (318)
|+|+.|+.... ...|..|++.|
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 78999999888 88999998875
No 51
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=91.35 E-value=0.085 Score=29.85 Aligned_cols=21 Identities=29% Similarity=0.574 Sum_probs=17.5
Q ss_pred eecCCCCCcCCCccchhhhhhh
Q 021063 132 YECKTCNRSFPSFQALGGHRAS 153 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rs 153 (318)
.+|+.||+.| ....|..|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 5799999999 56889999764
No 52
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.85 E-value=0.16 Score=48.33 Aligned_cols=58 Identities=21% Similarity=0.339 Sum_probs=46.4
Q ss_pred ccccchhhhhcCchhhhhhcc--cCCCC--ceeecC--CCccccCChhHHHHHhhhccCCCCCC
Q 021063 199 HMQAASAAATAANNNNTANNN--NKGGN--KIHECS--ICGSEFTSGQALGGHMRRHRAAVATG 256 (318)
Q Consensus 199 h~~~~c~k~~~~~~~l~~h~~--~htg~--kpy~C~--~Cgk~F~~~~~L~~H~r~H~~~~~~~ 256 (318)
+.+..|...|.....|..|.. .|+++ +||.|. .|++.|.+...|.+|..+|.+..+..
T Consensus 290 ~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 (467)
T COG5048 290 IKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAK 353 (467)
T ss_pred CCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccc
Confidence 344446666666666666666 67889 999999 89999999999999999999877655
No 53
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=90.05 E-value=0.16 Score=30.77 Aligned_cols=23 Identities=26% Similarity=0.515 Sum_probs=20.8
Q ss_pred eeecCCCCCcCCCccchhhhhhh
Q 021063 131 VYECKTCNRSFPSFQALGGHRAS 153 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rs 153 (318)
+|.|+.|++.|.+...+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58999999999999999999865
No 54
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=89.18 E-value=0.1 Score=45.99 Aligned_cols=28 Identities=36% Similarity=0.665 Sum_probs=23.8
Q ss_pred CceeecCCCccccCChhHHHHH-hhhccC
Q 021063 224 NKIHECSICGSEFTSGQALGGH-MRRHRA 251 (318)
Q Consensus 224 ~kpy~C~~Cgk~F~~~~~L~~H-~r~H~~ 251 (318)
.|.|+|-||.|..-++-.|..| |.+|..
T Consensus 32 akhfkchichkkl~sgpglsihcmqvhke 60 (341)
T KOG2893|consen 32 AKHFKCHICHKKLFSGPGLSIHCMQVHKE 60 (341)
T ss_pred hccceeeeehhhhccCCCceeehhhhhhh
Confidence 5789999999998888889888 677764
No 55
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=86.78 E-value=0.18 Score=54.38 Aligned_cols=43 Identities=21% Similarity=0.255 Sum_probs=30.3
Q ss_pred hhhcCchhhhhhcccCCCCceeecCCCccccCChhHHHHHhhhc
Q 021063 206 AATAANNNNTANNNNKGGNKIHECSICGSEFTSGQALGGHMRRH 249 (318)
Q Consensus 206 k~~~~~~~l~~h~~~htg~kpy~C~~Cgk~F~~~~~L~~H~r~H 249 (318)
+.+.....+.-+.-.+..-++| |.+|...|+...+|..|||.-
T Consensus 1309 ~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~~ 1351 (1406)
T KOG1146|consen 1309 FAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRSS 1351 (1406)
T ss_pred hccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHHh
Confidence 3333333333344444456778 999999999999999999963
No 56
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=86.77 E-value=0.24 Score=45.45 Aligned_cols=26 Identities=23% Similarity=0.589 Sum_probs=22.5
Q ss_pred CCCceeecCCCCCcCCCccchhhhhh
Q 021063 127 GGFYVYECKTCNRSFPSFQALGGHRA 152 (318)
Q Consensus 127 ~g~~~y~C~~C~K~F~s~~~L~~H~r 152 (318)
...|||+|++|+|.|.....|+-|+.
T Consensus 394 ~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 394 AKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred ccCCceeccccchhhccCccceeccc
Confidence 34489999999999999999999864
No 57
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=86.52 E-value=0.32 Score=36.54 Aligned_cols=25 Identities=36% Similarity=0.687 Sum_probs=22.0
Q ss_pred eeecCCCCCcCCCccchhhhhhhcC
Q 021063 131 VYECKTCNRSFPSFQALGGHRASHK 155 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rsHt 155 (318)
.+.|..|++.|.+...|..|++.+.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCcc
Confidence 5999999999999999999999753
No 58
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=82.97 E-value=0.99 Score=28.97 Aligned_cols=27 Identities=26% Similarity=0.632 Sum_probs=18.1
Q ss_pred CCceeecCCCccccCCh----hHHHHHhh-hc
Q 021063 223 GNKIHECSICGSEFTSG----QALGGHMR-RH 249 (318)
Q Consensus 223 g~kpy~C~~Cgk~F~~~----~~L~~H~r-~H 249 (318)
+....+|.+|++.|... .+|.+|++ .|
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 46788999999999875 78999994 44
No 59
>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=82.17 E-value=1.1 Score=26.99 Aligned_cols=24 Identities=13% Similarity=0.301 Sum_probs=18.5
Q ss_pred eecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCC
Q 021063 132 YECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEK 167 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k 167 (318)
|.|.+||..+.... .++.|+.|+.
T Consensus 2 ~~C~~CGy~y~~~~------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc------------CCCcCcCCCC
Confidence 88999998765432 6788999975
No 60
>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=82.01 E-value=0.85 Score=30.37 Aligned_cols=31 Identities=23% Similarity=0.486 Sum_probs=21.9
Q ss_pred ceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCC
Q 021063 130 YVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEK 167 (318)
Q Consensus 130 ~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k 167 (318)
+.|+|..||..|.....+ +. +.+..|+.|+.
T Consensus 4 Yey~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQKM------SD-DPLATCPECGG 34 (52)
T ss_pred EEEEeCCCCCEeEEEEec------CC-CCCCCCCCCCC
Confidence 579999999998744322 22 44567999986
No 61
>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=81.36 E-value=0.96 Score=28.32 Aligned_cols=32 Identities=22% Similarity=0.501 Sum_probs=22.6
Q ss_pred ceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCC
Q 021063 130 YVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKK 168 (318)
Q Consensus 130 ~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~ 168 (318)
+.|+|..||+.|.-...... .....|+.|+..
T Consensus 4 Y~y~C~~Cg~~fe~~~~~~~-------~~~~~CP~Cg~~ 35 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKISD-------DPLATCPECGGD 35 (41)
T ss_pred EEEEcCCCCCEEEEEEecCC-------CCCCCCCCCCCc
Confidence 57999999999865443321 345679999873
No 62
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=80.83 E-value=0.64 Score=41.06 Aligned_cols=44 Identities=23% Similarity=0.128 Sum_probs=33.2
Q ss_pred eecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCCCCcchhhcc
Q 021063 132 YECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSSASVPALAVL 179 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~~~~~~~~h~ 179 (318)
--|=+|++.|....-|..|++. |-|+|.+|.|+...--.|..||
T Consensus 11 pwcwycnrefddekiliqhqka----khfkchichkkl~sgpglsihc 54 (341)
T KOG2893|consen 11 PWCWYCNREFDDEKILIQHQKA----KHFKCHICHKKLFSGPGLSIHC 54 (341)
T ss_pred ceeeecccccchhhhhhhhhhh----ccceeeeehhhhccCCCceeeh
Confidence 3488999999999999998753 4499999998766553444444
No 63
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=80.32 E-value=1.3 Score=29.41 Aligned_cols=26 Identities=27% Similarity=0.727 Sum_probs=20.9
Q ss_pred ceeecCCCccccCCh-----hHHHHHhh-hcc
Q 021063 225 KIHECSICGSEFTSG-----QALGGHMR-RHR 250 (318)
Q Consensus 225 kpy~C~~Cgk~F~~~-----~~L~~H~r-~H~ 250 (318)
..-.|..|++.++.. ++|.+|++ +|.
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 345799999999876 59999998 564
No 64
>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=77.09 E-value=1.5 Score=27.97 Aligned_cols=31 Identities=19% Similarity=0.523 Sum_probs=22.8
Q ss_pred ceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCC
Q 021063 130 YVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEK 167 (318)
Q Consensus 130 ~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k 167 (318)
+.|+|..||..|...... .. ..+..|+.|+.
T Consensus 4 Yey~C~~Cg~~fe~~~~~------~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSI------SE-DDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEEc------CC-CCCCcCCCCCC
Confidence 679999999998654432 22 45678999986
No 65
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=75.98 E-value=2.1 Score=31.83 Aligned_cols=17 Identities=35% Similarity=0.950 Sum_probs=14.4
Q ss_pred CCceeecCCCccccCCh
Q 021063 223 GNKIHECSICGSEFTSG 239 (318)
Q Consensus 223 g~kpy~C~~Cgk~F~~~ 239 (318)
+...+.|..||..|.-+
T Consensus 50 a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 50 ATGIWKCRKCGAKFAGG 66 (89)
T ss_pred ccCeEEcCCCCCeeccc
Confidence 46899999999999854
No 66
>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=75.77 E-value=1.9 Score=33.69 Aligned_cols=16 Identities=31% Similarity=0.715 Sum_probs=13.8
Q ss_pred CceeecCCCccccCCh
Q 021063 224 NKIHECSICGSEFTSG 239 (318)
Q Consensus 224 ~kpy~C~~Cgk~F~~~ 239 (318)
..|-.|+.||..|.-.
T Consensus 24 k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 24 KDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCCccCCCCCCccCcc
Confidence 4788899999999876
No 67
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.13 E-value=1.9 Score=44.08 Aligned_cols=49 Identities=10% Similarity=0.023 Sum_probs=29.0
Q ss_pred cccCCCCCchhhccccccc-----ccc---chhhhhcCchhhhhhcccCCCCceeecC--CCc
Q 021063 181 TKNEYKDSYSTLHHHDQSH-----MQA---ASAAATAANNNNTANNNNKGGNKIHECS--ICG 233 (318)
Q Consensus 181 ~~~~~f~~~~~L~~H~~~h-----~~~---~c~k~~~~~~~l~~h~~~htg~kpy~C~--~Cg 233 (318)
.|...|-+...|.+|++.+ .|+ .++--|.....|+.|-+. ..|.|. .|-
T Consensus 187 ~C~~~fld~~el~rH~~~~h~~chfC~~~~~~neyy~~~~dLe~HfR~----~HflCE~~~C~ 245 (669)
T KOG2231|consen 187 FCHERFLDDDELYRHLRFDHEFCHFCDYKTGQNEYYNDYDDLEEHFRK----GHFLCEEEFCR 245 (669)
T ss_pred hhhhhhccHHHHHHhhccceeheeecCcccccchhcccchHHHHHhhh----cCccccccccc
Confidence 4555666667777777643 222 144556666777777543 357777 554
No 68
>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=73.19 E-value=2.2 Score=33.41 Aligned_cols=30 Identities=13% Similarity=0.282 Sum_probs=22.9
Q ss_pred eeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCCC
Q 021063 131 VYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSSA 171 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~~ 171 (318)
...|+.||+.| +.|++ .|..|++|+..|..
