Query 031966
Match_columns 150
No_of_seqs 233 out of 1718
Neff 9.7
Searched_HMMs 46136
Date Fri Mar 29 07:48:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031966.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031966hhsearch_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 3.1E-20 6.8E-25 131.6 4.7 109 3-113 140-261 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.8 1.1E-20 2.4E-25 133.8 2.3 84 4-89 172-265 (279)
3 KOG1074 Transcriptional repres 99.7 2.1E-17 4.5E-22 131.4 1.3 44 2-45 362-405 (958)
4 KOG3623 Homeobox transcription 99.5 2.6E-15 5.7E-20 118.3 1.0 73 17-89 890-972 (1007)
5 KOG1074 Transcriptional repres 99.4 1E-14 2.2E-19 116.4 -0.0 78 2-93 614-694 (958)
6 KOG3576 Ovo and related transc 99.3 1.4E-13 3E-18 94.2 -0.6 74 18-91 114-198 (267)
7 KOG3623 Homeobox transcription 99.3 9.6E-13 2.1E-17 104.1 1.0 51 3-53 904-954 (1007)
8 PHA02768 hypothetical protein; 99.2 5.4E-12 1.2E-16 69.1 2.0 44 21-84 5-48 (55)
9 KOG3576 Ovo and related transc 99.2 2.9E-12 6.4E-17 87.7 0.7 93 3-95 127-240 (267)
10 PHA00733 hypothetical protein 99.2 3.3E-11 7.2E-16 78.5 4.1 64 8-92 61-124 (128)
11 KOG3608 Zn finger proteins [Ge 99.1 2.1E-11 4.5E-16 89.7 0.2 96 2-98 188-322 (467)
12 PF13465 zf-H2C2_2: Zinc-finge 99.0 5.4E-11 1.2E-15 56.0 0.6 26 8-33 1-26 (26)
13 KOG3608 Zn finger proteins [Ge 98.8 2.5E-09 5.4E-14 79.0 3.5 90 1-91 271-376 (467)
14 PF13465 zf-H2C2_2: Zinc-finge 98.8 2.5E-09 5.4E-14 50.3 2.2 26 36-79 1-26 (26)
15 KOG3993 Transcription factor ( 98.8 2.1E-09 4.5E-14 80.9 1.2 91 3-93 277-382 (500)
16 PHA00732 hypothetical protein 98.7 1.5E-08 3.2E-13 60.4 2.7 47 21-91 1-48 (79)
17 PHA00616 hypothetical protein 98.6 1.9E-08 4.2E-13 52.6 1.3 33 21-53 1-33 (44)
18 PHA00616 hypothetical protein 98.5 2.9E-08 6.3E-13 51.9 0.9 33 67-99 1-33 (44)
19 PHA02768 hypothetical protein; 98.4 2.7E-07 5.9E-12 50.7 2.1 25 67-91 5-29 (55)
20 PHA00733 hypothetical protein 98.3 2.6E-07 5.6E-12 60.3 1.6 72 18-104 37-108 (128)
21 PF00096 zf-C2H2: Zinc finger, 98.3 4.2E-07 9.2E-12 41.2 1.7 23 68-90 1-23 (23)
22 PLN03086 PRLI-interacting fact 98.3 1.4E-06 3E-11 69.2 5.4 80 19-102 451-548 (567)
23 COG5189 SFP1 Putative transcri 98.2 8.2E-07 1.8E-11 65.0 2.1 71 18-88 346-419 (423)
24 PF00096 zf-C2H2: Zinc finger, 98.1 1.3E-06 2.9E-11 39.6 1.6 23 22-44 1-23 (23)
25 PLN03086 PRLI-interacting fact 98.1 2.9E-06 6.3E-11 67.4 4.3 77 6-88 465-561 (567)
26 PF13912 zf-C2H2_6: C2H2-type 98.0 3.8E-06 8.2E-11 39.6 1.4 26 67-92 1-26 (27)
27 PF05605 zf-Di19: Drought indu 97.9 2.1E-05 4.6E-10 43.5 4.1 51 21-91 2-53 (54)
28 PF13894 zf-C2H2_4: C2H2-type 97.9 9E-06 2E-10 36.8 1.8 24 68-91 1-24 (24)
29 PF13912 zf-C2H2_6: C2H2-type 97.8 1.4E-05 3.1E-10 37.5 1.4 25 21-45 1-25 (27)
30 PF13894 zf-C2H2_4: C2H2-type 97.6 3.9E-05 8.5E-10 34.6 1.8 23 22-44 1-23 (24)
31 PF12756 zf-C2H2_2: C2H2 type 97.5 5.8E-05 1.3E-09 46.6 2.2 68 23-91 1-74 (100)
32 smart00355 ZnF_C2H2 zinc finge 97.5 6.4E-05 1.4E-09 34.4 1.5 25 68-92 1-25 (26)
33 PF09237 GAGA: GAGA factor; I 97.5 0.00011 2.3E-09 39.5 2.2 33 63-95 20-52 (54)
34 PF09237 GAGA: GAGA factor; I 97.4 0.00016 3.5E-09 38.8 2.5 32 17-48 20-51 (54)
35 smart00355 ZnF_C2H2 zinc finge 97.3 0.00018 3.9E-09 32.8 2.0 24 22-45 1-24 (26)
36 PRK04860 hypothetical protein; 97.3 0.00015 3.2E-09 49.1 2.0 40 20-81 118-157 (160)
37 KOG3993 Transcription factor ( 97.1 8.7E-05 1.9E-09 56.6 -0.6 57 22-96 268-324 (500)
38 PHA00732 hypothetical protein 97.1 0.00046 9.9E-09 41.1 2.3 37 67-106 1-38 (79)
39 PF12874 zf-met: Zinc-finger o 96.9 0.00046 1E-08 31.6 1.3 23 68-90 1-23 (25)
40 PF12874 zf-met: Zinc-finger o 96.8 0.00062 1.4E-08 31.1 1.2 23 22-44 1-23 (25)
41 PF13909 zf-H2C2_5: C2H2-type 96.6 0.0014 3E-08 29.7 1.5 23 68-91 1-23 (24)
42 PF12171 zf-C2H2_jaz: Zinc-fin 96.5 0.0011 2.5E-08 30.9 0.9 22 22-43 2-23 (27)
43 PF12171 zf-C2H2_jaz: Zinc-fin 96.5 0.00084 1.8E-08 31.4 0.3 22 68-89 2-23 (27)
44 PF13913 zf-C2HC_2: zinc-finge 96.0 0.0045 9.8E-08 28.4 1.4 21 68-89 3-23 (25)
45 COG5048 FOG: Zn-finger [Genera 95.8 0.0048 1E-07 47.2 1.7 51 2-52 298-354 (467)
46 KOG1146 Homeobox protein [Gene 95.6 0.011 2.4E-07 51.3 3.1 85 5-89 448-540 (1406)
47 PF13913 zf-C2HC_2: zinc-finge 95.5 0.013 2.9E-07 26.8 1.8 21 22-43 3-23 (25)
48 PF13909 zf-H2C2_5: C2H2-type 95.4 0.014 3E-07 26.2 1.8 22 22-44 1-22 (24)
49 COG5048 FOG: Zn-finger [Genera 95.0 0.0087 1.9E-07 45.8 0.6 61 20-98 288-354 (467)
50 smart00451 ZnF_U1 U1-like zinc 94.9 0.029 6.3E-07 27.5 2.2 23 21-43 3-25 (35)
51 smart00451 ZnF_U1 U1-like zinc 94.6 0.022 4.8E-07 28.0 1.4 23 67-89 3-25 (35)
52 PF12756 zf-C2H2_2: C2H2 type 92.4 0.12 2.7E-06 31.4 2.4 24 21-44 50-73 (100)
53 PRK04860 hypothetical protein; 91.1 0.17 3.8E-06 34.3 2.1 35 66-104 118-152 (160)
54 PF09986 DUF2225: Uncharacteri 91.0 0.072 1.6E-06 37.9 0.2 54 19-80 3-61 (214)
55 PF09538 FYDLN_acid: Protein o 90.7 0.16 3.5E-06 32.1 1.5 17 64-80 23-39 (108)
56 PF05605 zf-Di19: Drought indu 89.9 0.24 5.2E-06 27.0 1.6 34 67-101 2-37 (54)
57 COG4049 Uncharacterized protei 89.3 0.21 4.6E-06 27.4 1.1 32 61-92 11-42 (65)
58 KOG2893 Zn finger protein [Gen 89.1 0.17 3.6E-06 36.4 0.8 47 23-91 12-59 (341)
59 cd00350 rubredoxin_like Rubred 87.6 0.41 8.9E-06 23.3 1.4 10 66-75 16-25 (33)
60 smart00614 ZnF_BED BED zinc fi 86.8 0.56 1.2E-05 25.1 1.8 25 67-91 18-48 (50)
61 COG1592 Rubrerythrin [Energy p 86.4 0.49 1.1E-05 32.2 1.7 12 63-74 145-156 (166)
62 PF05443 ROS_MUCR: ROS/MUCR tr 85.0 0.53 1.1E-05 30.9 1.3 29 65-96 70-98 (132)
63 KOG1146 Homeobox protein [Gene 84.8 0.84 1.8E-05 40.4 2.7 69 19-90 1282-1351(1406)
64 COG5189 SFP1 Putative transcri 84.7 0.49 1.1E-05 35.5 1.2 27 63-89 345-373 (423)
65 TIGR02300 FYDLN_acid conserved 84.6 0.69 1.5E-05 30.0 1.7 21 64-84 23-43 (129)
66 PF02892 zf-BED: BED zinc fing 84.3 0.98 2.1E-05 23.4 2.0 25 64-88 13-41 (45)
67 cd00729 rubredoxin_SM Rubredox 83.1 0.83 1.8E-05 22.4 1.3 10 66-75 17-26 (34)
68 smart00659 RPOLCX RNA polymera 83.0 1.1 2.4E-05 23.5 1.8 13 21-33 2-14 (44)
69 PRK00398 rpoP DNA-directed RNA 82.2 1 2.2E-05 23.6 1.5 13 21-33 3-15 (46)
70 KOG4167 Predicted DNA-binding 81.4 0.29 6.3E-06 40.5 -1.1 27 67-93 792-818 (907)
71 COG4049 Uncharacterized protei 80.6 0.78 1.7E-05 25.2 0.7 29 14-42 10-38 (65)
72 TIGR02098 MJ0042_CXXC MJ0042 f 80.5 1.4 3.1E-05 21.9 1.6 34 22-78 3-36 (38)
73 PF13719 zinc_ribbon_5: zinc-r 79.8 1.7 3.8E-05 21.7 1.8 34 22-78 3-36 (37)
74 TIGR02605 CxxC_CxxC_SSSS putat 79.6 0.55 1.2E-05 25.2 -0.1 13 21-33 5-17 (52)
75 PRK00464 nrdR transcriptional 79.5 0.45 9.7E-06 32.1 -0.6 18 66-83 27-44 (154)
76 smart00531 TFIIE Transcription 79.5 2.1 4.4E-05 28.6 2.6 40 17-78 95-134 (147)
77 PF04959 ARS2: Arsenite-resist 77.5 1.3 2.9E-05 31.4 1.3 31 63-93 73-103 (214)
78 COG2888 Predicted Zn-ribbon RN 77.2 2.2 4.7E-05 23.8 1.8 11 65-75 48-58 (61)
79 KOG4124 Putative transcription 76.4 0.72 1.6E-05 35.0 -0.3 68 19-86 347-417 (442)
80 PF03604 DNA_RNApol_7kD: DNA d 76.2 2.1 4.6E-05 20.7 1.4 11 66-76 16-26 (32)
81 PF13717 zinc_ribbon_4: zinc-r 74.3 3.5 7.7E-05 20.4 2.0 33 22-77 3-35 (36)
82 TIGR00373 conserved hypothetic 74.0 2.4 5.3E-05 28.6 1.8 24 14-37 102-125 (158)
83 KOG2186 Cell growth-regulating 73.6 3 6.5E-05 30.4 2.2 49 22-91 4-52 (276)
84 PF12013 DUF3505: Protein of u 72.1 2.9 6.3E-05 26.2 1.7 70 19-92 9-109 (109)
85 PF01927 Mut7-C: Mut7-C RNAse 71.0 3.8 8.2E-05 27.3 2.2 22 65-86 122-143 (147)
86 COG4530 Uncharacterized protei 70.8 2.1 4.6E-05 27.0 0.9 22 63-85 22-43 (129)
87 PRK06266 transcription initiat 70.6 2.8 6.1E-05 28.9 1.5 36 17-79 113-148 (178)
88 COG1996 RPC10 DNA-directed RNA 70.3 2.8 6.1E-05 22.5 1.1 13 19-31 4-16 (49)
89 smart00734 ZnF_Rad18 Rad18-lik 69.5 4.9 0.00011 18.3 1.8 20 22-42 2-21 (26)
90 PF04959 ARS2: Arsenite-resist 68.4 3.5 7.6E-05 29.4 1.6 28 17-44 73-100 (214)
91 PRK14890 putative Zn-ribbon RN 67.5 4.2 9E-05 22.7 1.5 10 66-75 47-56 (59)
92 PRK09678 DNA-binding transcrip 66.5 1.7 3.8E-05 25.3 -0.2 20 63-82 23-44 (72)
93 smart00834 CxxC_CXXC_SSSS Puta 66.2 2.9 6.2E-05 21.0 0.7 15 67-81 5-19 (41)
94 cd00924 Cyt_c_Oxidase_Vb Cytoc 65.8 2.4 5.1E-05 26.3 0.3 22 11-33 70-91 (97)
95 KOG2785 C2H2-type Zn-finger pr 65.4 6.1 0.00013 30.5 2.5 70 21-90 3-91 (390)
96 PF07754 DUF1610: Domain of un 63.9 3.5 7.6E-05 18.6 0.6 10 66-75 15-24 (24)
97 COG1997 RPL43A Ribosomal prote 63.0 4.3 9.2E-05 24.5 1.0 16 66-81 52-67 (89)
98 KOG2593 Transcription initiati 62.7 7.7 0.00017 30.5 2.6 24 14-37 121-144 (436)
99 PF09723 Zn-ribbon_8: Zinc rib 62.3 3.7 8E-05 21.1 0.6 15 67-81 5-19 (42)
100 KOG4167 Predicted DNA-binding 61.8 1.3 2.8E-05 36.9 -1.7 24 21-44 792-815 (907)
101 COG4957 Predicted transcriptio 61.1 4.5 9.7E-05 26.6 1.0 23 22-47 77-99 (148)
102 COG2331 Uncharacterized protei 58.8 2.3 5E-05 24.9 -0.6 11 21-31 12-22 (82)
103 PF10571 UPF0547: Uncharacteri 58.6 4.6 0.0001 18.5 0.5 10 69-78 16-25 (26)
104 PLN02294 cytochrome c oxidase 57.1 5.7 0.00012 27.2 1.0 19 60-79 135-153 (174)
105 PF08790 zf-LYAR: LYAR-type C2 56.9 3.6 7.8E-05 19.3 0.0 19 68-87 1-19 (28)
106 KOG3408 U1-like Zn-finger-cont 56.2 7.1 0.00015 25.2 1.2 25 20-44 56-80 (129)
107 KOG4173 Alpha-SNAP protein [In 55.9 3.8 8.3E-05 28.9 0.0 58 23-89 108-168 (253)
108 PRK03824 hypA hydrogenase nick 55.7 4.1 8.9E-05 26.8 0.2 15 20-34 69-83 (135)
109 smart00154 ZnF_AN1 AN1-like Zi 55.6 6.1 0.00013 20.0 0.7 14 67-80 12-25 (39)
110 KOG2785 C2H2-type Zn-finger pr 55.4 19 0.00042 27.9 3.6 69 20-89 165-242 (390)
111 PF05290 Baculo_IE-1: Baculovi 54.9 10 0.00022 24.9 1.8 21 16-36 75-95 (140)
112 PHA00626 hypothetical protein 54.0 7 0.00015 21.5 0.8 15 66-80 22-36 (59)
113 COG3091 SprT Zn-dependent meta 53.9 8.8 0.00019 25.8 1.4 14 19-33 115-128 (156)
114 PF01428 zf-AN1: AN1-like Zinc 52.7 6 0.00013 20.3 0.4 15 66-80 12-26 (43)
115 PF09845 DUF2072: Zn-ribbon co 52.6 6.4 0.00014 25.7 0.6 15 67-81 1-15 (131)
116 COG1571 Predicted DNA-binding 52.1 9 0.00019 30.2 1.5 18 64-81 364-381 (421)
117 PF10276 zf-CHCC: Zinc-finger 51.5 9.7 0.00021 19.4 1.1 12 66-77 28-39 (40)
118 KOG2231 Predicted E3 ubiquitin 51.5 16 0.00035 30.6 2.9 17 75-91 220-236 (669)
119 PF10013 DUF2256: Uncharacteri 51.0 8.2 0.00018 19.9 0.8 16 69-84 10-25 (42)
120 PF15269 zf-C2H2_7: Zinc-finge 49.5 11 0.00024 19.7 1.1 23 68-90 21-43 (54)
121 KOG2071 mRNA cleavage and poly 49.2 10 0.00023 31.0 1.5 29 65-93 416-444 (579)
122 PF01363 FYVE: FYVE zinc finge 48.5 11 0.00025 21.2 1.2 11 22-32 10-20 (69)
123 PRK12380 hydrogenase nickel in 48.4 10 0.00022 24.1 1.1 12 21-32 70-81 (113)
124 PF12013 DUF3505: Protein of u 47.7 18 0.00039 22.6 2.1 23 22-44 81-107 (109)
125 KOG3507 DNA-directed RNA polym 46.9 17 0.00037 20.2 1.6 13 66-78 36-48 (62)
126 KOG2482 Predicted C2H2-type Zn 46.1 12 0.00027 28.6 1.4 23 67-89 195-217 (423)
127 PRK14873 primosome assembly pr 45.8 12 0.00025 31.5 1.3 11 66-76 421-431 (665)
128 KOG3408 U1-like Zn-finger-cont 45.6 13 0.00028 24.0 1.2 26 64-89 54-79 (129)
129 PF13451 zf-trcl: Probable zin 45.4 11 0.00023 20.3 0.7 18 65-82 2-19 (49)
130 PRK03681 hypA hydrogenase nick 45.0 13 0.00029 23.6 1.3 12 20-31 69-80 (114)
131 KOG2636 Splicing factor 3a, su 44.4 15 0.00032 29.2 1.6 29 60-88 394-423 (497)
132 TIGR00100 hypA hydrogenase nic 44.0 14 0.0003 23.5 1.2 14 20-33 69-82 (115)
133 PF07975 C1_4: TFIIH C1-like d 43.9 8.5 0.00018 20.8 0.2 26 19-44 19-44 (51)
134 PRK05978 hypothetical protein; 42.9 9.1 0.0002 25.7 0.2 12 69-80 54-65 (148)
135 PRK00564 hypA hydrogenase nick 42.7 17 0.00036 23.3 1.4 14 20-33 70-83 (117)
136 PF06524 NOA36: NOA36 protein; 41.6 11 0.00024 27.7 0.6 75 16-91 137-233 (314)
137 PF04423 Rad50_zn_hook: Rad50 41.3 11 0.00023 20.4 0.3 12 69-80 22-33 (54)
138 PF13878 zf-C2H2_3: zinc-finge 40.6 23 0.00049 18.0 1.5 24 68-91 14-39 (41)
139 PF01215 COX5B: Cytochrome c o 40.1 14 0.0003 24.4 0.8 19 60-79 106-124 (136)
140 COG3364 Zn-ribbon containing p 39.9 15 0.00033 22.9 0.9 16 67-82 2-17 (112)
141 KOG2636 Splicing factor 3a, su 39.5 22 0.00048 28.3 1.9 29 14-42 394-423 (497)
142 COG4338 Uncharacterized protei 39.5 11 0.00024 20.0 0.2 17 69-85 14-30 (54)
143 KOG2231 Predicted E3 ubiquitin 38.7 26 0.00057 29.4 2.3 65 23-88 184-260 (669)
144 KOG2071 mRNA cleavage and poly 38.2 21 0.00045 29.4 1.6 26 19-44 416-441 (579)
145 COG1198 PriA Primosomal protei 37.6 22 0.00047 30.2 1.7 45 23-76 437-484 (730)
146 KOG0717 Molecular chaperone (D 37.6 20 0.00042 28.7 1.4 22 68-89 293-314 (508)
147 PF04780 DUF629: Protein of un 37.0 23 0.00051 28.3 1.7 32 63-94 53-85 (466)
148 KOG0717 Molecular chaperone (D 36.5 24 0.00052 28.2 1.7 22 22-43 293-314 (508)
149 KOG2482 Predicted C2H2-type Zn 35.6 22 0.00048 27.3 1.3 23 21-43 195-217 (423)
150 PF11931 DUF3449: Domain of un 35.3 12 0.00027 26.2 0.0 29 60-88 94-123 (196)
151 PF10263 SprT-like: SprT-like 35.2 18 0.00039 23.9 0.7 13 66-78 142-154 (157)
152 PRK04351 hypothetical protein; 35.0 22 0.00047 23.9 1.1 14 65-78 130-143 (149)
153 PF01286 XPA_N: XPA protein N- 34.8 17 0.00037 17.8 0.4 13 68-80 4-16 (34)
154 PF14353 CpXC: CpXC protein 34.4 19 0.00041 23.1 0.7 23 66-88 37-59 (128)
155 cd00065 FYVE FYVE domain; Zinc 34.4 29 0.00062 18.5 1.4 11 23-33 4-14 (57)
156 PTZ00043 cytochrome c oxidase 33.5 20 0.00044 25.8 0.8 16 64-79 178-193 (268)
157 PF06397 Desulfoferrod_N: Desu 33.2 21 0.00046 17.8 0.6 11 20-30 5-15 (36)
158 COG3677 Transposase and inacti 33.1 24 0.00052 23.0 1.0 15 19-33 51-65 (129)
159 COG1773 Rubredoxin [Energy pro 33.0 20 0.00042 19.8 0.5 13 21-33 3-15 (55)
160 COG5236 Uncharacterized conser 33.0 47 0.001 25.7 2.7 83 6-89 201-303 (493)
161 PTZ00448 hypothetical protein; 31.0 29 0.00063 26.9 1.3 23 67-89 314-336 (373)
162 smart00064 FYVE Protein presen 30.5 34 0.00074 19.1 1.3 11 22-32 11-21 (68)
163 COG4391 Uncharacterized protei 29.8 22 0.00048 20.0 0.4 12 67-78 48-59 (62)
164 PF14787 zf-CCHC_5: GAG-polypr 29.0 26 0.00056 17.4 0.5 16 69-84 4-19 (36)
165 smart00731 SprT SprT homologue 28.7 38 0.00083 22.3 1.5 12 66-77 132-143 (146)
166 PLN02748 tRNA dimethylallyltra 28.6 34 0.00073 27.5 1.4 25 65-89 416-441 (468)
167 COG5188 PRP9 Splicing factor 3 27.3 37 0.00081 26.2 1.3 28 61-88 368-396 (470)
