Query 037234
Match_columns 81
No_of_seqs 128 out of 1068
Neff 9.7
Searched_HMMs 46136
Date Fri Mar 29 10:06:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037234.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037234hhsearch_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 99.7 4.9E-18 1.1E-22 103.4 3.3 61 3-64 187-250 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.5 4.5E-15 9.8E-20 90.5 3.1 63 2-65 160-223 (279)
3 KOG3623 Homeobox transcription 99.5 3.9E-15 8.5E-20 100.3 0.5 61 3-64 894-957 (1007)
4 PHA02768 hypothetical protein; 99.2 5.6E-12 1.2E-16 60.5 1.3 43 3-45 5-48 (55)
5 KOG3623 Homeobox transcription 99.2 1.2E-11 2.6E-16 83.9 2.6 61 3-64 240-316 (1007)
6 KOG3576 Ovo and related transc 99.1 4.3E-12 9.3E-17 75.2 -0.6 60 4-64 118-180 (267)
7 PHA00733 hypothetical protein 99.0 5.1E-10 1.1E-14 62.6 4.8 50 2-51 72-122 (128)
8 KOG1074 Transcriptional repres 98.9 5.1E-10 1.1E-14 76.9 2.2 55 3-58 879-936 (958)
9 KOG3576 Ovo and related transc 98.9 3.9E-10 8.4E-15 67.1 0.7 50 2-51 144-196 (267)
10 KOG1074 Transcriptional repres 98.9 4.2E-10 9E-15 77.3 0.2 49 3-51 353-404 (958)
11 PHA00616 hypothetical protein 98.8 1.5E-09 3.2E-14 49.9 1.4 32 29-61 1-33 (44)
12 PHA00732 hypothetical protein 98.7 1.8E-08 3.8E-13 52.0 2.4 46 3-51 1-47 (79)
13 KOG3608 Zn finger proteins [Ge 98.6 3.1E-08 6.6E-13 63.2 2.0 55 4-60 264-322 (467)
14 PHA02768 hypothetical protein; 98.4 2.2E-07 4.7E-12 44.6 2.4 33 29-64 5-38 (55)
15 KOG3608 Zn finger proteins [Ge 98.3 9.1E-07 2E-11 56.6 4.4 64 2-65 236-300 (467)
16 PF13465 zf-H2C2_2: Zinc-finge 98.3 7.9E-07 1.7E-11 36.6 2.4 21 19-39 2-25 (26)
17 PLN03086 PRLI-interacting fact 98.2 2.2E-06 4.7E-11 57.9 4.8 62 2-66 452-513 (567)
18 PHA00733 hypothetical protein 98.2 6.8E-07 1.5E-11 50.0 1.9 61 2-65 39-107 (128)
19 PF00096 zf-C2H2: Zinc finger, 98.2 1.3E-06 2.8E-11 34.6 2.2 22 30-51 1-23 (23)
20 PHA00616 hypothetical protein 98.2 9.7E-07 2.1E-11 40.5 1.6 30 3-32 1-32 (44)
21 COG5189 SFP1 Putative transcri 98.1 5.5E-07 1.2E-11 56.9 0.4 49 1-49 347-419 (423)
22 PF05605 zf-Di19: Drought indu 98.1 8.3E-06 1.8E-10 39.1 4.1 46 3-51 2-52 (54)
23 PF13465 zf-H2C2_2: Zinc-finge 98.1 2.4E-06 5.2E-11 35.1 1.8 21 43-64 1-21 (26)
24 PLN03086 PRLI-interacting fact 98.0 1.4E-05 3E-10 54.1 4.6 59 2-64 477-548 (567)
25 PF13912 zf-C2H2_6: C2H2-type 97.9 7E-06 1.5E-10 33.7 1.5 23 29-51 1-24 (27)
26 PF00096 zf-C2H2: Zinc finger, 97.8 1.3E-05 2.8E-10 31.6 1.3 22 4-25 1-22 (23)
27 PF13894 zf-C2H2_4: C2H2-type 97.8 3.2E-05 6.8E-10 30.4 2.4 22 30-51 1-23 (24)
28 KOG3993 Transcription factor ( 97.7 3E-05 6.5E-10 50.7 2.3 49 3-51 295-379 (500)
29 smart00355 ZnF_C2H2 zinc finge 97.4 0.00013 2.9E-09 28.9 1.5 22 30-51 1-23 (26)
30 PF13912 zf-C2H2_6: C2H2-type 97.4 8E-05 1.7E-09 30.4 0.8 23 3-25 1-23 (27)
31 PF09237 GAGA: GAGA factor; I 97.3 0.00028 6.1E-09 33.3 2.6 30 27-57 22-52 (54)
32 PF13894 zf-C2H2_4: C2H2-type 97.3 0.00018 3.9E-09 28.1 1.7 22 4-25 1-22 (24)
33 PF12756 zf-C2H2_2: C2H2 type 97.1 0.00065 1.4E-08 35.6 3.2 47 5-51 1-73 (100)
34 PHA00732 hypothetical protein 97.1 0.00044 9.4E-09 35.7 2.3 33 29-65 1-35 (79)
35 smart00355 ZnF_C2H2 zinc finge 97.0 0.00088 1.9E-08 26.4 2.2 22 4-25 1-22 (26)
36 PF12874 zf-met: Zinc-finger o 96.8 0.00082 1.8E-08 26.8 1.4 21 30-50 1-22 (25)
37 KOG3993 Transcription factor ( 96.8 0.00019 4.2E-09 47.1 -0.9 48 4-51 268-318 (500)
38 PRK04860 hypothetical protein; 96.8 0.001 2.2E-08 38.6 2.1 23 40-63 127-149 (160)
39 PF09237 GAGA: GAGA factor; I 96.8 0.0013 2.7E-08 31.1 1.9 24 2-25 23-46 (54)
40 PF12874 zf-met: Zinc-finger o 96.1 0.0028 6.2E-08 25.1 1.0 21 4-24 1-21 (25)
41 PF13909 zf-H2C2_5: C2H2-type 96.0 0.0067 1.5E-07 23.9 1.8 21 30-51 1-22 (24)
42 PF12171 zf-C2H2_jaz: Zinc-fin 95.6 0.0034 7.3E-08 25.6 0.1 21 4-24 2-22 (27)
43 KOG2893 Zn finger protein [Gen 95.6 0.0051 1.1E-07 38.1 0.7 40 6-47 13-53 (341)
44 smart00451 ZnF_U1 U1-like zinc 95.1 0.021 4.5E-07 24.3 1.9 21 29-49 3-24 (35)
45 PRK04860 hypothetical protein; 95.1 0.021 4.5E-07 33.2 2.3 35 3-41 119-156 (160)
46 PF13913 zf-C2HC_2: zinc-finge 95.0 0.027 5.8E-07 22.6 1.9 20 5-25 4-23 (25)
47 COG5189 SFP1 Putative transcri 93.9 0.031 6.8E-07 36.0 1.3 24 26-49 346-372 (423)
48 KOG2186 Cell growth-regulating 92.7 0.084 1.8E-06 32.9 1.8 47 3-51 3-51 (276)
49 PF12756 zf-C2H2_2: C2H2 type 92.0 0.13 2.8E-06 26.7 1.7 23 3-25 50-72 (100)
50 KOG1146 Homeobox protein [Gene 91.3 0.14 3.1E-06 38.4 1.9 49 2-50 464-540 (1406)
51 COG5048 FOG: Zn-finger [Genera 90.4 0.066 1.4E-06 34.2 -0.4 57 3-60 289-354 (467)
52 COG1997 RPL43A Ribosomal prote 86.5 0.31 6.7E-06 25.6 0.6 29 3-39 35-64 (89)
53 PRK00464 nrdR transcriptional 86.3 0.15 3.2E-06 29.6 -0.7 40 4-43 1-43 (154)
54 COG4049 Uncharacterized protei 86.1 0.36 7.7E-06 23.3 0.7 26 26-51 14-40 (65)
55 PF09538 FYDLN_acid: Protein o 85.6 0.49 1.1E-05 25.8 1.2 30 4-42 10-40 (108)
56 smart00614 ZnF_BED BED zinc fi 84.0 0.99 2.1E-05 20.9 1.7 22 30-51 19-47 (50)
57 cd00350 rubredoxin_like Rubred 83.8 0.46 9.9E-06 20.2 0.4 23 4-36 2-25 (33)
58 PRK00398 rpoP DNA-directed RNA 83.2 0.54 1.2E-05 21.4 0.6 30 2-39 2-32 (46)
59 PHA00626 hypothetical protein 82.8 0.33 7.2E-06 23.4 -0.2 34 5-41 2-36 (59)
60 PF02892 zf-BED: BED zinc fing 82.7 1 2.2E-05 20.1 1.4 23 27-49 14-41 (45)
61 COG2888 Predicted Zn-ribbon RN 82.1 1 2.2E-05 22.0 1.3 8 28-35 49-57 (61)
62 PF04606 Ogr_Delta: Ogr/Delta- 81.2 0.32 6.8E-06 22.4 -0.6 37 5-41 1-40 (47)
63 PF15269 zf-C2H2_7: Zinc-finge 80.8 1.8 3.9E-05 20.0 1.8 22 30-51 21-43 (54)
64 PRK09678 DNA-binding transcrip 80.8 0.45 9.7E-06 24.1 -0.2 41 4-44 2-45 (72)
65 PF13719 zinc_ribbon_5: zinc-r 80.7 0.98 2.1E-05 19.7 0.9 32 5-39 4-36 (37)
66 PF05443 ROS_MUCR: ROS/MUCR tr 80.6 1.1 2.4E-05 25.4 1.3 24 28-55 71-95 (132)
67 PF04959 ARS2: Arsenite-resist 78.3 1.3 2.8E-05 27.1 1.2 24 2-25 76-99 (214)
68 KOG3408 U1-like Zn-finger-cont 77.3 1.6 3.4E-05 24.5 1.2 26 26-51 54-80 (129)
69 KOG4167 Predicted DNA-binding 76.6 0.59 1.3E-05 33.5 -0.6 23 29-51 792-815 (907)
70 PF13717 zinc_ribbon_4: zinc-r 76.6 1.3 2.8E-05 19.2 0.6 32 4-38 3-35 (36)
71 smart00659 RPOLCX RNA polymera 76.5 1.7 3.6E-05 19.8 1.0 26 3-37 2-28 (44)
72 COG1592 Rubrerythrin [Energy p 75.4 1.6 3.4E-05 25.7 1.0 8 4-11 135-142 (166)
73 TIGR02300 FYDLN_acid conserved 74.3 2 4.4E-05 24.2 1.2 33 3-44 9-42 (129)
74 PF04959 ARS2: Arsenite-resist 74.2 3.7 8E-05 25.2 2.4 24 28-51 76-100 (214)
75 TIGR02098 MJ0042_CXXC MJ0042 f 73.0 1.5 3.3E-05 18.9 0.4 33 4-39 3-36 (38)
76 PF08790 zf-LYAR: LYAR-type C2 71.9 1.1 2.5E-05 18.5 -0.1 18 31-49 2-20 (28)
77 smart00531 TFIIE Transcription 71.0 2.7 5.8E-05 24.0 1.2 12 29-40 99-111 (147)
78 PF09845 DUF2072: Zn-ribbon co 70.9 2.1 4.6E-05 24.2 0.8 15 3-17 1-15 (131)
79 KOG2482 Predicted C2H2-type Zn 70.5 6 0.00013 26.2 2.8 23 29-51 195-218 (423)
80 PF07754 DUF1610: Domain of un 67.8 2.7 5.8E-05 16.7 0.6 9 3-11 16-24 (24)
81 PF03604 DNA_RNApol_7kD: DNA d 67.8 2.1 4.7E-05 18.1 0.3 25 4-37 1-26 (32)
82 PRK14890 putative Zn-ribbon RN 66.6 3.4 7.3E-05 20.2 0.9 8 4-11 8-15 (59)
83 PF13451 zf-trcl: Probable zin 64.4 4 8.6E-05 19.1 0.9 33 2-34 3-39 (49)
84 KOG1146 Homeobox protein [Gene 64.4 3.6 7.9E-05 31.5 1.1 49 2-51 1283-1351(1406)
85 TIGR00373 conserved hypothetic 64.0 3.4 7.4E-05 23.9 0.7 16 29-44 109-125 (158)
86 smart00734 ZnF_Rad18 Rad18-lik 63.8 8.8 0.00019 15.3 1.8 19 5-24 3-21 (26)
87 smart00834 CxxC_CXXC_SSSS Puta 63.5 2.7 6E-05 18.2 0.2 29 3-36 5-34 (41)
88 PRK06266 transcription initiat 62.6 3.7 8.1E-05 24.3 0.7 13 4-16 118-130 (178)
89 COG5048 FOG: Zn-finger [Genera 62.3 6.7 0.00015 25.1 1.9 50 2-51 32-86 (467)
90 PF10571 UPF0547: Uncharacteri 62.0 5.1 0.00011 16.1 0.9 10 5-14 16-25 (26)
91 PF09723 Zn-ribbon_8: Zinc rib 60.1 3.1 6.7E-05 18.6 0.1 28 4-36 6-34 (42)
92 TIGR00280 L37a ribosomal prote 59.0 2.5 5.5E-05 22.4 -0.3 29 3-39 35-64 (91)
93 PTZ00255 60S ribosomal protein 58.5 4.4 9.6E-05 21.5 0.5 29 3-39 36-65 (90)
94 smart00154 ZnF_AN1 AN1-like Zi 58.2 5.2 0.00011 17.6 0.6 13 3-15 12-24 (39)
95 COG4957 Predicted transcriptio 57.2 12 0.00027 21.4 2.1 24 30-57 77-101 (148)
96 KOG2071 mRNA cleavage and poly 56.8 7.3 0.00016 27.4 1.4 25 27-51 416-441 (579)
97 KOG2482 Predicted C2H2-type Zn 56.7 7.7 0.00017 25.7 1.5 23 3-25 195-217 (423)
98 PF05191 ADK_lid: Adenylate ki 55.6 1.5 3.2E-05 19.1 -1.4 30 5-40 3-33 (36)
99 KOG2785 C2H2-type Zn-finger pr 55.5 41 0.00089 22.6 4.6 56 3-58 166-250 (390)
100 TIGR02605 CxxC_CxxC_SSSS putat 55.0 4.6 0.0001 18.6 0.2 29 3-36 5-34 (52)
101 KOG2593 Transcription initiati 54.9 11 0.00025 25.5 2.0 34 2-36 127-161 (436)
102 PLN03238 probable histone acet 54.8 25 0.00053 22.7 3.4 52 27-79 46-99 (290)
103 PF10013 DUF2256: Uncharacteri 54.8 7.8 0.00017 17.6 0.9 15 31-45 10-25 (42)
104 KOG1994 Predicted RNA binding 53.8 13 0.00028 23.2 2.0 22 26-47 236-258 (268)
105 KOG2857 Predicted MYND Zn-fing 53.6 7.3 0.00016 22.5 0.9 22 3-24 17-38 (157)
106 PF09986 DUF2225: Uncharacteri 53.6 5.5 0.00012 24.2 0.4 40 2-41 4-61 (214)
107 COG3364 Zn-ribbon containing p 51.5 9.6 0.00021 20.8 1.1 15 3-17 2-16 (112)
108 PRK03976 rpl37ae 50S ribosomal 51.3 3.6 7.9E-05 21.8 -0.5 29 3-39 36-65 (90)
109 KOG4173 Alpha-SNAP protein [In 50.4 7.2 0.00015 24.0 0.6 47 5-51 108-169 (253)
110 COG1571 Predicted DNA-binding 49.4 12 0.00027 25.3 1.6 29 5-42 352-381 (421)
111 PF01428 zf-AN1: AN1-like Zinc 48.4 4.9 0.00011 18.0 -0.3 12 3-14 13-24 (43)
112 PF01363 FYVE: FYVE zinc finge 47.8 6.6 0.00014 19.1 0.1 11 5-15 11-21 (69)
113 KOG0717 Molecular chaperone (D 47.6 19 0.0004 24.9 2.2 20 30-49 293-313 (508)
114 COG3091 SprT Zn-dependent meta 45.7 11 0.00024 21.9 0.9 11 3-14 117-127 (156)
115 smart00731 SprT SprT homologue 45.3 8.8 0.00019 21.7 0.4 11 3-13 112-122 (146)
116 COG5236 Uncharacterized conser 44.5 30 0.00065 23.2 2.7 19 6-24 223-241 (493)
117 PF02176 zf-TRAF: TRAF-type zi 43.8 8.1 0.00018 18.1 0.1 30 4-33 10-43 (60)
118 COG4888 Uncharacterized Zn rib 43.7 2.5 5.4E-05 22.9 -1.9 37 2-40 21-58 (104)
119 PF10537 WAC_Acf1_DNA_bd: ATP- 43.3 54 0.0012 17.7 3.4 36 2-37 2-39 (102)
120 PLN02294 cytochrome c oxidase 43.2 11 0.00023 22.5 0.5 12 28-39 140-152 (174)
121 PF06397 Desulfoferrod_N: Desu 42.9 9.3 0.0002 16.7 0.2 10 3-12 6-15 (36)
122 cd00065 FYVE FYVE domain; Zinc 41.9 15 0.00033 16.9 0.9 26 5-40 4-30 (57)
123 PF13821 DUF4187: Domain of un 41.7 42 0.00091 15.9 2.4 20 27-46 25-45 (55)
124 smart00064 FYVE Protein presen 41.2 17 0.00037 17.5 1.0 26 5-40 12-38 (68)
125 PF12760 Zn_Tnp_IS1595: Transp 40.5 8 0.00017 17.5 -0.2 8 4-11 19-26 (46)
126 PRK04351 hypothetical protein; 40.5 11 0.00025 21.7 0.4 12 27-38 130-142 (149)
127 KOG2907 RNA polymerase I trans 40.3 14 0.00029 20.5 0.6 35 4-40 75-114 (116)
128 PF12013 DUF3505: Protein of u 40.1 25 0.00053 18.8 1.6 18 7-24 88-105 (109)
129 KOG4727 U1-like Zn-finger prot 39.9 23 0.00051 21.2 1.6 21 29-49 75-96 (193)
130 COG3677 Transposase and inacti 38.8 14 0.00031 20.7 0.6 15 3-17 53-67 (129)
131 COG1773 Rubredoxin [Energy pro 37.7 13 0.00029 17.8 0.3 15 2-16 2-16 (55)
132 PF04423 Rad50_zn_hook: Rad50 37.6 9.8 0.00021 17.7 -0.2 12 5-16 22-33 (54)
133 PF10263 SprT-like: SprT-like 37.1 8 0.00017 21.9 -0.6 7 5-11 125-131 (157)
134 PRK05978 hypothetical protein; 36.6 19 0.0004 20.9 0.8 8 5-12 35-42 (148)
135 PF14353 CpXC: CpXC protein 35.9 16 0.00035 20.1 0.5 18 3-20 38-55 (128)
136 PTZ00448 hypothetical protein; 35.5 34 0.00074 22.9 2.0 23 3-25 314-336 (373)
137 COG5112 UFD2 U1-like Zn-finger 35.4 15 0.00034 20.1 0.4 21 29-49 55-76 (126)
138 PF09963 DUF2197: Uncharacteri 35.3 18 0.0004 17.4 0.6 33 5-37 4-40 (56)
139 PF09889 DUF2116: Uncharacteri 34.1 23 0.00049 17.2 0.8 12 3-14 2-14 (59)
140 PF04780 DUF629: Protein of un 34.1 33 0.00072 23.7 1.8 24 28-51 56-80 (466)
141 PF08274 PhnA_Zn_Ribbon: PhnA 34.1 20 0.00043 14.9 0.5 23 5-36 4-27 (30)
142 KOG3507 DNA-directed RNA polym 34.0 22 0.00047 17.4 0.7 27 4-39 21-48 (62)
143 cd00729 rubredoxin_SM Rubredox 33.6 17 0.00038 15.4 0.3 24 3-36 2-26 (34)
144 PF13878 zf-C2H2_3: zinc-finge 33.0 46 0.001 14.7 1.7 22 30-51 14-38 (41)
145 PF11494 Ta0938: Ta0938; Inte 32.2 9 0.00019 20.6 -0.8 36 3-43 14-52 (105)
146 PF07282 OrfB_Zn_ribbon: Putat 32.1 38 0.00082 16.3 1.5 13 27-39 44-57 (69)
147 PRK00432 30S ribosomal protein 31.8 28 0.0006 16.2 0.9 12 27-38 35-47 (50)
148 COG1996 RPC10 DNA-directed RNA 30.9 16 0.00036 17.1 0.0 28 2-37 5-33 (49)
149 PF10276 zf-CHCC: Zinc-finger 30.9 15 0.00033 16.4 -0.1 10 4-13 30-39 (40)
150 KOG0717 Molecular chaperone (D 30.8 32 0.0007 23.8 1.3 26 30-55 461-487 (508)
151 COG3357 Predicted transcriptio 30.6 25 0.00053 18.8 0.6 14 2-15 57-70 (97)
152 PLN02748 tRNA dimethylallyltra 30.4 49 0.0011 22.9 2.1 22 3-24 418-440 (468)
153 PF02591 DUF164: Putative zinc 30.4 68 0.0015 14.9 2.2 10 27-36 44-54 (56)
154 COG1656 Uncharacterized conser 30.2 92 0.002 18.5 3.0 45 5-49 99-151 (165)
155 TIGR00622 ssl1 transcription f 29.2 32 0.0007 19.0 1.0 40 2-41 14-68 (112)
156 COG4530 Uncharacterized protei 29.2 33 0.00072 19.0 1.0 11 3-13 26-36 (129)
157 KOG2231 Predicted E3 ubiquitin 28.4 80 0.0017 23.0 2.9 19 6-24 185-203 (669)
158 PRK08222 hydrogenase 4 subunit 28.2 51 0.0011 19.5 1.8 18 3-20 114-131 (181)
159 PF01927 Mut7-C: Mut7-C RNAse 28.0 41 0.00089 19.1 1.3 42 4-45 92-141 (147)
160 PLN00104 MYST -like histone ac 27.5 78 0.0017 21.9 2.7 25 27-51 196-221 (450)
161 PF14690 zf-ISL3: zinc-finger 27.2 37 0.00081 14.9 0.9 11 2-12 1-11 (47)
162 COG4338 Uncharacterized protei 27.1 27 0.00059 16.4 0.4 15 31-45 14-29 (54)