T Consensus 9 KR~Cp~CG~kF---YDLnk--------~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 9 KRTCPSCGAKF---YDLNK--------DPIVCPKCGTEFPP 38 (108)
T ss_pred cccCCCCcchh---ccCCC--------CCccCCCCCCccCc
Confidence 37899999987 45542 47789999998853
No 69
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=73.09 E-value=1.2 Score=30.18 Aligned_cols=28 Identities=18% Similarity=0.265 Sum_probs=24.3
Q ss_pred CCCCceeecCCCCCcCCCccchhhhhhh
Q 021063 126 AGGFYVYECKTCNRSFPSFQALGGHRAS 153 (318)
Q Consensus 126 h~g~~~y~C~~C~K~F~s~~~L~~H~rs 153 (318)
+.|+..+.|+-|++.|.......+|...
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 3788899999999999999999999643
No 70
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=71.51 E-value=2.2 Score=37.53 Aligned_cols=43 Identities=12% Similarity=0.157 Sum_probs=29.9
Q ss_pred ceeecCCCCCcCCCccchhhhhhh---c-------CCCCC-----ccCCCCCCCCCCC
Q 021063 130 YVYECKTCNRSFPSFQALGGHRAS---H-------KKPKA-----ALAEAPEKKSSAS 172 (318)
Q Consensus 130 ~~y~C~~C~K~F~s~~~L~~H~rs---H-------t~~kp-----~~C~~C~k~f~~~ 172 (318)
+.+.|++|++.|....-+.+..+. . .+..| ..|+.|+.+|...
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 469999999999998776666543 1 22333 3588998877543
No 71
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=71.38 E-value=2.5 Score=39.96 Aligned_cols=28 Identities=25% Similarity=0.608 Sum_probs=24.3
Q ss_pred CCceeecCCCccccCChhHHHHHhh--hcc
Q 021063 223 GNKIHECSICGSEFTSGQALGGHMR--RHR 250 (318)
Q Consensus 223 g~kpy~C~~Cgk~F~~~~~L~~H~r--~H~ 250 (318)
++-++.|.+|.|.|.+..+...|+. .|.
T Consensus 65 ~~~~~~c~~c~k~~~s~~a~~~hl~Sk~h~ 94 (390)
T KOG2785|consen 65 AESVVYCEACNKSFASPKAHENHLKSKKHV 94 (390)
T ss_pred cccceehHHhhccccChhhHHHHHHHhhcc
Confidence 4778999999999999999999985 454
No 72
>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=70.00 E-value=2.9 Score=37.51 Aligned_cols=95 Identities=18% Similarity=0.214 Sum_probs=56.6
Q ss_pred CCCceeecCCCCCcCCCccchhhhhhhcC--CCCCccCCCCCCCCCCCcchhhccCcccCCCCCchhhccccccccccch
Q 021063 127 GGFYVYECKTCNRSFPSFQALGGHRASHK--KPKAALAEAPEKKSSASVPALAVLPTKNEYKDSYSTLHHHDQSHMQAAS 204 (318)
Q Consensus 127 ~g~~~y~C~~C~K~F~s~~~L~~H~rsHt--~~kp~~C~~C~k~f~~~~~~~~h~~~~~~~f~~~~~L~~H~~~h~~~~c 204 (318)
.|.+.|+|..|+. |--...--.|+++-. ....|+|.-|++.-.++ +..|-..|-+ .|.+.-
T Consensus 138 hGGrif~CsfC~~-flCEDDQFEHQAsCQvLe~E~~KC~SCNrlGq~s------CLRCK~cfCd-----dHvrrK----- 200 (314)
T PF06524_consen 138 HGGRIFKCSFCDN-FLCEDDQFEHQASCQVLESETFKCQSCNRLGQYS------CLRCKICFCD-----DHVRRK----- 200 (314)
T ss_pred CCCeEEEeecCCC-eeeccchhhhhhhhhhhhcccccccccccccchh------hhheeeeehh-----hhhhhc-----
Confidence 4558999999987 444445556777632 22358898888755433 1111111111 122211
Q ss_pred hhhhcCchhhhhhcccCCCCceeecCCCccccCChhHHHHHhhhccC
Q 021063 205 AAATAANNNNTANNNNKGGNKIHECSICGSEFTSGQALGGHMRRHRA 251 (318)
Q Consensus 205 ~k~~~~~~~l~~h~~~htg~kpy~C~~Cgk~F~~~~~L~~H~r~H~~ 251 (318)
.|. . ...+++.|+.||........|..-.|+|.-
T Consensus 201 --g~k----------y-~k~k~~PCPKCg~et~eTkdLSmStR~hky 234 (314)
T PF06524_consen 201 --GFK----------Y-EKGKPIPCPKCGYETQETKDLSMSTRSHKY 234 (314)
T ss_pred --ccc----------c-ccCCCCCCCCCCCcccccccceeeeecchh
Confidence 111 1 135899999999999888888877777753
No 73
>PRK14873 primosome assembly protein PriA; Provisional
Probab=69.63 E-value=2.8 Score=43.31 Aligned_cols=40 Identities=10% Similarity=0.098 Sum_probs=24.6
Q ss_pred CCCcee-ecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCC
Q 021063 127 GGFYVY-ECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEK 167 (318)
Q Consensus 127 ~g~~~y-~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k 167 (318)
-|.-++ .|..||..+... .-...+..|.......|.+|+.
T Consensus 378 rGyap~l~C~~Cg~~~~C~-~C~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 378 RGYVPSLACARCRTPARCR-HCTGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred CCCCCeeEhhhCcCeeECC-CCCCceeEecCCCeeECCCCcC
Confidence 344444 888888877653 3333444555556677888875
No 74
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=69.12 E-value=2.1 Score=34.73 Aligned_cols=28 Identities=29% Similarity=0.597 Sum_probs=17.8
Q ss_pred CceeecCCCccccCChhHHHHHhhhccCCCC
Q 021063 224 NKIHECSICGSEFTSGQALGGHMRRHRAAVA 254 (318)
Q Consensus 224 ~kpy~C~~Cgk~F~~~~~L~~H~r~H~~~~~ 254 (318)
+.--.|-+||+.|.. |++|++.|+|..|
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCCH
Confidence 455689999999985 4999999987543
No 75
>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=67.92 E-value=4.5 Score=24.57 Aligned_cols=25 Identities=12% Similarity=0.174 Sum_probs=18.2
Q ss_pred eeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCC
Q 021063 131 VYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEK 167 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k 167 (318)
.|.|.+||..+... +.|..|++|+.
T Consensus 2 ~~~C~~CG~i~~g~------------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE------------EAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC------------cCCCcCcCCCC
Confidence 58999999875432 24678999985
No 76
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=64.87 E-value=3.1 Score=28.23 Aligned_cols=29 Identities=21% Similarity=0.510 Sum_probs=25.1
Q ss_pred CCCceeecCCCccccCChhHHHHHhhhcc
Q 021063 222 GGNKIHECSICGSEFTSGQALGGHMRRHR 250 (318)
Q Consensus 222 tg~kpy~C~~Cgk~F~~~~~L~~H~r~H~ 250 (318)
-||--+.|+-||+.|.....+.+|.-.-+
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 47889999999999999999999985433
No 77
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=64.25 E-value=1.4 Score=44.90 Aligned_cols=28 Identities=32% Similarity=0.628 Sum_probs=25.3
Q ss_pred CceeecCCCccccCChhHHHHHhhhccC
Q 021063 224 NKIHECSICGSEFTSGQALGGHMRRHRA 251 (318)
Q Consensus 224 ~kpy~C~~Cgk~F~~~~~L~~H~r~H~~ 251 (318)
.-.|.|..|+|.|---..+..||++|+-
T Consensus 790 ~giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 790 TGIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred CceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 3479999999999999999999999974
No 78
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=64.20 E-value=4.3 Score=30.55 Aligned_cols=18 Identities=22% Similarity=0.479 Sum_probs=14.6
Q ss_pred CCceeecCCCccccCChh
Q 021063 223 GNKIHECSICGSEFTSGQ 240 (318)
Q Consensus 223 g~kpy~C~~Cgk~F~~~~ 240 (318)
+.-.++|..|++.|.-+.
T Consensus 51 a~GIW~C~~C~~~~AGGA 68 (90)
T PTZ00255 51 AVGIWRCKGCKKTVAGGA 68 (90)
T ss_pred eeEEEEcCCCCCEEeCCc
Confidence 467899999999998553
No 79
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=64.18 E-value=3.6 Score=26.67 Aligned_cols=30 Identities=13% Similarity=0.122 Sum_probs=21.3
Q ss_pred eeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCC
Q 021063 131 VYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSS 170 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~ 170 (318)
.|.|+.||..|.....-. .+.|+.|+..+.
T Consensus 3 ~y~C~~CG~~~~~~~~~~----------~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEYGT----------GVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCCCC----------ceECCCCCCeEE
Confidence 699999999875532211 578999997654
No 80
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.75 E-value=3.8 Score=41.92 Aligned_cols=83 Identities=22% Similarity=0.223 Sum_probs=43.7
Q ss_pred ecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCCCCcchhhccCcccCCCCCchhhcccccccc--cc--ch----
Q 021063 133 ECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSSASVPALAVLPTKNEYKDSYSTLHHHDQSHM--QA--AS---- 204 (318)
Q Consensus 133 ~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~~~~~~~~h~~~~~~~f~~~~~L~~H~~~h~--~~--~c---- 204 (318)
.|+.|...|-....|..|++.+. |.|..|.+.- .+..+|.+...|..|.|.+. |+ .|
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~-----------~~neyy~~~~dLe~HfR~~HflCE~~~C~~~~ 248 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKT-----------GQNEYYNDYDDLEEHFRKGHFLCEEEFCRTKK 248 (669)
T ss_pred cchhhhhhhccHHHHHHhhccce----eheeecCccc-----------ccchhcccchHHHHHhhhcCccccccccccce
Confidence 45555555555555555554432 3444443211 11236777788988876542 33 23
Q ss_pred -hhhhcCchhhhhhcccCCCCceeecC
Q 021063 205 -AAATAANNNNTANNNNKGGNKIHECS 230 (318)
Q Consensus 205 -~k~~~~~~~l~~h~~~htg~kpy~C~ 230 (318)
.-.|.....|++|.+.+.-++-|-|.