168 PRK06260 threonine synthase; V 27.3 47 0.001 25.9 2.0 11 22-32 4-14 (397)
169 PTZ00448 hypothetical protein; 26.7 50 0.0011 25.7 1.9 23 21-43 314-336 (373)
170 PLN02748 tRNA dimethylallyltra 26.5 51 0.0011 26.5 2.0 26 19-44 416-442 (468)
171 TIGR00622 ssl1 transcription f 26.2 50 0.0011 21.1 1.6 24 21-44 81-104 (112)
172 TIGR00686 phnA alkylphosphonat 26.1 42 0.00092 21.2 1.2 15 66-80 18-32 (109)
173 COG5151 SSL1 RNA polymerase II 26.0 68 0.0015 24.4 2.5 26 66-91 387-412 (421)
174 PRK00762 hypA hydrogenase nick 25.9 27 0.00058 22.5 0.4 14 20-34 69-82 (124)
175 PF05191 ADK_lid: Adenylate ki 25.7 32 0.00069 17.0 0.5 11 68-78 2-12 (36)
176 TIGR00416 sms DNA repair prote 25.7 52 0.0011 26.3 2.0 11 21-31 7-17 (454)
177 TIGR01206 lysW lysine biosynth 25.6 29 0.00062 19.0 0.4 12 68-79 3-14 (54)
178 PRK11823 DNA repair protein Ra 25.2 54 0.0012 26.1 2.0 12 20-31 6-17 (446)
179 PF00301 Rubredoxin: Rubredoxi 25.0 35 0.00077 18.0 0.7 12 68-79 2-13 (47)
180 COG1656 Uncharacterized conser 25.0 49 0.0011 22.6 1.5 23 66-88 129-151 (165)
181 PF02748 PyrI_C: Aspartate car 24.7 34 0.00073 18.5 0.5 19 15-33 29-47 (52)
182 COG3357 Predicted transcriptio 24.6 36 0.00078 20.8 0.7 14 20-33 57-70 (97)
183 cd00730 rubredoxin Rubredoxin; 24.3 31 0.00067 18.5 0.3 12 68-79 2-13 (50)
184 PF12907 zf-met2: Zinc-binding 24.2 24 0.00053 18.0 -0.1 26 68-93 2-31 (40)
185 PF06220 zf-U1: U1 zinc finger 23.5 76 0.0017 15.8 1.7 15 21-35 3-17 (38)
186 PLN03238 probable histone acet 23.4 1.1E+02 0.0023 23.1 3.0 26 19-44 46-71 (290)
187 PF01780 Ribosomal_L37ae: Ribo 23.3 39 0.00085 20.6 0.7 11 66-76 34-44 (90)
188 KOG0978 E3 ubiquitin ligase in 23.2 29 0.00062 29.3 0.1 21 66-86 677-697 (698)
189 PTZ00303 phosphatidylinositol 23.2 31 0.00068 29.7 0.3 13 22-34 461-473 (1374)
190 KOG1842 FYVE finger-containing 23.1 39 0.00085 26.9 0.8 28 66-93 14-42 (505)
191 COG1675 TFA1 Transcription ini 23.0 69 0.0015 22.2 1.9 20 16-35 108-127 (176)
192 PF01096 TFIIS_C: Transcriptio 22.9 39 0.00084 16.9 0.5 10 68-77 29-38 (39)
193 PF03811 Zn_Tnp_IS1: InsA N-te 22.8 53 0.0012 16.2 1.0 19 9-27 17-35 (36)
194 PRK10220 hypothetical protein; 22.5 69 0.0015 20.3 1.7 16 66-81 19-34 (111)
195 PF04780 DUF629: Protein of un 22.2 67 0.0015 25.9 2.0 25 20-44 56-81 (466)
196 PF08209 Sgf11: Sgf11 (transcr 21.9 44 0.00095 16.2 0.6 23 67-90 4-26 (33)
197 TIGR00319 desulf_FeS4 desulfof 21.5 51 0.0011 15.7 0.8 12 20-31 6-17 (34)
198 KOG3352 Cytochrome c oxidase, 21.3 43 0.00094 22.5 0.6 18 60-78 127-144 (153)
199 TIGR00244 transcriptional regu 21.3 39 0.00085 22.6 0.4 18 66-83 27-44 (147)
200 cd00974 DSRD Desulforedoxin (D 21.0 52 0.0011 15.7 0.8 11 21-31 4-14 (34)
201 cd01121 Sms Sms (bacterial rad 20.7 70 0.0015 24.9 1.8 10 67-76 14-23 (372)
202 KOG2807 RNA polymerase II tran 20.5 1.8E+02 0.004 22.4 3.8 72 20-91 289-369 (378)
203 PRK04023 DNA polymerase II lar 20.5 82 0.0018 28.0 2.2 13 66-78 662-674 (1121)
204 KOG1280 Uncharacterized conser 20.2 1.6E+02 0.0034 22.9 3.4 25 19-43 77-101 (381)
205 PRK08222 hydrogenase 4 subunit 20.1 78 0.0017 21.8 1.8 21 19-39 112-132 (181)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.80 E-value=3.1e-20 Score=131.60 Aligned_cols=109 Identities=21% Similarity=0.257 Sum_probs=90.5
Q ss_pred cccccccchhhhhcCC---CCceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCc----cc------ccccccCCCCcee
Q 031966 3 LTRSNRAKLPIKKRLA---SDVFECKTCNRQFPSFQALGGHRASHKKPRLINGET----KT------LSSTTATKPKLHE 69 (150)
Q Consensus 3 f~~~~~l~~h~~~h~~---~~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~----~~------~h~~~h~~~kp~~ 69 (150)
+...++|.+|.++|-. .+.+.|++|||.|.+.-.|..|+|+|+ -++.|.. +. .|+|+|+|||||.
T Consensus 140 ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~ 217 (279)
T KOG2462|consen 140 YSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFS 217 (279)
T ss_pred cccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCCcc
Confidence 4567789999998853 467899999999999999999999996 4555555 22 7999999999999
Q ss_pred ccccccccccchHHHHHhHhcccchhhcccccccccCCCCcccc
Q 031966 70 CSICGQEFAMGQALGGHMRRHRIAMNESLNSAVIVSQSPPVLRR 113 (150)
Q Consensus 70 C~~Cgk~f~~~~~l~~H~~~h~~~~~~~~~~~~~~~~~~~~~~~ 113 (150)
|..|+|+|+.+++|+.||++|.+.++..+..+...+...+-+.+
T Consensus 218 C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnK 261 (279)
T KOG2462|consen 218 CPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNK 261 (279)
T ss_pred CCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHH
Confidence 99999999999999999999999999999888877766554444
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.80 E-value=1.1e-20 Score=133.85 Aligned_cols=84 Identities=24% Similarity=0.382 Sum_probs=75.7
Q ss_pred ccccccchhhhhcCCCCceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCccc----------ccccccCCCCceecccc
Q 031966 4 TRSNRAKLPIKKRLASDVFECKTCNRQFPSFQALGGHRASHKKPRLINGETKT----------LSSTTATKPKLHECSIC 73 (150)
Q Consensus 4 ~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~~~----------~h~~~h~~~kp~~C~~C 73 (150)
..--.|+.|+++|+ -+++|.+|||.|.++.-|..|+|+|+|||||.|..+. .|+.+|++.|+|.|..|
T Consensus 172 vSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C 249 (279)
T KOG2462|consen 172 VSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRC 249 (279)
T ss_pred eehHHHhhHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcch
Confidence 34456899999998 6899999999999999999999999999999987721 79999999999999999
Q ss_pred ccccccchHHHHHhHh
Q 031966 74 GQEFAMGQALGGHMRR 89 (150)
Q Consensus 74 gk~f~~~~~l~~H~~~ 89 (150)
+|.|+..+.|.+|...
T Consensus 250 ~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 250 GKSFALKSYLNKHSES 265 (279)
T ss_pred hhHHHHHHHHHHhhhh
Confidence 9999999999999764
No 3
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.65 E-value=2.1e-17 Score=131.45 Aligned_cols=44 Identities=16% Similarity=0.444 Sum_probs=40.9
Q ss_pred ccccccccchhhhhcCCCCceecCCCCCcCCCHHHHHhhHHhcC
Q 031966 2 LLTRSNRAKLPIKKRLASDVFECKTCNRQFPSFQALGGHRASHK 45 (150)
Q Consensus 2 ~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~h~ 45 (150)
||...+.|+.|+|.|+||+||+|++||..|.++.+|+.|...|.
T Consensus 362 vfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~ 405 (958)
T KOG1074|consen 362 VFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHR 405 (958)
T ss_pred hcCchhhhhhhhhccCCCCCeeecccccccccccceeeeeeecc
Confidence 68889999999999999999999999999999999999976664
No 4
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.51 E-value=2.6e-15 Score=118.32 Aligned_cols=73 Identities=18% Similarity=0.381 Sum_probs=62.4
Q ss_pred CCCCceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCccc----------ccccccCCCCceeccccccccccchHHHHH
Q 031966 17 LASDVFECKTCNRQFPSFQALGGHRASHKKPRLINGETKT----------LSSTTATKPKLHECSICGQEFAMGQALGGH 86 (150)
Q Consensus 17 ~~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~~~----------~h~~~h~~~kp~~C~~Cgk~f~~~~~l~~H 86 (150)
+.+-+|.|+.|+|.|...+.|.+|.--|+|.|||+|..+. .|.|.|+|||||.|..|+|.|+..+.+.+|
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQH 969 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQH 969 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhh
Confidence 3456788888888888888888888888888888887721 677888999999999999999999999999
Q ss_pred hHh
Q 031966 87 MRR 89 (150)
Q Consensus 87 ~~~ 89 (150)
|..
T Consensus 970 MNH 972 (1007)
T KOG3623|consen 970 MNH 972 (1007)
T ss_pred hcc
Confidence 863
No 5
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.45 E-value=1e-14 Score=116.40 Aligned_cols=78 Identities=24% Similarity=0.453 Sum_probs=70.2
Q ss_pred ccccccccchhhhhcCCCCceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCcccccccccCCCCceecc---ccccccc
Q 031966 2 LLTRSNRAKLPIKKRLASDVFECKTCNRQFPSFQALGGHRASHKKPRLINGETKTLSSTTATKPKLHECS---ICGQEFA 78 (150)
Q Consensus 2 ~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~~~~h~~~h~~~kp~~C~---~Cgk~f~ 78 (150)
|+...+.|+.|+|+|+|||||+|.+||++|..+.+|+.|+-+|...-+++ -+|.|+ +|-+.|.
T Consensus 614 VlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R--------------~q~ScP~~~ic~~kft 679 (958)
T KOG1074|consen 614 VLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPAR--------------VQFSCPSTFICQKKFT 679 (958)
T ss_pred cccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCcccc--------------ccccCCchhhhccccc
Confidence 45778899999999999999999999999999999999999997655542 578899 9999999
Q ss_pred cchHHHHHhHhcccc
Q 031966 79 MGQALGGHMRRHRIA 93 (150)
Q Consensus 79 ~~~~l~~H~~~h~~~ 93 (150)
....|.+|+++|.+.
T Consensus 680 n~V~lpQhIriH~~~ 694 (958)
T KOG1074|consen 680 NAVTLPQHIRIHLGG 694 (958)
T ss_pred ccccccceEEeecCC
Confidence 999999999999854
No 6
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.33 E-value=1.4e-13 Score=94.16 Aligned_cols=74 Identities=23% Similarity=0.418 Sum_probs=58.1
Q ss_pred CCCceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCc----c------cccccccCCCCceeccccccccccchHHHHHh
Q 031966 18 ASDVFECKTCNRQFPSFQALGGHRASHKKPRLINGET----K------TLSSTTATKPKLHECSICGQEFAMGQALGGHM 87 (150)
Q Consensus 18 ~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~----~------~~h~~~h~~~kp~~C~~Cgk~f~~~~~l~~H~ 87 (150)
+.-.|.|.+|+|.|.....|.+|++-|...+.+.|.. + ..|.++|+|.+||+|..|+|+|.....|..|.
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 3456888888888888888888888887766655433 1 17888889999999999999999999999998
Q ss_pred H-hcc
Q 031966 88 R-RHR 91 (150)
Q Consensus 88 ~-~h~ 91 (150)
+ +|.
T Consensus 194 ~kvhg 198 (267)
T KOG3576|consen 194 KKVHG 198 (267)
T ss_pred HHHcC
Confidence 6 454
No 7
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.27 E-value=9.6e-13 Score=104.14 Aligned_cols=51 Identities=12% Similarity=0.288 Sum_probs=27.3
Q ss_pred cccccccchhhhhcCCCCceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCC
Q 031966 3 LTRSNRAKLPIKKRLASDVFECKTCNRQFPSFQALGGHRASHKKPRLINGE 53 (150)
Q Consensus 3 f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~ 53 (150)
|.+.++|.+|.--|+|.|||+|.+|.|+|..+.+|..|+|.|+|+|||+|+
T Consensus 904 FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCd 954 (1007)
T KOG3623|consen 904 FQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCD 954 (1007)
T ss_pred HHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhh
Confidence 445555555555555555555555555555555555555555555555553
No 8
>PHA02768 hypothetical protein; Provisional
Probab=99.22 E-value=5.4e-12 Score=69.13 Aligned_cols=44 Identities=16% Similarity=0.201 Sum_probs=39.6
Q ss_pred ceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCcccccccccCCCCceeccccccccccchHHH
Q 031966 21 VFECKTCNRQFPSFQALGGHRASHKKPRLINGETKTLSSTTATKPKLHECSICGQEFAMGQALG 84 (150)
Q Consensus 21 ~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~~~~h~~~h~~~kp~~C~~Cgk~f~~~~~l~ 84 (150)
-|.|+.||+.|...++|..|+++| + ++|+|..|++.|+..+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H------------------~--k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKH------------------N--TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhc------------------C--CcccCCcccceecccceeE
Confidence 389999999999999999999999 4 6889999999999887764
No 9
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.20 E-value=2.9e-12 Score=87.72 Aligned_cols=93 Identities=17% Similarity=0.166 Sum_probs=74.1
Q ss_pred cccccccchhhhhcCCCCceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCc----cc------ccc-ccc---------
Q 031966 3 LTRSNRAKLPIKKRLASDVFECKTCNRQFPSFQALGGHRASHKKPRLINGET----KT------LSS-TTA--------- 62 (150)
Q Consensus 3 f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~----~~------~h~-~~h--------- 62 (150)
|.-..-|.+|++.|+.-+.|-|..|||.|...-.|++|+|+|+|.+||+|.. ++ .|. ++|
T Consensus 127 F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yayk 206 (267)
T KOG3576|consen 127 FGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYK 206 (267)
T ss_pred hhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHH
Confidence 4445567889999999999999999999999999999999999999999866 11 222 122
Q ss_pred -CCCCceeccccccccccchHHHHHhHhcccchh
Q 031966 63 -TKPKLHECSICGQEFAMGQALGGHMRRHRIAMN 95 (150)
Q Consensus 63 -~~~kp~~C~~Cgk~f~~~~~l~~H~~~h~~~~~ 95 (150)
..+|-|.|..||..-.....+..|++.|+...+
T Consensus 207 err~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 207 ERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred HhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 456789999999999999999999998776543
No 10
>PHA00733 hypothetical protein
Probab=99.16 E-value=3.3e-11 Score=78.50 Aligned_cols=64 Identities=20% Similarity=0.344 Sum_probs=52.5
Q ss_pred ccchhhhhcCCCCceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCcccccccccCCCCceeccccccccccchHHHHHh
Q 031966 8 RAKLPIKKRLASDVFECKTCNRQFPSFQALGGHRASHKKPRLINGETKTLSSTTATKPKLHECSICGQEFAMGQALGGHM 87 (150)
Q Consensus 8 ~l~~h~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~~~~h~~~h~~~kp~~C~~Cgk~f~~~~~l~~H~ 87 (150)
.|..|+..+ +++||.|+.||+.|.....|..|++.| +.+|.|..|++.|.....|..|+
T Consensus 61 ~l~~~~~~~-~~kPy~C~~Cgk~Fss~s~L~~H~r~h--------------------~~~~~C~~CgK~F~~~~sL~~H~ 119 (128)
T PHA00733 61 YLYKLLTSK-AVSPYVCPLCLMPFSSSVSLKQHIRYT--------------------EHSKVCPVCGKEFRNTDSTLDHV 119 (128)
T ss_pred HHHhhcccC-CCCCccCCCCCCcCCCHHHHHHHHhcC--------------------CcCccCCCCCCccCCHHHHHHHH
Confidence 345554444 588999999999999999999998865 24689999999999999999999
Q ss_pred Hhccc
Q 031966 88 RRHRI 92 (150)
Q Consensus 88 ~~h~~ 92 (150)
...++
T Consensus 120 ~~~h~ 124 (128)
T PHA00733 120 CKKHN 124 (128)
T ss_pred HHhcC
Confidence 87654
No 11
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.08 E-value=2.1e-11 Score=89.72 Aligned_cols=96 Identities=17% Similarity=0.234 Sum_probs=74.0
Q ss_pred ccccccccchhhhhcCCCCceecCCCCCcCCCHHHHHhhHHhc--CCCCCCCCCc--cc---------------------
Q 031966 2 LLTRSNRAKLPIKKRLASDVFECKTCNRQFPSFQALGGHRASH--KKPRLINGET--KT--------------------- 56 (150)
Q Consensus 2 ~f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~h--~~~k~~~c~~--~~--------------------- 56 (150)
+|..+..|+.|++.|++||...|..||..|++...|-.|.+.. ....+|.|.. +.
