Query psy7479
Match_columns 170
No_of_seqs 210 out of 1279
Neff 9.2
Searched_HMMs 46136
Date Fri Aug 16 19:22:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7479.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7479hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4577|consensus 99.9 8E-29 1.7E-33 184.9 -2.5 144 16-164 32-203 (383)
2 KOG1701|consensus 99.9 1.9E-27 4.2E-32 185.8 -3.5 131 13-153 270-402 (468)
3 KOG1701|consensus 99.9 5.6E-26 1.2E-30 177.7 1.4 123 15-142 332-463 (468)
4 KOG2272|consensus 99.9 1.7E-23 3.7E-28 153.9 -1.7 120 14-140 192-311 (332)
5 KOG1044|consensus 99.8 7.6E-22 1.6E-26 159.5 2.7 120 13-139 129-248 (670)
6 KOG2272|consensus 99.8 5.2E-21 1.1E-25 140.9 -0.0 121 14-143 134-254 (332)
7 KOG1703|consensus 99.8 1.8E-20 4E-25 154.5 -0.3 118 15-138 361-478 (479)
8 KOG1703|consensus 99.8 1.5E-19 3.3E-24 149.0 2.9 121 16-143 302-422 (479)
9 KOG1044|consensus 99.7 1.1E-16 2.3E-21 130.0 5.8 125 11-142 10-191 (670)
10 PF00412 LIM: LIM domain; Int 99.6 6.4E-16 1.4E-20 92.0 5.3 58 84-142 1-58 (58)
11 PF00412 LIM: LIM domain; Int 99.5 2.9E-15 6.2E-20 89.2 2.7 57 20-78 1-58 (58)
12 KOG1700|consensus 99.5 4.4E-15 9.5E-20 109.3 0.4 125 14-142 4-167 (200)
13 smart00132 LIM Zinc-binding do 98.8 2.1E-09 4.5E-14 58.2 2.5 37 83-119 1-37 (39)
14 smart00132 LIM Zinc-binding do 98.8 3.2E-09 6.9E-14 57.5 2.7 37 19-55 1-38 (39)
15 KOG4577|consensus 98.7 4.5E-10 9.8E-15 84.9 -2.9 66 82-150 34-99 (383)
16 KOG0490|consensus 98.4 2.4E-08 5.2E-13 75.2 -1.4 116 22-141 1-119 (235)
17 KOG1702|consensus 98.4 1.2E-08 2.6E-13 73.8 -3.6 85 83-170 6-91 (264)
18 KOG1700|consensus 97.6 1E-05 2.3E-10 59.7 -0.5 64 14-79 105-168 (200)
19 KOG1702|consensus 97.5 1.2E-05 2.5E-10 58.6 -1.9 61 17-79 4-64 (264)
20 PF08394 Arc_trans_TRASH: Arch 94.3 0.017 3.7E-07 30.6 0.5 33 84-119 1-33 (37)
21 PF14446 Prok-RING_1: Prokaryo 89.6 0.23 4.9E-06 28.7 1.4 37 83-119 7-51 (54)
22 PF10367 Vps39_2: Vacuolar sor 89.4 0.28 6.1E-06 32.0 2.0 32 15-46 76-108 (109)
23 PF14471 DUF4428: Domain of un 89.1 0.44 9.6E-06 27.1 2.4 30 111-141 1-30 (51)
24 smart00504 Ubox Modified RING 88.8 0.21 4.5E-06 29.3 0.9 46 45-93 2-47 (63)
25 PF08394 Arc_trans_TRASH: Arch 88.7 0.26 5.7E-06 26.1 1.2 32 20-54 1-33 (37)
26 PF10367 Vps39_2: Vacuolar sor 87.5 0.44 9.5E-06 31.1 2.0 28 83-110 80-107 (109)
27 KOG0490|consensus 85.3 0.18 3.8E-06 37.7 -0.9 52 87-140 2-54 (235)
28 PF14835 zf-RING_6: zf-RING of 85.0 0.97 2.1E-05 27.0 2.3 46 45-95 8-54 (65)
29 PF13920 zf-C3HC4_3: Zinc fing 84.1 0.65 1.4E-05 26.0 1.3 44 46-92 4-48 (50)
30 PF09943 DUF2175: Uncharacteri 83.9 1.6 3.4E-05 28.6 3.1 34 110-143 3-36 (101)
31 PF12773 DZR: Double zinc ribb 82.1 1.2 2.5E-05 24.9 1.8 9 83-91 31-39 (50)
32 PF06677 Auto_anti-p27: Sjogre 81.6 1.1 2.3E-05 24.3 1.5 22 46-73 19-40 (41)
33 PF07191 zinc-ribbons_6: zinc- 81.5 3.2 7E-05 25.3 3.7 59 46-120 3-61 (70)
34 PRK14890 putative Zn-ribbon RN 80.9 1.3 2.8E-05 26.0 1.7 14 17-30 7-20 (59)
35 KOG0320|consensus 80.3 0.53 1.1E-05 34.0 -0.1 53 40-93 127-179 (187)
36 PF11781 RRN7: RNA polymerase 79.2 1.1 2.4E-05 23.5 1.0 25 45-75 9-33 (36)
37 COG1645 Uncharacterized Zn-fin 78.5 1.3 2.7E-05 30.5 1.4 23 46-75 30-52 (131)
38 PF09943 DUF2175: Uncharacteri 77.2 0.91 2E-05 29.7 0.3 31 83-113 4-34 (101)
39 KOG1813|consensus 76.3 1.4 3.1E-05 34.3 1.3 47 44-93 241-287 (313)
40 PF14634 zf-RING_5: zinc-RING 74.5 2 4.4E-05 23.3 1.3 40 47-88 2-43 (44)
41 COG1645 Uncharacterized Zn-fin 73.9 1.7 3.7E-05 29.8 1.0 22 112-139 31-52 (131)
42 PF13248 zf-ribbon_3: zinc-rib 72.1 2.1 4.6E-05 20.6 0.9 9 83-91 4-12 (26)
43 PF06906 DUF1272: Protein of u 71.2 3.7 8.1E-05 23.8 1.8 45 46-92 7-52 (57)
44 COG2888 Predicted Zn-ribbon RN 70.3 1.9 4.1E-05 25.3 0.5 11 17-27 9-19 (61)
45 COG0068 HypF Hydrogenase matur 70.1 6.7 0.00014 34.5 3.9 86 13-119 97-183 (750)
46 PF00645 zf-PARP: Poly(ADP-rib 70.1 2.5 5.4E-05 26.3 1.1 16 15-30 5-20 (82)
47 cd02249 ZZ Zinc finger, ZZ typ 69.3 4.6 0.0001 22.2 2.0 12 130-141 22-33 (46)
48 PF01258 zf-dskA_traR: Prokary 68.9 0.63 1.4E-05 24.3 -1.6 28 112-140 6-33 (36)
49 COG2191 Formylmethanofuran deh 67.0 1.6 3.5E-05 32.2 -0.3 31 110-141 173-203 (206)
50 PF10235 Cript: Microtubule-as 66.7 3.6 7.8E-05 26.4 1.3 43 39-93 39-81 (90)
51 smart00291 ZnF_ZZ Zinc-binding 66.2 5.6 0.00012 21.6 1.9 11 130-140 26-36 (44)
52 PRK14559 putative protein seri 64.5 6.1 0.00013 34.6 2.7 12 19-30 3-14 (645)
53 COG4847 Uncharacterized protei 64.5 7.2 0.00016 25.2 2.3 29 110-138 7-35 (103)
54 PRK00420 hypothetical protein; 64.1 4.4 9.5E-05 27.1 1.4 24 45-74 24-47 (112)
55 PF06689 zf-C4_ClpX: ClpX C4-t 64.0 12 0.00027 20.0 2.9 31 111-141 3-34 (41)
56 PF07754 DUF1610: Domain of un 63.9 4.2 9E-05 19.3 0.9 11 20-30 1-11 (24)
57 PF10083 DUF2321: Uncharacteri 63.8 2.7 5.9E-05 29.7 0.4 54 66-123 27-82 (158)
58 PF13240 zinc_ribbon_2: zinc-r 62.8 4.1 8.9E-05 19.0 0.8 8 84-91 2-9 (23)
59 PF10886 DUF2685: Protein of u 62.6 6.6 0.00014 22.6 1.7 26 18-43 2-27 (54)
60 COG5152 Uncharacterized conser 61.4 1.8 3.8E-05 31.9 -0.9 48 43-93 195-242 (259)
61 PF00569 ZZ: Zinc finger, ZZ t 61.4 10 0.00023 20.8 2.4 11 130-140 27-37 (46)
62 PF13923 zf-C3HC4_2: Zinc fing 60.9 3.1 6.6E-05 21.9 0.2 38 47-87 1-39 (39)
63 COG2191 Formylmethanofuran deh 59.7 4 8.6E-05 30.2 0.6 31 45-77 173-203 (206)
64 PF13639 zf-RING_2: Ring finge 59.7 23 0.0005 18.8 3.6 33 112-144 3-36 (44)
65 PF04570 DUF581: Protein of un 57.5 8.2 0.00018 22.6 1.6 26 46-71 18-43 (58)
66 KOG2462|consensus 56.9 2.6 5.6E-05 32.6 -0.7 40 14-54 127-171 (279)
67 cd02341 ZZ_ZZZ3 Zinc finger, Z 56.8 9.6 0.00021 21.3 1.8 11 131-141 26-36 (48)
68 KOG3579|consensus 56.4 12 0.00027 29.2 2.8 51 15-72 266-316 (352)
69 cd02335 ZZ_ADA2 Zinc finger, Z 56.1 12 0.00025 20.9 2.1 12 130-141 23-34 (49)
70 cd00162 RING RING-finger (Real 55.0 6.9 0.00015 20.3 1.0 26 65-90 18-44 (45)
71 cd02336 ZZ_RSC8 Zinc finger, Z 54.3 13 0.00029 20.4 2.0 30 111-141 2-33 (45)
72 KOG2462|consensus 51.7 7 0.00015 30.3 0.8 15 41-55 127-141 (279)
73 PF10170 C6_DPF: Cysteine-rich 51.6 39 0.00084 22.0 4.1 31 111-141 51-81 (97)
74 PLN03208 E3 ubiquitin-protein 50.2 11 0.00023 27.8 1.6 47 44-93 18-80 (193)
75 PF04810 zf-Sec23_Sec24: Sec23 49.9 11 0.00024 20.0 1.2 30 18-52 3-32 (40)
76 PF13834 DUF4193: Domain of un 49.7 4.7 0.0001 26.2 -0.3 29 109-137 70-98 (99)
77 PF10764 Gin: Inhibitor of sig 49.4 26 0.00055 19.4 2.7 29 111-142 1-29 (46)
78 cd02340 ZZ_NBR1_like Zinc fing 48.8 17 0.00036 19.7 1.9 9 132-140 24-32 (43)
79 cd02338 ZZ_PCMF_like Zinc fing 48.6 17 0.00037 20.3 2.0 12 130-141 23-34 (49)
80 PF12674 Zn_ribbon_2: Putative 48.4 7.2 0.00016 24.5 0.4 28 112-139 3-34 (81)
81 PF13717 zinc_ribbon_4: zinc-r 48.1 6.2 0.00013 20.6 0.1 10 83-92 4-13 (36)
82 PF11571 Med27: Mediator compl 47.4 4.3 9.3E-05 25.9 -0.8 16 74-91 49-64 (90)
83 PF06827 zf-FPG_IleRS: Zinc fi 46.6 9.8 0.00021 18.7 0.7 10 83-92 3-12 (30)
84 PF07503 zf-HYPF: HypF finger; 46.2 8.9 0.00019 20.0 0.5 32 19-55 1-32 (35)
85 PF02069 Metallothio_Pro: Prok 46.1 8.6 0.00019 22.0 0.4 28 111-139 9-37 (52)
86 TIGR02098 MJ0042_CXXC MJ0042 f 46.0 6.3 0.00014 20.5 -0.1 10 110-119 26-35 (38)
87 KOG0978|consensus 44.5 3 6.6E-05 36.5 -2.3 48 45-95 644-692 (698)
88 PF09723 Zn-ribbon_8: Zinc rib 44.5 5.7 0.00012 21.4 -0.4 9 83-91 7-15 (42)
89 cd02342 ZZ_UBA_plant Zinc fing 43.4 23 0.0005 19.4 1.8 29 112-141 3-34 (43)
90 KOG3002|consensus 43.4 14 0.00031 29.1 1.5 43 45-92 49-91 (299)
91 PRK14873 primosome assembly pr 42.3 17 0.00037 32.1 1.9 58 31-90 370-431 (665)
92 TIGR00599 rad18 DNA repair pro 41.4 9.6 0.00021 31.3 0.2 12 17-28 26-37 (397)
93 KOG0320|consensus 41.3 21 0.00045 26.0 1.9 47 107-153 129-175 (187)
94 COG3813 Uncharacterized protei 40.9 20 0.00042 22.0 1.4 44 47-92 8-52 (84)
95 KOG2932|consensus 40.9 11 0.00023 29.9 0.4 43 46-92 92-134 (389)
96 PF13719 zinc_ribbon_5: zinc-r 39.3 11 0.00024 19.7 0.2 9 83-91 4-12 (37)
97 PF08792 A2L_zn_ribbon: A2L zi 39.3 23 0.0005 18.1 1.4 23 46-73 5-27 (33)
98 PF10122 Mu-like_Com: Mu-like 38.9 5.6 0.00012 22.6 -1.0 9 83-91 6-14 (51)
99 KOG4443|consensus 38.6 14 0.0003 32.2 0.7 44 67-120 83-126 (694)
100 PF07649 C1_3: C1-like domain; 38.0 16 0.00035 17.9 0.7 9 111-119 2-10 (30)
101 COG1198 PriA Primosomal protei 37.5 23 0.00051 31.6 2.0 40 45-90 445-484 (730)
102 PF00130 C1_1: Phorbol esters/ 37.5 18 0.00038 20.2 0.9 15 15-29 9-23 (53)
103 PF11077 DUF2616: Protein of u 36.9 26 0.00055 25.4 1.8 34 46-79 138-172 (173)
104 cd02345 ZZ_dah Zinc finger, ZZ 36.5 29 0.00062 19.4 1.6 10 132-141 25-34 (49)
105 KOG1734|consensus 36.4 10 0.00022 29.5 -0.4 17 14-30 221-237 (328)
106 TIGR00143 hypF [NiFe] hydrogen 36.2 37 0.0008 30.3 3.0 86 13-119 64-150 (711)
107 PF00096 zf-C2H2: Zinc finger, 35.8 16 0.00034 16.3 0.4 10 110-119 1-10 (23)
108 PF12677 DUF3797: Domain of un 34.8 27 0.00059 19.6 1.3 28 17-44 13-42 (49)
109 TIGR00595 priA primosomal prot 34.8 47 0.001 28.3 3.3 29 61-90 234-262 (505)
110 PF14569 zf-UDP: Zinc-binding 34.7 28 0.00061 21.7 1.5 13 130-142 35-47 (80)
111 KOG4739|consensus 34.7 43 0.00094 25.4 2.8 31 61-93 19-49 (233)
112 PRK14559 putative protein seri 34.1 34 0.00073 30.1 2.4 15 13-27 11-25 (645)
113 KOG2893|consensus 33.8 15 0.00032 28.1 0.1 36 83-122 12-47 (341)
114 COG2075 RPL24A Ribosomal prote 33.2 43 0.00093 20.1 2.0 28 111-138 5-37 (66)
115 PF14570 zf-RING_4: RING/Ubox 33.0 16 0.00035 20.5 0.2 22 69-90 24-46 (48)
116 PF14255 Cys_rich_CPXG: Cystei 32.4 19 0.00042 20.5 0.5 29 83-112 2-30 (52)
117 PF04564 U-box: U-box domain; 32.2 28 0.00061 21.0 1.2 48 43-93 3-51 (73)
118 PF15451 DUF4632: Domain of un 32.1 20 0.00044 21.1 0.5 19 152-170 44-62 (71)
119 TIGR00373 conserved hypothetic 31.9 11 0.00024 26.7 -0.7 31 17-55 109-139 (158)
120 PHA02610 uvsY.-2 hypothetical 31.8 38 0.00082 19.3 1.5 26 18-43 2-27 (53)
121 PHA02768 hypothetical protein; 31.2 17 0.00036 21.1 0.1 43 83-127 7-49 (55)
122 smart00531 TFIIE Transcription 30.7 12 0.00026 26.1 -0.7 36 17-55 99-134 (147)
123 PRK00807 50S ribosomal protein 30.4 34 0.00074 19.4 1.3 10 19-28 3-12 (52)
124 PRK06266 transcription initiat 29.7 15 0.00033 26.6 -0.4 31 17-55 117-147 (178)