T Consensus 249 f~~~~~~ei~lk~~~~~~~~e~~~~~~ 275 (669)
T KOG2231|consen 249 FYVAFELEIELKAHNRFIQHEKCYICR 275 (669)
T ss_pred eeehhHHHHHHHhhccccchheeccCC
Confidence 23334455666665444447777774
No 81
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=62.41 E-value=4.6 Score=33.28 Aligned_cols=37 Identities=11% Similarity=0.131 Sum_probs=25.8
Q ss_pred CceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCC
Q 021063 129 FYVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKS 169 (318)
Q Consensus 129 ~~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f 169 (318)
...|.|+.|++.|....++..- +. ...|.|+.|+...
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~---d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLL---DM-DGTFTCPRCGEEL 133 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhc---CC-CCcEECCCCCCEE
Confidence 3479999999999865544431 11 3349999999765
No 82
>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=62.40 E-value=4.4 Score=40.46 Aligned_cols=37 Identities=14% Similarity=0.084 Sum_probs=23.6
Q ss_pred eecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCC
Q 021063 132 YECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKS 169 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f 169 (318)
..|..||...... .-...+..|.......|.+|+...
T Consensus 214 ~~C~~Cg~~~~C~-~C~~~l~~h~~~~~l~Ch~Cg~~~ 250 (505)
T TIGR00595 214 LLCRSCGYILCCP-NCDVSLTYHKKEGKLRCHYCGYQE 250 (505)
T ss_pred eEhhhCcCccCCC-CCCCceEEecCCCeEEcCCCcCcC
Confidence 4788888776653 334455556666667788887543
No 83
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=61.95 E-value=5.5 Score=26.40 Aligned_cols=30 Identities=13% Similarity=0.339 Sum_probs=21.3
Q ss_pred ceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCC
Q 021063 130 YVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKS 169 (318)
Q Consensus 130 ~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f 169 (318)
..|.|-.||+.|.. -.......|+.|+..-
T Consensus 5 ~~Y~C~~Cg~~~~~----------~~~~~~irCp~Cg~rI 34 (49)
T COG1996 5 MEYKCARCGREVEL----------DQETRGIRCPYCGSRI 34 (49)
T ss_pred EEEEhhhcCCeeeh----------hhccCceeCCCCCcEE
Confidence 47999999999821 1233457899998654
No 84
>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=61.95 E-value=5.5 Score=31.88 Aligned_cols=20 Identities=20% Similarity=0.321 Sum_probs=15.5
Q ss_pred CceeecCCCccccCChhHHH
Q 021063 224 NKIHECSICGSEFTSGQALG 243 (318)
Q Consensus 224 ~kpy~C~~Cgk~F~~~~~L~ 243 (318)
..|-.|..||..|.-...++
T Consensus 24 k~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 24 RRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred CCCccCCCcCCccCcchhhc
Confidence 57889999999987664444
No 85
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=59.89 E-value=4 Score=34.89 Aligned_cols=32 Identities=13% Similarity=0.171 Sum_probs=26.0
Q ss_pred ceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCC
Q 021063 130 YVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSS 170 (318)
Q Consensus 130 ~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~ 170 (318)
.-|.|+.|++.|....++. --|.|+.||....
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME---------YGFRCPQCGEMLE 147 (178)
T ss_pred CEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCCe
Confidence 4699999999998888774 2599999997653
No 86
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=59.82 E-value=5.8 Score=41.34 Aligned_cols=12 Identities=42% Similarity=0.803 Sum_probs=9.2
Q ss_pred CceeecCCCccc
Q 021063 224 NKIHECSICGSE 235 (318)
Q Consensus 224 ~kpy~C~~Cgk~ 235 (318)
..|..|+.||..
T Consensus 473 ~~p~~Cp~Cgs~ 484 (730)
T COG1198 473 PIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCC
Confidence 577888888865
No 87
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=59.30 E-value=20 Score=28.17 Aligned_cols=27 Identities=19% Similarity=0.269 Sum_probs=23.8
Q ss_pred CceeecCCCccccCChhHHHHHhhhcc
Q 021063 224 NKIHECSICGSEFTSGQALGGHMRRHR 250 (318)
Q Consensus 224 ~kpy~C~~Cgk~F~~~~~L~~H~r~H~ 250 (318)
...|+|..|...|--.-+.-.|...|.
T Consensus 79 ~~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 79 SHRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred ccceeCCCCCCccccccchhhhhhccC
Confidence 568999999999999988888888775
No 88
>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=59.16 E-value=4.5 Score=33.87 Aligned_cols=31 Identities=10% Similarity=-0.004 Sum_probs=26.0
Q ss_pred ceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCC
Q 021063 130 YVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKS 169 (318)
Q Consensus 130 ~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f 169 (318)
.-|.|+.|+..|....++.. -|.|+.||...
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~~---------~F~Cp~Cg~~L 138 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAMEL---------NFTCPRCGAML 138 (158)
T ss_pred CeEECCCCCcEeeHHHHHHc---------CCcCCCCCCEe
Confidence 46999999999998888862 59999999764
No 89
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=59.10 E-value=5.5 Score=33.61 Aligned_cols=13 Identities=38% Similarity=0.956 Sum_probs=10.7
Q ss_pred CCCceeecCCCcc
Q 021063 222 GGNKIHECSICGS 234 (318)
Q Consensus 222 tg~kpy~C~~Cgk 234 (318)
-|+-|-+|++||.
T Consensus 145 ~ge~P~~CPiCga 157 (166)
T COG1592 145 EGEAPEVCPICGA 157 (166)
T ss_pred cCCCCCcCCCCCC
Confidence 3688999999983
No 90
>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=58.09 E-value=5.6 Score=30.00 Aligned_cols=18 Identities=33% Similarity=0.868 Sum_probs=14.6
Q ss_pred CCceeecCCCccccCChh
Q 021063 223 GNKIHECSICGSEFTSGQ 240 (318)
Q Consensus 223 g~kpy~C~~Cgk~F~~~~ 240 (318)
+.-.++|..|++.|.-+.
T Consensus 50 a~GIW~C~~C~~~~AGGA 67 (91)
T TIGR00280 50 STGIWTCRKCGAKFAGGA 67 (91)
T ss_pred eeEEEEcCCCCCEEeCCc
Confidence 367899999999998553
No 91
>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=56.65 E-value=7.9 Score=30.01 Aligned_cols=26 Identities=23% Similarity=0.415 Sum_probs=23.6
Q ss_pred eeec----CCCccccCChhHHHHHhhhccC
Q 021063 226 IHEC----SICGSEFTSGQALGGHMRRHRA 251 (318)
Q Consensus 226 py~C----~~Cgk~F~~~~~L~~H~r~H~~ 251 (318)
-|.| ..|+..+.+...+..|++.++|
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 4899 9999999999999999998764
No 92
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=56.43 E-value=9.1 Score=24.75 Aligned_cols=29 Identities=14% Similarity=0.212 Sum_probs=21.6
Q ss_pred eeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCC
Q 021063 131 VYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSS 170 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~ 170 (318)
.|.|..||..|.-. ...+..|+.|+..-.
T Consensus 2 ~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~rIl 30 (44)
T smart00659 2 IYICGECGRENEIK-----------SKDVVRCRECGYRIL 30 (44)
T ss_pred EEECCCCCCEeecC-----------CCCceECCCCCceEE
Confidence 59999999988643 234578999987654
No 93
>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=56.21 E-value=8.9 Score=21.75 Aligned_cols=21 Identities=19% Similarity=0.564 Sum_probs=16.6
Q ss_pred eecCCCccccCChhHHHHHhhh
Q 021063 227 HECSICGSEFTSGQALGGHMRR 248 (318)
Q Consensus 227 y~C~~Cgk~F~~~~~L~~H~r~ 248 (318)
..|++|++.+ ....+..|...
T Consensus 2 v~CPiC~~~v-~~~~in~HLD~ 22 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLDS 22 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHHH
Confidence 3699999999 55788888763
No 94
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=56.08 E-value=9.5 Score=32.17 Aligned_cols=24 Identities=17% Similarity=0.422 Sum_probs=20.2
Q ss_pred eeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCC
Q 021063 131 VYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEK 167 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k 167 (318)
.|.|++||.. |.++-|-.|++|+.
T Consensus 134 ~~vC~vCGy~-------------~~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYT-------------HEGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCc-------------ccCCCCCcCCCCCC
Confidence 8999999764 56788999999984
No 95
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=56.07 E-value=22 Score=37.05 Aligned_cols=34 Identities=24% Similarity=0.332 Sum_probs=21.6
Q ss_pred eecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCCCC
Q 021063 132 YECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSSAS 172 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~~~ 172 (318)
-.|..|++.|.....+...++ +.|..||..|...
T Consensus 461 dtC~~C~kkFfSlsK~L~~RK-------HHCRkCGrVFC~~ 494 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRA-------HHCRSCGIRLCVF 494 (1374)
T ss_pred CcccCcCCccccccccccccc-------ccccCCccccCcc
Confidence 579999999976533222222 3477788877443
No 96
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=53.42 E-value=8.6 Score=39.54 Aligned_cols=42 Identities=21% Similarity=0.390 Sum_probs=28.7
Q ss_pred cee-ecCCCCCcCCCccchhhhhhhcCCCCCc-cCCCCCCCCCCC
Q 021063 130 YVY-ECKTCNRSFPSFQALGGHRASHKKPKAA-LAEAPEKKSSAS 172 (318)
Q Consensus 130 ~~y-~C~~C~K~F~s~~~L~~H~rsHt~~kp~-~C~~C~k~f~~~ 172 (318)
||| .|..||-.|.--.+|---| -+|.-+.| .|+.|.+.+..+
T Consensus 121 YPF~~CT~CGPRfTIi~alPYDR-~nTsM~~F~lC~~C~~EY~dP 164 (750)
T COG0068 121 YPFINCTNCGPRFTIIEALPYDR-ENTSMADFPLCPFCDKEYKDP 164 (750)
T ss_pred ccccccCCCCcceeeeccCCCCc-ccCccccCcCCHHHHHHhcCc
Confidence 455 6999999998887776543 34444444 488888877554
No 97
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=52.76 E-value=8.7 Score=26.94 Aligned_cols=14 Identities=29% Similarity=0.740 Sum_probs=6.7
Q ss_pred CceeecCCCccccC
Q 021063 224 NKIHECSICGSEFT 237 (318)
Q Consensus 224 ~kpy~C~~Cgk~F~ 237 (318)
.+.|.|..||..|=
T Consensus 23 ~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 23 RRRHHCRNCGRVVC 36 (69)
T ss_dssp S-EEE-TTT--EEE
T ss_pred eeeEccCCCCCEEC
Confidence 46677777777665
No 98
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=52.29 E-value=7.2 Score=29.35 Aligned_cols=17 Identities=47% Similarity=1.116 Sum_probs=14.1
Q ss_pred CCceeecCCCccccCCh
Q 021063 223 GNKIHECSICGSEFTSG 239 (318)
Q Consensus 223 g~kpy~C~~Cgk~F~~~ 239 (318)
+.-.++|..|++.|.-+
T Consensus 51 a~GIW~C~~C~~~~AGG 67 (90)
T PRK03976 51 GTGIWECRKCGAKFAGG 67 (90)
T ss_pred EEEEEEcCCCCCEEeCC
Confidence 35789999999999854
No 99
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=49.86 E-value=7.5 Score=32.41 Aligned_cols=12 Identities=17% Similarity=-0.053 Sum_probs=7.2
Q ss_pred ccCCCCCCCCCC
Q 021063 160 ALAEAPEKKSSA 171 (318)
Q Consensus 160 ~~C~~C~k~f~~ 171 (318)
++|+.|+++|..