163 PRK12387 formate hydrogenlyase 26.6 51 0.0011 19.3 1.6 16 3-18 114-129 (180)
164 PF14787 zf-CCHC_5: GAG-polypr 26.4 38 0.00083 14.8 0.8 14 5-18 4-17 (36)
165 KOG2747 Histone acetyltransfer 26.2 82 0.0018 21.4 2.6 49 27-78 156-205 (396)
166 cd00924 Cyt_c_Oxidase_Vb Cytoc 25.4 32 0.00069 18.5 0.5 14 27-40 77-91 (97)
167 COG4068 Uncharacterized protei 25.4 38 0.00082 16.5 0.7 11 3-13 7-18 (64)
168 cd00730 rubredoxin Rubredoxin; 25.1 30 0.00065 16.1 0.3 13 4-16 2-14 (50)
169 PTZ00043 cytochrome c oxidase 25.1 32 0.0007 21.6 0.6 15 2-16 180-194 (268)
170 TIGR03831 YgiT_finger YgiT-typ 25.0 33 0.00071 14.9 0.5 11 4-14 33-43 (46)
171 PF06220 zf-U1: U1 zinc finger 24.9 63 0.0014 14.0 1.3 12 2-13 2-13 (38)
172 PF09855 DUF2082: Nucleic-acid 24.6 37 0.0008 16.7 0.6 9 4-12 1-9 (64)
173 cd00974 DSRD Desulforedoxin (D 24.6 35 0.00076 14.2 0.5 11 3-13 4-14 (34)
174 PF14369 zf-RING_3: zinc-finge 24.5 37 0.0008 14.5 0.5 9 6-14 24-32 (35)
175 PF13453 zf-TFIIB: Transcripti 24.3 69 0.0015 13.9 1.5 17 5-21 21-37 (41)
176 COG4306 Uncharacterized protei 24.2 23 0.00051 20.1 -0.1 17 27-43 66-83 (160)
177 PF07975 C1_4: TFIIH C1-like d 23.9 34 0.00074 16.1 0.4 18 3-20 21-38 (51)
178 KOG3002 Zn finger protein [Gen 23.9 71 0.0015 20.7 1.9 58 3-63 80-142 (299)
179 TIGR00319 desulf_FeS4 desulfof 23.5 37 0.0008 14.1 0.5 11 3-13 7-17 (34)
180 KOG0562 Predicted hydrolase (H 23.5 90 0.002 18.7 2.1 25 27-51 151-176 (184)
181 PF01096 TFIIS_C: Transcriptio 23.4 32 0.00068 15.0 0.2 10 29-38 28-38 (39)
182 PF01286 XPA_N: XPA protein N- 23.4 23 0.0005 15.2 -0.2 13 5-17 5-17 (34)
183 PF01780 Ribosomal_L37ae: Ribo 23.4 44 0.00094 17.7 0.8 30 2-39 34-64 (90)
184 PF01215 COX5B: Cytochrome c o 23.2 19 0.00042 20.5 -0.6 13 2-14 111-123 (136)
185 PF08792 A2L_zn_ribbon: A2L zi 22.5 35 0.00077 14.4 0.3 8 6-13 24-31 (33)
186 KOG3497 DNA-directed RNA polym 22.4 54 0.0012 16.1 0.9 14 28-41 3-17 (69)
187 PF08209 Sgf11: Sgf11 (transcr 22.2 48 0.001 14.1 0.7 19 4-23 5-23 (33)
188 PF10083 DUF2321: Uncharacteri 22.2 68 0.0015 18.9 1.5 21 27-47 66-87 (158)
189 PF01194 RNA_pol_N: RNA polyme 22.2 66 0.0014 15.7 1.2 16 2-17 3-18 (60)
190 PF13240 zinc_ribbon_2: zinc-r 22.1 36 0.00077 13.0 0.2 6 6-11 16-21 (23)
191 PF08271 TF_Zn_Ribbon: TFIIB z 21.3 54 0.0012 14.4 0.8 28 4-38 1-29 (43)
192 smart00132 LIM Zinc-binding do 21.3 52 0.0011 13.3 0.7 10 4-13 28-37 (39)
193 smart00440 ZnF_C2C2 C2C2 Zinc 21.0 58 0.0013 14.2 0.8 34 4-39 1-39 (40)
194 PRK01343 zinc-binding protein; 20.9 59 0.0013 15.7 0.9 11 4-14 10-20 (57)
195 KOG0978 E3 ubiquitin ligase in 20.3 34 0.00075 24.8 0.0 17 28-44 677-694 (698)
196 TIGR00100 hypA hydrogenase nic 20.0 34 0.00073 18.7 -0.0 10 30-39 71-81 (115)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.71 E-value=4.9e-18 Score=103.36 Aligned_cols=61 Identities=18% Similarity=0.352 Sum_probs=57.2
Q ss_pred ccccCcCCcCCCChhHHHHHHHh--cCCceEe-ecCcccCChhHHHHHHHHhcCCCCCCCCCCcc
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKN--CGRIWYC-VCGSDFKHKRSLKDHIKAFGHGHAALGIECFE 64 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~--~~~p~~C-~C~~~f~~~~~l~~H~~~~~~~~~p~~~~~~~ 64 (81)
|++|..|||.|...+.|+.|+|+ |+|||.| .|+++|..++||+.||++| .+.|+|.|..+.
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTH-S~~K~~qC~~C~ 250 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTH-SDVKKHQCPRCG 250 (279)
T ss_pred CcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhh-cCCccccCcchh
Confidence 68899999999999999999996 8999999 9999999999999999999 899999997654
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.54 E-value=4.5e-15 Score=90.54 Aligned_cols=63 Identities=21% Similarity=0.387 Sum_probs=58.2
Q ss_pred CccccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccCChhHHHHHHHHhcCCCCCCCCCCccC
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFKHKRSLKDHIKAFGHGHAALGIECFEE 65 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~~~~~l~~H~~~~~~~~~p~~~~~~~~ 65 (81)
+.+.|..|+|.|+....|..|++++.-+.+| +||+.|.+.=-|+.|+|+| +|||||.|.-+..
T Consensus 160 ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTH-TGEKPF~C~hC~k 223 (279)
T KOG2462|consen 160 KAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTH-TGEKPFSCPHCGK 223 (279)
T ss_pred ccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccc-cCCCCccCCcccc
Confidence 4678999999999999999999998889999 9999999999999999999 9999999976654
No 3
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.49 E-value=3.9e-15 Score=100.27 Aligned_cols=61 Identities=23% Similarity=0.462 Sum_probs=57.2
Q ss_pred ccccCcCCcCCCChhHHHHHHH--hcCCceEe-ecCcccCChhHHHHHHHHhcCCCCCCCCCCcc
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEK--NCGRIWYC-VCGSDFKHKRSLKDHIKAFGHGHAALGIECFE 64 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~--~~~~p~~C-~C~~~f~~~~~l~~H~~~~~~~~~p~~~~~~~ 64 (81)
+|.|..|.|.|.-.+.|.+|.. +|.+||+| +|.++|.++..|+.|+|+| .|+|||.||.+-
T Consensus 894 myaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLH-SGEKPfQCdKCl 957 (1007)
T KOG3623|consen 894 MYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLH-SGEKPFQCDKCL 957 (1007)
T ss_pred cchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhc-cCCCcchhhhhh
Confidence 6899999999999999999998 48999999 9999999999999999999 999999998764
No 4
>PHA02768 hypothetical protein; Provisional
Probab=99.20 E-value=5.6e-12 Score=60.45 Aligned_cols=43 Identities=12% Similarity=0.087 Sum_probs=38.9
Q ss_pred ccccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccCChhHHH
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFKHKRSLK 45 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~~~~~l~ 45 (81)
-|.|+.||+.|....+|..|++++.++++| .|++.|...+.|+
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcCCcccCCcccceecccceeE
Confidence 478999999999999999999998789999 9999999887764
No 5
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.18 E-value=1.2e-11 Score=83.89 Aligned_cols=61 Identities=25% Similarity=0.439 Sum_probs=54.2
Q ss_pred ccccCcCCcCCCChhHHHHHHHhc---------------CCceEe-ecCcccCChhHHHHHHHHhcCCCCCCCCCCcc
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKNC---------------GRIWYC-VCGSDFKHKRSLKDHIKAFGHGHAALGIECFE 64 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~~---------------~~p~~C-~C~~~f~~~~~l~~H~~~~~~~~~p~~~~~~~ 64 (81)
-|.|..|..+|.....|.+|+.++ -+-|+| .|+++|..+..|+.|+|+| .|+|||.|..+.
T Consensus 240 nfsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIH-SGEKPfeCpnCk 316 (1007)
T KOG3623|consen 240 NFSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIH-SGEKPFECPNCK 316 (1007)
T ss_pred CCcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheee-cCCCCcCCcccc
Confidence 467999999999999999999741 256899 9999999999999999999 899999998765
No 6
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.15 E-value=4.3e-12 Score=75.23 Aligned_cols=60 Identities=25% Similarity=0.428 Sum_probs=34.5
Q ss_pred cccCcCCcCCCChhHHHHHHHhc--CCceEe-ecCcccCChhHHHHHHHHhcCCCCCCCCCCcc
Q 037234 4 SKRKKCGKPFAVKGDWRTHEKNC--GRIWYC-VCGSDFKHKRSLKDHIKAFGHGHAALGIECFE 64 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~~~--~~p~~C-~C~~~f~~~~~l~~H~~~~~~~~~p~~~~~~~ 64 (81)
|.|..|+|.|.....|.+|++.+ .+.+.| .||+.|...-.|++|+|+| +|-+||.|..++
T Consensus 118 ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rth-tgvrpykc~~c~ 180 (267)
T KOG3576|consen 118 FTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTH-TGVRPYKCSLCE 180 (267)
T ss_pred eeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccc-cCccccchhhhh
Confidence 45666666666666666665532 344555 6666666666666666666 566666555444
No 7
>PHA00733 hypothetical protein
Probab=99.04 E-value=5.1e-10 Score=62.56 Aligned_cols=50 Identities=24% Similarity=0.401 Sum_probs=40.5
Q ss_pred CccccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccCChhHHHHHHHHh
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
+||.|..|++.|.....|..|+++...++.| .|++.|.....|..|+...
T Consensus 72 kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~~sL~~H~~~~ 122 (128)
T PHA00733 72 SPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTDSTLDHVCKK 122 (128)
T ss_pred CCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccCCHHHHHHHHHHh
Confidence 5788888888888888888888765567888 8888888888888887755
No 8
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.92 E-value=5.1e-10 Score=76.86 Aligned_cols=55 Identities=20% Similarity=0.428 Sum_probs=49.7
Q ss_pred ccccCcCCcCCCChhHHHHHHHh--cCCceEe-ecCcccCChhHHHHHHHHhcCCCCCC
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKN--CGRIWYC-VCGSDFKHKRSLKDHIKAFGHGHAAL 58 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~--~~~p~~C-~C~~~f~~~~~l~~H~~~~~~~~~p~ 58 (81)
.+.|.+||+.|...+.|.+|+++ +++||.| .|++.|..+.+|+.||.+| .+..|.
T Consensus 879 ~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH-~w~q~~ 936 (958)
T KOG1074|consen 879 AHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTH-MWVQPP 936 (958)
T ss_pred hhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccc-cccCCC
Confidence 36799999999999999999997 6899999 9999999999999999999 565544
No 9
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=98.89 E-value=3.9e-10 Score=67.06 Aligned_cols=50 Identities=28% Similarity=0.501 Sum_probs=45.7
Q ss_pred CccccCcCCcCCCChhHHHHHHHh--cCCceEe-ecCcccCChhHHHHHHHHh
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKN--CGRIWYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~--~~~p~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
|-|.|..||+.|.....|++|+++ |.+||+| .|+++|+++-+|..|++.-
T Consensus 144 kr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kv 196 (267)
T KOG3576|consen 144 KRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKV 196 (267)
T ss_pred HHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHH
Confidence 357799999999999999999996 7899999 9999999999999997755
No 10
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.86 E-value=4.2e-10 Score=77.27 Aligned_cols=49 Identities=31% Similarity=0.576 Sum_probs=46.1
Q ss_pred ccccCcCCcCCCChhHHHHHHHh--cCCceEe-ecCcccCChhHHHHHHHHh
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKN--CGRIWYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~--~~~p~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
+++|..|.|.|...+.|+.|.|+ |++||+| +||.+|+++.+|+.|...|
T Consensus 353 khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH 404 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRH 404 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeeeeec
Confidence 57899999999999999999995 8999999 9999999999999998877
No 11
>PHA00616 hypothetical protein
Probab=98.83 E-value=1.5e-09 Score=49.85 Aligned_cols=32 Identities=28% Similarity=0.734 Sum_probs=27.9
Q ss_pred ceEe-ecCcccCChhHHHHHHHHhcCCCCCCCCC
Q 037234 29 IWYC-VCGSDFKHKRSLKDHIKAFGHGHAALGIE 61 (81)
Q Consensus 29 p~~C-~C~~~f~~~~~l~~H~~~~~~~~~p~~~~ 61 (81)
||+| .||+.|...++|..|++.| +|++++.++
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~-hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSV-HKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHh-cCCCcccee
Confidence 6789 9999999999999999998 899888765
No 12
>PHA00732 hypothetical protein
Probab=98.67 E-value=1.8e-08 Score=52.02 Aligned_cols=46 Identities=20% Similarity=0.351 Sum_probs=38.1
Q ss_pred ccccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccCChhHHHHHHHHh
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
||.|..|++.|.....|..|++....++.| .|++.|. .+..|.+..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeC---Chhhhhccc
Confidence 689999999999999999999853346799 9999998 467777543
No 13
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.57 E-value=3.1e-08 Score=63.16 Aligned_cols=55 Identities=15% Similarity=0.288 Sum_probs=26.5
Q ss_pred cccCcCCcCCCChhHHHHHHHh---cCCceEe-ecCcccCChhHHHHHHHHhcCCCCCCCC
Q 037234 4 SKRKKCGKPFAVKGDWRTHEKN---CGRIWYC-VCGSDFKHKRSLKDHIKAFGHGHAALGI 60 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~~---~~~p~~C-~C~~~f~~~~~l~~H~~~~~~~~~p~~~ 60 (81)
|+|+.|.......+.|..|++. ..+||+| .|...|.+.+.|..|..+| + +..|.|
T Consensus 264 ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~H-S-~~~y~C 322 (467)
T KOG3608|consen 264 YKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVH-S-KTVYQC 322 (467)
T ss_pred ccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhc-c-ccceec
Confidence 4455555444444555555543 2345555 5555555555555555544 2 334444
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.42 E-value=2.2e-07 Score=44.63 Aligned_cols=33 Identities=18% Similarity=0.555 Sum_probs=26.9
Q ss_pred ceEe-ecCcccCChhHHHHHHHHhcCCCCCCCCCCcc
Q 037234 29 IWYC-VCGSDFKHKRSLKDHIKAFGHGHAALGIECFE 64 (81)
Q Consensus 29 p~~C-~C~~~f~~~~~l~~H~~~~~~~~~p~~~~~~~ 64 (81)
-|.| .||+.|...++|..|+++| + ++|.|..+.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H-~--k~~kc~~C~ 38 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKH-N--TNLKLSNCK 38 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhc-C--CcccCCccc
Confidence 4789 9999999999999999999 5 466554443
No 15
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.34 E-value=9.1e-07 Score=56.63 Aligned_cols=64 Identities=19% Similarity=0.254 Sum_probs=57.5
Q ss_pred CccccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccCChhHHHHHHHHhcCCCCCCCCCCccC
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFKHKRSLKDHIKAFGHGHAALGIECFEE 65 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~~~~~l~~H~~~~~~~~~p~~~~~~~~ 65 (81)
.+|.|..|-|.|.....|..|+..+..-|+| +|.......+.|..|++.-+...|||.||.++.