125 TIGR00570 cdk7 CDK-activating 29.2 27 0.00058 27.7 0.9 29 65-93 26-55 (309)
126 PF10080 DUF2318: Predicted me 28.5 37 0.00081 22.3 1.4 26 111-141 37-62 (102)
127 PRK14714 DNA polymerase II lar 27.4 78 0.0017 30.2 3.6 54 44-120 667-720 (1337)
128 COG5432 RAD18 RING-finger-cont 27.1 20 0.00043 28.2 -0.1 44 45-91 26-69 (391)
129 PF13894 zf-C2H2_4: C2H2-type 26.8 28 0.00061 15.1 0.4 10 110-119 1-10 (24)
130 PF00628 PHD: PHD-finger; Int 26.7 56 0.0012 17.8 1.8 27 20-46 2-30 (51)
131 TIGR02605 CxxC_CxxC_SSSS putat 25.8 22 0.00048 19.8 -0.1 9 83-91 7-15 (52)
132 PRK04023 DNA polymerase II lar 25.8 60 0.0013 30.2 2.5 37 45-93 639-675 (1121)
133 PRK00398 rpoP DNA-directed RNA 25.7 28 0.0006 19.0 0.3 27 83-119 5-31 (46)
134 TIGR03826 YvyF flagellar opero 25.4 57 0.0012 22.6 1.9 24 110-142 82-105 (137)
135 smart00834 CxxC_CXXC_SSSS Puta 25.4 19 0.00042 18.7 -0.3 9 83-91 7-15 (41)
136 smart00659 RPOLCX RNA polymera 25.0 30 0.00066 18.9 0.4 9 83-91 4-12 (44)
137 COG4357 Zinc finger domain con 24.7 6.8 0.00015 25.4 -2.5 50 83-134 37-86 (105)
138 cd02344 ZZ_HERC2 Zinc finger, 24.6 53 0.0012 18.1 1.3 11 130-140 23-33 (45)
139 PRK12495 hypothetical protein; 24.5 28 0.00061 26.2 0.3 10 83-92 44-53 (226)
140 PF04981 NMD3: NMD3 family ; 24.3 53 0.0012 24.8 1.8 25 47-79 1-25 (236)
141 PRK11595 DNA utilization prote 24.0 45 0.00098 25.0 1.3 23 69-91 22-44 (227)
142 COG1381 RecO Recombinational D 23.9 44 0.00094 25.6 1.2 28 110-138 155-182 (251)
143 PRK13796 GTPase YqeH; Provisio 23.7 38 0.00083 27.4 0.9 10 130-139 33-42 (365)
144 smart00547 ZnF_RBZ Zinc finger 23.5 45 0.00098 15.4 0.8 6 83-88 18-23 (26)
145 PHA02929 N1R/p28-like protein; 23.1 60 0.0013 24.8 1.8 28 66-93 201-228 (238)
146 KOG3476|consensus 23.1 9 0.00019 24.3 -2.2 37 45-93 55-91 (100)
147 cd02334 ZZ_dystrophin Zinc fin 22.6 82 0.0018 17.6 1.9 11 131-141 24-34 (49)
148 PF08746 zf-RING-like: RING-li 22.6 19 0.00042 19.5 -0.7 11 20-30 1-11 (43)
149 COG0266 Nei Formamidopyrimidin 22.6 48 0.001 25.9 1.2 25 83-109 247-271 (273)
150 COG1813 Predicted transcriptio 22.4 97 0.0021 22.3 2.6 36 112-150 6-43 (165)
151 PRK05580 primosome assembly pr 22.1 1.1E+02 0.0024 27.1 3.5 58 31-90 368-430 (679)
152 PRK00085 recO DNA repair prote 21.9 45 0.00098 25.1 1.0 32 106-138 146-177 (247)
153 PF13912 zf-C2H2_6: C2H2-type 21.7 39 0.00085 15.6 0.4 10 110-119 2-11 (27)
154 cd02343 ZZ_EF Zinc finger, ZZ 21.7 1E+02 0.0022 17.3 2.1 12 131-142 23-34 (48)
155 PF05502 Dynactin_p62: Dynacti 21.4 51 0.0011 27.9 1.3 36 83-120 28-63 (483)
156 PF12874 zf-met: Zinc-finger o 21.0 41 0.0009 15.2 0.4 10 110-119 1-10 (25)
157 PF04161 Arv1: Arv1-like famil 21.0 55 0.0012 24.3 1.2 11 45-55 1-11 (208)
158 PF13901 DUF4206: Domain of un 20.9 40 0.00086 24.9 0.5 6 83-88 154-159 (202)
159 smart00184 RING Ring finger. E 20.5 47 0.001 16.1 0.6 12 64-75 15-26 (39)
160 PF02591 DUF164: Putative zinc 20.4 15 0.00033 21.0 -1.5 10 46-55 24-33 (56)
161 PF08271 TF_Zn_Ribbon: TFIIB z 20.3 47 0.001 17.7 0.6 7 46-52 2-8 (43)
162 PF12171 zf-C2H2_jaz: Zinc-fin 20.3 62 0.0013 15.1 1.0 10 110-119 2-11 (27)
163 PRK08359 transcription factor; 20.0 1.2E+02 0.0025 22.1 2.7 27 112-139 9-38 (176)
No 1
>KOG4577|consensus
Probab=99.94 E-value=8e-29 Score=184.90 Aligned_cols=144 Identities=38% Similarity=0.858 Sum_probs=127.9
Q ss_pred CcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccCCc
Q psy7479 16 GLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFE 95 (170)
Q Consensus 16 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~ 95 (170)
..++|++|.+.|.++++++++++.||..|++|+.|...|. ..+|.++|.+||+++|.++|+. +|..|...|.+..
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~---drCFsR~~s~yCkedFfKrfGT--KCsaC~~GIpPtq 106 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLA---DRCFSREGSVYCKEDFFKRFGT--KCSACQEGIPPTQ 106 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHH---HHHhhcCCceeehHHHHHHhCC--cchhhcCCCChHH
Confidence 6799999999999999999999999999999999999997 5689999999999999999999 9999999999865
Q ss_pred eEEecCCcccccCccccccCCcccccCCeEEEe-CCeeccHHhHHHHhh-------------------------hcc--c
Q psy7479 96 MVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC-DNKILCEYDYEERQV-------------------------FAN--I 147 (170)
Q Consensus 96 ~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~-~~~~~C~~c~~~~~~-------------------------~~~--~ 147 (170)
.+..|.+.+||..||.|..|+++|..|++||+. |+++.|+..|++... ..+ .
T Consensus 107 VVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~~l~gd~~nKRPRTTItAKqLETLK~AY 186 (383)
T KOG4577|consen 107 VVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCNELEGDASNKRPRTTITAKQLETLKQAY 186 (383)
T ss_pred HHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccccccccccccCCCcceeeHHHHHHHHHHh
Confidence 566799999999999999999999889999975 689999999975432 111 2
Q ss_pred cCCCCchHHhhhhccee
Q psy7479 148 AYNPSSLAHLRRQVTLQ 164 (170)
Q Consensus 148 ~~~~~~~~~~~~~~~~~ 164 (170)
..+|++++|+||+|++.
T Consensus 187 n~SpKPARHVREQLsse 203 (383)
T KOG4577|consen 187 NTSPKPARHVREQLSSE 203 (383)
T ss_pred cCCCchhHHHHHHhhhc
Confidence 33489999999999875
No 2
>KOG1701|consensus
Probab=99.92 E-value=1.9e-27 Score=185.84 Aligned_cols=131 Identities=26% Similarity=0.586 Sum_probs=115.8
Q ss_pred CCCCcccccccccccccc-eeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccc
Q psy7479 13 ASGGLKECASCGKRITER-FLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVI 91 (170)
Q Consensus 13 ~~~~~~~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i 91 (170)
......+|.+|+|.|.+. ..+.||++.||..||+|..|++.|. ++.||..|+++||+.||..... +|..|+++|
T Consensus 270 ~~~~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~--Gq~FY~v~~k~~CE~cyq~tle---kC~~Cg~~I 344 (468)
T KOG1701|consen 270 VEDYFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLA--GQSFYQVDGKPYCEGCYQDTLE---KCNKCGEPI 344 (468)
T ss_pred hhhhhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhc--cccccccCCcccchHHHHHHHH---HHhhhhhHH
Confidence 344566999999999987 3488999999999999999999997 6889999999999999998876 999999999
Q ss_pred cCCceEEecCCcccccCccccccCCcccccCCeEEEe-CCeeccHHhHHHHhhhccccCCCCc
Q psy7479 92 PAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC-DNKILCEYDYEERQVFANIAYNPSS 153 (170)
Q Consensus 92 ~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~-~~~~~C~~c~~~~~~~~~~~~~~~~ 153 (170)
+ |++++|.|+.||+.||+|..|++.| .|..|.+. ++++||..+|.++ |++++.-++.
T Consensus 345 ~--d~iLrA~GkayHp~CF~Cv~C~r~l-dgipFtvd~~n~v~Cv~dfh~k--fAPrCs~C~~ 402 (468)
T KOG1701|consen 345 M--DRILRALGKAYHPGCFTCVVCARCL-DGIPFTVDSQNNVYCVPDFHKK--FAPRCSVCGN 402 (468)
T ss_pred H--HHHHHhcccccCCCceEEEEecccc-CCccccccCCCceeeehhhhhh--cCcchhhccC
Confidence 5 5899999999999999999999999 88899874 7999999999998 6666655443
No 3
>KOG1701|consensus
Probab=99.91 E-value=5.6e-26 Score=177.71 Aligned_cols=123 Identities=27% Similarity=0.636 Sum_probs=108.9
Q ss_pred CCcccccccccccccceeEEeCCccccccCccccccccccccCCCee-EEeCCccccccceecccccccccccccccccC
Q psy7479 15 GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTL-YQKANLILCKRDYLRLFGTTGYCAACTKVIPA 93 (170)
Q Consensus 15 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~-~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~ 93 (170)
..+.+|..|++.|.++ +|.|+|+.||+.||+|..|.+.|+ +-.| ...++++||..||+++|++ +|+.|+++|++
T Consensus 332 ~tlekC~~Cg~~I~d~-iLrA~GkayHp~CF~Cv~C~r~ld--gipFtvd~~n~v~Cv~dfh~kfAP--rCs~C~~PI~P 406 (468)
T KOG1701|consen 332 DTLEKCNKCGEPIMDR-ILRALGKAYHPGCFTCVVCARCLD--GIPFTVDSQNNVYCVPDFHKKFAP--RCSVCGNPILP 406 (468)
T ss_pred HHHHHHhhhhhHHHHH-HHHhcccccCCCceEEEEeccccC--CccccccCCCceeeehhhhhhcCc--chhhccCCccC
Confidence 3567899999999999 799999999999999999999997 3445 5778999999999999999 99999999976
Q ss_pred C---ce--EEecCCcccccCccccccCCcccc---cCCeEEEeCCeeccHHhHHHHh
Q psy7479 94 F---EM--VMRAKNNVYHLECFACQQCNHRFC---VGDRFYLCDNKILCEYDYEERQ 142 (170)
Q Consensus 94 ~---~~--~~~~~~~~~H~~Cf~C~~C~~~l~---~~~~~~~~~~~~~C~~c~~~~~ 142 (170)
. |. .|.++++.||.+|++|+.|+.+|+ .+...|..||.++|+.|..+++
T Consensus 407 ~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch~~Rl 463 (468)
T KOG1701|consen 407 RDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCHLKRL 463 (468)
T ss_pred CCCCcceEEEEEccccccccceehhhcCccccccCCCCcceeccCceeechhhhhhh
Confidence 3 21 467999999999999999999996 3567899999999999998874
No 4
>KOG2272|consensus
Probab=99.86 E-value=1.7e-23 Score=153.95 Aligned_cols=120 Identities=32% Similarity=0.754 Sum_probs=111.3
Q ss_pred CCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccC
Q psy7479 14 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 93 (170)
Q Consensus 14 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~ 93 (170)
.-+.++|..|.++|.+. ++.++|+.||.+.|+|+.|.+++- +...|++.|..||+.+|.++|+. .|..|+..|.+
T Consensus 192 ~mgipiCgaC~rpIeer-vi~amgKhWHveHFvCa~CekPFl--GHrHYEkkGlaYCe~h~~qLfG~--~CF~C~~~i~G 266 (332)
T KOG2272|consen 192 KMGIPICGACRRPIEER-VIFAMGKHWHVEHFVCAKCEKPFL--GHRHYEKKGLAYCETHYHQLFGN--LCFICNRVIGG 266 (332)
T ss_pred ccCCcccccccCchHHH-HHHHhccccchhheeehhcCCccc--chhhhhhcCchhHHHHHHHHhhh--hheecCCccCc
Confidence 35789999999999987 789999999999999999999985 56789999999999999999998 99999999966
Q ss_pred CceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHH
Q psy7479 94 FEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEE 140 (170)
Q Consensus 94 ~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~ 140 (170)
.++.+.++.|.++||.|+.|++.|.....|++.|-.|.|+.||++
T Consensus 267 --~vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~r 311 (332)
T KOG2272|consen 267 --DVVSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDR 311 (332)
T ss_pred --cHHHHhhhhhccccccccccccccccccceeeeccchHHHHHHhh
Confidence 788999999999999999999999778899999999999999985
No 5
>KOG1044|consensus
Probab=99.84 E-value=7.6e-22 Score=159.48 Aligned_cols=120 Identities=32% Similarity=0.682 Sum_probs=111.1
Q ss_pred CCCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceeccccccccccccccccc
Q psy7479 13 ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIP 92 (170)
Q Consensus 13 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~ 92 (170)
...+...|++|++.|..+.++.|+++.||..||+|..|+..|. ..|+.++|.+||+.||.+.|+. +|..|.+.|.