T Consensus 29 ~~c~~c~~~f~~ 40 (154)
T PRK00464 29 RECLACGKRFTT 40 (154)
T ss_pred eeccccCCcceE
Confidence 556666666643
No 100
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=49.54 E-value=8.9 Score=31.01 Aligned_cols=27 Identities=22% Similarity=0.354 Sum_probs=22.2
Q ss_pred ceeecCCCccccCChhHHHHHhhhccCCCC
Q 021063 225 KIHECSICGSEFTSGQALGGHMRRHRAAVA 254 (318)
Q Consensus 225 kpy~C~~Cgk~F~~~~~L~~H~r~H~~~~~ 254 (318)
--..|-.|||.|. .|++|+.+|.|-.|
T Consensus 75 D~IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 75 DYIICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred CeEEEeccCcchH---HHHHHHhcccCCCH
Confidence 3457999999997 58999999998654
No 101
>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=44.77 E-value=11 Score=23.19 Aligned_cols=33 Identities=15% Similarity=0.211 Sum_probs=19.3
Q ss_pred eecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCC
Q 021063 132 YECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKS 169 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f 169 (318)
++|+.|+..|.-...... .......|..|+..|
T Consensus 3 ~~CP~C~~~~~v~~~~~~-----~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLG-----ANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcC-----CCCCEEECCCCCCEE
Confidence 678888887755433221 111236788887766
No 102
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=44.65 E-value=19 Score=24.85 Aligned_cols=33 Identities=9% Similarity=-0.010 Sum_probs=20.6
Q ss_pred ceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCC
Q 021063 130 YVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEK 167 (318)
Q Consensus 130 ~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k 167 (318)
-.|.|+.||+.-..+- .+.-+--.+|.|+.|+-
T Consensus 26 v~F~CPnCGe~~I~Rc-----~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPCPNCGEVEIYRC-----AKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeCCCCCceeeehh-----hhHHHcCCceECCCcCc
Confidence 4699999997543321 22222345799998873
No 103
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=44.15 E-value=9 Score=31.05 Aligned_cols=26 Identities=23% Similarity=0.471 Sum_probs=16.5
Q ss_pred eeecCCCCCcCCCccchhhhhhhcCCCCC
Q 021063 131 VYECKTCNRSFPSFQALGGHRASHKKPKA 159 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rsHt~~kp 159 (318)
--.|-+|||.|. .|++|.+.|.|-.|
T Consensus 72 ~i~clecGk~~k---~LkrHL~~~~gltp 97 (132)
T PF05443_consen 72 YIICLECGKKFK---TLKRHLRTHHGLTP 97 (132)
T ss_dssp -EE-TBT--EES---BHHHHHHHTT-S-H
T ss_pred eeEEccCCcccc---hHHHHHHHccCCCH
Confidence 468999999875 57999999977554
No 104
>PRK05580 primosome assembly protein PriA; Validated
Probab=44.12 E-value=14 Score=38.41 Aligned_cols=36 Identities=8% Similarity=0.077 Sum_probs=18.5
Q ss_pred eecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCC
Q 021063 132 YECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKK 168 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~ 168 (318)
..|..||..+... .-...+..|.......|.+|+..
T Consensus 382 ~~C~~Cg~~~~C~-~C~~~l~~h~~~~~l~Ch~Cg~~ 417 (679)
T PRK05580 382 LLCRDCGWVAECP-HCDASLTLHRFQRRLRCHHCGYQ 417 (679)
T ss_pred eEhhhCcCccCCC-CCCCceeEECCCCeEECCCCcCC
Confidence 4677777665442 12222333444455667666654
No 105
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=43.97 E-value=7.2 Score=40.04 Aligned_cols=26 Identities=19% Similarity=0.655 Sum_probs=24.1
Q ss_pred ceeecCCCCCcCCCccchhhhhhhcC
Q 021063 130 YVYECKTCNRSFPSFQALGGHRASHK 155 (318)
Q Consensus 130 ~~y~C~~C~K~F~s~~~L~~H~rsHt 155 (318)
-.|.|..|+|+|-....+..||++|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 47999999999999999999999995
No 106
>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=43.21 E-value=5.4 Score=30.04 Aligned_cols=16 Identities=38% Similarity=0.985 Sum_probs=12.5
Q ss_pred CceeecCCCccccCCh
Q 021063 224 NKIHECSICGSEFTSG 239 (318)
Q Consensus 224 ~kpy~C~~Cgk~F~~~ 239 (318)
.-.++|..|++.|.-+
T Consensus 51 ~GIW~C~~C~~~~AGG 66 (90)
T PF01780_consen 51 TGIWKCKKCGKKFAGG 66 (90)
T ss_dssp TTEEEETTTTEEEE-B
T ss_pred eEEeecCCCCCEEeCC
Confidence 4579999999999743
No 107
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=42.75 E-value=19 Score=22.07 Aligned_cols=15 Identities=33% Similarity=0.682 Sum_probs=12.0
Q ss_pred CCceeecCCCccccC
Q 021063 223 GNKIHECSICGSEFT 237 (318)
Q Consensus 223 g~kpy~C~~Cgk~F~ 237 (318)
..+..+|+.|+..|.
T Consensus 22 ~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 22 KGRKVRCSKCGHVFF 36 (36)
T ss_pred CCcEEECCCCCCEeC
Confidence 356789999998884
No 108
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=42.65 E-value=20 Score=32.13 Aligned_cols=35 Identities=9% Similarity=0.208 Sum_probs=21.9
Q ss_pred CCCceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCC
Q 021063 127 GGFYVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKS 169 (318)
Q Consensus 127 ~g~~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f 169 (318)
+-++.|.|..|...+-. ++-....--.|..|.+.|
T Consensus 108 ~~drqFaC~~Cd~~WwR--------rvp~rKeVSRCr~C~~rY 142 (278)
T PF15135_consen 108 SVDRQFACSSCDHMWWR--------RVPQRKEVSRCRKCRKRY 142 (278)
T ss_pred ccceeeeccccchHHHh--------ccCccccccccccccccc
Confidence 44578999999776533 222233335677787776
No 109
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=42.48 E-value=18 Score=22.85 Aligned_cols=25 Identities=24% Similarity=0.539 Sum_probs=19.3
Q ss_pred eeecCCCccccCChh--HHHHHhhhcc
Q 021063 226 IHECSICGSEFTSGQ--ALGGHMRRHR 250 (318)
Q Consensus 226 py~C~~Cgk~F~~~~--~L~~H~r~H~ 250 (318)
.-.|..||..|.... .-..|.+.|.
T Consensus 13 ~~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred CcCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 358999999998654 5677888875
No 110
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=41.77 E-value=9.8 Score=34.12 Aligned_cols=27 Identities=22% Similarity=0.444 Sum_probs=21.3
Q ss_pred CceeecCCCccccCChhHHHHHhhhccC
Q 021063 224 NKIHECSICGSEFTSGQALGGHMRRHRA 251 (318)
Q Consensus 224 ~kpy~C~~Cgk~F~~~~~L~~H~r~H~~ 251 (318)
..-|.|-.|++.|-. -.+..|...-+.
T Consensus 27 n~~fSCIDC~k~F~~-~sYknH~kCITE 53 (276)
T KOG2186|consen 27 NAYFSCIDCGKTFER-VSYKNHTKCITE 53 (276)
T ss_pred CCeeEEeeccccccc-chhhhhhhhcch
Confidence 378999999999988 677788765554
No 111
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.44 E-value=14 Score=28.76 Aligned_cols=15 Identities=7% Similarity=0.120 Sum_probs=12.8
Q ss_pred CceeecCCCccccCC
Q 021063 224 NKIHECSICGSEFTS 238 (318)
Q Consensus 224 ~kpy~C~~Cgk~F~~ 238 (318)
..|-.|+.||++|..
T Consensus 24 rdPiVsPytG~s~P~ 38 (129)
T COG4530 24 RDPIVSPYTGKSYPR 38 (129)
T ss_pred CCccccCcccccchH
Confidence 678999999999953
No 112
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=41.31 E-value=18 Score=24.10 Aligned_cols=15 Identities=40% Similarity=0.875 Sum_probs=10.4
Q ss_pred CceeecCCCccccCC
Q 021063 224 NKIHECSICGSEFTS 238 (318)
Q Consensus 224 ~kpy~C~~Cgk~F~~ 238 (318)
.+.|.|..||+.|-.
T Consensus 16 ~rk~~Cr~Cg~~~C~ 30 (57)
T cd00065 16 RRRHHCRNCGRIFCS 30 (57)
T ss_pred ccccccCcCcCCcCh
Confidence 456777777777764
No 113
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=39.55 E-value=10 Score=35.63 Aligned_cols=23 Identities=26% Similarity=0.534 Sum_probs=17.2
Q ss_pred CCceeecCCCccccCChhHHHHH
Q 021063 223 GNKIHECSICGSEFTSGQALGGH 245 (318)
Q Consensus 223 g~kpy~C~~Cgk~F~~~~~L~~H 245 (318)
..|+|+|++|.+.+.-.-.|.-|
T Consensus 395 ~nk~~r~~i~~~~~k~~~~l~~~ 417 (442)
T KOG4124|consen 395 ENKPYRCEVCSKRYKNLNGLKYH 417 (442)
T ss_pred ccCcccChhhhhhhccCCCCCce
Confidence 47999999999888765554433
No 114
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=39.50 E-value=9.1 Score=22.25 Aligned_cols=20 Identities=25% Similarity=0.689 Sum_probs=13.5
Q ss_pred eecCCCccccCChhHHHHHhh
Q 021063 227 HECSICGSEFTSGQALGGHMR 247 (318)
Q Consensus 227 y~C~~Cgk~F~~~~~L~~H~r 247 (318)
|.|-.|++.| .+...+.|..
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~ 20 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTS 20 (28)
T ss_dssp EEETTTTEEE-EGGGTTT---
T ss_pred CeeecCCCCc-CcCCcCCCCc
Confidence 5788999999 5666666654
No 115
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=39.07 E-value=15 Score=20.83 Aligned_cols=12 Identities=33% Similarity=0.872 Sum_probs=9.4
Q ss_pred eeecCCCccccC
Q 021063 226 IHECSICGSEFT 237 (318)
Q Consensus 226 py~C~~Cgk~F~ 237 (318)
.-.|+.||..|.