T Consensus 188 ~~~~k~~LreH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCp 267 (467)
T KOG3608|consen 188 HMGNKYRLREHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCP 267 (467)
T ss_pred hhccHHHHHHHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhhccccc
Confidence 3667888999999999999999999999999999888887543 3344555533 00
Q ss_pred -------------cccc-ccCCCCceeccccccccccchHHHHHhHhcccchhhcc
Q 031966 57 -------------LSST-TATKPKLHECSICGQEFAMGQALGGHMRRHRIAMNESL 98 (150)
Q Consensus 57 -------------~h~~-~h~~~kp~~C~~Cgk~f~~~~~l~~H~~~h~~~~~~~~ 98 (150)
.|++ .|+..|||+|..|.+.|.+.+.|.+|..+|. +....+
T Consensus 268 lCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C 322 (467)
T KOG3608|consen 268 LCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQC 322 (467)
T ss_pred ccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceec
Confidence 3443 4688999999999999999999999999887 444443
No 12
>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=99.03 E-value=5.4e-11 Score=56.05 Aligned_cols=26 Identities=12% Similarity=0.525 Sum_probs=23.8
Q ss_pred ccchhhhhcCCCCceecCCCCCcCCC
Q 031966 8 RAKLPIKKRLASDVFECKTCNRQFPS 33 (150)
Q Consensus 8 ~l~~h~~~h~~~~~~~C~~C~k~f~~ 33 (150)
+|..|+++|+|++||.|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 47899999999999999999999863
No 13
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.84 E-value=2.5e-09 Score=78.99 Aligned_cols=90 Identities=19% Similarity=0.361 Sum_probs=72.0
Q ss_pred Cccccccccchhhh-hcCCCCceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCc--cc----------cccc-ccCC--
Q 031966 1 MLLTRSNRAKLPIK-KRLASDVFECKTCNRQFPSFQALGGHRASHKKPRLINGET--KT----------LSST-TATK-- 64 (150)
Q Consensus 1 m~f~~~~~l~~h~~-~h~~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~--~~----------~h~~-~h~~-- 64 (150)
|.....++|..|++ .|+.+|||+|+.|++.|.+.+.|..|..+|+ +-.|.|+. .. .|.+ .|.|
T Consensus 271 mtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~n 349 (467)
T KOG3608|consen 271 MTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNN 349 (467)
T ss_pred cCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCC
Confidence 44556788999998 5888999999999999999999999999998 66788765 11 3443 3334
Q ss_pred CCceeccccccccccchHHHHHhHhcc
Q 031966 65 PKLHECSICGQEFAMGQALGGHMRRHR 91 (150)
Q Consensus 65 ~kp~~C~~Cgk~f~~~~~l~~H~~~h~ 91 (150)
+-+|.|..|.+.|.+..+|..|+...+
T Consensus 350 p~~Y~CH~Cdr~ft~G~~L~~HL~kkH 376 (467)
T KOG3608|consen 350 PILYACHCCDRFFTSGKSLSAHLMKKH 376 (467)
T ss_pred CCceeeecchhhhccchhHHHHHHHhh
Confidence 457999999999999999999986533
No 14
>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=98.83 E-value=2.5e-09 Score=50.28 Aligned_cols=26 Identities=35% Similarity=0.649 Sum_probs=22.2
Q ss_pred HHHhhHHhcCCCCCCCCCcccccccccCCCCceecccccccccc
Q 031966 36 ALGGHRASHKKPRLINGETKTLSSTTATKPKLHECSICGQEFAM 79 (150)
Q Consensus 36 ~L~~H~~~h~~~k~~~c~~~~~h~~~h~~~kp~~C~~Cgk~f~~ 79 (150)
+|.+|+++| ++++||.|+.|++.|.+
T Consensus 1 ~l~~H~~~H------------------~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTH------------------TGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHH------------------SSSSSEEESSSSEEESS
T ss_pred CHHHHhhhc------------------CCCCCCCCCCCcCeeCc
Confidence 477888887 88899999999999964
No 15
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.77 E-value=2.1e-09 Score=80.90 Aligned_cols=91 Identities=20% Similarity=0.338 Sum_probs=62.5
Q ss_pred cccccccchhhhhcCCCCceecCCCCCcCCCHHHHHhhHHhcCCCCCCC-CCc---cc---------cccccc--CCCCc
Q 031966 3 LTRSNRAKLPIKKRLASDVFECKTCNRQFPSFQALGGHRASHKKPRLIN-GET---KT---------LSSTTA--TKPKL 67 (150)
Q Consensus 3 f~~~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~-c~~---~~---------~h~~~h--~~~kp 67 (150)
|...+.|..|.-...----|+|.+|+|.|+.+.||..|+|+|.-..... -.. +. .-.+.. ..+--
T Consensus 277 YeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi 356 (500)
T KOG3993|consen 277 YEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGI 356 (500)
T ss_pred hhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCce
Confidence 4556677777644444445999999999999999999999995322211 000 00 000100 22337
Q ss_pred eeccccccccccchHHHHHhHhcccc
Q 031966 68 HECSICGQEFAMGQALGGHMRRHRIA 93 (150)
Q Consensus 68 ~~C~~Cgk~f~~~~~l~~H~~~h~~~ 93 (150)
|.|.+|||.|.+...|+.|+.+|...
T Consensus 357 ~~C~~C~KkFrRqAYLrKHqlthq~~ 382 (500)
T KOG3993|consen 357 FSCHTCGKKFRRQAYLRKHQLTHQRA 382 (500)
T ss_pred eecHHhhhhhHHHHHHHHhHHhhhcc
Confidence 99999999999999999999987654
No 16
>PHA00732 hypothetical protein
Probab=98.68 E-value=1.5e-08 Score=60.45 Aligned_cols=47 Identities=28% Similarity=0.631 Sum_probs=38.8
Q ss_pred ceecCCCCCcCCCHHHHHhhHHh-cCCCCCCCCCcccccccccCCCCceeccccccccccchHHHHHhHhcc
Q 031966 21 VFECKTCNRQFPSFQALGGHRAS-HKKPRLINGETKTLSSTTATKPKLHECSICGQEFAMGQALGGHMRRHR 91 (150)
Q Consensus 21 ~~~C~~C~k~f~~~~~L~~H~~~-h~~~k~~~c~~~~~h~~~h~~~kp~~C~~Cgk~f~~~~~l~~H~~~h~ 91 (150)
||.|..||+.|.....|..|++. | . ++.|+.||+.|. .|..|..++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H------------------~---~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNH------------------T---LTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhccc------------------C---CCccCCCCCEeC---ChhhhhcccC
Confidence 68999999999999999999984 5 2 357999999997 4778875543
No 17
>PHA00616 hypothetical protein
Probab=98.59 E-value=1.9e-08 Score=52.58 Aligned_cols=33 Identities=21% Similarity=0.351 Sum_probs=28.4
Q ss_pred ceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCC
Q 031966 21 VFECKTCNRQFPSFQALGGHRASHKKPRLINGE 53 (150)
Q Consensus 21 ~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~ 53 (150)
||.|..||+.|...+.|..|++.|+|++++.|+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 689999999999999999999999666555543
No 18
>PHA00616 hypothetical protein
Probab=98.52 E-value=2.9e-08 Score=51.93 Aligned_cols=33 Identities=18% Similarity=0.309 Sum_probs=29.9
Q ss_pred ceeccccccccccchHHHHHhHhcccchhhccc
Q 031966 67 LHECSICGQEFAMGQALGGHMRRHRIAMNESLN 99 (150)
Q Consensus 67 p~~C~~Cgk~f~~~~~l~~H~~~h~~~~~~~~~ 99 (150)
||.|..||+.|...+.|..|++.|+|+.+...+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 689999999999999999999999999776554
No 19
>PHA02768 hypothetical protein; Provisional
Probab=98.36 E-value=2.7e-07 Score=50.66 Aligned_cols=25 Identities=32% Similarity=0.723 Sum_probs=23.9
Q ss_pred ceeccccccccccchHHHHHhHhcc
Q 031966 67 LHECSICGQEFAMGQALGGHMRRHR 91 (150)
Q Consensus 67 p~~C~~Cgk~f~~~~~l~~H~~~h~ 91 (150)
-|.|++||+.|+..++|..|+++|+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN 29 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC
Confidence 4799999999999999999999999
No 20
>PHA00733 hypothetical protein
Probab=98.31 E-value=2.6e-07 Score=60.26 Aligned_cols=72 Identities=13% Similarity=0.031 Sum_probs=52.1
Q ss_pred CCCceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCcccccccccCCCCceeccccccccccchHHHHHhHhcccchhhc
Q 031966 18 ASDVFECKTCNRQFPSFQALGGHRASHKKPRLINGETKTLSSTTATKPKLHECSICGQEFAMGQALGGHMRRHRIAMNES 97 (150)
Q Consensus 18 ~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~~~~h~~~h~~~kp~~C~~Cgk~f~~~~~l~~H~~~h~~~~~~~ 97 (150)
..+++.|.+|.+.|..+..|..+.... .++. +.+++||.|..||+.|.....|..|++.|. .+..
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~------------~~~~-~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~--~~~~ 101 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLY------------KLLT-SKAVSPYVCPLCLMPFSSSVSLKQHIRYTE--HSKV 101 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHH------------hhcc-cCCCCCccCCCCCCcCCCHHHHHHHHhcCC--cCcc
Confidence 357899999999999988888773221 1111 245789999999999999999999999763 2344
Q ss_pred ccccccc
Q 031966 98 LNSAVIV 104 (150)
Q Consensus 98 ~~~~~~~ 104 (150)
+..+...
T Consensus 102 C~~CgK~ 108 (128)
T PHA00733 102 CPVCGKE 108 (128)
T ss_pred CCCCCCc
Confidence 4444433
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=98.29 E-value=4.2e-07 Score=41.24 Aligned_cols=23 Identities=48% Similarity=0.982 Sum_probs=21.6
Q ss_pred eeccccccccccchHHHHHhHhc
Q 031966 68 HECSICGQEFAMGQALGGHMRRH 90 (150)
Q Consensus 68 ~~C~~Cgk~f~~~~~l~~H~~~h 90 (150)
|.|+.|++.|.....|..|++.|
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 22
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.28 E-value=1.4e-06 Score=69.21 Aligned_cols=80 Identities=13% Similarity=0.245 Sum_probs=58.9
Q ss_pred CCceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCC--cc------cccccccCCCCceecccccccccc----------c
Q 031966 19 SDVFECKTCNRQFPSFQALGGHRASHKKPRLINGE--TK------TLSSTTATKPKLHECSICGQEFAM----------G 80 (150)
Q Consensus 19 ~~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~--~~------~~h~~~h~~~kp~~C~~Cgk~f~~----------~ 80 (150)
++.+.|..|++.|. ...|..|+.+|. +++.|. .. ..|..+|..++++.|..|++.|.. .
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~CpCg~~~~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~ 527 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCPCGVVLEKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRL 527 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CCccCCCCCCcchhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhh
Confidence 45578999999986 577899998874 566663 21 168888899999999999998852 3
Q ss_pred hHHHHHhHhcccchhhcccccc
Q 031966 81 QALGGHMRRHRIAMNESLNSAV 102 (150)
Q Consensus 81 ~~l~~H~~~h~~~~~~~~~~~~ 102 (150)
..|..|..++ |.+...|..+.
T Consensus 528 s~Lt~HE~~C-G~rt~~C~~Cg 548 (567)
T PLN03086 528 RGMSEHESIC-GSRTAPCDSCG 548 (567)
T ss_pred hhHHHHHHhc-CCcceEccccC
Confidence 4788888885 66666665543
No 23
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=98.19 E-value=8.2e-07 Score=65.04 Aligned_cols=71 Identities=18% Similarity=0.409 Sum_probs=48.5
Q ss_pred CCCceecCC--CCCcCCCHHHHHhhHHh-cCCCCCCCCCcccccccccCCCCceeccccccccccchHHHHHhH
Q 031966 18 ASDVFECKT--CNRQFPSFQALGGHRAS-HKKPRLINGETKTLSSTTATKPKLHECSICGQEFAMGQALGGHMR 88 (150)
Q Consensus 18 ~~~~~~C~~--C~k~f~~~~~L~~H~~~-h~~~k~~~c~~~~~h~~~h~~~kp~~C~~Cgk~f~~~~~l~~H~~ 88 (150)
++|||+|++ |.|.|.....|+-|+.- |...+.-.-..--.+...-...|||.|++|+|.|.....|+-|+.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 469999986 99999999999999742 322111110000011112256799999999999999999988864
No 24
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.14 E-value=1.3e-06 Score=39.55 Aligned_cols=23 Identities=30% Similarity=0.710 Sum_probs=21.4
Q ss_pred eecCCCCCcCCCHHHHHhhHHhc
Q 031966 22 FECKTCNRQFPSFQALGGHRASH 44 (150)
Q Consensus 22 ~~C~~C~k~f~~~~~L~~H~~~h 44 (150)
|.|+.|++.|.....|..|++.|
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 78999999999999999999865
No 25
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.13 E-value=2.9e-06 Score=67.41 Aligned_cols=77 Identities=17% Similarity=0.264 Sum_probs=60.6
Q ss_pred ccccchhhhhcCCCCceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCccc--------------------ccccccCCC
Q 031966 6 SNRAKLPIKKRLASDVFECKTCNRQFPSFQALGGHRASHKKPRLINGETKT--------------------LSSTTATKP 65 (150)
Q Consensus 6 ~~~l~~h~~~h~~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~~~--------------------~h~~~h~~~ 65 (150)
...|..|+++|+ +++.|. ||+.+ ....|..|+.+|..++++.|..+. .|... .|.
T Consensus 465 ~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~-CG~ 539 (567)
T PLN03086 465 QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESI-CGS 539 (567)
T ss_pred hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHh-cCC
Confidence 356889999874 899999 99765 668999999999999999886521 35555 488
Q ss_pred CceeccccccccccchHHHHHhH
Q 031966 66 KLHECSICGQEFAMGQALGGHMR 88 (150)
Q Consensus 66 kp~~C~~Cgk~f~~~~~l~~H~~ 88 (150)
+++.|..||+.|..+ .|..|+.
T Consensus 540 rt~~C~~Cgk~Vrlr-dm~~H~~ 561 (567)
T PLN03086 540 RTAPCDSCGRSVMLK-EMDIHQI 561 (567)
T ss_pred cceEccccCCeeeeh-hHHHHHH
Confidence 999999999988655 4566664
No 26
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.97 E-value=3.8e-06 Score=39.57 Aligned_cols=26 Identities=38% Similarity=0.618 Sum_probs=23.9
Q ss_pred ceeccccccccccchHHHHHhHhccc
Q 031966 67 LHECSICGQEFAMGQALGGHMRRHRI 92 (150)
Q Consensus 67 p~~C~~Cgk~f~~~~~l~~H~~~h~~ 92 (150)
||.|..|++.|.....|..|++.|.+
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 68999999999999999999998764
No 27
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=97.93 E-value=2.1e-05 Score=43.45 Aligned_cols=51 Identities=25% Similarity=0.494 Sum_probs=38.4
Q ss_pred ceecCCCCCcCCCHHHHHhhHHh-cCCCCCCCCCcccccccccCCCCceeccccccccccchHHHHHhHhcc
Q 031966 21 VFECKTCNRQFPSFQALGGHRAS-HKKPRLINGETKTLSSTTATKPKLHECSICGQEFAMGQALGGHMRRHR 91 (150)
Q Consensus 21 ~~~C~~C~k~f~~~~~L~~H~~~-h~~~k~~~c~~~~~h~~~h~~~kp~~C~~Cgk~f~~~~~l~~H~~~h~ 91 (150)
.|.|+.|++. .....|..|... |. ...+.+.|+.|...+. .+|..|+..++
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~-----------------~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHR-----------------SESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCc-----------------CCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 4899999995 556789999754 42 2235789999998654 49999998754
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.88 E-value=9e-06 Score=36.83 Aligned_cols=24 Identities=42% Similarity=0.899 Sum_probs=20.1
Q ss_pred eeccccccccccchHHHHHhHhcc
Q 031966 68 HECSICGQEFAMGQALGGHMRRHR 91 (150)
Q Consensus 68 ~~C~~Cgk~f~~~~~l~~H~~~h~ 91 (150)
|.|+.|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 789999999999999999998763
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=97.76 E-value=1.4e-05 Score=37.55 Aligned_cols=25 Identities=44% Similarity=0.869 Sum_probs=23.1
Q ss_pred ceecCCCCCcCCCHHHHHhhHHhcC
Q 031966 21 VFECKTCNRQFPSFQALGGHRASHK 45 (150)
Q Consensus 21 ~~~C~~C~k~f~~~~~L~~H~~~h~ 45 (150)
||.|..|++.|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 6899999999999999999998873
No 30
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.63 E-value=3.9e-05 Score=34.63 Aligned_cols=23 Identities=35% Similarity=0.756 Sum_probs=19.5
Q ss_pred eecCCCCCcCCCHHHHHhhHHhc
Q 031966 22 FECKTCNRQFPSFQALGGHRASH 44 (150)
Q Consensus 22 ~~C~~C~k~f~~~~~L~~H~~~h 44 (150)
|.|+.|++.|.+...|..|++.|
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 78999999999999999999875
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.53 E-value=5.8e-05 Score=46.56 Aligned_cols=68 Identities=21% Similarity=0.301 Sum_probs=22.3
Q ss_pred ecCCCCCcCCCHHHHHhhHHhcCC-CCCC---CCCc--ccccccccCCCCceeccccccccccchHHHHHhHhcc
Q 031966 23 ECKTCNRQFPSFQALGGHRASHKK-PRLI---NGET--KTLSSTTATKPKLHECSICGQEFAMGQALGGHMRRHR 91 (150)
Q Consensus 23 ~C~~C~k~f~~~~~L~~H~~~h~~-~k~~---~c~~--~~~h~~~h~~~kp~~C~~Cgk~f~~~~~l~~H~~~h~ 91 (150)
+|..|+..|.....|..|+....+ ..+- .... .....+. .....+.|..|++.|.....|..|++.+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~-~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRK-KVKESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp -------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred Ccccccccccccccccccccccccccccccccccccccccccccc-ccCCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 489999999999999999854322 2110 0000 0111111 12237999999999999999999999753
No 32
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.49 E-value=6.4e-05 Score=34.42 Aligned_cols=25 Identities=40% Similarity=0.709 Sum_probs=22.3
Q ss_pred eeccccccccccchHHHHHhHhccc
Q 031966 68 HECSICGQEFAMGQALGGHMRRHRI 92 (150)
Q Consensus 68 ~~C~~Cgk~f~~~~~l~~H~~~h~~ 92 (150)
|.|..|++.|.....|..|++.|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~~ 25 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHXX 25 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhcc
Confidence 5799999999999999999997753
No 33
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.45 E-value=0.00011 Score=39.47 Aligned_cols=33 Identities=18% Similarity=0.396 Sum_probs=24.1
Q ss_pred CCCCceeccccccccccchHHHHHhHhcccchh
Q 031966 63 TKPKLHECSICGQEFAMGQALGGHMRRHRIAMN 95 (150)
Q Consensus 63 ~~~kp~~C~~Cgk~f~~~~~l~~H~~~h~~~~~ 95 (150)
..+.|..|++|+..++...+|++|+.++++.++
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 456899999999999999999999998877665
No 34
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=97.39 E-value=0.00016 Score=38.77 Aligned_cols=32 Identities=13% Similarity=0.202 Sum_probs=22.6
Q ss_pred CCCCceecCCCCCcCCCHHHHHhhHHhcCCCC
Q 031966 17 LASDVFECKTCNRQFPSFQALGGHRASHKKPR 48 (150)
Q Consensus 17 ~~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~k 48 (150)
..+.|-.|++|+..+.+..+|.+|+.++.+.|
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhccc
Confidence 46789999999999999999999997765444
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.34 E-value=0.00018 Score=32.85 Aligned_cols=24 Identities=33% Similarity=0.693 Sum_probs=21.8
Q ss_pred eecCCCCCcCCCHHHHHhhHHhcC
Q 031966 22 FECKTCNRQFPSFQALGGHRASHK 45 (150)
Q Consensus 22 ~~C~~C~k~f~~~~~L~~H~~~h~ 45 (150)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999998773
No 36
>PRK04860 hypothetical protein; Provisional
Probab=97.29 E-value=0.00015 Score=49.05 Aligned_cols=40 Identities=18% Similarity=0.444 Sum_probs=32.8
Q ss_pred CceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCcccccccccCCCCceeccccccccccch
Q 031966 20 DVFECKTCNRQFPSFQALGGHRASHKKPRLINGETKTLSSTTATKPKLHECSICGQEFAMGQ 81 (150)
Q Consensus 20 ~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~~~~h~~~h~~~kp~~C~~Cgk~f~~~~ 81 (150)
-+|.|. |++ ....+.+|.++| +++++|.|..|++.|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~------------------~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVV------------------RGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHh------------------cCCccEECCCCCceeEEec
Confidence 479998 987 566788899988 7888999999999886543
No 37
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.11 E-value=8.7e-05 Score=56.55 Aligned_cols=57 Identities=23% Similarity=0.461 Sum_probs=46.5
Q ss_pred eecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCcccccccccCCCCceeccccccccccchHHHHHhHhcccchhh
Q 031966 22 FECKTCNRQFPSFQALGGHRASHKKPRLINGETKTLSSTTATKPKLHECSICGQEFAMGQALGGHMRRHRIAMNE 96 (150)
Q Consensus 22 ~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~~~~h~~~h~~~kp~~C~~Cgk~f~~~~~l~~H~~~h~~~~~~ 96 (150)
|.|..|...|...-.|.+|+-.. ..-.-|+|++|+|.|+-..+|..|+|.|......
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~R------------------IV~vEYrCPEC~KVFsCPANLASHRRWHKPR~ea 324 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPR------------------IVHVEYRCPECDKVFSCPANLASHRRWHKPRPEA 324 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCe------------------eEEeeecCCcccccccCchhhhhhhcccCCchhh
Confidence 88999999999999999886322 1224599999999999999999999999765433
No 38
>PHA00732 hypothetical protein
Probab=97.06 E-value=0.00046 Score=41.14 Aligned_cols=37 Identities=27% Similarity=0.408 Sum_probs=28.6
Q ss_pred ceeccccccccccchHHHHHhHh-cccchhhcccccccccC
Q 031966 67 LHECSICGQEFAMGQALGGHMRR-HRIAMNESLNSAVIVSQ 106 (150)
Q Consensus 67 p~~C~~Cgk~f~~~~~l~~H~~~-h~~~~~~~~~~~~~~~~ 106 (150)
||.|..||+.|.....|..|++. |.+. .+..+.....