T Consensus 129 ~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~---gey~skdg~pyce~dy~~~fgv--kc~~c~~fis 203 (670)
T KOG1044|consen 129 ESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLN---GEYMSKDGVPYCEKDYQAKFGV--KCEECEKFIS 203 (670)
T ss_pred cccCCccccchhhhhhccceeeeeccceeeeeeehhhhccccc---ceeeccCCCcchhhhhhhhcCe--ehHHhhhhhh
Confidence 3347788999999999998899999999999999999999996 5699999999999999999998 9999999997
Q ss_pred CCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHH
Q psy7479 93 AFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYE 139 (170)
Q Consensus 93 ~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~ 139 (170)
+ .++.|.|+.||+.|-+|+.|+.+|..|+++|+....+|-..|-.
T Consensus 204 g--kvLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~q 248 (670)
T KOG1044|consen 204 G--KVLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCKQ 248 (670)
T ss_pred h--hhhhccCcccCcchhhhhhhccccccchheeeccccccCCcccc
Confidence 7 89999999999999999999999999999999999988877754
No 6
>KOG2272|consensus
Probab=99.80 E-value=5.2e-21 Score=140.91 Aligned_cols=121 Identities=27% Similarity=0.457 Sum_probs=108.2
Q ss_pred CCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccC
Q psy7479 14 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 93 (170)
Q Consensus 14 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~ 93 (170)
..+.-+|.+|+..|.+. .+...+..||+..|+|..|++.|. +.-....|.+||..|+.+.--| .|..|.++|
T Consensus 134 ~~g~YvC~KCh~~iD~~-~l~fr~d~yH~yHFkCt~C~keL~---sdaRevk~eLyClrChD~mgip--iCgaC~rpI-- 205 (332)
T KOG2272|consen 134 GRGRYVCQKCHAHIDEQ-PLTFRGDPYHPYHFKCTTCGKELT---SDAREVKGELYCLRCHDKMGIP--ICGACRRPI-- 205 (332)
T ss_pred ccceeehhhhhhhcccc-cccccCCCCCccceeccccccccc---chhhhhccceeccccccccCCc--ccccccCch--
Confidence 44567899999999885 688999999999999999999997 3456778899999999987766 999999999
Q ss_pred CceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhh
Q psy7479 94 FEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQV 143 (170)
Q Consensus 94 ~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~ 143 (170)
+|+++.++|+.||.+.|+|+.|.+|+ .|-+.|++.|..||+.+|.++|.
T Consensus 206 eervi~amgKhWHveHFvCa~CekPF-lGHrHYEkkGlaYCe~h~~qLfG 254 (332)
T KOG2272|consen 206 EERVIFAMGKHWHVEHFVCAKCEKPF-LGHRHYEKKGLAYCETHYHQLFG 254 (332)
T ss_pred HHHHHHHhccccchhheeehhcCCcc-cchhhhhhcCchhHHHHHHHHhh
Confidence 46899999999999999999999999 78899999999999999999853
No 7
>KOG1703|consensus
Probab=99.78 E-value=1.8e-20 Score=154.47 Aligned_cols=118 Identities=26% Similarity=0.587 Sum_probs=107.9
Q ss_pred CCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccCC
Q psy7479 15 GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAF 94 (170)
Q Consensus 15 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~ 94 (170)
...+.|.+|.++|.+. .|.|.+..||++||.|..|++.|. +..|+..+|.+||+.||.+++.+ +|..|.++|...
T Consensus 361 ~~~p~C~~C~~~i~~~-~v~a~~~~wH~~cf~C~~C~~~~~--~~~~~~~~~~pyce~~~~~~~~~--~~~~~~~p~~~~ 435 (479)
T KOG1703|consen 361 PFRPNCKRCLLPILEE-GVCALGRLWHPECFVCADCGKPLK--NSSFFESDGEPYCEDHYKKLFTT--KCDYCKKPVEFG 435 (479)
T ss_pred hhCccccccCCchHHh-HhhhccCeechhceeeecccCCCC--CCcccccCCccchhhhHhhhccc--cchhccchhHhh
Confidence 4678899999999999 577889999999999999999997 46699999999999999999998 999999998755
Q ss_pred ceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhH
Q psy7479 95 EMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138 (170)
Q Consensus 95 ~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~ 138 (170)
+..+.+.+..||..||+|..|.+.| .+..|+...++++|..|+
T Consensus 436 ~~~ie~~~~~~h~~~F~c~~c~~~l-~~~~~~~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 436 SRQIEADGSPFHGDCFRCANCMKKL-TKKTFFETLDKPLCQKHF 478 (479)
T ss_pred hhHhhccCccccccceehhhhhccc-cCCceeecCCccccccCC
Confidence 6788999999999999999999999 788899999999999885
No 8
>KOG1703|consensus
Probab=99.76 E-value=1.5e-19 Score=149.03 Aligned_cols=121 Identities=24% Similarity=0.507 Sum_probs=110.3
Q ss_pred CcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccCCc
Q psy7479 16 GLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFE 95 (170)
Q Consensus 16 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~ 95 (170)
..+.|..|...|.+..++.++++.||+.+|.|..|+..+.. ..+...+|++||..|+...+.+ .|.+|+++|.+
T Consensus 302 ~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~--~~~~~~~g~~~c~~~~~~~~~p--~C~~C~~~i~~-- 375 (479)
T KOG1703|consen 302 TRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILD--GGPRELDGKILCHECFHAPFRP--NCKRCLLPILE-- 375 (479)
T ss_pred ccccccccccCcccceeEeeccccccccceeeccccccccC--CCccccCCCccHHHHHHHhhCc--cccccCCchHH--
Confidence 45899999999999447899999999999999999999974 3468899999999999999998 99999999965
Q ss_pred eEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhh
Q psy7479 96 MVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQV 143 (170)
Q Consensus 96 ~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~ 143 (170)
.+|.+.+..||++||.|..|+++| .+..|+..++.+||..||.+++.
T Consensus 376 ~~v~a~~~~wH~~cf~C~~C~~~~-~~~~~~~~~~~pyce~~~~~~~~ 422 (479)
T KOG1703|consen 376 EGVCALGRLWHPECFVCADCGKPL-KNSSFFESDGEPYCEDHYKKLFT 422 (479)
T ss_pred hHhhhccCeechhceeeecccCCC-CCCcccccCCccchhhhHhhhcc
Confidence 788999999999999999999999 78889999999999999999854
No 9
>KOG1044|consensus
Probab=99.66 E-value=1.1e-16 Score=129.98 Aligned_cols=125 Identities=23% Similarity=0.558 Sum_probs=99.1
Q ss_pred CCCCCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCC-ccccccceec-------------
Q psy7479 11 GGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKAN-LILCKRDYLR------------- 76 (170)
Q Consensus 11 ~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~-~~yC~~c~~~------------- 76 (170)
++.......|.+|.+.-.+. ++.+.++.||..||+|..|+..|.+.+ ||.+++ ++|+......
T Consensus 10 ~~~~~~~i~c~~c~~kc~ge-vlrv~d~~fhi~cf~c~~cg~~la~~g--ff~k~~~~~ygt~~c~~~~~gevvsa~gkt 86 (670)
T KOG1044|consen 10 PQTGKQGIKCDKCRKKCSGE-VLRVNDNHFHINCFQCKKCGRNLAEGG--FFTKPENRLYGTDDCRAFVEGEVVSTLGKT 86 (670)
T ss_pred ccccccceehhhhCCccccc-eeEeeccccceeeeeccccCCCccccc--ceecccceeecccchhhhccceeEecccce
Confidence 34455567899999999998 899999999999999999999998643 555443 5666533221
Q ss_pred -------------------------------------------ccccccccccccccccCCceEEecCCcccccCccccc
Q psy7479 77 -------------------------------------------LFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQ 113 (170)
Q Consensus 77 -------------------------------------------~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~ 113 (170)
..++ ..|++|+..|.. +..+.|.++.||..||+|.
T Consensus 87 yh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~p-s~cagc~~~lk~-gq~llald~qwhv~cfkc~ 164 (670)
T KOG1044|consen 87 YHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGP-STCAGCGEELKN-GQALLALDKQWHVSCFKCK 164 (670)
T ss_pred eccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCC-ccccchhhhhhc-cceeeeeccceeeeeeehh
Confidence 0011 149999998865 4788999999999999999
Q ss_pred cCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479 114 QCNHRFCVGDRFYLCDNKILCEYDYEERQ 142 (170)
Q Consensus 114 ~C~~~l~~~~~~~~~~~~~~C~~c~~~~~ 142 (170)
.|+..| ..+|+..+|.+||..+|.+.|
T Consensus 165 ~c~~vL--~gey~skdg~pyce~dy~~~f 191 (670)
T KOG1044|consen 165 SCSAVL--NGEYMSKDGVPYCEKDYQAKF 191 (670)
T ss_pred hhcccc--cceeeccCCCcchhhhhhhhc
Confidence 999999 457999999999999998876
No 10
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.63 E-value=6.4e-16 Score=92.02 Aligned_cols=58 Identities=36% Similarity=0.745 Sum_probs=52.1
Q ss_pred cccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ 142 (170)
Q Consensus 84 C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~ 142 (170)
|.+|+++|.+.+.++.+.|+.||++||+|..|+++| .+..|+..+|++||..||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l-~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPL-NDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBT-TTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCcc-CCCeeEeECCEEECHHHHhhhC
Confidence 789999999877677899999999999999999999 4555999999999999999874
No 11
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.54 E-value=2.9e-15 Score=89.19 Aligned_cols=57 Identities=39% Similarity=0.864 Sum_probs=50.7
Q ss_pred ccccccccccceeE-EeCCccccccCccccccccccccCCCeeEEeCCccccccceeccc
Q psy7479 20 CASCGKRITERFLL-KALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLF 78 (170)
Q Consensus 20 C~~C~~~I~~~~~~-~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~ 78 (170)
|.+|+++|.+..++ .++|+.||++||+|..|+++|.. ..++..+|++||+.||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~--~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLND--GDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTT--SSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCC--CeeEeECCEEECHHHHhhhC
Confidence 78999999987554 69999999999999999999974 34999999999999998765
No 12
>KOG1700|consensus
Probab=99.49 E-value=4.4e-15 Score=109.28 Aligned_cols=125 Identities=22% Similarity=0.548 Sum_probs=103.5
Q ss_pred CCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceeccccccc-----------
Q psy7479 14 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTG----------- 82 (170)
Q Consensus 14 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~----------- 82 (170)
+.....|..|++.++-.+.+...|..||+.||+|..|.+.|.. ..+..+++.+||+.+|...+++.+
T Consensus 4 ~~~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~--~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~ 81 (200)
T KOG1700|consen 4 TGTTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTL--SGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAG 81 (200)
T ss_pred ccccchhhhccCcchHHHHHhccCcchhhhHHhcccccccccc--ccccccccccccccchHhhhCcccccccccccccC
Confidence 3455689999999998766778899999999999999999973 457789999999997655433310
Q ss_pred ----------------------------ccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeecc
Q psy7479 83 ----------------------------YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILC 134 (170)
Q Consensus 83 ----------------------------~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C 134 (170)
.|..|++.+.+.+ .+...+..||..||+|+.|+..| ....+...++.+||
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~E-k~~~~~~~~hk~cfrc~~~~~~l-s~~~~~~~~g~l~~ 159 (200)
T KOG1700|consen 82 GLGKDGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLE-KVTGNGLEFHKSCFRCTHCGKKL-SPKNYAALEGVLYC 159 (200)
T ss_pred CCCcccccccccccccchhHHhhhccccccccccceeeehH-HHhhhhhhhhhhheeeccccccc-CCcchhhcCCcccc
Confidence 3999999998754 44677999999999999999999 67788888999999
Q ss_pred HHhHHHHh
Q psy7479 135 EYDYEERQ 142 (170)
Q Consensus 135 ~~c~~~~~ 142 (170)
..++..++
T Consensus 160 ~~~~~~~~ 167 (200)
T KOG1700|consen 160 KHHFAQLF 167 (200)
T ss_pred chhhheee
Confidence 99887764
No 13
>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=98.84 E-value=2.1e-09 Score=58.23 Aligned_cols=37 Identities=43% Similarity=0.909 Sum_probs=33.6
Q ss_pred ccccccccccCCceEEecCCcccccCccccccCCccc
Q psy7479 83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRF 119 (170)
Q Consensus 83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 119 (170)
+|.+|+++|.+.+..+.+.++.||++||+|..|+++|
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L 37 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPL 37 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcC
Confidence 5889999998765788899999999999999999998
No 14
>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=98.82 E-value=3.2e-09 Score=57.49 Aligned_cols=37 Identities=46% Similarity=1.076 Sum_probs=33.4
Q ss_pred cccccccccccc-eeEEeCCccccccCccccccccccc
Q psy7479 19 ECASCGKRITER-FLLKALDLFWHEDCLKCGCCDCRLG 55 (170)
Q Consensus 19 ~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~ 55 (170)
.|.+|+++|.+. ..+.++++.||+.||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 489999999986 6788899999999999999999984
No 15
>KOG4577|consensus
Probab=98.74 E-value=4.5e-10 Score=84.91 Aligned_cols=66 Identities=21% Similarity=0.569 Sum_probs=57.9
Q ss_pred cccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhhhccccCC
Q psy7479 82 GYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANIAYN 150 (170)
Q Consensus 82 ~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~~ 150 (170)
++|++|.+.|.. ..++.+.++.||..|++|+.|+.+| ++..+.+++.+||+.+|.++|..+..+..
T Consensus 34 p~CagC~q~IlD-rFilKvl~R~wHs~CLkCs~C~~qL--~drCFsR~~s~yCkedFfKrfGTKCsaC~ 99 (383)
T KOG4577|consen 34 PICAGCDQHILD-RFILKVLDRHWHSSCLKCSDCHDQL--ADRCFSREGSVYCKEDFFKRFGTKCSACQ 99 (383)
T ss_pred ccccchHHHHHH-HHHHHHHhhhhhhhhcchhhhhhHH--HHHHhhcCCceeehHHHHHHhCCcchhhc
Confidence 399999999964 4577899999999999999999999 56777899999999999999887777666
No 16
>KOG0490|consensus
Probab=98.42 E-value=2.4e-08 Score=75.22 Aligned_cols=116 Identities=41% Similarity=0.823 Sum_probs=97.3
Q ss_pred ccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceec--ccccccccccccccccCCceEEe
Q psy7479 22 SCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLR--LFGTTGYCAACTKVIPAFEMVMR 99 (170)
Q Consensus 22 ~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~--~~~~~~~C~~C~~~i~~~~~~~~ 99 (170)
.|+..|.+.+.+.+.+..||..|.+|..|...|.. ....+..+|..||..+|.. .+.. +|.+|...+...+.+..
T Consensus 1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~g~~~~~~d~~~~~~~~~--rr~rt~~~~~ql~~ler 77 (235)
T KOG0490|consen 1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGV-GDTCFSKDGSIYCKRDYQREFKFSK--RCARCKFTISQLDELER 77 (235)
T ss_pred CCCccccchHHhhcccHHHHHHHHhhhhhcchhcc-CCCcccCCCcccccccchhhhhccc--cccCCCCCcCHHHHHHH
Confidence 37778888877777899999999999999999962 2445555999999999998 5655 99999999977677888
Q ss_pred cCCcccccCccccccCCcccccCCeEEEeCC-eeccHHhHHHH
Q psy7479 100 AKNNVYHLECFACQQCNHRFCVGDRFYLCDN-KILCEYDYEER 141 (170)
Q Consensus 100 ~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~-~~~C~~c~~~~ 141 (170)
+..+. |.-||.|..|...+..+..+.+.+. +..|...+.+.