T Consensus 14 ~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 14 AKFCPHCGYDFE 25 (26)
T ss_pred cCcCCCCCCCCc
Confidence 347899999885
No 116
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=38.76 E-value=26 Score=32.47 Aligned_cols=28 Identities=25% Similarity=0.322 Sum_probs=24.3
Q ss_pred CCceeecCCCccccCChhHHHHHhhhcc
Q 021063 223 GNKIHECSICGSEFTSGQALGGHMRRHR 250 (318)
Q Consensus 223 g~kpy~C~~Cgk~F~~~~~L~~H~r~H~ 250 (318)
..-.|+|+.|...|-.-.+.-.|...|.
T Consensus 385 ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 385 SSGRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred cccceechhhhhhhhhhhHHHHHHHHhh
Confidence 3568999999999999999888988775
No 117
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=37.94 E-value=25 Score=21.66 Aligned_cols=15 Identities=33% Similarity=0.857 Sum_probs=12.4
Q ss_pred CCceeecCCCccccC
Q 021063 223 GNKIHECSICGSEFT 237 (318)
Q Consensus 223 g~kpy~C~~Cgk~F~ 237 (318)
+.+..+|+.|+..|.
T Consensus 22 ~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 22 GGRKVRCPKCGHVFR 36 (37)
T ss_pred CCcEEECCCCCcEee
Confidence 467889999998885
No 118
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=37.22 E-value=14 Score=30.38 Aligned_cols=33 Identities=33% Similarity=0.536 Sum_probs=23.2
Q ss_pred CceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCC
Q 021063 129 FYVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKS 169 (318)
Q Consensus 129 ~~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f 169 (318)
.+.|.|..|+..+. +|.++ ..+.|.|..|+..+
T Consensus 121 ~~~~~C~~C~~~~~------r~~~~--~~~~~~C~~C~~~l 153 (157)
T PF10263_consen 121 KYVYRCPSCGREYK------RHRRS--KRKRYRCGRCGGPL 153 (157)
T ss_pred ceEEEcCCCCCEee------eeccc--chhhEECCCCCCEE
Confidence 46899999998873 44444 23348899998655
No 119
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=36.82 E-value=15 Score=29.57 Aligned_cols=15 Identities=40% Similarity=1.026 Sum_probs=13.6
Q ss_pred eeecCCCccccCChh
Q 021063 226 IHECSICGSEFTSGQ 240 (318)
Q Consensus 226 py~C~~Cgk~F~~~~ 240 (318)
||+|-.||+.|..+.
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 789999999999876
No 120
>COG1773 Rubredoxin [Energy production and conversion]
Probab=36.45 E-value=16 Score=24.84 Aligned_cols=13 Identities=38% Similarity=0.938 Sum_probs=11.1
Q ss_pred ceeecCCCccccC
Q 021063 225 KIHECSICGSEFT 237 (318)
Q Consensus 225 kpy~C~~Cgk~F~ 237 (318)
+.|+|.+||..|-
T Consensus 2 ~~~~C~~CG~vYd 14 (55)
T COG1773 2 KRWRCSVCGYVYD 14 (55)
T ss_pred CceEecCCceEec
Confidence 4699999999886
No 121
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the 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=36.26 E-value=36 Score=20.37 Aligned_cols=27 Identities=15% Similarity=0.281 Sum_probs=15.9
Q ss_pred eecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCC
Q 021063 132 YECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKS 169 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f 169 (318)
|.|..||..+. |. ...+.+|..|+..-
T Consensus 1 Y~C~~Cg~~~~----~~-------~~~~irC~~CG~RI 27 (32)
T PF03604_consen 1 YICGECGAEVE----LK-------PGDPIRCPECGHRI 27 (32)
T ss_dssp EBESSSSSSE-----BS-------TSSTSSBSSSS-SE
T ss_pred CCCCcCCCeeE----cC-------CCCcEECCcCCCeE
Confidence 67888888765 11 12346788887643
No 123
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=36.22 E-value=16 Score=26.36 Aligned_cols=38 Identities=8% Similarity=0.078 Sum_probs=19.5
Q ss_pred eecCCCCCcCCCccchhhhhhhcCCCCCccCC--CCCCCCCC
Q 021063 132 YECKTCNRSFPSFQALGGHRASHKKPKAALAE--APEKKSSA 171 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~--~C~k~f~~ 171 (318)
+.|+.||....-...-..+. -..++-+.|. .|+.+|..
T Consensus 2 m~CP~Cg~~a~irtSr~~s~--~~~~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITD--TTKERYHQCQNVNCSATFIT 41 (72)
T ss_pred ccCCCCCCccEEEEChhcCh--hhheeeeecCCCCCCCEEEE
Confidence 46777776542222211111 1345556676 67777753
No 124
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=35.62 E-value=21 Score=19.97 Aligned_cols=9 Identities=22% Similarity=0.848 Sum_probs=8.0
Q ss_pred eeecCCCCC
Q 021063 131 VYECKTCNR 139 (318)
Q Consensus 131 ~y~C~~C~K 139 (318)
.|.|+.||+
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 799999985
No 125
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=35.50 E-value=20 Score=33.66 Aligned_cols=29 Identities=21% Similarity=0.456 Sum_probs=24.4
Q ss_pred eeecCCCCCcCCCccchhhhhhh--cCCCCC
Q 021063 131 VYECKTCNRSFPSFQALGGHRAS--HKKPKA 159 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rs--Ht~~kp 159 (318)
.++|-+|.|.|+.+..|+.|||. |....|
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinP 225 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINP 225 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCC
Confidence 47899999999999999999986 655444
No 126
>PF15269 zf-C2H2_7: Zinc-finger
Probab=35.02 E-value=24 Score=22.84 Aligned_cols=24 Identities=21% Similarity=0.267 Sum_probs=20.4
Q ss_pred eeecCCCccccCChhHHHHHhhhc
Q 021063 226 IHECSICGSEFTSGQALGGHMRRH 249 (318)
Q Consensus 226 py~C~~Cgk~F~~~~~L~~H~r~H 249 (318)
.|+|-.|..+..-++.|-.||+.-
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred cceeecCCcccchHHHHHHHHHHH
Confidence 378999998888999999999853
No 127
>PHA00626 hypothetical protein
Probab=34.70 E-value=20 Score=24.37 Aligned_cols=16 Identities=19% Similarity=0.326 Sum_probs=13.5
Q ss_pred CceeecCCCccccCCh
Q 021063 224 NKIHECSICGSEFTSG 239 (318)
Q Consensus 224 ~kpy~C~~Cgk~F~~~ 239 (318)
...|+|..||..|+..
T Consensus 21 snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 21 SDDYVCCDCGYNDSKD 36 (59)
T ss_pred CcceEcCCCCCeechh
Confidence 5689999999999854
No 128
>PRK04023 DNA polymerase II large subunit; Validated
Probab=33.77 E-value=41 Score=36.27 Aligned_cols=13 Identities=46% Similarity=0.828 Sum_probs=9.1
Q ss_pred ceeecCCCccccC
Q 021063 225 KIHECSICGSEFT 237 (318)
Q Consensus 225 kpy~C~~Cgk~F~ 237 (318)
.+|.|+.||..-.
T Consensus 662 ~~y~CPKCG~El~ 674 (1121)
T PRK04023 662 EEDECEKCGREPT 674 (1121)
T ss_pred CCCcCCCCCCCCC
Confidence 4577888886554
No 129
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=33.08 E-value=22 Score=22.21 Aligned_cols=14 Identities=29% Similarity=0.667 Sum_probs=12.3
Q ss_pred eeecCCCccccCCh
Q 021063 226 IHECSICGSEFTSG 239 (318)
Q Consensus 226 py~C~~Cgk~F~~~ 239 (318)
||+|..|++.|=..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 89999999999754
No 130
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=33.05 E-value=72 Score=24.98 Aligned_cols=26 Identities=15% Similarity=0.143 Sum_probs=19.2
Q ss_pred eeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCC
Q 021063 131 VYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKK 168 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~ 168 (318)
.+.|..|+..|.... ..+.|+.|+..
T Consensus 70 ~~~C~~Cg~~~~~~~------------~~~~CP~Cgs~ 95 (113)
T PRK12380 70 QAWCWDCSQVVEIHQ------------HDAQCPHCHGE 95 (113)
T ss_pred EEEcccCCCEEecCC------------cCccCcCCCCC
Confidence 699999998886543 23569999853
No 131
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=32.83 E-value=28 Score=32.71 Aligned_cols=31 Identities=32% Similarity=0.548 Sum_probs=25.5
Q ss_pred ceeecCCCccccCChhHHHHHhh--hccCCCCC
Q 021063 225 KIHECSICGSEFTSGQALGGHMR--RHRAAVAT 255 (318)
Q Consensus 225 kpy~C~~Cgk~F~~~~~L~~H~r--~H~~~~~~ 255 (318)
-.++|-.|.|.|..+..|+.||| .|+.-.|.
T Consensus 194 ~r~~CLyCekifrdkntLkeHMrkK~HrrinPk 226 (423)
T KOG2482|consen 194 ERLRCLYCEKIFRDKNTLKEHMRKKRHRRINPK 226 (423)
T ss_pred hhheeeeeccccCCcHHHHHHHHhccCcccCCC
Confidence 35899999999999999999997 47655443
No 132
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=32.62 E-value=24 Score=35.51 Aligned_cols=27 Identities=26% Similarity=0.603 Sum_probs=22.5
Q ss_pred CceeecCCCccccCChhHHHHHhhhcc
Q 021063 224 NKIHECSICGSEFTSGQALGGHMRRHR 250 (318)
Q Consensus 224 ~kpy~C~~Cgk~F~~~~~L~~H~r~H~ 250 (318)
.+|.+|..||..|-.......||-.|-
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 578999999999999888777776664
No 133
>KOG0782 consensus Predicted diacylglycerol kinase [Signal transduction mechanisms]
Probab=32.59 E-value=65 Score=32.51 Aligned_cols=12 Identities=25% Similarity=0.487 Sum_probs=9.6
Q ss_pred hhhhhHHHHHHH
Q 021063 73 EEDQDMANCLIM 84 (318)
Q Consensus 73 ~eeed~a~cli~ 84 (318)
+.++|+.+|++.
