Query 038614
Match_columns 263
No_of_seqs 321 out of 1908
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 12:50:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038614.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038614hhsearch_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 99.8 4.8E-19 1E-23 153.3 5.4 106 121-228 128-242 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.7 6.5E-19 1.4E-23 152.5 2.3 127 91-223 133-265 (279)
3 KOG1074 Transcriptional repres 99.4 5.9E-14 1.3E-18 136.4 1.1 54 122-175 352-405 (958)
4 KOG3623 Homeobox transcription 99.3 9.3E-14 2E-18 133.2 -1.3 77 149-225 892-974 (1007)
5 KOG3576 Ovo and related transc 99.2 1.3E-12 2.8E-17 108.9 -0.7 110 120-229 114-240 (267)
6 KOG3576 Ovo and related transc 99.2 3.6E-12 7.9E-17 106.2 -0.1 79 148-226 114-199 (267)
7 KOG1074 Transcriptional repres 99.0 7.8E-11 1.7E-15 115.0 1.0 88 122-227 604-694 (958)
8 KOG3623 Homeobox transcription 99.0 1.1E-10 2.4E-15 112.3 0.6 98 124-222 211-330 (1007)
9 PHA02768 hypothetical protein; 98.7 6.5E-09 1.4E-13 69.5 1.6 44 151-218 5-48 (55)
10 KOG3608 Zn finger proteins [Ge 98.7 9E-09 2E-13 92.3 2.8 129 87-225 236-377 (467)
11 KOG3608 Zn finger proteins [Ge 98.6 8.8E-09 1.9E-13 92.4 -0.6 112 113-226 197-317 (467)
12 PLN03086 PRLI-interacting fact 98.5 1.1E-07 2.4E-12 91.7 4.4 92 123-221 453-560 (567)
13 PHA00733 hypothetical protein 98.5 8.8E-08 1.9E-12 76.0 2.6 55 148-226 70-124 (128)
14 KOG3993 Transcription factor ( 98.3 1.2E-07 2.5E-12 87.0 -1.0 104 123-226 267-381 (500)
15 PHA02768 hypothetical protein; 98.2 4.1E-07 8.8E-12 60.9 0.8 44 124-169 6-49 (55)
16 PF13465 zf-H2C2_2: Zinc-finge 98.1 4.2E-07 9E-12 51.8 -0.2 23 191-213 4-26 (26)
17 PF13465 zf-H2C2_2: Zinc-finge 98.1 1.1E-06 2.5E-11 50.0 0.6 25 139-163 2-26 (26)
18 PHA00732 hypothetical protein 98.0 5.1E-06 1.1E-10 60.3 2.6 48 151-226 1-49 (79)
19 PHA00616 hypothetical protein 97.9 3E-06 6.5E-11 54.1 0.5 33 151-183 1-33 (44)
20 PLN03086 PRLI-interacting fact 97.9 1.5E-05 3.2E-10 77.2 4.7 72 149-224 451-537 (567)
21 PF00096 zf-C2H2: Zinc finger, 97.8 1.2E-05 2.6E-10 44.1 1.6 23 202-224 1-23 (23)
22 PHA00616 hypothetical protein 97.7 1.2E-05 2.6E-10 51.3 1.2 29 201-229 1-29 (44)
23 PHA00733 hypothetical protein 97.7 4.2E-05 9.1E-10 60.7 3.5 82 90-175 42-123 (128)
24 COG5189 SFP1 Putative transcri 97.6 3.4E-05 7.3E-10 68.8 2.3 70 149-222 347-419 (423)
25 PF13912 zf-C2H2_6: C2H2-type 97.5 5.1E-05 1.1E-09 43.2 1.5 26 201-226 1-26 (27)
26 PF13894 zf-C2H2_4: C2H2-type 97.3 0.00018 3.9E-09 39.2 1.8 23 202-224 1-23 (24)
27 PF00096 zf-C2H2: Zinc finger, 97.2 0.0001 2.2E-09 40.3 0.7 23 152-174 1-23 (23)
28 KOG3993 Transcription factor ( 97.1 0.00043 9.3E-09 64.0 3.8 54 122-175 294-380 (500)
29 PF13912 zf-C2H2_6: C2H2-type 97.1 0.00024 5.2E-09 40.4 1.1 26 151-176 1-26 (27)
30 PF12756 zf-C2H2_2: C2H2 type 97.0 0.00041 8.9E-09 51.5 2.1 72 153-225 1-74 (100)
31 smart00355 ZnF_C2H2 zinc finge 96.9 0.00065 1.4E-08 37.4 1.8 25 202-226 1-25 (26)
32 PF05605 zf-Di19: Drought indu 96.9 0.0012 2.7E-08 44.1 3.3 51 151-225 2-53 (54)
33 PHA00732 hypothetical protein 96.8 0.00065 1.4E-08 49.2 1.9 47 123-175 1-48 (79)
34 PF13894 zf-C2H2_4: C2H2-type 96.5 0.001 2.2E-08 36.1 0.8 23 152-174 1-23 (24)
35 smart00355 ZnF_C2H2 zinc finge 96.0 0.0042 9.2E-08 34.0 1.5 24 152-175 1-24 (26)
36 PF12874 zf-met: Zinc-finger o 95.7 0.0061 1.3E-07 33.7 1.4 23 202-224 1-23 (25)
37 PF09237 GAGA: GAGA factor; I 95.6 0.012 2.5E-07 38.7 2.5 29 198-226 21-49 (54)
38 PF12874 zf-met: Zinc-finger o 95.0 0.008 1.7E-07 33.2 0.3 23 152-174 1-23 (25)
39 PF13909 zf-H2C2_5: C2H2-type 95.0 0.017 3.6E-07 31.7 1.6 23 202-225 1-23 (24)
40 PF12171 zf-C2H2_jaz: Zinc-fin 94.7 0.015 3.2E-07 33.0 0.9 23 202-224 2-24 (27)
41 PRK04860 hypothetical protein; 94.6 0.018 3.8E-07 47.4 1.6 22 192-213 134-155 (160)
42 PF09237 GAGA: GAGA factor; I 94.3 0.026 5.7E-07 37.0 1.5 33 147-179 20-52 (54)
43 PF12171 zf-C2H2_jaz: Zinc-fin 94.1 0.029 6.3E-07 31.8 1.3 23 152-174 2-24 (27)
44 KOG1146 Homeobox protein [Gene 94.1 0.043 9.4E-07 57.6 3.4 78 146-223 460-540 (1406)
45 PF13913 zf-C2HC_2: zinc-finge 93.2 0.057 1.2E-06 30.2 1.5 21 202-223 3-23 (25)
46 KOG2893 Zn finger protein [Gen 93.1 0.026 5.6E-07 48.8 -0.1 47 125-175 12-59 (341)
47 PRK04860 hypothetical protein; 93.0 0.04 8.7E-07 45.3 1.0 36 150-189 118-153 (160)
48 PF12756 zf-C2H2_2: C2H2 type 92.9 0.05 1.1E-06 40.0 1.3 24 151-174 50-73 (100)
49 COG5189 SFP1 Putative transcri 92.8 0.064 1.4E-06 48.3 2.0 58 115-172 341-419 (423)
50 COG5048 FOG: Zn-finger [Genera 92.4 0.14 3E-06 47.0 3.7 60 122-181 288-353 (467)
51 PF05605 zf-Di19: Drought indu 91.6 0.13 2.8E-06 34.2 1.9 50 123-175 2-53 (54)
52 KOG2893 Zn finger protein [Gen 90.3 0.098 2.1E-06 45.4 0.5 30 198-227 31-61 (341)
53 COG5048 FOG: Zn-finger [Genera 89.7 0.16 3.5E-06 46.5 1.4 59 150-228 288-350 (467)
54 PF13909 zf-H2C2_5: C2H2-type 89.2 0.15 3.2E-06 27.8 0.4 23 152-175 1-23 (24)
55 smart00451 ZnF_U1 U1-like zinc 88.5 0.29 6.2E-06 29.0 1.5 23 201-223 3-25 (35)
56 smart00451 ZnF_U1 U1-like zinc 87.8 0.29 6.4E-06 29.0 1.2 23 151-173 3-25 (35)
57 PF09986 DUF2225: Uncharacteri 82.3 0.77 1.7E-05 39.5 1.7 24 149-172 3-26 (214)
58 KOG1146 Homeobox protein [Gene 82.1 0.67 1.5E-05 49.1 1.4 70 150-226 1283-1353(1406)
59 PF09538 FYDLN_acid: Protein o 72.8 2.2 4.8E-05 32.7 1.6 16 199-214 24-39 (108)
60 COG4049 Uncharacterized protei 69.0 2.1 4.5E-05 28.7 0.6 27 197-223 13-39 (65)
61 smart00614 ZnF_BED BED zinc fi 65.9 4.6 0.0001 26.1 1.8 25 201-225 18-48 (50)
62 PRK00464 nrdR transcriptional 65.0 3.3 7.2E-05 33.8 1.2 46 125-170 2-47 (154)
63 PF02892 zf-BED: BED zinc fing 64.9 4.9 0.00011 25.1 1.7 25 198-222 13-41 (45)
64 PF05443 ROS_MUCR: ROS/MUCR tr 63.9 4.1 8.9E-05 32.4 1.5 27 199-228 70-96 (132)
65 KOG4124 Putative transcription 63.4 3.7 8E-05 37.8 1.2 69 149-221 347-418 (442)
66 PF09538 FYDLN_acid: Protein o 62.4 5.3 0.00012 30.6 1.8 29 125-164 11-39 (108)
67 PRK12380 hydrogenase nickel in 61.5 12 0.00026 28.8 3.7 55 87-159 40-94 (113)
68 PRK03824 hypA hydrogenase nick 58.8 13 0.00029 29.5 3.6 68 87-160 40-116 (135)
69 PF09723 Zn-ribbon_8: Zinc rib 58.0 5.2 0.00011 25.0 0.9 31 122-159 4-34 (42)
70 COG1198 PriA Primosomal protei 57.1 8.3 0.00018 39.2 2.6 13 198-210 472-484 (730)
71 KOG4167 Predicted DNA-binding 55.4 2.8 6E-05 42.1 -1.0 26 201-226 792-817 (907)
72 PRK00398 rpoP DNA-directed RNA 54.8 7.4 0.00016 24.7 1.3 13 151-163 3-15 (46)
73 PRK03681 hypA hydrogenase nick 54.7 19 0.00041 27.7 3.7 57 87-160 40-96 (114)
74 COG4049 Uncharacterized protei 54.2 4.9 0.00011 27.0 0.3 27 146-172 12-38 (65)
75 PF06524 NOA36: NOA36 protein; 53.6 8.5 0.00019 34.0 1.8 103 113-228 132-236 (314)
76 PRK00564 hypA hydrogenase nick 53.1 21 0.00046 27.6 3.8 57 87-160 40-97 (117)
77 TIGR02098 MJ0042_CXXC MJ0042 f 53.1 9.7 0.00021 22.9 1.5 12 201-212 25-36 (38)
78 TIGR00100 hypA hydrogenase nic 52.1 21 0.00045 27.5 3.6 56 87-160 40-95 (115)
79 PF09845 DUF2072: Zn-ribbon co 51.7 7 0.00015 30.9 0.9 15 201-215 1-15 (131)
80 COG1592 Rubrerythrin [Energy p 51.4 8.6 0.00019 31.8 1.4 12 198-209 146-157 (166)
81 smart00734 ZnF_Rad18 Rad18-lik 51.3 10 0.00022 21.2 1.3 20 202-222 2-21 (26)
82 PF01155 HypA: Hydrogenase exp 51.1 7.4 0.00016 29.9 0.9 56 87-160 40-95 (113)
83 PF05443 ROS_MUCR: ROS/MUCR tr 50.7 7.2 0.00016 31.0 0.8 28 149-179 70-97 (132)
84 COG4957 Predicted transcriptio 50.1 7.2 0.00016 31.0 0.7 25 201-228 76-100 (148)
85 PF13717 zinc_ribbon_4: zinc-r 49.3 11 0.00025 22.7 1.4 33 125-162 4-36 (36)
86 PRK06266 transcription initiat 48.4 8.1 0.00017 32.3 0.8 19 149-167 115-133 (178)
87 TIGR00622 ssl1 transcription f 48.2 33 0.00071 26.5 4.0 28 199-226 79-106 (112)
88 PRK00762 hypA hydrogenase nick 46.8 28 0.00062 27.2 3.7 61 87-159 40-100 (124)
89 smart00531 TFIIE Transcription 46.2 16 0.00035 29.3 2.2 19 148-166 96-114 (147)
90 TIGR02300 FYDLN_acid conserved 45.7 16 0.00035 28.8 2.1 33 125-168 11-43 (129)
91 PF12013 DUF3505: Protein of u 45.5 14 0.00031 27.9 1.8 26 201-226 80-109 (109)
92 PF10571 UPF0547: Uncharacteri 44.8 11 0.00023 21.2 0.7 11 202-212 15-25 (26)
93 cd00350 rubredoxin_like Rubred 43.2 16 0.00035 21.5 1.3 24 124-159 2-25 (33)
94 COG1996 RPC10 DNA-directed RNA 43.0 13 0.00028 24.3 1.0 12 150-161 5-16 (49)
95 KOG4167 Predicted DNA-binding 42.2 5.1 0.00011 40.3 -1.5 27 150-176 791-817 (907)
96 PF13719 zinc_ribbon_5: zinc-r 42.1 16 0.00036 22.1 1.3 33 125-162 4-36 (37)
97 TIGR00373 conserved hypothetic 41.8 14 0.00031 30.1 1.3 21 147-167 105-125 (158)
98 KOG2186 Cell growth-regulating 41.2 16 0.00034 32.2 1.5 23 152-175 4-26 (276)
99 TIGR02605 CxxC_CxxC_SSSS putat 41.0 14 0.00031 23.8 1.0 31 122-159 4-34 (52)
100 COG3364 Zn-ribbon containing p 40.0 14 0.00031 27.9 0.9 16 201-216 2-17 (112)
101 smart00834 CxxC_CXXC_SSSS Puta 38.9 15 0.00032 22.2 0.8 16 201-216 5-20 (41)
102 smart00659 RPOLCX RNA polymera 38.4 21 0.00045 22.7 1.4 26 124-160 3-28 (44)
103 PRK14873 primosome assembly pr 37.9 17 0.00038 36.6 1.5 47 153-210 385-431 (665)
104 cd00924 Cyt_c_Oxidase_Vb Cytoc 37.6 16 0.00036 27.4 1.0 19 193-212 72-90 (97)
105 PF13878 zf-C2H2_3: zinc-finge 37.5 26 0.00057 21.7 1.7 24 202-225 14-39 (41)
106 TIGR00244 transcriptional regu 36.5 21 0.00045 28.9 1.4 45 125-169 2-46 (147)
107 PF07754 DUF1610: Domain of un 36.2 18 0.00039 20.0 0.7 11 199-209 14-24 (24)
108 PHA00626 hypothetical protein 35.8 18 0.0004 24.3 0.9 15 199-213 21-35 (59)
109 COG0375 HybF Zn finger protein 35.8 43 0.00092 26.0 3.0 55 86-158 39-93 (115)
110 KOG2231 Predicted E3 ubiquitin 35.8 20 0.00043 36.1 1.4 89 124-225 100-206 (669)
111 PF09986 DUF2225: Uncharacteri 34.2 12 0.00026 32.2 -0.3 25 199-223 3-27 (214)
112 KOG2071 mRNA cleavage and poly 34.1 23 0.0005 34.9 1.6 28 199-226 416-443 (579)
113 PF08790 zf-LYAR: LYAR-type C2 34.0 18 0.0004 20.7 0.6 21 202-223 1-21 (28)
114 COG3677 Transposase and inacti 33.9 26 0.00057 27.6 1.6 16 198-213 50-65 (129)
115 COG1997 RPL43A Ribosomal prote 33.5 31 0.00068 25.3 1.8 16 199-214 51-66 (89)
116 PRK04023 DNA polymerase II lar 33.2 43 0.00092 35.4 3.3 13 200-212 662-674 (1121)
117 KOG0320 Predicted E3 ubiquitin 32.7 21 0.00046 29.8 0.9 19 147-165 127-145 (187)
118 COG4957 Predicted transcriptio 31.4 19 0.00042 28.7 0.5 25 152-179 77-101 (148)
119 PF03604 DNA_RNApol_7kD: DNA d 31.3 34 0.00075 20.2 1.4 25 125-160 2-26 (32)
120 COG5236 Uncharacterized conser 31.2 35 0.00076 31.6 2.2 20 203-222 222-241 (493)
121 KOG2785 C2H2-type Zn-finger pr 30.8 15 0.00033 34.2 -0.2 72 152-223 4-90 (390)
122 COG1594 RPB9 DNA-directed RNA 29.2 26 0.00056 27.0 0.8 40 124-163 73-112 (113)
123 smart00154 ZnF_AN1 AN1-like Zi 28.5 30 0.00064 21.3 0.9 14 201-214 12-25 (39)
124 PLN02294 cytochrome c oxidase 28.4 28 0.00061 28.9 1.0 20 193-213 134-153 (174)
125 KOG3408 U1-like Zn-finger-cont 27.8 30 0.00064 27.1 0.9 26 198-223 54-79 (129)
126 PF15269 zf-C2H2_7: Zinc-finge 27.4 34 0.00074 21.9 1.0 25 201-225 20-44 (54)
127 PF04959 ARS2: Arsenite-resist 27.1 38 0.00081 29.2 1.6 26 198-223 74-99 (214)
128 KOG2186 Cell growth-regulating 26.5 29 0.00063 30.6 0.8 47 123-172 3-49 (276)
129 cd00729 rubredoxin_SM Rubredox 26.4 44 0.00096 19.8 1.3 24 124-159 3-26 (34)
130 PRK14890 putative Zn-ribbon RN 25.7 46 0.001 22.6 1.5 11 199-209 46-56 (59)
131 TIGR00595 priA primosomal prot 25.4 42 0.00091 32.7 1.7 48 153-210 215-262 (505)
132 PF01428 zf-AN1: AN1-like Zinc 25.2 30 0.00064 21.6 0.5 15 200-214 12-26 (43)
133 TIGR00143 hypF [NiFe] hydrogen 25.1 16 0.00035 37.2 -1.2 9 201-209 140-148 (711)
134 COG1327 Predicted transcriptio 24.6 44 0.00096 27.2 1.4 19 149-167 26-44 (156)
135 KOG2593 Transcription initiati 24.4 47 0.001 31.6 1.8 45 139-208 116-160 (436)
136 PRK09678 DNA-binding transcrip 23.6 31 0.00067 24.4 0.3 42 124-167 2-45 (72)
137 PF01096 TFIIS_C: Transcriptio 22.9 23 0.00049 21.7 -0.4 12 151-162 28-39 (39)
138 KOG2636 Splicing factor 3a, su 22.9 46 0.001 31.8 1.4 28 195-222 395-423 (497)
139 COG5236 Uncharacterized conser 22.7 59 0.0013 30.1 2.0 15 209-223 289-303 (493)
140 smart00440 ZnF_C2C2 C2C2 Zinc 22.4 44 0.00096 20.6 0.8 12 151-162 28-39 (40)
141 TIGR03510 XapX XapX domain. Th 22.2 35 0.00077 22.3 0.4 12 245-256 17-28 (49)
142 COG1773 Rubredoxin [Energy pro 22.1 40 0.00087 22.6 0.6 14 200-213 2-15 (55)
143 PF07975 C1_4: TFIIH C1-like d 21.8 40 0.00086 22.2 0.6 27 149-175 19-45 (51)
144 PRK05580 primosome assembly pr 21.8 59 0.0013 32.9 2.0 46 152-210 382-430 (679)
145 COG0068 HypF Hydrogenase matur 21.5 51 0.0011 33.4 1.5 53 154-209 126-181 (750)
146 KOG3408 U1-like Zn-finger-cont 20.9 42 0.0009 26.3 0.6 26 148-173 54-79 (129)
147 PF12013 DUF3505: Protein of u 20.3 54 0.0012 24.7 1.1 24 152-175 81-108 (109)
148 PF10276 zf-CHCC: Zinc-finger 20.3 47 0.001 20.7 0.6 12 200-211 28-39 (40)
149 PF04423 Rad50_zn_hook: Rad50 20.2 42 0.00091 21.9 0.4 12 203-214 22-33 (54)
150 PF04959 ARS2: Arsenite-resist 20.1 45 0.00097 28.8 0.7 28 148-175 74-101 (214)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.76 E-value=4.8e-19 Score=153.30 Aligned_cols=106 Identities=21% Similarity=0.296 Sum_probs=87.0
Q ss_pred CccccCCCCCCCcccccchhhhhcccC---CCCccccCcccccccChhhhhhhhhhcCCCcccccCCCCcccc------c
Q 038614 121 EYVRGKSDDGDNDEEEDKEEDESSLVS---RTNKYKCKTCKKEFRSYQALGGHKASHKKIKIHHNGSSDAAAA------G 191 (263)
Q Consensus 121 ~~~~~c~~c~~~~~~~~~~~~h~~~h~---~~kp~kC~~C~k~F~s~~~L~~H~~~H~~~kp~~~~~~~~~~~------~ 191 (263)
...+.|.+||+.+.....|.+|...|- ..+.+.|..|+|+|.+..+|..|+++|+ -++.|.+|++.|. .