T Consensus 78 ~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 78 AFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred hhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 88888 9999999999998878888888765 89998887654
No 17
>KOG1702|consensus
Probab=98.39 E-value=1.2e-08 Score=73.84 Aligned_cols=85 Identities=21% Similarity=0.381 Sum_probs=70.4
Q ss_pred ccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhhhccccCCCCchHH-hhhhc
Q psy7479 83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANIAYNPSSLAH-LRRQV 161 (170)
Q Consensus 83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~~~~~~~~-~~~~~ 161 (170)
.|..|++.+.+.| -+.-+++.||..||+|..|+.+| .-.+|-..+.++||..+|.+. +++.++.+|+..+. ...++
T Consensus 6 n~~~cgk~vYPvE-~v~cldk~whk~cfkce~c~mtl-nmKnyKgy~kkpycn~hYpkq-~at~~adTPEm~Rik~n~en 82 (264)
T KOG1702|consen 6 NREDCGKTVYPVE-EVKCLDKVWHKQCFKCEVCGMTL-NMKNYKGYDKKPYCNPHYPKQ-VATVMADTPEMRRIKENTEN 82 (264)
T ss_pred hhhhhccccccHH-HHhhHHHHHHHHhheeeeccCCh-hhhhccccccCCCcCcccccc-eeeeecCCHHHHHHHhhhcc
Confidence 6788999888754 34778999999999999999999 677888899999999999876 48888888988855 44457
Q ss_pred ceeeecccC
Q psy7479 162 TLQVLWIRE 170 (170)
Q Consensus 162 ~~~~~~~~~ 170 (170)
.++|-|++|
T Consensus 83 qS~vkY~~e 91 (264)
T KOG1702|consen 83 QSNVKYHAE 91 (264)
T ss_pred chhhhhHHH
Confidence 788888865
No 18
>KOG1700|consensus
Probab=97.61 E-value=1e-05 Score=59.74 Aligned_cols=64 Identities=23% Similarity=0.577 Sum_probs=53.5
Q ss_pred CCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccc
Q psy7479 14 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 79 (170)
Q Consensus 14 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~ 79 (170)
......|..|++.++..+.+...+..||..||+|..|+..|.. ..+...++.+||...+..++-
T Consensus 105 ~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~--~~~~~~~g~l~~~~~~~~~~~ 168 (200)
T KOG1700|consen 105 AGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSP--KNYAALEGVLYCKHHFAQLFK 168 (200)
T ss_pred hccccccccccceeeehHHHhhhhhhhhhhheeecccccccCC--cchhhcCCccccchhhheeec
Confidence 3455779999999998877788899999999999999999973 557888999999877766553
No 19
>KOG1702|consensus
Probab=97.46 E-value=1.2e-05 Score=58.57 Aligned_cols=61 Identities=25% Similarity=0.506 Sum_probs=51.0
Q ss_pred cccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccc
Q psy7479 17 LKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 79 (170)
Q Consensus 17 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~ 79 (170)
...|..|++.++..+.+.-+++.||..||+|..|+.+|.. ..+-..+.++||..+|.+..+
T Consensus 4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnm--KnyKgy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNM--KNYKGYDKKPYCNPHYPKQVA 64 (264)
T ss_pred cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhh--hhccccccCCCcCccccccee
Confidence 4567889999998777888999999999999999999973 445668899999999987543
No 20
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=94.25 E-value=0.017 Score=30.59 Aligned_cols=33 Identities=33% Similarity=0.748 Sum_probs=22.4
Q ss_pred cccccccccCCceEEecCCcccccCccccccCCccc
Q psy7479 84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRF 119 (170)
Q Consensus 84 C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 119 (170)
|..|+++|.+...++...++.|| |-|..|.+.|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~f 33 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQF 33 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE---EECHHHHHHH
Confidence 66788888775556777788887 4455555544
No 21
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=89.60 E-value=0.23 Score=28.66 Aligned_cols=37 Identities=24% Similarity=0.652 Sum_probs=24.8
Q ss_pred ccccccccccCCceEEe--cCCcccccCcc----cccc--CCccc
Q psy7479 83 YCAACTKVIPAFEMVMR--AKNNVYHLECF----ACQQ--CNHRF 119 (170)
Q Consensus 83 ~C~~C~~~i~~~~~~~~--~~~~~~H~~Cf----~C~~--C~~~l 119 (170)
+|..|+++|...+.++. .=+..||.+|+ .|.. |+..+
T Consensus 7 ~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred cChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence 89999999965444443 33667888887 3655 55543
No 22
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=89.37 E-value=0.28 Score=32.03 Aligned_cols=32 Identities=25% Similarity=0.571 Sum_probs=20.4
Q ss_pred CCcccccccccccccc-eeEEeCCccccccCcc
Q psy7479 15 GGLKECASCGKRITER-FLLKALDLFWHEDCLK 46 (170)
Q Consensus 15 ~~~~~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~ 46 (170)
.....|..|+++|... .++...|..+|..|++
T Consensus 76 ~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 3456688888888765 3344456667777753
No 23
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=89.10 E-value=0.44 Score=27.15 Aligned_cols=30 Identities=20% Similarity=0.490 Sum_probs=23.4
Q ss_pred ccccCCcccccCCeEEEeCCeeccHHhHHHH
Q psy7479 111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEER 141 (170)
Q Consensus 111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~ 141 (170)
.|..|+..++.-..+-+.|| .+|..|+.+.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 48889999855455667788 6999999875
No 24
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=88.76 E-value=0.21 Score=29.32 Aligned_cols=46 Identities=7% Similarity=0.030 Sum_probs=33.6
Q ss_pred ccccccccccccCCCeeEEeCCccccccceecccccccccccccccccC
Q psy7479 45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 93 (170)
Q Consensus 45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~ 93 (170)
|.|..|+..+. .......|..||..+..+.+...+.|..|++++..
T Consensus 2 ~~Cpi~~~~~~---~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~ 47 (63)
T smart00504 2 FLCPISLEVMK---DPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTH 47 (63)
T ss_pred cCCcCCCCcCC---CCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence 57888888886 34667788999999887654333478888887744
No 25
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=88.74 E-value=0.26 Score=26.08 Aligned_cols=32 Identities=25% Similarity=0.596 Sum_probs=21.9
Q ss_pred ccccccccccc-eeEEeCCccccccCcccccccccc
Q psy7479 20 CASCGKRITER-FLLKALDLFWHEDCLKCGCCDCRL 54 (170)
Q Consensus 20 C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l 54 (170)
|..|+.+|.+. .++...++.|| |-|..|...+
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~f 33 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQF 33 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE---EECHHHHHHH
Confidence 67899999887 44667888887 4445554443
No 26
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=87.50 E-value=0.44 Score=31.09 Aligned_cols=28 Identities=25% Similarity=0.502 Sum_probs=18.8
Q ss_pred ccccccccccCCceEEecCCcccccCcc
Q psy7479 83 YCAACTKVIPAFEMVMRAKNNVYHLECF 110 (170)
Q Consensus 83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf 110 (170)
.|..|+++|.....++...|..+|..|+
T Consensus 80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CccCcCCcCCCceEEEeCCCeEEecccc
Confidence 6888888886533345555667777775
No 27
>KOG0490|consensus
Probab=85.26 E-value=0.18 Score=37.73 Aligned_cols=52 Identities=27% Similarity=0.706 Sum_probs=39.3
Q ss_pred ccccccCCceEEecCCcccccCccccccCCccccc-CCeEEEeCCeeccHHhHHH
Q psy7479 87 CTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCV-GDRFYLCDNKILCEYDYEE 140 (170)
Q Consensus 87 C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~~~~~~~~~~~C~~c~~~ 140 (170)
|+..|.+ ...+.+.+..||..|..|..|...+.. ...|.. +|..||...+..
T Consensus 2 ~~~~~~~-~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~ 54 (235)
T KOG0490|consen 2 CGRQILD-RYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQR 54 (235)
T ss_pred CCccccc-hHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchh
Confidence 5556644 234556689999999999999999942 334554 999999999987
No 28
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=85.01 E-value=0.97 Score=27.03 Aligned_cols=46 Identities=20% Similarity=0.379 Sum_probs=24.1
Q ss_pred ccccccccccccCCCee-EEeCCccccccceecccccccccccccccccCCc
Q psy7479 45 LKCGCCDCRLGEVGSTL-YQKANLILCKRDYLRLFGTTGYCAACTKVIPAFE 95 (170)
Q Consensus 45 f~C~~C~~~l~~~~~~~-~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~ 95 (170)
++|+.|...|. ..+ ...=..+||..|....++. .|+.|+.|....|
T Consensus 8 LrCs~C~~~l~---~pv~l~~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD 54 (65)
T PF14835_consen 8 LRCSICFDILK---EPVCLGGCEHIFCSSCIRDCIGS--ECPVCHTPAWIQD 54 (65)
T ss_dssp TS-SSS-S--S---S-B---SSS--B-TTTGGGGTTT--B-SSS--B-S-SS
T ss_pred cCCcHHHHHhc---CCceeccCccHHHHHHhHHhcCC--CCCCcCChHHHHH
Confidence 58888988886 233 3555688999999988887 8999998886544
No 29
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=84.05 E-value=0.65 Score=26.03 Aligned_cols=44 Identities=18% Similarity=0.392 Sum_probs=29.9
Q ss_pred cccccccccccCCCeeEEeCCcc-ccccceeccccccccccccccccc
Q psy7479 46 KCGCCDCRLGEVGSTLYQKANLI-LCKRDYLRLFGTTGYCAACTKVIP 92 (170)
Q Consensus 46 ~C~~C~~~l~~~~~~~~~~~~~~-yC~~c~~~~~~~~~~C~~C~~~i~ 92 (170)
.|..|..... ...+..=|.. +|..|..+......+|..|..+|.
T Consensus 4 ~C~iC~~~~~---~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 4 ECPICFENPR---DVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp B-TTTSSSBS---SEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred CCccCCccCC---ceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 4666666653 3456677777 999999877533348999999884
No 30
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=83.89 E-value=1.6 Score=28.61 Aligned_cols=34 Identities=15% Similarity=0.328 Sum_probs=23.7
Q ss_pred cccccCCcccccCCeEEEeCCeeccHHhHHHHhh
Q psy7479 110 FACQQCNHRFCVGDRFYLCDNKILCEYDYEERQV 143 (170)
Q Consensus 110 f~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~ 143 (170)
++|..|+.++-.|+.|.+..+.+.--.||.....
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~~ 36 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREKAS 36 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHHHh
Confidence 3577777777677777777667777777766543
No 31
>PF12773 DZR: Double zinc ribbon
Probab=82.06 E-value=1.2 Score=24.94 Aligned_cols=9 Identities=22% Similarity=0.597 Sum_probs=4.2
Q ss_pred ccccccccc
Q psy7479 83 YCAACTKVI 91 (170)
Q Consensus 83 ~C~~C~~~i 91 (170)
.|..|+..+
T Consensus 31 ~C~~Cg~~~ 39 (50)
T PF12773_consen 31 ICPNCGAEN 39 (50)
T ss_pred CCcCCcCCC
Confidence 355555443
No 32
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=81.57 E-value=1.1 Score=24.34 Aligned_cols=22 Identities=27% Similarity=0.531 Sum_probs=15.3
Q ss_pred cccccccccccCCCeeEEeCCccccccc
Q psy7479 46 KCGCCDCRLGEVGSTLYQKANLILCKRD 73 (170)
Q Consensus 46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c 73 (170)
.|..|+.+| +..++|+.||..|
T Consensus 19 ~Cp~C~~PL------~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPL------MRDKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCee------EEecCCCEECCCC
Confidence 466777776 3357888888765
No 33
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=81.50 E-value=3.2 Score=25.25 Aligned_cols=59 Identities=19% Similarity=0.450 Sum_probs=28.4
Q ss_pred cccccccccccCCCeeEEeCCccccccceecccccccccccccccccCCceEEecCCcccccCccccccCCcccc
Q psy7479 46 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFC 120 (170)
Q Consensus 46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 120 (170)
.|..|+.+|. ..++..+|..|...... .+.|+.|+.++ .++.|-|.. =|.|..|+..++
T Consensus 3 ~CP~C~~~L~-------~~~~~~~C~~C~~~~~~-~a~CPdC~~~L----e~LkACGAv----dYFC~~c~gLiS 61 (70)
T PF07191_consen 3 TCPKCQQELE-------WQGGHYHCEACQKDYKK-EAFCPDCGQPL----EVLKACGAV----DYFCNHCHGLIS 61 (70)
T ss_dssp B-SSS-SBEE-------EETTEEEETTT--EEEE-EEE-TTT-SB-----EEEEETTEE----EEE-TTTT-EE-
T ss_pred cCCCCCCccE-------EeCCEEECcccccccee-cccCCCcccHH----HHHHHhccc----ceeeccCCceee
Confidence 4667777764 22356667777543221 23899999888 455555521 135778887774
No 34
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=80.92 E-value=1.3 Score=26.01 Aligned_cols=14 Identities=43% Similarity=0.899 Sum_probs=8.1
Q ss_pred cccccccccccccc
Q psy7479 17 LKECASCGKRITER 30 (170)
Q Consensus 17 ~~~C~~C~~~I~~~ 30 (170)
.+.|..|+..|.+.
T Consensus 7 ~~~CtSCg~~i~~~ 20 (59)
T PRK14890 7 PPKCTSCGIEIAPR 20 (59)
T ss_pred CccccCCCCcccCC
Confidence 34566666666544
No 35
>KOG0320|consensus
Probab=80.27 E-value=0.53 Score=33.99 Aligned_cols=53 Identities=23% Similarity=0.414 Sum_probs=38.4
Q ss_pred ccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccC
Q psy7479 40 WHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 93 (170)
Q Consensus 40 ~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~ 93 (170)
--..+++|..|=....+ ...+..+=|.+||..|.........+|..|++.|..
T Consensus 127 ~~~~~~~CPiCl~~~se-k~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 127 RKEGTYKCPICLDSVSE-KVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred ccccccCCCceecchhh-ccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 34567888888776652 123457889999999998765444489999998853
No 36
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=79.20 E-value=1.1 Score=23.51 Aligned_cols=25 Identities=24% Similarity=0.519 Sum_probs=17.2
Q ss_pred ccccccccccccCCCeeEEeCCcccccccee
Q psy7479 45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYL 75 (170)
Q Consensus 45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~ 75 (170)
+.|..|+.. .+...+|..||..|-.
T Consensus 9 ~~C~~C~~~------~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR------WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe------EeEccCCEEEhhhCce
Confidence 347777654 2677889999977643
No 37
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=78.48 E-value=1.3 Score=30.47 Aligned_cols=23 Identities=22% Similarity=0.475 Sum_probs=17.5
Q ss_pred cccccccccccCCCeeEEeCCcccccccee
Q psy7479 46 KCGCCDCRLGEVGSTLYQKANLILCKRDYL 75 (170)
Q Consensus 46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~ 75 (170)
.|..|+.+| | .++|.+||..|-.