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~~---~C~~CgKsF~ 38 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTLT---KCPVCNKSYR 38 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCCC---ccCCCCCEeC
Confidence 68899999999999999999984 6643 4555554444
No 39
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.95 E-value=0.00046 Score=31.57 Aligned_cols=23 Identities=30% Similarity=0.730 Sum_probs=21.1
Q ss_pred eeccccccccccchHHHHHhHhc
Q 031966 68 HECSICGQEFAMGQALGGHMRRH 90 (150)
Q Consensus 68 ~~C~~Cgk~f~~~~~l~~H~~~h 90 (150)
|.|..|++.|.....|..|++.+
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 68999999999999999999764
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.84 E-value=0.00062 Score=31.12 Aligned_cols=23 Identities=39% Similarity=0.716 Sum_probs=21.0
Q ss_pred eecCCCCCcCCCHHHHHhhHHhc
Q 031966 22 FECKTCNRQFPSFQALGGHRASH 44 (150)
Q Consensus 22 ~~C~~C~k~f~~~~~L~~H~~~h 44 (150)
|.|.+|++.|.....|..|++.+
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 68999999999999999998764
No 41
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.62 E-value=0.0014 Score=29.68 Aligned_cols=23 Identities=26% Similarity=0.602 Sum_probs=18.4
Q ss_pred eeccccccccccchHHHHHhHhcc
Q 031966 68 HECSICGQEFAMGQALGGHMRRHR 91 (150)
Q Consensus 68 ~~C~~Cgk~f~~~~~l~~H~~~h~ 91 (150)
|.|..|+.... ...|.+|++.|.
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 889999999865
No 42
>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=96.53 E-value=0.0011 Score=30.94 Aligned_cols=22 Identities=36% Similarity=0.694 Sum_probs=20.3
Q ss_pred eecCCCCCcCCCHHHHHhhHHh
Q 031966 22 FECKTCNRQFPSFQALGGHRAS 43 (150)
Q Consensus 22 ~~C~~C~k~f~~~~~L~~H~~~ 43 (150)
|.|..|++.|.....+..|+++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 7899999999999999999865
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=96.49 E-value=0.00084 Score=31.41 Aligned_cols=22 Identities=27% Similarity=0.605 Sum_probs=20.3
Q ss_pred eeccccccccccchHHHHHhHh
Q 031966 68 HECSICGQEFAMGQALGGHMRR 89 (150)
Q Consensus 68 ~~C~~Cgk~f~~~~~l~~H~~~ 89 (150)
|.|..|++.|.+...|..|++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 6799999999999999999875
No 44
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.02 E-value=0.0045 Score=28.42 Aligned_cols=21 Identities=33% Similarity=0.700 Sum_probs=17.8
Q ss_pred eeccccccccccchHHHHHhHh
Q 031966 68 HECSICGQEFAMGQALGGHMRR 89 (150)
Q Consensus 68 ~~C~~Cgk~f~~~~~l~~H~~~ 89 (150)
..|+.||+.| ..+.|.+|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 3699999999 78889999765
No 45
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.82 E-value=0.0048 Score=47.24 Aligned_cols=51 Identities=20% Similarity=0.314 Sum_probs=45.4
Q ss_pred ccccccccchhhh--hcCCC--CceecC--CCCCcCCCHHHHHhhHHhcCCCCCCCC
Q 031966 2 LLTRSNRAKLPIK--KRLAS--DVFECK--TCNRQFPSFQALGGHRASHKKPRLING 52 (150)
Q Consensus 2 ~f~~~~~l~~h~~--~h~~~--~~~~C~--~C~k~f~~~~~L~~H~~~h~~~k~~~c 52 (150)
.|.....|..|.+ .|+++ +++.|. .|++.|.+...+..|...|.+.+++.+
T Consensus 298 ~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 (467)
T COG5048 298 SFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKE 354 (467)
T ss_pred CccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccc
Confidence 4778889999999 89999 999999 799999999999999999987776554
No 46
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=95.59 E-value=0.011 Score=51.26 Aligned_cols=85 Identities=15% Similarity=0.172 Sum_probs=57.8
Q ss_pred cccccchhhh-hcCCCCceecCCCCCcCCCHHHHHhhHHhcCCCCC-CCCCcccccc------cccCCCCceeccccccc
Q 031966 5 RSNRAKLPIK-KRLASDVFECKTCNRQFPSFQALGGHRASHKKPRL-INGETKTLSS------TTATKPKLHECSICGQE 76 (150)
Q Consensus 5 ~~~~l~~h~~-~h~~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~-~~c~~~~~h~------~~h~~~kp~~C~~Cgk~ 76 (150)
+...+..|+. .|+-.+.|.|..|+..|.....|..|+|.-.-+.. --|.....|. ..-.+.+||.|..|..+
T Consensus 448 s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~s 527 (1406)
T KOG1146|consen 448 SKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYS 527 (1406)
T ss_pred hhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeee
Confidence 3334444443 45556889999999999999999999987321111 1122211111 12245689999999999
Q ss_pred cccchHHHHHhHh
Q 031966 77 FAMGQALGGHMRR 89 (150)
Q Consensus 77 f~~~~~l~~H~~~ 89 (150)
+....+|.+|+..
T Consensus 528 tttng~LsihlqS 540 (1406)
T KOG1146|consen 528 TTTNGNLSIHLQS 540 (1406)
T ss_pred eecchHHHHHHHH
Confidence 9999999999974
No 47
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.47 E-value=0.013 Score=26.83 Aligned_cols=21 Identities=29% Similarity=0.615 Sum_probs=17.6
Q ss_pred eecCCCCCcCCCHHHHHhhHHh
Q 031966 22 FECKTCNRQFPSFQALGGHRAS 43 (150)
Q Consensus 22 ~~C~~C~k~f~~~~~L~~H~~~ 43 (150)
..|..||+.| ....|..|+.+
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 67888999764
No 48
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.38 E-value=0.014 Score=26.24 Aligned_cols=22 Identities=23% Similarity=0.510 Sum_probs=17.7
Q ss_pred eecCCCCCcCCCHHHHHhhHHhc
Q 031966 22 FECKTCNRQFPSFQALGGHRASH 44 (150)
Q Consensus 22 ~~C~~C~k~f~~~~~L~~H~~~h 44 (150)
|+|..|+.... ...|..|++.|
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhh
Confidence 78999999888 89999999875
No 49
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.96 E-value=0.0087 Score=45.82 Aligned_cols=61 Identities=26% Similarity=0.419 Sum_probs=51.9
Q ss_pred CceecCCCCCcCCCHHHHHhhHH--hcCCCCCCCCCcccccccccCCC--Cceecc--ccccccccchHHHHHhHhcccc
Q 031966 20 DVFECKTCNRQFPSFQALGGHRA--SHKKPRLINGETKTLSSTTATKP--KLHECS--ICGQEFAMGQALGGHMRRHRIA 93 (150)
Q Consensus 20 ~~~~C~~C~k~f~~~~~L~~H~~--~h~~~k~~~c~~~~~h~~~h~~~--kp~~C~--~Cgk~f~~~~~l~~H~~~h~~~ 93 (150)
.++.|..|...|.....|..|.+ .| .++ +|+.|+ .|++.|.+...+..|...|.+.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h------------------~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~ 349 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNH------------------SGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSI 349 (467)
T ss_pred cCCCCccccCCcccccccccccccccc------------------ccccCCceeeeccCCCccccccccccCCcccccCC
Confidence 46889999999999999999988 66 666 888888 7999999999999999999887
Q ss_pred hhhcc
Q 031966 94 MNESL 98 (150)
Q Consensus 94 ~~~~~ 98 (150)
.....
T Consensus 350 ~~~~~ 354 (467)
T COG5048 350 SPAKE 354 (467)
T ss_pred Ccccc
Confidence 65443
No 50
>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=94.86 E-value=0.029 Score=27.54 Aligned_cols=23 Identities=30% Similarity=0.521 Sum_probs=20.4
Q ss_pred ceecCCCCCcCCCHHHHHhhHHh
Q 031966 21 VFECKTCNRQFPSFQALGGHRAS 43 (150)
Q Consensus 21 ~~~C~~C~k~f~~~~~L~~H~~~ 43 (150)
+|.|.+|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999999999754
No 51
>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=94.60 E-value=0.022 Score=27.97 Aligned_cols=23 Identities=17% Similarity=0.472 Sum_probs=20.7
Q ss_pred ceeccccccccccchHHHHHhHh
Q 031966 67 LHECSICGQEFAMGQALGGHMRR 89 (150)
Q Consensus 67 p~~C~~Cgk~f~~~~~l~~H~~~ 89 (150)
+|.|..|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999999999864
No 52
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=92.40 E-value=0.12 Score=31.37 Aligned_cols=24 Identities=42% Similarity=0.713 Sum_probs=21.5
Q ss_pred ceecCCCCCcCCCHHHHHhhHHhc
Q 031966 21 VFECKTCNRQFPSFQALGGHRASH 44 (150)
Q Consensus 21 ~~~C~~C~k~f~~~~~L~~H~~~h 44 (150)
.+.|..|++.|.+...|..|++.+
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 589999999999999999999876
No 53
>PRK04860 hypothetical protein; Provisional
Probab=91.08 E-value=0.17 Score=34.26 Aligned_cols=35 Identities=14% Similarity=0.049 Sum_probs=29.4
Q ss_pred CceeccccccccccchHHHHHhHhcccchhhcccccccc
Q 031966 66 KLHECSICGQEFAMGQALGGHMRRHRIAMNESLNSAVIV 104 (150)
Q Consensus 66 kp~~C~~Cgk~f~~~~~l~~H~~~h~~~~~~~~~~~~~~ 104 (150)
-+|.|. |++ ....+.+|.++|+++++..+..+...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~ 152 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGET 152 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCce
Confidence 479998 988 78889999999999998888776543
No 54
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=90.99 E-value=0.072 Score=37.87 Aligned_cols=54 Identities=13% Similarity=0.260 Sum_probs=31.5
Q ss_pred CCceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCcccccccccCCCCc-----eeccccccccccc
Q 031966 19 SDVFECKTCNRQFPSFQALGGHRASHKKPRLINGETKTLSSTTATKPKL-----HECSICGQEFAMG 80 (150)
Q Consensus 19 ~~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~~~~h~~~h~~~kp-----~~C~~Cgk~f~~~ 80 (150)
++...|++|++.|....-.....+.-..+.-+. ....+..| ..|+.||.+|...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~--------~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFC--------PRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCc--------cccCCCCCeeeeEEECCCCCCccccc
Confidence 467899999999988765554443321111110 00123333 5799999887654
No 55
>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=90.67 E-value=0.16 Score=32.10 Aligned_cols=17 Identities=29% Similarity=0.587 Sum_probs=13.8
Q ss_pred CCCceeccccccccccc
Q 031966 64 KPKLHECSICGQEFAMG 80 (150)
Q Consensus 64 ~~kp~~C~~Cgk~f~~~ 80 (150)
+..|-.|+.||..|.-.
T Consensus 23 nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 23 NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCCCccCCCCCCccCcc
Confidence 34688899999998766
No 56
>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=89.89 E-value=0.24 Score=27.04 Aligned_cols=34 Identities=24% Similarity=0.338 Sum_probs=23.2
Q ss_pred ceeccccccccccchHHHHHhHh-cccch-hhccccc
Q 031966 67 LHECSICGQEFAMGQALGGHMRR-HRIAM-NESLNSA 101 (150)
Q Consensus 67 p~~C~~Cgk~f~~~~~l~~H~~~-h~~~~-~~~~~~~ 101 (150)
.|.|++||+. .....|..|... |..+. ...+..+
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC 37 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPIC 37 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCc
Confidence 4889999995 456789999875 55543 3344444
No 57
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=89.26 E-value=0.21 Score=27.40 Aligned_cols=32 Identities=16% Similarity=0.309 Sum_probs=26.4
Q ss_pred ccCCCCceeccccccccccchHHHHHhHhccc
Q 031966 61 TATKPKLHECSICGQEFAMGQALGGHMRRHRI 92 (150)
Q Consensus 61 ~h~~~kp~~C~~Cgk~f~~~~~l~~H~~~h~~ 92 (150)
+-.||.-+.|+.||..|.......+|...-++
T Consensus 11 ~RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 11 DRDGEEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred ccCCceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 33688889999999999999999999865333
No 58
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=89.12 E-value=0.17 Score=36.39 Aligned_cols=47 Identities=34% Similarity=0.618 Sum_probs=36.2
Q ss_pred ecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCcccccccccCCCCceeccccccccccchHHHHH-hHhcc
Q 031966 23 ECKTCNRQFPSFQALGGHRASHKKPRLINGETKTLSSTTATKPKLHECSICGQEFAMGQALGGH-MRRHR 91 (150)
Q Consensus 23 ~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~~~~h~~~h~~~kp~~C~~Cgk~f~~~~~l~~H-~~~h~ 91 (150)
.|=.|++.|-....|..|++ .|-|+|.+|.|..-+...|..| +++|.
T Consensus 12 wcwycnrefddekiliqhqk----------------------akhfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQK----------------------AKHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred eeeecccccchhhhhhhhhh----------------------hccceeeeehhhhccCCCceeehhhhhh
Confidence 48889999999988888864 3578999999777666677666 45554
No 59
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=87.64 E-value=0.41 Score=23.31 Aligned_cols=10 Identities=30% Similarity=0.916 Sum_probs=8.1
Q ss_pred Cceecccccc
Q 031966 66 KLHECSICGQ 75 (150)
Q Consensus 66 kp~~C~~Cgk 75 (150)
.++.|+.||.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 5788999985
No 60
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=86.77 E-value=0.56 Score=25.11 Aligned_cols=25 Identities=28% Similarity=0.732 Sum_probs=19.8
Q ss_pred ceeccccccccccc-----hHHHHHhH-hcc
Q 031966 67 LHECSICGQEFAMG-----QALGGHMR-RHR 91 (150)
Q Consensus 67 p~~C~~Cgk~f~~~-----~~l~~H~~-~h~ 91 (150)
--.|..|++.++.. ++|.+|++ .|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 35699999998765 69999998 564
No 61
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=86.40 E-value=0.49 Score=32.25 Aligned_cols=12 Identities=33% Similarity=0.780 Sum_probs=10.1
Q ss_pred CCCCceeccccc
Q 031966 63 TKPKLHECSICG 74 (150)
Q Consensus 63 ~~~kp~~C~~Cg 74 (150)
.|+-|-.|+.||
T Consensus 145 ~ge~P~~CPiCg 156 (166)
T COG1592 145 EGEAPEVCPICG 156 (166)
T ss_pred cCCCCCcCCCCC
Confidence 457788999998
No 62
>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=84.96 E-value=0.53 Score=30.87 Aligned_cols=29 Identities=34% Similarity=0.631 Sum_probs=17.6
Q ss_pred CCceeccccccccccchHHHHHhHhcccchhh
Q 031966 65 PKLHECSICGQEFAMGQALGGHMRRHRIAMNE 96 (150)
Q Consensus 65 ~kp~~C~~Cgk~f~~~~~l~~H~~~h~~~~~~ 96 (150)
+.--.|-+||+.|.. |++|.+.|.|..+.
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~gltp~ 98 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLTPE 98 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-HH
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCCHH
Confidence 345679999998765 48999999777543
No 63
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=84.78 E-value=0.84 Score=40.38 Aligned_cols=69 Identities=20% Similarity=0.310 Sum_probs=46.5
Q ss_pred CCceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCcc-cccccccCCCCceeccccccccccchHHHHHhHhc
Q 031966 19 SDVFECKTCNRQFPSFQALGGHRASHKKPRLINGETK-TLSSTTATKPKLHECSICGQEFAMGQALGGHMRRH 90 (150)
Q Consensus 19 ~~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~~-~~h~~~h~~~kp~~C~~Cgk~f~~~~~l~~H~~~h 90 (150)
..+|.|..|.-.|.....|..|++.- .+.++.... ..+...+...++| |..|...|+....|..|+++-
T Consensus 1282 ~~~~~~~~~~~~~~~~~~l~~~~~k~--~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~~ 1351 (1406)
T KOG1146|consen 1282 THRYLCRQCKMAFDGEAPLTAHQRKF--CFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRSS 1351 (1406)
T ss_pred chhHHHHHHHhhhcchhHHHHHHHHH--HhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHHh
Confidence 35688888888888888888887322 111111111 1233334555677 999999999999999999963
No 64
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=84.75 E-value=0.49 Score=35.51 Aligned_cols=27 Identities=22% Similarity=0.480 Sum_probs=23.7
Q ss_pred CCCCceeccc--cccccccchHHHHHhHh
Q 031966 63 TKPKLHECSI--CGQEFAMGQALGGHMRR 89 (150)
Q Consensus 63 ~~~kp~~C~~--Cgk~f~~~~~l~~H~~~ 89 (150)
.++|||+|++ |.|.|.....|+-|+.-
T Consensus 345 ~d~KpykCpV~gC~K~YknqnGLKYH~lh 373 (423)
T COG5189 345 KDGKPYKCPVEGCNKKYKNQNGLKYHMLH 373 (423)
T ss_pred ecCceecCCCCCchhhhccccchhhhhhc
Confidence 3469999987 99999999999999875
No 65
>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=84.60 E-value=0.69 Score=29.95 Aligned_cols=21 Identities=19% Similarity=0.287 Sum_probs=15.4
Q ss_pred CCCceeccccccccccchHHH
Q 031966 64 KPKLHECSICGQEFAMGQALG 84 (150)
Q Consensus 64 ~~kp~~C~~Cgk~f~~~~~l~ 84 (150)
+..|-.|+.||..|.-...++
T Consensus 23 nk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 23 NRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred CCCCccCCCcCCccCcchhhc
Confidence 446889999999986664444
No 66
>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=84.33 E-value=0.98 Score=23.36 Aligned_cols=25 Identities=24% Similarity=0.588 Sum_probs=16.4
Q ss_pred CCCceeccccccccccc----hHHHHHhH
Q 031966 64 KPKLHECSICGQEFAMG----QALGGHMR 88 (150)
Q Consensus 64 ~~kp~~C~~Cgk~f~~~----~~l~~H~~ 88 (150)
+..-..|..|++.+... +.|.+|++
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 44567899999998764 78999984
No 67
>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=83.07 E-value=0.83 Score=22.44 Aligned_cols=10 Identities=40% Similarity=1.089 Sum_probs=7.7
Q ss_pred Cceecccccc
Q 031966 66 KLHECSICGQ 75 (150)
Q Consensus 66 kp~~C~~Cgk 75 (150)
.|..|+.||.
T Consensus 17 ~p~~CP~Cg~ 26 (34)
T cd00729 17 APEKCPICGA 26 (34)
T ss_pred CCCcCcCCCC
Confidence 4678999985
No 68
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=82.99 E-value=1.1 Score=23.45 Aligned_cols=13 Identities=23% Similarity=0.736 Sum_probs=10.2
Q ss_pred ceecCCCCCcCCC
Q 031966 21 VFECKTCNRQFPS 33 (150)
Q Consensus 21 ~~~C~~C~k~f~~ 33 (150)
.|.|..||..|..
T Consensus 2 ~Y~C~~Cg~~~~~ 14 (44)
T smart00659 2 IYICGECGRENEI 14 (44)
T ss_pred EEECCCCCCEeec
Confidence 4889999987753
No 69
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=82.18 E-value=1 Score=23.59 Aligned_cols=13 Identities=23% Similarity=0.797 Sum_probs=9.7
Q ss_pred ceecCCCCCcCCC
Q 031966 21 VFECKTCNRQFPS 33 (150)
Q Consensus 21 ~~~C~~C~k~f~~ 33 (150)
.|.|..||..|..
T Consensus 3 ~y~C~~CG~~~~~ 15 (46)
T PRK00398 3 EYKCARCGREVEL 15 (46)
T ss_pred EEECCCCCCEEEE
Confidence 5889999876643
No 70
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=81.40 E-value=0.29 Score=40.51 Aligned_cols=27 Identities=30% Similarity=0.618 Sum_probs=24.2
Q ss_pred ceeccccccccccchHHHHHhHhcccc
Q 031966 67 LHECSICGQEFAMGQALGGHMRRHRIA 93 (150)
Q Consensus 67 p~~C~~Cgk~f~~~~~l~~H~~~h~~~ 93 (150)
-|.|.+|+|.|-.-.++..||++|.-.
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~q 818 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQQ 818 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHHH
Confidence 489999999999999999999999744
No 71
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=80.59 E-value=0.78 Score=25.21 Aligned_cols=29 Identities=17% Similarity=0.361 Sum_probs=24.9
Q ss_pred hhcCCCCceecCCCCCcCCCHHHHHhhHH
Q 031966 14 KKRLASDVFECKTCNRQFPSFQALGGHRA 42 (150)
Q Consensus 14 ~~h~~~~~~~C~~C~k~f~~~~~L~~H~~ 42 (150)
...-||.-++|+-||..|.......+|..