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQG 205 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQG 205 (279)
T ss_pred CCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhc
Confidence 345688889998888888888887763 3677889999999999999999988888 4577888888762 3
Q ss_pred ccccccCCcceecCccccccCCchhhhhHhhhhcCCC
Q 038614 192 GDAVVMDQRVFKCPFCDKVFDSGQALGGHKKIHFTYL 228 (263)
Q Consensus 192 h~~~h~g~kp~~C~~Cgk~F~~~~~L~~H~r~H~~~~ 228 (263)
|+|+|||||||.|+.|+|+|...++|+.|+++|.+-.
T Consensus 206 HiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K 242 (279)
T KOG2462|consen 206 HIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVK 242 (279)
T ss_pred ccccccCCCCccCCcccchhcchHHHHHHHHhhcCCc
Confidence 8888999999999999999999999999999988754
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.73 E-value=6.5e-19 Score=152.50 Aligned_cols=127 Identities=19% Similarity=0.158 Sum_probs=106.2
Q ss_pred HHHHHHhhcccccccccccccccceeeccCCccccCCCCCCCcccccchhhhhcccCCCCccccCcccccccChhhhhhh
Q 038614 91 VAMCLLKLSRDNWLQKDKQVVVAEAVVDEDEYVRGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKEFRSYQALGGH 170 (263)
Q Consensus 91 ~a~cl~mlsr~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~F~s~~~L~~H 170 (263)
+..|..+++...-|....+ .+ ........+.|..|++.+.....|..|+++|+ -+++|.+|||.|....-|.+|
T Consensus 133 c~eCgk~ysT~snLsrHkQ---~H-~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGH 206 (279)
T KOG2462|consen 133 CPECGKSYSTSSNLSRHKQ---TH-RSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGH 206 (279)
T ss_pred ccccccccccccccchhhc---cc-ccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcc
Confidence 3347777777776653321 11 22233567899999999999999999999988 789999999999999999999
Q ss_pred hhhcCCCcccccCCCCccc-----cc-ccccccCCcceecCccccccCCchhhhhHhhh
Q 038614 171 KASHKKIKIHHNGSSDAAA-----AG-GDAVVMDQRVFKCPFCDKVFDSGQALGGHKKI 223 (263)
Q Consensus 171 ~~~H~~~kp~~~~~~~~~~-----~~-h~~~h~g~kp~~C~~Cgk~F~~~~~L~~H~r~ 223 (263)
+|+|+|||||.|.-|++.| ++ |+++|.+.|.|+|..|+|.|...+-|.+|.-.
T Consensus 207 iRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 207 IRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred cccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 9999999999988887766 33 99999999999999999999999999999754
No 3
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.39 E-value=5.9e-14 Score=136.39 Aligned_cols=54 Identities=11% Similarity=0.150 Sum_probs=50.5
Q ss_pred ccccCCCCCCCcccccchhhhhcccCCCCccccCcccccccChhhhhhhhhhcC
Q 038614 122 YVRGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKEFRSYQALGGHKASHK 175 (263)
Q Consensus 122 ~~~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~F~s~~~L~~H~~~H~ 175 (263)
...+|-.|.+.|...+.|+.|.+.|++++||+|.+||..|..+.+|+.|...|+
T Consensus 352 ~khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~ 405 (958)
T KOG1074|consen 352 FKHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHR 405 (958)
T ss_pred ccchhhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeeeeecc
Confidence 345899999999999999999999999999999999999999999999987776
No 4
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.34 E-value=9.3e-14 Score=133.16 Aligned_cols=77 Identities=21% Similarity=0.378 Sum_probs=50.5
Q ss_pred CCccccCcccccccChhhhhhhhhhcCCCcccccCCCCccc------ccccccccCCcceecCccccccCCchhhhhHhh
Q 038614 149 TNKYKCKTCKKEFRSYQALGGHKASHKKIKIHHNGSSDAAA------AGGDAVVMDQRVFKCPFCDKVFDSGQALGGHKK 222 (263)
Q Consensus 149 ~kp~kC~~C~k~F~s~~~L~~H~~~H~~~kp~~~~~~~~~~------~~h~~~h~g~kp~~C~~Cgk~F~~~~~L~~H~r 222 (263)
...|.|+.|+|+|...+.|.+|+--|+|.+||+|..|.+.| ..|.|+|.|+|||.|..|+|+|........||.
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhc
Confidence 34455555555555555555555555555555555554444 124555668899999999999999999999997
Q ss_pred hhc
Q 038614 223 IHF 225 (263)
Q Consensus 223 ~H~ 225 (263)
--+
T Consensus 972 HRY 974 (1007)
T KOG3623|consen 972 HRY 974 (1007)
T ss_pred cch
Confidence 544
No 5
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.22 E-value=1.3e-12 Score=108.85 Aligned_cols=110 Identities=15% Similarity=0.148 Sum_probs=87.2
Q ss_pred CCccccCCCCCCCcccccchhhhhcccCCCCccccCcccccccChhhhhhhhhhcCCCcccccCCCCccccc------cc
Q 038614 120 DEYVRGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKEFRSYQALGGHKASHKKIKIHHNGSSDAAAAG------GD 193 (263)
Q Consensus 120 ~~~~~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~F~s~~~L~~H~~~H~~~kp~~~~~~~~~~~~------h~ 193 (263)
+...+.|..|++.|.-..-|.+|++-|..-+.|.|..|||.|...-.|++|.++|+|.+||+|..|.+.|.+ |.
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 345678888999988877788888888888889999999999988889999999999999988888877632 32
Q ss_pred c-ccc----------CCcceecCccccccCCchhhhhHhhhhcCCCC
Q 038614 194 A-VVM----------DQRVFKCPFCDKVFDSGQALGGHKKIHFTYLA 229 (263)
Q Consensus 194 ~-~h~----------g~kp~~C~~Cgk~F~~~~~L~~H~r~H~~~~~ 229 (263)
+ +|. ..|.|.|..||.+-.....+..|.+.|....+
T Consensus 194 ~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 194 KKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred HHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 1 121 25678999999888888888888888876543
No 6
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.17 E-value=3.6e-12 Score=106.16 Aligned_cols=79 Identities=24% Similarity=0.456 Sum_probs=71.8
Q ss_pred CCCccccCcccccccChhhhhhhhhhcCCCcccccCCCCccc------ccccccccCCcceecCccccccCCchhhhhHh
Q 038614 148 RTNKYKCKTCKKEFRSYQALGGHKASHKKIKIHHNGSSDAAA------AGGDAVVMDQRVFKCPFCDKVFDSGQALGGHK 221 (263)
Q Consensus 148 ~~kp~kC~~C~k~F~s~~~L~~H~~~H~~~kp~~~~~~~~~~------~~h~~~h~g~kp~~C~~Cgk~F~~~~~L~~H~ 221 (263)
....|.|.+|+|.|.....|.+|++.|...|.|.|.||++.| .+|.|+|+|-+||+|..|+|+|.+...|..|.
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 455799999999999999999999999999999999999876 46999999999999999999999999999997
Q ss_pred h-hhcC
Q 038614 222 K-IHFT 226 (263)
Q Consensus 222 r-~H~~ 226 (263)
+ +|..
T Consensus 194 ~kvhgv 199 (267)
T KOG3576|consen 194 KKVHGV 199 (267)
T ss_pred HHHcCc
Confidence 5 5643
No 7
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.00 E-value=7.8e-11 Score=114.97 Aligned_cols=88 Identities=22% Similarity=0.274 Sum_probs=78.7
Q ss_pred ccccCCCCCCCcccccchhhhhcccCCCCccccCcccccccChhhhhhhhhhcCCCcccccCCCCcccccccccccCCcc
Q 038614 122 YVRGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKEFRSYQALGGHKASHKKIKIHHNGSSDAAAAGGDAVVMDQRV 201 (263)
Q Consensus 122 ~~~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~F~s~~~L~~H~~~H~~~kp~~~~~~~~~~~~h~~~h~g~kp 201 (263)
.+-+|-.|-+.....+.|+.|.++|+|++||+|.+||+.|..+.+|+.|+-+|+..-+++ -+
T Consensus 604 dPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R------------------~q 665 (958)
T KOG1074|consen 604 DPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPAR------------------VQ 665 (958)
T ss_pred CccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCcccc------------------cc
Confidence 344799999999999999999999999999999999999999999999999998654332 47
Q ss_pred eecC---ccccccCCchhhhhHhhhhcCC
Q 038614 202 FKCP---FCDKVFDSGQALGGHKKIHFTY 227 (263)
Q Consensus 202 ~~C~---~Cgk~F~~~~~L~~H~r~H~~~ 227 (263)
|.|+ +|.+.|..+-.|..|+|+|.++
T Consensus 666 ~ScP~~~ic~~kftn~V~lpQhIriH~~~ 694 (958)
T KOG1074|consen 666 FSCPSTFICQKKFTNAVTLPQHIRIHLGG 694 (958)
T ss_pred ccCCchhhhcccccccccccceEEeecCC
Confidence 8999 9999999999999999999965
No 8
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=98.97 E-value=1.1e-10 Score=112.34 Aligned_cols=98 Identities=15% Similarity=0.218 Sum_probs=62.2
Q ss_pred ccCCCCCCCcccccchhhhhcc---cCCCCccccCcccccccChhhhhhhhhhcCCC-------------cccccCCCCc
Q 038614 124 RGKSDDGDNDEEEDKEEDESSL---VSRTNKYKCKTCKKEFRSYQALGGHKASHKKI-------------KIHHNGSSDA 187 (263)
Q Consensus 124 ~~c~~c~~~~~~~~~~~~h~~~---h~~~kp~kC~~C~k~F~s~~~L~~H~~~H~~~-------------kp~~~~~~~~ 187 (263)
..|..|...+.....++.|++. .... .|.|..|..+|.+...|.+|+.+|... +-|+|..|++
T Consensus 211 ltcpycdrgykrltslkeHikyrhekne~-nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgK 289 (1007)
T KOG3623|consen 211 LTCPYCDRGYKRLTSLKEHIKYRHEKNEP-NFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGK 289 (1007)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHhhCCC-CCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccch
Confidence 3566666555555455554422 1222 255666666666666666666666532 2234666666
Q ss_pred cc------ccccccccCCcceecCccccccCCchhhhhHhh
Q 038614 188 AA------AGGDAVVMDQRVFKCPFCDKVFDSGQALGGHKK 222 (263)
Q Consensus 188 ~~------~~h~~~h~g~kp~~C~~Cgk~F~~~~~L~~H~r 222 (263)
.| ..|.|+|.|+|||+|+.|+|+|........||-
T Consensus 290 AFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmS 330 (1007)
T KOG3623|consen 290 AFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMS 330 (1007)
T ss_pred hhhhHHHHHhhheeecCCCCcCCcccccccccCCccccccc
Confidence 55 125667778999999999999999999999974
No 9
>PHA02768 hypothetical protein; Provisional
Probab=98.69 E-value=6.5e-09 Score=69.49 Aligned_cols=44 Identities=16% Similarity=0.311 Sum_probs=38.5
Q ss_pred ccccCcccccccChhhhhhhhhhcCCCcccccCCCCcccccccccccCCcceecCccccccCCchhhh
Q 038614 151 KYKCKTCKKEFRSYQALGGHKASHKKIKIHHNGSSDAAAAGGDAVVMDQRVFKCPFCDKVFDSGQALG 218 (263)
Q Consensus 151 p~kC~~C~k~F~s~~~L~~H~~~H~~~kp~~~~~~~~~~~~h~~~h~g~kp~~C~~Cgk~F~~~~~L~ 218 (263)
-|+|+.|||.|...++|..|+++|+ ++|+|..|++.|...+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~------------------------k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN------------------------TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC------------------------CcccCCcccceecccceeE
Confidence 3899999999999999999999886 4778999999998877663
No 10
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.68 E-value=9e-09 Score=92.33 Aligned_cols=129 Identities=16% Similarity=0.241 Sum_probs=100.6
Q ss_pred CHHHHHHHHHhhcccccccccccccccceeeccCCccccCCCCCCCcccccchhhhhcc-cCCCCccccCcccccccChh
Q 038614 87 SDREVAMCLLKLSRDNWLQKDKQVVVAEAVVDEDEYVRGKSDDGDNDEEEDKEEDESSL-VSRTNKYKCKTCKKEFRSYQ 165 (263)
Q Consensus 87 ~ee~~a~cl~mlsr~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~-h~~~kp~kC~~C~k~F~s~~ 165 (263)
.....+.|...|+.+..+.... ...+ ..++|..|+......+.|..|++. |...|||+|..|.+.|....
T Consensus 236 n~fqC~~C~KrFaTeklL~~Hv----~rHv-----n~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~es 306 (467)
T KOG3608|consen 236 NSFQCAQCFKRFATEKLLKSHV----VRHV-----NCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRES 306 (467)
T ss_pred CchHHHHHHHHHhHHHHHHHHH----HHhh-----hcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHH
Confidence 4567788888888888887332 1111 346899999999988899999864 77889999999999999999
Q ss_pred hhhhhhhhcCCCcccccCC--CCccc------ccccc-cccC--CcceecCccccccCCchhhhhHhhh-hc
Q 038614 166 ALGGHKASHKKIKIHHNGS--SDAAA------AGGDA-VVMD--QRVFKCPFCDKVFDSGQALGGHKKI-HF 225 (263)
Q Consensus 166 ~L~~H~~~H~~~kp~~~~~--~~~~~------~~h~~-~h~g--~kp~~C~~Cgk~F~~~~~L~~H~r~-H~ 225 (263)
.|..|..+|. +-.|.|.+ |..++ .+|.+ .|.| +-+|.|..|.+.|.++.+|..|++. |.