T Consensus 30 hCp~Cg~PL------F-~KdG~v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTPL------F-RKDGEVFCPVCGY 52 (131)
T ss_pred hCcccCCcc------e-eeCCeEECCCCCc
Confidence 477788877 3 3999999988753
No 38
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=77.16 E-value=0.91 Score=29.69 Aligned_cols=31 Identities=29% Similarity=0.461 Sum_probs=23.2
Q ss_pred ccccccccccCCceEEecCCcccccCccccc
Q psy7479 83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQ 113 (170)
Q Consensus 83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~ 113 (170)
+|..|+++|..++..-...+..-|-.||.=.
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~ 34 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREK 34 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHH
Confidence 7999999998755554455677899998743
No 39
>KOG1813|consensus
Probab=76.32 E-value=1.4 Score=34.35 Aligned_cols=47 Identities=17% Similarity=0.335 Sum_probs=34.7
Q ss_pred CccccccccccccCCCeeEEeCCccccccceecccccccccccccccccC
Q psy7479 44 CLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 93 (170)
Q Consensus 44 Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~ 93 (170)
=|.|..|.+... ..+...-+..+|+.|..+.+...++|..|++.+.+
T Consensus 241 Pf~c~icr~~f~---~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 241 PFKCFICRKYFY---RPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred Cccccccccccc---cchhhcCCceeehhhhccccccCCcceeccccccc
Confidence 367777888775 44667778888999988766543489999988865
No 40
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=74.52 E-value=2 Score=23.33 Aligned_cols=40 Identities=20% Similarity=0.463 Sum_probs=23.9
Q ss_pred ccccccccccCCCeeEEeCCccccccceeccc--cccccccccc
Q psy7479 47 CGCCDCRLGEVGSTLYQKANLILCKRDYLRLF--GTTGYCAACT 88 (170)
Q Consensus 47 C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~--~~~~~C~~C~ 88 (170)
|..|...+.+....+...=|.++|..|..+.. .. .|..|+
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~--~CP~C~ 43 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSV--KCPICR 43 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCC--CCcCCC
Confidence 45555555322234456667778888877666 33 677665
No 41
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=73.88 E-value=1.7 Score=29.83 Aligned_cols=22 Identities=23% Similarity=0.596 Sum_probs=18.6
Q ss_pred cccCCcccccCCeEEEeCCeeccHHhHH
Q psy7479 112 CQQCNHRFCVGDRFYLCDNKILCEYDYE 139 (170)
Q Consensus 112 C~~C~~~l~~~~~~~~~~~~~~C~~c~~ 139 (170)
|..|+.+| |- ++|.+||..|-.
T Consensus 31 Cp~Cg~PL-----F~-KdG~v~CPvC~~ 52 (131)
T COG1645 31 CPKCGTPL-----FR-KDGEVFCPVCGY 52 (131)
T ss_pred CcccCCcc-----ee-eCCeEECCCCCc
Confidence 88899998 55 899999999973
No 42
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=72.13 E-value=2.1 Score=20.56 Aligned_cols=9 Identities=33% Similarity=1.062 Sum_probs=4.7
Q ss_pred ccccccccc
Q psy7479 83 YCAACTKVI 91 (170)
Q Consensus 83 ~C~~C~~~i 91 (170)
.|..|+..|
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 455555544
No 43
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=71.19 E-value=3.7 Score=23.77 Aligned_cols=45 Identities=18% Similarity=0.424 Sum_probs=29.2
Q ss_pred cccccccccccCC-CeeEEeCCccccccceeccccccccccccccccc
Q psy7479 46 KCGCCDCRLGEVG-STLYQKANLILCKRDYLRLFGTTGYCAACTKVIP 92 (170)
Q Consensus 46 ~C~~C~~~l~~~~-~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~ 92 (170)
.|..|++.|.... ..+.-.-.=.||.+|....+.. .|..|+..+.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~--~CPNCgGelv 52 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNG--VCPNCGGELV 52 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcC--cCcCCCCccc
Confidence 4566778776322 2333334456888888888665 8999987653
No 44
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=70.28 E-value=1.9 Score=25.31 Aligned_cols=11 Identities=45% Similarity=1.050 Sum_probs=6.3
Q ss_pred ccccccccccc
Q psy7479 17 LKECASCGKRI 27 (170)
Q Consensus 17 ~~~C~~C~~~I 27 (170)
.+.|..|+..|
T Consensus 9 ~~~CtSCg~~i 19 (61)
T COG2888 9 PPVCTSCGREI 19 (61)
T ss_pred CceeccCCCEe
Confidence 35566666655
No 45
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=70.09 E-value=6.7 Score=34.51 Aligned_cols=86 Identities=19% Similarity=0.354 Sum_probs=56.0
Q ss_pred CCCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCcccccccee-cccccccccccccccc
Q psy7479 13 ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYL-RLFGTTGYCAACTKVI 91 (170)
Q Consensus 13 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~-~~~~~~~~C~~C~~~i 91 (170)
......+|..|-+.|.+. .++.||--=-.|..||-.+. +-...+|=..... +.| +.|..|.+
T Consensus 97 I~pD~a~C~~Cl~Ei~dp-----~~rrY~YPF~~CT~CGPRfT-------Ii~alPYDR~nTsM~~F---~lC~~C~~-- 159 (750)
T COG0068 97 IPPDAATCEDCLEEIFDP-----NSRRYLYPFINCTNCGPRFT-------IIEALPYDRENTSMADF---PLCPFCDK-- 159 (750)
T ss_pred cCCchhhhHHHHHHhcCC-----CCcceeccccccCCCCccee-------eeccCCCCcccCccccC---cCCHHHHH--
Confidence 456778999999998876 35667766678999986653 2233333221111 112 26777765
Q ss_pred cCCceEEecCCcccccCccccccCCccc
Q psy7479 92 PAFEMVMRAKNNVYHLECFACQQCNHRF 119 (170)
Q Consensus 92 ~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 119 (170)
.+-...++.||..=..|..|+-.+
T Consensus 160 ----EY~dP~nRRfHAQp~aCp~CGP~~ 183 (750)
T COG0068 160 ----EYKDPLNRRFHAQPIACPKCGPHL 183 (750)
T ss_pred ----HhcCccccccccccccCcccCCCe
Confidence 233456888999888899998766
No 46
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=70.07 E-value=2.5 Score=26.28 Aligned_cols=16 Identities=31% Similarity=0.796 Sum_probs=12.1
Q ss_pred CCcccccccccccccc
Q psy7479 15 GGLKECASCGKRITER 30 (170)
Q Consensus 15 ~~~~~C~~C~~~I~~~ 30 (170)
++...|.+|++.|..+
T Consensus 5 s~Ra~Ck~C~~~I~kg 20 (82)
T PF00645_consen 5 SGRAKCKGCKKKIAKG 20 (82)
T ss_dssp SSTEBETTTSCBE-TT
T ss_pred CCCccCcccCCcCCCC
Confidence 4556899999999766
No 47
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=69.28 E-value=4.6 Score=22.19 Aligned_cols=12 Identities=25% Similarity=0.382 Sum_probs=8.4
Q ss_pred CeeccHHhHHHH
Q psy7479 130 NKILCEYDYEER 141 (170)
Q Consensus 130 ~~~~C~~c~~~~ 141 (170)
+--+|..||...
T Consensus 22 d~dLC~~Cf~~~ 33 (46)
T cd02249 22 DFDLCSSCYAKG 33 (46)
T ss_pred CCcCHHHHHCcC
Confidence 445799998754
No 48
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=68.92 E-value=0.63 Score=24.29 Aligned_cols=28 Identities=21% Similarity=0.474 Sum_probs=14.7
Q ss_pred cccCCcccccCCeEEEeCCeeccHHhHHH
Q psy7479 112 CQQCNHRFCVGDRFYLCDNKILCEYDYEE 140 (170)
Q Consensus 112 C~~C~~~l~~~~~~~~~~~~~~C~~c~~~ 140 (170)
|..|+.++ ...+.....+..+|..|...
T Consensus 6 C~~CGe~I-~~~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 6 CEDCGEPI-PEERLVAVPGATLCVECQER 33 (36)
T ss_dssp -TTTSSBE-EHHHHHHCTTECS-HHHHHH
T ss_pred ccccCChH-HHHHHHhCCCcEECHHHhCc
Confidence 66666666 33333445566677777654
No 49
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=67.01 E-value=1.6 Score=32.19 Aligned_cols=31 Identities=23% Similarity=0.519 Sum_probs=25.0
Q ss_pred cccccCCcccccCCeEEEeCCeeccHHhHHHH
Q psy7479 110 FACQQCNHRFCVGDRFYLCDNKILCEYDYEER 141 (170)
Q Consensus 110 f~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~ 141 (170)
-+|+.|+..+ ....-...+|+++|+.|+.+.
T Consensus 173 v~C~kCGE~~-~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELF-MEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCccc-ccchhhhcCCceecccccccc
Confidence 5799999998 455566689999999998753
No 50
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=66.70 E-value=3.6 Score=26.39 Aligned_cols=43 Identities=23% Similarity=0.472 Sum_probs=29.1
Q ss_pred cccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccC
Q psy7479 39 FWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 93 (170)
Q Consensus 39 ~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~ 93 (170)
.|-+.=-.|..|...+.+ .|.-||..|..+. +.|+-|++.|..
T Consensus 39 Py~~~~~~C~~CK~~v~q--------~g~~YCq~CAYkk----GiCamCGKki~d 81 (90)
T PF10235_consen 39 PYAPYSSKCKICKTKVHQ--------PGAKYCQTCAYKK----GICAMCGKKILD 81 (90)
T ss_pred cccccCcccccccccccc--------CCCccChhhhccc----CcccccCCeecc
Confidence 344433467788777742 2566999996553 389999999854
No 51
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=66.21 E-value=5.6 Score=21.64 Aligned_cols=11 Identities=18% Similarity=0.446 Sum_probs=7.8
Q ss_pred CeeccHHhHHH
Q psy7479 130 NKILCEYDYEE 140 (170)
Q Consensus 130 ~~~~C~~c~~~ 140 (170)
+.-+|..||.+
T Consensus 26 d~dlC~~Cf~~ 36 (44)
T smart00291 26 DYDLCQSCFAK 36 (44)
T ss_pred CccchHHHHhC
Confidence 34479999875
No 52
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=64.52 E-value=6.1 Score=34.62 Aligned_cols=12 Identities=17% Similarity=0.429 Sum_probs=6.7
Q ss_pred cccccccccccc
Q psy7479 19 ECASCGKRITER 30 (170)
Q Consensus 19 ~C~~C~~~I~~~ 30 (170)
+|..|+..+.++
T Consensus 3 ~Cp~Cg~~n~~~ 14 (645)
T PRK14559 3 ICPQCQFENPNN 14 (645)
T ss_pred cCCCCCCcCCCC
Confidence 466666655444
No 53
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=64.48 E-value=7.2 Score=25.17 Aligned_cols=29 Identities=14% Similarity=0.311 Sum_probs=13.9
Q ss_pred cccccCCcccccCCeEEEeCCeeccHHhH
Q psy7479 110 FACQQCNHRFCVGDRFYLCDNKILCEYDY 138 (170)
Q Consensus 110 f~C~~C~~~l~~~~~~~~~~~~~~C~~c~ 138 (170)
|+|..|+.++..|+.|.+....+.--.|+
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl 35 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECL 35 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHH
Confidence 34555555555555555443333333444
No 54
>PRK00420 hypothetical protein; Validated
Probab=64.11 E-value=4.4 Score=27.13 Aligned_cols=24 Identities=21% Similarity=0.418 Sum_probs=15.2
Q ss_pred ccccccccccccCCCeeEEeCCccccccce
Q psy7479 45 LKCGCCDCRLGEVGSTLYQKANLILCKRDY 74 (170)
Q Consensus 45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~ 74 (170)
-.|..|+.+| |-.++|+.||..|-
T Consensus 24 ~~CP~Cg~pL------f~lk~g~~~Cp~Cg 47 (112)
T PRK00420 24 KHCPVCGLPL------FELKDGEVVCPVHG 47 (112)
T ss_pred CCCCCCCCcc------eecCCCceECCCCC
Confidence 4577787766 33377777666553
No 55
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=63.99 E-value=12 Score=20.05 Aligned_cols=31 Identities=16% Similarity=0.285 Sum_probs=19.4
Q ss_pred ccccCCcccccCCeEEEeC-CeeccHHhHHHH
Q psy7479 111 ACQQCNHRFCVGDRFYLCD-NKILCEYDYEER 141 (170)
Q Consensus 111 ~C~~C~~~l~~~~~~~~~~-~~~~C~~c~~~~ 141 (170)
.|+.|+++.........-. +...|..|....
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~~ 34 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQA 34 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHHH
Confidence 5888999885555555443 778899998764
No 56
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=63.86 E-value=4.2 Score=19.32 Aligned_cols=11 Identities=55% Similarity=1.301 Sum_probs=4.9
Q ss_pred ccccccccccc
Q psy7479 20 CASCGKRITER 30 (170)
Q Consensus 20 C~~C~~~I~~~ 30 (170)
|..|+..|.+.
T Consensus 1 C~sC~~~i~~r 11 (24)
T PF07754_consen 1 CTSCGRPIAPR 11 (24)
T ss_pred CccCCCcccCc
Confidence 34444444443
No 57
>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=63.81 E-value=2.7 Score=29.66 Aligned_cols=54 Identities=15% Similarity=0.276 Sum_probs=36.4
Q ss_pred CccccccceecccccccccccccccccCCceE--EecCCcccccCccccccCCcccccCC
Q psy7479 66 NLILCKRDYLRLFGTTGYCAACTKVIPAFEMV--MRAKNNVYHLECFACQQCNHRFCVGD 123 (170)
Q Consensus 66 ~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~~~--~~~~~~~~H~~Cf~C~~C~~~l~~~~ 123 (170)
..-||..|-.+... .|..|+.+|.|...+ +...+..|+. =--|..||++++...
T Consensus 27 ~~~fC~kCG~~tI~---~Cp~C~~~IrG~y~v~gv~~~g~~~~~-PsYC~~CGkpyPWt~ 82 (158)
T PF10083_consen 27 REKFCSKCGAKTIT---SCPNCSTPIRGDYHVEGVFGLGGHYEA-PSYCHNCGKPYPWTE 82 (158)
T ss_pred HHHHHHHhhHHHHH---HCcCCCCCCCCceecCCeeeeCCCCCC-ChhHHhCCCCCchHH
Confidence 35689999888776 799999999874211 1233455552 234889999986543
No 58
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=62.77 E-value=4.1 Score=19.00 Aligned_cols=8 Identities=38% Similarity=0.982 Sum_probs=3.2
Q ss_pred cccccccc
Q psy7479 84 CAACTKVI 91 (170)
Q Consensus 84 C~~C~~~i 91 (170)
|..|+..|
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 33444433
No 59
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=62.57 E-value=6.6 Score=22.59 Aligned_cols=26 Identities=15% Similarity=0.336 Sum_probs=17.4
Q ss_pred ccccccccccccceeEEeCCcccccc
Q psy7479 18 KECASCGKRITERFLLKALDLFWHED 43 (170)
Q Consensus 18 ~~C~~C~~~I~~~~~~~~~~~~~H~~ 43 (170)
.+|..|+.+|....++...+..-|+.