T Consensus 10 ~~RDGE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 10 RDRDGEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred eccCCceeeeCCchhHHHHHhHHHHHHhh
Confidence 34568888999999999999999999974
No 72
>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=80.54 E-value=1.4 Score=21.91 Aligned_cols=34 Identities=21% Similarity=0.567 Sum_probs=22.2
Q ss_pred eecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCcccccccccCCCCceeccccccccc
Q 031966 22 FECKTCNRQFPSFQALGGHRASHKKPRLINGETKTLSSTTATKPKLHECSICGQEFA 78 (150)
Q Consensus 22 ~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~~~~h~~~h~~~kp~~C~~Cgk~f~ 78 (150)
+.|+.|+..|.-...... ....-..|+.||..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~-----------------------~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLG-----------------------ANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcC-----------------------CCCCEEECCCCCCEEE
Confidence 679999988766544211 1122578999998774
No 73
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=79.84 E-value=1.7 Score=21.66 Aligned_cols=34 Identities=21% Similarity=0.519 Sum_probs=23.1
Q ss_pred eecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCcccccccccCCCCceeccccccccc
Q 031966 22 FECKTCNRQFPSFQALGGHRASHKKPRLINGETKTLSSTTATKPKLHECSICGQEFA 78 (150)
Q Consensus 22 ~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~~~~h~~~h~~~kp~~C~~Cgk~f~ 78 (150)
..|+.|+..|.-...- +- .+.+..+|..|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~-----l~------------------~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK-----LP------------------AGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHH-----cc------------------cCCcEEECCCCCcEee
Confidence 4688999888765541 11 3345778999998774
No 74
>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=79.56 E-value=0.55 Score=25.23 Aligned_cols=13 Identities=23% Similarity=0.904 Sum_probs=10.5
Q ss_pred ceecCCCCCcCCC
Q 031966 21 VFECKTCNRQFPS 33 (150)
Q Consensus 21 ~~~C~~C~k~f~~ 33 (150)
-|+|..||..|..
T Consensus 5 ey~C~~Cg~~fe~ 17 (52)
T TIGR02605 5 EYRCTACGHRFEV 17 (52)
T ss_pred EEEeCCCCCEeEE
Confidence 3889999998864
No 75
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=79.49 E-value=0.45 Score=32.07 Aligned_cols=18 Identities=28% Similarity=0.704 Sum_probs=13.6
Q ss_pred CceeccccccccccchHH
Q 031966 66 KLHECSICGQEFAMGQAL 83 (150)
Q Consensus 66 kp~~C~~Cgk~f~~~~~l 83 (150)
+-+.|+.||+.|.....+
T Consensus 27 ~~~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 27 RRRECLACGKRFTTFERV 44 (154)
T ss_pred eeeeccccCCcceEeEec
Confidence 348999999999865443
No 76
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=79.47 E-value=2.1 Score=28.55 Aligned_cols=40 Identities=18% Similarity=0.488 Sum_probs=26.2
Q ss_pred CCCCceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCcccccccccCCCCceeccccccccc
Q 031966 17 LASDVFECKTCNRQFPSFQALGGHRASHKKPRLINGETKTLSSTTATKPKLHECSICGQEFA 78 (150)
Q Consensus 17 ~~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~~~~h~~~h~~~kp~~C~~Cgk~f~ 78 (150)
.+..-|.|+.|++.|.....+.. .. . ..-|.|+.||....
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~---~d------------------~-~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQL---LD------------------M-DGTFTCPRCGEELE 134 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHh---cC------------------C-CCcEECCCCCCEEE
Confidence 34567999999999986443321 01 1 12399999997654
No 77
>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=77.49 E-value=1.3 Score=31.45 Aligned_cols=31 Identities=16% Similarity=0.369 Sum_probs=23.6
Q ss_pred CCCCceeccccccccccchHHHHHhHhcccc
Q 031966 63 TKPKLHECSICGQEFAMGQALGGHMRRHRIA 93 (150)
Q Consensus 63 ~~~kp~~C~~Cgk~f~~~~~l~~H~~~h~~~ 93 (150)
..+.-|.|..|+|.|.-..-..+|+..-+.+
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 4556799999999999999999999875544
No 78
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=77.22 E-value=2.2 Score=23.81 Aligned_cols=11 Identities=27% Similarity=0.619 Sum_probs=9.0
Q ss_pred CCceecccccc
Q 031966 65 PKLHECSICGQ 75 (150)
Q Consensus 65 ~kp~~C~~Cgk 75 (150)
..+|.|+.||.
T Consensus 48 g~~Y~Cp~CGF 58 (61)
T COG2888 48 GNPYRCPKCGF 58 (61)
T ss_pred CCceECCCcCc
Confidence 36899999984
No 79
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=76.37 E-value=0.72 Score=35.03 Aligned_cols=68 Identities=16% Similarity=0.359 Sum_probs=42.0
Q ss_pred CCceecCC--CCCcCCCHHHHHhhHHh-cCCCCCCCCCcccccccccCCCCceeccccccccccchHHHHH
Q 031966 19 SDVFECKT--CNRQFPSFQALGGHRAS-HKKPRLINGETKTLSSTTATKPKLHECSICGQEFAMGQALGGH 86 (150)
Q Consensus 19 ~~~~~C~~--C~k~f~~~~~L~~H~~~-h~~~k~~~c~~~~~h~~~h~~~kp~~C~~Cgk~f~~~~~l~~H 86 (150)
.++|+|.+ |.+.++....|+.|... |-......-....-|+-.....|+|+|++|.+.+.....|.-|
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~ 417 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYH 417 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCce
Confidence 47899975 99999888877776532 2111000001111344444667999999999988776665544
No 80
>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=76.20 E-value=2.1 Score=20.74 Aligned_cols=11 Identities=27% Similarity=0.767 Sum_probs=7.3
Q ss_pred Cceeccccccc
Q 031966 66 KLHECSICGQE 76 (150)
Q Consensus 66 kp~~C~~Cgk~ 76 (150)
.+..|..||..
T Consensus 16 ~~irC~~CG~R 26 (32)
T PF03604_consen 16 DPIRCPECGHR 26 (32)
T ss_dssp STSSBSSSS-S
T ss_pred CcEECCcCCCe
Confidence 35679999854
No 81
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=74.31 E-value=3.5 Score=20.43 Aligned_cols=33 Identities=24% Similarity=0.542 Sum_probs=22.5
Q ss_pred eecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCcccccccccCCCCceecccccccc
Q 031966 22 FECKTCNRQFPSFQALGGHRASHKKPRLINGETKTLSSTTATKPKLHECSICGQEF 77 (150)
Q Consensus 22 ~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~~~~h~~~h~~~kp~~C~~Cgk~f 77 (150)
..|+.|+..|.-..... - ...+-.+|..||..|
T Consensus 3 i~Cp~C~~~y~i~d~~i-----p------------------~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKI-----P------------------PKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHC-----C------------------CCCcEEECCCCCCEe
Confidence 56888988887655431 1 233567899999876
No 82
>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=74.02 E-value=2.4 Score=28.62 Aligned_cols=24 Identities=17% Similarity=0.214 Sum_probs=18.2
Q ss_pred hhcCCCCceecCCCCCcCCCHHHH
Q 031966 14 KKRLASDVFECKTCNRQFPSFQAL 37 (150)
Q Consensus 14 ~~h~~~~~~~C~~C~k~f~~~~~L 37 (150)
....+..-|.|+.|+..|+....+
T Consensus 102 ~~e~~~~~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 102 EFETNNMFFICPNMCVRFTFNEAM 125 (158)
T ss_pred hhccCCCeEECCCCCcEeeHHHHH
Confidence 334455679999999999887776
No 83
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=73.57 E-value=3 Score=30.37 Aligned_cols=49 Identities=18% Similarity=0.440 Sum_probs=35.1
Q ss_pred eecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCcccccccccCCCCceeccccccccccchHHHHHhHhcc
Q 031966 22 FECKTCNRQFPSFQALGGHRASHKKPRLINGETKTLSSTTATKPKLHECSICGQEFAMGQALGGHMRRHR 91 (150)
Q Consensus 22 ~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~~~~h~~~h~~~kp~~C~~Cgk~f~~~~~l~~H~~~h~ 91 (150)
|.|..||....-+ .+.+|+-.. .+ .-|.|--||+.|-. .....|..--+
T Consensus 4 FtCnvCgEsvKKp-~vekH~srC------------------rn-~~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 4 FTCNVCGESVKKP-QVEKHMSRC------------------RN-AYFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred Eehhhhhhhcccc-chHHHHHhc------------------cC-CeeEEeeccccccc-chhhhhhhhcc
Confidence 7899999876654 455677544 33 57899999999987 66677765433
No 84
>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=72.09 E-value=2.9 Score=26.21 Aligned_cols=70 Identities=14% Similarity=0.226 Sum_probs=44.2
Q ss_pred CCceecCCCCCcCCCHHHHHhhHH-hcCCCCC------------CC---CCc--cc---------ccccccCCCCceec-
Q 031966 19 SDVFECKTCNRQFPSFQALGGHRA-SHKKPRL------------IN---GET--KT---------LSSTTATKPKLHEC- 70 (150)
Q Consensus 19 ~~~~~C~~C~k~f~~~~~L~~H~~-~h~~~k~------------~~---c~~--~~---------~h~~~h~~~kp~~C- 70 (150)
.+...|..|+.+... +.+..|.+ .|...+. +. .+. .. ..+..+ .-|.|
T Consensus 9 ~~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gLp~~---~G~~C~ 84 (109)
T PF12013_consen 9 YRVLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGLPVY---DGYRCQ 84 (109)
T ss_pred CCEEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCCCCCC---CCeeee
Confidence 355779999987765 77888887 3322111 10 000 00 122222 23889
Q ss_pred ---cccccccccchHHHHHhHhccc
Q 031966 71 ---SICGQEFAMGQALGGHMRRHRI 92 (150)
Q Consensus 71 ---~~Cgk~f~~~~~l~~H~~~h~~ 92 (150)
..|+..+.+...+.+|.+.++|
T Consensus 85 ~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 85 CDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred cCCCCCCcEeccHHHHHHHHHHhcC
Confidence 9999999999999999987654
No 85
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=71.04 E-value=3.8 Score=27.26 Aligned_cols=22 Identities=18% Similarity=0.424 Sum_probs=17.0
Q ss_pred CCceeccccccccccchHHHHH
Q 031966 65 PKLHECSICGQEFAMGQALGGH 86 (150)
Q Consensus 65 ~kp~~C~~Cgk~f~~~~~l~~H 86 (150)
+.=+.|+.|||.|-..+++.+-
T Consensus 122 ~~f~~C~~C~kiyW~GsH~~~~ 143 (147)
T PF01927_consen 122 DEFWRCPGCGKIYWEGSHWRRM 143 (147)
T ss_pred CeEEECCCCCCEecccccHHHH
Confidence 4467899999999887766543
No 86
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=70.85 E-value=2.1 Score=26.97 Aligned_cols=22 Identities=5% Similarity=0.009 Sum_probs=15.3
Q ss_pred CCCCceeccccccccccchHHHH
Q 031966 63 TKPKLHECSICGQEFAMGQALGG 85 (150)
Q Consensus 63 ~~~kp~~C~~Cgk~f~~~~~l~~ 85 (150)
.+..|..|++||++| -.+.+..
T Consensus 22 LNrdPiVsPytG~s~-P~s~fe~ 43 (129)
T COG4530 22 LNRDPIVSPYTGKSY-PRSYFEE 43 (129)
T ss_pred cCCCccccCcccccc-hHHHHHh
Confidence 345688899999999 3444443
No 87
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=70.63 E-value=2.8 Score=28.92 Aligned_cols=36 Identities=22% Similarity=0.452 Sum_probs=26.1
Q ss_pred CCCCceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCcccccccccCCCCceecccccccccc
Q 031966 17 LASDVFECKTCNRQFPSFQALGGHRASHKKPRLINGETKTLSSTTATKPKLHECSICGQEFAM 79 (150)
Q Consensus 17 ~~~~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~~~~h~~~h~~~kp~~C~~Cgk~f~~ 79 (150)
....-|.|+.|+..|+....+. .-|.|+.||-....
T Consensus 113 ~~~~~Y~Cp~C~~rytf~eA~~---------------------------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTFDEAME---------------------------YGFRCPQCGEMLEE 148 (178)
T ss_pred cCCCEEECCCCCcEEeHHHHhh---------------------------cCCcCCCCCCCCee
Confidence 3445689999999998776642 24889999976543
No 88
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=70.28 E-value=2.8 Score=22.47 Aligned_cols=13 Identities=23% Similarity=0.751 Sum_probs=10.9
Q ss_pred CCceecCCCCCcC
Q 031966 19 SDVFECKTCNRQF 31 (150)
Q Consensus 19 ~~~~~C~~C~k~f 31 (150)
...|.|..||+.|
T Consensus 4 ~~~Y~C~~Cg~~~ 16 (49)
T COG1996 4 MMEYKCARCGREV 16 (49)
T ss_pred eEEEEhhhcCCee
Confidence 3569999999988
No 89
>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=69.50 E-value=4.9 Score=18.35 Aligned_cols=20 Identities=20% Similarity=0.512 Sum_probs=15.3
Q ss_pred eecCCCCCcCCCHHHHHhhHH
Q 031966 22 FECKTCNRQFPSFQALGGHRA 42 (150)
Q Consensus 22 ~~C~~C~k~f~~~~~L~~H~~ 42 (150)
..|++|++.+ ....+..|..
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 4699999998 5567777764
No 90
>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=68.38 E-value=3.5 Score=29.38 Aligned_cols=28 Identities=18% Similarity=0.377 Sum_probs=21.7
Q ss_pred CCCCceecCCCCCcCCCHHHHHhhHHhc
Q 031966 17 LASDVFECKTCNRQFPSFQALGGHRASH 44 (150)
Q Consensus 17 ~~~~~~~C~~C~k~f~~~~~L~~H~~~h 44 (150)
..+..|.|..|+|.|.-...+..|+..-
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nK 100 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNK 100 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhc
Confidence 3455799999999999999999998653
No 91
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=67.50 E-value=4.2 Score=22.69 Aligned_cols=10 Identities=30% Similarity=0.717 Sum_probs=8.5
Q ss_pred Cceecccccc
Q 031966 66 KLHECSICGQ 75 (150)
Q Consensus 66 kp~~C~~Cgk 75 (150)
.+|.|+.||.
T Consensus 47 ~~Y~CP~CGF 56 (59)
T PRK14890 47 NPYTCPKCGF 56 (59)
T ss_pred CceECCCCCC
Confidence 6899999984
No 92
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=66.48 E-value=1.7 Score=25.31 Aligned_cols=20 Identities=30% Similarity=0.675 Sum_probs=15.0
Q ss_pred CCCCceecc--ccccccccchH
Q 031966 63 TKPKLHECS--ICGQEFAMGQA 82 (150)
Q Consensus 63 ~~~kp~~C~--~Cgk~f~~~~~ 82 (150)
..++-+.|. +||..|.....
T Consensus 23 ~~~~Y~qC~N~eCg~tF~t~es 44 (72)
T PRK09678 23 TKERYHQCQNVNCSATFITYES 44 (72)
T ss_pred hheeeeecCCCCCCCEEEEEEE
Confidence 445678898 89999987644
No 93
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=66.18 E-value=2.9 Score=20.96 Aligned_cols=15 Identities=33% Similarity=0.654 Sum_probs=11.6
Q ss_pred ceeccccccccccch
Q 031966 67 LHECSICGQEFAMGQ 81 (150)
Q Consensus 67 p~~C~~Cgk~f~~~~ 81 (150)
-|.|..||..|....
T Consensus 5 ~y~C~~Cg~~fe~~~ 19 (41)
T smart00834 5 EYRCEDCGHTFEVLQ 19 (41)
T ss_pred EEEcCCCCCEEEEEE
Confidence 478999999886543
No 94
>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=65.80 E-value=2.4 Score=26.28 Aligned_cols=22 Identities=14% Similarity=0.235 Sum_probs=16.5
Q ss_pred hhhhhcCCCCceecCCCCCcCCC
Q 031966 11 LPIKKRLASDVFECKTCNRQFPS 33 (150)
Q Consensus 11 ~h~~~h~~~~~~~C~~C~k~f~~ 33 (150)
..+..+.| ++++|.+||..|..
T Consensus 70 ~W~~l~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 70 IWMWLEKG-KPKRCPECGHVFKL 91 (97)
T ss_pred EEEEEeCC-CceeCCCCCcEEEE
Confidence 34555666 79999999998853
No 95
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=65.44 E-value=6.1 Score=30.51 Aligned_cols=70 Identities=23% Similarity=0.401 Sum_probs=46.1
Q ss_pred ceecCCCCCcCCCHHHHHhhHHh--c---CCCCCCCCCc-----cc---------ccccccCCCCceeccccccccccch
Q 031966 21 VFECKTCNRQFPSFQALGGHRAS--H---KKPRLINGET-----KT---------LSSTTATKPKLHECSICGQEFAMGQ 81 (150)
Q Consensus 21 ~~~C~~C~k~f~~~~~L~~H~~~--h---~~~k~~~c~~-----~~---------~h~~~h~~~kp~~C~~Cgk~f~~~~ 81 (150)
-|.|..|...|......+.|.++ | ...+.+.-.. +. .-...-.++-++.|..|.|.|....
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s~~ 82 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFASPK 82 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccChh
Confidence 38899999999998887888764 3 1111111100 10 1111124556899999999999999
Q ss_pred HHHHHhHhc
Q 031966 82 ALGGHMRRH 90 (150)
Q Consensus 82 ~l~~H~~~h 90 (150)
+...|+..-
T Consensus 83 a~~~hl~Sk 91 (390)
T KOG2785|consen 83 AHENHLKSK 91 (390)
T ss_pred hHHHHHHHh
Confidence 999998753
No 96
>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=63.94 E-value=3.5 Score=18.59 Aligned_cols=10 Identities=30% Similarity=0.667 Sum_probs=8.4
Q ss_pred Cceecccccc
Q 031966 66 KLHECSICGQ 75 (150)
Q Consensus 66 kp~~C~~Cgk 75 (150)
.+|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 5799999984
No 97
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=63.02 E-value=4.3 Score=24.54 Aligned_cols=16 Identities=38% Similarity=0.889 Sum_probs=12.6
Q ss_pred Cceeccccccccccch
Q 031966 66 KLHECSICGQEFAMGQ 81 (150)
Q Consensus 66 kp~~C~~Cgk~f~~~~ 81 (150)
.-|.|..||..|....
T Consensus 52 GIW~C~kCg~~fAGga 67 (89)
T COG1997 52 GIWKCRKCGAKFAGGA 67 (89)
T ss_pred CeEEcCCCCCeecccc
Confidence 3588999999997654
No 98
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=62.73 E-value=7.7 Score=30.48 Aligned_cols=24 Identities=21% Similarity=0.628 Sum_probs=17.8
Q ss_pred hhcCCCCceecCCCCCcCCCHHHH
Q 031966 14 KKRLASDVFECKTCNRQFPSFQAL 37 (150)
Q Consensus 14 ~~h~~~~~~~C~~C~k~f~~~~~L 37 (150)
+.-+...-|.|+.|.+.|.....+
T Consensus 121 ~d~t~~~~Y~Cp~C~kkyt~Lea~ 144 (436)
T KOG2593|consen 121 RDDTNVAGYVCPNCQKKYTSLEAL 144 (436)
T ss_pred hhccccccccCCccccchhhhHHH
Confidence 334555679999999999775554
No 99
>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=62.31 E-value=3.7 Score=21.07 Aligned_cols=15 Identities=40% Similarity=0.760 Sum_probs=11.7
Q ss_pred ceeccccccccccch
Q 031966 67 LHECSICGQEFAMGQ 81 (150)
Q Consensus 67 p~~C~~Cgk~f~~~~ 81 (150)
-|.|..||..|....