T Consensus 236 n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~ 300 (467)
T KOG3608|consen 236 NSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDT 300 (467)
T ss_pred CchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHHHhhhccCCCccccchhh
Confidence 4789999999999999999999877788999 999999999999999997768899999998874
No 16
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.30 E-value=7.9e-07 Score=36.56 Aligned_cols=21 Identities=29% Similarity=0.738 Sum_probs=13.3
Q ss_pred HHHHHHh--cCCceEe-ecCcccC
Q 037234 19 WRTHEKN--CGRIWYC-VCGSDFK 39 (81)
Q Consensus 19 l~~h~~~--~~~p~~C-~C~~~f~ 39 (81)
|..|+++ +++||.| .|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 5566664 5666777 6666664
No 17
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.25 E-value=2.2e-06 Score=57.87 Aligned_cols=62 Identities=19% Similarity=0.326 Sum_probs=44.8
Q ss_pred CccccCcCCcCCCChhHHHHHHHhcCCceEeecCcccCChhHHHHHHHHhcCCCCCCCCCCccCC
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKNCGRIWYCVCGSDFKHKRSLKDHIKAFGHGHAALGIECFEED 66 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~~~~p~~C~C~~~f~~~~~l~~H~~~~~~~~~p~~~~~~~~~ 66 (81)
+.+.|..|++.|. ...|..|+.++.+++.|.|+..+ .+..|..|+++| .+.+++.|..+...
T Consensus 452 ~H~~C~~Cgk~f~-~s~LekH~~~~Hkpv~CpCg~~~-~R~~L~~H~~th-Cp~Kpi~C~fC~~~ 513 (567)
T PLN03086 452 NHVHCEKCGQAFQ-QGEMEKHMKVFHEPLQCPCGVVL-EKEQMVQHQAST-CPLRLITCRFCGDM 513 (567)
T ss_pred cCccCCCCCCccc-hHHHHHHHHhcCCCccCCCCCCc-chhHHHhhhhcc-CCCCceeCCCCCCc
Confidence 3567888888875 56688888875577777677544 567788888877 78888888776643
No 18
>PHA00733 hypothetical protein
Probab=98.23 E-value=6.8e-07 Score=50.01 Aligned_cols=61 Identities=15% Similarity=0.079 Sum_probs=48.1
Q ss_pred CccccCcCCcCCCChhHHHHHHH------h-cCCceEe-ecCcccCChhHHHHHHHHhcCCCCCCCCCCccC
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEK------N-CGRIWYC-VCGSDFKHKRSLKDHIKAFGHGHAALGIECFEE 65 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~------~-~~~p~~C-~C~~~f~~~~~l~~H~~~~~~~~~p~~~~~~~~ 65 (81)
+++.|..|.+.|.....|..+.. + +.+||.| .|++.|.....|..|++.+ ..+|.|..++.
T Consensus 39 ~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h---~~~~~C~~CgK 107 (128)
T PHA00733 39 KRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT---EHSKVCPVCGK 107 (128)
T ss_pred hhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC---CcCccCCCCCC
Confidence 46789999988888777766622 2 4789999 9999999999999999875 34688876654
No 19
>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=98.23 E-value=1.3e-06 Score=34.64 Aligned_cols=22 Identities=36% Similarity=0.961 Sum_probs=15.1
Q ss_pred eEe-ecCcccCChhHHHHHHHHh
Q 037234 30 WYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 30 ~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
|.| .|++.|.+...|..|++.|
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 567 7777777777777776653
No 20
>PHA00616 hypothetical protein
Probab=98.18 E-value=9.7e-07 Score=40.54 Aligned_cols=30 Identities=17% Similarity=0.088 Sum_probs=27.1
Q ss_pred ccccCcCCcCCCChhHHHHHHHh--cCCceEe
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKN--CGRIWYC 32 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~--~~~p~~C 32 (81)
||.|..||+.|..+..|..|++. +++++.|
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 78999999999999999999995 6788876
No 21
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=98.14 E-value=5.5e-07 Score=56.88 Aligned_cols=49 Identities=24% Similarity=0.409 Sum_probs=40.5
Q ss_pred CCccccCc--CCcCCCChhHHHHHHHhc---------------------CCceEe-ecCcccCChhHHHHHHH
Q 037234 1 MISSKRKK--CGKPFAVKGDWRTHEKNC---------------------GRIWYC-VCGSDFKHKRSLKDHIK 49 (81)
Q Consensus 1 ~kp~~C~~--C~k~f~~~~~l~~h~~~~---------------------~~p~~C-~C~~~f~~~~~l~~H~~ 49 (81)
+|||+|++ |.|.|.....|+-|+..| .+||+| +|++++.+...|+.|+.
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceeccc
Confidence 48999986 999999998899888631 279999 99999999988887754
No 22
>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=98.11 E-value=8.3e-06 Score=39.08 Aligned_cols=46 Identities=22% Similarity=0.344 Sum_probs=36.6
Q ss_pred ccccCcCCcCCCChhHHHHHHHh-c---CCceEe-ecCcccCChhHHHHHHHHh
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKN-C---GRIWYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~-~---~~p~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
.|.|+.|++ ......|..|... + .+.+.| +|...+. .+|..|+...
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~ 52 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQ 52 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHh
Confidence 589999999 5667789999884 2 457899 9988655 4899998876
No 23
>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=98.10 E-value=2.4e-06 Score=35.08 Aligned_cols=21 Identities=14% Similarity=0.331 Sum_probs=18.7
Q ss_pred HHHHHHHHhcCCCCCCCCCCcc
Q 037234 43 SLKDHIKAFGHGHAALGIECFE 64 (81)
Q Consensus 43 ~l~~H~~~~~~~~~p~~~~~~~ 64 (81)
+|..|+++| +|++||.|+.++
T Consensus 1 ~l~~H~~~H-~~~k~~~C~~C~ 21 (26)
T PF13465_consen 1 NLRRHMRTH-TGEKPYKCPYCG 21 (26)
T ss_dssp HHHHHHHHH-SSSSSEEESSSS
T ss_pred CHHHHhhhc-CCCCCCCCCCCc
Confidence 588999999 999999998765
No 24
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.98 E-value=1.4e-05 Score=54.11 Aligned_cols=59 Identities=19% Similarity=0.325 Sum_probs=47.8
Q ss_pred CccccCcCCcCCCChhHHHHHHHh--cCCceEe-ecCcccC----------ChhHHHHHHHHhcCCCCCCCCCCcc
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKN--CGRIWYC-VCGSDFK----------HKRSLKDHIKAFGHGHAALGIECFE 64 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~--~~~p~~C-~C~~~f~----------~~~~l~~H~~~~~~~~~p~~~~~~~ 64 (81)
+|+.|+ |++.+ ....|..|+.+ ..+++.| .|++.|. ..+.|..|+... |.+++.|..+.
T Consensus 477 kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~C--G~rt~~C~~Cg 548 (567)
T PLN03086 477 EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESIC--GSRTAPCDSCG 548 (567)
T ss_pred CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhHHHHHHhc--CCcceEccccC
Confidence 478899 99754 67889999885 4899999 9999985 245799999875 89999987664
No 25
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.91 E-value=7e-06 Score=33.73 Aligned_cols=23 Identities=26% Similarity=0.707 Sum_probs=17.9
Q ss_pred ceEe-ecCcccCChhHHHHHHHHh
Q 037234 29 IWYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 29 p~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
||.| .|++.|.....|..|++.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 5778 8888888888888887766
No 26
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.79 E-value=1.3e-05 Score=31.64 Aligned_cols=22 Identities=32% Similarity=0.604 Sum_probs=20.3
Q ss_pred cccCcCCcCCCChhHHHHHHHh
Q 037234 4 SKRKKCGKPFAVKGDWRTHEKN 25 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~~ 25 (81)
|.|..|++.|.....|..|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 6899999999999999999874
No 27
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.78 E-value=3.2e-05 Score=30.42 Aligned_cols=22 Identities=32% Similarity=1.017 Sum_probs=14.4
Q ss_pred eEe-ecCcccCChhHHHHHHHHh
Q 037234 30 WYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 30 ~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
|.| .|++.|.+...|..|++.+
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 567 7777777777777777665
No 28
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.68 E-value=3e-05 Score=50.75 Aligned_cols=49 Identities=22% Similarity=0.550 Sum_probs=41.8
Q ss_pred ccccCcCCcCCCChhHHHHHHHh----------cCC-------------------------ceEe-ecCcccCChhHHHH
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKN----------CGR-------------------------IWYC-VCGSDFKHKRSLKD 46 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~----------~~~-------------------------p~~C-~C~~~f~~~~~l~~ 46 (81)
-|+|+.|+|.|.-..||..|.|= +.. .|.| .|++.|.+..-|+.
T Consensus 295 EYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrK 374 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRK 374 (500)
T ss_pred eecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHH
Confidence 48999999999999999999871 111 3789 99999999999999
Q ss_pred HHHHh
Q 037234 47 HIKAF 51 (81)
Q Consensus 47 H~~~~ 51 (81)
|+-+|
T Consensus 375 Hqlth 379 (500)
T KOG3993|consen 375 HQLTH 379 (500)
T ss_pred hHHhh
Confidence 98777
No 29
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.36 E-value=0.00013 Score=28.90 Aligned_cols=22 Identities=41% Similarity=0.952 Sum_probs=15.5
Q ss_pred eEe-ecCcccCChhHHHHHHHHh
Q 037234 30 WYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 30 ~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
|.| .|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 356 7777777777777777755
No 30
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.36 E-value=8e-05 Score=30.44 Aligned_cols=23 Identities=26% Similarity=0.573 Sum_probs=21.4
Q ss_pred ccccCcCCcCCCChhHHHHHHHh
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKN 25 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~ 25 (81)
||.|..|++.|.....|..|++.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~ 23 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRS 23 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCT
T ss_pred CCCCCccCCccCChhHHHHHhHH
Confidence 68999999999999999999975
No 31
>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=97.34 E-value=0.00028 Score=33.32 Aligned_cols=30 Identities=23% Similarity=0.532 Sum_probs=21.8
Q ss_pred CCceEe-ecCcccCChhHHHHHHHHhcCCCCC
Q 037234 27 GRIWYC-VCGSDFKHKRSLKDHIKAFGHGHAA 57 (81)
Q Consensus 27 ~~p~~C-~C~~~f~~~~~l~~H~~~~~~~~~p 57 (81)
..|-.| .|+..+.+..+|..|+.++ ++.||
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~-H~~k~ 52 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIR-HFKKP 52 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHH-TTTS-
T ss_pred CCCCCCCcchhhccchhhHHHHHHHH-hcccC
Confidence 578899 9999999999999999988 77776
No 32
>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=97.32 E-value=0.00018 Score=28.13 Aligned_cols=22 Identities=32% Similarity=0.582 Sum_probs=18.3
Q ss_pred cccCcCCcCCCChhHHHHHHHh
Q 037234 4 SKRKKCGKPFAVKGDWRTHEKN 25 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~~ 25 (81)
|.|+.|++.|.....|..|+.+
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~ 22 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRT 22 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHh
Confidence 6899999999999999999874
No 33
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.15 E-value=0.00065 Score=35.59 Aligned_cols=47 Identities=21% Similarity=0.523 Sum_probs=20.5
Q ss_pred ccCcCCcCCCChhHHHHHHHh-c------------------------CCceEe-ecCcccCChhHHHHHHHHh
Q 037234 5 KRKKCGKPFAVKGDWRTHEKN-C------------------------GRIWYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 5 ~C~~C~k~f~~~~~l~~h~~~-~------------------------~~p~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
.|..|+..|.....|..|+.. + ...+.| .|++.|.+...|..|++.+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 377888888888888888751 0 124789 9999999999999999976
No 34
>PHA00732 hypothetical protein
Probab=97.14 E-value=0.00044 Score=35.69 Aligned_cols=33 Identities=18% Similarity=0.371 Sum_probs=26.1
Q ss_pred ceEe-ecCcccCChhHHHHHHHH-hcCCCCCCCCCCccC
Q 037234 29 IWYC-VCGSDFKHKRSLKDHIKA-FGHGHAALGIECFEE 65 (81)
Q Consensus 29 p~~C-~C~~~f~~~~~l~~H~~~-~~~~~~p~~~~~~~~ 65 (81)
||.| .|++.|.+..+|..|++. | . ++.|+.++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H-~---~~~C~~CgK 35 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNH-T---LTKCPVCNK 35 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhccc-C---CCccCCCCC
Confidence 6889 999999999999999985 5 4 345655543
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.99 E-value=0.00088 Score=26.36 Aligned_cols=22 Identities=27% Similarity=0.557 Sum_probs=20.0
Q ss_pred cccCcCCcCCCChhHHHHHHHh
Q 037234 4 SKRKKCGKPFAVKGDWRTHEKN 25 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~~ 25 (81)
|.|..|++.|.....|..|++.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~ 22 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRT 22 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHH
Confidence 5799999999999999999874
No 36
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.83 E-value=0.00082 Score=26.79 Aligned_cols=21 Identities=33% Similarity=1.099 Sum_probs=14.8
Q ss_pred eEe-ecCcccCChhHHHHHHHH
Q 037234 30 WYC-VCGSDFKHKRSLKDHIKA 50 (81)
Q Consensus 30 ~~C-~C~~~f~~~~~l~~H~~~ 50 (81)
|.| .|.+.|.+...|..|++.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTT
T ss_pred CCCCCCCCCcCCHHHHHHHHCc
Confidence 567 777777777777777653
No 37
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=96.80 E-value=0.00019 Score=47.11 Aligned_cols=48 Identities=15% Similarity=0.188 Sum_probs=41.8
Q ss_pred cccCcCCcCCCChhHHHHHHH--hcCCceEe-ecCcccCChhHHHHHHHHh
Q 037234 4 SKRKKCGKPFAVKGDWRTHEK--NCGRIWYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~--~~~~p~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
|.|..|...|.....|.+|.= |-..-|+| .|+|.|+-..||..|.|.|
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWH 318 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWH 318 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhccc
Confidence 779999988999999999874 33457999 9999999999999999988
No 38
>PRK04860 hypothetical protein; Provisional
Probab=96.78 E-value=0.001 Score=38.63 Aligned_cols=23 Identities=17% Similarity=0.327 Sum_probs=11.8
Q ss_pred ChhHHHHHHHHhcCCCCCCCCCCc
Q 037234 40 HKRSLKDHIKAFGHGHAALGIECF 63 (81)
Q Consensus 40 ~~~~l~~H~~~~~~~~~p~~~~~~ 63 (81)
...++..|.+++ .|+++|.|..+
T Consensus 127 ~~~~~rrH~ri~-~g~~~YrC~~C 149 (160)
T PRK04860 127 HQLTVRRHNRVV-RGEAVYRCRRC 149 (160)
T ss_pred eeCHHHHHHHHh-cCCccEECCCC
Confidence 444455555555 55555555443
No 39
>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=96.76 E-value=0.0013 Score=31.13 Aligned_cols=24 Identities=17% Similarity=0.228 Sum_probs=17.9
Q ss_pred CccccCcCCcCCCChhHHHHHHHh
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKN 25 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~ 25 (81)
.|..|+.|+..+.+..+|.+|+.+
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~ 46 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEI 46 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHH
T ss_pred CCCCCCcchhhccchhhHHHHHHH
Confidence 578899999999999999999985
No 40
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.14 E-value=0.0028 Score=25.15 Aligned_cols=21 Identities=24% Similarity=0.412 Sum_probs=19.5
Q ss_pred cccCcCCcCCCChhHHHHHHH
Q 037234 4 SKRKKCGKPFAVKGDWRTHEK 24 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~ 24 (81)
|.|..|++.|.....+..|++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 579999999999999999986
No 41
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.01 E-value=0.0067 Score=23.87 Aligned_cols=21 Identities=33% Similarity=0.667 Sum_probs=11.7
Q ss_pred eEe-ecCcccCChhHHHHHHHHh
Q 037234 30 WYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 30 ~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
|+| .|.-... ...|..|++.+
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 456 6665555 66666676654
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=95.60 E-value=0.0034 Score=25.58 Aligned_cols=21 Identities=24% Similarity=0.374 Sum_probs=10.9
Q ss_pred cccCcCCcCCCChhHHHHHHH
Q 037234 4 SKRKKCGKPFAVKGDWRTHEK 24 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~ 24 (81)
|.|..|++.|.....+..|++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 345555555555555555443
No 43
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=95.55 E-value=0.0051 Score=38.05 Aligned_cols=40 Identities=20% Similarity=0.378 Sum_probs=32.2
Q ss_pred cCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccCChhHHHHH
Q 037234 6 RKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFKHKRSLKDH 47 (81)
Q Consensus 6 C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~~~~~l~~H 47 (81)
|=.|++.|-...-|.+|++ .+.|+| +|-+.+.+--.|..|
T Consensus 13 cwycnrefddekiliqhqk--akhfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQK--AKHFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhhhhhhhhh--hccceeeeehhhhccCCCceee
Confidence 6779999999999999998 478999 998776665555444
No 44
>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=95.14 E-value=0.021 Score=24.34 Aligned_cols=21 Identities=33% Similarity=0.861 Sum_probs=15.3
Q ss_pred ceEe-ecCcccCChhHHHHHHH
Q 037234 29 IWYC-VCGSDFKHKRSLKDHIK 49 (81)
Q Consensus 29 p~~C-~C~~~f~~~~~l~~H~~ 49 (81)
+|.| .|...|.....+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 5677 78887877777777754
No 45
>PRK04860 hypothetical protein; Provisional
Probab=95.12 E-value=0.021 Score=33.24 Aligned_cols=35 Identities=23% Similarity=0.491 Sum_probs=28.8
Q ss_pred ccccCcCCcCCCChhHHHHHHHh--cCCceEe-ecCcccCCh
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKN--CGRIWYC-VCGSDFKHK 41 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~--~~~p~~C-~C~~~f~~~ 41 (81)
+|.|. |++ ....+.+|.++ ++++|.| .|+..|...