T Consensus 2 ~~CvVCKqpi~~a~~v~T~~G~VH~g 27 (54)
T PF10886_consen 2 EICVVCKQPIDDALVVETESGPVHPG 27 (54)
T ss_pred CeeeeeCCccCcceEEEcCCCccCcH
Confidence 46888888887765555555566654
No 60
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=61.43 E-value=1.8 Score=31.92 Aligned_cols=48 Identities=19% Similarity=0.376 Sum_probs=34.2
Q ss_pred cCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccC
Q psy7479 43 DCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 93 (170)
Q Consensus 43 ~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~ 93 (170)
.=|.|..|.+... +.+...-|.-+|..|+.+.+...+.|..|++...+
T Consensus 195 IPF~C~iCKkdy~---spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G 242 (259)
T COG5152 195 IPFLCGICKKDYE---SPVVTECGHSFCSLCAIRKYQKGDECGVCGKATYG 242 (259)
T ss_pred Cceeehhchhhcc---chhhhhcchhHHHHHHHHHhccCCcceecchhhcc
Confidence 3478888887764 45666777888888887765433478888887765
No 61
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=61.41 E-value=10 Score=20.78 Aligned_cols=11 Identities=27% Similarity=0.483 Sum_probs=7.9
Q ss_pred CeeccHHhHHH
Q psy7479 130 NKILCEYDYEE 140 (170)
Q Consensus 130 ~~~~C~~c~~~ 140 (170)
+.-+|..||.+
T Consensus 27 d~dLC~~C~~~ 37 (46)
T PF00569_consen 27 DYDLCEDCFSK 37 (46)
T ss_dssp S-EEEHHHHHH
T ss_pred CCchhhHHHhC
Confidence 34489999986
No 62
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=60.88 E-value=3.1 Score=21.87 Aligned_cols=38 Identities=18% Similarity=0.431 Sum_probs=20.0
Q ss_pred ccccccccccCCCe-eEEeCCccccccceecccccccccccc
Q psy7479 47 CGCCDCRLGEVGST-LYQKANLILCKRDYLRLFGTTGYCAAC 87 (170)
Q Consensus 47 C~~C~~~l~~~~~~-~~~~~~~~yC~~c~~~~~~~~~~C~~C 87 (170)
|..|...+. .. ....=|..||.+|..+......+|..|
T Consensus 1 C~iC~~~~~---~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELR---DPVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-S---SEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCccc---CcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 344555553 23 456677788888876554332255443
No 63
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=59.74 E-value=4 Score=30.21 Aligned_cols=31 Identities=16% Similarity=0.215 Sum_probs=24.9
Q ss_pred ccccccccccccCCCeeEEeCCccccccceecc
Q psy7479 45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77 (170)
Q Consensus 45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~ 77 (170)
-+|+.|+..+.+ ......+|+++|..||.+.
T Consensus 173 v~C~kCGE~~~e--~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFME--PRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCccccc--chhhhcCCceecccccccc
Confidence 689999998863 3456789999999998754
No 64
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=59.66 E-value=23 Score=18.84 Aligned_cols=33 Identities=15% Similarity=0.230 Sum_probs=20.3
Q ss_pred cccCCcccccCCeEEEeC-CeeccHHhHHHHhhh
Q psy7479 112 CQQCNHRFCVGDRFYLCD-NKILCEYDYEERQVF 144 (170)
Q Consensus 112 C~~C~~~l~~~~~~~~~~-~~~~C~~c~~~~~~~ 144 (170)
|..|...+..++...... +..|+..|..+.+..
T Consensus 3 C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~ 36 (44)
T PF13639_consen 3 CPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKR 36 (44)
T ss_dssp ETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHH
T ss_pred CcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHh
Confidence 566666664445555444 777788887765433
No 65
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=57.51 E-value=8.2 Score=22.60 Aligned_cols=26 Identities=15% Similarity=0.359 Sum_probs=14.0
Q ss_pred cccccccccccCCCeeEEeCCccccc
Q psy7479 46 KCGCCDCRLGEVGSTLYQKANLILCK 71 (170)
Q Consensus 46 ~C~~C~~~l~~~~~~~~~~~~~~yC~ 71 (170)
.|..|++.|......|..+..+.+|.
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS 43 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCS 43 (58)
T ss_pred HHHccCCCCCCCCCeeeecccccccc
Confidence 35556667763333344555666664
No 66
>KOG2462|consensus
Probab=56.94 E-value=2.6 Score=32.62 Aligned_cols=40 Identities=20% Similarity=0.367 Sum_probs=22.2
Q ss_pred CCCcccccccccccccceeEEeCCcccc-----ccCcccccccccc
Q psy7479 14 SGGLKECASCGKRITERFLLKALDLFWH-----EDCLKCGCCDCRL 54 (170)
Q Consensus 14 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H-----~~Cf~C~~C~~~l 54 (170)
....-+|..|++......-+ ..-+.+| +.=|.|..|++.-
T Consensus 127 ~~~r~~c~eCgk~ysT~snL-srHkQ~H~~~~s~ka~~C~~C~K~Y 171 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNL-SRHKQTHRSLDSKKAFSCKYCGKVY 171 (279)
T ss_pred cCCceecccccccccccccc-chhhcccccccccccccCCCCCcee
Confidence 44556788888876543111 1122233 4557888887764
No 67
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=56.79 E-value=9.6 Score=21.32 Aligned_cols=11 Identities=18% Similarity=0.042 Sum_probs=8.0
Q ss_pred eeccHHhHHHH
Q psy7479 131 KILCEYDYEER 141 (170)
Q Consensus 131 ~~~C~~c~~~~ 141 (170)
--+|..||...
T Consensus 26 ~DlC~~C~~~~ 36 (48)
T cd02341 26 FDLCQDCVVKG 36 (48)
T ss_pred CccCHHHHhCc
Confidence 34799998764
No 68
>KOG3579|consensus
Probab=56.44 E-value=12 Score=29.18 Aligned_cols=51 Identities=14% Similarity=0.381 Sum_probs=34.9
Q ss_pred CCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCcccccc
Q psy7479 15 GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKR 72 (170)
Q Consensus 15 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~ 72 (170)
...-.|.-|++.+.+...+.--.-.-|+-||-|+. ..|.. +...|.+||..
T Consensus 266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSR--esIK~-----Qg~sgevYCPS 316 (352)
T KOG3579|consen 266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSR--ESIKQ-----QGASGEVYCPS 316 (352)
T ss_pred CCceeehhhhhhhccCceeecCCCcccceecccCH--HHHHh-----hcCCCceeCCC
Confidence 34456889999999886677777788999998752 33321 23456788864
No 69
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=56.06 E-value=12 Score=20.89 Aligned_cols=12 Identities=17% Similarity=0.174 Sum_probs=8.4
Q ss_pred CeeccHHhHHHH
Q psy7479 130 NKILCEYDYEER 141 (170)
Q Consensus 130 ~~~~C~~c~~~~ 141 (170)
+--+|..||...
T Consensus 23 d~dLC~~Cf~~g 34 (49)
T cd02335 23 DFDLCLECFSAG 34 (49)
T ss_pred CcchhHHhhhCc
Confidence 344799998754
No 70
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=54.96 E-value=6.9 Score=20.29 Aligned_cols=26 Identities=12% Similarity=0.429 Sum_probs=12.2
Q ss_pred CCccccccceeccccc-cccccccccc
Q psy7479 65 ANLILCKRDYLRLFGT-TGYCAACTKV 90 (170)
Q Consensus 65 ~~~~yC~~c~~~~~~~-~~~C~~C~~~ 90 (170)
=|..||..|..+.+.. ..+|..|+..
T Consensus 18 C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 18 CGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 3445555555433211 1257766654
No 71
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=54.27 E-value=13 Score=20.45 Aligned_cols=30 Identities=23% Similarity=0.409 Sum_probs=19.3
Q ss_pred ccccCCcccccCCeEEEe--CCeeccHHhHHHH
Q psy7479 111 ACQQCNHRFCVGDRFYLC--DNKILCEYDYEER 141 (170)
Q Consensus 111 ~C~~C~~~l~~~~~~~~~--~~~~~C~~c~~~~ 141 (170)
.|..|+..+ ...+|.-. .+..+|..||.+-
T Consensus 2 ~C~~Cg~D~-t~vryh~~~~~~~dLC~~CF~~G 33 (45)
T cd02336 2 HCFTCGNDC-TRVRYHNLKAKKYDLCPSCYQEG 33 (45)
T ss_pred cccCCCCcc-CceEEEecCCCccccChHHHhCc
Confidence 477777777 34444432 2567899999753
No 72
>KOG2462|consensus
Probab=51.66 E-value=7 Score=30.32 Aligned_cols=15 Identities=20% Similarity=0.383 Sum_probs=12.0
Q ss_pred cccCccccccccccc
Q psy7479 41 HEDCLKCGCCDCRLG 55 (170)
Q Consensus 41 H~~Cf~C~~C~~~l~ 55 (170)
-...++|..|++.+.
T Consensus 127 ~~~r~~c~eCgk~ys 141 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYS 141 (279)
T ss_pred cCCceeccccccccc
Confidence 345679999999986
No 73
>PF10170 C6_DPF: Cysteine-rich domain; InterPro: IPR018785 This entry represents the N-terminal approximately 100 amino acids of a family of proteins found in a range of organisms, including human, chicken and Drosophila [, , ]. It contains between six and eight highly conserved cysteine residues and a characteristic DPF sequence motif. One member is putatively named as receptor for egg jelly protein but this could not confirmed.
Probab=51.57 E-value=39 Score=22.00 Aligned_cols=31 Identities=26% Similarity=0.518 Sum_probs=23.7
Q ss_pred ccccCCcccccCCeEEEeCCeeccHHhHHHH
Q psy7479 111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEER 141 (170)
Q Consensus 111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~ 141 (170)
.|+.|+++.=.+....+.-.+-+|..|..+.
T Consensus 51 ~CS~C~~~VC~~~~CSlFYtkrFC~pC~~~~ 81 (97)
T PF10170_consen 51 PCSICGKPVCVGQDCSLFYTKRFCLPCVKRN 81 (97)
T ss_pred cccccCCceEcCCCccEEeeCceeHHHHHHH
Confidence 4899999875666666666677999998754
No 74
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=50.23 E-value=11 Score=27.82 Aligned_cols=47 Identities=11% Similarity=0.287 Sum_probs=28.6
Q ss_pred CccccccccccccCCCeeEEeCCccccccceeccc----------------ccccccccccccccC
Q psy7479 44 CLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLF----------------GTTGYCAACTKVIPA 93 (170)
Q Consensus 44 Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~----------------~~~~~C~~C~~~i~~ 93 (170)
-|.|..|...+. ......=|..||..|..+.. ....+|..|...|..
T Consensus 18 ~~~CpICld~~~---dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 18 DFDCNICLDQVR---DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred ccCCccCCCcCC---CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 366777766654 23455667777777764321 011379999988865
No 75
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=49.91 E-value=11 Score=20.05 Aligned_cols=30 Identities=17% Similarity=0.476 Sum_probs=12.2
Q ss_pred ccccccccccccceeEEeCCccccccCcccccccc
Q psy7479 18 KECASCGKRITERFLLKALDLFWHEDCLKCGCCDC 52 (170)
Q Consensus 18 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~ 52 (170)
..|..|+--|..--.+...++.| +|..|+.
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w-----~C~~C~~ 32 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTW-----ICNFCGT 32 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEE-----EETTT--
T ss_pred cccCCCCCEECCcceEcCCCCEE-----ECcCCCC
Confidence 45666666665543344444554 5666654
No 76
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=49.70 E-value=4.7 Score=26.24 Aligned_cols=29 Identities=17% Similarity=0.228 Sum_probs=17.6
Q ss_pred ccccccCCcccccCCeEEEeCCeeccHHh
Q psy7479 109 CFACQQCNHRFCVGDRFYLCDNKILCEYD 137 (170)
Q Consensus 109 Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c 137 (170)
=|+|+.|--.--.++--...+|+++|..|
T Consensus 70 EFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 70 EFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred ceeeeeeeeEechhhhccccCCCEecccc
Confidence 37788776543112212345799999887
No 77
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=49.38 E-value=26 Score=19.43 Aligned_cols=29 Identities=17% Similarity=0.261 Sum_probs=18.9
Q ss_pred ccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479 111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ 142 (170)
Q Consensus 111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~ 142 (170)
.|..|+++. .+. ....|..+|..|..+++
T Consensus 1 ~CiiC~~~~--~~G-I~I~~~fIC~~CE~~iv 29 (46)
T PF10764_consen 1 KCIICGKEK--EEG-IHIYGKFICSDCEKEIV 29 (46)
T ss_pred CeEeCCCcC--CCC-EEEECeEehHHHHHHhc
Confidence 366777776 222 33567888999977764
No 78
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=48.85 E-value=17 Score=19.74 Aligned_cols=9 Identities=33% Similarity=0.324 Sum_probs=6.2
Q ss_pred eccHHhHHH
Q psy7479 132 ILCEYDYEE 140 (170)
Q Consensus 132 ~~C~~c~~~ 140 (170)
-+|..||..
T Consensus 24 dLC~~C~~~ 32 (43)
T cd02340 24 DLCESCEAK 32 (43)
T ss_pred cchHHhhCc
Confidence 378888764
No 79
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=48.55 E-value=17 Score=20.26 Aligned_cols=12 Identities=25% Similarity=0.432 Sum_probs=8.6
Q ss_pred CeeccHHhHHHH
Q psy7479 130 NKILCEYDYEER 141 (170)
Q Consensus 130 ~~~~C~~c~~~~ 141 (170)
+--+|..||...
T Consensus 23 d~dlC~~Cf~~~ 34 (49)
T cd02338 23 DYDLCADCYDSG 34 (49)
T ss_pred CCccchhHHhCC
Confidence 344899999854
No 80
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=48.39 E-value=7.2 Score=24.46 Aligned_cols=28 Identities=29% Similarity=0.691 Sum_probs=16.0
Q ss_pred cccCCcccccCCeEEE-eC---CeeccHHhHH
Q psy7479 112 CQQCNHRFCVGDRFYL-CD---NKILCEYDYE 139 (170)
Q Consensus 112 C~~C~~~l~~~~~~~~-~~---~~~~C~~c~~ 139 (170)
|..|+.||.....+.. .| +.-||..||.
T Consensus 3 CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~ 34 (81)
T PF12674_consen 3 CQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQ 34 (81)
T ss_pred CCcCcCccCCccccccccCCCCchhHHHHHhc
Confidence 6777777743332222 12 4568888885
No 81
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=48.06 E-value=6.2 Score=20.57 Aligned_cols=10 Identities=20% Similarity=0.594 Sum_probs=4.9
Q ss_pred cccccccccc
Q psy7479 83 YCAACTKVIP 92 (170)
Q Consensus 83 ~C~~C~~~i~ 92 (170)
.|..|+....
T Consensus 4 ~Cp~C~~~y~ 13 (36)
T PF13717_consen 4 TCPNCQAKYE 13 (36)
T ss_pred ECCCCCCEEe
Confidence 4555555443
No 82
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=47.38 E-value=4.3 Score=25.93 Aligned_cols=16 Identities=44% Similarity=0.949 Sum_probs=12.5
Q ss_pred eecccccccccccccccc
Q psy7479 74 YLRLFGTTGYCAACTKVI 91 (170)
Q Consensus 74 ~~~~~~~~~~C~~C~~~i 91 (170)
|..+|.. .|.+|++.+
T Consensus 49 Y~~lfs~--pC~~C~klL 64 (90)
T PF11571_consen 49 YRNLFST--PCKKCGKLL 64 (90)
T ss_pred Hhhhccc--hhhHHHhHh
Confidence 4556776 899999988
No 83
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=46.57 E-value=9.8 Score=18.69 Aligned_cols=10 Identities=30% Similarity=0.677 Sum_probs=4.8
Q ss_pred cccccccccc
Q psy7479 83 YCAACTKVIP 92 (170)
Q Consensus 83 ~C~~C~~~i~ 92 (170)
+|.+|+..|.