T Consensus 307 dL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~ 377 (467)
T KOG3608|consen 307 DLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHG 377 (467)
T ss_pred HHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhc
Confidence 9999999999 55688877 55443 23554 3445 4579999999999999999999754 44
No 11
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.57 E-value=8.8e-09 Score=92.41 Aligned_cols=112 Identities=21% Similarity=0.247 Sum_probs=78.1
Q ss_pred cceeeccCCccccCCCCCCCcccccchhhhhcccC--CCCccccCcccccccChhhhhhhhhhcCCCcccccCCCCcc--
Q 038614 113 AEAVVDEDEYVRGKSDDGDNDEEEDKEEDESSLVS--RTNKYKCKTCKKEFRSYQALGGHKASHKKIKIHHNGSSDAA-- 188 (263)
Q Consensus 113 ~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~h~--~~kp~kC~~C~k~F~s~~~L~~H~~~H~~~kp~~~~~~~~~-- 188 (263)
.+...+.+++..-|..||.-|.....+-.|.+-.+ ...+|+|..|.|.|.....|..|+..|-. -|+|..|+-.
T Consensus 197 eH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn--~ykCplCdmtc~ 274 (467)
T KOG3608|consen 197 EHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN--CYKCPLCDMTCS 274 (467)
T ss_pred HHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh--cccccccccCCC
Confidence 34445566666777777777777766666654333 33477888888888888888888777754 3556665532
Q ss_pred ----ccccccc-ccCCcceecCccccccCCchhhhhHhhhhcC
Q 038614 189 ----AAGGDAV-VMDQRVFKCPFCDKVFDSGQALGGHKKIHFT 226 (263)
Q Consensus 189 ----~~~h~~~-h~g~kp~~C~~Cgk~F~~~~~L~~H~r~H~~ 226 (263)
..+|++. |...|||+|..|.+.|...+.|.+|..+|..
T Consensus 275 ~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS~ 317 (467)
T KOG3608|consen 275 SASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHSK 317 (467)
T ss_pred ChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhccc
Confidence 2346553 6678899999999999999999999888874
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.48 E-value=1.1e-07 Score=91.73 Aligned_cols=92 Identities=12% Similarity=0.197 Sum_probs=69.2
Q ss_pred cccCCCCCCCcccccchhhhhcccCCCCccccCcccccccChhhhhhhhhhcCCCcccccCCCCcccc------------
Q 038614 123 VRGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKEFRSYQALGGHKASHKKIKIHHNGSSDAAAA------------ 190 (263)
Q Consensus 123 ~~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~F~s~~~L~~H~~~H~~~kp~~~~~~~~~~~------------ 190 (263)
.+.|..|++.|. ...+..|..+++ ++|.|. ||+.| ....|..|+++|...+++.|.||...+.
T Consensus 453 H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~ 527 (567)
T PLN03086 453 HVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRL 527 (567)
T ss_pred CccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhh
Confidence 347889988885 466788888774 789998 98755 5688899999999999999999886542
Q ss_pred ----cccccccCCcceecCccccccCCchhhhhHh
Q 038614 191 ----GGDAVVMDQRVFKCPFCDKVFDSGQALGGHK 221 (263)
Q Consensus 191 ----~h~~~h~g~kp~~C~~Cgk~F~~~~~L~~H~ 221 (263)
.|... .|.+++.|..||+.|... .|..|+
T Consensus 528 s~Lt~HE~~-CG~rt~~C~~Cgk~Vrlr-dm~~H~ 560 (567)
T PLN03086 528 RGMSEHESI-CGSRTAPCDSCGRSVMLK-EMDIHQ 560 (567)
T ss_pred hhHHHHHHh-cCCcceEccccCCeeeeh-hHHHHH
Confidence 24443 478899999999888664 445554
No 13
>PHA00733 hypothetical protein
Probab=98.46 E-value=8.8e-08 Score=75.96 Aligned_cols=55 Identities=24% Similarity=0.388 Sum_probs=44.4
Q ss_pred CCCccccCcccccccChhhhhhhhhhcCCCcccccCCCCcccccccccccCCcceecCccccccCCchhhhhHhhhhcC
Q 038614 148 RTNKYKCKTCKKEFRSYQALGGHKASHKKIKIHHNGSSDAAAAGGDAVVMDQRVFKCPFCDKVFDSGQALGGHKKIHFT 226 (263)
Q Consensus 148 ~~kp~kC~~C~k~F~s~~~L~~H~~~H~~~kp~~~~~~~~~~~~h~~~h~g~kp~~C~~Cgk~F~~~~~L~~H~r~H~~ 226 (263)
+.+||.|..|++.|.+...|..|++.|. .+|.|..|++.|.....|..|++...+
T Consensus 70 ~~kPy~C~~Cgk~Fss~s~L~~H~r~h~------------------------~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 70 AVSPYVCPLCLMPFSSSVSLKQHIRYTE------------------------HSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCccCCCCCCcCCCHHHHHHHHhcCC------------------------cCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 4678888888888888888877766542 368999999999999999999887543
No 14
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.27 E-value=1.2e-07 Score=86.98 Aligned_cols=104 Identities=18% Similarity=0.202 Sum_probs=73.5
Q ss_pred cccCCCCCCCcccccchhhhhcccCCCCccccCcccccccChhhhhhhhhhcCCCccccc--------CCCCccccc-cc
Q 038614 123 VRGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKEFRSYQALGGHKASHKKIKIHHN--------GSSDAAAAG-GD 193 (263)
Q Consensus 123 ~~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~F~s~~~L~~H~~~H~~~kp~~~--------~~~~~~~~~-h~ 193 (263)
.|.|..|-..+++.-.|..|.-.....--|+|..|+|+|.-..+|..|+|.|+-..-... ........+ -.
T Consensus 267 dyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 267 DYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 467999999998887788886444444569999999999999999999999985432211 000000000 01
Q ss_pred ccc--cCCcceecCccccccCCchhhhhHhhhhcC
Q 038614 194 AVV--MDQRVFKCPFCDKVFDSGQALGGHKKIHFT 226 (263)
Q Consensus 194 ~~h--~g~kp~~C~~Cgk~F~~~~~L~~H~r~H~~ 226 (263)
+.. ..+-.|.|.+|+|.|.....|+.|+.+|..
T Consensus 347 rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred ccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 111 113489999999999999999999988874
No 15
>PHA02768 hypothetical protein; Provisional
Probab=98.21 E-value=4.1e-07 Score=60.87 Aligned_cols=44 Identities=9% Similarity=-0.101 Sum_probs=40.2
Q ss_pred ccCCCCCCCcccccchhhhhcccCCCCccccCcccccccChhhhhh
Q 038614 124 RGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKEFRSYQALGG 169 (263)
Q Consensus 124 ~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~F~s~~~L~~ 169 (263)
|.|++||+.|...+.|..|+++|+ ++|+|..|++.|.+.+.|..
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~~ 49 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYIE 49 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecccceeEE
Confidence 589999999999999999999999 79999999999998877653
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=98.13 E-value=4.2e-07 Score=51.81 Aligned_cols=23 Identities=26% Similarity=0.707 Sum_probs=18.4
Q ss_pred cccccccCCcceecCccccccCC
Q 038614 191 GGDAVVMDQRVFKCPFCDKVFDS 213 (263)
Q Consensus 191 ~h~~~h~g~kp~~C~~Cgk~F~~ 213 (263)
+|+++|+|+|||.|++|++.|.+
T Consensus 4 ~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 4 RHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHSSSSSEEESSSSEEESS
T ss_pred HHhhhcCCCCCCCCCCCcCeeCc
Confidence 45566668899999999999964
No 17
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.06 E-value=1.1e-06 Score=49.97 Aligned_cols=25 Identities=24% Similarity=0.466 Sum_probs=22.1
Q ss_pred hhhhhcccCCCCccccCcccccccC
Q 038614 139 EEDESSLVSRTNKYKCKTCKKEFRS 163 (263)
Q Consensus 139 ~~~h~~~h~~~kp~kC~~C~k~F~s 163 (263)
|..|+++|++++||+|..|++.|.+
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 5689999999999999999999863
No 18
>PHA00732 hypothetical protein
Probab=97.96 E-value=5.1e-06 Score=60.26 Aligned_cols=48 Identities=29% Similarity=0.589 Sum_probs=38.2
Q ss_pred ccccCcccccccChhhhhhhhhh-cCCCcccccCCCCcccccccccccCCcceecCccccccCCchhhhhHhhhhcC
Q 038614 151 KYKCKTCKKEFRSYQALGGHKAS-HKKIKIHHNGSSDAAAAGGDAVVMDQRVFKCPFCDKVFDSGQALGGHKKIHFT 226 (263)
Q Consensus 151 p~kC~~C~k~F~s~~~L~~H~~~-H~~~kp~~~~~~~~~~~~h~~~h~g~kp~~C~~Cgk~F~~~~~L~~H~r~H~~ 226 (263)
||.|..|++.|.+...|..|++. |. ++.|+.|++.|. .|..|.+++..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~-------------------------~~~C~~CgKsF~---~l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT-------------------------LTKCPVCNKSYR---RLNQHFYSQYD 49 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC-------------------------CCccCCCCCEeC---ChhhhhcccCC
Confidence 58899999999999999999874 43 246999999997 47778766554
No 19
>PHA00616 hypothetical protein
Probab=97.91 E-value=3e-06 Score=54.07 Aligned_cols=33 Identities=24% Similarity=0.293 Sum_probs=29.8
Q ss_pred ccccCcccccccChhhhhhhhhhcCCCcccccC
Q 038614 151 KYKCKTCKKEFRSYQALGGHKASHKKIKIHHNG 183 (263)
Q Consensus 151 p~kC~~C~k~F~s~~~L~~H~~~H~~~kp~~~~ 183 (263)
||+|..||+.|..++.|..|++.|+|++++.+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 699999999999999999999999988877643
No 20
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.86 E-value=1.5e-05 Score=77.20 Aligned_cols=72 Identities=18% Similarity=0.425 Sum_probs=58.9
Q ss_pred CCccccCcccccccChhhhhhhhhhcCCCcccccCCCCccc-----ccccccccCCcceecCccccccCCc---------
Q 038614 149 TNKYKCKTCKKEFRSYQALGGHKASHKKIKIHHNGSSDAAA-----AGGDAVVMDQRVFKCPFCDKVFDSG--------- 214 (263)
Q Consensus 149 ~kp~kC~~C~k~F~s~~~L~~H~~~H~~~kp~~~~~~~~~~-----~~h~~~h~g~kp~~C~~Cgk~F~~~--------- 214 (263)
++.+.|..|++.|. ...|..|+++|. +++.|. |+..+ ..|..+|.+.+++.|.+|++.|..+
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~ 526 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVLEKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDR 526 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCcchhHHHhhhhccCCCCceeCCCCCCccccCccccchhhh
Confidence 45679999999996 678999999985 778887 87543 3488889999999999999999633
Q ss_pred -hhhhhHhhhh
Q 038614 215 -QALGGHKKIH 224 (263)
Q Consensus 215 -~~L~~H~r~H 224 (263)
..|..|..++
T Consensus 527 ~s~Lt~HE~~C 537 (567)
T PLN03086 527 LRGMSEHESIC 537 (567)
T ss_pred hhhHHHHHHhc
Confidence 4789999886
No 21
>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=97.79 E-value=1.2e-05 Score=44.07 Aligned_cols=23 Identities=43% Similarity=0.920 Sum_probs=21.9
Q ss_pred eecCccccccCCchhhhhHhhhh
Q 038614 202 FKCPFCDKVFDSGQALGGHKKIH 224 (263)
Q Consensus 202 ~~C~~Cgk~F~~~~~L~~H~r~H 224 (263)
|.|+.|++.|.+...|..|++.|
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 78999999999999999999986
No 22
>PHA00616 hypothetical protein
Probab=97.73 E-value=1.2e-05 Score=51.30 Aligned_cols=29 Identities=14% Similarity=0.282 Sum_probs=27.0
Q ss_pred ceecCccccccCCchhhhhHhhhhcCCCC
Q 038614 201 VFKCPFCDKVFDSGQALGGHKKIHFTYLA 229 (263)
Q Consensus 201 p~~C~~Cgk~F~~~~~L~~H~r~H~~~~~ 229 (263)
||+|+.||+.|.+.+.|..|++.|+++..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~ 29 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK 29 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc
Confidence 69999999999999999999999999744
No 23
>PHA00733 hypothetical protein
Probab=97.66 E-value=4.2e-05 Score=60.65 Aligned_cols=82 Identities=11% Similarity=0.016 Sum_probs=58.8
Q ss_pred HHHHHHHhhcccccccccccccccceeeccCCccccCCCCCCCcccccchhhhhcccCCCCccccCcccccccChhhhhh
Q 038614 90 EVAMCLLKLSRDNWLQKDKQVVVAEAVVDEDEYVRGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKEFRSYQALGG 169 (263)
Q Consensus 90 ~~a~cl~mlsr~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~F~s~~~L~~ 169 (263)
..++|-..+.....+..... + ...+...+..++.|..|++.|.....+..|++.+ ..+|.|.+|++.|.....|..
T Consensus 42 ~~~~~~~~~~~~~~l~~~~~-l-~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~ 117 (128)
T PHA00733 42 IRAVVKTLIYNPQLLDESSY-L-YKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNTDSTLD 117 (128)
T ss_pred HHHHHhhhccChhhhcchHH-H-HhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCHHHHHH
Confidence 34456666665555542210 0 1112333467889999999999999999999876 457999999999999999999
Q ss_pred hhhhcC
Q 038614 170 HKASHK 175 (263)
Q Consensus 170 H~~~H~ 175 (263)
|++...
T Consensus 118 H~~~~h 123 (128)
T PHA00733 118 HVCKKH 123 (128)
T ss_pred HHHHhc
Confidence 987654
No 24
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.59 E-value=3.4e-05 Score=68.78 Aligned_cols=70 Identities=26% Similarity=0.564 Sum_probs=50.1
Q ss_pred CCccccCc--ccccccChhhhhhhhhh-cCCCcccccCCCCcccccccccccCCcceecCccccccCCchhhhhHhh
Q 038614 149 TNKYKCKT--CKKEFRSYQALGGHKAS-HKKIKIHHNGSSDAAAAGGDAVVMDQRVFKCPFCDKVFDSGQALGGHKK 222 (263)
Q Consensus 149 ~kp~kC~~--C~k~F~s~~~L~~H~~~-H~~~kp~~~~~~~~~~~~h~~~h~g~kp~~C~~Cgk~F~~~~~L~~H~r 222 (263)
+|||+|++ |.|.+.....|+.|+.- |...+..... .-..+.-.....|||.|++|+|++.....|+.|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p----~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENP----SPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCC----CccccccccccCCceeccccchhhccCccceeccc
Confidence 48999987 99999999999999753 4333222100 11122223446799999999999999999999864
No 25
>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=97.50 E-value=5.1e-05 Score=43.23 Aligned_cols=26 Identities=42% Similarity=0.705 Sum_probs=24.4
Q ss_pred ceecCccccccCCchhhhhHhhhhcC
Q 038614 201 VFKCPFCDKVFDSGQALGGHKKIHFT 226 (263)
Q Consensus 201 p~~C~~Cgk~F~~~~~L~~H~r~H~~ 226 (263)
||.|..|++.|.+...|..|++.|..
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 68999999999999999999999864
No 26
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.26 E-value=0.00018 Score=39.20 Aligned_cols=23 Identities=43% Similarity=0.943 Sum_probs=19.9
Q ss_pred eecCccccccCCchhhhhHhhhh
Q 038614 202 FKCPFCDKVFDSGQALGGHKKIH 224 (263)
Q Consensus 202 ~~C~~Cgk~F~~~~~L~~H~r~H 224 (263)
|.|++|++.|.+...|..|+++|
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 78999999999999999999987
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.24 E-value=0.0001 Score=40.31 Aligned_cols=23 Identities=43% Similarity=0.777 Sum_probs=21.4
Q ss_pred cccCcccccccChhhhhhhhhhc
Q 038614 152 YKCKTCKKEFRSYQALGGHKASH 174 (263)
Q Consensus 152 ~kC~~C~k~F~s~~~L~~H~~~H 174 (263)
|+|..|++.|.....|..|++.|
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 78999999999999999999875
No 28
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.12 E-value=0.00043 Score=64.04 Aligned_cols=54 Identities=17% Similarity=0.222 Sum_probs=45.3
Q ss_pred ccccCCCCCCCcccccchhhhhcccCC---------------------------------CCccccCcccccccChhhhh
Q 038614 122 YVRGKSDDGDNDEEEDKEEDESSLVSR---------------------------------TNKYKCKTCKKEFRSYQALG 168 (263)
Q Consensus 122 ~~~~c~~c~~~~~~~~~~~~h~~~h~~---------------------------------~kp~kC~~C~k~F~s~~~L~ 168 (263)
..|.|.+|++.|...-+|..|.|-|.- ..-|.|..|+|.|+....|.