T Consensus 5 ey~C~~Cg~~fe~~~ 19 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQ 19 (42)
T ss_pred EEEeCCCCCEEEEEE
Confidence 488999998886543
No 100
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=61.81 E-value=1.3 Score=36.91 Aligned_cols=24 Identities=25% Similarity=0.747 Sum_probs=22.3
Q ss_pred ceecCCCCCcCCCHHHHHhhHHhc
Q 031966 21 VFECKTCNRQFPSFQALGGHRASH 44 (150)
Q Consensus 21 ~~~C~~C~k~f~~~~~L~~H~~~h 44 (150)
-|.|.+|+|.|-.-..++.||++|
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHH
Confidence 489999999999999999999998
No 101
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=61.14 E-value=4.5 Score=26.55 Aligned_cols=23 Identities=26% Similarity=0.377 Sum_probs=19.0
Q ss_pred eecCCCCCcCCCHHHHHhhHHhcCCC
Q 031966 22 FECKTCNRQFPSFQALGGHRASHKKP 47 (150)
Q Consensus 22 ~~C~~C~k~f~~~~~L~~H~~~h~~~ 47 (150)
..|-++||.|.+ |++|..+|-+-
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gm 99 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGL 99 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCC
Confidence 469999999964 99999998554
No 102
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.79 E-value=2.3 Score=24.94 Aligned_cols=11 Identities=36% Similarity=1.207 Sum_probs=9.2
Q ss_pred ceecCCCCCcC
Q 031966 21 VFECKTCNRQF 31 (150)
Q Consensus 21 ~~~C~~C~k~f 31 (150)
.|+|..||..|
T Consensus 12 ~Y~c~~cg~~~ 22 (82)
T COG2331 12 SYECTECGNRF 22 (82)
T ss_pred EEeecccchHH
Confidence 48999999876
No 103
>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=58.56 E-value=4.6 Score=18.52 Aligned_cols=10 Identities=40% Similarity=1.062 Sum_probs=8.1
Q ss_pred eccccccccc
Q 031966 69 ECSICGQEFA 78 (150)
Q Consensus 69 ~C~~Cgk~f~ 78 (150)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 5889998885
No 104
>PLN02294 cytochrome c oxidase subunit Vb
Probab=57.13 E-value=5.7 Score=27.18 Aligned_cols=19 Identities=32% Similarity=0.597 Sum_probs=14.3
Q ss_pred cccCCCCceecccccccccc
Q 031966 60 TTATKPKLHECSICGQEFAM 79 (150)
Q Consensus 60 ~~h~~~kp~~C~~Cgk~f~~ 79 (150)
..+.| +|+.|++||..|.-
T Consensus 135 ~L~kG-kp~RCpeCG~~fkL 153 (174)
T PLN02294 135 WLEKG-KSFECPVCTQYFEL 153 (174)
T ss_pred EecCC-CceeCCCCCCEEEE
Confidence 34444 79999999998863
No 105
>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=56.94 E-value=3.6 Score=19.29 Aligned_cols=19 Identities=26% Similarity=0.739 Sum_probs=11.9
Q ss_pred eeccccccccccchHHHHHh
Q 031966 68 HECSICGQEFAMGQALGGHM 87 (150)
Q Consensus 68 ~~C~~Cgk~f~~~~~l~~H~ 87 (150)
|.|--|++.|. ....+.|-
T Consensus 1 ~sCiDC~~~F~-~~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDFD-GDSYKSHT 19 (28)
T ss_dssp EEETTTTEEEE-GGGTTT--
T ss_pred CeeecCCCCcC-cCCcCCCC
Confidence 57888999994 44444553
No 106
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=56.18 E-value=7.1 Score=25.15 Aligned_cols=25 Identities=32% Similarity=0.523 Sum_probs=22.0
Q ss_pred CceecCCCCCcCCCHHHHHhhHHhc
Q 031966 20 DVFECKTCNRQFPSFQALGGHRASH 44 (150)
Q Consensus 20 ~~~~C~~C~k~f~~~~~L~~H~~~h 44 (150)
-.|.|-.|.+-|.....|..|.++.
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHhcc
Confidence 4589999999999999999998753
No 107
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=55.94 E-value=3.8 Score=28.94 Aligned_cols=58 Identities=24% Similarity=0.477 Sum_probs=39.9
Q ss_pred ecCCCCCcCCCHHHHHhhHH-hcCCCCCCCCCcccccccccCCCCceecc--ccccccccchHHHHHhHh
Q 031966 23 ECKTCNRQFPSFQALGGHRA-SHKKPRLINGETKTLSSTTATKPKLHECS--ICGQEFAMGQALGGHMRR 89 (150)
Q Consensus 23 ~C~~C~k~f~~~~~L~~H~~-~h~~~k~~~c~~~~~h~~~h~~~kp~~C~--~Cgk~f~~~~~l~~H~~~ 89 (150)
.|.+|.+.|.+..-|..|+. .|..- | ...+-.|.--|.|- .|+-.|.+......|+..
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~--F-------qa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~ 168 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSL--F-------QALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIR 168 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHH--H-------HHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHH
Confidence 69999999999988888873 34100 0 00111344558885 499999999999999864
No 108
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=55.72 E-value=4.1 Score=26.76 Aligned_cols=15 Identities=20% Similarity=0.744 Sum_probs=12.2
Q ss_pred CceecCCCCCcCCCH
Q 031966 20 DVFECKTCNRQFPSF 34 (150)
Q Consensus 20 ~~~~C~~C~k~f~~~ 34 (150)
..+.|..||..|...
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 568999999888654
No 109
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=55.63 E-value=6.1 Score=19.97 Aligned_cols=14 Identities=29% Similarity=0.596 Sum_probs=11.5
Q ss_pred ceeccccccccccc
Q 031966 67 LHECSICGQEFAMG 80 (150)
Q Consensus 67 p~~C~~Cgk~f~~~ 80 (150)
||.|..|++.|=..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 89999999888543
No 110
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=55.42 E-value=19 Score=27.89 Aligned_cols=69 Identities=19% Similarity=0.210 Sum_probs=45.6
Q ss_pred CceecCCCCCcCCCHHHHHhhHHhcCC----CCCCCCCccc--ccccccCCCCceeccccc---cccccchHHHHHhHh
Q 031966 20 DVFECKTCNRQFPSFQALGGHRASHKK----PRLINGETKT--LSSTTATKPKLHECSICG---QEFAMGQALGGHMRR 89 (150)
Q Consensus 20 ~~~~C~~C~k~f~~~~~L~~H~~~h~~----~k~~~c~~~~--~h~~~h~~~kp~~C~~Cg---k~f~~~~~l~~H~~~ 89 (150)
-|-.|-.|++.+.....-..||..+.| ++.|.-+... ..+. -.-..-|.|-.|+ +.|.+-.+.+.||..
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLg-eKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLG-EKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHH-HHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 356799999999999888899976644 2223222111 0000 0112357788888 999999999999974
No 111
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=54.93 E-value=10 Score=24.92 Aligned_cols=21 Identities=19% Similarity=0.466 Sum_probs=14.8
Q ss_pred cCCCCceecCCCCCcCCCHHH
Q 031966 16 RLASDVFECKTCNRQFPSFQA 36 (150)
Q Consensus 16 h~~~~~~~C~~C~k~f~~~~~ 36 (150)
-...+.|+|++|..++.....
T Consensus 75 F~d~~lYeCnIC~etS~ee~F 95 (140)
T PF05290_consen 75 FLDPKLYECNICKETSAEERF 95 (140)
T ss_pred ecCCCceeccCcccccchhhc
Confidence 345578999999987654433
No 112
>PHA00626 hypothetical protein
Probab=53.97 E-value=7 Score=21.54 Aligned_cols=15 Identities=20% Similarity=0.286 Sum_probs=12.5
Q ss_pred Cceeccccccccccc
Q 031966 66 KLHECSICGQEFAMG 80 (150)
Q Consensus 66 kp~~C~~Cgk~f~~~ 80 (150)
..|.|+.||..|+..
T Consensus 22 nrYkCkdCGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCDCGYNDSKD 36 (59)
T ss_pred cceEcCCCCCeechh
Confidence 579999999988653
No 113
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=53.91 E-value=8.8 Score=25.79 Aligned_cols=14 Identities=14% Similarity=0.783 Sum_probs=10.0
Q ss_pred CCceecCCCCCcCCC
Q 031966 19 SDVFECKTCNRQFPS 33 (150)
Q Consensus 19 ~~~~~C~~C~k~f~~ 33 (150)
..+|.|. |+..|.+
T Consensus 115 ~~~Y~C~-C~q~~l~ 128 (156)
T COG3091 115 TYPYRCQ-CQQHYLR 128 (156)
T ss_pred ceeEEee-cCCccch
Confidence 3478888 8887654
No 114
>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=52.68 E-value=6 Score=20.35 Aligned_cols=15 Identities=27% Similarity=0.780 Sum_probs=9.8
Q ss_pred Cceeccccccccccc
Q 031966 66 KLHECSICGQEFAMG 80 (150)
Q Consensus 66 kp~~C~~Cgk~f~~~ 80 (150)
-|+.|..|++.|=..
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 589999999988543
No 115
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=52.58 E-value=6.4 Score=25.73 Aligned_cols=15 Identities=40% Similarity=0.995 Sum_probs=12.1
Q ss_pred ceeccccccccccch
Q 031966 67 LHECSICGQEFAMGQ 81 (150)
Q Consensus 67 p~~C~~Cgk~f~~~~ 81 (150)
|++|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 678999999998665
No 116
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=52.09 E-value=9 Score=30.15 Aligned_cols=18 Identities=17% Similarity=0.281 Sum_probs=13.7
Q ss_pred CCCceeccccccccccch
Q 031966 64 KPKLHECSICGQEFAMGQ 81 (150)
Q Consensus 64 ~~kp~~C~~Cgk~f~~~~ 81 (150)
|..-|+|+.||..+....
T Consensus 364 G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 364 GRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCCcccccccccCCccc
Confidence 444899999999876653
No 117
>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=51.55 E-value=9.7 Score=19.45 Aligned_cols=12 Identities=25% Similarity=0.764 Sum_probs=10.3
Q ss_pred Cceecccccccc
Q 031966 66 KLHECSICGQEF 77 (150)
Q Consensus 66 kp~~C~~Cgk~f 77 (150)
++-.|++||..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 478899999887
No 118
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=51.47 E-value=16 Score=30.55 Aligned_cols=17 Identities=18% Similarity=0.276 Sum_probs=9.6
Q ss_pred cccccchHHHHHhHhcc
Q 031966 75 QEFAMGQALGGHMRRHR 91 (150)
Q Consensus 75 k~f~~~~~l~~H~~~h~ 91 (150)
.-|.....|..|.+.++
T Consensus 220 eyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 220 EYYNDYDDLEEHFRKGH 236 (669)
T ss_pred hhcccchHHHHHhhhcC
Confidence 34455666666666543
No 119
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=51.02 E-value=8.2 Score=19.94 Aligned_cols=16 Identities=25% Similarity=0.789 Sum_probs=12.6
Q ss_pred eccccccccccchHHH
Q 031966 69 ECSICGQEFAMGQALG 84 (150)
Q Consensus 69 ~C~~Cgk~f~~~~~l~ 84 (150)
.|..||+.|+...-..
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 4999999998775543
No 120
>PF15269 zf-C2H2_7: Zinc-finger
Probab=49.51 E-value=11 Score=19.72 Aligned_cols=23 Identities=22% Similarity=0.268 Sum_probs=18.0
Q ss_pred eeccccccccccchHHHHHhHhc
Q 031966 68 HECSICGQEFAMGQALGGHMRRH 90 (150)
Q Consensus 68 ~~C~~Cgk~f~~~~~l~~H~~~h 90 (150)
|+|-.|.......+.|-.||+-.
T Consensus 21 ykcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred ceeecCCcccchHHHHHHHHHHH
Confidence 56888887777888888888753
No 121
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=49.19 E-value=10 Score=30.98 Aligned_cols=29 Identities=24% Similarity=0.409 Sum_probs=24.6
Q ss_pred CCceeccccccccccchHHHHHhHhcccc
Q 031966 65 PKLHECSICGQEFAMGQALGGHMRRHRIA 93 (150)
Q Consensus 65 ~kp~~C~~Cgk~f~~~~~l~~H~~~h~~~ 93 (150)
..|-.|..||..|........||.+|...
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~dw 444 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHDDW 444 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhhhh
Confidence 45788999999999999888888888655
No 122
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=48.48 E-value=11 Score=21.20 Aligned_cols=11 Identities=27% Similarity=0.942 Sum_probs=4.9
Q ss_pred eecCCCCCcCC
Q 031966 22 FECKTCNRQFP 32 (150)
Q Consensus 22 ~~C~~C~k~f~ 32 (150)
-.|..|++.|.
T Consensus 10 ~~C~~C~~~F~ 20 (69)
T PF01363_consen 10 SNCMICGKKFS 20 (69)
T ss_dssp SB-TTT--B-B
T ss_pred CcCcCcCCcCC
Confidence 45888888885
No 123
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=48.40 E-value=10 Score=24.07 Aligned_cols=12 Identities=17% Similarity=0.332 Sum_probs=8.7
Q ss_pred ceecCCCCCcCC
Q 031966 21 VFECKTCNRQFP 32 (150)
Q Consensus 21 ~~~C~~C~k~f~ 32 (150)
.+.|..||..|.
T Consensus 70 ~~~C~~Cg~~~~ 81 (113)
T PRK12380 70 QAWCWDCSQVVE 81 (113)
T ss_pred EEEcccCCCEEe
Confidence 477888886664
No 124
>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=47.73 E-value=18 Score=22.57 Aligned_cols=23 Identities=17% Similarity=0.395 Sum_probs=20.9
Q ss_pred eec----CCCCCcCCCHHHHHhhHHhc
Q 031966 22 FEC----KTCNRQFPSFQALGGHRASH 44 (150)
Q Consensus 22 ~~C----~~C~k~f~~~~~L~~H~~~h 44 (150)
|.| ..|+....+...+..|.+.+
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~ 107 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKE 107 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHh
Confidence 889 99999999999999998765
No 125
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=46.90 E-value=17 Score=20.23 Aligned_cols=13 Identities=23% Similarity=0.659 Sum_probs=9.7
Q ss_pred Cceeccccccccc
Q 031966 66 KLHECSICGQEFA 78 (150)
Q Consensus 66 kp~~C~~Cgk~f~ 78 (150)
..+.|.+||....
T Consensus 36 D~irCReCG~RIl 48 (62)
T KOG3507|consen 36 DVIRCRECGYRIL 48 (62)
T ss_pred CcEehhhcchHHH
Confidence 4788999996543
No 126
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=46.12 E-value=12 Score=28.60 Aligned_cols=23 Identities=30% Similarity=0.550 Sum_probs=21.2
Q ss_pred ceeccccccccccchHHHHHhHh
Q 031966 67 LHECSICGQEFAMGQALGGHMRR 89 (150)
Q Consensus 67 p~~C~~Cgk~f~~~~~l~~H~~~ 89 (150)
.+.|-.|.+.|..+..|+.||+.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 47899999999999999999985
No 127
>PRK14873 primosome assembly protein PriA; Provisional
Probab=45.75 E-value=12 Score=31.49 Aligned_cols=11 Identities=27% Similarity=0.773 Sum_probs=8.4
Q ss_pred Cceeccccccc
Q 031966 66 KLHECSICGQE 76 (150)
Q Consensus 66 kp~~C~~Cgk~ 76 (150)
.|+.|+.||..
T Consensus 421 ~p~~Cp~Cgs~ 431 (665)
T PRK14873 421 PDWRCPRCGSD 431 (665)
T ss_pred cCccCCCCcCC
Confidence 47889999854
No 128
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=45.65 E-value=13 Score=24.01 Aligned_cols=26 Identities=23% Similarity=0.374 Sum_probs=22.6
Q ss_pred CCCceeccccccccccchHHHHHhHh
Q 031966 64 KPKLHECSICGQEFAMGQALGGHMRR 89 (150)
Q Consensus 64 ~~kp~~C~~Cgk~f~~~~~l~~H~~~ 89 (150)
|.-.|-|-+|.+-|.....|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 33458899999999999999999875
No 129
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=45.36 E-value=11 Score=20.26 Aligned_cols=18 Identities=33% Similarity=0.674 Sum_probs=14.0
Q ss_pred CCceeccccccccccchH
Q 031966 65 PKLHECSICGQEFAMGQA 82 (150)
Q Consensus 65 ~kp~~C~~Cgk~f~~~~~ 82 (150)
.+.+.|..||..|.....
T Consensus 2 Dk~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAG 19 (49)
T ss_pred CeeEEcccCCCeEEEehh
Confidence 467899999999976543
No 130
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=44.99 E-value=13 Score=23.56 Aligned_cols=12 Identities=25% Similarity=0.556 Sum_probs=8.5
Q ss_pred CceecCCCCCcC
Q 031966 20 DVFECKTCNRQF 31 (150)
Q Consensus 20 ~~~~C~~C~k~f 31 (150)
-.+.|..||..|
T Consensus 69 ~~~~C~~Cg~~~ 80 (114)
T PRK03681 69 AECWCETCQQYV 80 (114)
T ss_pred cEEEcccCCCee
Confidence 357788888655
No 131
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=44.39 E-value=15 Score=29.19 Aligned_cols=29 Identities=21% Similarity=0.360 Sum_probs=24.8
Q ss_pred cccCCCCceeccccc-cccccchHHHHHhH
Q 031966 60 TTATKPKLHECSICG-QEFAMGQALGGHMR 88 (150)
Q Consensus 60 ~~h~~~kp~~C~~Cg-k~f~~~~~l~~H~~ 88 (150)
+.|.-...|.|.+|| +++..+.++.+|..
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 456667789999999 99999999999975
No 132
>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=44.01 E-value=14 Score=23.53 Aligned_cols=14 Identities=21% Similarity=0.622 Sum_probs=9.5
Q ss_pred CceecCCCCCcCCC
Q 031966 20 DVFECKTCNRQFPS 33 (150)
Q Consensus 20 ~~~~C~~C~k~f~~ 33 (150)
-...|..||+.|..
T Consensus 69 ~~~~C~~Cg~~~~~ 82 (115)
T TIGR00100 69 VECECEDCSEEVSP 82 (115)
T ss_pred cEEEcccCCCEEec
Confidence 34778888876643
No 133
>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=43.94 E-value=8.5 Score=20.82 Aligned_cols=26 Identities=23% Similarity=0.372 Sum_probs=15.9
Q ss_pred CCceecCCCCCcCCCHHHHHhhHHhc
Q 031966 19 SDVFECKTCNRQFPSFQALGGHRASH 44 (150)
Q Consensus 19 ~~~~~C~~C~k~f~~~~~L~~H~~~h 44 (150)
...|+|+.|.+.|-..-.+-.|...|
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH 44 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLH 44 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-
T ss_pred CCeEECCCCCCccccCcChhhhcccc
Confidence 35799999999999888888787766
No 134
>PRK05978 hypothetical protein; Provisional
Probab=42.91 E-value=9.1 Score=25.66 Aligned_cols=12 Identities=33% Similarity=1.099 Sum_probs=8.6
Q ss_pred eccccccccccc
Q 031966 69 ECSICGQEFAMG 80 (150)
Q Consensus 69 ~C~~Cgk~f~~~ 80 (150)
.|+.||..|...
T Consensus 54 ~C~~CG~~~~~~ 65 (148)
T PRK05978 54 HCAACGEDFTHH 65 (148)
T ss_pred CccccCCccccC
Confidence 488888877643
No 135
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=42.73 E-value=17 Score=23.26 Aligned_cols=14 Identities=36% Similarity=0.804 Sum_probs=10.0
Q ss_pred CceecCCCCCcCCC
Q 031966 20 DVFECKTCNRQFPS 33 (150)
Q Consensus 20 ~~~~C~~C~k~f~~ 33 (150)
-.+.|..||..|..
T Consensus 70 ~~~~C~~Cg~~~~~ 83 (117)
T PRK00564 70 VELECKDCSHVFKP 83 (117)
T ss_pred CEEEhhhCCCcccc
Confidence 35788999877643
No 136
>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=41.64 E-value=11 Score=27.67 Aligned_cols=75 Identities=20% Similarity=0.264 Sum_probs=45.1
Q ss_pred cCCCCceecCCCCCcCCCHHHHHhhHHhc--CCCCCCCCCcc----------------ccccc----ccCCCCceecccc
Q 031966 16 RLASDVFECKTCNRQFPSFQALGGHRASH--KKPRLINGETK----------------TLSST----TATKPKLHECSIC 73 (150)
Q Consensus 16 h~~~~~~~C~~C~k~f~~~~~L~~H~~~h--~~~k~~~c~~~----------------~~h~~----~h~~~kp~~C~~C 73 (150)
..|.+.|+|..|....-.-. --.|+.+- .....|+|... ..|++ .....+++.|+.|
T Consensus 137 ~hGGrif~CsfC~~flCEDD-QFEHQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKC 215 (314)
T PF06524_consen 137 DHGGRIFKCSFCDNFLCEDD-QFEHQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKC 215 (314)
T ss_pred cCCCeEEEeecCCCeeeccc-hhhhhhhhhhhhcccccccccccccchhhhheeeeehhhhhhhcccccccCCCCCCCCC
Confidence 45778999999986544333 33465543 11223443320 03433 2244579999999
Q ss_pred ccccccchHHHHHhHhcc
Q 031966 74 GQEFAMGQALGGHMRRHR 91 (150)
Q Consensus 74 gk~f~~~~~l~~H~~~h~ 91 (150)
|........|..-.|+|.
T Consensus 216 g~et~eTkdLSmStR~hk 233 (314)
T PF06524_consen 216 GYETQETKDLSMSTRSHK 233 (314)
T ss_pred CCcccccccceeeeecch
Confidence 988877777776666664
No 137
>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=41.32 E-value=11 Score=20.39 Aligned_cols=12 Identities=25% Similarity=0.825 Sum_probs=6.6
Q ss_pred eccccccccccc
Q 031966 69 ECSICGQEFAMG 80 (150)
Q Consensus 69 ~C~~Cgk~f~~~ 80 (150)
.|+.|++.|...