T Consensus 3 ~C~rC~~~~~ 12 (30)
T PF06827_consen 3 KCPRCWNYIE 12 (30)
T ss_dssp B-TTT--BBE
T ss_pred cCccCCCcce
Confidence 6777777763
No 84
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=46.18 E-value=8.9 Score=19.96 Aligned_cols=32 Identities=22% Similarity=0.473 Sum_probs=19.0
Q ss_pred cccccccccccceeEEeCCccccccCccccccccccc
Q psy7479 19 ECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLG 55 (170)
Q Consensus 19 ~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 55 (170)
+|..|.+.+.+. .++.||..=..|..||-.+.
T Consensus 1 lC~~C~~Ey~~p-----~~RR~~~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 1 LCDDCLKEYFDP-----SNRRFHYQFISCTNCGPRYS 32 (35)
T ss_dssp --HHHHHHHCST-----TSTTTT-TT--BTTCC-SCC
T ss_pred CCHHHHHHHcCC-----CCCcccCcCccCCCCCCCEE
Confidence 366676665544 47889999999999987763
No 85
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=46.13 E-value=8.6 Score=21.98 Aligned_cols=28 Identities=25% Similarity=0.394 Sum_probs=13.7
Q ss_pred ccccCCcccccCCeEEEeCCeecc-HHhHH
Q psy7479 111 ACQQCNHRFCVGDRFYLCDNKILC-EYDYE 139 (170)
Q Consensus 111 ~C~~C~~~l~~~~~~~~~~~~~~C-~~c~~ 139 (170)
.|..|...++. ..-+.+||+.|| ..|..
T Consensus 9 aC~~C~C~V~~-~~Ai~~dGk~YCS~aCA~ 37 (52)
T PF02069_consen 9 ACPSCSCVVSE-EEAIQKDGKYYCSEACAN 37 (52)
T ss_dssp SSTT----B-T-TTSEESSS-EESSHHHHH
T ss_pred cCCCCEeEECc-hHhHHhCCEeeecHHHhc
Confidence 36777777733 445558888887 44543
No 86
>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=46.02 E-value=6.3 Score=20.51 Aligned_cols=10 Identities=30% Similarity=1.032 Sum_probs=6.1
Q ss_pred cccccCCccc
Q psy7479 110 FACQQCNHRF 119 (170)
Q Consensus 110 f~C~~C~~~l 119 (170)
++|..|+..|
T Consensus 26 v~C~~C~~~~ 35 (38)
T TIGR02098 26 VRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEE
Confidence 4566666655
No 87
>KOG0978|consensus
Probab=44.54 E-value=3 Score=36.51 Aligned_cols=48 Identities=23% Similarity=0.540 Sum_probs=29.2
Q ss_pred ccccccccccccCCCeeEEeCCccccccceeccccc-ccccccccccccCCc
Q psy7479 45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGT-TGYCAACTKVIPAFE 95 (170)
Q Consensus 45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~-~~~C~~C~~~i~~~~ 95 (170)
++|+.|+..-. ......=+.+||..|...++.. +.+|+.|+.++.++|
T Consensus 644 LkCs~Cn~R~K---d~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD 692 (698)
T KOG0978|consen 644 LKCSVCNTRWK---DAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAND 692 (698)
T ss_pred eeCCCccCchh---hHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence 46777764432 2234555677777776655432 127888888886644
No 88
>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=44.53 E-value=5.7 Score=21.42 Aligned_cols=9 Identities=22% Similarity=0.733 Sum_probs=4.4
Q ss_pred ccccccccc
Q psy7479 83 YCAACTKVI 91 (170)
Q Consensus 83 ~C~~C~~~i 91 (170)
+|..|+..+
T Consensus 7 ~C~~Cg~~f 15 (42)
T PF09723_consen 7 RCEECGHEF 15 (42)
T ss_pred EeCCCCCEE
Confidence 455555443
No 89
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=43.44 E-value=23 Score=19.36 Aligned_cols=29 Identities=21% Similarity=0.513 Sum_probs=15.1
Q ss_pred cccCCc-ccccCCeEEEe--CCeeccHHhHHHH
Q psy7479 112 CQQCNH-RFCVGDRFYLC--DNKILCEYDYEER 141 (170)
Q Consensus 112 C~~C~~-~l~~~~~~~~~--~~~~~C~~c~~~~ 141 (170)
|..|+. +| .|.+|.-. .+.-+|..||.+.
T Consensus 3 CDgCg~~PI-~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 3 CDGCGVLPI-TGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCcc-cccceEeCCCCCCccHHHHhhhh
Confidence 444553 33 44444432 2344788888764
No 90
>KOG3002|consensus
Probab=43.37 E-value=14 Score=29.12 Aligned_cols=43 Identities=19% Similarity=0.364 Sum_probs=33.1
Q ss_pred ccccccccccccCCCeeEEeCCccccccceeccccccccccccccccc
Q psy7479 45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIP 92 (170)
Q Consensus 45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~ 92 (170)
+-|..|...|. ...++=.+|.+.|..|-.++.. +|..|..+|.
T Consensus 49 leCPvC~~~l~--~Pi~QC~nGHlaCssC~~~~~~---~CP~Cr~~~g 91 (299)
T KOG3002|consen 49 LDCPVCFNPLS--PPIFQCDNGHLACSSCRTKVSN---KCPTCRLPIG 91 (299)
T ss_pred ccCchhhccCc--ccceecCCCcEehhhhhhhhcc---cCCccccccc
Confidence 56777777875 2346677899999999876665 8999999885
No 91
>PRK14873 primosome assembly protein PriA; Provisional
Probab=42.31 E-value=17 Score=32.06 Aligned_cols=58 Identities=14% Similarity=0.040 Sum_probs=30.6
Q ss_pred eeEEeCCccccccCccccccccccc----cCCCeeEEeCCccccccceeccccccccccccccc
Q psy7479 31 FLLKALDLFWHEDCLKCGCCDCRLG----EVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKV 90 (170)
Q Consensus 31 ~~~~~~~~~~H~~Cf~C~~C~~~l~----~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~ 90 (170)
.++...++.-...=+.|..|+..+. +....|...++.+.|.-|-...... .|..|+..
T Consensus 370 qvll~lnRrGyap~l~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~--~Cp~Cgs~ 431 (665)
T PRK14873 370 PVLVQVPRRGYVPSLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAAPDW--RCPRCGSD 431 (665)
T ss_pred cEEEEecCCCCCCeeEhhhCcCeeECCCCCCceeEecCCCeeECCCCcCCCcCc--cCCCCcCC
Confidence 4444444433333344444444442 1111233445678899996655443 89999874
No 92
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.41 E-value=9.6 Score=31.34 Aligned_cols=12 Identities=17% Similarity=0.385 Sum_probs=6.0
Q ss_pred cccccccccccc
Q psy7479 17 LKECASCGKRIT 28 (170)
Q Consensus 17 ~~~C~~C~~~I~ 28 (170)
.-.|..|...+.
T Consensus 26 ~l~C~IC~d~~~ 37 (397)
T TIGR00599 26 SLRCHICKDFFD 37 (397)
T ss_pred ccCCCcCchhhh
Confidence 345555555443
No 93
>KOG0320|consensus
Probab=41.25 E-value=21 Score=25.97 Aligned_cols=47 Identities=9% Similarity=0.067 Sum_probs=33.9
Q ss_pred cCccccccCCcccccCCeEEEeCCeeccHHhHHHHhhhccccCCCCc
Q psy7479 107 LECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANIAYNPSS 153 (170)
Q Consensus 107 ~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~~~~~ 153 (170)
..+|+|..|=........+...=|.++|+.|....+.....++.+..
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~k 175 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRK 175 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCccc
Confidence 35788888877763333355566999999999988777777776544
No 94
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.94 E-value=20 Score=21.98 Aligned_cols=44 Identities=18% Similarity=0.367 Sum_probs=26.7
Q ss_pred ccccccccccC-CCeeEEeCCccccccceeccccccccccccccccc
Q psy7479 47 CGCCDCRLGEV-GSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIP 92 (170)
Q Consensus 47 C~~C~~~l~~~-~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~ 92 (170)
|.-|++-|... +....-.-.-.||.+|...++.. .|..|+..+.
T Consensus 8 CECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~g--~CPnCGGelv 52 (84)
T COG3813 8 CECCDRDLPPDSTDARICTFECTFCADCAENRLHG--LCPNCGGELV 52 (84)
T ss_pred CcccCCCCCCCCCceeEEEEeeehhHhHHHHhhcC--cCCCCCchhh
Confidence 45577777521 11122222345788888877776 8999987553
No 95
>KOG2932|consensus
Probab=40.94 E-value=11 Score=29.91 Aligned_cols=43 Identities=16% Similarity=0.346 Sum_probs=25.6
Q ss_pred cccccccccccCCCeeEEeCCccccccceeccccccccccccccccc
Q psy7479 46 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIP 92 (170)
Q Consensus 46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~ 92 (170)
-|..|+.+|.-.+ -.+.=+.+||.+|....-.. .|..|...|.
T Consensus 92 fCd~Cd~PI~IYG--RmIPCkHvFCl~CAr~~~dK--~Cp~C~d~Vq 134 (389)
T KOG2932|consen 92 FCDRCDFPIAIYG--RMIPCKHVFCLECARSDSDK--ICPLCDDRVQ 134 (389)
T ss_pred eecccCCcceeee--cccccchhhhhhhhhcCccc--cCcCcccHHH
Confidence 4677777775222 12445566777776544433 7888877663
No 96
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=39.30 E-value=11 Score=19.70 Aligned_cols=9 Identities=22% Similarity=0.748 Sum_probs=4.7
Q ss_pred ccccccccc
Q psy7479 83 YCAACTKVI 91 (170)
Q Consensus 83 ~C~~C~~~i 91 (170)
.|..|+...
T Consensus 4 ~CP~C~~~f 12 (37)
T PF13719_consen 4 TCPNCQTRF 12 (37)
T ss_pred ECCCCCceE
Confidence 455555544
No 97
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=39.27 E-value=23 Score=18.08 Aligned_cols=23 Identities=17% Similarity=0.297 Sum_probs=12.2
Q ss_pred cccccccccccCCCeeEEeCCccccccc
Q psy7479 46 KCGCCDCRLGEVGSTLYQKANLILCKRD 73 (170)
Q Consensus 46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c 73 (170)
+|..|+..+- +...++..+|..|
T Consensus 5 ~C~~C~~~~i-----~~~~~~~~~C~~C 27 (33)
T PF08792_consen 5 KCSKCGGNGI-----VNKEDDYEVCIFC 27 (33)
T ss_pred EcCCCCCCeE-----EEecCCeEEcccC
Confidence 4555655441 3355566666555
No 98
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=38.94 E-value=5.6 Score=22.57 Aligned_cols=9 Identities=33% Similarity=1.080 Sum_probs=4.6
Q ss_pred ccccccccc
Q psy7479 83 YCAACTKVI 91 (170)
Q Consensus 83 ~C~~C~~~i 91 (170)
+|..|++.+
T Consensus 6 RC~~CnklL 14 (51)
T PF10122_consen 6 RCGHCNKLL 14 (51)
T ss_pred eccchhHHH
Confidence 455555544
No 99
>KOG4443|consensus
Probab=38.57 E-value=14 Score=32.23 Aligned_cols=44 Identities=25% Similarity=0.479 Sum_probs=27.2
Q ss_pred ccccccceecccccccccccccccccCCceEEecCCcccccCccccccCCcccc
Q psy7479 67 LILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFC 120 (170)
Q Consensus 67 ~~yC~~c~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 120 (170)
-++|+.|-..+.. .|.+|. ++.+ ..+..+.++|+.|..|+..+.
T Consensus 83 f~~Ck~cDvsyh~------yc~~P~--~~~v--~sg~~~ckk~~~c~qc~~~lp 126 (694)
T KOG4443|consen 83 FLLCKRCDVSYHC------YCQKPP--NDKV--PSGPWLCKKCTRCRQCDSTLP 126 (694)
T ss_pred ccccccccccccc------cccCCc--cccc--cCcccccHHHHhhhhcccccc
Confidence 4567776544322 244444 2222 346778889999999999883
No 100
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=38.01 E-value=16 Score=17.92 Aligned_cols=9 Identities=22% Similarity=0.896 Sum_probs=2.0
Q ss_pred ccccCCccc
Q psy7479 111 ACQQCNHRF 119 (170)
Q Consensus 111 ~C~~C~~~l 119 (170)
.|..|++++
T Consensus 2 ~C~~C~~~~ 10 (30)
T PF07649_consen 2 RCDACGKPI 10 (30)
T ss_dssp --TTTS---
T ss_pred cCCcCCCcC
Confidence 344444444
No 101
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=37.54 E-value=23 Score=31.56 Aligned_cols=40 Identities=20% Similarity=0.338 Sum_probs=26.4
Q ss_pred ccccccccccccCCCeeEEeCCccccccceeccccccccccccccc
Q psy7479 45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKV 90 (170)
Q Consensus 45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~ 90 (170)
++|..|+..|. +....+.+.|..|-.+.--+ ..|..|+..
T Consensus 445 ~~Cp~Cd~~lt-----~H~~~~~L~CH~Cg~~~~~p-~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLT-----LHKATGQLRCHYCGYQEPIP-QSCPECGSE 484 (730)
T ss_pred ccCCCCCcceE-----EecCCCeeEeCCCCCCCCCC-CCCCCCCCC
Confidence 34555555553 55667889999997664333 289999875
No 102
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=37.54 E-value=18 Score=20.16 Aligned_cols=15 Identities=33% Similarity=0.499 Sum_probs=10.1
Q ss_pred CCccccccccccccc
Q psy7479 15 GGLKECASCGKRITE 29 (170)
Q Consensus 15 ~~~~~C~~C~~~I~~ 29 (170)
.....|..|++.|.+
T Consensus 9 ~~~~~C~~C~~~i~g 23 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWG 23 (53)
T ss_dssp SSTEB-TTSSSBECS
T ss_pred CCCCCCcccCcccCC
Confidence 455679999998843
No 103
>PF11077 DUF2616: Protein of unknown function (DUF2616); InterPro: IPR020201 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf52; it is a family of uncharacterised viral proteins.
Probab=36.85 E-value=26 Score=25.39 Aligned_cols=34 Identities=26% Similarity=0.477 Sum_probs=22.7
Q ss_pred cccccccccccCCCe-eEEeCCccccccceecccc
Q psy7479 46 KCGCCDCRLGEVGST-LYQKANLILCKRDYLRLFG 79 (170)
Q Consensus 46 ~C~~C~~~l~~~~~~-~~~~~~~~yC~~c~~~~~~ 79 (170)
+|-.|+......+.. ++..+..++|..|...+|.
T Consensus 138 kC~QC~~~~~~~~~~~~~~F~~~lFC~~ClFPLF~ 172 (173)
T PF11077_consen 138 KCVQCSQKCENVGAKIFTYFNFNLFCKNCLFPLFD 172 (173)
T ss_pred ccCcCCCCcccccceeEEecChhhcccccCccccc
Confidence 344455554433455 7788899999999877663
No 104
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=36.46 E-value=29 Score=19.36 Aligned_cols=10 Identities=30% Similarity=0.388 Sum_probs=7.5
Q ss_pred eccHHhHHHH
Q psy7479 132 ILCEYDYEER 141 (170)
Q Consensus 132 ~~C~~c~~~~ 141 (170)
-+|..||...