T Consensus 294 vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLr 373 (500)
T KOG3993|consen 294 VEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLR 373 (500)
T ss_pred eeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHH
Confidence 357999999999999999888876631 12488999999999999999
Q ss_pred hhhhhcC
Q 038614 169 GHKASHK 175 (263)
Q Consensus 169 ~H~~~H~ 175 (263)
.|+.+|.
T Consensus 374 KHqlthq 380 (500)
T KOG3993|consen 374 KHQLTHQ 380 (500)
T ss_pred HhHHhhh
Confidence 9987775
No 29
>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=97.06 E-value=0.00024 Score=40.37 Aligned_cols=26 Identities=42% Similarity=0.756 Sum_probs=23.8
Q ss_pred ccccCcccccccChhhhhhhhhhcCC
Q 038614 151 KYKCKTCKKEFRSYQALGGHKASHKK 176 (263)
Q Consensus 151 p~kC~~C~k~F~s~~~L~~H~~~H~~ 176 (263)
+|+|..|++.|....+|..|++.|.+
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 68999999999999999999998853
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.00 E-value=0.00041 Score=51.46 Aligned_cols=72 Identities=24% Similarity=0.405 Sum_probs=22.4
Q ss_pred ccCcccccccChhhhhhhhhhcCCCc-ccccCCCCc-ccccccccccCCcceecCccccccCCchhhhhHhhhhc
Q 038614 153 KCKTCKKEFRSYQALGGHKASHKKIK-IHHNGSSDA-AAAGGDAVVMDQRVFKCPFCDKVFDSGQALGGHKKIHF 225 (263)
Q Consensus 153 kC~~C~k~F~s~~~L~~H~~~H~~~k-p~~~~~~~~-~~~~h~~~h~g~kp~~C~~Cgk~F~~~~~L~~H~r~H~ 225 (263)
+|..|+..|.....|..|+....+.. +-...+... ....+.+.. -...+.|..|++.|.+...|..|++.+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~-~~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKK-VKESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp -------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred Cccccccccccccccccccccccccccccccccccccccccccccc-cCCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 58899999999999999986543322 111111111 111121111 1237999999999999999999999753
No 31
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.89 E-value=0.00065 Score=37.40 Aligned_cols=25 Identities=44% Similarity=0.852 Sum_probs=22.9
Q ss_pred eecCccccccCCchhhhhHhhhhcC
Q 038614 202 FKCPFCDKVFDSGQALGGHKKIHFT 226 (263)
Q Consensus 202 ~~C~~Cgk~F~~~~~L~~H~r~H~~ 226 (263)
|.|..|++.|.....|..|++.|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~~ 25 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHXX 25 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhcc
Confidence 6899999999999999999998864
No 32
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=96.85 E-value=0.0012 Score=44.08 Aligned_cols=51 Identities=24% Similarity=0.436 Sum_probs=38.5
Q ss_pred ccccCcccccccChhhhhhhhh-hcCCCcccccCCCCcccccccccccCCcceecCccccccCCchhhhhHhhhhc
Q 038614 151 KYKCKTCKKEFRSYQALGGHKA-SHKKIKIHHNGSSDAAAAGGDAVVMDQRVFKCPFCDKVFDSGQALGGHKKIHF 225 (263)
Q Consensus 151 p~kC~~C~k~F~s~~~L~~H~~-~H~~~kp~~~~~~~~~~~~h~~~h~g~kp~~C~~Cgk~F~~~~~L~~H~r~H~ 225 (263)
.|.|+.|++. .....|..|.. .|..+ .+.+.|++|...+. ..|..|++.+.
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~---------------------~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSE---------------------SKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCC---------------------CCCccCCCchhhhh--hHHHHHHHHhc
Confidence 4899999995 55678999955 35432 35789999998765 48999988754
No 33
>PHA00732 hypothetical protein
Probab=96.82 E-value=0.00065 Score=49.23 Aligned_cols=47 Identities=19% Similarity=0.136 Sum_probs=38.3
Q ss_pred cccCCCCCCCcccccchhhhhcc-cCCCCccccCcccccccChhhhhhhhhhcC
Q 038614 123 VRGKSDDGDNDEEEDKEEDESSL-VSRTNKYKCKTCKKEFRSYQALGGHKASHK 175 (263)
Q Consensus 123 ~~~c~~c~~~~~~~~~~~~h~~~-h~~~kp~kC~~C~k~F~s~~~L~~H~~~H~ 175 (263)
++.|..|++.|.....+..|++. |. ++.|..|++.|. .|..|..++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CCccCCCCCEeC---ChhhhhcccC
Confidence 36799999999999999999874 55 468999999998 4777875544
No 34
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=96.50 E-value=0.001 Score=36.06 Aligned_cols=23 Identities=39% Similarity=0.814 Sum_probs=19.4
Q ss_pred cccCcccccccChhhhhhhhhhc
Q 038614 152 YKCKTCKKEFRSYQALGGHKASH 174 (263)
Q Consensus 152 ~kC~~C~k~F~s~~~L~~H~~~H 174 (263)
|.|..|++.|.+...|..|++.|
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 68999999999999999998875
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=95.97 E-value=0.0042 Score=33.97 Aligned_cols=24 Identities=42% Similarity=0.809 Sum_probs=21.8
Q ss_pred cccCcccccccChhhhhhhhhhcC
Q 038614 152 YKCKTCKKEFRSYQALGGHKASHK 175 (263)
Q Consensus 152 ~kC~~C~k~F~s~~~L~~H~~~H~ 175 (263)
|+|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 689999999999999999998775
No 36
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=95.69 E-value=0.0061 Score=33.73 Aligned_cols=23 Identities=35% Similarity=0.735 Sum_probs=21.3
Q ss_pred eecCccccccCCchhhhhHhhhh
Q 038614 202 FKCPFCDKVFDSGQALGGHKKIH 224 (263)
Q Consensus 202 ~~C~~Cgk~F~~~~~L~~H~r~H 224 (263)
|.|.+|++.|.+...|..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 68999999999999999999865
No 37
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=95.57 E-value=0.012 Score=38.67 Aligned_cols=29 Identities=24% Similarity=0.533 Sum_probs=21.4
Q ss_pred CCcceecCccccccCCchhhhhHhhhhcC
Q 038614 198 DQRVFKCPFCDKVFDSGQALGGHKKIHFT 226 (263)
Q Consensus 198 g~kp~~C~~Cgk~F~~~~~L~~H~r~H~~ 226 (263)
.+.|..|++|+..+.+..+|.+|+.++.+
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhc
Confidence 46799999999999999999999987665
No 38
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.97 E-value=0.008 Score=33.23 Aligned_cols=23 Identities=35% Similarity=0.671 Sum_probs=21.1
Q ss_pred cccCcccccccChhhhhhhhhhc
Q 038614 152 YKCKTCKKEFRSYQALGGHKASH 174 (263)
Q Consensus 152 ~kC~~C~k~F~s~~~L~~H~~~H 174 (263)
|.|.+|++.|.+...|..|++++
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 67999999999999999998865
No 39
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.96 E-value=0.017 Score=31.69 Aligned_cols=23 Identities=35% Similarity=0.664 Sum_probs=18.8
Q ss_pred eecCccccccCCchhhhhHhhhhc
Q 038614 202 FKCPFCDKVFDSGQALGGHKKIHF 225 (263)
Q Consensus 202 ~~C~~Cgk~F~~~~~L~~H~r~H~ 225 (263)
|+|+.|..... ...|..|++.|.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 78999999998 889999999864
No 40
>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=94.66 E-value=0.015 Score=33.02 Aligned_cols=23 Identities=43% Similarity=0.719 Sum_probs=20.9
Q ss_pred eecCccccccCCchhhhhHhhhh
Q 038614 202 FKCPFCDKVFDSGQALGGHKKIH 224 (263)
Q Consensus 202 ~~C~~Cgk~F~~~~~L~~H~r~H 224 (263)
|-|..|++.|.+...|..|++..
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 41
>PRK04860 hypothetical protein; Provisional
Probab=94.62 E-value=0.018 Score=47.42 Aligned_cols=22 Identities=23% Similarity=0.519 Sum_probs=15.2
Q ss_pred ccccccCCcceecCccccccCC
Q 038614 192 GDAVVMDQRVFKCPFCDKVFDS 213 (263)
Q Consensus 192 h~~~h~g~kp~~C~~Cgk~F~~ 213 (263)
|.++|+++++|.|..|++.|..
T Consensus 134 H~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 134 HNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred HHHHhcCCccEECCCCCceeEE
Confidence 4445556778888888887754
No 42
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=94.28 E-value=0.026 Score=37.03 Aligned_cols=33 Identities=18% Similarity=0.224 Sum_probs=23.5
Q ss_pred CCCCccccCcccccccChhhhhhhhhhcCCCcc
Q 038614 147 SRTNKYKCKTCKKEFRSYQALGGHKASHKKIKI 179 (263)
Q Consensus 147 ~~~kp~kC~~C~k~F~s~~~L~~H~~~H~~~kp 179 (263)
..+.|..|.+|+..+.+..+|.+|+.++.+.||
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 356789999999999999999999988776664
No 43
>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=94.10 E-value=0.029 Score=31.76 Aligned_cols=23 Identities=35% Similarity=0.635 Sum_probs=20.8
Q ss_pred cccCcccccccChhhhhhhhhhc
Q 038614 152 YKCKTCKKEFRSYQALGGHKASH 174 (263)
Q Consensus 152 ~kC~~C~k~F~s~~~L~~H~~~H 174 (263)
|.|..|++.|.....|..|+++.
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 44
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=94.05 E-value=0.043 Score=57.58 Aligned_cols=78 Identities=19% Similarity=0.299 Sum_probs=53.1
Q ss_pred cCCCCccccCcccccccChhhhhhhhhh-cC-CCcccccCCCCcccc-cccccccCCcceecCccccccCCchhhhhHhh
Q 038614 146 VSRTNKYKCKTCKKEFRSYQALGGHKAS-HK-KIKIHHNGSSDAAAA-GGDAVVMDQRVFKCPFCDKVFDSGQALGGHKK 222 (263)
Q Consensus 146 h~~~kp~kC~~C~k~F~s~~~L~~H~~~-H~-~~kp~~~~~~~~~~~-~h~~~h~g~kp~~C~~Cgk~F~~~~~L~~H~r 222 (263)
+...+.|+|..|+..|...+.|..|+|+ |. ....|...+...... +......+-++|.|..|...|..+.+|-+|+.
T Consensus 460 ~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~Lsihlq 539 (1406)
T KOG1146|consen 460 HSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQ 539 (1406)
T ss_pred ecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHH
Confidence 5556889999999999999999999997 32 222121111100000 11111234679999999999999999999986
Q ss_pred h
Q 038614 223 I 223 (263)
Q Consensus 223 ~ 223 (263)
.
T Consensus 540 S 540 (1406)
T KOG1146|consen 540 S 540 (1406)
T ss_pred H
Confidence 4
No 45
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=93.23 E-value=0.057 Score=30.19 Aligned_cols=21 Identities=38% Similarity=0.877 Sum_probs=18.0
Q ss_pred eecCccccccCCchhhhhHhhh
Q 038614 202 FKCPFCDKVFDSGQALGGHKKI 223 (263)
Q Consensus 202 ~~C~~Cgk~F~~~~~L~~H~r~ 223 (263)
..|+.||+.| ....|..|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4799999999 67888999875
No 46
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=93.09 E-value=0.026 Score=48.85 Aligned_cols=47 Identities=21% Similarity=0.229 Sum_probs=38.9
Q ss_pred cCCCCCCCcccccchhhhhcccCCCCccccCcccccccChhhhhhh-hhhcC
Q 038614 125 GKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKEFRSYQALGGH-KASHK 175 (263)
Q Consensus 125 ~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~F~s~~~L~~H-~~~H~ 175 (263)
=||-|..+|+++..|..|++ .|-|+|.+|.|.+-+--.|..| +++|+
T Consensus 12 wcwycnrefddekiliqhqk----akhfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQK----AKHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred eeeecccccchhhhhhhhhh----hccceeeeehhhhccCCCceeehhhhhh
Confidence 38999999999888877764 4669999999988888888888 66776
No 47
>PRK04860 hypothetical protein; Provisional
Probab=93.03 E-value=0.04 Score=45.31 Aligned_cols=36 Identities=14% Similarity=0.301 Sum_probs=28.2
Q ss_pred CccccCcccccccChhhhhhhhhhcCCCcccccCCCCccc
Q 038614 150 NKYKCKTCKKEFRSYQALGGHKASHKKIKIHHNGSSDAAA 189 (263)
Q Consensus 150 kp~kC~~C~k~F~s~~~L~~H~~~H~~~kp~~~~~~~~~~ 189 (263)
-+|.|. |++ ....+.+|.++|+++++|.|..|...+
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l 153 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETL 153 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCcee
Confidence 368887 887 566778888888888888888887654
No 48
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=92.93 E-value=0.05 Score=39.99 Aligned_cols=24 Identities=42% Similarity=0.798 Sum_probs=21.4
Q ss_pred ccccCcccccccChhhhhhhhhhc
Q 038614 151 KYKCKTCKKEFRSYQALGGHKASH 174 (263)
Q Consensus 151 p~kC~~C~k~F~s~~~L~~H~~~H 174 (263)
.+.|..|++.|.+...|..|++.+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCc
Confidence 699999999999999999999865
No 49
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=92.84 E-value=0.064 Score=48.32 Aligned_cols=58 Identities=12% Similarity=0.241 Sum_probs=41.4
Q ss_pred eeeccCCccccCC--CCCCCcccccchhhhhcc-c------------------CCCCccccCcccccccChhhhhhhhh
Q 038614 115 AVVDEDEYVRGKS--DDGDNDEEEDKEEDESSL-V------------------SRTNKYKCKTCKKEFRSYQALGGHKA 172 (263)
Q Consensus 115 ~~~~~~~~~~~c~--~c~~~~~~~~~~~~h~~~-h------------------~~~kp~kC~~C~k~F~s~~~L~~H~~ 172 (263)
.+.--++++|.|. -|++.+....-|+.|+.- | ...|||+|++|+|.+.....|+.|+.
T Consensus 341 ~l~v~d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 341 MLKVKDGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred eeEeecCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 3444456888887 477877766555555421 1 23589999999999999999988865
No 50
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.36 E-value=0.14 Score=47.02 Aligned_cols=60 Identities=17% Similarity=0.122 Sum_probs=54.4
Q ss_pred ccccCCCCCCCcccccchhhhhc--ccCCC--CccccC--cccccccChhhhhhhhhhcCCCcccc
Q 038614 122 YVRGKSDDGDNDEEEDKEEDESS--LVSRT--NKYKCK--TCKKEFRSYQALGGHKASHKKIKIHH 181 (263)
Q Consensus 122 ~~~~c~~c~~~~~~~~~~~~h~~--~h~~~--kp~kC~--~C~k~F~s~~~L~~H~~~H~~~kp~~ 181 (263)
..+.|..|...+.....+..|.+ .|+++ +++.|. .|++.|.....+..|...|.+.+++.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAK 353 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccc
Confidence 46788899999999999999999 89999 999999 79999999999999999999887654
No 51
>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=91.59 E-value=0.13 Score=34.21 Aligned_cols=50 Identities=14% Similarity=0.112 Sum_probs=36.0
Q ss_pred cccCCCCCCCcccccchhhhhc-ccCC-CCccccCcccccccChhhhhhhhhhcC
Q 038614 123 VRGKSDDGDNDEEEDKEEDESS-LVSR-TNKYKCKTCKKEFRSYQALGGHKASHK 175 (263)
Q Consensus 123 ~~~c~~c~~~~~~~~~~~~h~~-~h~~-~kp~kC~~C~k~F~s~~~L~~H~~~H~ 175 (263)
.|.|.-|++.++ ...|..|.. .|.. .+.+.|++|...+. .+|..|+..+.
T Consensus 2 ~f~CP~C~~~~~-~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKGFS-ESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCccC-HHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 468999999544 567888864 3544 35799999998655 48888877643
No 52
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=90.35 E-value=0.098 Score=45.36 Aligned_cols=30 Identities=33% Similarity=0.583 Sum_probs=25.6
Q ss_pred CCcceecCccccccCCchhhhhH-hhhhcCC
Q 038614 198 DQRVFKCPFCDKVFDSGQALGGH-KKIHFTY 227 (263)
Q Consensus 198 g~kp~~C~~Cgk~F~~~~~L~~H-~r~H~~~ 227 (263)
..|.|+|.+|.|...++-.|..| +.+|..-
T Consensus 31 kakhfkchichkkl~sgpglsihcmqvhket 61 (341)
T KOG2893|consen 31 KAKHFKCHICHKKLFSGPGLSIHCMQVHKET 61 (341)
T ss_pred hhccceeeeehhhhccCCCceeehhhhhhhh
Confidence 46889999999999999999998 7788754
No 53
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=89.65 E-value=0.16 Score=46.54 Aligned_cols=59 Identities=29% Similarity=0.511 Sum_probs=43.5
Q ss_pred CccccCcccccccChhhhhhhhh--hcCCCcccccCCCCcccccccccccCCcceecC--ccccccCCchhhhhHhhhhc
Q 038614 150 NKYKCKTCKKEFRSYQALGGHKA--SHKKIKIHHNGSSDAAAAGGDAVVMDQRVFKCP--FCDKVFDSGQALGGHKKIHF 225 (263)
Q Consensus 150 kp~kC~~C~k~F~s~~~L~~H~~--~H~~~kp~~~~~~~~~~~~h~~~h~g~kp~~C~--~Cgk~F~~~~~L~~H~r~H~ 225 (263)
.++.|..|...|.....|..|.+ .|.++. .++|.|+ .|++.|.+...+..|..+|+
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~--------------------~~~~~~p~~~~~~~~~~~~~~~~~~~~~~ 347 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGES--------------------LKPFSCPYSLCGKLFSRNDALKRHILLHT 347 (467)
T ss_pred cCCCCccccCCcccccccccccccccccccc--------------------CCceeeeccCCCccccccccccCCccccc
Confidence 46888888888888888888877 455430 1677777 68888888888888888877
Q ss_pred CCC
Q 038614 226 TYL 228 (263)
Q Consensus 226 ~~~ 228 (263)
+-.