T Consensus 106 ~~~~~L~~~~r~ 117 (1004)
T KOG0782|consen 106 ISNPDLTNCQRK 117 (1004)
T ss_pred cCChhHHHHHHh
Confidence 567899999874
No 134
>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=32.32 E-value=48 Score=21.32 Aligned_cols=27 Identities=19% Similarity=0.299 Sum_probs=15.4
Q ss_pred eecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCC
Q 021063 132 YECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEK 167 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k 167 (318)
+.|+.||.. ....|.. ...|+|..|.+
T Consensus 19 ~~CP~Cg~~--~~~~~~~-------~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST--KHYRLKT-------RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe--eeEEeCC-------CCeEECCCCCC
Confidence 668888865 2222222 45577777754
No 135
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=32.22 E-value=22 Score=31.91 Aligned_cols=39 Identities=13% Similarity=0.186 Sum_probs=31.1
Q ss_pred eeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCCC
Q 021063 131 VYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSSA 171 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~~ 171 (318)
-|.|..||..-... .|..|+-.-.+ .-|.|..|++.|-.
T Consensus 3 ~FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~ 41 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER 41 (276)
T ss_pred EEehhhhhhhcccc-chHHHHHhccC-CeeEEeeccccccc
Confidence 48999999987754 66679877666 56899999999966
No 136
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=31.82 E-value=8.6 Score=36.33 Aligned_cols=43 Identities=16% Similarity=0.163 Sum_probs=22.2
Q ss_pred CceeecCCCCCcCCCccch---hhh-hhhcCCCCC-ccCCCCCCCCCC
Q 021063 129 FYVYECKTCNRSFPSFQAL---GGH-RASHKKPKA-ALAEAPEKKSSA 171 (318)
Q Consensus 129 ~~~y~C~~C~K~F~s~~~L---~~H-~rsHt~~kp-~~C~~C~k~f~~ 171 (318)
.+.|.|.+|.+++...... .+| +..|...|. |+|..|++....
T Consensus 250 ~kav~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt~s 297 (344)
T PF09332_consen 250 CKAVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRTIS 297 (344)
T ss_dssp EEEEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EEEE
T ss_pred EEEEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCeeee
Confidence 4579999998876555443 344 334555555 789999987543
No 137
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=31.63 E-value=24 Score=23.39 Aligned_cols=18 Identities=33% Similarity=0.682 Sum_probs=14.5
Q ss_pred CceeecCCCccccCChhH
Q 021063 224 NKIHECSICGSEFTSGQA 241 (318)
Q Consensus 224 ~kpy~C~~Cgk~F~~~~~ 241 (318)
.+++.|..||+.|.....
T Consensus 2 Dk~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAG 19 (49)
T ss_pred CeeEEcccCCCeEEEehh
Confidence 578999999999876543
No 138
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=30.41 E-value=24 Score=34.18 Aligned_cols=32 Identities=16% Similarity=0.372 Sum_probs=0.0
Q ss_pred eecCCCCCcCCCccchhhhhhhcCCCCCccCCCCC
Q 021063 132 YECKTCNRSFPSFQALGGHRASHKKPKAALAEAPE 166 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~ 166 (318)
|.|+.|.+.| ..|..-+-.-...-.|.|..|+
T Consensus 129 Y~Cp~C~kky---t~Lea~~L~~~~~~~F~C~~C~ 160 (436)
T KOG2593|consen 129 YVCPNCQKKY---TSLEALQLLDNETGEFHCENCG 160 (436)
T ss_pred ccCCccccch---hhhHHHHhhcccCceEEEecCC
No 139
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.59 E-value=34 Score=27.74 Aligned_cols=39 Identities=15% Similarity=0.208 Sum_probs=23.7
Q ss_pred ceeecCCCCCcCCCc---cchh--hhhhhcCC----CCCccCCCCCCC
Q 021063 130 YVYECKTCNRSFPSF---QALG--GHRASHKK----PKAALAEAPEKK 168 (318)
Q Consensus 130 ~~y~C~~C~K~F~s~---~~L~--~H~rsHt~----~kp~~C~~C~k~ 168 (318)
..|.|..||..|... ..|. .+...|-- ..-+.|+.|+..
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 369999999988764 2221 12233322 234679999854
No 140
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=29.31 E-value=27 Score=32.82 Aligned_cols=104 Identities=20% Similarity=0.291 Sum_probs=60.6
Q ss_pred eeecCC--CCCcCCCccchhhhhhhcCCCCCccCCCCC---CCCCCCcchhhccCcccCCCCCchhhcccccc-------
Q 021063 131 VYECKT--CNRSFPSFQALGGHRASHKKPKAALAEAPE---KKSSASVPALAVLPTKNEYKDSYSTLHHHDQS------- 198 (318)
Q Consensus 131 ~y~C~~--C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~---k~f~~~~~~~~h~~~~~~~f~~~~~L~~H~~~------- 198 (318)
.|.|+. |..+......|..|..+-.+ .+.|.+|- +.|.....+ |. ...|..|...
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~--~~~C~~C~~nKk~F~~E~~l----------F~-~~~Lr~H~~~G~~e~GF 217 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHG--FVLCSECIGNKKDFWNEIRL----------FR-SSTLRDHKNGGLEEEGF 217 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcC--cEEhHhhhcCcccCccceee----------ee-cccccccccCCccccCc
Confidence 488886 77777777889999876322 25576664 234322111 11 1344444322
Q ss_pred --c-cccchhhhhcCchhhhhhcccCCCCceeecCCCc----cccCChhHHHHHhhh
Q 021063 199 --H-MQAASAAATAANNNNTANNNNKGGNKIHECSICG----SEFTSGQALGGHMRR 248 (318)
Q Consensus 199 --h-~~~~c~k~~~~~~~l~~h~~~htg~kpy~C~~Cg----k~F~~~~~L~~H~r~ 248 (318)
| .|.-|.+.|..-..|.+|++.. .|+=|.|..-+ .-|..-..|-+|.+.
T Consensus 218 KGHP~C~FC~~~FYdDDEL~~HcR~~-HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~ 273 (493)
T COG5236 218 KGHPLCIFCKIYFYDDDELRRHCRLR-HEACHICDMVGPIRYQYFKSYEDLEAHFRN 273 (493)
T ss_pred CCCchhhhccceecChHHHHHHHHhh-hhhhhhhhccCccchhhhhCHHHHHHHhhc
Confidence 1 1333888899999999998753 24444443322 237777788888763
No 141
>PLN02748 tRNA dimethylallyltransferase
Probab=29.27 E-value=31 Score=34.12 Aligned_cols=28 Identities=21% Similarity=0.421 Sum_probs=23.2
Q ss_pred CceeecCCCcc-ccCChhHHHHHhh--hccC
Q 021063 224 NKIHECSICGS-EFTSGQALGGHMR--RHRA 251 (318)
Q Consensus 224 ~kpy~C~~Cgk-~F~~~~~L~~H~r--~H~~ 251 (318)
-+.|.|++|++ +|.....+..|++ .|+.
T Consensus 416 ~~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~ 446 (468)
T PLN02748 416 WTQYVCEACGNKVLRGAHEWEQHKQGRGHRK 446 (468)
T ss_pred cccccccCCCCcccCCHHHHHHHhcchHHHH
Confidence 37799999997 8999999999985 5654
No 142
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=29.24 E-value=9 Score=35.29 Aligned_cols=36 Identities=14% Similarity=0.203 Sum_probs=13.4
Q ss_pred eeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCC
Q 021063 131 VYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKS 169 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f 169 (318)
.-.|++||.. +....|..--. .|.|-..|..|+...
T Consensus 172 ~g~CPvCGs~-P~~s~l~~~~~--~G~R~L~Cs~C~t~W 207 (290)
T PF04216_consen 172 RGYCPVCGSP-PVLSVLRGGER--EGKRYLHCSLCGTEW 207 (290)
T ss_dssp -SS-TTT----EEEEEEE--------EEEEEETTT--EE
T ss_pred CCcCCCCCCc-CceEEEecCCC--CccEEEEcCCCCCee
Confidence 3589999974 33344433222 244555677776543
No 143
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=29.23 E-value=35 Score=28.30 Aligned_cols=37 Identities=16% Similarity=0.357 Sum_probs=27.2
Q ss_pred CCceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCC
Q 021063 128 GFYVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKS 169 (318)
Q Consensus 128 g~~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f 169 (318)
..++|.|. |+..|.+ -++|-.+-.|+ .|.|..|+...
T Consensus 114 ~~~~Y~C~-C~q~~l~---~RRhn~~~~g~-~YrC~~C~gkL 150 (156)
T COG3091 114 TTYPYRCQ-CQQHYLR---IRRHNTVRRGE-VYRCGKCGGKL 150 (156)
T ss_pred cceeEEee-cCCccch---hhhcccccccc-eEEeccCCceE
Confidence 45789999 9998654 34555556677 89999998653
No 144
>PF15325 MRI: Modulator of retrovirus infection
Probab=28.64 E-value=1.4e+02 Score=22.85 Aligned_cols=6 Identities=67% Similarity=0.977 Sum_probs=3.1
Q ss_pred hhhhhH
Q 021063 73 EEDQDM 78 (318)
Q Consensus 73 ~eeed~ 78 (318)
+||||+
T Consensus 91 eEdeD~ 96 (106)
T PF15325_consen 91 EEDEDA 96 (106)
T ss_pred chhhHH
Confidence 455554
No 145
>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=28.62 E-value=26 Score=30.85 Aligned_cols=29 Identities=17% Similarity=0.475 Sum_probs=22.1
Q ss_pred CCceeecCCCccccCChhHHHHHhhhccC
Q 021063 223 GNKIHECSICGSEFTSGQALGGHMRRHRA 251 (318)
Q Consensus 223 g~kpy~C~~Cgk~F~~~~~L~~H~r~H~~ 251 (318)
.+-.|.|.+|+|.|.-..-+..|+..-+.
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 46789999999999999999999875433
No 146
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=28.47 E-value=31 Score=28.59 Aligned_cols=13 Identities=31% Similarity=0.956 Sum_probs=10.1
Q ss_pred CCCceeecCCCccc
Q 021063 222 GGNKIHECSICGSE 235 (318)
Q Consensus 222 tg~kpy~C~~Cgk~ 235 (318)
.|+ .|.|..|+-.
T Consensus 137 ~g~-~YrC~~C~gk 149 (156)
T COG3091 137 RGE-VYRCGKCGGK 149 (156)
T ss_pred ccc-eEEeccCCce
Confidence 356 9999999853
No 147
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=28.37 E-value=87 Score=24.55 Aligned_cols=27 Identities=11% Similarity=0.148 Sum_probs=18.6
Q ss_pred eeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCC
Q 021063 131 VYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKK 168 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~ 168 (318)
.+.|..|+..|...... .+.|+.|+..
T Consensus 70 ~~~C~~Cg~~~~~~~~~-----------~~~CP~Cgs~ 96 (114)
T PRK03681 70 ECWCETCQQYVTLLTQR-----------VRRCPQCHGD 96 (114)
T ss_pred EEEcccCCCeeecCCcc-----------CCcCcCcCCC
Confidence 69999999877543211 1569999854
No 148
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=27.97 E-value=29 Score=26.69 Aligned_cols=16 Identities=38% Similarity=0.966 Sum_probs=13.7
Q ss_pred eeecCCCccccCChhH
Q 021063 226 IHECSICGSEFTSGQA 241 (318)
Q Consensus 226 py~C~~Cgk~F~~~~~ 241 (318)
||+|--||..|..++.