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 68898 987 66778899986 6889999 999887654
No 46
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.01 E-value=0.027 Score=22.63 Aligned_cols=20 Identities=30% Similarity=0.476 Sum_probs=12.7
Q ss_pred ccCcCCcCCCChhHHHHHHHh
Q 037234 5 KRKKCGKPFAVKGDWRTHEKN 25 (81)
Q Consensus 5 ~C~~C~k~f~~~~~l~~h~~~ 25 (81)
.|+.||+.| ....|..|+.+
T Consensus 4 ~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred cCCCCCCEE-CHHHHHHHHHh
Confidence 477777777 34456666653
No 47
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=93.91 E-value=0.031 Score=35.98 Aligned_cols=24 Identities=29% Similarity=0.677 Sum_probs=21.1
Q ss_pred cCCceEe---ecCcccCChhHHHHHHH
Q 037234 26 CGRIWYC---VCGSDFKHKRSLKDHIK 49 (81)
Q Consensus 26 ~~~p~~C---~C~~~f~~~~~l~~H~~ 49 (81)
+++||+| .|.+.+.+...|+.|+.
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~l 372 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHML 372 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhh
Confidence 4699999 69999999999999875
No 48
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=92.74 E-value=0.084 Score=32.91 Aligned_cols=47 Identities=26% Similarity=0.465 Sum_probs=37.1
Q ss_pred ccccCcCCcCCCChhHHHHHHHh-cCCceEe-ecCcccCChhHHHHHHHHh
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKN-CGRIWYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~-~~~p~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
-|.|..||.+.. +..+.+|+.. ...-|.| -|++.|.. ..+..|...-
T Consensus 3 ~FtCnvCgEsvK-Kp~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~kCI 51 (276)
T KOG2186|consen 3 FFTCNVCGESVK-KPQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTKCI 51 (276)
T ss_pred EEehhhhhhhcc-ccchHHHHHhccCCeeEEeeccccccc-chhhhhhhhc
Confidence 478999997644 5668889986 3567899 99999998 6788887765
No 49
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=91.96 E-value=0.13 Score=26.68 Aligned_cols=23 Identities=22% Similarity=0.403 Sum_probs=20.4
Q ss_pred ccccCcCCcCCCChhHHHHHHHh
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKN 25 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~ 25 (81)
++.|..|++.|.....|..|++.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHH
T ss_pred CCCCCccCCCCcCHHHHHHHHcC
Confidence 47899999999999999999995
No 50
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=91.30 E-value=0.14 Score=38.39 Aligned_cols=49 Identities=18% Similarity=0.382 Sum_probs=41.1
Q ss_pred CccccCcCCcCCCChhHHHHHHHh---------------------------cCCceEe-ecCcccCChhHHHHHHHH
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKN---------------------------CGRIWYC-VCGSDFKHKRSLKDHIKA 50 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~---------------------------~~~p~~C-~C~~~f~~~~~l~~H~~~ 50 (81)
+.++|++|+-.|.....|..|||. +.++|.| .|-..++.+.+|..|+..
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCcccceeeeeeeecchHHHHHHHH
Confidence 468899999999999999999884 0257889 999999999999999763
No 51
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.44 E-value=0.066 Score=34.22 Aligned_cols=57 Identities=25% Similarity=0.437 Sum_probs=48.2
Q ss_pred ccccCcCCcCCCChhHHHHHHH--h--cC--CceEe---ecCcccCChhHHHHHHHHhcCCCCCCCC
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEK--N--CG--RIWYC---VCGSDFKHKRSLKDHIKAFGHGHAALGI 60 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~--~--~~--~p~~C---~C~~~f~~~~~l~~H~~~~~~~~~p~~~ 60 (81)
++.|..|...|.....+..|.+ . ++ +++.| .|++.|.+...+..|..+| .+-.++.+
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~ 354 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLH-TSISPAKE 354 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccc-cCCCcccc
Confidence 5778999999999999999998 5 46 89999 3999999999999999988 67666543
No 52
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=86.52 E-value=0.31 Score=25.60 Aligned_cols=29 Identities=31% Similarity=0.749 Sum_probs=20.2
Q ss_pred ccccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccC
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFK 39 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~ 39 (81)
.|.|+.|++. .+.++....|.| .|+..|.
T Consensus 35 ~~~Cp~C~~~--------~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 35 KHVCPFCGRT--------TVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred CCcCCCCCCc--------ceeeeccCeEEcCCCCCeec
Confidence 6889999875 222344557899 9988775
No 53
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=86.35 E-value=0.15 Score=29.58 Aligned_cols=40 Identities=23% Similarity=0.359 Sum_probs=21.9
Q ss_pred cccCcCCcCCCChh-HHHHHHHh-cCCceEe-ecCcccCChhH
Q 037234 4 SKRKKCGKPFAVKG-DWRTHEKN-CGRIWYC-VCGSDFKHKRS 43 (81)
Q Consensus 4 ~~C~~C~k~f~~~~-~l~~h~~~-~~~p~~C-~C~~~f~~~~~ 43 (81)
.+|+.||..++... ....-.+. -.+.++| .||++|.....
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFER 43 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeEe
Confidence 37999997653321 11000010 1234899 99999986533
No 54
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=86.05 E-value=0.36 Score=23.32 Aligned_cols=26 Identities=19% Similarity=0.519 Sum_probs=19.8
Q ss_pred cCCceEe-ecCcccCChhHHHHHHHHh
Q 037234 26 CGRIWYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 26 ~~~p~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
|+..+.| .|+..|.....+..|....
T Consensus 14 GE~~lrCPRC~~~FR~~K~Y~RHVNKa 40 (65)
T COG4049 14 GEEFLRCPRCGMVFRRRKDYIRHVNKA 40 (65)
T ss_pred CceeeeCCchhHHHHHhHHHHHHhhHH
Confidence 5667788 8888888888888876644
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=85.59 E-value=0.49 Score=25.84 Aligned_cols=30 Identities=23% Similarity=0.504 Sum_probs=23.0
Q ss_pred cccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccCChh
Q 037234 4 SKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFKHKR 42 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~~~~ 42 (81)
..|+.||+.|--.. ..|..| .||..|.-..
T Consensus 10 R~Cp~CG~kFYDLn---------k~PivCP~CG~~~~~~~ 40 (108)
T PF09538_consen 10 RTCPSCGAKFYDLN---------KDPIVCPKCGTEFPPEP 40 (108)
T ss_pred ccCCCCcchhccCC---------CCCccCCCCCCccCccc
Confidence 57999998776442 468899 9999888773
No 56
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=84.00 E-value=0.99 Score=20.89 Aligned_cols=22 Identities=23% Similarity=0.671 Sum_probs=16.2
Q ss_pred eEe-ecCcccCCh-----hHHHHHHH-Hh
Q 037234 30 WYC-VCGSDFKHK-----RSLKDHIK-AF 51 (81)
Q Consensus 30 ~~C-~C~~~f~~~-----~~l~~H~~-~~ 51 (81)
-.| .|++.+... ++|..|++ .|
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~h 47 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRKH 47 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhHC
Confidence 467 888877654 68999988 44
No 57
>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=83.76 E-value=0.46 Score=20.19 Aligned_cols=23 Identities=30% Similarity=0.742 Sum_probs=14.6
Q ss_pred cccCcCCcCCCChhHHHHHHHhcCCceEe-ecCc
Q 037234 4 SKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGS 36 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~ 36 (81)
|.|..||..+... ..++.| .|+.
T Consensus 2 ~~C~~CGy~y~~~----------~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGE----------EAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCC----------cCCCcCcCCCC
Confidence 6788887654322 257788 8864
No 58
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=83.17 E-value=0.54 Score=21.42 Aligned_cols=30 Identities=23% Similarity=0.474 Sum_probs=19.7
Q ss_pred CccccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccC
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFK 39 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~ 39 (81)
..|.|..||..|..... .....| .||..+.
T Consensus 2 ~~y~C~~CG~~~~~~~~--------~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 2 AEYKCARCGREVELDEY--------GTGVRCPYCGYRIL 32 (46)
T ss_pred CEEECCCCCCEEEECCC--------CCceECCCCCCeEE
Confidence 56899999987654332 126788 8886543
No 59
>PHA00626 hypothetical protein
Probab=82.76 E-value=0.33 Score=23.40 Aligned_cols=34 Identities=21% Similarity=0.327 Sum_probs=20.1
Q ss_pred ccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccCCh
Q 037234 5 KRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFKHK 41 (81)
Q Consensus 5 ~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~~~ 41 (81)
.|+.||..-..+..... -....|.| .||..|+..
T Consensus 2 ~CP~CGS~~Ivrcg~cr---~~snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMR---GWSDDYVCCDCGYNDSKD 36 (59)
T ss_pred CCCCCCCceeeeeceec---ccCcceEcCCCCCeechh
Confidence 58888864222221111 11468999 999888754
No 60
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=82.69 E-value=1 Score=20.13 Aligned_cols=23 Identities=35% Similarity=0.597 Sum_probs=13.9
Q ss_pred CCceEe-ecCcccCC----hhHHHHHHH
Q 037234 27 GRIWYC-VCGSDFKH----KRSLKDHIK 49 (81)
Q Consensus 27 ~~p~~C-~C~~~f~~----~~~l~~H~~ 49 (81)
..-..| .|++.+.. .++|..|++
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 345678 88877765 377888884
No 61
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=82.10 E-value=1 Score=22.00 Aligned_cols=8 Identities=38% Similarity=1.161 Sum_probs=3.8
Q ss_pred CceEe-ecC
Q 037234 28 RIWYC-VCG 35 (81)
Q Consensus 28 ~p~~C-~C~ 35 (81)
.+|.| .||
T Consensus 49 ~~Y~Cp~CG 57 (61)
T COG2888 49 NPYRCPKCG 57 (61)
T ss_pred CceECCCcC
Confidence 34555 444
No 62
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=81.25 E-value=0.32 Score=22.42 Aligned_cols=37 Identities=16% Similarity=0.370 Sum_probs=22.3
Q ss_pred ccCcCCcCCCChhHHHHHHHhcCCceEe---ecCcccCCh
Q 037234 5 KRKKCGKPFAVKGDWRTHEKNCGRIWYC---VCGSDFKHK 41 (81)
Q Consensus 5 ~C~~C~k~f~~~~~l~~h~~~~~~p~~C---~C~~~f~~~ 41 (81)
.|+.||...........+..+.+.-++| .||..|...
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFVAN 40 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEEEE
Confidence 4888887655554433333334556778 599887643
No 63
>PF15269 zf-C2H2_7: Zinc-finger
Probab=80.84 E-value=1.8 Score=19.98 Aligned_cols=22 Identities=27% Similarity=0.484 Sum_probs=17.6
Q ss_pred eEe-ecCcccCChhHHHHHHHHh
Q 037234 30 WYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 30 ~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
|+| +|.....-++.|-.|++..
T Consensus 21 ykcfqcpftc~~kshl~nhmky~ 43 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKYS 43 (54)
T ss_pred ceeecCCcccchHHHHHHHHHHH
Confidence 578 9988888888888888754
No 64
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=80.81 E-value=0.45 Score=24.14 Aligned_cols=41 Identities=15% Similarity=0.242 Sum_probs=24.9
Q ss_pred cccCcCCcCCCChhHHHHHHHhcCCceEe---ecCcccCChhHH
Q 037234 4 SKRKKCGKPFAVKGDWRTHEKNCGRIWYC---VCGSDFKHKRSL 44 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~~~~~p~~C---~C~~~f~~~~~l 44 (81)
+.|+.||........-.....+.++-++| .||.+|.....+
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred ccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEEEEEEE
Confidence 46999987653333222222223566788 799999876554
No 65
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=80.67 E-value=0.98 Score=19.68 Aligned_cols=32 Identities=31% Similarity=0.548 Sum_probs=21.7
Q ss_pred ccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccC
Q 037234 5 KRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFK 39 (81)
Q Consensus 5 ~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~ 39 (81)
.|+.|+..|.....-. ..+....+| .|+..|.
T Consensus 4 ~CP~C~~~f~v~~~~l---~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKL---PAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHHc---ccCCcEEECCCCCcEee
Confidence 5889998887665421 123457789 9988764
No 66
>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=80.65 E-value=1.1 Score=25.36 Aligned_cols=24 Identities=38% Similarity=0.808 Sum_probs=14.3
Q ss_pred CceEe-ecCcccCChhHHHHHHHHhcCCC
Q 037234 28 RIWYC-VCGSDFKHKRSLKDHIKAFGHGH 55 (81)
Q Consensus 28 ~p~~C-~C~~~f~~~~~l~~H~~~~~~~~ 55 (81)
.-..| .||+.|... ..|++.| +|-
T Consensus 71 d~i~clecGk~~k~L---krHL~~~-~gl 95 (132)
T PF05443_consen 71 DYIICLECGKKFKTL---KRHLRTH-HGL 95 (132)
T ss_dssp S-EE-TBT--EESBH---HHHHHHT-T-S
T ss_pred CeeEEccCCcccchH---HHHHHHc-cCC
Confidence 34579 999988765 8899988 553
No 67
>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=78.28 E-value=1.3 Score=27.09 Aligned_cols=24 Identities=29% Similarity=0.185 Sum_probs=18.7
Q ss_pred CccccCcCCcCCCChhHHHHHHHh
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKN 25 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~ 25 (81)
..|.|..|+|.|.-...+..|+..
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHH
T ss_pred CEECCCCCCcccCChHHHHHHHhh
Confidence 358899999999999999999874
No 68
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=77.28 E-value=1.6 Score=24.46 Aligned_cols=26 Identities=35% Similarity=0.706 Sum_probs=21.1
Q ss_pred cCCceEe-ecCcccCChhHHHHHHHHh
Q 037234 26 CGRIWYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 26 ~~~p~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
|.-.|.| .|.+-|.....|..|.++-
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhcc
Confidence 3445889 9999999999999997643
No 69
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=76.57 E-value=0.59 Score=33.46 Aligned_cols=23 Identities=35% Similarity=0.681 Sum_probs=21.3
Q ss_pred ceEe-ecCcccCChhHHHHHHHHh
Q 037234 29 IWYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 29 p~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
.|.| .|++.|....++..||++|
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~H 815 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTH 815 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHH
Confidence 4889 9999999999999999988
No 70
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=76.55 E-value=1.3 Score=19.23 Aligned_cols=32 Identities=22% Similarity=0.463 Sum_probs=21.4
Q ss_pred cccCcCCcCCCChhHHHHHHHhcCCceEe-ecCccc
Q 037234 4 SKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDF 38 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f 38 (81)
..|+.|+..|........ ...+-.+| .|+..|
T Consensus 3 i~Cp~C~~~y~i~d~~ip---~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIP---PKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCC---CCCcEEECCCCCCEe
Confidence 368889888877654321 23456788 898776
No 71
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=76.52 E-value=1.7 Score=19.85 Aligned_cols=26 Identities=23% Similarity=0.494 Sum_probs=18.1
Q ss_pred ccccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcc
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSD 37 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~ 37 (81)
.|.|..||..|... ...+..| .||..
T Consensus 2 ~Y~C~~Cg~~~~~~---------~~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRENEIK---------SKDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCEeecC---------CCCceECCCCCce
Confidence 48899999876644 1346788 88754
No 72
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=75.36 E-value=1.6 Score=25.71 Aligned_cols=8 Identities=25% Similarity=0.272 Sum_probs=4.1
Q ss_pred cccCcCCc
Q 037234 4 SKRKKCGK 11 (81)
Q Consensus 4 ~~C~~C~k 11 (81)
|.|.+||.
T Consensus 135 ~vC~vCGy 142 (166)
T COG1592 135 WVCPVCGY 142 (166)
T ss_pred EEcCCCCC
Confidence 45555543
No 73
>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=74.29 E-value=2 Score=24.19 Aligned_cols=33 Identities=18% Similarity=0.166 Sum_probs=23.3
Q ss_pred ccccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccCChhHH
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFKHKRSL 44 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~~~~~l 44 (81)
...|+.||+.|--.. ..|..| .||..|.....+
T Consensus 9 Kr~Cp~cg~kFYDLn---------k~p~vcP~cg~~~~~~~~~ 42 (129)
T TIGR02300 9 KRICPNTGSKFYDLN---------RRPAVSPYTGEQFPPEEAL 42 (129)
T ss_pred cccCCCcCccccccC---------CCCccCCCcCCccCcchhh
Confidence 356999998776432 468899 999887665343
No 74
>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=74.24 E-value=3.7 Score=25.17 Aligned_cols=24 Identities=33% Similarity=0.714 Sum_probs=19.8
Q ss_pred CceEe-ecCcccCChhHHHHHHHHh
Q 037234 28 RIWYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 28 ~p~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
.-|.| .|+|.|.-..-+..|+..-
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~nK 100 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFNK 100 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHHH
T ss_pred CEECCCCCCcccCChHHHHHHHhhc
Confidence 45889 9999999999999998765
No 75
>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=72.95 E-value=1.5 Score=18.88 Aligned_cols=33 Identities=21% Similarity=0.351 Sum_probs=20.9
Q ss_pred cccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccC
Q 037234 4 SKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFK 39 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~ 39 (81)
..|+.|+..|........ .......| .|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~---~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLG---ANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcC---CCCCEEECCCCCCEEE
Confidence 568999988776654321 11235688 8887764
No 76
>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=71.94 E-value=1.1 Score=18.48 Aligned_cols=18 Identities=39% Similarity=0.755 Sum_probs=7.4
Q ss_pred Ee-ecCcccCChhHHHHHHH
Q 037234 31 YC-VCGSDFKHKRSLKDHIK 49 (81)
Q Consensus 31 ~C-~C~~~f~~~~~l~~H~~ 49 (81)
.| .|++.| ....++.|..