T Consensus 348 ~~~ 350 (467)
T COG5048 348 SIS 350 (467)
T ss_pred CCC
Confidence 643
No 54
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=89.15 E-value=0.15 Score=27.80 Aligned_cols=23 Identities=30% Similarity=0.559 Sum_probs=17.6
Q ss_pred cccCcccccccChhhhhhhhhhcC
Q 038614 152 YKCKTCKKEFRSYQALGGHKASHK 175 (263)
Q Consensus 152 ~kC~~C~k~F~s~~~L~~H~~~H~ 175 (263)
|+|..|..... ...|..|++.|.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 78999998887 889999988753
No 55
>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=88.52 E-value=0.29 Score=29.02 Aligned_cols=23 Identities=26% Similarity=0.530 Sum_probs=20.4
Q ss_pred ceecCccccccCCchhhhhHhhh
Q 038614 201 VFKCPFCDKVFDSGQALGGHKKI 223 (263)
Q Consensus 201 p~~C~~Cgk~F~~~~~L~~H~r~ 223 (263)
+|-|..|++.|....++..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999999999764
No 56
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=87.77 E-value=0.29 Score=28.98 Aligned_cols=23 Identities=22% Similarity=0.508 Sum_probs=20.3
Q ss_pred ccccCcccccccChhhhhhhhhh
Q 038614 151 KYKCKTCKKEFRSYQALGGHKAS 173 (263)
Q Consensus 151 p~kC~~C~k~F~s~~~L~~H~~~ 173 (263)
+|.|..|++.|....++..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999999888764
No 57
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=82.26 E-value=0.77 Score=39.51 Aligned_cols=24 Identities=29% Similarity=0.624 Sum_probs=18.0
Q ss_pred CCccccCcccccccChhhhhhhhh
Q 038614 149 TNKYKCKTCKKEFRSYQALGGHKA 172 (263)
Q Consensus 149 ~kp~kC~~C~k~F~s~~~L~~H~~ 172 (263)
++.+.|++|++.|....-..+..+
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r 26 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIR 26 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCce
Confidence 356899999999988766555544
No 58
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=82.14 E-value=0.67 Score=49.10 Aligned_cols=70 Identities=21% Similarity=0.363 Sum_probs=45.1
Q ss_pred CccccCcccccccChhhhhhhhhhcCCCcccccCCCCccc-ccccccccCCcceecCccccccCCchhhhhHhhhhcC
Q 038614 150 NKYKCKTCKKEFRSYQALGGHKASHKKIKIHHNGSSDAAA-AGGDAVVMDQRVFKCPFCDKVFDSGQALGGHKKIHFT 226 (263)
Q Consensus 150 kp~kC~~C~k~F~s~~~L~~H~~~H~~~kp~~~~~~~~~~-~~h~~~h~g~kp~~C~~Cgk~F~~~~~L~~H~r~H~~ 226 (263)
.+|.|..|.-.|.....|..|++ . +...+..... .-+...+-.-++| |..|...|....+|..|+|+-..
T Consensus 1283 ~~~~~~~~~~~~~~~~~l~~~~~--k----~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~~~~ 1353 (1406)
T KOG1146|consen 1283 HRYLCRQCKMAFDGEAPLTAHQR--K----FCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRSSAH 1353 (1406)
T ss_pred hhHHHHHHHhhhcchhHHHHHHH--H----HHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHHhhh
Confidence 45778888888888877777762 1 1001111110 1133334445678 99999999999999999997443
No 59
>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=72.79 E-value=2.2 Score=32.69 Aligned_cols=16 Identities=25% Similarity=0.629 Sum_probs=13.5
Q ss_pred CcceecCccccccCCc
Q 038614 199 QRVFKCPFCDKVFDSG 214 (263)
Q Consensus 199 ~kp~~C~~Cgk~F~~~ 214 (263)
..|-.|+.||..|.-.
T Consensus 24 k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 24 KDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCCccCCCCCCccCcc
Confidence 4688899999999776
No 60
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=68.95 E-value=2.1 Score=28.71 Aligned_cols=27 Identities=22% Similarity=0.466 Sum_probs=23.5
Q ss_pred cCCcceecCccccccCCchhhhhHhhh
Q 038614 197 MDQRVFKCPFCDKVFDSGQALGGHKKI 223 (263)
Q Consensus 197 ~g~kp~~C~~Cgk~F~~~~~L~~H~r~ 223 (263)
-|+--+.|+.||+.|.......+|...
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 367789999999999999999999754
No 61
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=65.92 E-value=4.6 Score=26.14 Aligned_cols=25 Identities=28% Similarity=0.525 Sum_probs=19.5
Q ss_pred ceecCccccccCCc-----hhhhhHhh-hhc
Q 038614 201 VFKCPFCDKVFDSG-----QALGGHKK-IHF 225 (263)
Q Consensus 201 p~~C~~Cgk~F~~~-----~~L~~H~r-~H~ 225 (263)
--.|..|++.+... ++|.+|++ .|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 34699999998765 58999988 564
No 62
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=65.00 E-value=3.3 Score=33.79 Aligned_cols=46 Identities=13% Similarity=0.167 Sum_probs=25.9
Q ss_pred cCCCCCCCcccccchhhhhcccCCCCccccCcccccccChhhhhhh
Q 038614 125 GKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKEFRSYQALGGH 170 (263)
Q Consensus 125 ~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~F~s~~~L~~H 170 (263)
.|..||..+..-.....-..-...++.|+|..||+.|..+-.+..-
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~~~~~ 47 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFERVELV 47 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEeccCc
Confidence 5888887663221111110101123349999999999987665543
No 63
>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=64.92 E-value=4.9 Score=25.12 Aligned_cols=25 Identities=36% Similarity=0.683 Sum_probs=16.3
Q ss_pred CCcceecCccccccCCc----hhhhhHhh
Q 038614 198 DQRVFKCPFCDKVFDSG----QALGGHKK 222 (263)
Q Consensus 198 g~kp~~C~~Cgk~F~~~----~~L~~H~r 222 (263)
+..-..|..|++.+... +.|..|++
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 45667899999998775 78888883
No 64
>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=63.91 E-value=4.1 Score=32.38 Aligned_cols=27 Identities=26% Similarity=0.447 Sum_probs=17.2
Q ss_pred CcceecCccccccCCchhhhhHhhhhcCCC
Q 038614 199 QRVFKCPFCDKVFDSGQALGGHKKIHFTYL 228 (263)
Q Consensus 199 ~kp~~C~~Cgk~F~~~~~L~~H~r~H~~~~ 228 (263)
+.-..|-+|||.|.. |.+|++.|+|-.
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~glt 96 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLT 96 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCC
Confidence 445689999999965 699999998753
No 65
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=63.37 E-value=3.7 Score=37.75 Aligned_cols=69 Identities=23% Similarity=0.509 Sum_probs=42.5
Q ss_pred CCccccCc--ccccccChhhhhhhhhh-cCCCcccccCCCCcccccccccccCCcceecCccccccCCchhhhhHh
Q 038614 149 TNKYKCKT--CKKEFRSYQALGGHKAS-HKKIKIHHNGSSDAAAAGGDAVVMDQRVFKCPFCDKVFDSGQALGGHK 221 (263)
Q Consensus 149 ~kp~kC~~--C~k~F~s~~~L~~H~~~-H~~~kp~~~~~~~~~~~~h~~~h~g~kp~~C~~Cgk~F~~~~~L~~H~ 221 (263)
.++|+|.+ |.+.+.....|..|... |... .. .-.+...-|.....-.|+|.|++|.+++...-.|..|.
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~--i~--~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~ 418 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSP--IT--TPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHR 418 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCC--CC--CCCCCCCCcceeeeccCcccChhhhhhhccCCCCCcee
Confidence 46899976 99998887777777542 2211 00 00001112333334579999999999988776666554
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=62.44 E-value=5.3 Score=30.61 Aligned_cols=29 Identities=17% Similarity=0.256 Sum_probs=21.2
Q ss_pred cCCCCCCCcccccchhhhhcccCCCCccccCcccccccCh
Q 038614 125 GKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKEFRSY 164 (263)
Q Consensus 125 ~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~F~s~ 164 (263)
.|..||..|... ++.|..|..||..|.-.
T Consensus 11 ~Cp~CG~kFYDL-----------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAKFYDL-----------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcchhccC-----------CCCCccCCCCCCccCcc
Confidence 688888888754 34677788888887655
No 67
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=61.54 E-value=12 Score=28.77 Aligned_cols=55 Identities=11% Similarity=0.027 Sum_probs=37.7
Q ss_pred CHHHHHHHHHhhcccccccccccccccceeeccCCccccCCCCCCCcccccchhhhhcccCCCCccccCcccc
Q 038614 87 SDREVAMCLLKLSRDNWLQKDKQVVVAEAVVDEDEYVRGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKK 159 (263)
Q Consensus 87 ~ee~~a~cl~mlsr~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k 159 (263)
..+.+.+|.-.++++...+... -.+..-.-...|..|+..|... ...|.|+.||.
T Consensus 40 ~pe~L~f~f~~~~~~T~~egA~------L~I~~vp~~~~C~~Cg~~~~~~------------~~~~~CP~Cgs 94 (113)
T PRK12380 40 EESAVRFSFEIVCHGTVAQGCD------LHIVYKPAQAWCWDCSQVVEIH------------QHDAQCPHCHG 94 (113)
T ss_pred CHHHHHHHHHHHhCCCccCCCE------EEEEeeCcEEEcccCCCEEecC------------CcCccCcCCCC
Confidence 7889999999999998877332 2233334456888998776532 13466888884
No 68
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=58.83 E-value=13 Score=29.47 Aligned_cols=68 Identities=19% Similarity=0.208 Sum_probs=39.5
Q ss_pred CHHHHHHHHHhhcccccccccccccccceeeccCCccccCCCCCCCccccc---c------hhhhhcccCCCCccccCcc
Q 038614 87 SDREVAMCLLKLSRDNWLQKDKQVVVAEAVVDEDEYVRGKSDDGDNDEEED---K------EEDESSLVSRTNKYKCKTC 157 (263)
Q Consensus 87 ~ee~~a~cl~mlsr~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~---~------~~~h~~~h~~~kp~kC~~C 157 (263)
..+.+.+|.-.+..+...+.. .-.+......+.|..||..+.-.. . ...|.-.-....-+.|+.|
T Consensus 40 ~pe~L~fafe~l~~gt~~ega------~L~i~~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~C 113 (135)
T PRK03824 40 DKEIVEFALNELLKGTILEGA------EIIFEEEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKC 113 (135)
T ss_pred hHHHHHHHHHHHHcCCcccCC------EEEEEecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCC
Confidence 678888999988888877622 222333345678888987765431 1 1112111122345678888
Q ss_pred ccc
Q 038614 158 KKE 160 (263)
Q Consensus 158 ~k~ 160 (263)
|..
T Consensus 114 gs~ 116 (135)
T PRK03824 114 GSR 116 (135)
T ss_pred CCC
Confidence 843
No 69
>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=58.03 E-value=5.2 Score=25.02 Aligned_cols=31 Identities=16% Similarity=0.287 Sum_probs=19.8
Q ss_pred ccccCCCCCCCcccccchhhhhcccCCCCccccCcccc
Q 038614 122 YVRGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKK 159 (263)
Q Consensus 122 ~~~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k 159 (263)
+.|.|.+||..|+.... +.. ...-.|..||.
T Consensus 4 Yey~C~~Cg~~fe~~~~------~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQS------ISE-DDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEE------cCC-CCCCcCCCCCC
Confidence 35678888888875322 222 45667888876
No 70
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=57.07 E-value=8.3 Score=39.25 Aligned_cols=13 Identities=23% Similarity=0.534 Sum_probs=10.3
Q ss_pred CCcceecCccccc
Q 038614 198 DQRVFKCPFCDKV 210 (263)
Q Consensus 198 g~kp~~C~~Cgk~ 210 (263)
...|+.|+.||-.
T Consensus 472 ~~~p~~Cp~Cgs~ 484 (730)
T COG1198 472 EPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCC
Confidence 4678999999865
No 71
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=55.44 E-value=2.8 Score=42.05 Aligned_cols=26 Identities=35% Similarity=0.562 Sum_probs=24.4
Q ss_pred ceecCccccccCCchhhhhHhhhhcC
Q 038614 201 VFKCPFCDKVFDSGQALGGHKKIHFT 226 (263)
Q Consensus 201 p~~C~~Cgk~F~~~~~L~~H~r~H~~ 226 (263)
.|.|.+|+|+|-.-..+..||++|.-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 69999999999999999999999984
No 72
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=54.76 E-value=7.4 Score=24.68 Aligned_cols=13 Identities=38% Similarity=0.979 Sum_probs=8.6
Q ss_pred ccccCcccccccC
Q 038614 151 KYKCKTCKKEFRS 163 (263)
Q Consensus 151 p~kC~~C~k~F~s 163 (263)
.|+|..||..|..
T Consensus 3 ~y~C~~CG~~~~~ 15 (46)
T PRK00398 3 EYKCARCGREVEL 15 (46)
T ss_pred EEECCCCCCEEEE
Confidence 4777777766543
No 73
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=54.70 E-value=19 Score=27.73 Aligned_cols=57 Identities=12% Similarity=0.135 Sum_probs=37.6
Q ss_pred CHHHHHHHHHhhcccccccccccccccceeeccCCccccCCCCCCCcccccchhhhhcccCCCCccccCccccc
Q 038614 87 SDREVAMCLLKLSRDNWLQKDKQVVVAEAVVDEDEYVRGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKE 160 (263)
Q Consensus 87 ~ee~~a~cl~mlsr~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~ 160 (263)
..+.+.+|.-.+.++...+.. .-.+....-...|..|+..|.... ...+.|+.||..
T Consensus 40 ~p~~L~f~f~~~~~~t~~egA------~L~i~~~p~~~~C~~Cg~~~~~~~-----------~~~~~CP~Cgs~ 96 (114)
T PRK03681 40 ETSSLAFCFDLVCRGTVAEGC------KLHLEEQEAECWCETCQQYVTLLT-----------QRVRRCPQCHGD 96 (114)
T ss_pred CHHHHHHHHHHHhCCCccCCC------EEEEEeeCcEEEcccCCCeeecCC-----------ccCCcCcCcCCC
Confidence 788999999999998877632 223333345568889987665321 112679988843
No 74
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=54.24 E-value=4.9 Score=27.00 Aligned_cols=27 Identities=19% Similarity=0.309 Sum_probs=22.8
Q ss_pred cCCCCccccCcccccccChhhhhhhhh
Q 038614 146 VSRTNKYKCKTCKKEFRSYQALGGHKA 172 (263)
Q Consensus 146 h~~~kp~kC~~C~k~F~s~~~L~~H~~ 172 (263)
.-|+.-++|+-|+..|.......+|..
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhh
Confidence 346778999999999999998888854
No 75
>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=53.60 E-value=8.5 Score=34.05 Aligned_cols=103 Identities=17% Similarity=0.172 Sum_probs=56.4
Q ss_pred cceeeccCCccccCCCCCCCcccccchhhhhcc--cCCCCccccCcccccccChhhhhhhhhhcCCCcccccCCCCcccc
Q 038614 113 AEAVVDEDEYVRGKSDDGDNDEEEDKEEDESSL--VSRTNKYKCKTCKKEFRSYQALGGHKASHKKIKIHHNGSSDAAAA 190 (263)
Q Consensus 113 ~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~--h~~~kp~kC~~C~k~F~s~~~L~~H~~~H~~~kp~~~~~~~~~~~ 190 (263)
...+|..++.+|.|..|..-.-+.+.+ .|+.. ......|+|.-|++. .+++-|.- +--||.....
T Consensus 132 ~R~vw~hGGrif~CsfC~~flCEDDQF-EHQAsCQvLe~E~~KC~SCNrl-Gq~sCLRC-----------K~cfCddHvr 198 (314)
T PF06524_consen 132 ERGVWDHGGRIFKCSFCDNFLCEDDQF-EHQASCQVLESETFKCQSCNRL-GQYSCLRC-----------KICFCDDHVR 198 (314)
T ss_pred ecccccCCCeEEEeecCCCeeeccchh-hhhhhhhhhhcccccccccccc-cchhhhhe-----------eeeehhhhhh
Confidence 456677788888888877654444333 23211 122345778777642 22222211 0112221111
Q ss_pred cccccccCCcceecCccccccCCchhhhhHhhhhcCCC
Q 038614 191 GGDAVVMDQRVFKCPFCDKVFDSGQALGGHKKIHFTYL 228 (263)
Q Consensus 191 ~h~~~h~g~kp~~C~~Cgk~F~~~~~L~~H~r~H~~~~ 228 (263)
+-.......+++.||.||.-...-..|..-.|+|.=+.