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 899999999754
No 138
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=40.59 E-value=23 Score=18.04 Aligned_cols=24 Identities=21% Similarity=0.441 Sum_probs=17.3
Q ss_pred eecccccccccc--chHHHHHhHhcc
Q 031966 68 HECSICGQEFAM--GQALGGHMRRHR 91 (150)
Q Consensus 68 ~~C~~Cgk~f~~--~~~l~~H~~~h~ 91 (150)
-.|+.||-.|.. ...-..|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 579999977764 456667777664
No 139
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=40.12 E-value=14 Score=24.40 Aligned_cols=19 Identities=32% Similarity=0.587 Sum_probs=14.6
Q ss_pred cccCCCCceecccccccccc
Q 031966 60 TTATKPKLHECSICGQEFAM 79 (150)
Q Consensus 60 ~~h~~~kp~~C~~Cgk~f~~ 79 (150)
..+.| +|..|.+||..|.-
T Consensus 106 ~l~~g-~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 106 WLHKG-KPQRCPECGQVFKL 124 (136)
T ss_dssp EEETT-SEEEETTTEEEEEE
T ss_pred EEeCC-CccCCCCCCeEEEE
Confidence 44555 59999999998863
No 140
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=39.90 E-value=15 Score=22.88 Aligned_cols=16 Identities=38% Similarity=0.924 Sum_probs=12.4
Q ss_pred ceeccccccccccchH
Q 031966 67 LHECSICGQEFAMGQA 82 (150)
Q Consensus 67 p~~C~~Cgk~f~~~~~ 82 (150)
|+.|..||..|...+.
T Consensus 2 pH~CtrCG~vf~~g~~ 17 (112)
T COG3364 2 PHQCTRCGEVFDDGSE 17 (112)
T ss_pred CceecccccccccccH
Confidence 6789999999987543
No 141
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=39.50 E-value=22 Score=28.25 Aligned_cols=29 Identities=17% Similarity=0.309 Sum_probs=23.5
Q ss_pred hhcCCCCceecCCCC-CcCCCHHHHHhhHH
Q 031966 14 KKRLASDVFECKTCN-RQFPSFQALGGHRA 42 (150)
Q Consensus 14 ~~h~~~~~~~C~~C~-k~f~~~~~L~~H~~ 42 (150)
+.|.-..-|.|++|| +++.-...+.+|-.
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 456667889999999 88888888888864
No 142
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.47 E-value=11 Score=20.04 Aligned_cols=17 Identities=18% Similarity=0.585 Sum_probs=13.2
Q ss_pred eccccccccccchHHHH
Q 031966 69 ECSICGQEFAMGQALGG 85 (150)
Q Consensus 69 ~C~~Cgk~f~~~~~l~~ 85 (150)
.|+.|++.|++..-..+
T Consensus 14 ICpvCqRPFsWRkKW~~ 30 (54)
T COG4338 14 ICPVCQRPFSWRKKWAR 30 (54)
T ss_pred hhhhhcCchHHHHHHHH
Confidence 59999999998765544
No 143
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.75 E-value=26 Score=29.38 Aligned_cols=65 Identities=15% Similarity=0.207 Sum_probs=33.9
Q ss_pred ecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCc-------cc--ccccccCCCCceecc--ccc-cccccchHHHHHhH
Q 031966 23 ECKTCNRQFPSFQALGGHRASHKKPRLINGET-------KT--LSSTTATKPKLHECS--ICG-QEFAMGQALGGHMR 88 (150)
Q Consensus 23 ~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~-------~~--~h~~~h~~~kp~~C~--~Cg-k~f~~~~~l~~H~~ 88 (150)
.|..|...|.....|.+|++.+.-.-.| |+. +. .-+..|-.+.-|.|. .|. +.|...-.+..+++
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h~~chf-C~~~~~~neyy~~~~dLe~HfR~~HflCE~~~C~~~~f~~~~~~ei~lk 260 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDHEFCHF-CDYKTGQNEYYNDYDDLEEHFRKGHFLCEEEFCRTKKFYVAFELEIELK 260 (669)
T ss_pred cchhhhhhhccHHHHHHhhccceeheee-cCcccccchhcccchHHHHHhhhcCccccccccccceeeehhHHHHHHH
Confidence 4777878887777777777643211111 211 11 223445556678887 564 44444434444444
No 144
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=38.17 E-value=21 Score=29.36 Aligned_cols=26 Identities=23% Similarity=0.465 Sum_probs=21.9
Q ss_pred CCceecCCCCCcCCCHHHHHhhHHhc
Q 031966 19 SDVFECKTCNRQFPSFQALGGHRASH 44 (150)
Q Consensus 19 ~~~~~C~~C~k~f~~~~~L~~H~~~h 44 (150)
.++-.|..||..|........||..|
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhh
Confidence 46789999999999998888777766
No 145
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=37.65 E-value=22 Score=30.25 Aligned_cols=45 Identities=20% Similarity=0.359 Sum_probs=23.5
Q ss_pred ecCCCCCcCCCH---HHHHhhHHhcCCCCCCCCCcccccccccCCCCceeccccccc
Q 031966 23 ECKTCNRQFPSF---QALGGHRASHKKPRLINGETKTLSSTTATKPKLHECSICGQE 76 (150)
Q Consensus 23 ~C~~C~k~f~~~---~~L~~H~~~h~~~k~~~c~~~~~h~~~h~~~kp~~C~~Cgk~ 76 (150)
.|..||..+..+ ..|..|+ ......|..+. +....|..|+.||..
T Consensus 437 ~C~~Cg~v~~Cp~Cd~~lt~H~----~~~~L~CH~Cg-----~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 437 LCRDCGYIAECPNCDSPLTLHK----ATGQLRCHYCG-----YQEPIPQSCPECGSE 484 (730)
T ss_pred ecccCCCcccCCCCCcceEEec----CCCeeEeCCCC-----CCCCCCCCCCCCCCC
Confidence 466676655432 2233333 33334443322 245678899999854
No 146
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=37.64 E-value=20 Score=28.70 Aligned_cols=22 Identities=23% Similarity=0.542 Sum_probs=19.8
Q ss_pred eeccccccccccchHHHHHhHh
Q 031966 68 HECSICGQEFAMGQALGGHMRR 89 (150)
Q Consensus 68 ~~C~~Cgk~f~~~~~l~~H~~~ 89 (150)
+-|.+|.|.|.+..+|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 6699999999999999999764
No 147
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=37.04 E-value=23 Score=28.35 Aligned_cols=32 Identities=19% Similarity=0.451 Sum_probs=25.9
Q ss_pred CCCCceeccccccccccchHHHHHhHh-cccch
Q 031966 63 TKPKLHECSICGQEFAMGQALGGHMRR-HRIAM 94 (150)
Q Consensus 63 ~~~kp~~C~~Cgk~f~~~~~l~~H~~~-h~~~~ 94 (150)
..-+=+.|+.|.+.|.....+..|+.. |.+.-
T Consensus 53 ~sWrFWiCp~CskkF~d~~~~~~H~~~eH~~~l 85 (466)
T PF04780_consen 53 KSWRFWICPRCSKKFSDAESCLSHMEQEHPAGL 85 (466)
T ss_pred CceeEeeCCcccceeCCHHHHHHHHHHhhhhhc
Confidence 344567899999999999999999984 76653
No 148
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=36.55 E-value=24 Score=28.22 Aligned_cols=22 Identities=36% Similarity=0.680 Sum_probs=19.8
Q ss_pred eecCCCCCcCCCHHHHHhhHHh
Q 031966 22 FECKTCNRQFPSFQALGGHRAS 43 (150)
Q Consensus 22 ~~C~~C~k~f~~~~~L~~H~~~ 43 (150)
+-|.+|.|.|.+.-.|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7899999999999999999754
No 149
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=35.65 E-value=22 Score=27.28 Aligned_cols=23 Identities=22% Similarity=0.459 Sum_probs=21.1
Q ss_pred ceecCCCCCcCCCHHHHHhhHHh
Q 031966 21 VFECKTCNRQFPSFQALGGHRAS 43 (150)
Q Consensus 21 ~~~C~~C~k~f~~~~~L~~H~~~ 43 (150)
.+.|-.|.|.|..+..|..|||.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 48899999999999999999975
No 150
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=35.33 E-value=12 Score=26.23 Aligned_cols=29 Identities=24% Similarity=0.434 Sum_probs=0.0
Q ss_pred cccCCCCceeccccc-cccccchHHHHHhH
Q 031966 60 TTATKPKLHECSICG-QEFAMGQALGGHMR 88 (150)
Q Consensus 60 ~~h~~~kp~~C~~Cg-k~f~~~~~l~~H~~ 88 (150)
+.|.-.+-|.|.+|| ..|..+.++.+|..
T Consensus 94 KLhGL~~ey~CEICGN~~Y~GrkaFekHF~ 123 (196)
T PF11931_consen 94 KLHGLGVEYKCEICGNQSYKGRKAFEKHFQ 123 (196)
T ss_dssp ------------------------------
T ss_pred HHhCCCCeeeeEeCCCcceecHHHHHHhcC
Confidence 344556779999998 67777888888864
No 151
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=35.16 E-value=18 Score=23.94 Aligned_cols=13 Identities=31% Similarity=0.703 Sum_probs=9.4
Q ss_pred Cceeccccccccc
Q 031966 66 KLHECSICGQEFA 78 (150)
Q Consensus 66 kp~~C~~Cgk~f~ 78 (150)
.-|.|..|+..|.
T Consensus 142 ~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 142 KRYRCGRCGGPLV 154 (157)
T ss_pred hhEECCCCCCEEE
Confidence 3588999986654
No 152
>PRK04351 hypothetical protein; Provisional
Probab=35.01 E-value=22 Score=23.85 Aligned_cols=14 Identities=21% Similarity=0.510 Sum_probs=10.3
Q ss_pred CCceeccccccccc
Q 031966 65 PKLHECSICGQEFA 78 (150)
Q Consensus 65 ~kp~~C~~Cgk~f~ 78 (150)
.+-|.|..|+-.+.
T Consensus 130 ~~~yrCg~C~g~L~ 143 (149)
T PRK04351 130 TKRYRCGKCRGKLK 143 (149)
T ss_pred CCcEEeCCCCcEee
Confidence 46789999986654
No 153
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=34.84 E-value=17 Score=17.85 Aligned_cols=13 Identities=31% Similarity=0.825 Sum_probs=6.8
Q ss_pred eeccccccccccc
Q 031966 68 HECSICGQEFAMG 80 (150)
Q Consensus 68 ~~C~~Cgk~f~~~ 80 (150)
-.|.+||+.|..+
T Consensus 4 ~~C~eC~~~f~dS 16 (34)
T PF01286_consen 4 PKCDECGKPFMDS 16 (34)
T ss_dssp EE-TTT--EES-S
T ss_pred chHhHhCCHHHHH
Confidence 3699999998654
No 154
>PF14353 CpXC: CpXC protein
Probab=34.42 E-value=19 Score=23.14 Aligned_cols=23 Identities=26% Similarity=0.431 Sum_probs=16.9
Q ss_pred CceeccccccccccchHHHHHhH
Q 031966 66 KLHECSICGQEFAMGQALGGHMR 88 (150)
Q Consensus 66 kp~~C~~Cgk~f~~~~~l~~H~~ 88 (150)
--|.|+.||..|.-...+.-|..
T Consensus 37 ~~~~CP~Cg~~~~~~~p~lY~D~ 59 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLLYHDP 59 (128)
T ss_pred CEEECCCCCCceecCCCEEEEcC
Confidence 36899999999987666555543
No 155
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=34.38 E-value=29 Score=18.55 Aligned_cols=11 Identities=27% Similarity=0.866 Sum_probs=7.2
Q ss_pred ecCCCCCcCCC
Q 031966 23 ECKTCNRQFPS 33 (150)
Q Consensus 23 ~C~~C~k~f~~ 33 (150)
.|..|++.|..
T Consensus 4 ~C~~C~~~F~~ 14 (57)
T cd00065 4 SCMGCGKPFTL 14 (57)
T ss_pred cCcccCccccC
Confidence 46677777754
No 156
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=33.52 E-value=20 Score=25.79 Aligned_cols=16 Identities=31% Similarity=0.592 Sum_probs=13.0
Q ss_pred CCCceecccccccccc
Q 031966 64 KPKLHECSICGQEFAM 79 (150)
Q Consensus 64 ~~kp~~C~~Cgk~f~~ 79 (150)
..++.+|.+||..|.-
T Consensus 178 EGkpqRCpECGqVFKL 193 (268)
T PTZ00043 178 EGFLYRCGECDQIFML 193 (268)
T ss_pred CCCCccCCCCCcEEEE
Confidence 3468999999999864
No 157
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=33.20 E-value=21 Score=17.76 Aligned_cols=11 Identities=18% Similarity=0.963 Sum_probs=5.9
Q ss_pred CceecCCCCCc
Q 031966 20 DVFECKTCNRQ 30 (150)
Q Consensus 20 ~~~~C~~C~k~ 30 (150)
+-|+|..||..
T Consensus 5 ~~YkC~~CGni 15 (36)
T PF06397_consen 5 EFYKCEHCGNI 15 (36)
T ss_dssp EEEE-TTT--E
T ss_pred cEEEccCCCCE
Confidence 35899999854
No 158
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.13 E-value=24 Score=23.01 Aligned_cols=15 Identities=27% Similarity=0.866 Sum_probs=9.8
Q ss_pred CCceecCCCCCcCCC
Q 031966 19 SDVFECKTCNRQFPS 33 (150)
Q Consensus 19 ~~~~~C~~C~k~f~~ 33 (150)
...|+|..|++.|..
T Consensus 51 ~qRyrC~~C~~tf~~ 65 (129)
T COG3677 51 HQRYKCKSCGSTFTV 65 (129)
T ss_pred ccccccCCcCcceee
Confidence 455777777777644
No 159
>COG1773 Rubredoxin [Energy production and conversion]
Probab=33.04 E-value=20 Score=19.76 Aligned_cols=13 Identities=15% Similarity=0.692 Sum_probs=10.6
Q ss_pred ceecCCCCCcCCC
Q 031966 21 VFECKTCNRQFPS 33 (150)
Q Consensus 21 ~~~C~~C~k~f~~ 33 (150)
.|+|..||..|.-
T Consensus 3 ~~~C~~CG~vYd~ 15 (55)
T COG1773 3 RWRCSVCGYVYDP 15 (55)
T ss_pred ceEecCCceEecc
Confidence 5899999988754
No 160
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=32.98 E-value=47 Score=25.65 Aligned_cols=83 Identities=17% Similarity=0.150 Sum_probs=49.7
Q ss_pred ccccchhhhhcCCCCc----eecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCccc----------ccccccCCCCceecc
Q 031966 6 SNRAKLPIKKRLASDV----FECKTCNRQFPSFQALGGHRASHKKPRLINGETKT----------LSSTTATKPKLHECS 71 (150)
Q Consensus 6 ~~~l~~h~~~h~~~~~----~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~~~----------~h~~~h~~~kp~~C~ 71 (150)
+.-|+.|...-..+.- -.|..|.+.|-....|..|+|.. .++-+-|+.-. ..+..|-..-.|.|.
T Consensus 201 ~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~FYdDDEL~~HcR~~-HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~~hy~ct 279 (493)
T COG5236 201 SSTLRDHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLR-HEACHICDMVGPIRYQYFKSYEDLEAHFRNAHYCCT 279 (493)
T ss_pred cccccccccCCccccCcCCCchhhhccceecChHHHHHHHHhh-hhhhhhhhccCccchhhhhCHHHHHHHhhcCceEEE
Confidence 3456666554322222 35999999999999999998753 24445555411 111223344456665
Q ss_pred c--c--c--cccccchHHHHHhHh
Q 031966 72 I--C--G--QEFAMGQALGGHMRR 89 (150)
Q Consensus 72 ~--C--g--k~f~~~~~l~~H~~~ 89 (150)
+ | | ..|.....|..|+..
T Consensus 280 ~qtc~~~k~~vf~~~~el~~h~~~ 303 (493)
T COG5236 280 FQTCRVGKCYVFPYHTELLEHLTR 303 (493)
T ss_pred EEEEecCcEEEeccHHHHHHHHHH
Confidence 4 3 2 467777888888754
No 161
>PTZ00448 hypothetical protein; Provisional
Probab=31.02 E-value=29 Score=26.90 Aligned_cols=23 Identities=22% Similarity=0.424 Sum_probs=20.9
Q ss_pred ceeccccccccccchHHHHHhHh
Q 031966 67 LHECSICGQEFAMGQALGGHMRR 89 (150)
Q Consensus 67 p~~C~~Cgk~f~~~~~l~~H~~~ 89 (150)
.|.|..|+-.|......+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999988999999986
No 162
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.77 E-value=22 Score=19.97 Aligned_cols=12 Identities=17% Similarity=0.592 Sum_probs=9.6
Q ss_pred ceeccccccccc
Q 031966 67 LHECSICGQEFA 78 (150)
Q Consensus 67 p~~C~~Cgk~f~ 78 (150)
-..|++|++.|.
T Consensus 48 ev~CPYC~t~y~ 59 (62)
T COG4391 48 EVVCPYCSTRYR 59 (62)
T ss_pred cEecCccccEEE
Confidence 357999999885
No 164
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=29.00 E-value=26 Score=17.44 Aligned_cols=16 Identities=25% Similarity=0.603 Sum_probs=9.7
Q ss_pred eccccccccccchHHH
Q 031966 69 ECSICGQEFAMGQALG 84 (150)
Q Consensus 69 ~C~~Cgk~f~~~~~l~ 84 (150)
.|..|+|.|-+.+...
T Consensus 4 ~CprC~kg~Hwa~~C~ 19 (36)
T PF14787_consen 4 LCPRCGKGFHWASECR 19 (36)
T ss_dssp C-TTTSSSCS-TTT--
T ss_pred cCcccCCCcchhhhhh
Confidence 5888999987776654
No 165
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=28.68 E-value=38 Score=22.31 Aligned_cols=12 Identities=25% Similarity=0.728 Sum_probs=8.6
Q ss_pred Cceecccccccc
Q 031966 66 KLHECSICGQEF 77 (150)
Q Consensus 66 kp~~C~~Cgk~f 77 (150)
.-|.|..|+-.+
T Consensus 132 ~~y~C~~C~g~l 143 (146)
T smart00731 132 SRYRCGKCGGKL 143 (146)
T ss_pred ceEEcCCCCCEE
Confidence 558888887654
No 166
>PLN02748 tRNA dimethylallyltransferase
Probab=28.63 E-value=34 Score=27.54 Aligned_cols=25 Identities=16% Similarity=0.260 Sum_probs=21.6
Q ss_pred CCceecccccc-ccccchHHHHHhHh
Q 031966 65 PKLHECSICGQ-EFAMGQALGGHMRR 89 (150)
Q Consensus 65 ~kp~~C~~Cgk-~f~~~~~l~~H~~~ 89 (150)
.+.|.|..|++ .+.....+..|++.
T Consensus 416 ~~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 416 WTQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred cccccccCCCCcccCCHHHHHHHhcc
Confidence 46789999997 79999999999865
No 167
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=27.33 E-value=37 Score=26.23 Aligned_cols=28 Identities=21% Similarity=0.366 Sum_probs=22.6
Q ss_pred ccCCCCceeccccc-cccccchHHHHHhH
Q 031966 61 TATKPKLHECSICG-QEFAMGQALGGHMR 88 (150)
Q Consensus 61 ~h~~~kp~~C~~Cg-k~f~~~~~l~~H~~ 88 (150)
.|.-.+-|.|..|| +.+.....+.+|..
T Consensus 368 lhgLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 368 LHGLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred hcCCCcceeeeecccccccchHHHHhhhh
Confidence 45556789999999 88888888888864
No 168
>PRK06260 threonine synthase; Validated
Probab=27.32 E-value=47 Score=25.88 Aligned_cols=11 Identities=18% Similarity=1.005 Sum_probs=8.9
Q ss_pred eecCCCCCcCC
Q 031966 22 FECKTCNRQFP 32 (150)
Q Consensus 22 ~~C~~C~k~f~ 32 (150)
++|..||+.|.
T Consensus 4 ~~C~~cg~~~~ 14 (397)
T PRK06260 4 LKCIECGKEYD 14 (397)
T ss_pred EEECCCCCCCC
Confidence 78999998764
No 169
>PTZ00448 hypothetical protein; Provisional
Probab=26.71 E-value=50 Score=25.65 Aligned_cols=23 Identities=30% Similarity=0.573 Sum_probs=19.6
Q ss_pred ceecCCCCCcCCCHHHHHhhHHh
Q 031966 21 VFECKTCNRQFPSFQALGGHRAS 43 (150)
Q Consensus 21 ~~~C~~C~k~f~~~~~L~~H~~~ 43 (150)
.|.|..|+-.|......+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 68899999999888888788765
No 170
>PLN02748 tRNA dimethylallyltransferase
Probab=26.50 E-value=51 Score=26.54 Aligned_cols=26 Identities=12% Similarity=0.383 Sum_probs=21.4
Q ss_pred CCceecCCCCC-cCCCHHHHHhhHHhc
Q 031966 19 SDVFECKTCNR-QFPSFQALGGHRASH 44 (150)
Q Consensus 19 ~~~~~C~~C~k-~f~~~~~L~~H~~~h 44 (150)
.+.|.|+.|++ .+.-......|.+..