T Consensus 2 sCiDC~~~F-~~~~y~~Ht~ 20 (28)
T PF08790_consen 2 SCIDCSKDF-DGDSYKSHTS 20 (28)
T ss_dssp EETTTTEEE-EGGGTTT---
T ss_pred eeecCCCCc-CcCCcCCCCc
Confidence 45 566665 3334444443
No 77
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=71.05 E-value=2.7 Score=23.99 Aligned_cols=12 Identities=25% Similarity=0.802 Sum_probs=6.7
Q ss_pred ceEe-ecCcccCC
Q 037234 29 IWYC-VCGSDFKH 40 (81)
Q Consensus 29 p~~C-~C~~~f~~ 40 (81)
-|.| .|+..|..
T Consensus 99 ~Y~Cp~C~~~y~~ 111 (147)
T smart00531 99 YYKCPNCQSKYTF 111 (147)
T ss_pred EEECcCCCCEeeH
Confidence 4556 66655553
No 78
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=70.93 E-value=2.1 Score=24.19 Aligned_cols=15 Identities=27% Similarity=0.561 Sum_probs=13.1
Q ss_pred ccccCcCCcCCCChh
Q 037234 3 SSKRKKCGKPFAVKG 17 (81)
Q Consensus 3 p~~C~~C~k~f~~~~ 17 (81)
||.|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 789999999998765
No 79
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=70.52 E-value=6 Score=26.18 Aligned_cols=23 Identities=30% Similarity=0.652 Sum_probs=18.3
Q ss_pred ceEe-ecCcccCChhHHHHHHHHh
Q 037234 29 IWYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 29 p~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
.+.| .|.+.|..+.-|..|||.-
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK 218 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKK 218 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhc
Confidence 3568 8888888888888888855
No 80
>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=67.82 E-value=2.7 Score=16.71 Aligned_cols=9 Identities=22% Similarity=0.364 Sum_probs=6.4
Q ss_pred ccccCcCCc
Q 037234 3 SSKRKKCGK 11 (81)
Q Consensus 3 p~~C~~C~k 11 (81)
+|.|+.||+
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 577888873
No 81
>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=67.79 E-value=2.1 Score=18.14 Aligned_cols=25 Identities=28% Similarity=0.559 Sum_probs=14.3
Q ss_pred cccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcc
Q 037234 4 SKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSD 37 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~ 37 (81)
|.|..||..+.... ..+.+| .||..
T Consensus 1 Y~C~~Cg~~~~~~~---------~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVELKP---------GDPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-BST---------SSTSSBSSSS-S
T ss_pred CCCCcCCCeeEcCC---------CCcEECCcCCCe
Confidence 57888887655322 235577 77754
No 82
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=66.56 E-value=3.4 Score=20.15 Aligned_cols=8 Identities=38% Similarity=0.733 Sum_probs=4.1
Q ss_pred cccCcCCc
Q 037234 4 SKRKKCGK 11 (81)
Q Consensus 4 ~~C~~C~k 11 (81)
..|..|+.
T Consensus 8 ~~CtSCg~ 15 (59)
T PRK14890 8 PKCTSCGI 15 (59)
T ss_pred ccccCCCC
Confidence 34555554
No 83
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=64.42 E-value=4 Score=19.13 Aligned_cols=33 Identities=18% Similarity=0.324 Sum_probs=19.8
Q ss_pred CccccCcCCcCCCChhHHHHHHHh-c--CCceEe-ec
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKN-C--GRIWYC-VC 34 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~-~--~~p~~C-~C 34 (81)
+.+.|..||..|+....-+..... | ..|..| .|
T Consensus 3 k~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~C 39 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSC 39 (49)
T ss_pred eeEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHH
Confidence 467788888887766544433332 2 246666 66
No 84
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=64.38 E-value=3.6 Score=31.53 Aligned_cols=49 Identities=14% Similarity=0.327 Sum_probs=41.1
Q ss_pred CccccCcCCcCCCChhHHHHHHHh----c---------------CCceEe-ecCcccCChhHHHHHHHHh
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKN----C---------------GRIWYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~----~---------------~~p~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
.+|.|..|...|.....|..|++. + ..+| | .|-..|.....|+.|++..
T Consensus 1283 ~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~~ 1351 (1406)
T KOG1146|consen 1283 HRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRSS 1351 (1406)
T ss_pred hhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHHh
Confidence 578999999999999999999871 0 1234 9 9999999999999999976
No 85
>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=63.98 E-value=3.4 Score=23.94 Aligned_cols=16 Identities=13% Similarity=0.440 Sum_probs=7.4
Q ss_pred ceEe-ecCcccCChhHH
Q 037234 29 IWYC-VCGSDFKHKRSL 44 (81)
Q Consensus 29 p~~C-~C~~~f~~~~~l 44 (81)
-|.| .|+..|+..-.+
T Consensus 109 ~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAM 125 (158)
T ss_pred eEECCCCCcEeeHHHHH
Confidence 3445 555544444333
No 86
>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=63.76 E-value=8.8 Score=15.29 Aligned_cols=19 Identities=11% Similarity=0.092 Sum_probs=11.7
Q ss_pred ccCcCCcCCCChhHHHHHHH
Q 037234 5 KRKKCGKPFAVKGDWRTHEK 24 (81)
Q Consensus 5 ~C~~C~k~f~~~~~l~~h~~ 24 (81)
.|+.|++.+ ....+..|..
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 477787776 4455556654
No 87
>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=63.46 E-value=2.7 Score=18.17 Aligned_cols=29 Identities=24% Similarity=0.572 Sum_probs=17.5
Q ss_pred ccccCcCCcCCCChhHHHHHHHhcCCceEe-ecCc
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGS 36 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~ 36 (81)
.|+|..||..|........ .....| .||.
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~-----~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISD-----DPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCC-----CCCCCCCCCCC
Confidence 3779999987765433211 234567 7775
No 88
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=62.60 E-value=3.7 Score=24.31 Aligned_cols=13 Identities=15% Similarity=0.186 Sum_probs=6.6
Q ss_pred cccCcCCcCCCCh
Q 037234 4 SKRKKCGKPFAVK 16 (81)
Q Consensus 4 ~~C~~C~k~f~~~ 16 (81)
|.|+.|+..|+..
T Consensus 118 Y~Cp~C~~rytf~ 130 (178)
T PRK06266 118 FFCPNCHIRFTFD 130 (178)
T ss_pred EECCCCCcEEeHH
Confidence 4555555554443
No 89
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=62.28 E-value=6.7 Score=25.07 Aligned_cols=50 Identities=16% Similarity=0.341 Sum_probs=40.1
Q ss_pred CccccCcCCcCCCChhHHHHHHHh--cCCceEe---ecCcccCChhHHHHHHHHh
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKN--CGRIWYC---VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~--~~~p~~C---~C~~~f~~~~~l~~H~~~~ 51 (81)
.++.|..|...|........|.+. +++++.| .|...+.....+..|.+.+
T Consensus 32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (467)
T COG5048 32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTH 86 (467)
T ss_pred chhhcccccccccccchhhhhcccccccCCccccccccccccCCcchhhhhcccc
Confidence 356788888889988888888885 6788888 5777788888888887777
No 90
>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=61.98 E-value=5.1 Score=16.08 Aligned_cols=10 Identities=30% Similarity=0.560 Sum_probs=6.5
Q ss_pred ccCcCCcCCC
Q 037234 5 KRKKCGKPFA 14 (81)
Q Consensus 5 ~C~~C~k~f~ 14 (81)
.|+.||..|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 4777776664
No 91
>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=60.08 E-value=3.1 Score=18.56 Aligned_cols=28 Identities=29% Similarity=0.552 Sum_probs=17.4
Q ss_pred cccCcCCcCCCChhHHHHHHHhcCCceEe-ecCc
Q 037234 4 SKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGS 36 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~ 36 (81)
|+|..||..|.....+.. ..+..| .||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~-----~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE-----DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCC-----CCCCcCCCCCC
Confidence 778888877765543222 245567 7765
No 92
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=59.04 E-value=2.5 Score=22.42 Aligned_cols=29 Identities=31% Similarity=0.699 Sum_probs=17.1
Q ss_pred ccccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccC
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFK 39 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~ 39 (81)
.|.|+.|++.-.. +...-.|.| .|++.|.
T Consensus 35 ~y~CpfCgk~~vk--------R~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 35 KYVCPFCGKKTVK--------RGSTGIWTCRKCGAKFA 64 (91)
T ss_pred CccCCCCCCCceE--------EEeeEEEEcCCCCCEEe
Confidence 5778888753111 122346788 8887765
No 93
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=58.52 E-value=4.4 Score=21.46 Aligned_cols=29 Identities=24% Similarity=0.455 Sum_probs=17.1
Q ss_pred ccccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccC
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFK 39 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~ 39 (81)
.|.|+.|++.-.. +...-.|.| .|++.|.
T Consensus 36 ~y~CpfCgk~~vk--------R~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 36 KYFCPFCGKHAVK--------RQAVGIWRCKGCKKTVA 65 (90)
T ss_pred CccCCCCCCCcee--------eeeeEEEEcCCCCCEEe
Confidence 5778888753111 112346788 8887765
No 94
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=58.17 E-value=5.2 Score=17.62 Aligned_cols=13 Identities=31% Similarity=0.583 Sum_probs=8.5
Q ss_pred ccccCcCCcCCCC
Q 037234 3 SSKRKKCGKPFAV 15 (81)
Q Consensus 3 p~~C~~C~k~f~~ 15 (81)
|+.|..|++.|-.
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 5667777766654
No 95
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=57.22 E-value=12 Score=21.41 Aligned_cols=24 Identities=38% Similarity=0.600 Sum_probs=17.0
Q ss_pred eEe-ecCcccCChhHHHHHHHHhcCCCCC
Q 037234 30 WYC-VCGSDFKHKRSLKDHIKAFGHGHAA 57 (81)
Q Consensus 30 ~~C-~C~~~f~~~~~l~~H~~~~~~~~~p 57 (81)
..| .+|+.|. +|++|+.+| .|-.|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~-~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTH-YGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcc-cCCCH
Confidence 358 8888774 678899887 55433
No 96
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=56.80 E-value=7.3 Score=27.39 Aligned_cols=25 Identities=20% Similarity=0.445 Sum_probs=20.6
Q ss_pred CCceEe-ecCcccCChhHHHHHHHHh
Q 037234 27 GRIWYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 27 ~~p~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
..|-+| .||.+|........|+..|
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhh
Confidence 567899 9999999988777777666
No 97
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=56.72 E-value=7.7 Score=25.70 Aligned_cols=23 Identities=22% Similarity=0.317 Sum_probs=20.7
Q ss_pred ccccCcCCcCCCChhHHHHHHHh
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKN 25 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~ 25 (81)
.+.|-.|.+.|..+..|+.||+.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 35799999999999999999984
No 98
>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=55.62 E-value=1.5 Score=19.13 Aligned_cols=30 Identities=20% Similarity=0.391 Sum_probs=15.8
Q ss_pred ccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccCC
Q 037234 5 KRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFKH 40 (81)
Q Consensus 5 ~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~~ 40 (81)
.|..||+.|....+. ...+-.| .||-.+.+
T Consensus 3 ~C~~Cg~~Yh~~~~p------P~~~~~Cd~cg~~L~q 33 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNP------PKVEGVCDNCGGELVQ 33 (36)
T ss_dssp EETTTTEEEETTTB--------SSTTBCTTTTEBEBE
T ss_pred CcCCCCCccccccCC------CCCCCccCCCCCeeEe
Confidence 577777776644332 1234466 66654443
No 99
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=55.50 E-value=41 Score=22.64 Aligned_cols=56 Identities=18% Similarity=0.311 Sum_probs=41.8
Q ss_pred ccccCcCCcCCCChhHHHHHHHh--c-----------------------CCceEe-ecC---cccCChhHHHHHHHHhcC
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKN--C-----------------------GRIWYC-VCG---SDFKHKRSLKDHIKAFGH 53 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~--~-----------------------~~p~~C-~C~---~~f~~~~~l~~H~~~~~~ 53 (81)
|--|..|++.+.....-..||.. + ..-+.| .|. +.|......+.||..-++
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~K~H 245 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRDKGH 245 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhhccC
Confidence 44588899998888777778762 1 134568 887 999999999999987655
Q ss_pred CCCCC
Q 037234 54 GHAAL 58 (81)
Q Consensus 54 ~~~p~ 58 (81)
..-+|
T Consensus 246 Ckl~y 250 (390)
T KOG2785|consen 246 CKLPY 250 (390)
T ss_pred cccCC
Confidence 55565
No 100
>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=55.01 E-value=4.6 Score=18.57 Aligned_cols=29 Identities=24% Similarity=0.547 Sum_probs=17.9
Q ss_pred ccccCcCCcCCCChhHHHHHHHhcCCceEe-ecCc
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGS 36 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~ 36 (81)
-|+|..||..|.....+.. ..+..| .||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~-----~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSD-----DPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecCC-----CCCCCCCCCCC
Confidence 3789999987775532211 234568 8875
No 101
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=54.91 E-value=11 Score=25.53 Aligned_cols=34 Identities=18% Similarity=0.336 Sum_probs=22.0
Q ss_pred CccccCcCCcCCCChhHHHHHHHhcCCceEe-ecCc
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGS 36 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~ 36 (81)
..|.|+.|.+.|.....+..-- .-.-.|.| .|+-
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~L~~-~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQLLD-NETGEFHCENCGG 161 (436)
T ss_pred ccccCCccccchhhhHHHHhhc-ccCceEEEecCCC
Confidence 3588999999888766544211 11346888 8863
No 102
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=54.80 E-value=25 Score=22.72 Aligned_cols=52 Identities=23% Similarity=0.395 Sum_probs=32.4
Q ss_pred CCceEe-ecCcccCChhHHHHHHHHhcCCCCCCCCCCc-cCCCCccccccccCCC
Q 037234 27 GRIWYC-VCGSDFKHKRSLKDHIKAFGHGHAALGIECF-EEDDEPASEIEHDGGI 79 (81)
Q Consensus 27 ~~p~~C-~C~~~f~~~~~l~~H~~~~~~~~~p~~~~~~-~~~~~~~~~~~~~~~~ 79 (81)
...|.| .|-+-|.....|..|+... .-..|=+.+-- +.+++..+..+.||..
T Consensus 46 ~~lyiCe~Clky~~~~~~l~~H~~~C-~~r~PPG~eIYr~~~~~~~sifEVDG~~ 99 (290)
T PLN03238 46 TKLYICEYCLKYMRKKKSLLRHLAKC-DIRQPPGGGIYGAVTEGPLSVFEVDGKK 99 (290)
T ss_pred CeEEEcCCCcchhCCHHHHHHHHHhC-CCCCCCcCEeEecCCCCcEEEEEEeCCc
Confidence 457889 9999999999999998754 22122111111 1124457778877753
No 103
>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=54.75 E-value=7.8 Score=17.55 Aligned_cols=15 Identities=33% Similarity=0.935 Sum_probs=11.2
Q ss_pred Ee-ecCcccCChhHHH
Q 037234 31 YC-VCGSDFKHKRSLK 45 (81)
Q Consensus 31 ~C-~C~~~f~~~~~l~ 45 (81)
.| .|++.|+.+....
T Consensus 10 ~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCcccCCcchHHHHHH
Confidence 57 8888888876653
No 104
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=53.84 E-value=13 Score=23.25 Aligned_cols=22 Identities=32% Similarity=0.880 Sum_probs=18.9
Q ss_pred cCCceEe-ecCcccCChhHHHHH
Q 037234 26 CGRIWYC-VCGSDFKHKRSLKDH 47 (81)
Q Consensus 26 ~~~p~~C-~C~~~f~~~~~l~~H 47 (81)
....|.| .||-.|.....|..|
T Consensus 236 R~eh~YC~fCG~~y~~~edl~eh 258 (268)
T KOG1994|consen 236 RSEHYYCFFCGIKYKDEEDLYEH 258 (268)
T ss_pred hccceEEEEeccccCCHHHHHHh
Confidence 3457899 999999999999876
No 105
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=53.58 E-value=7.3 Score=22.46 Aligned_cols=22 Identities=23% Similarity=0.460 Sum_probs=19.7
Q ss_pred ccccCcCCcCCCChhHHHHHHH
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEK 24 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~ 24 (81)
.|+|+.|.-.|.....++.|+.
T Consensus 17 KYKCpkC~vPYCSl~CfKiHk~ 38 (157)
T KOG2857|consen 17 KYKCPKCSVPYCSLPCFKIHKS 38 (157)
T ss_pred hccCCCCCCccccchhhhhccC
Confidence 5899999999999999999876
No 106
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=53.57 E-value=5.5 Score=24.24 Aligned_cols=40 Identities=23% Similarity=0.341 Sum_probs=27.2
Q ss_pred CccccCcCCcCCCChhHHHHHHHh------------cCCc-----eEe-ecCcccCCh
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKN------------CGRI-----WYC-VCGSDFKHK 41 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~------------~~~p-----~~C-~C~~~f~~~ 41 (81)
|...|+.|++.|..+.......++ +..| ..| .||-++...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 667899999999987655544442 1233 368 899776643
No 107
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=51.47 E-value=9.6 Score=20.75 Aligned_cols=15 Identities=20% Similarity=0.510 Sum_probs=12.4
Q ss_pred ccccCcCCcCCCChh
Q 037234 3 SSKRKKCGKPFAVKG 17 (81)
Q Consensus 3 p~~C~~C~k~f~~~~ 17 (81)
||.|..||..|..-+
T Consensus 2 pH~CtrCG~vf~~g~ 16 (112)
T COG3364 2 PHQCTRCGEVFDDGS 16 (112)
T ss_pred Cceeccccccccccc
Confidence 788999999888753
No 108
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=51.29 E-value=3.6 Score=21.78 Aligned_cols=29 Identities=31% Similarity=0.749 Sum_probs=16.2
Q ss_pred ccccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccC
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFK 39 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~ 39 (81)
.|.|+.|++.-.. +...-.|.| .|++.|.