T Consensus 199 rKg~ky~k~k~~PCPKCg~et~eTkdLSmStR~hkyGR 236 (314)
T PF06524_consen 199 RKGFKYEKGKPIPCPKCGYETQETKDLSMSTRSHKYGR 236 (314)
T ss_pred hcccccccCCCCCCCCCCCcccccccceeeeecchhcc
Confidence 10011223579999999998888888888788877443
No 76
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=53.12 E-value=21 Score=27.59 Aligned_cols=57 Identities=7% Similarity=0.057 Sum_probs=36.9
Q ss_pred CHHHHHHHHHhhcccc-cccccccccccceeeccCCccccCCCCCCCcccccchhhhhcccCCCCccccCccccc
Q 038614 87 SDREVAMCLLKLSRDN-WLQKDKQVVVAEAVVDEDEYVRGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKE 160 (263)
Q Consensus 87 ~ee~~a~cl~mlsr~~-~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~ 160 (263)
..+.+.+|.-.+.++. ..+. ..-.+....-...|..|+..|..... .-+.|+.||..
T Consensus 40 ~pe~L~faf~~~~~~T~~~eg------a~L~Ie~vp~~~~C~~Cg~~~~~~~~-----------~~~~CP~Cgs~ 97 (117)
T PRK00564 40 DKSLFVSAFETFREESLVCKD------AILDIVDEKVELECKDCSHVFKPNAL-----------DYGVCEKCHSK 97 (117)
T ss_pred CHHHHHHHHHHHhcCCcccCC------CEEEEEecCCEEEhhhCCCccccCCc-----------cCCcCcCCCCC
Confidence 7889999999999998 5652 22233334456688888877654211 11348888843
No 77
>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=53.07 E-value=9.7 Score=22.93 Aligned_cols=12 Identities=25% Similarity=0.670 Sum_probs=9.3
Q ss_pred ceecCccccccC
Q 038614 201 VFKCPFCDKVFD 212 (263)
Q Consensus 201 p~~C~~Cgk~F~ 212 (263)
...|+.|+..|.
T Consensus 25 ~v~C~~C~~~~~ 36 (38)
T TIGR02098 25 KVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCEEE
Confidence 567999988774
No 78
>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=52.12 E-value=21 Score=27.53 Aligned_cols=56 Identities=9% Similarity=0.204 Sum_probs=37.3
Q ss_pred CHHHHHHHHHhhcccccccccccccccceeeccCCccccCCCCCCCcccccchhhhhcccCCCCccccCccccc
Q 038614 87 SDREVAMCLLKLSRDNWLQKDKQVVVAEAVVDEDEYVRGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKE 160 (263)
Q Consensus 87 ~ee~~a~cl~mlsr~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~ 160 (263)
..+.+.+|.-.+.++..++.. .-.+....-...|..|+..|.... ..+.|+.||..
T Consensus 40 ~p~~L~faf~~~~~~t~~ega------~L~I~~~p~~~~C~~Cg~~~~~~~------------~~~~CP~Cgs~ 95 (115)
T TIGR00100 40 NPSQLQFAFEVVREGTVAEGA------KLNIEDEPVECECEDCSEEVSPEI------------DLYRCPKCHGI 95 (115)
T ss_pred CHHHHHHHHHHHhCCCccCCC------EEEEEeeCcEEEcccCCCEEecCC------------cCccCcCCcCC
Confidence 778899999999998887732 222333344567888887765422 13678888743
No 79
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=51.68 E-value=7 Score=30.95 Aligned_cols=15 Identities=33% Similarity=0.946 Sum_probs=13.0
Q ss_pred ceecCccccccCCch
Q 038614 201 VFKCPFCDKVFDSGQ 215 (263)
Q Consensus 201 p~~C~~Cgk~F~~~~ 215 (263)
||+|..||+.|..++
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 689999999998876
No 80
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=51.42 E-value=8.6 Score=31.79 Aligned_cols=12 Identities=25% Similarity=0.697 Sum_probs=9.7
Q ss_pred CCcceecCcccc
Q 038614 198 DQRVFKCPFCDK 209 (263)
Q Consensus 198 g~kp~~C~~Cgk 209 (263)
|+-|-.||+||-
T Consensus 146 ge~P~~CPiCga 157 (166)
T COG1592 146 GEAPEVCPICGA 157 (166)
T ss_pred CCCCCcCCCCCC
Confidence 567889999983
No 81
>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=51.31 E-value=10 Score=21.20 Aligned_cols=20 Identities=20% Similarity=0.597 Sum_probs=15.7
Q ss_pred eecCccccccCCchhhhhHhh
Q 038614 202 FKCPFCDKVFDSGQALGGHKK 222 (263)
Q Consensus 202 ~~C~~Cgk~F~~~~~L~~H~r 222 (263)
..||+|++.+ ....+..|..
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3699999998 5567778875
No 82
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=51.14 E-value=7.4 Score=29.90 Aligned_cols=56 Identities=14% Similarity=0.246 Sum_probs=34.0
Q ss_pred CHHHHHHHHHhhcccccccccccccccceeeccCCccccCCCCCCCcccccchhhhhcccCCCCccccCccccc
Q 038614 87 SDREVAMCLLKLSRDNWLQKDKQVVVAEAVVDEDEYVRGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKE 160 (263)
Q Consensus 87 ~ee~~a~cl~mlsr~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~ 160 (263)
..+.+.+|.-.+.++.+++... -.+....-...|..|+..|.-... .+.|+.||..
T Consensus 40 ~pe~L~f~f~~~~~~T~~e~a~------L~Ie~~p~~~~C~~Cg~~~~~~~~------------~~~CP~Cgs~ 95 (113)
T PF01155_consen 40 EPEALRFAFEVLAEGTILEGAE------LEIEEVPARARCRDCGHEFEPDEF------------DFSCPRCGSP 95 (113)
T ss_dssp -HHHHHHHHHHHHCCSTTTT-E------EEEEEE--EEEETTTS-EEECHHC------------CHH-SSSSSS
T ss_pred CHHHHHHHHHHHhCCCCccCCE------EEEEecCCcEECCCCCCEEecCCC------------CCCCcCCcCC
Confidence 6788999999999999887432 222223345678888888764321 1568888754
No 83
>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=50.72 E-value=7.2 Score=31.01 Aligned_cols=28 Identities=25% Similarity=0.539 Sum_probs=17.7
Q ss_pred CCccccCcccccccChhhhhhhhhhcCCCcc
Q 038614 149 TNKYKCKTCKKEFRSYQALGGHKASHKKIKI 179 (263)
Q Consensus 149 ~kp~kC~~C~k~F~s~~~L~~H~~~H~~~kp 179 (263)
+.-..|-+|||.|.. |.+|.+.|.|-.|
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 345679999999876 6899999977655
No 84
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=50.08 E-value=7.2 Score=31.01 Aligned_cols=25 Identities=24% Similarity=0.323 Sum_probs=21.2
Q ss_pred ceecCccccccCCchhhhhHhhhhcCCC
Q 038614 201 VFKCPFCDKVFDSGQALGGHKKIHFTYL 228 (263)
Q Consensus 201 p~~C~~Cgk~F~~~~~L~~H~r~H~~~~ 228 (263)
-..|-+|||.|. .|++|+.+|++-.
T Consensus 76 ~IicLEDGkkfK---SLKRHL~t~~gmT 100 (148)
T COG4957 76 YIICLEDGKKFK---SLKRHLTTHYGLT 100 (148)
T ss_pred eEEEeccCcchH---HHHHHHhcccCCC
Confidence 457999999995 4999999999864
No 85
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=49.35 E-value=11 Score=22.71 Aligned_cols=33 Identities=18% Similarity=0.361 Sum_probs=21.9
Q ss_pred cCCCCCCCcccccchhhhhcccCCCCccccCccccccc
Q 038614 125 GKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKEFR 162 (263)
Q Consensus 125 ~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~F~ 162 (263)
.|..|+..|.-.+.. +-......+|..|+..|.
T Consensus 4 ~Cp~C~~~y~i~d~~-----ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEK-----IPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred ECCCCCCEEeCCHHH-----CCCCCcEEECCCCCCEeC
Confidence 677888887754332 223445689999998873
No 86
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=48.38 E-value=8.1 Score=32.28 Aligned_cols=19 Identities=21% Similarity=0.469 Sum_probs=14.3
Q ss_pred CCccccCcccccccChhhh
Q 038614 149 TNKYKCKTCKKEFRSYQAL 167 (263)
Q Consensus 149 ~kp~kC~~C~k~F~s~~~L 167 (263)
..-|.|+.|++.|...-++
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~ 133 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAM 133 (178)
T ss_pred CCEEECCCCCcEEeHHHHh
Confidence 3468898898888777665
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=48.23 E-value=33 Score=26.50 Aligned_cols=28 Identities=21% Similarity=0.460 Sum_probs=23.5
Q ss_pred CcceecCccccccCCchhhhhHhhhhcC
Q 038614 199 QRVFKCPFCDKVFDSGQALGGHKKIHFT 226 (263)
Q Consensus 199 ~kp~~C~~Cgk~F~~~~~L~~H~r~H~~ 226 (263)
...|+|+.|...|--.-..-.|...|.-
T Consensus 79 ~~~y~C~~C~~~FC~dCD~fiHe~Lh~C 106 (112)
T TIGR00622 79 SHRYVCAVCKNVFCVDCDVFVHESLHCC 106 (112)
T ss_pred ccceeCCCCCCccccccchhhhhhccCC
Confidence 3479999999999988888888888874
No 88
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.84 E-value=28 Score=27.16 Aligned_cols=61 Identities=13% Similarity=0.192 Sum_probs=37.3
Q ss_pred CHHHHHHHHHhhcccccccccccccccceeeccCCccccCCCCCCCcccccchhhhhcccCCCCccccCcccc
Q 038614 87 SDREVAMCLLKLSRDNWLQKDKQVVVAEAVVDEDEYVRGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKK 159 (263)
Q Consensus 87 ~ee~~a~cl~mlsr~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k 159 (263)
..+.+.+|.-.++++...+.. .-.+....-...| .|+..|........| ..-.+.|+.||.
T Consensus 40 ~pe~L~faf~~~~~gT~~egA------~L~I~~vp~~~~C-~Cg~~~~~~~~~~~~-----~~~~~~CP~Cgs 100 (124)
T PRK00762 40 NPEQLRFMLDVLAEGTIAEDA------DLIVEMIPVEIEC-ECGYEGVVDEDEIDH-----YAAVIECPVCGN 100 (124)
T ss_pred CHHHHHHHHHHHhCCCCcCCC------EEEEEecCeeEEe-eCcCcccccccchhc-----cccCCcCcCCCC
Confidence 788899999999998877632 2233334456689 899776543210001 001257999883
No 89
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=46.22 E-value=16 Score=29.34 Aligned_cols=19 Identities=26% Similarity=0.725 Sum_probs=13.7
Q ss_pred CCCccccCcccccccChhh
Q 038614 148 RTNKYKCKTCKKEFRSYQA 166 (263)
Q Consensus 148 ~~kp~kC~~C~k~F~s~~~ 166 (263)
...-|.|+.|++.|....+
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea 114 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEA 114 (147)
T ss_pred CCcEEECcCCCCEeeHHHH
Confidence 4456889999988875544
No 90
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=45.67 E-value=16 Score=28.76 Aligned_cols=33 Identities=12% Similarity=0.018 Sum_probs=24.7
Q ss_pred cCCCCCCCcccccchhhhhcccCCCCccccCcccccccChhhhh
Q 038614 125 GKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKEFRSYQALG 168 (263)
Q Consensus 125 ~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~F~s~~~L~ 168 (263)
.|..||..|... ++.|..|..||..|.....+.
T Consensus 11 ~Cp~cg~kFYDL-----------nk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 11 ICPNTGSKFYDL-----------NRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred cCCCcCcccccc-----------CCCCccCCCcCCccCcchhhc
Confidence 688899988754 456888999999886654443
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=45.48 E-value=14 Score=27.85 Aligned_cols=26 Identities=19% Similarity=0.511 Sum_probs=23.0
Q ss_pred ceec----CccccccCCchhhhhHhhhhcC
Q 038614 201 VFKC----PFCDKVFDSGQALGGHKKIHFT 226 (263)
Q Consensus 201 p~~C----~~Cgk~F~~~~~L~~H~r~H~~ 226 (263)
-|.| ..|++.+.+...+..|.+.+.|
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3899 9999999999999999987653
No 92
>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=44.80 E-value=11 Score=21.18 Aligned_cols=11 Identities=36% Similarity=0.869 Sum_probs=9.0
Q ss_pred eecCccccccC
Q 038614 202 FKCPFCDKVFD 212 (263)
Q Consensus 202 ~~C~~Cgk~F~ 212 (263)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 37999999885
No 93
>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=43.18 E-value=16 Score=21.49 Aligned_cols=24 Identities=17% Similarity=0.174 Sum_probs=15.6
Q ss_pred ccCCCCCCCcccccchhhhhcccCCCCccccCcccc
Q 038614 124 RGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKK 159 (263)
Q Consensus 124 ~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k 159 (263)
+.|..||..+... +.++.|.+|+-
T Consensus 2 ~~C~~CGy~y~~~------------~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGE------------EAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCC------------cCCCcCcCCCC
Confidence 4677777665432 25678888874
No 94
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=43.03 E-value=13 Score=24.30 Aligned_cols=12 Identities=42% Similarity=1.046 Sum_probs=9.8
Q ss_pred CccccCcccccc
Q 038614 150 NKYKCKTCKKEF 161 (263)
Q Consensus 150 kp~kC~~C~k~F 161 (263)
.-|+|..||+.|
T Consensus 5 ~~Y~C~~Cg~~~ 16 (49)
T COG1996 5 MEYKCARCGREV 16 (49)
T ss_pred EEEEhhhcCCee
Confidence 358899999888
No 95
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=42.19 E-value=5.1 Score=40.28 Aligned_cols=27 Identities=22% Similarity=0.605 Sum_probs=24.4
Q ss_pred CccccCcccccccChhhhhhhhhhcCC
Q 038614 150 NKYKCKTCKKEFRSYQALGGHKASHKK 176 (263)
Q Consensus 150 kp~kC~~C~k~F~s~~~L~~H~~~H~~ 176 (263)
.-|.|..|+|+|-.-..+..||++|.-
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 469999999999999999999999973
No 96
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=42.07 E-value=16 Score=22.08 Aligned_cols=33 Identities=21% Similarity=0.322 Sum_probs=21.9
Q ss_pred cCCCCCCCcccccchhhhhcccCCCCccccCccccccc
Q 038614 125 GKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKEFR 162 (263)
Q Consensus 125 ~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~F~ 162 (263)
.|..|+..|.-.++ ++..+.+..+|..|+..|.
T Consensus 4 ~CP~C~~~f~v~~~-----~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDD-----KLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHH-----HcccCCcEEECCCCCcEee
Confidence 57788887765432 1223455789999998874
No 97
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=41.76 E-value=14 Score=30.09 Aligned_cols=21 Identities=14% Similarity=0.251 Sum_probs=15.5
Q ss_pred CCCCccccCcccccccChhhh
Q 038614 147 SRTNKYKCKTCKKEFRSYQAL 167 (263)
Q Consensus 147 ~~~kp~kC~~C~k~F~s~~~L 167 (263)
....-|.|+.|+..|....++
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAM 125 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHH
Confidence 344568888888888777776
No 98
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=41.16 E-value=16 Score=32.24 Aligned_cols=23 Identities=13% Similarity=0.518 Sum_probs=13.1
Q ss_pred cccCcccccccChhhhhhhhhhcC
Q 038614 152 YKCKTCKKEFRSYQALGGHKASHK 175 (263)
Q Consensus 152 ~kC~~C~k~F~s~~~L~~H~~~H~ 175 (263)
|.|.+||....-. .|..|+-..+
T Consensus 4 FtCnvCgEsvKKp-~vekH~srCr 26 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRCR 26 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhcc
Confidence 6777777665433 3455654444
No 99
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=40.98 E-value=14 Score=23.81 Aligned_cols=31 Identities=19% Similarity=0.180 Sum_probs=18.0
Q ss_pred ccccCCCCCCCcccccchhhhhcccCCCCccccCcccc
Q 038614 122 YVRGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKK 159 (263)
Q Consensus 122 ~~~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k 159 (263)
+.|.|.+|+..|+..... .. ...-.|..||.
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 346788888877743211 11 33456888874
No 100
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=40.04 E-value=14 Score=27.93 Aligned_cols=16 Identities=38% Similarity=0.899 Sum_probs=13.3
Q ss_pred ceecCccccccCCchh
Q 038614 201 VFKCPFCDKVFDSGQA 216 (263)
Q Consensus 201 p~~C~~Cgk~F~~~~~ 216 (263)
||.|..||..|..++.
T Consensus 2 pH~CtrCG~vf~~g~~ 17 (112)
T COG3364 2 PHQCTRCGEVFDDGSE 17 (112)
T ss_pred CceecccccccccccH
Confidence 7899999999988644
No 101
>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=38.89 E-value=15 Score=22.24 Aligned_cols=16 Identities=25% Similarity=0.650 Sum_probs=12.3
Q ss_pred ceecCccccccCCchh
Q 038614 201 VFKCPFCDKVFDSGQA 216 (263)
Q Consensus 201 p~~C~~Cgk~F~~~~~ 216 (263)
-|+|..||..|.-...