T Consensus 416 ~~~~~Ce~C~~~~~~G~~eW~~Hlksr 442 (468)
T PLN02748 416 WTQYVCEACGNKVLRGAHEWEQHKQGR 442 (468)
T ss_pred cccccccCCCCcccCCHHHHHHHhcch
Confidence 46789999997 798888898888543
No 171
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.19 E-value=50 Score=21.06 Aligned_cols=24 Identities=21% Similarity=0.332 Sum_probs=13.3
Q ss_pred ceecCCCCCcCCCHHHHHhhHHhc
Q 031966 21 VFECKTCNRQFPSFQALGGHRASH 44 (150)
Q Consensus 21 ~~~C~~C~k~f~~~~~L~~H~~~h 44 (150)
.|+|+.|.+.|-..-++-.|...|
T Consensus 81 ~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 81 RYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred ceeCCCCCCccccccchhhhhhcc
Confidence 355666666665555555555444
No 172
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=26.15 E-value=42 Score=21.19 Aligned_cols=15 Identities=20% Similarity=0.328 Sum_probs=11.7
Q ss_pred Cceeccccccccccc
Q 031966 66 KLHECSICGQEFAMG 80 (150)
Q Consensus 66 kp~~C~~Cgk~f~~~ 80 (150)
..|.|++|+..++..
T Consensus 18 ~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 18 TQLICPSCLYEWNEN 32 (109)
T ss_pred CeeECcccccccccc
Confidence 468999999877654
No 173
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=26.04 E-value=68 Score=24.43 Aligned_cols=26 Identities=19% Similarity=0.273 Sum_probs=21.0
Q ss_pred CceeccccccccccchHHHHHhHhcc
Q 031966 66 KLHECSICGQEFAMGQALGGHMRRHR 91 (150)
Q Consensus 66 kp~~C~~Cgk~f~~~~~l~~H~~~h~ 91 (150)
-.|.|+.|...|-.....-.|...|-
T Consensus 387 ~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 387 GRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred cceechhhhhhhhhhhHHHHHHHHhh
Confidence 46999999999988888777877664
No 174
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=25.91 E-value=27 Score=22.55 Aligned_cols=14 Identities=21% Similarity=0.252 Sum_probs=10.3
Q ss_pred CceecCCCCCcCCCH
Q 031966 20 DVFECKTCNRQFPSF 34 (150)
Q Consensus 20 ~~~~C~~C~k~f~~~ 34 (150)
-.+.| .||..|...
T Consensus 69 ~~~~C-~Cg~~~~~~ 82 (124)
T PRK00762 69 VEIEC-ECGYEGVVD 82 (124)
T ss_pred eeEEe-eCcCccccc
Confidence 35789 999887653
No 175
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=25.72 E-value=32 Score=17.00 Aligned_cols=11 Identities=27% Similarity=0.875 Sum_probs=8.0
Q ss_pred eeccccccccc
Q 031966 68 HECSICGQEFA 78 (150)
Q Consensus 68 ~~C~~Cgk~f~ 78 (150)
+.|+.||+.|.
T Consensus 2 r~C~~Cg~~Yh 12 (36)
T PF05191_consen 2 RICPKCGRIYH 12 (36)
T ss_dssp EEETTTTEEEE
T ss_pred cCcCCCCCccc
Confidence 45888888774
No 176
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=25.71 E-value=52 Score=26.28 Aligned_cols=11 Identities=27% Similarity=0.773 Sum_probs=8.6
Q ss_pred ceecCCCCCcC
Q 031966 21 VFECKTCNRQF 31 (150)
Q Consensus 21 ~~~C~~C~k~f 31 (150)
.|.|..||..+
T Consensus 7 ~y~C~~Cg~~~ 17 (454)
T TIGR00416 7 KFVCQHCGADS 17 (454)
T ss_pred eEECCcCCCCC
Confidence 59999999653
No 177
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=25.64 E-value=29 Score=18.99 Aligned_cols=12 Identities=42% Similarity=1.024 Sum_probs=9.1
Q ss_pred eecccccccccc
Q 031966 68 HECSICGQEFAM 79 (150)
Q Consensus 68 ~~C~~Cgk~f~~ 79 (150)
|+|+.||..+.-
T Consensus 3 ~~CP~CG~~iev 14 (54)
T TIGR01206 3 FECPDCGAEIEL 14 (54)
T ss_pred cCCCCCCCEEec
Confidence 679999987643
No 178
>PRK11823 DNA repair protein RadA; Provisional
Probab=25.24 E-value=54 Score=26.13 Aligned_cols=12 Identities=17% Similarity=0.733 Sum_probs=9.1
Q ss_pred CceecCCCCCcC
Q 031966 20 DVFECKTCNRQF 31 (150)
Q Consensus 20 ~~~~C~~C~k~f 31 (150)
..|.|..||..+
T Consensus 6 ~~y~C~~Cg~~~ 17 (446)
T PRK11823 6 TAYVCQECGAES 17 (446)
T ss_pred CeEECCcCCCCC
Confidence 359999999653
No 179
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=25.02 E-value=35 Score=18.01 Aligned_cols=12 Identities=25% Similarity=0.872 Sum_probs=8.9
Q ss_pred eecccccccccc
Q 031966 68 HECSICGQEFAM 79 (150)
Q Consensus 68 ~~C~~Cgk~f~~ 79 (150)
|.|..||..+..
T Consensus 2 y~C~~CgyvYd~ 13 (47)
T PF00301_consen 2 YQCPVCGYVYDP 13 (47)
T ss_dssp EEETTTSBEEET
T ss_pred cCCCCCCEEEcC
Confidence 678888877654
No 180
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=24.97 E-value=49 Score=22.60 Aligned_cols=23 Identities=17% Similarity=0.467 Sum_probs=17.4
Q ss_pred CceeccccccccccchHHHHHhH
Q 031966 66 KLHECSICGQEFAMGQALGGHMR 88 (150)
Q Consensus 66 kp~~C~~Cgk~f~~~~~l~~H~~ 88 (150)
.-|.|+.||+.|-..+++..-.+
T Consensus 129 ~f~~C~~CgkiYW~GsHw~~m~~ 151 (165)
T COG1656 129 EFYRCPKCGKIYWKGSHWRRMVE 151 (165)
T ss_pred ceeECCCCcccccCchHHHHHHH
Confidence 45779999999988877665444
No 181
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=24.67 E-value=34 Score=18.52 Aligned_cols=19 Identities=16% Similarity=0.343 Sum_probs=12.6
Q ss_pred hcCCCCceecCCCCCcCCC
Q 031966 15 KRLASDVFECKTCNRQFPS 33 (150)
Q Consensus 15 ~h~~~~~~~C~~C~k~f~~ 33 (150)
...+...|+|..|++.+..
T Consensus 29 ~~~~~~~~rC~YCe~~~~~ 47 (52)
T PF02748_consen 29 IDKEPIKLRCHYCERIITE 47 (52)
T ss_dssp EETTTCEEEETTT--EEEH
T ss_pred EeCCCCEEEeeCCCCEecc
Confidence 3456678999999988754
No 182
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=24.64 E-value=36 Score=20.80 Aligned_cols=14 Identities=29% Similarity=0.662 Sum_probs=11.9
Q ss_pred CceecCCCCCcCCC
Q 031966 20 DVFECKTCNRQFPS 33 (150)
Q Consensus 20 ~~~~C~~C~k~f~~ 33 (150)
+|-.|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 58899999998865
No 183
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=24.31 E-value=31 Score=18.50 Aligned_cols=12 Identities=42% Similarity=0.910 Sum_probs=8.9
Q ss_pred eecccccccccc
Q 031966 68 HECSICGQEFAM 79 (150)
Q Consensus 68 ~~C~~Cgk~f~~ 79 (150)
|.|..||..|..
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 678888877653
No 184
>PF12907 zf-met2: Zinc-binding
Probab=24.19 E-value=24 Score=17.99 Aligned_cols=26 Identities=31% Similarity=0.482 Sum_probs=18.8
Q ss_pred eeccccccccc---cchHHHHHhHh-cccc
Q 031966 68 HECSICGQEFA---MGQALGGHMRR-HRIA 93 (150)
Q Consensus 68 ~~C~~Cgk~f~---~~~~l~~H~~~-h~~~ 93 (150)
+.|.+|-..|. ....|..|... |...
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~ 31 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKN 31 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCC
Confidence 46889987665 45679999874 6554
No 185
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=23.46 E-value=76 Score=15.80 Aligned_cols=15 Identities=13% Similarity=0.476 Sum_probs=6.0
Q ss_pred ceecCCCCCcCCCHH
Q 031966 21 VFECKTCNRQFPSFQ 35 (150)
Q Consensus 21 ~~~C~~C~k~f~~~~ 35 (150)
.|-|+.|...|...+
T Consensus 3 ryyCdyC~~~~~~d~ 17 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDS 17 (38)
T ss_dssp S-B-TTT--B-S--S
T ss_pred CeecccccceecCCC
Confidence 488999999984433
No 186
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=23.35 E-value=1.1e+02 Score=23.09 Aligned_cols=26 Identities=19% Similarity=0.388 Sum_probs=22.7
Q ss_pred CCceecCCCCCcCCCHHHHHhhHHhc
Q 031966 19 SDVFECKTCNRQFPSFQALGGHRASH 44 (150)
Q Consensus 19 ~~~~~C~~C~k~f~~~~~L~~H~~~h 44 (150)
+.-|.|+.|-+-|.....|.+|+...
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~C 71 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAKC 71 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHhC
Confidence 45699999999999999999998743
No 187
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=23.29 E-value=39 Score=20.62 Aligned_cols=11 Identities=27% Similarity=0.836 Sum_probs=6.3
Q ss_pred Cceeccccccc
Q 031966 66 KLHECSICGQE 76 (150)
Q Consensus 66 kp~~C~~Cgk~ 76 (150)
..|.|+.||+.
T Consensus 34 ~ky~Cp~Cgk~ 44 (90)
T PF01780_consen 34 AKYTCPFCGKT 44 (90)
T ss_dssp S-BEESSSSSS
T ss_pred CCCcCCCCCCc
Confidence 45667777654
No 188
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=23.23 E-value=29 Score=29.33 Aligned_cols=21 Identities=19% Similarity=0.496 Sum_probs=16.3
Q ss_pred CceeccccccccccchHHHHH
Q 031966 66 KLHECSICGQEFAMGQALGGH 86 (150)
Q Consensus 66 kp~~C~~Cgk~f~~~~~l~~H 86 (150)
|.-+||.|+.+|...+.+..|
T Consensus 677 RqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 677 RQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred hcCCCCCCCCCCCcccccccC
Confidence 445799999999988766554
No 189
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=23.15 E-value=31 Score=29.72 Aligned_cols=13 Identities=38% Similarity=0.848 Sum_probs=10.2
Q ss_pred eecCCCCCcCCCH
Q 031966 22 FECKTCNRQFPSF 34 (150)
Q Consensus 22 ~~C~~C~k~f~~~ 34 (150)
-.|..|++.|...
T Consensus 461 dtC~~C~kkFfSl 473 (1374)
T PTZ00303 461 DSCPSCGRAFISL 473 (1374)
T ss_pred CcccCcCCccccc
Confidence 4699999999653
No 190
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=23.12 E-value=39 Score=26.92 Aligned_cols=28 Identities=25% Similarity=0.328 Sum_probs=24.0
Q ss_pred CceeccccccccccchHHHHHhHh-cccc
Q 031966 66 KLHECSICGQEFAMGQALGGHMRR-HRIA 93 (150)
Q Consensus 66 kp~~C~~Cgk~f~~~~~l~~H~~~-h~~~ 93 (150)
.-|.|+.|.+.|..-..|..|... |.++
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 468999999999999999999976 5544
No 191
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=22.97 E-value=69 Score=22.18 Aligned_cols=20 Identities=10% Similarity=0.464 Sum_probs=12.3
Q ss_pred cCCCCceecCCCCCcCCCHH
Q 031966 16 RLASDVFECKTCNRQFPSFQ 35 (150)
Q Consensus 16 h~~~~~~~C~~C~k~f~~~~ 35 (150)
-+...-|.|+.|.-.|+...
T Consensus 108 ~~~~~~y~C~~~~~r~sfde 127 (176)
T COG1675 108 ETENNYYVCPNCHVKYSFDE 127 (176)
T ss_pred hccCCceeCCCCCCcccHHH
Confidence 34555688877776665433
No 192
>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=22.95 E-value=39 Score=16.92 Aligned_cols=10 Identities=30% Similarity=0.932 Sum_probs=8.4
Q ss_pred eecccccccc
Q 031966 68 HECSICGQEF 77 (150)
Q Consensus 68 ~~C~~Cgk~f 77 (150)
|.|..||..|
T Consensus 29 y~C~~C~~~w 38 (39)
T PF01096_consen 29 YVCCNCGHRW 38 (39)
T ss_dssp EEESSSTEEE
T ss_pred EEeCCCCCee
Confidence 8899999876
No 193
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=22.77 E-value=53 Score=16.24 Aligned_cols=19 Identities=26% Similarity=0.475 Sum_probs=11.2
Q ss_pred cchhhhhcCCCCceecCCC
Q 031966 9 AKLPIKKRLASDVFECKTC 27 (150)
Q Consensus 9 l~~h~~~h~~~~~~~C~~C 27 (150)
+..|-+...|...|.|..|
T Consensus 17 v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 17 VKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred ceeCCCCCCCCEeEecCcC
Confidence 4455555556666777666
No 194
>PRK10220 hypothetical protein; Provisional
Probab=22.51 E-value=69 Score=20.30 Aligned_cols=16 Identities=19% Similarity=0.528 Sum_probs=12.0
Q ss_pred Cceeccccccccccch
Q 031966 66 KLHECSICGQEFAMGQ 81 (150)
Q Consensus 66 kp~~C~~Cgk~f~~~~ 81 (150)
..|.|++|+..++...
T Consensus 19 ~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 19 GMYICPECAHEWNDAE 34 (111)
T ss_pred CeEECCcccCcCCccc
Confidence 4689999998776543
No 195
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=22.24 E-value=67 Score=25.86 Aligned_cols=25 Identities=20% Similarity=0.553 Sum_probs=21.4
Q ss_pred CceecCCCCCcCCCHHHHHhhHH-hc
Q 031966 20 DVFECKTCNRQFPSFQALGGHRA-SH 44 (150)
Q Consensus 20 ~~~~C~~C~k~f~~~~~L~~H~~-~h 44 (150)
+=+.|+.|++.|.....+..|+. .|
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH 81 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEH 81 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhh
Confidence 45689999999999999999985 45
No 196
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=21.90 E-value=44 Score=16.24 Aligned_cols=23 Identities=26% Similarity=0.637 Sum_probs=14.3
Q ss_pred ceeccccccccccchHHHHHhHhc
Q 031966 67 LHECSICGQEFAMGQALGGHMRRH 90 (150)
Q Consensus 67 p~~C~~Cgk~f~~~~~l~~H~~~h 90 (150)
-+.|+.|++.+. .+-+..|+..-
T Consensus 4 ~~~C~nC~R~v~-a~RfA~HLekC 26 (33)
T PF08209_consen 4 YVECPNCGRPVA-ASRFAPHLEKC 26 (33)
T ss_dssp EEE-TTTSSEEE-GGGHHHHHHHH
T ss_pred eEECCCCcCCcc-hhhhHHHHHHH
Confidence 478999998764 34455665543
No 197
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=21.54 E-value=51 Score=15.74 Aligned_cols=12 Identities=25% Similarity=0.935 Sum_probs=9.0
Q ss_pred CceecCCCCCcC
Q 031966 20 DVFECKTCNRQF 31 (150)
Q Consensus 20 ~~~~C~~C~k~f 31 (150)
+-|+|..||...
T Consensus 6 ~~ykC~~Cgniv 17 (34)
T TIGR00319 6 QVYKCEVCGNIV 17 (34)
T ss_pred cEEEcCCCCcEE
Confidence 368999998654
No 198
>KOG3352 consensus Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion]
Probab=21.33 E-value=43 Score=22.50 Aligned_cols=18 Identities=22% Similarity=0.521 Sum_probs=12.9
Q ss_pred cccCCCCceeccccccccc
Q 031966 60 TTATKPKLHECSICGQEFA 78 (150)
Q Consensus 60 ~~h~~~kp~~C~~Cgk~f~ 78 (150)
..+.| +..+|.+||..|.
T Consensus 127 wl~Kg-e~~rc~eCG~~fk 144 (153)
T KOG3352|consen 127 WLEKG-ETQRCPECGHYFK 144 (153)
T ss_pred EEEcC-CcccCCcccceEE
Confidence 34444 4667999998885
No 199
>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=21.30 E-value=39 Score=22.63 Aligned_cols=18 Identities=22% Similarity=0.469 Sum_probs=13.4
Q ss_pred CceeccccccccccchHH
Q 031966 66 KLHECSICGQEFAMGQAL 83 (150)
Q Consensus 66 kp~~C~~Cgk~f~~~~~l 83 (150)
+--.|..||+.|.+....
T Consensus 27 RRReC~~C~~RFTTyErv 44 (147)
T TIGR00244 27 RRRECLECHERFTTFERA 44 (147)
T ss_pred ecccCCccCCccceeeec
Confidence 345799999999876433
No 200
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=21.04 E-value=52 Score=15.72 Aligned_cols=11 Identities=27% Similarity=0.975 Sum_probs=8.0
Q ss_pred ceecCCCCCcC
Q 031966 21 VFECKTCNRQF 31 (150)
Q Consensus 21 ~~~C~~C~k~f 31 (150)
-|+|..||...
T Consensus 4 ~ykC~~CGniv 14 (34)
T cd00974 4 VYKCEICGNIV 14 (34)
T ss_pred EEEcCCCCcEE
Confidence 58888888654
No 201
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=20.68 E-value=70 Score=24.87 Aligned_cols=10 Identities=40% Similarity=0.950 Sum_probs=7.1
Q ss_pred ceeccccccc
Q 031966 67 LHECSICGQE 76 (150)
Q Consensus 67 p~~C~~Cgk~ 76 (150)
-.+|+.|+..
T Consensus 14 ~g~cp~c~~w 23 (372)
T cd01121 14 LGKCPECGEW 23 (372)
T ss_pred cEECcCCCCc
Confidence 4578889764
No 202
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=20.50 E-value=1.8e+02 Score=22.37 Aligned_cols=72 Identities=14% Similarity=0.095 Sum_probs=41.5
Q ss_pred CceecCCCCCcCCCHHHHHhhHHhcCCCCCCCCCc-----ccccc----cccCCCCceeccccccccccchHHHHHhHhc
Q 031966 20 DVFECKTCNRQFPSFQALGGHRASHKKPRLINGET-----KTLSS----TTATKPKLHECSICGQEFAMGQALGGHMRRH 90 (150)
Q Consensus 20 ~~~~C~~C~k~f~~~~~L~~H~~~h~~~k~~~c~~-----~~~h~----~~h~~~kp~~C~~Cgk~f~~~~~l~~H~~~h 90 (150)
-|-.|+.|+-..-...+|.+-.+---.-++|.-.. ...+- ..-.+.-.|.|..|...|--....-.|...|
T Consensus 289 LP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 289 LPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred CCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhccceeeccchHHHHhhhh
Confidence 36788999988888888876433212222221100 00000 0113334699999999988777777776666
Q ss_pred c
Q 031966 91 R 91 (150)
Q Consensus 91 ~ 91 (150)
-
T Consensus 369 ~ 369 (378)
T KOG2807|consen 369 N 369 (378)
T ss_pred c
Confidence 4
No 203
>PRK04023 DNA polymerase II large subunit; Validated
Probab=20.50 E-value=82 Score=28.05 Aligned_cols=13 Identities=38% Similarity=0.820 Sum_probs=8.4
Q ss_pred Cceeccccccccc
Q 031966 66 KLHECSICGQEFA 78 (150)
Q Consensus 66 kp~~C~~Cgk~f~ 78 (150)
.++.|+.||..-.
T Consensus 662 ~~y~CPKCG~El~ 674 (1121)
T PRK04023 662 EEDECEKCGREPT 674 (1121)
T ss_pred CCCcCCCCCCCCC
Confidence 3567888875443
No 204
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=20.23 E-value=1.6e+02 Score=22.88 Aligned_cols=25 Identities=24% Similarity=0.363 Sum_probs=20.4
Q ss_pred CCceecCCCCCcCCCHHHHHhhHHh
Q 031966 19 SDVFECKTCNRQFPSFQALGGHRAS 43 (150)
Q Consensus 19 ~~~~~C~~C~k~f~~~~~L~~H~~~ 43 (150)
+..|.|++|++.=-+...+..|...
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s 101 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLS 101 (381)
T ss_pred cccccCCcccccccchhHHHHHhhh
Confidence 4579999999988888888888743
No 205
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=20.13 E-value=78 Score=21.80 Aligned_cols=21 Identities=19% Similarity=0.487 Sum_probs=16.5
Q ss_pred CCceecCCCCCcCCCHHHHHh
Q 031966 19 SDVFECKTCNRQFPSFQALGG 39 (150)
Q Consensus 19 ~~~~~C~~C~k~f~~~~~L~~ 39 (150)
.....|..||+.|.....+..
T Consensus 112 ~~~~~C~~Cg~~f~~~k~i~~ 132 (181)
T PRK08222 112 FHLQRCSRCERPFAPQKTVAL 132 (181)
T ss_pred cccCcCcccCCccCcHhHHHH
Confidence 357889999999997666554
Done!