T Consensus 36 ~y~CpfCgk~~vk--------R~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 36 KHVCPVCGRPKVK--------RVGTGIWECRKCGAKFA 65 (90)
T ss_pred CccCCCCCCCceE--------EEEEEEEEcCCCCCEEe
Confidence 4677777653111 112236788 8877665
No 109
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=50.36 E-value=7.2 Score=24.02 Aligned_cols=47 Identities=23% Similarity=0.425 Sum_probs=36.8
Q ss_pred ccCcCCcCCCChhHHHHHHHh------------cCCceEe---ecCcccCChhHHHHHHHHh
Q 037234 5 KRKKCGKPFAVKGDWRTHEKN------------CGRIWYC---VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 5 ~C~~C~k~f~~~~~l~~h~~~------------~~~p~~C---~C~~~f~~~~~l~~H~~~~ 51 (81)
.|..|.+.|.....|..|+.- |.--|.| .|+..|.+...-..|+-..
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~ 169 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRM 169 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHh
Confidence 699999999999888888751 3335789 6999999888888886544
No 110
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=49.43 E-value=12 Score=25.31 Aligned_cols=29 Identities=17% Similarity=0.422 Sum_probs=19.9
Q ss_pred ccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccCChh
Q 037234 5 KRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFKHKR 42 (81)
Q Consensus 5 ~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~~~~ 42 (81)
.|+.||....+ .|..-|+| .||..+....
T Consensus 352 ~Cp~Cg~~m~S---------~G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGRMKS---------AGRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCchhh---------cCCCCcccccccccCCccc
Confidence 68899864222 24448999 9998877653
No 111
>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=48.43 E-value=4.9 Score=17.95 Aligned_cols=12 Identities=50% Similarity=0.877 Sum_probs=5.2
Q ss_pred ccccCcCCcCCC
Q 037234 3 SSKRKKCGKPFA 14 (81)
Q Consensus 3 p~~C~~C~k~f~ 14 (81)
|+.|..|++.|-
T Consensus 13 ~~~C~~C~~~FC 24 (43)
T PF01428_consen 13 PFKCKHCGKSFC 24 (43)
T ss_dssp HEE-TTTS-EE-
T ss_pred CeECCCCCcccC
Confidence 455666666554
No 112
>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=47.81 E-value=6.6 Score=19.10 Aligned_cols=11 Identities=36% Similarity=0.778 Sum_probs=4.6
Q ss_pred ccCcCCcCCCC
Q 037234 5 KRKKCGKPFAV 15 (81)
Q Consensus 5 ~C~~C~k~f~~ 15 (81)
.|..|++.|..
T Consensus 11 ~C~~C~~~F~~ 21 (69)
T PF01363_consen 11 NCMICGKKFSL 21 (69)
T ss_dssp B-TTT--B-BS
T ss_pred cCcCcCCcCCC
Confidence 47788888843
No 113
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=47.57 E-value=19 Score=24.91 Aligned_cols=20 Identities=45% Similarity=1.034 Sum_probs=17.3
Q ss_pred eEe-ecCcccCChhHHHHHHH
Q 037234 30 WYC-VCGSDFKHKRSLKDHIK 49 (81)
Q Consensus 30 ~~C-~C~~~f~~~~~l~~H~~ 49 (81)
+.| +|.+.|.+...|..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 789 99999999988888855
No 114
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=45.72 E-value=11 Score=21.94 Aligned_cols=11 Identities=9% Similarity=0.464 Sum_probs=6.1
Q ss_pred ccccCcCCcCCC
Q 037234 3 SSKRKKCGKPFA 14 (81)
Q Consensus 3 p~~C~~C~k~f~ 14 (81)
+|.|. |+..|.
T Consensus 117 ~Y~C~-C~q~~l 127 (156)
T COG3091 117 PYRCQ-CQQHYL 127 (156)
T ss_pred eEEee-cCCccc
Confidence 45666 665543
No 115
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=45.31 E-value=8.8 Score=21.74 Aligned_cols=11 Identities=18% Similarity=0.661 Sum_probs=5.7
Q ss_pred ccccCcCCcCC
Q 037234 3 SSKRKKCGKPF 13 (81)
Q Consensus 3 p~~C~~C~k~f 13 (81)
.|.|..|+..+
T Consensus 112 ~y~C~~C~~~~ 122 (146)
T smart00731 112 PYRCTGCGQRY 122 (146)
T ss_pred EEECCCCCCCC
Confidence 35565565443
No 116
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=44.47 E-value=30 Score=23.17 Aligned_cols=19 Identities=21% Similarity=0.217 Sum_probs=12.5
Q ss_pred cCcCCcCCCChhHHHHHHH
Q 037234 6 RKKCGKPFAVKGDWRTHEK 24 (81)
Q Consensus 6 C~~C~k~f~~~~~l~~h~~ 24 (81)
|..|...|-.-..|.+|++
T Consensus 223 C~FC~~~FYdDDEL~~HcR 241 (493)
T COG5236 223 CIFCKIYFYDDDELRRHCR 241 (493)
T ss_pred hhhccceecChHHHHHHHH
Confidence 6666666666666666666
No 117
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=43.81 E-value=8.1 Score=18.09 Aligned_cols=30 Identities=13% Similarity=0.184 Sum_probs=13.7
Q ss_pred cccCc-CCcCCCChhHHHHHHH-h-cCCceEe-e
Q 037234 4 SKRKK-CGKPFAVKGDWRTHEK-N-CGRIWYC-V 33 (81)
Q Consensus 4 ~~C~~-C~k~f~~~~~l~~h~~-~-~~~p~~C-~ 33 (81)
..|+. |+..-.....|..|.. . ..++..| .
T Consensus 10 v~C~~~cc~~~i~r~~l~~H~~~~C~~~~v~C~~ 43 (60)
T PF02176_consen 10 VPCPNGCCNEMIPRKELDDHLENECPKRPVPCPY 43 (60)
T ss_dssp EE-TT--S-BEEECCCHHHHHHTTSTTSEEE-SS
T ss_pred eeCCCCCcccceeHHHHHHHHHccCCCCcEECCC
Confidence 34554 3323233456777777 3 3456666 5
No 118
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=43.69 E-value=2.5 Score=22.87 Aligned_cols=37 Identities=16% Similarity=0.243 Sum_probs=20.2
Q ss_pred CccccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccCC
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFKH 40 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~~ 40 (81)
+.|.|+.||.--.....+..-. ..-...| .||.+|.-
T Consensus 21 k~FtCp~Cghe~vs~ctvkk~~--~~g~~~Cg~CGls~e~ 58 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTVKKTV--NIGTAVCGNCGLSFEC 58 (104)
T ss_pred ceEecCccCCeeeeEEEEEecC--ceeEEEcccCcceEEE
Confidence 4578999986544433322111 1224467 88877653
No 119
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=43.33 E-value=54 Score=17.67 Aligned_cols=36 Identities=17% Similarity=0.254 Sum_probs=27.9
Q ss_pred CccccCcCCcCCCChhHHHHHHHh-cCCceEe-ecCcc
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKN-CGRIWYC-VCGSD 37 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~-~~~p~~C-~C~~~ 37 (81)
.-|.|+.-|..|..-......+.. ..+.|.| ..|+.
T Consensus 2 eVf~i~~T~EiF~dYe~Y~~R~~~y~~~vwtC~~TGk~ 39 (102)
T PF10537_consen 2 EVFYIPFTGEIFRDYEEYLKRMILYNQRVWTCEITGKS 39 (102)
T ss_pred ceEEeCCCCcccCCHHHHHHHHHHHhCCeeEEecCCCC
Confidence 456788888899998887776664 6788999 87765
No 120
>PLN02294 cytochrome c oxidase subunit Vb
Probab=43.15 E-value=11 Score=22.47 Aligned_cols=12 Identities=33% Similarity=0.908 Sum_probs=6.1
Q ss_pred CceEe-ecCcccC
Q 037234 28 RIWYC-VCGSDFK 39 (81)
Q Consensus 28 ~p~~C-~C~~~f~ 39 (81)
+|..| .||..|.
T Consensus 140 kp~RCpeCG~~fk 152 (174)
T PLN02294 140 KSFECPVCTQYFE 152 (174)
T ss_pred CceeCCCCCCEEE
Confidence 34555 5555444
No 121
>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=42.92 E-value=9.3 Score=16.68 Aligned_cols=10 Identities=30% Similarity=0.481 Sum_probs=5.2
Q ss_pred ccccCcCCcC
Q 037234 3 SSKRKKCGKP 12 (81)
Q Consensus 3 p~~C~~C~k~ 12 (81)
-|+|..||..
T Consensus 6 ~YkC~~CGni 15 (36)
T PF06397_consen 6 FYKCEHCGNI 15 (36)
T ss_dssp EEE-TTT--E
T ss_pred EEEccCCCCE
Confidence 4788888865
No 122
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=41.93 E-value=15 Score=16.93 Aligned_cols=26 Identities=38% Similarity=0.763 Sum_probs=15.2
Q ss_pred ccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccCC
Q 037234 5 KRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFKH 40 (81)
Q Consensus 5 ~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~~ 40 (81)
.|..|++.|... .+.+.| .||+.|-.
T Consensus 4 ~C~~C~~~F~~~----------~rk~~Cr~Cg~~~C~ 30 (57)
T cd00065 4 SCMGCGKPFTLT----------RRRHHCRNCGRIFCS 30 (57)
T ss_pred cCcccCccccCC----------ccccccCcCcCCcCh
Confidence 477787777652 234456 66665543
No 123
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=41.69 E-value=42 Score=15.94 Aligned_cols=20 Identities=25% Similarity=0.727 Sum_probs=16.1
Q ss_pred CCceEe-ecCcccCChhHHHH
Q 037234 27 GRIWYC-VCGSDFKHKRSLKD 46 (81)
Q Consensus 27 ~~p~~C-~C~~~f~~~~~l~~ 46 (81)
.+-+-| .||..|.....|..
T Consensus 25 ~~~~YC~~Cg~~Y~d~~dL~~ 45 (55)
T PF13821_consen 25 EEHNYCFWCGTKYDDEEDLER 45 (55)
T ss_pred hhCceeeeeCCccCCHHHHHh
Confidence 566789 99999999887753
No 124
>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 PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=40.54 E-value=8 Score=17.47 Aligned_cols=8 Identities=25% Similarity=0.480 Sum_probs=4.5
Q ss_pred cccCcCCc
Q 037234 4 SKRKKCGK 11 (81)
Q Consensus 4 ~~C~~C~k 11 (81)
+.|+.||.
T Consensus 19 ~~CP~Cg~ 26 (46)
T PF12760_consen 19 FVCPHCGS 26 (46)
T ss_pred CCCCCCCC
Confidence 44666664
No 126
>PRK04351 hypothetical protein; Provisional
Probab=40.52 E-value=11 Score=21.66 Aligned_cols=12 Identities=17% Similarity=0.686 Sum_probs=6.1
Q ss_pred CCceEe-ecCccc
Q 037234 27 GRIWYC-VCGSDF 38 (81)
Q Consensus 27 ~~p~~C-~C~~~f 38 (81)
..-|.| .|+-.+
T Consensus 130 ~~~yrCg~C~g~L 142 (149)
T PRK04351 130 TKRYRCGKCRGKL 142 (149)
T ss_pred CCcEEeCCCCcEe
Confidence 345566 665443
No 127
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=40.29 E-value=14 Score=20.51 Aligned_cols=35 Identities=20% Similarity=0.368 Sum_probs=18.5
Q ss_pred cccCcCCcCCCChhHHHHHHHh---c-CCceEe-ecCcccCC
Q 037234 4 SKRKKCGKPFAVKGDWRTHEKN---C-GRIWYC-VCGSDFKH 40 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~~---~-~~p~~C-~C~~~f~~ 40 (81)
++|+.||-.=..-..++ +|+ | ..-|.| .|+..|+.
T Consensus 75 ~kCpkCghe~m~Y~T~Q--lRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQ--LRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred ccCcccCCchhhhhhhh--cccccCCceEEEEcCccceeeec
Confidence 56888875322222221 232 3 245778 88877754
No 128
>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=40.13 E-value=25 Score=18.81 Aligned_cols=18 Identities=28% Similarity=0.370 Sum_probs=9.1
Q ss_pred CcCCcCCCChhHHHHHHH
Q 037234 7 KKCGKPFAVKGDWRTHEK 24 (81)
Q Consensus 7 ~~C~k~f~~~~~l~~h~~ 24 (81)
..|+........+..|.+
T Consensus 88 ~~C~y~~~~~~~m~~H~~ 105 (109)
T PF12013_consen 88 PHCGYITRSKKTMRKHWR 105 (109)
T ss_pred CCCCcEeccHHHHHHHHH
Confidence 555555555555555543
No 129
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=39.93 E-value=23 Score=21.16 Aligned_cols=21 Identities=38% Similarity=0.774 Sum_probs=18.0
Q ss_pred ceEe-ecCcccCChhHHHHHHH
Q 037234 29 IWYC-VCGSDFKHKRSLKDHIK 49 (81)
Q Consensus 29 p~~C-~C~~~f~~~~~l~~H~~ 49 (81)
-|.| +|...|...-+++.|+.
T Consensus 75 GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ceeeeecceeehhhHHHHHHhc
Confidence 5889 99999999999888764
No 130
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=38.83 E-value=14 Score=20.73 Aligned_cols=15 Identities=40% Similarity=0.702 Sum_probs=12.1
Q ss_pred ccccCcCCcCCCChh
Q 037234 3 SSKRKKCGKPFAVKG 17 (81)
Q Consensus 3 p~~C~~C~k~f~~~~ 17 (81)
-|+|..|++.|....
T Consensus 53 RyrC~~C~~tf~~~~ 67 (129)
T COG3677 53 RYKCKSCGSTFTVET 67 (129)
T ss_pred ccccCCcCcceeeec
Confidence 488999999887654
No 131
>COG1773 Rubredoxin [Energy production and conversion]
Probab=37.70 E-value=13 Score=17.82 Aligned_cols=15 Identities=13% Similarity=0.261 Sum_probs=9.8
Q ss_pred CccccCcCCcCCCCh
Q 037234 2 ISSKRKKCGKPFAVK 16 (81)
Q Consensus 2 kp~~C~~C~k~f~~~ 16 (81)
+.|+|..||..|--.
T Consensus 2 ~~~~C~~CG~vYd~e 16 (55)
T COG1773 2 KRWRCSVCGYVYDPE 16 (55)
T ss_pred CceEecCCceEeccc
Confidence 457788887665543
No 132
>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=37.64 E-value=9.8 Score=17.74 Aligned_cols=12 Identities=25% Similarity=0.603 Sum_probs=5.8
Q ss_pred ccCcCCcCCCCh
Q 037234 5 KRKKCGKPFAVK 16 (81)
Q Consensus 5 ~C~~C~k~f~~~ 16 (81)
.|+.|++.|...
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 688898877654
No 133
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=37.15 E-value=8 Score=21.86 Aligned_cols=7 Identities=29% Similarity=0.990 Sum_probs=3.0
Q ss_pred ccCcCCc
Q 037234 5 KRKKCGK 11 (81)
Q Consensus 5 ~C~~C~k 11 (81)
.|..|+.
T Consensus 125 ~C~~C~~ 131 (157)
T PF10263_consen 125 RCPSCGR 131 (157)
T ss_pred EcCCCCC
Confidence 3444443
No 134
>PRK05978 hypothetical protein; Provisional
Probab=36.56 E-value=19 Score=20.90 Aligned_cols=8 Identities=25% Similarity=0.717 Sum_probs=4.3
Q ss_pred ccCcCCcC
Q 037234 5 KRKKCGKP 12 (81)
Q Consensus 5 ~C~~C~k~ 12 (81)
+|+.||+.
T Consensus 35 rCP~CG~G 42 (148)
T PRK05978 35 RCPACGEG 42 (148)
T ss_pred cCCCCCCC
Confidence 45556554
No 135
>PF14353 CpXC: CpXC protein
Probab=35.86 E-value=16 Score=20.08 Aligned_cols=18 Identities=22% Similarity=0.311 Sum_probs=12.8
Q ss_pred ccccCcCCcCCCChhHHH
Q 037234 3 SSKRKKCGKPFAVKGDWR 20 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~ 20 (81)
.|.|+.||..|.....+.
T Consensus 38 ~~~CP~Cg~~~~~~~p~l 55 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLL 55 (128)
T ss_pred EEECCCCCCceecCCCEE
Confidence 478999998876654443
No 136
>PTZ00448 hypothetical protein; Provisional
Probab=35.50 E-value=34 Score=22.89 Aligned_cols=23 Identities=13% Similarity=0.291 Sum_probs=18.2
Q ss_pred ccccCcCCcCCCChhHHHHHHHh
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKN 25 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~ 25 (81)
.|.|..|+-.|........|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 46788898888777777788775
No 137
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=35.37 E-value=15 Score=20.13 Aligned_cols=21 Identities=33% Similarity=0.725 Sum_probs=17.9
Q ss_pred ceEe-ecCcccCChhHHHHHHH
Q 037234 29 IWYC-VCGSDFKHKRSLKDHIK 49 (81)
Q Consensus 29 p~~C-~C~~~f~~~~~l~~H~~ 49 (81)
.+.| .|.+-|.+...|..|.+
T Consensus 55 qhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 55 QHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred eeeeehhHHHHHHHHHHHHHhc
Confidence 3678 99999999999988865
No 138
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=35.31 E-value=18 Score=17.42 Aligned_cols=33 Identities=18% Similarity=0.268 Sum_probs=17.3
Q ss_pred ccCcCCcCCCChhHHHHHHHh---cCCceEe-ecCcc
Q 037234 5 KRKKCGKPFAVKGDWRTHEKN---CGRIWYC-VCGSD 37 (81)
Q Consensus 5 ~C~~C~k~f~~~~~l~~h~~~---~~~p~~C-~C~~~ 37 (81)
+|..|++.+..-.......+. ....|.| .|...
T Consensus 4 kC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~R 40 (56)
T PF09963_consen 4 KCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKER 40 (56)
T ss_pred EEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHH
Confidence 577777765554333333332 2345777 77443
No 139
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=34.14 E-value=23 Score=17.24 Aligned_cols=12 Identities=42% Similarity=0.808 Sum_probs=7.8
Q ss_pred ccc-cCcCCcCCC
Q 037234 3 SSK-RKKCGKPFA 14 (81)
Q Consensus 3 p~~-C~~C~k~f~ 14 (81)
||+ |..||+...