T Consensus 5 ~y~C~~Cg~~fe~~~~ 20 (41)
T smart00834 5 EYRCEDCGHTFEVLQK 20 (41)
T ss_pred EEEcCCCCCEEEEEEe
Confidence 4899999999865443
No 102
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=38.43 E-value=21 Score=22.70 Aligned_cols=26 Identities=15% Similarity=0.349 Sum_probs=16.4
Q ss_pred ccCCCCCCCcccccchhhhhcccCCCCccccCccccc
Q 038614 124 RGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKE 160 (263)
Q Consensus 124 ~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~ 160 (263)
|.|.+||.+++.. ...+.+|..||..
T Consensus 3 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK-----------SKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC-----------CCCceECCCCCce
Confidence 5677788776643 2245677777743
No 103
>PRK14873 primosome assembly protein PriA; Provisional
Probab=37.86 E-value=17 Score=36.63 Aligned_cols=47 Identities=17% Similarity=0.287 Sum_probs=26.4
Q ss_pred ccCcccccccChhhhhhhhhhcCCCcccccCCCCcccccccccccCCcceecCccccc
Q 038614 153 KCKTCKKEFRSYQALGGHKASHKKIKIHHNGSSDAAAAGGDAVVMDQRVFKCPFCDKV 210 (263)
Q Consensus 153 kC~~C~k~F~s~~~L~~H~~~H~~~kp~~~~~~~~~~~~h~~~h~g~kp~~C~~Cgk~ 210 (263)
.|..||..+.-.. -...+..|.......|.+|+.. ..|..|+.||..
T Consensus 385 ~C~~Cg~~~~C~~-C~~~L~~h~~~~~l~Ch~CG~~----------~~p~~Cp~Cgs~ 431 (665)
T PRK14873 385 ACARCRTPARCRH-CTGPLGLPSAGGTPRCRWCGRA----------APDWRCPRCGSD 431 (665)
T ss_pred EhhhCcCeeECCC-CCCceeEecCCCeeECCCCcCC----------CcCccCCCCcCC
Confidence 5777776654321 1122333444444557777641 247899999865
No 104
>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=37.65 E-value=16 Score=27.38 Aligned_cols=19 Identities=26% Similarity=0.537 Sum_probs=15.1
Q ss_pred cccccCCcceecCccccccC
Q 038614 193 DAVVMDQRVFKCPFCDKVFD 212 (263)
Q Consensus 193 ~~~h~g~kp~~C~~Cgk~F~ 212 (263)
+.++.| +|+.|+.||..|.
T Consensus 72 ~~l~~g-~~~rC~eCG~~fk 90 (97)
T cd00924 72 MWLEKG-KPKRCPECGHVFK 90 (97)
T ss_pred EEEeCC-CceeCCCCCcEEE
Confidence 445556 7999999999885
No 105
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=37.50 E-value=26 Score=21.75 Aligned_cols=24 Identities=33% Similarity=0.614 Sum_probs=17.8
Q ss_pred eecCccccccCCch--hhhhHhhhhc
Q 038614 202 FKCPFCDKVFDSGQ--ALGGHKKIHF 225 (263)
Q Consensus 202 ~~C~~Cgk~F~~~~--~L~~H~r~H~ 225 (263)
-.|+.||..|..+. .-..|.+-|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 58999999887643 4567777774
No 106
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=36.47 E-value=21 Score=28.93 Aligned_cols=45 Identities=9% Similarity=0.067 Sum_probs=24.5
Q ss_pred cCCCCCCCcccccchhhhhcccCCCCccccCcccccccChhhhhh
Q 038614 125 GKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKEFRSYQALGG 169 (263)
Q Consensus 125 ~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~F~s~~~L~~ 169 (263)
.|..|+...+.--+...-..-.+-.+.=.|..|++.|..+-.+..
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~ 46 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAEL 46 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccc
Confidence 466677654432221111111122345689999999998865543
No 107
>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=36.17 E-value=18 Score=19.98 Aligned_cols=11 Identities=36% Similarity=0.809 Sum_probs=8.8
Q ss_pred CcceecCcccc
Q 038614 199 QRVFKCPFCDK 209 (263)
Q Consensus 199 ~kp~~C~~Cgk 209 (263)
..+|.|+.||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 35899999985
No 108
>PHA00626 hypothetical protein
Probab=35.84 E-value=18 Score=24.27 Aligned_cols=15 Identities=13% Similarity=0.173 Sum_probs=12.7
Q ss_pred CcceecCccccccCC
Q 038614 199 QRVFKCPFCDKVFDS 213 (263)
Q Consensus 199 ~kp~~C~~Cgk~F~~ 213 (263)
...|+|+.||+.|..
T Consensus 21 snrYkCkdCGY~ft~ 35 (59)
T PHA00626 21 SDDYVCCDCGYNDSK 35 (59)
T ss_pred CcceEcCCCCCeech
Confidence 468999999999964
No 109
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=35.81 E-value=43 Score=25.99 Aligned_cols=55 Identities=15% Similarity=0.254 Sum_probs=38.0
Q ss_pred cCHHHHHHHHHhhcccccccccccccccceeeccCCccccCCCCCCCcccccchhhhhcccCCCCccccCccc
Q 038614 86 LSDREVAMCLLKLSRDNWLQKDKQVVVAEAVVDEDEYVRGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCK 158 (263)
Q Consensus 86 ~~ee~~a~cl~mlsr~~~~~~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~ 158 (263)
...+.+.+|.-.++++...+... -.+....-...|..|+..+.... -.|.|+.|+
T Consensus 39 v~~~~l~FaFev~~egT~aega~------l~Ie~~p~~~~C~~C~~~~~~e~------------~~~~CP~C~ 93 (115)
T COG0375 39 VEPEALRFAFEVVAEGTIAEGAE------LHIEEEPAECWCLDCGQEVELEE------------LDYRCPKCG 93 (115)
T ss_pred cCHHHHHHHHHHHhccCcccCCE------EEEEEeccEEEeccCCCeecchh------------heeECCCCC
Confidence 37899999999999999988432 22334445568888866654321 235699998
No 110
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.77 E-value=20 Score=36.08 Aligned_cols=89 Identities=19% Similarity=0.193 Sum_probs=0.0
Q ss_pred ccCCCCCCCcccccchhhhhcccCCCCccccCcccccccChhhhhhhh-hhcCCCcccccCCCCcccccccccccCCc--
Q 038614 124 RGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKEFRSYQALGGHK-ASHKKIKIHHNGSSDAAAAGGDAVVMDQR-- 200 (263)
Q Consensus 124 ~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~F~s~~~L~~H~-~~H~~~kp~~~~~~~~~~~~h~~~h~g~k-- 200 (263)
..|..|...+.. ......|..| -.|.+...|..|+ ..|..-.-..|....+.+..-.++++...
T Consensus 100 ~~C~~C~~~~~~------------~~~~~~~~~c-~~~~s~~~Lk~H~~~~H~~~~c~lC~~~~kif~~e~k~Yt~~el~ 166 (669)
T KOG2231|consen 100 HSCHICDRRFRA------------LYNKKECLHC-TEFKSVENLKNHMRDQHKLHLCSLCLQNLKIFINERKLYTRAELN 166 (669)
T ss_pred hhcCccccchhh------------hcccCCCccc-cchhHHHHHHHHHHHhhhhhccccccccceeeeeeeehehHHHHH
Q ss_pred -------c--------eecCccccccCCchhhhhHhhhhc
Q 038614 201 -------V--------FKCPFCDKVFDSGQALGGHKKIHF 225 (263)
Q Consensus 201 -------p--------~~C~~Cgk~F~~~~~L~~H~r~H~ 225 (263)
+ -.|..|...|-....|.+|++.+.
T Consensus 167 ~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~h 206 (669)
T KOG2231|consen 167 LHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRFDH 206 (669)
T ss_pred HHHhcCCCccccccCCccchhhhhhhccHHHHHHhhccce
No 111
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=34.16 E-value=12 Score=32.18 Aligned_cols=25 Identities=24% Similarity=0.716 Sum_probs=20.3
Q ss_pred CcceecCccccccCCchhhhhHhhh
Q 038614 199 QRVFKCPFCDKVFDSGQALGGHKKI 223 (263)
Q Consensus 199 ~kp~~C~~Cgk~F~~~~~L~~H~r~ 223 (263)
+|.+.||+|++.|.....+.+..|+
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~ 27 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRV 27 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceE
Confidence 4678999999999988777777654
No 112
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=34.11 E-value=23 Score=34.89 Aligned_cols=28 Identities=25% Similarity=0.417 Sum_probs=24.1
Q ss_pred CcceecCccccccCCchhhhhHhhhhcC
Q 038614 199 QRVFKCPFCDKVFDSGQALGGHKKIHFT 226 (263)
Q Consensus 199 ~kp~~C~~Cgk~F~~~~~L~~H~r~H~~ 226 (263)
.+|.+|..||.+|........||-.|..
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhhh
Confidence 5689999999999999888888877764
No 113
>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=33.98 E-value=18 Score=20.72 Aligned_cols=21 Identities=33% Similarity=0.703 Sum_probs=13.5
Q ss_pred eecCccccccCCchhhhhHhhh
Q 038614 202 FKCPFCDKVFDSGQALGGHKKI 223 (263)
Q Consensus 202 ~~C~~Cgk~F~~~~~L~~H~r~ 223 (263)
|.|-.|++.| .+.....|...
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~C 21 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTSC 21 (28)
T ss_dssp EEETTTTEEE-EGGGTTT----
T ss_pred CeeecCCCCc-CcCCcCCCCcc
Confidence 5788999999 66666666544
No 114
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.86 E-value=26 Score=27.61 Aligned_cols=16 Identities=25% Similarity=0.727 Sum_probs=12.3
Q ss_pred CCcceecCccccccCC
Q 038614 198 DQRVFKCPFCDKVFDS 213 (263)
Q Consensus 198 g~kp~~C~~Cgk~F~~ 213 (263)
|...|.|+.|++.|..
T Consensus 50 ~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 50 GHQRYKCKSCGSTFTV 65 (129)
T ss_pred cccccccCCcCcceee
Confidence 3557899999998853
No 115
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=33.49 E-value=31 Score=25.34 Aligned_cols=16 Identities=31% Similarity=0.821 Sum_probs=12.4
Q ss_pred CcceecCccccccCCc
Q 038614 199 QRVFKCPFCDKVFDSG 214 (263)
Q Consensus 199 ~kp~~C~~Cgk~F~~~ 214 (263)
.....|..||..|.-+
T Consensus 51 ~GIW~C~kCg~~fAGg 66 (89)
T COG1997 51 TGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCeEEcCCCCCeeccc
Confidence 3478899999998654
No 116
>PRK04023 DNA polymerase II large subunit; Validated
Probab=33.21 E-value=43 Score=35.36 Aligned_cols=13 Identities=15% Similarity=0.296 Sum_probs=9.1
Q ss_pred cceecCccccccC
Q 038614 200 RVFKCPFCDKVFD 212 (263)
Q Consensus 200 kp~~C~~Cgk~F~ 212 (263)
.++.|+.||..-.
T Consensus 662 ~~y~CPKCG~El~ 674 (1121)
T PRK04023 662 EEDECEKCGREPT 674 (1121)
T ss_pred CCCcCCCCCCCCC
Confidence 3577999986543
No 117
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.68 E-value=21 Score=29.84 Aligned_cols=19 Identities=21% Similarity=0.541 Sum_probs=13.2
Q ss_pred CCCCccccCcccccccChh
Q 038614 147 SRTNKYKCKTCKKEFRSYQ 165 (263)
Q Consensus 147 ~~~kp~kC~~C~k~F~s~~ 165 (263)
..+..|+|.+|--.|..+.
T Consensus 127 ~~~~~~~CPiCl~~~sek~ 145 (187)
T KOG0320|consen 127 RKEGTYKCPICLDSVSEKV 145 (187)
T ss_pred ccccccCCCceecchhhcc
Confidence 3455699999987766544
No 118
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=31.37 E-value=19 Score=28.65 Aligned_cols=25 Identities=28% Similarity=0.394 Sum_probs=21.1
Q ss_pred cccCcccccccChhhhhhhhhhcCCCcc
Q 038614 152 YKCKTCKKEFRSYQALGGHKASHKKIKI 179 (263)
Q Consensus 152 ~kC~~C~k~F~s~~~L~~H~~~H~~~kp 179 (263)
..|-.|||.|.+ |++|..+|-+--|
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCH
Confidence 569999999965 8999999988665
No 119
>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=31.32 E-value=34 Score=20.16 Aligned_cols=25 Identities=16% Similarity=0.304 Sum_probs=14.0
Q ss_pred cCCCCCCCcccccchhhhhcccCCCCccccCccccc
Q 038614 125 GKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKE 160 (263)
Q Consensus 125 ~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~ 160 (263)
.|.+|+..++.. ...+.+|..||..
T Consensus 2 ~C~~Cg~~~~~~-----------~~~~irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAEVELK-----------PGDPIRCPECGHR 26 (32)
T ss_dssp BESSSSSSE-BS-----------TSSTSSBSSSS-S
T ss_pred CCCcCCCeeEcC-----------CCCcEECCcCCCe
Confidence 566777766522 2235678888743
No 120
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=31.19 E-value=35 Score=31.55 Aligned_cols=20 Identities=30% Similarity=0.604 Sum_probs=12.0
Q ss_pred ecCccccccCCchhhhhHhh
Q 038614 203 KCPFCDKVFDSGQALGGHKK 222 (263)
Q Consensus 203 ~C~~Cgk~F~~~~~L~~H~r 222 (263)
.|.+|...|..-..|..|+|
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR 241 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCR 241 (493)
T ss_pred hhhhccceecChHHHHHHHH
Confidence 36666666666666666554
No 121
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=30.79 E-value=15 Score=34.20 Aligned_cols=72 Identities=24% Similarity=0.412 Sum_probs=0.0
Q ss_pred cccCcccccccChhhhhhhhhh--cC-------------CCcccccCCCCcccccccccccCCcceecCccccccCCchh
Q 038614 152 YKCKTCKKEFRSYQALGGHKAS--HK-------------KIKIHHNGSSDAAAAGGDAVVMDQRVFKCPFCDKVFDSGQA 216 (263)
Q Consensus 152 ~kC~~C~k~F~s~~~L~~H~~~--H~-------------~~kp~~~~~~~~~~~~h~~~h~g~kp~~C~~Cgk~F~~~~~ 216 (263)
|.|..|...|...-.-..|.++ |. +...|.-.........-...-.++-++.|..|.|.|.+..+
T Consensus 4 ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s~~a 83 (390)
T KOG2785|consen 4 FTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFASPKA 83 (390)
T ss_pred ceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccChhh
Q ss_pred hhhHhhh
Q 038614 217 LGGHKKI 223 (263)
Q Consensus 217 L~~H~r~ 223 (263)
-..|+..
T Consensus 84 ~~~hl~S 90 (390)
T KOG2785|consen 84 HENHLKS 90 (390)
T ss_pred HHHHHHH
No 122
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=29.18 E-value=26 Score=27.00 Aligned_cols=40 Identities=20% Similarity=0.285 Sum_probs=21.6
Q ss_pred ccCCCCCCCcccccchhhhhcccCCCCccccCcccccccC
Q 038614 124 RGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKEFRS 163 (263)
Q Consensus 124 ~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~F~s 163 (263)
+.|..||.....--.++....--....-|+|..||..|+.
T Consensus 73 ~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wre 112 (113)
T COG1594 73 EKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWRE 112 (113)
T ss_pred ccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEeec
Confidence 4678888754433222211111111234899999988864
No 123
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=28.53 E-value=30 Score=21.29 Aligned_cols=14 Identities=36% Similarity=0.833 Sum_probs=12.2
Q ss_pred ceecCccccccCCc
Q 038614 201 VFKCPFCDKVFDSG 214 (263)
Q Consensus 201 p~~C~~Cgk~F~~~ 214 (263)
||.|..|++.|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 89999999999654
No 124
>PLN02294 cytochrome c oxidase subunit Vb
Probab=28.44 E-value=28 Score=28.86 Aligned_cols=20 Identities=25% Similarity=0.652 Sum_probs=14.8
Q ss_pred cccccCCcceecCccccccCC
Q 038614 193 DAVVMDQRVFKCPFCDKVFDS 213 (263)
Q Consensus 193 ~~~h~g~kp~~C~~Cgk~F~~ 213 (263)
+.++.| +|++|++||..|.-
T Consensus 134 f~L~kG-kp~RCpeCG~~fkL 153 (174)
T PLN02294 134 FWLEKG-KSFECPVCTQYFEL 153 (174)
T ss_pred EEecCC-CceeCCCCCCEEEE
Confidence 344444 79999999999853
No 125
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=27.79 E-value=30 Score=27.07 Aligned_cols=26 Identities=31% Similarity=0.443 Sum_probs=22.8
Q ss_pred CCcceecCccccccCCchhhhhHhhh
Q 038614 198 DQRVFKCPFCDKVFDSGQALGGHKKI 223 (263)
Q Consensus 198 g~kp~~C~~Cgk~F~~~~~L~~H~r~ 223 (263)
|.-.|-|-.|.+-|.+..+|..|.|+
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 44578999999999999999999874
No 126
>PF15269 zf-C2H2_7: Zinc-finger
Probab=27.37 E-value=34 Score=21.92 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=19.9
Q ss_pred ceecCccccccCCchhhhhHhhhhc
Q 038614 201 VFKCPFCDKVFDSGQALGGHKKIHF 225 (263)
Q Consensus 201 p~~C~~Cgk~F~~~~~L~~H~r~H~ 225 (263)
-|+|-+|..+..-+++|-.||+--.