T Consensus 2 pH~CtrCG~vf~~g~~ 17 (112)
T COG3364 2 PHQCTRCGEVFDDGSE 17 (112)
T ss_pred CceecccccccccccH
Confidence 7899999999998654
No 149
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.86 E-value=13 Score=32.43 Aligned_cols=50 Identities=18% Similarity=0.244 Sum_probs=35.7
Q ss_pred ccchhhhhcCchhhhhhcc----------cCCCCceeecC--CCccccCChhHHHHHhh-hcc
Q 021063 201 QAASAAATAANNNNTANNN----------NKGGNKIHECS--ICGSEFTSGQALGGHMR-RHR 250 (318)
Q Consensus 201 ~~~c~k~~~~~~~l~~h~~----------~htg~kpy~C~--~Cgk~F~~~~~L~~H~r-~H~ 250 (318)
|..|.+.|....-|..|+. +..|.-.|+|- -|+-.|.+...-..||. +|.
T Consensus 109 Cs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 109 CSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred hHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhcc
Confidence 3447777777766666632 22456789994 59999999999999985 564
No 150
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=27.83 E-value=38 Score=26.60 Aligned_cols=27 Identities=11% Similarity=0.106 Sum_probs=20.3
Q ss_pred eeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCC
Q 021063 131 VYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKS 169 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f 169 (318)
...|..|++.|..... -+.|+.|+...
T Consensus 70 ~~~C~~Cg~~~~~~~~------------~~~CP~Cgs~~ 96 (115)
T TIGR00100 70 ECECEDCSEEVSPEID------------LYRCPKCHGIM 96 (115)
T ss_pred EEEcccCCCEEecCCc------------CccCcCCcCCC
Confidence 5999999998876432 36799998643
No 151
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=27.21 E-value=30 Score=34.87 Aligned_cols=27 Identities=22% Similarity=0.363 Sum_probs=23.1
Q ss_pred CceeecCCCCCcCCCccchhhhhhhcC
Q 021063 129 FYVYECKTCNRSFPSFQALGGHRASHK 155 (318)
Q Consensus 129 ~~~y~C~~C~K~F~s~~~L~~H~rsHt 155 (318)
.++.+|..||+.|........||-.|.
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhh
Confidence 457899999999999998888887774
No 152
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=27.15 E-value=17 Score=31.42 Aligned_cols=15 Identities=13% Similarity=0.011 Sum_probs=12.0
Q ss_pred CCccCCCCCCCCCCC
Q 021063 158 KAALAEAPEKKSSAS 172 (318)
Q Consensus 158 kp~~C~~C~k~f~~~ 172 (318)
-||.|.+|.+.|..+
T Consensus 195 IPF~C~iCKkdy~sp 209 (259)
T COG5152 195 IPFLCGICKKDYESP 209 (259)
T ss_pred Cceeehhchhhccch
Confidence 479999999988644
No 153
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=26.95 E-value=36 Score=33.13 Aligned_cols=26 Identities=27% Similarity=0.592 Sum_probs=21.1
Q ss_pred CCCCceeecCCCc-cccCChhHHHHHh
Q 021063 221 KGGNKIHECSICG-SEFTSGQALGGHM 246 (318)
Q Consensus 221 htg~kpy~C~~Cg-k~F~~~~~L~~H~ 246 (318)
|.=.+-|.|.||| +++.-..++.+|-
T Consensus 396 HGL~~ey~CEICGNy~Y~GrkaF~RHF 422 (497)
T KOG2636|consen 396 HGLDIEYNCEICGNYVYKGRKAFDRHF 422 (497)
T ss_pred cCCCcccceeeccCccccCcHHHHHHh
Confidence 3345679999999 8888888898885
No 154
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=26.93 E-value=29 Score=32.68 Aligned_cols=44 Identities=20% Similarity=0.373 Sum_probs=32.1
Q ss_pred CceeecCC--CCCcCCCccchhhhhhh-c--------------C----CCCCccCCCCCCCCCCC
Q 021063 129 FYVYECKT--CNRSFPSFQALGGHRAS-H--------------K----KPKAALAEAPEKKSSAS 172 (318)
Q Consensus 129 ~~~y~C~~--C~K~F~s~~~L~~H~rs-H--------------t----~~kp~~C~~C~k~f~~~ 172 (318)
.++|+|.+ |.+.+.....|..|... | + ..|+|+|++|.+.+...
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~ 411 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNL 411 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccC
Confidence 36899987 99999988888777432 3 2 24788898888877554
No 155
>PLN02294 cytochrome c oxidase subunit Vb
Probab=26.84 E-value=41 Score=28.44 Aligned_cols=15 Identities=33% Similarity=0.733 Sum_probs=13.2
Q ss_pred CceeecCCCccccCC
Q 021063 224 NKIHECSICGSEFTS 238 (318)
Q Consensus 224 ~kpy~C~~Cgk~F~~ 238 (318)
.+|++|..||..|.-
T Consensus 139 Gkp~RCpeCG~~fkL 153 (174)
T PLN02294 139 GKSFECPVCTQYFEL 153 (174)
T ss_pred CCceeCCCCCCEEEE
Confidence 689999999999873
No 156
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=26.84 E-value=16 Score=32.16 Aligned_cols=24 Identities=33% Similarity=0.826 Sum_probs=19.6
Q ss_pred CceeecCCCccccCChhHHHHHhh
Q 021063 224 NKIHECSICGSEFTSGQALGGHMR 247 (318)
Q Consensus 224 ~kpy~C~~Cgk~F~~~~~L~~H~r 247 (318)
.|.+.|++|++.|....-+.+..|
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r 26 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIR 26 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCce
Confidence 578899999999998876666655
No 157
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=26.39 E-value=20 Score=29.59 Aligned_cols=10 Identities=20% Similarity=0.800 Sum_probs=6.2
Q ss_pred eeecCCCCCc
Q 021063 131 VYECKTCNRS 140 (318)
Q Consensus 131 ~y~C~~C~K~ 140 (318)
.|.|..||..
T Consensus 112 ~l~C~~Cg~~ 121 (146)
T PF07295_consen 112 TLVCENCGHE 121 (146)
T ss_pred eEecccCCCE
Confidence 4667666653
No 158
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=26.26 E-value=33 Score=21.21 Aligned_cols=13 Identities=23% Similarity=0.705 Sum_probs=8.0
Q ss_pred CceeecCCCcccc
Q 021063 224 NKIHECSICGSEF 236 (318)
Q Consensus 224 ~kpy~C~~Cgk~F 236 (318)
.+.|+|.+||...
T Consensus 4 ~~~YkC~~CGniV 16 (36)
T PF06397_consen 4 GEFYKCEHCGNIV 16 (36)
T ss_dssp TEEEE-TTT--EE
T ss_pred ccEEEccCCCCEE
Confidence 5789999999754
No 159
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=26.15 E-value=38 Score=27.69 Aligned_cols=34 Identities=21% Similarity=0.309 Sum_probs=23.5
Q ss_pred CceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCC
Q 021063 129 FYVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKS 169 (318)
Q Consensus 129 ~~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f 169 (318)
.+.|+|..|+..+. .|+++.. ...|.|..|+-.+
T Consensus 110 ~~~y~C~~C~~~~~------~~rr~~~-~~~y~C~~C~g~l 143 (146)
T smart00731 110 KYPYRCTGCGQRYL------RVRRSNN-VSRYRCGKCGGKL 143 (146)
T ss_pred eEEEECCCCCCCCc------eEccccC-cceEEcCCCCCEE
Confidence 46899999998764 3443332 2568999898655
No 160
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=26.06 E-value=28 Score=22.11 Aligned_cols=15 Identities=27% Similarity=0.612 Sum_probs=10.2
Q ss_pred ceeecCCCccccCCh
Q 021063 225 KIHECSICGSEFTSG 239 (318)
Q Consensus 225 kpy~C~~Cgk~F~~~ 239 (318)
-|++|..|++.|=..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 689999999999754
No 161
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=25.87 E-value=35 Score=35.74 Aligned_cols=12 Identities=17% Similarity=0.473 Sum_probs=6.6
Q ss_pred eecCCCCCcCCC
Q 021063 132 YECKTCNRSFPS 143 (318)
Q Consensus 132 y~C~~C~K~F~s 143 (318)
-.|..||..|..
T Consensus 436 l~C~~Cg~v~~C 447 (730)
T COG1198 436 LLCRDCGYIAEC 447 (730)
T ss_pred eecccCCCcccC
Confidence 356666655544
No 162
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=25.78 E-value=47 Score=26.21 Aligned_cols=28 Identities=25% Similarity=0.436 Sum_probs=19.3
Q ss_pred eeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCC
Q 021063 131 VYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKS 169 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f 169 (318)
.+.|..||..|..... .-+.|+.|+...
T Consensus 71 ~~~C~~Cg~~~~~~~~-----------~~~~CP~Cgs~~ 98 (117)
T PRK00564 71 ELECKDCSHVFKPNAL-----------DYGVCEKCHSKN 98 (117)
T ss_pred EEEhhhCCCccccCCc-----------cCCcCcCCCCCc
Confidence 6999999988866422 113499998543
No 163
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=25.64 E-value=38 Score=20.85 Aligned_cols=30 Identities=10% Similarity=0.212 Sum_probs=18.4
Q ss_pred eecCCCCCcCCCccchhhhhhhcCCCCCccCCCC
Q 021063 132 YECKTCNRSFPSFQALGGHRASHKKPKAALAEAP 165 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C 165 (318)
-.|+.|+.. ..+.+|-....|...|.|..|
T Consensus 6 v~CP~C~s~----~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 6 VHCPRCQST----EGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeCCCCCCC----CcceeCCCCCCCCEeEecCcC
Confidence 467777654 335566666666666777665
No 164
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=25.21 E-value=45 Score=23.00 Aligned_cols=11 Identities=27% Similarity=0.664 Sum_probs=9.4
Q ss_pred CceeecCCCcc
Q 021063 224 NKIHECSICGS 234 (318)
Q Consensus 224 ~kpy~C~~Cgk 234 (318)
..+|+|+.||.
T Consensus 46 ~~~Y~CP~CGF 56 (59)
T PRK14890 46 SNPYTCPKCGF 56 (59)
T ss_pred CCceECCCCCC
Confidence 57899999984
No 165
>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=24.78 E-value=36 Score=26.21 Aligned_cols=24 Identities=21% Similarity=0.426 Sum_probs=21.8
Q ss_pred eec----CCCCCcCCCccchhhhhhhcC
Q 021063 132 YEC----KTCNRSFPSFQALGGHRASHK 155 (318)
Q Consensus 132 y~C----~~C~K~F~s~~~L~~H~rsHt 155 (318)
|.| ..|+..+.+...+..|.+.+.