T Consensus 2 ~HkHC~~CG~~Ip 14 (59)
T PF09889_consen 2 PHKHCPVCGKPIP 14 (59)
T ss_pred CCCcCCcCCCcCC
Confidence 444 888887644
No 140
>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=34.10 E-value=33 Score=23.68 Aligned_cols=24 Identities=29% Similarity=0.742 Sum_probs=19.9
Q ss_pred CceEe-ecCcccCChhHHHHHHHHh
Q 037234 28 RIWYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 28 ~p~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
+-+.| .|.+.|.....+..|+..-
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~e 80 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQE 80 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHh
Confidence 35678 8999999999999998744
No 141
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=34.09 E-value=20 Score=14.93 Aligned_cols=23 Identities=30% Similarity=0.780 Sum_probs=9.0
Q ss_pred ccCcCCcCCCChhHHHHHHHhcCCceEe-ecCc
Q 037234 5 KRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGS 36 (81)
Q Consensus 5 ~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~ 36 (81)
+|+.|+..+.. .....+.| .|+.
T Consensus 4 ~Cp~C~se~~y---------~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTY---------EDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----E---------E-SSSEEETTTTE
T ss_pred CCCCCCCccee---------ccCCEEeCCcccc
Confidence 47777665544 12346677 7764
No 142
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=33.97 E-value=22 Score=17.37 Aligned_cols=27 Identities=22% Similarity=0.492 Sum_probs=15.7
Q ss_pred cccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccC
Q 037234 4 SKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFK 39 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~ 39 (81)
|.|..|+.--. |+ ...++.| .||....
T Consensus 21 YiCgdC~~en~----lk-----~~D~irCReCG~RIl 48 (62)
T KOG3507|consen 21 YICGDCGQENT----LK-----RGDVIRCRECGYRIL 48 (62)
T ss_pred EEecccccccc----cc-----CCCcEehhhcchHHH
Confidence 66777764221 11 2357888 8986543
No 143
>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=33.56 E-value=17 Score=15.37 Aligned_cols=24 Identities=21% Similarity=0.336 Sum_probs=15.6
Q ss_pred ccccCcCCcCCCChhHHHHHHHhcCCceEe-ecCc
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGS 36 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~ 36 (81)
-|.|..||..+... ..|..| .|+.
T Consensus 2 ~~~C~~CG~i~~g~----------~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGE----------EAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECC----------cCCCcCcCCCC
Confidence 47889998654321 246788 8875
No 144
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=32.95 E-value=46 Score=14.66 Aligned_cols=22 Identities=27% Similarity=0.363 Sum_probs=13.9
Q ss_pred eEe-ecCcccCCh--hHHHHHHHHh
Q 037234 30 WYC-VCGSDFKHK--RSLKDHIKAF 51 (81)
Q Consensus 30 ~~C-~C~~~f~~~--~~l~~H~~~~ 51 (81)
..| .||-.|... ..-..|.+.|
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHH
Confidence 477 888776643 4456676666
No 145
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=32.20 E-value=9 Score=20.63 Aligned_cols=36 Identities=22% Similarity=0.516 Sum_probs=14.7
Q ss_pred ccccCcCCcCCCChhHHHHHHHh-cCCceEe--ecCcccCChhH
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKN-CGRIWYC--VCGSDFKHKRS 43 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~-~~~p~~C--~C~~~f~~~~~ 43 (81)
.-.|..||+.+... ++.+ +++.|-| .|.+-|.+.-+
T Consensus 14 e~~CalCG~tWg~~-----y~Ev~G~rLfFCCd~ca~EF~nmi~ 52 (105)
T PF11494_consen 14 EMGCALCGATWGDY-----YEEVDGERLFFCCDDCAKEFKNMIN 52 (105)
T ss_dssp GGS-SS---S---S-----S-B-TT--BSSS--SSSS-TTS-TH
T ss_pred cccccccCCcHHHH-----HHhhcCCEEEEEcHHHHHHHHHHHH
Confidence 34588888775522 2223 6777766 89988887533
No 146
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=32.07 E-value=38 Score=16.33 Aligned_cols=13 Identities=38% Similarity=1.165 Sum_probs=8.3
Q ss_pred CCceEe-ecCcccC
Q 037234 27 GRIWYC-VCGSDFK 39 (81)
Q Consensus 27 ~~p~~C-~C~~~f~ 39 (81)
.+.|.| .||..+.
T Consensus 44 ~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 44 GRVFTCPNCGFEMD 57 (69)
T ss_pred cceEEcCCCCCEEC
Confidence 456777 7776543
No 147
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=31.82 E-value=28 Score=16.21 Aligned_cols=12 Identities=33% Similarity=0.750 Sum_probs=7.7
Q ss_pred CCceEe-ecCccc
Q 037234 27 GRIWYC-VCGSDF 38 (81)
Q Consensus 27 ~~p~~C-~C~~~f 38 (81)
...+.| .||..+
T Consensus 35 ~~r~~C~~Cgyt~ 47 (50)
T PRK00432 35 LDRWHCGKCGYTE 47 (50)
T ss_pred CCcEECCCcCCEE
Confidence 356778 787653
No 148
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=30.94 E-value=16 Score=17.07 Aligned_cols=28 Identities=29% Similarity=0.610 Sum_probs=18.0
Q ss_pred CccccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcc
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSD 37 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~ 37 (81)
..|+|..||+.|... . ......| .||..
T Consensus 5 ~~Y~C~~Cg~~~~~~---~-----~~~~irCp~Cg~r 33 (49)
T COG1996 5 MEYKCARCGREVELD---Q-----ETRGIRCPYCGSR 33 (49)
T ss_pred EEEEhhhcCCeeehh---h-----ccCceeCCCCCcE
Confidence 358899999987211 1 2346688 88754
No 149
>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=30.85 E-value=15 Score=16.37 Aligned_cols=10 Identities=20% Similarity=0.494 Sum_probs=5.2
Q ss_pred cccCcCCcCC
Q 037234 4 SKRKKCGKPF 13 (81)
Q Consensus 4 ~~C~~C~k~f 13 (81)
..|+.|+..|
T Consensus 30 ~~CpYCg~~y 39 (40)
T PF10276_consen 30 VVCPYCGTRY 39 (40)
T ss_dssp EEETTTTEEE
T ss_pred EECCCCCCEE
Confidence 3456665543
No 150
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=30.84 E-value=32 Score=23.83 Aligned_cols=26 Identities=31% Similarity=0.678 Sum_probs=21.3
Q ss_pred eEe-ecCcccCChhHHHHHHHHhcCCC
Q 037234 30 WYC-VCGSDFKHKRSLKDHIKAFGHGH 55 (81)
Q Consensus 30 ~~C-~C~~~f~~~~~l~~H~~~~~~~~ 55 (81)
..| .|+..|.++..|-.|++..+++.
T Consensus 461 ~~C~tCr~~FdSRnkLF~Hlk~tgHa~ 487 (508)
T KOG0717|consen 461 ISCTTCRESFDSRNKLFAHLKKTGHAR 487 (508)
T ss_pred HhhhhhhhhccchhHHHHHhhhcCCee
Confidence 468 99999999999999998764443
No 151
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=30.64 E-value=25 Score=18.79 Aligned_cols=14 Identities=36% Similarity=0.567 Sum_probs=10.4
Q ss_pred CccccCcCCcCCCC
Q 037234 2 ISSKRKKCGKPFAV 15 (81)
Q Consensus 2 kp~~C~~C~k~f~~ 15 (81)
+|-.|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 47778888877665
No 152
>PLN02748 tRNA dimethylallyltransferase
Probab=30.43 E-value=49 Score=22.86 Aligned_cols=22 Identities=18% Similarity=0.525 Sum_probs=13.7
Q ss_pred ccccCcCCc-CCCChhHHHHHHH
Q 037234 3 SSKRKKCGK-PFAVKGDWRTHEK 24 (81)
Q Consensus 3 p~~C~~C~k-~f~~~~~l~~h~~ 24 (81)
.|.|..|++ .+.....+..|++
T Consensus 418 ~~~Ce~C~~~~~~G~~eW~~Hlk 440 (468)
T PLN02748 418 QYVCEACGNKVLRGAHEWEQHKQ 440 (468)
T ss_pred cccccCCCCcccCCHHHHHHHhc
Confidence 456777775 5666666666665
No 153
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=30.38 E-value=68 Score=14.93 Aligned_cols=10 Identities=40% Similarity=1.139 Sum_probs=5.2
Q ss_pred CCceEe-ecCc
Q 037234 27 GRIWYC-VCGS 36 (81)
Q Consensus 27 ~~p~~C-~C~~ 36 (81)
.....| .||+
T Consensus 44 ~~i~~Cp~CgR 54 (56)
T PF02591_consen 44 DEIVFCPNCGR 54 (56)
T ss_pred CCeEECcCCCc
Confidence 344555 5554
No 154
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=30.23 E-value=92 Score=18.49 Aligned_cols=45 Identities=11% Similarity=0.327 Sum_probs=24.8
Q ss_pred ccCcCCcCCCChhH--HHH-----HHHhcCCceEe-ecCcccCChhHHHHHHH
Q 037234 5 KRKKCGKPFAVKGD--WRT-----HEKNCGRIWYC-VCGSDFKHKRSLKDHIK 49 (81)
Q Consensus 5 ~C~~C~k~f~~~~~--l~~-----h~~~~~~p~~C-~C~~~f~~~~~l~~H~~ 49 (81)
.|+.|+....-.+. ... +......-+.| .||+.|=.-+++..-.+
T Consensus 99 RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw~~m~~ 151 (165)
T COG1656 99 RCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGSHWRRMVE 151 (165)
T ss_pred cCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccccCchHHHHHHH
Confidence 59999865443322 111 11112445679 99998766666544333
No 155
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.20 E-value=32 Score=19.00 Aligned_cols=40 Identities=13% Similarity=0.297 Sum_probs=27.3
Q ss_pred CccccCcCCcCCCChhHHHHHHHh-------cCCce-------Ee-ecCcccCCh
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKN-------CGRIW-------YC-VCGSDFKHK 41 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~-------~~~p~-------~C-~C~~~f~~~ 41 (81)
-|-.|+.||.......+|.+.... .+.++ .| .|...|...
T Consensus 14 LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~ 68 (112)
T TIGR00622 14 LPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKP 68 (112)
T ss_pred CCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCc
Confidence 367799999988888888876551 11221 38 888888754
No 156
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.18 E-value=33 Score=19.01 Aligned_cols=11 Identities=18% Similarity=0.268 Sum_probs=4.9
Q ss_pred ccccCcCCcCC
Q 037234 3 SSKRKKCGKPF 13 (81)
Q Consensus 3 p~~C~~C~k~f 13 (81)
|..|+.||++|
T Consensus 26 PiVsPytG~s~ 36 (129)
T COG4530 26 PIVSPYTGKSY 36 (129)
T ss_pred ccccCcccccc
Confidence 33444444444
No 157
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.38 E-value=80 Score=23.00 Aligned_cols=19 Identities=21% Similarity=0.308 Sum_probs=10.2
Q ss_pred cCcCCcCCCChhHHHHHHH
Q 037234 6 RKKCGKPFAVKGDWRTHEK 24 (81)
Q Consensus 6 C~~C~k~f~~~~~l~~h~~ 24 (81)
|..|...|.....|..|++
T Consensus 185 C~~C~~~fld~~el~rH~~ 203 (669)
T KOG2231|consen 185 CKFCHERFLDDDELYRHLR 203 (669)
T ss_pred chhhhhhhccHHHHHHhhc
Confidence 4455555555555555554
No 158
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=28.24 E-value=51 Score=19.49 Aligned_cols=18 Identities=22% Similarity=0.504 Sum_probs=13.0
Q ss_pred ccccCcCCcCCCChhHHH
Q 037234 3 SSKRKKCGKPFAVKGDWR 20 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~ 20 (81)
...|..||+.|.....+.
T Consensus 114 ~~~C~~Cg~~f~~~k~i~ 131 (181)
T PRK08222 114 LQRCSRCERPFAPQKTVA 131 (181)
T ss_pred cCcCcccCCccCcHhHHH
Confidence 456899999998665444
No 159
>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=28.02 E-value=41 Score=19.09 Aligned_cols=42 Identities=19% Similarity=0.484 Sum_probs=22.5
Q ss_pred cccCcCCcCCCChhHHHHHHH----h---cCCceEe-ecCcccCChhHHH
Q 037234 4 SKRKKCGKPFAVKGDWRTHEK----N---CGRIWYC-VCGSDFKHKRSLK 45 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~----~---~~~p~~C-~C~~~f~~~~~l~ 45 (81)
-.|..|+..+.....-...-. + ...-+.| .|++.|=.-+.+.
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~ 141 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHWR 141 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccHH
Confidence 358899875544332111001 1 2345789 9998765544443
No 160
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=27.47 E-value=78 Score=21.88 Aligned_cols=25 Identities=28% Similarity=0.724 Sum_probs=21.1
Q ss_pred CCceEe-ecCcccCChhHHHHHHHHh
Q 037234 27 GRIWYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 27 ~~p~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
...|.| .|-+-|.....|..|+...
T Consensus 196 ~~lyiCe~Cl~y~~~~~~~~~H~~~C 221 (450)
T PLN00104 196 SKLYFCEFCLKFMKRKEQLQRHMKKC 221 (450)
T ss_pred CeEEEchhhhhhhcCHHHHHHHHhcC
Confidence 356889 9999999999999998744
No 161
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=27.24 E-value=37 Score=14.92 Aligned_cols=11 Identities=27% Similarity=0.757 Sum_probs=7.5
Q ss_pred CccccCcCCcC
Q 037234 2 ISSKRKKCGKP 12 (81)
Q Consensus 2 kp~~C~~C~k~ 12 (81)
+|..|+.||..
T Consensus 1 ~~~~Cp~Cg~~ 11 (47)
T PF14690_consen 1 KPPRCPHCGSP 11 (47)
T ss_pred CCccCCCcCCC
Confidence 36678888843
No 162
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.13 E-value=27 Score=16.35 Aligned_cols=15 Identities=27% Similarity=0.767 Sum_probs=10.9
Q ss_pred Ee-ecCcccCChhHHH
Q 037234 31 YC-VCGSDFKHKRSLK 45 (81)
Q Consensus 31 ~C-~C~~~f~~~~~l~ 45 (81)
.| .|++.|+++..+.
T Consensus 14 ICpvCqRPFsWRkKW~ 29 (54)
T COG4338 14 ICPVCQRPFSWRKKWA 29 (54)
T ss_pred hhhhhcCchHHHHHHH
Confidence 57 8888888776553
No 163
>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional
Probab=26.63 E-value=51 Score=19.34 Aligned_cols=16 Identities=38% Similarity=0.872 Sum_probs=10.6
Q ss_pred ccccCcCCcCCCChhH
Q 037234 3 SSKRKKCGKPFAVKGD 18 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~ 18 (81)
++.|..||+.|.....
T Consensus 114 ~~~C~~CG~~f~~~~~ 129 (180)
T PRK12387 114 LCNCRVCGRPFAVQKE 129 (180)
T ss_pred cccchhhCCccccHHH
Confidence 3567778887775543
No 164
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=26.37 E-value=38 Score=14.77 Aligned_cols=14 Identities=29% Similarity=0.567 Sum_probs=8.2
Q ss_pred ccCcCCcCCCChhH
Q 037234 5 KRKKCGKPFAVKGD 18 (81)
Q Consensus 5 ~C~~C~k~f~~~~~ 18 (81)
.|..|++.|...+.
T Consensus 4 ~CprC~kg~Hwa~~ 17 (36)
T PF14787_consen 4 LCPRCGKGFHWASE 17 (36)
T ss_dssp C-TTTSSSCS-TTT
T ss_pred cCcccCCCcchhhh
Confidence 57888887765543
No 165
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=26.22 E-value=82 Score=21.40 Aligned_cols=49 Identities=27% Similarity=0.401 Sum_probs=31.4
Q ss_pred CCceEe-ecCcccCChhHHHHHHHHhcCCCCCCCCCCccCCCCccccccccCC
Q 037234 27 GRIWYC-VCGSDFKHKRSLKDHIKAFGHGHAALGIECFEEDDEPASEIEHDGG 78 (81)
Q Consensus 27 ~~p~~C-~C~~~f~~~~~l~~H~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~ 78 (81)
...|.| .|-+-+.....|+.|+... .-..|=+.+- =-++++|..|.||.
T Consensus 156 ~~lYiCEfCLkY~~s~~~l~rH~~kC-~~rhPPG~EI--YR~~~iSvfEVDG~ 205 (396)
T KOG2747|consen 156 DKLYICEFCLKYMKSRTSLQRHLKKC-KLRHPPGNEI--YRKGNISVFEVDGR 205 (396)
T ss_pred CeEEEehHHHhHhchHHHHHHHHHhc-CCCCCCccee--eecCCEEEEEecCc
Confidence 356789 9999999999999999876 2222211100 02444777777764
No 166
>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=25.39 E-value=32 Score=18.45 Aligned_cols=14 Identities=43% Similarity=0.816 Sum_probs=10.9
Q ss_pred CCceEe-ecCcccCC
Q 037234 27 GRIWYC-VCGSDFKH 40 (81)
Q Consensus 27 ~~p~~C-~C~~~f~~ 40 (81)
.+|.+| .||..|.-
T Consensus 77 g~~~rC~eCG~~fkL 91 (97)
T cd00924 77 GKPKRCPECGHVFKL 91 (97)
T ss_pred CCceeCCCCCcEEEE
Confidence 368899 89988753
No 167
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=25.39 E-value=38 Score=16.55 Aligned_cols=11 Identities=27% Similarity=0.604 Sum_probs=7.3
Q ss_pred ccc-cCcCCcCC
Q 037234 3 SSK-RKKCGKPF 13 (81)
Q Consensus 3 p~~-C~~C~k~f 13 (81)
||+ |..||+..
T Consensus 7 PH~HC~VCg~aI 18 (64)
T COG4068 7 PHRHCVVCGKAI 18 (64)
T ss_pred CCccccccCCcC
Confidence 444 88888753
No 168
>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=25.13 E-value=30 Score=16.15 Aligned_cols=13 Identities=15% Similarity=0.353 Sum_probs=9.6
Q ss_pred cccCcCCcCCCCh
Q 037234 4 SKRKKCGKPFAVK 16 (81)
Q Consensus 4 ~~C~~C~k~f~~~ 16 (81)
|.|..||..+.-.