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky~l 44 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKYSL 44 (54)
T ss_pred cceeecCCcccchHHHHHHHHHHHh
Confidence 3678888888888999999987543
No 127
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=27.09 E-value=38 Score=29.23 Aligned_cols=26 Identities=27% Similarity=0.662 Sum_probs=20.4
Q ss_pred CCcceecCccccccCCchhhhhHhhh
Q 038614 198 DQRVFKCPFCDKVFDSGQALGGHKKI 223 (263)
Q Consensus 198 g~kp~~C~~Cgk~F~~~~~L~~H~r~ 223 (263)
.+.-|.|+.|+|.|.-..-...|+..
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 45579999999999999999999765
No 128
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=26.51 E-value=29 Score=30.64 Aligned_cols=47 Identities=17% Similarity=0.266 Sum_probs=31.0
Q ss_pred cccCCCCCCCcccccchhhhhcccCCCCccccCcccccccChhhhhhhhh
Q 038614 123 VRGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKKEFRSYQALGGHKA 172 (263)
Q Consensus 123 ~~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k~F~s~~~L~~H~~ 172 (263)
.|.|..||+...-. .+..|+..-.+ ..|.|-.|++.|.. -....|..
T Consensus 3 ~FtCnvCgEsvKKp-~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 3 FFTCNVCGESVKKP-QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EEehhhhhhhcccc-chHHHHHhccC-CeeEEeeccccccc-chhhhhhh
Confidence 35788888876643 34456644444 67889999999987 44555544
No 129
>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=26.39 E-value=44 Score=19.82 Aligned_cols=24 Identities=25% Similarity=0.199 Sum_probs=15.2
Q ss_pred ccCCCCCCCcccccchhhhhcccCCCCccccCcccc
Q 038614 124 RGKSDDGDNDEEEDKEEDESSLVSRTNKYKCKTCKK 159 (263)
Q Consensus 124 ~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~~C~k 159 (263)
+.|..||...... +.|..|.+|+.
T Consensus 3 ~~C~~CG~i~~g~------------~~p~~CP~Cg~ 26 (34)
T cd00729 3 WVCPVCGYIHEGE------------EAPEKCPICGA 26 (34)
T ss_pred EECCCCCCEeECC------------cCCCcCcCCCC
Confidence 4677777665421 24568888875
No 130
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=25.69 E-value=46 Score=22.59 Aligned_cols=11 Identities=27% Similarity=0.848 Sum_probs=9.1
Q ss_pred CcceecCcccc
Q 038614 199 QRVFKCPFCDK 209 (263)
Q Consensus 199 ~kp~~C~~Cgk 209 (263)
..+|.|+.||.
T Consensus 46 ~~~Y~CP~CGF 56 (59)
T PRK14890 46 SNPYTCPKCGF 56 (59)
T ss_pred CCceECCCCCC
Confidence 46899999985
No 131
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.35 E-value=42 Score=32.69 Aligned_cols=48 Identities=17% Similarity=0.194 Sum_probs=26.7
Q ss_pred ccCcccccccChhhhhhhhhhcCCCcccccCCCCcccccccccccCCcceecCccccc
Q 038614 153 KCKTCKKEFRSYQALGGHKASHKKIKIHHNGSSDAAAAGGDAVVMDQRVFKCPFCDKV 210 (263)
Q Consensus 153 kC~~C~k~F~s~~~L~~H~~~H~~~kp~~~~~~~~~~~~h~~~h~g~kp~~C~~Cgk~ 210 (263)
.|..||....-.. -...+..|.......|.+|+.. ..-|..|+.|+..
T Consensus 215 ~C~~Cg~~~~C~~-C~~~l~~h~~~~~l~Ch~Cg~~---------~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 215 LCRSCGYILCCPN-CDVSLTYHKKEGKLRCHYCGYQ---------EPIPKTCPQCGSE 262 (505)
T ss_pred EhhhCcCccCCCC-CCCceEEecCCCeEEcCCCcCc---------CCCCCCCCCCCCC
Confidence 5777776654321 1223444444444556666542 2457789999853
No 132
>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=25.22 E-value=30 Score=21.59 Aligned_cols=15 Identities=40% Similarity=0.698 Sum_probs=10.1
Q ss_pred cceecCccccccCCc
Q 038614 200 RVFKCPFCDKVFDSG 214 (263)
Q Consensus 200 kp~~C~~Cgk~F~~~ 214 (263)
-||.|..|++.|-..
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 489999999999654
No 133
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=25.09 E-value=16 Score=37.16 Aligned_cols=9 Identities=33% Similarity=0.951 Sum_probs=5.5
Q ss_pred ceecCcccc
Q 038614 201 VFKCPFCDK 209 (263)
Q Consensus 201 p~~C~~Cgk 209 (263)
+-.|+.||-
T Consensus 140 ~~~C~~Cgp 148 (711)
T TIGR00143 140 PIACPRCGP 148 (711)
T ss_pred CccCCCCCc
Confidence 446777764
No 134
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=24.65 E-value=44 Score=27.17 Aligned_cols=19 Identities=16% Similarity=0.646 Sum_probs=14.5
Q ss_pred CCccccCcccccccChhhh
Q 038614 149 TNKYKCKTCKKEFRSYQAL 167 (263)
Q Consensus 149 ~kp~kC~~C~k~F~s~~~L 167 (263)
++.-.|..|++.|..+-..
T Consensus 26 RRRReC~~C~~RFTTfE~~ 44 (156)
T COG1327 26 RRRRECLECGERFTTFERA 44 (156)
T ss_pred hhhhcccccccccchhhee
Confidence 4456899999999887544
No 135
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=24.36 E-value=47 Score=31.56 Aligned_cols=45 Identities=27% Similarity=0.476 Sum_probs=0.0
Q ss_pred hhhhhcccCCCCccccCcccccccChhhhhhhhhhcCCCcccccCCCCcccccccccccCCcceecCccc
Q 038614 139 EEDESSLVSRTNKYKCKTCKKEFRSYQALGGHKASHKKIKIHHNGSSDAAAAGGDAVVMDQRVFKCPFCD 208 (263)
Q Consensus 139 ~~~h~~~h~~~kp~kC~~C~k~F~s~~~L~~H~~~H~~~kp~~~~~~~~~~~~h~~~h~g~kp~~C~~Cg 208 (263)
+....+-.+...-|.|+.|.+.|...-++..--..-. .|.|..|+
T Consensus 116 led~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~-------------------------~F~C~~C~ 160 (436)
T KOG2593|consen 116 LEDRLRDDTNVAGYVCPNCQKKYTSLEALQLLDNETG-------------------------EFHCENCG 160 (436)
T ss_pred HHHHhhhccccccccCCccccchhhhHHHHhhcccCc-------------------------eEEEecCC
No 136
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=23.57 E-value=31 Score=24.42 Aligned_cols=42 Identities=10% Similarity=0.161 Sum_probs=25.4
Q ss_pred ccCCCCCCCcccccchhhhhcccCCCCccccC--cccccccChhhh
Q 038614 124 RGKSDDGDNDEEEDKEEDESSLVSRTNKYKCK--TCKKEFRSYQAL 167 (263)
Q Consensus 124 ~~c~~c~~~~~~~~~~~~h~~~h~~~kp~kC~--~C~k~F~s~~~L 167 (263)
..|..||............ ....+.-++|. .||.+|.....+
T Consensus 2 m~CP~Cg~~a~irtSr~~s--~~~~~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYIT--DTTKERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred ccCCCCCCccEEEEChhcC--hhhheeeeecCCCCCCCEEEEEEEE
Confidence 3577777765332221111 12456778998 899999876654
No 137
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=22.89 E-value=23 Score=21.74 Aligned_cols=12 Identities=33% Similarity=0.880 Sum_probs=9.0
Q ss_pred ccccCccccccc
Q 038614 151 KYKCKTCKKEFR 162 (263)
Q Consensus 151 p~kC~~C~k~F~ 162 (263)
-|.|..|++.|+
T Consensus 28 fy~C~~C~~~wr 39 (39)
T PF01096_consen 28 FYVCCNCGHRWR 39 (39)
T ss_dssp EEEESSSTEEEE
T ss_pred EEEeCCCCCeeC
Confidence 488888888763
No 138
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=22.87 E-value=46 Score=31.79 Aligned_cols=28 Identities=18% Similarity=0.396 Sum_probs=22.9
Q ss_pred cccCCcceecCccc-cccCCchhhhhHhh
Q 038614 195 VVMDQRVFKCPFCD-KVFDSGQALGGHKK 222 (263)
Q Consensus 195 ~h~g~kp~~C~~Cg-k~F~~~~~L~~H~r 222 (263)
+|.=.+-|.|.+|| +++.-..++.+|..
T Consensus 395 LHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 395 LHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hcCCCcccceeeccCccccCcHHHHHHhH
Confidence 34446689999999 99999999999954
No 139
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=22.66 E-value=59 Score=30.14 Aligned_cols=15 Identities=27% Similarity=0.107 Sum_probs=10.6
Q ss_pred cccCCchhhhhHhhh
Q 038614 209 KVFDSGQALGGHKKI 223 (263)
Q Consensus 209 k~F~~~~~L~~H~r~ 223 (263)
.+|.....|..|+-.
T Consensus 289 ~vf~~~~el~~h~~~ 303 (493)
T COG5236 289 YVFPYHTELLEHLTR 303 (493)
T ss_pred EEeccHHHHHHHHHH
Confidence 467777778888644
No 140
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=22.37 E-value=44 Score=20.58 Aligned_cols=12 Identities=33% Similarity=0.949 Sum_probs=9.1
Q ss_pred ccccCccccccc
Q 038614 151 KYKCKTCKKEFR 162 (263)
Q Consensus 151 p~kC~~C~k~F~ 162 (263)
-|.|..|+..|.
T Consensus 28 fy~C~~C~~~w~ 39 (40)
T smart00440 28 FYVCTKCGHRWR 39 (40)
T ss_pred EEEeCCCCCEeC
Confidence 488888887764
No 141
>TIGR03510 XapX XapX domain. This model describes an uncharacterized small, hydrophobic protein of about 50 amino acids, found between the xapB and xapR genes of the E. coli xanthosine utilization system, and homologous regions in other small proteins, such as the N-terminal region of DUF1427 (Pfam model pfam07235). We name this domain XapX, as it comprises the full length of the protein encoded between the genes for the well-studied XapB and XapR proteins.
Probab=22.18 E-value=35 Score=22.27 Aligned_cols=12 Identities=25% Similarity=0.512 Sum_probs=10.0
Q ss_pred CCCCCCCCCCCC
Q 038614 245 KFIDLNLPAPED 256 (263)
Q Consensus 245 ~~~dlnlpa~~~ 256 (263)
+.+|++.|||+-
T Consensus 17 ~~l~vp~PAPP~ 28 (49)
T TIGR03510 17 SLLKVPSPAPPV 28 (49)
T ss_pred HHhCCCCCCCch
Confidence 468999999973
No 142
>COG1773 Rubredoxin [Energy production and conversion]
Probab=22.11 E-value=40 Score=22.56 Aligned_cols=14 Identities=29% Similarity=1.001 Sum_probs=11.5
Q ss_pred cceecCccccccCC
Q 038614 200 RVFKCPFCDKVFDS 213 (263)
Q Consensus 200 kp~~C~~Cgk~F~~ 213 (263)
+.|+|..||..|.-
T Consensus 2 ~~~~C~~CG~vYd~ 15 (55)
T COG1773 2 KRWRCSVCGYVYDP 15 (55)
T ss_pred CceEecCCceEecc
Confidence 36899999999854
No 143
>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=21.84 E-value=40 Score=22.21 Aligned_cols=27 Identities=26% Similarity=0.551 Sum_probs=15.5
Q ss_pred CCccccCcccccccChhhhhhhhhhcC
Q 038614 149 TNKYKCKTCKKEFRSYQALGGHKASHK 175 (263)
Q Consensus 149 ~kp~kC~~C~k~F~s~~~L~~H~~~H~ 175 (263)
...|+|+.|++.|-..=.+-.|...|.
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 356999999999988888777765553
No 144
>PRK05580 primosome assembly protein PriA; Validated
Probab=21.77 E-value=59 Score=32.93 Aligned_cols=46 Identities=15% Similarity=0.219 Sum_probs=23.7
Q ss_pred cccCcccccccCh---hhhhhhhhhcCCCcccccCCCCcccccccccccCCcceecCccccc
Q 038614 152 YKCKTCKKEFRSY---QALGGHKASHKKIKIHHNGSSDAAAAGGDAVVMDQRVFKCPFCDKV 210 (263)
Q Consensus 152 ~kC~~C~k~F~s~---~~L~~H~~~H~~~kp~~~~~~~~~~~~h~~~h~g~kp~~C~~Cgk~ 210 (263)
..|..||..+.-. ..|..| .......|.+|+.. ...|..|+.||..
T Consensus 382 ~~C~~Cg~~~~C~~C~~~l~~h----~~~~~l~Ch~Cg~~---------~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 382 LLCRDCGWVAECPHCDASLTLH----RFQRRLRCHHCGYQ---------EPIPKACPECGST 430 (679)
T ss_pred eEhhhCcCccCCCCCCCceeEE----CCCCeEECCCCcCC---------CCCCCCCCCCcCC
Confidence 3466666554321 223333 33333446666532 2457789999764
No 145
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=21.45 E-value=51 Score=33.41 Aligned_cols=53 Identities=17% Similarity=0.303 Sum_probs=28.1
Q ss_pred cCcccccccChhhhhhhhhhcCCCcccc-cCCCCccccc--ccccccCCcceecCcccc
Q 038614 154 CKTCKKEFRSYQALGGHKASHKKIKIHH-NGSSDAAAAG--GDAVVMDQRVFKCPFCDK 209 (263)
Q Consensus 154 C~~C~k~F~s~~~L~~H~~~H~~~kp~~-~~~~~~~~~~--h~~~h~g~kp~~C~~Cgk 209 (263)
|..||-.|+--.+|-- -|-++..+.|. |.+|.+.+.. ..|-| -.|.-|+.||-
T Consensus 126 CT~CGPRfTIi~alPY-DR~nTsM~~F~lC~~C~~EY~dP~nRRfH--AQp~aCp~CGP 181 (750)
T COG0068 126 CTNCGPRFTIIEALPY-DRENTSMADFPLCPFCDKEYKDPLNRRFH--AQPIACPKCGP 181 (750)
T ss_pred cCCCCcceeeeccCCC-CcccCccccCcCCHHHHHHhcCccccccc--cccccCcccCC
Confidence 6667766665555432 23344444443 5565543321 22333 24778999985
No 146
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=20.88 E-value=42 Score=26.28 Aligned_cols=26 Identities=23% Similarity=0.457 Sum_probs=22.9
Q ss_pred CCCccccCcccccccChhhhhhhhhh
Q 038614 148 RTNKYKCKTCKKEFRSYQALGGHKAS 173 (263)
Q Consensus 148 ~~kp~kC~~C~k~F~s~~~L~~H~~~ 173 (263)
|-..|-|-.|.+-|....+|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 55679999999999999999999764
No 147
>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=20.27 E-value=54 Score=24.65 Aligned_cols=24 Identities=25% Similarity=0.488 Sum_probs=21.5
Q ss_pred ccc----CcccccccChhhhhhhhhhcC
Q 038614 152 YKC----KTCKKEFRSYQALGGHKASHK 175 (263)
Q Consensus 152 ~kC----~~C~k~F~s~~~L~~H~~~H~ 175 (263)
|.| ..|+..+.+...+..|.+.+.
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~H 108 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEH 108 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhc
Confidence 899 999999999999999987654
No 148
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=20.27 E-value=47 Score=20.67 Aligned_cols=12 Identities=25% Similarity=0.960 Sum_probs=10.4
Q ss_pred cceecCcccccc
Q 038614 200 RVFKCPFCDKVF 211 (263)
Q Consensus 200 kp~~C~~Cgk~F 211 (263)
++-.|+.|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 478999999987
No 149
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=20.22 E-value=42 Score=21.92 Aligned_cols=12 Identities=33% Similarity=1.024 Sum_probs=6.6
Q ss_pred ecCccccccCCc
Q 038614 203 KCPFCDKVFDSG 214 (263)
Q Consensus 203 ~C~~Cgk~F~~~ 214 (263)
.||.|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 899999999653
No 150
>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=20.09 E-value=45 Score=28.77 Aligned_cols=28 Identities=21% Similarity=0.501 Sum_probs=21.0
Q ss_pred CCCccccCcccccccChhhhhhhhhhcC
Q 038614 148 RTNKYKCKTCKKEFRSYQALGGHKASHK 175 (263)
Q Consensus 148 ~~kp~kC~~C~k~F~s~~~L~~H~~~H~ 175 (263)
.+..|.|..|+|.|.-...+..|+..-.
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcC
Confidence 4456999999999999999999977543
Done!