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 999 999999999999999988754
No 166
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=24.19 E-value=39 Score=27.42 Aligned_cols=25 Identities=20% Similarity=0.296 Sum_probs=20.9
Q ss_pred eecCCCCCcCCCccchhhhhhhcCCCCC
Q 021063 132 YECKTCNRSFPSFQALGGHRASHKKPKA 159 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rsHt~~kp 159 (318)
..|-+|||.|. .|++|+.+|-+-.|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 57999999984 69999999977655
No 167
>PRK04351 hypothetical protein; Provisional
Probab=24.01 E-value=41 Score=27.81 Aligned_cols=34 Identities=24% Similarity=0.461 Sum_probs=23.6
Q ss_pred CceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCCC
Q 021063 129 FYVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKSS 170 (318)
Q Consensus 129 ~~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f~ 170 (318)
.+.|.|..|+..+.+ +++ |. ...|.|..|+-.+.
T Consensus 110 ~y~Y~C~~Cg~~~~r------~Rr-~n-~~~yrCg~C~g~L~ 143 (149)
T PRK04351 110 NYLYECQSCGQQYLR------KRR-IN-TKRYRCGKCRGKLK 143 (149)
T ss_pred eEEEECCCCCCEeee------eee-cC-CCcEEeCCCCcEee
Confidence 478999999976643 222 32 36699999987653
No 168
>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=23.88 E-value=56 Score=20.06 Aligned_cols=30 Identities=10% Similarity=0.155 Sum_probs=17.1
Q ss_pred eecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCC
Q 021063 132 YECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKS 169 (318)
Q Consensus 132 y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f 169 (318)
+.|+.||+.|.-. .-....+-.|+.|+..+
T Consensus 2 r~C~~Cg~~Yh~~--------~~pP~~~~~Cd~cg~~L 31 (36)
T PF05191_consen 2 RICPKCGRIYHIE--------FNPPKVEGVCDNCGGEL 31 (36)
T ss_dssp EEETTTTEEEETT--------TB--SSTTBCTTTTEBE
T ss_pred cCcCCCCCccccc--------cCCCCCCCccCCCCCee
Confidence 5688999887532 22233345677776543
No 169
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=23.68 E-value=10 Score=33.00 Aligned_cols=46 Identities=22% Similarity=0.270 Sum_probs=31.4
Q ss_pred ecCCCCCcCCCccchhhhhh-hc---------CCCCCccCCC--CCCCCCCCcchhhc
Q 021063 133 ECKTCNRSFPSFQALGGHRA-SH---------KKPKAALAEA--PEKKSSASVPALAV 178 (318)
Q Consensus 133 ~C~~C~K~F~s~~~L~~H~r-sH---------t~~kp~~C~~--C~k~f~~~~~~~~h 178 (318)
.|.+|.|.|++...|..|.. .| .|.-.|.|-+ |..+|.+......|
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH 165 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDH 165 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhH
Confidence 79999999999999988864 24 3444577754 77777665333333
No 170
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=22.23 E-value=49 Score=21.14 Aligned_cols=16 Identities=31% Similarity=0.746 Sum_probs=13.1
Q ss_pred ecCCCccccCChhHHH
Q 021063 228 ECSICGSEFTSGQALG 243 (318)
Q Consensus 228 ~C~~Cgk~F~~~~~L~ 243 (318)
.|.+||+.|+....+.
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 5999999999876554
No 171
>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=21.81 E-value=45 Score=29.37 Aligned_cols=26 Identities=15% Similarity=0.291 Sum_probs=20.6
Q ss_pred CCceeecCCCCCcCCCccchhhhhhh
Q 021063 128 GFYVYECKTCNRSFPSFQALGGHRAS 153 (318)
Q Consensus 128 g~~~y~C~~C~K~F~s~~~L~~H~rs 153 (318)
.+..|.|+.|+|.|.-......|+..
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhh
Confidence 44579999999999999999999765
No 172
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=21.59 E-value=1e+02 Score=29.10 Aligned_cols=18 Identities=22% Similarity=0.228 Sum_probs=13.4
Q ss_pred cccCChhHHHHHhhhccC
Q 021063 234 SEFTSGQALGGHMRRHRA 251 (318)
Q Consensus 234 k~F~~~~~L~~H~r~H~~ 251 (318)
.+|...-.|..|+..-++
T Consensus 289 ~vf~~~~el~~h~~~~h~ 306 (493)
T COG5236 289 YVFPYHTELLEHLTRFHK 306 (493)
T ss_pred EEeccHHHHHHHHHHHhh
Confidence 478888899999765443
No 173
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=21.54 E-value=46 Score=25.46 Aligned_cols=15 Identities=33% Similarity=0.716 Sum_probs=13.0
Q ss_pred CceeecCCCccccCC
Q 021063 224 NKIHECSICGSEFTS 238 (318)
Q Consensus 224 ~kpy~C~~Cgk~F~~ 238 (318)
.+|++|..||..|.-
T Consensus 77 g~~~rC~eCG~~fkL 91 (97)
T cd00924 77 GKPKRCPECGHVFKL 91 (97)
T ss_pred CCceeCCCCCcEEEE
Confidence 489999999999863
No 174
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=21.45 E-value=28 Score=21.83 Aligned_cols=9 Identities=0% Similarity=-0.034 Sum_probs=4.0
Q ss_pred ccCCCCCCC
Q 021063 160 ALAEAPEKK 168 (318)
Q Consensus 160 ~~C~~C~k~ 168 (318)
|.|..|+..
T Consensus 29 y~C~~C~~~ 37 (40)
T smart00440 29 YVCTKCGHR 37 (40)
T ss_pred EEeCCCCCE
Confidence 444444443
No 175
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=21.22 E-value=47 Score=21.75 Aligned_cols=13 Identities=23% Similarity=0.825 Sum_probs=10.2
Q ss_pred eeecCCCccccCC
Q 021063 226 IHECSICGSEFTS 238 (318)
Q Consensus 226 py~C~~Cgk~F~~ 238 (318)
.|+|.+||..|--
T Consensus 1 ky~C~~CgyvYd~ 13 (47)
T PF00301_consen 1 KYQCPVCGYVYDP 13 (47)
T ss_dssp EEEETTTSBEEET
T ss_pred CcCCCCCCEEEcC
Confidence 4899999987753
No 176
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=21.00 E-value=59 Score=31.61 Aligned_cols=19 Identities=21% Similarity=0.478 Sum_probs=14.8
Q ss_pred CCceeecCCCccccCChhH
Q 021063 223 GNKIHECSICGSEFTSGQA 241 (318)
Q Consensus 223 g~kpy~C~~Cgk~F~~~~~ 241 (318)
|..-|+|..||..+....-
T Consensus 364 G~~g~rC~kCg~~~~~~~~ 382 (421)
T COG1571 364 GRNGFRCKKCGTRARETLI 382 (421)
T ss_pred CCCCcccccccccCCcccc
Confidence 4448999999998886643
No 177
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=20.85 E-value=66 Score=30.04 Aligned_cols=39 Identities=10% Similarity=0.028 Sum_probs=23.1
Q ss_pred CCceeecCCCCCcCCCccchhhhhhhcCCCCCccCCCCCCCC
Q 021063 128 GFYVYECKTCNRSFPSFQALGGHRASHKKPKAALAEAPEKKS 169 (318)
Q Consensus 128 g~~~y~C~~C~K~F~s~~~L~~H~rsHt~~kp~~C~~C~k~f 169 (318)
++..-.|++||..-. .+-+ +.....|.|-..|..|+-..
T Consensus 184 ~~~~~~CPvCGs~P~-~s~v--~~~~~~G~RyL~CslC~teW 222 (309)
T PRK03564 184 GEQRQFCPVCGSMPV-SSVV--QIGTTQGLRYLHCNLCESEW 222 (309)
T ss_pred ccCCCCCCCCCCcch-hhee--eccCCCCceEEEcCCCCCcc
Confidence 334578999997532 2211 22234566667788887654
No 178
>KOG0782 consensus Predicted diacylglycerol kinase [Signal transduction mechanisms]
Probab=20.78 E-value=32 Score=34.64 Aligned_cols=15 Identities=20% Similarity=0.441 Sum_probs=10.8
Q ss_pred eeecCCCccccCChh
Q 021063 226 IHECSICGSEFTSGQ 240 (318)
Q Consensus 226 py~C~~Cgk~F~~~~ 240 (318)
...|+.|...|-.+-
T Consensus 276 AisCSWCKqayH~Kv 290 (1004)
T KOG0782|consen 276 AISCSWCKQAYHLKV 290 (1004)
T ss_pred EEEehHHHHHhhcch
Confidence 457888888776654
No 179
>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=20.44 E-value=35 Score=22.80 Aligned_cols=27 Identities=22% Similarity=0.293 Sum_probs=16.3
Q ss_pred CceeecCCCCCcCCCccchhhhhhhcC
Q 021063 129 FYVYECKTCNRSFPSFQALGGHRASHK 155 (318)
Q Consensus 129 ~~~y~C~~C~K~F~s~~~L~~H~rsHt 155 (318)
...|+|+.|...|--.=.+-.|...|.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH~ 45 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLHN 45 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-S
T ss_pred CCeEECCCCCCccccCcChhhhccccC
Confidence 357999999999988778888877774
No 180
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=20.40 E-value=42 Score=22.30 Aligned_cols=12 Identities=42% Similarity=0.991 Sum_probs=9.9
Q ss_pred eecCCCccccCC
Q 021063 227 HECSICGSEFTS 238 (318)
Q Consensus 227 y~C~~Cgk~F~~ 238 (318)
|+|.+||..|.-
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 889999988763
No 181
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=20.21 E-value=26 Score=25.04 Aligned_cols=39 Identities=13% Similarity=0.194 Sum_probs=19.7
Q ss_pred eeecCCCCCcCCCcc---chhhhhhhcCCCCCccCCCCCCCC
Q 021063 131 VYECKTCNRSFPSFQ---ALGGHRASHKKPKAALAEAPEKKS 169 (318)
Q Consensus 131 ~y~C~~C~K~F~s~~---~L~~H~rsHt~~kp~~C~~C~k~f 169 (318)
-.+|+-|++.|+-.. .+..|.......+...|..|...+
T Consensus 10 ~~~~~cC~~~y~C~~CHde~~~H~~~~~~~~~v~Cg~C~~~~ 51 (71)
T PF05495_consen 10 AIRFPCCGKYYPCRFCHDELEDHPFDRWPVKRVICGKCRTEQ 51 (71)
T ss_dssp EEEETTTTEEESSHHHHHHCSSS---TTT--EEEETTT--EE
T ss_pred EEECCcccCeecHHHHHHHhccCccccccccCeECCCCCCcc
Confidence 477888888887653 344443333333455666666544
Done!