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 7889998776643
No 169
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=25.13 E-value=32 Score=21.56 Aligned_cols=15 Identities=13% Similarity=0.324 Sum_probs=9.4
Q ss_pred CccccCcCCcCCCCh
Q 037234 2 ISSKRKKCGKPFAVK 16 (81)
Q Consensus 2 kp~~C~~C~k~f~~~ 16 (81)
++++|..||..|...
T Consensus 180 kpqRCpECGqVFKLV 194 (268)
T PTZ00043 180 FLYRCGECDQIFMLV 194 (268)
T ss_pred CCccCCCCCcEEEEE
Confidence 456677777666543
No 170
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=25.01 E-value=33 Score=14.87 Aligned_cols=11 Identities=18% Similarity=0.534 Sum_probs=7.1
Q ss_pred cccCcCCcCCC
Q 037234 4 SKRKKCGKPFA 14 (81)
Q Consensus 4 ~~C~~C~k~f~ 14 (81)
+.|+.||..+.
T Consensus 33 ~~C~~CGE~~~ 43 (46)
T TIGR03831 33 LVCPQCGEEYL 43 (46)
T ss_pred cccccCCCEee
Confidence 45777876554
No 171
>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=24.88 E-value=63 Score=14.02 Aligned_cols=12 Identities=17% Similarity=0.055 Sum_probs=3.9
Q ss_pred CccccCcCCcCC
Q 037234 2 ISSKRKKCGKPF 13 (81)
Q Consensus 2 kp~~C~~C~k~f 13 (81)
+.|-|..|...|
T Consensus 2 ~ryyCdyC~~~~ 13 (38)
T PF06220_consen 2 PRYYCDYCKKYL 13 (38)
T ss_dssp -S-B-TTT--B-
T ss_pred cCeeccccccee
Confidence 346677776665
No 172
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=24.60 E-value=37 Score=16.74 Aligned_cols=9 Identities=44% Similarity=0.744 Sum_probs=6.9
Q ss_pred cccCcCCcC
Q 037234 4 SKRKKCGKP 12 (81)
Q Consensus 4 ~~C~~C~k~ 12 (81)
|.|+.||..
T Consensus 1 y~C~KCg~~ 9 (64)
T PF09855_consen 1 YKCPKCGNE 9 (64)
T ss_pred CCCCCCCCc
Confidence 678888864
No 173
>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=24.59 E-value=35 Score=14.20 Aligned_cols=11 Identities=27% Similarity=0.413 Sum_probs=7.3
Q ss_pred ccccCcCCcCC
Q 037234 3 SSKRKKCGKPF 13 (81)
Q Consensus 3 p~~C~~C~k~f 13 (81)
-|+|..||...
T Consensus 4 ~ykC~~CGniv 14 (34)
T cd00974 4 VYKCEICGNIV 14 (34)
T ss_pred EEEcCCCCcEE
Confidence 46777777643
No 174
>PF14369 zf-RING_3: zinc-finger
Probab=24.45 E-value=37 Score=14.49 Aligned_cols=9 Identities=22% Similarity=0.534 Sum_probs=6.8
Q ss_pred cCcCCcCCC
Q 037234 6 RKKCGKPFA 14 (81)
Q Consensus 6 C~~C~k~f~ 14 (81)
|+.|+..|.
T Consensus 24 CP~C~~gFv 32 (35)
T PF14369_consen 24 CPRCHGGFV 32 (35)
T ss_pred CcCCCCcEe
Confidence 888887775
No 175
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=24.26 E-value=69 Score=13.86 Aligned_cols=17 Identities=18% Similarity=0.337 Sum_probs=9.3
Q ss_pred ccCcCCcCCCChhHHHH
Q 037234 5 KRKKCGKPFAVKGDWRT 21 (81)
Q Consensus 5 ~C~~C~k~f~~~~~l~~ 21 (81)
.|..|+-.+.....|.+
T Consensus 21 ~C~~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 21 VCPSCGGIWFDAGELEK 37 (41)
T ss_pred ECCCCCeEEccHHHHHH
Confidence 46666665555554443
No 176
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.24 E-value=23 Score=20.09 Aligned_cols=17 Identities=29% Similarity=0.641 Sum_probs=12.4
Q ss_pred CCceEe-ecCcccCChhH
Q 037234 27 GRIWYC-VCGSDFKHKRS 43 (81)
Q Consensus 27 ~~p~~C-~C~~~f~~~~~ 43 (81)
+-|--| .||+.|.+...
T Consensus 66 e~psfchncgs~fpwter 83 (160)
T COG4306 66 EPPSFCHNCGSRFPWTER 83 (160)
T ss_pred CCcchhhcCCCCCCcHHH
Confidence 346668 99999988643
No 177
>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=23.95 E-value=34 Score=16.10 Aligned_cols=18 Identities=22% Similarity=0.355 Sum_probs=8.6
Q ss_pred ccccCcCCcCCCChhHHH
Q 037234 3 SSKRKKCGKPFAVKGDWR 20 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~ 20 (81)
.|.|+.|...|-.--.+-
T Consensus 21 ~y~C~~C~~~FC~dCD~f 38 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVF 38 (51)
T ss_dssp EE--TTTT--B-HHHHHT
T ss_pred eEECCCCCCccccCcChh
Confidence 488999988877555443
No 178
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=23.90 E-value=71 Score=20.74 Aligned_cols=58 Identities=16% Similarity=0.115 Sum_probs=29.3
Q ss_pred ccccCcCCcCCCChhHHHHHHHhcCCceEe-----ecCcccCChhHHHHHHHHhcCCCCCCCCCCc
Q 037234 3 SSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-----VCGSDFKHKRSLKDHIKAFGHGHAALGIECF 63 (81)
Q Consensus 3 p~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-----~C~~~f~~~~~l~~H~~~~~~~~~p~~~~~~ 63 (81)
+.+|+.|...+.....+..-.-+-...+.| .|.+.|..... ..|.+.- .. +||.|...
T Consensus 80 ~~~CP~Cr~~~g~~R~~amEkV~e~~~vpC~~~~~GC~~~~~Y~~~-~~HE~~C-~f-~~~~CP~p 142 (299)
T KOG3002|consen 80 SNKCPTCRLPIGNIRCRAMEKVAEAVLVPCKNAKLGCTKSFPYGEK-SKHEKVC-EF-RPCSCPVP 142 (299)
T ss_pred cccCCccccccccHHHHHHHHHHHhceecccccccCCceeeccccc-ccccccc-cc-CCcCCCCC
Confidence 456888877777544333211122233344 35555655544 4565544 22 56666555
No 179
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=23.48 E-value=37 Score=14.09 Aligned_cols=11 Identities=27% Similarity=0.425 Sum_probs=7.3
Q ss_pred ccccCcCCcCC
Q 037234 3 SSKRKKCGKPF 13 (81)
Q Consensus 3 p~~C~~C~k~f 13 (81)
-|+|..||...
T Consensus 7 ~ykC~~Cgniv 17 (34)
T TIGR00319 7 VYKCEVCGNIV 17 (34)
T ss_pred EEEcCCCCcEE
Confidence 46777777643
No 180
>KOG0562 consensus Predicted hydrolase (HIT family) [General function prediction only]
Probab=23.48 E-value=90 Score=18.69 Aligned_cols=25 Identities=24% Similarity=0.276 Sum_probs=18.7
Q ss_pred CCceEe-ecCcccCChhHHHHHHHHh
Q 037234 27 GRIWYC-VCGSDFKHKRSLKDHIKAF 51 (81)
Q Consensus 27 ~~p~~C-~C~~~f~~~~~l~~H~~~~ 51 (81)
+.+..| .|+..-.....|+.|++.+
T Consensus 151 k~dLrC~~Cq~~~~~~~kLK~Hl~~~ 176 (184)
T KOG0562|consen 151 KEDLRCWRCQTFGPHFPKLKAHLREE 176 (184)
T ss_pred ccceeehhhhhcccccHHHHHHHHHH
Confidence 457789 9984445667889998876
No 181
>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=23.42 E-value=32 Score=14.99 Aligned_cols=10 Identities=30% Similarity=1.148 Sum_probs=7.2
Q ss_pred ceEe-ecCccc
Q 037234 29 IWYC-VCGSDF 38 (81)
Q Consensus 29 p~~C-~C~~~f 38 (81)
-|.| .|++.|
T Consensus 28 fy~C~~C~~~w 38 (39)
T PF01096_consen 28 FYVCCNCGHRW 38 (39)
T ss_dssp EEEESSSTEEE
T ss_pred EEEeCCCCCee
Confidence 4678 888765
No 182
>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=23.37 E-value=23 Score=15.22 Aligned_cols=13 Identities=46% Similarity=0.797 Sum_probs=5.6
Q ss_pred ccCcCCcCCCChh
Q 037234 5 KRKKCGKPFAVKG 17 (81)
Q Consensus 5 ~C~~C~k~f~~~~ 17 (81)
.|..|++.|..+.
T Consensus 5 ~C~eC~~~f~dSy 17 (34)
T PF01286_consen 5 KCDECGKPFMDSY 17 (34)
T ss_dssp E-TTT--EES-SS
T ss_pred hHhHhCCHHHHHH
Confidence 5777777766543
No 183
>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=23.37 E-value=44 Score=17.75 Aligned_cols=30 Identities=30% Similarity=0.650 Sum_probs=18.8
Q ss_pred CccccCcCCcCCCChhHHHHHHHhcCCceEe-ecCcccC
Q 037234 2 ISSKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDFK 39 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f~ 39 (81)
..|.|+.|++.-.- +...-.|.| .|++.|.
T Consensus 34 ~ky~Cp~Cgk~~vk--------R~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 34 AKYTCPFCGKTSVK--------RVATGIWKCKKCGKKFA 64 (90)
T ss_dssp S-BEESSSSSSEEE--------EEETTEEEETTTTEEEE
T ss_pred CCCcCCCCCCceeE--------EeeeEEeecCCCCCEEe
Confidence 36889999975211 122336899 9987765
No 184
>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=23.19 E-value=19 Score=20.54 Aligned_cols=13 Identities=23% Similarity=0.616 Sum_probs=7.4
Q ss_pred CccccCcCCcCCC
Q 037234 2 ISSKRKKCGKPFA 14 (81)
Q Consensus 2 kp~~C~~C~k~f~ 14 (81)
+|.+|..||..|.
T Consensus 111 ~~~RCpeCG~~fk 123 (136)
T PF01215_consen 111 KPQRCPECGQVFK 123 (136)
T ss_dssp SEEEETTTEEEEE
T ss_pred CccCCCCCCeEEE
Confidence 3556666665554
No 185
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=22.48 E-value=35 Score=14.39 Aligned_cols=8 Identities=38% Similarity=0.750 Sum_probs=4.1
Q ss_pred cCcCCcCC
Q 037234 6 RKKCGKPF 13 (81)
Q Consensus 6 C~~C~k~f 13 (81)
|..|+..|
T Consensus 24 C~~Cg~~~ 31 (33)
T PF08792_consen 24 CIFCGSSF 31 (33)
T ss_pred cccCCcEe
Confidence 55555443
No 186
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=22.40 E-value=54 Score=16.13 Aligned_cols=14 Identities=29% Similarity=0.517 Sum_probs=10.2
Q ss_pred CceEe-ecCcccCCh
Q 037234 28 RIWYC-VCGSDFKHK 41 (81)
Q Consensus 28 ~p~~C-~C~~~f~~~ 41 (81)
.|..| .||+....+
T Consensus 3 iPiRCFtCGKvig~K 17 (69)
T KOG3497|consen 3 IPIRCFTCGKVIGDK 17 (69)
T ss_pred eeeEeeecccccccc
Confidence 36788 898876654
No 187
>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=22.25 E-value=48 Score=14.08 Aligned_cols=19 Identities=26% Similarity=0.620 Sum_probs=8.8
Q ss_pred cccCcCCcCCCChhHHHHHH
Q 037234 4 SKRKKCGKPFAVKGDWRTHE 23 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~ 23 (81)
+.|+.|++.+... -+..|+
T Consensus 5 ~~C~nC~R~v~a~-RfA~HL 23 (33)
T PF08209_consen 5 VECPNCGRPVAAS-RFAPHL 23 (33)
T ss_dssp EE-TTTSSEEEGG-GHHHHH
T ss_pred EECCCCcCCcchh-hhHHHH
Confidence 4567777654432 244444
No 188
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=22.20 E-value=68 Score=18.86 Aligned_cols=21 Identities=19% Similarity=0.493 Sum_probs=16.1
Q ss_pred CCceEe-ecCcccCChhHHHHH
Q 037234 27 GRIWYC-VCGSDFKHKRSLKDH 47 (81)
Q Consensus 27 ~~p~~C-~C~~~f~~~~~l~~H 47 (81)
..|..| .||+.|.|..+-..-
T Consensus 66 ~~PsYC~~CGkpyPWt~~~L~a 87 (158)
T PF10083_consen 66 EAPSYCHNCGKPYPWTENALEA 87 (158)
T ss_pred CCChhHHhCCCCCchHHHHHHH
Confidence 468889 999999987664433
No 189
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=22.16 E-value=66 Score=15.72 Aligned_cols=16 Identities=31% Similarity=0.391 Sum_probs=10.2
Q ss_pred CccccCcCCcCCCChh
Q 037234 2 ISSKRKKCGKPFAVKG 17 (81)
Q Consensus 2 kp~~C~~C~k~f~~~~ 17 (81)
.|-+|-.||+....+.
T Consensus 3 iPVRCFTCGkvi~~~~ 18 (60)
T PF01194_consen 3 IPVRCFTCGKVIGNKW 18 (60)
T ss_dssp -SSS-STTTSBTCGHH
T ss_pred CceecCCCCCChhHhH
Confidence 3677888888776554
No 190
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=22.11 E-value=36 Score=13.04 Aligned_cols=6 Identities=33% Similarity=0.899 Sum_probs=3.1
Q ss_pred cCcCCc
Q 037234 6 RKKCGK 11 (81)
Q Consensus 6 C~~C~k 11 (81)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 555554
No 191
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (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 seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=21.32 E-value=54 Score=14.38 Aligned_cols=28 Identities=25% Similarity=0.293 Sum_probs=13.9
Q ss_pred cccCcCCcCCCChhHHHHHHHhcCCceEe-ecCccc
Q 037234 4 SKRKKCGKPFAVKGDWRTHEKNCGRIWYC-VCGSDF 38 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~~~~~p~~C-~C~~~f 38 (81)
|+|+.|+.... ... ...--+.| .||...
T Consensus 1 m~Cp~Cg~~~~-~~D------~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 1 MKCPNCGSKEI-VFD------PERGELVCPNCGLVL 29 (43)
T ss_dssp ESBTTTSSSEE-EEE------TTTTEEEETTT-BBE
T ss_pred CCCcCCcCCce-EEc------CCCCeEECCCCCCEe
Confidence 46888876531 111 01234578 887543
No 192
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=21.26 E-value=52 Score=13.25 Aligned_cols=10 Identities=60% Similarity=1.079 Sum_probs=5.6
Q ss_pred cccCcCCcCC
Q 037234 4 SKRKKCGKPF 13 (81)
Q Consensus 4 ~~C~~C~k~f 13 (81)
|.|..|++.+
T Consensus 28 f~C~~C~~~L 37 (39)
T smart00132 28 FKCSKCGKPL 37 (39)
T ss_pred CCCcccCCcC
Confidence 4566666544
No 193
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=21.04 E-value=58 Score=14.23 Aligned_cols=34 Identities=21% Similarity=0.439 Sum_probs=18.2
Q ss_pred cccCcCCcCCCChhHHHHHHHh---c-CCceEe-ecCcccC
Q 037234 4 SKRKKCGKPFAVKGDWRTHEKN---C-GRIWYC-VCGSDFK 39 (81)
Q Consensus 4 ~~C~~C~k~f~~~~~l~~h~~~---~-~~p~~C-~C~~~f~ 39 (81)
+.|+.|+..-..... ..++. + ..-|.| .|+..+.
T Consensus 1 ~~Cp~C~~~~a~~~q--~Q~RsaDE~mT~fy~C~~C~~~w~ 39 (40)
T smart00440 1 APCPKCGNREATFFQ--LQTRSADEPMTVFYVCTKCGHRWR 39 (40)
T ss_pred CcCCCCCCCeEEEEE--EcccCCCCCCeEEEEeCCCCCEeC
Confidence 468888754332222 22333 2 234788 8987654
No 194
>PRK01343 zinc-binding protein; Provisional
Probab=20.93 E-value=59 Score=15.72 Aligned_cols=11 Identities=36% Similarity=0.736 Sum_probs=8.8
Q ss_pred cccCcCCcCCC
Q 037234 4 SKRKKCGKPFA 14 (81)
Q Consensus 4 ~~C~~C~k~f~ 14 (81)
..|+.|++.+.
T Consensus 10 ~~CP~C~k~~~ 20 (57)
T PRK01343 10 RPCPECGKPST 20 (57)
T ss_pred CcCCCCCCcCc
Confidence 45999999865
No 195
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=20.26 E-value=34 Score=24.84 Aligned_cols=17 Identities=24% Similarity=0.478 Sum_probs=11.0
Q ss_pred CceEe-ecCcccCChhHH
Q 037234 28 RIWYC-VCGSDFKHKRSL 44 (81)
Q Consensus 28 ~p~~C-~C~~~f~~~~~l 44 (81)
+--+| .|+.+|...--+
T Consensus 677 RqRKCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 677 RQRKCPKCNAAFGANDVH 694 (698)
T ss_pred hcCCCCCCCCCCCccccc
Confidence 44578 888888765443
No 196
>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=20.03 E-value=34 Score=18.72 Aligned_cols=10 Identities=20% Similarity=0.664 Sum_probs=4.7
Q ss_pred eEe-ecCcccC
Q 037234 30 WYC-VCGSDFK 39 (81)
Q Consensus 30 ~~C-~C~~~f~ 39 (81)
..| .|+..|.
T Consensus 71 ~~C~~Cg~~~~ 81 (115)
T TIGR00100 71 CECEDCSEEVS 81 (115)
T ss_pred EEcccCCCEEe
Confidence 345 5554443
Done!