T Consensus 25 dLC~~Cf~~~ 34 (49)
T cd02345 25 SLCLGCYTKG 34 (49)
T ss_pred CchHHHHhCC
Confidence 3799998754
No 105
>KOG1734|consensus
Probab=36.43 E-value=10 Score=29.48 Aligned_cols=17 Identities=29% Similarity=0.509 Sum_probs=11.0
Q ss_pred CCCcccccccccccccc
Q psy7479 14 SGGLKECASCGKRITER 30 (170)
Q Consensus 14 ~~~~~~C~~C~~~I~~~ 30 (170)
.....+|+.|++.|...
T Consensus 221 hl~d~vCaVCg~~~~~s 237 (328)
T KOG1734|consen 221 HLSDSVCAVCGQQIDVS 237 (328)
T ss_pred CCCcchhHhhcchheee
Confidence 34456788888777543
No 106
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=36.19 E-value=37 Score=30.26 Aligned_cols=86 Identities=17% Similarity=0.433 Sum_probs=52.6
Q ss_pred CCCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccce-ecccccccccccccccc
Q psy7479 13 ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY-LRLFGTTGYCAACTKVI 91 (170)
Q Consensus 13 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~-~~~~~~~~~C~~C~~~i 91 (170)
.+....+|..|-+.|.+. .++.|+--=..|..||-.+. +....+|=.... ...|. .|..|.+..
T Consensus 64 ippD~a~C~~Cl~E~~dp-----~~Rry~YpF~nCt~CGPr~~-------i~~~lpydr~~t~m~~f~---~C~~C~~ey 128 (711)
T TIGR00143 64 IPADVATCSDCLEEMLDK-----NDRRYLYPFISCTHCGPRFT-------IIEALPYDRENTSMADFP---LCPDCAKEY 128 (711)
T ss_pred cCCchhhHHHHHHHhcCC-----CcccccCCcccccCCCCCeE-------EeecCCCCCCCcCCCCCc---CCHHHHHHh
Confidence 355778899999988765 25667666678889986653 222222211100 11122 677776544
Q ss_pred cCCceEEecCCcccccCccccccCCccc
Q psy7479 92 PAFEMVMRAKNNVYHLECFACQQCNHRF 119 (170)
Q Consensus 92 ~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 119 (170)
-...++.||-.=-.|..|+-.|
T Consensus 129 ------~~p~~rr~h~~~~~C~~Cgp~l 150 (711)
T TIGR00143 129 ------KDPLDRRFHAQPIACPRCGPQL 150 (711)
T ss_pred ------cCCccccCCCCCccCCCCCcEE
Confidence 2335677888777888888776
No 107
>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=35.76 E-value=16 Score=16.30 Aligned_cols=10 Identities=30% Similarity=1.112 Sum_probs=7.8
Q ss_pred cccccCCccc
Q psy7479 110 FACQQCNHRF 119 (170)
Q Consensus 110 f~C~~C~~~l 119 (170)
|.|..|++.+
T Consensus 1 y~C~~C~~~f 10 (23)
T PF00096_consen 1 YKCPICGKSF 10 (23)
T ss_dssp EEETTTTEEE
T ss_pred CCCCCCCCcc
Confidence 5688888877
No 108
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=34.82 E-value=27 Score=19.59 Aligned_cols=28 Identities=18% Similarity=0.377 Sum_probs=21.0
Q ss_pred cccccccccccccc--eeEEeCCccccccC
Q psy7479 17 LKECASCGKRITER--FLLKALDLFWHEDC 44 (170)
Q Consensus 17 ~~~C~~C~~~I~~~--~~~~~~~~~~H~~C 44 (170)
...|+.|+....+. ..+.+.+..|+..|
T Consensus 13 Y~~Cp~CGN~~vGngEG~liV~edtfkRtC 42 (49)
T PF12677_consen 13 YCKCPKCGNDKVGNGEGTLIVEEDTFKRTC 42 (49)
T ss_pred hccCcccCCcEeecCcceEEEeccceeeee
Confidence 46799999876543 45778888898877
No 109
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.79 E-value=47 Score=28.27 Aligned_cols=29 Identities=14% Similarity=0.142 Sum_probs=20.1
Q ss_pred eEEeCCccccccceeccccccccccccccc
Q psy7479 61 LYQKANLILCKRDYLRLFGTTGYCAACTKV 90 (170)
Q Consensus 61 ~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~ 90 (170)
|...++.+.|..|-...-.+ ..|..|+..
T Consensus 234 ~h~~~~~l~Ch~Cg~~~~~~-~~Cp~C~s~ 262 (505)
T TIGR00595 234 YHKKEGKLRCHYCGYQEPIP-KTCPQCGSE 262 (505)
T ss_pred EecCCCeEEcCCCcCcCCCC-CCCCCCCCC
Confidence 55567788899996554322 289999863
No 110
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=34.69 E-value=28 Score=21.66 Aligned_cols=13 Identities=23% Similarity=0.304 Sum_probs=5.7
Q ss_pred CeeccHHhHHHHh
Q psy7479 130 NKILCEYDYEERQ 142 (170)
Q Consensus 130 ~~~~C~~c~~~~~ 142 (170)
+-|.|+.||+-..
T Consensus 35 ~fPvCr~CyEYEr 47 (80)
T PF14569_consen 35 AFPVCRPCYEYER 47 (80)
T ss_dssp -----HHHHHHHH
T ss_pred CCccchhHHHHHh
Confidence 4557999997443
No 111
>KOG4739|consensus
Probab=34.69 E-value=43 Score=25.45 Aligned_cols=31 Identities=16% Similarity=0.330 Sum_probs=24.4
Q ss_pred eEEeCCccccccceecccccccccccccccccC
Q psy7479 61 LYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 93 (170)
Q Consensus 61 ~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~ 93 (170)
|..-=..++|..|.....+. .|.-|++.|..
T Consensus 19 ~LTaC~HvfC~~C~k~~~~~--~C~lCkk~ir~ 49 (233)
T KOG4739|consen 19 FLTACRHVFCEPCLKASSPD--VCPLCKKSIRI 49 (233)
T ss_pred eeeechhhhhhhhcccCCcc--ccccccceeee
Confidence 44556788999998888876 89999998744
No 112
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=34.12 E-value=34 Score=30.15 Aligned_cols=15 Identities=20% Similarity=0.643 Sum_probs=9.2
Q ss_pred CCCCccccccccccc
Q psy7479 13 ASGGLKECASCGKRI 27 (170)
Q Consensus 13 ~~~~~~~C~~C~~~I 27 (170)
...+...|..|+.++
T Consensus 11 n~~~akFC~~CG~~l 25 (645)
T PRK14559 11 NPNNNRFCQKCGTSL 25 (645)
T ss_pred CCCCCccccccCCCC
Confidence 345566677776665
No 113
>KOG2893|consensus
Probab=33.84 E-value=15 Score=28.09 Aligned_cols=36 Identities=19% Similarity=0.640 Sum_probs=17.7
Q ss_pred ccccccccccCCceEEecCCcccccCccccccCCcccccC
Q psy7479 83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVG 122 (170)
Q Consensus 83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~ 122 (170)
-|..|+..+.. |.++.-..+ ..+|+|..|++.|-.|
T Consensus 12 wcwycnrefdd-ekiliqhqk---akhfkchichkkl~sg 47 (341)
T KOG2893|consen 12 WCWYCNREFDD-EKILIQHQK---AKHFKCHICHKKLFSG 47 (341)
T ss_pred eeeecccccch-hhhhhhhhh---hccceeeeehhhhccC
Confidence 46666665532 222221112 2457777777776333
No 114
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=33.24 E-value=43 Score=20.10 Aligned_cols=28 Identities=25% Similarity=0.540 Sum_probs=16.4
Q ss_pred ccccCCcccccCCe--EEEeCCeec--c-HHhH
Q psy7479 111 ACQQCNHRFCVGDR--FYLCDNKIL--C-EYDY 138 (170)
Q Consensus 111 ~C~~C~~~l~~~~~--~~~~~~~~~--C-~~c~ 138 (170)
+|+.|+..|..|.. |+..||.++ | ..|.
T Consensus 5 ~CsFcG~~I~PGtG~m~Vr~Dg~v~~FcssKc~ 37 (66)
T COG2075 5 VCSFCGKKIEPGTGIMYVRNDGKVLRFCSSKCE 37 (66)
T ss_pred EecCcCCccCCCceEEEEecCCeEEEEechhHH
Confidence 47778888755543 333567654 5 4443
No 115
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=33.03 E-value=16 Score=20.50 Aligned_cols=22 Identities=23% Similarity=0.709 Sum_probs=10.0
Q ss_pred ccccceecccc-ccccccccccc
Q psy7479 69 LCKRDYLRLFG-TTGYCAACTKV 90 (170)
Q Consensus 69 yC~~c~~~~~~-~~~~C~~C~~~ 90 (170)
.|..||.+... ..++|.+|.++
T Consensus 24 IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 24 ICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp --HHHHHHHTTSS-SB-TTT--B
T ss_pred HHHHHHHHHHhccCCCCCCCCCC
Confidence 57777765442 23488888765
No 116
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=32.42 E-value=19 Score=20.52 Aligned_cols=29 Identities=24% Similarity=0.494 Sum_probs=15.2
Q ss_pred ccccccccccCCceEEecCCcccccCcccc
Q psy7479 83 YCAACTKVIPAFEMVMRAKNNVYHLECFAC 112 (170)
Q Consensus 83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C 112 (170)
.|+.|+..|.. ..-.+..++.|-.+|-.|
T Consensus 2 ~CPyCge~~~~-~iD~s~~~Q~yiEDC~vC 30 (52)
T PF14255_consen 2 QCPYCGEPIEI-LIDPSAGDQEYIEDCQVC 30 (52)
T ss_pred CCCCCCCeeEE-EEecCCCCeeEEeehhhc
Confidence 46667766632 112234455666666554
No 117
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=32.20 E-value=28 Score=21.02 Aligned_cols=48 Identities=8% Similarity=0.048 Sum_probs=30.3
Q ss_pred cCccccccccccccCCCeeEEeCCccccccceeccccc-ccccccccccccC
Q psy7479 43 DCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGT-TGYCAACTKVIPA 93 (170)
Q Consensus 43 ~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~-~~~C~~C~~~i~~ 93 (170)
+=|.|..++..+. ......+|..|...+..+.+.. .+.|..++.++..
T Consensus 3 ~~f~CpIt~~lM~---dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 3 DEFLCPITGELMR---DPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGGB-TTTSSB-S---SEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred cccCCcCcCcHhh---CceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 4478888888875 5677888899988876554432 2378888888755
No 118
>PF15451 DUF4632: Domain of unknown function (DUF4632)
Probab=32.10 E-value=20 Score=21.06 Aligned_cols=19 Identities=26% Similarity=0.394 Sum_probs=14.9
Q ss_pred CchHHhhhhcceeeecccC
Q psy7479 152 SSLAHLRRQVTLQVLWIRE 170 (170)
Q Consensus 152 ~~~~~~~~~~~~~~~~~~~ 170 (170)
.+.+..++.|.+.|||-+|
T Consensus 44 ~parrwrrplpsnvlycpe 62 (71)
T PF15451_consen 44 APARRWRRPLPSNVLYCPE 62 (71)
T ss_pred hHHHHhccCCCccceechh
Confidence 3467788899999998664
No 119
>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=31.89 E-value=11 Score=26.74 Aligned_cols=31 Identities=19% Similarity=0.282 Sum_probs=20.9
Q ss_pred cccccccccccccceeEEeCCccccccCccccccccccc
Q psy7479 17 LKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLG 55 (170)
Q Consensus 17 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 55 (170)
.=+|..|+....-.+++. .=|.|..||..|.
T Consensus 109 ~Y~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAME--------LNFTCPRCGAMLD 139 (158)
T ss_pred eEECCCCCcEeeHHHHHH--------cCCcCCCCCCEee
Confidence 346888887665554332 1388999998885
No 120
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=31.84 E-value=38 Score=19.28 Aligned_cols=26 Identities=19% Similarity=0.341 Sum_probs=15.8
Q ss_pred ccccccccccccceeEEeCCcccccc
Q psy7479 18 KECASCGKRITERFLLKALDLFWHED 43 (170)
Q Consensus 18 ~~C~~C~~~I~~~~~~~~~~~~~H~~ 43 (170)
.+|..|+.||...-.+.-....-|+.
T Consensus 2 ~iCvvCK~Pi~~al~v~T~~Gpvh~g 27 (53)
T PHA02610 2 KICVVCKQPIEKALVVETEKGPVHPG 27 (53)
T ss_pred ceeeeeCCchhhceEEecCCCCCCCh
Confidence 46888888886664444444455543
No 121
>PHA02768 hypothetical protein; Provisional
Probab=31.17 E-value=17 Score=21.06 Aligned_cols=43 Identities=12% Similarity=0.167 Sum_probs=21.4
Q ss_pred ccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEE
Q psy7479 83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYL 127 (170)
Q Consensus 83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~ 127 (170)
.|..|++...-.. .+ ..-..-|..=++|..|++.+.....+.+
T Consensus 7 ~C~~CGK~Fs~~~-~L-~~H~r~H~k~~kc~~C~k~f~~~s~l~~ 49 (55)
T PHA02768 7 ECPICGEIYIKRK-SM-ITHLRKHNTNLKLSNCKRISLRTGEYIE 49 (55)
T ss_pred CcchhCCeeccHH-HH-HHHHHhcCCcccCCcccceecccceeEE
Confidence 5666666553311 11 1122235556677777777644444443
No 122
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=30.73 E-value=12 Score=26.12 Aligned_cols=36 Identities=22% Similarity=0.453 Sum_probs=19.2
Q ss_pred cccccccccccccceeEEeCCccccccCccccccccccc
Q psy7479 17 LKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLG 55 (170)
Q Consensus 17 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 55 (170)
.=.|+.|+.......++...+. ..=|.|..|+..|.
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~~d~---~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQLLDM---DGTFTCPRCGEELE 134 (147)
T ss_pred EEECcCCCCEeeHHHHHHhcCC---CCcEECCCCCCEEE
Confidence 3457777766654432222221 23377777777764
No 123
>PRK00807 50S ribosomal protein L24e; Validated
Probab=30.35 E-value=34 Score=19.42 Aligned_cols=10 Identities=50% Similarity=1.175 Sum_probs=6.4
Q ss_pred cccccccccc
Q psy7479 19 ECASCGKRIT 28 (170)
Q Consensus 19 ~C~~C~~~I~ 28 (170)
.|..|+..|.
T Consensus 3 ~C~fcG~~I~ 12 (52)
T PRK00807 3 TCSFCGKEIE 12 (52)
T ss_pred ccCCCCCeEc
Confidence 4666666665
No 124
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=29.68 E-value=15 Score=26.64 Aligned_cols=31 Identities=23% Similarity=0.403 Sum_probs=20.4
Q ss_pred cccccccccccccceeEEeCCccccccCccccccccccc
Q psy7479 17 LKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLG 55 (170)
Q Consensus 17 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 55 (170)
.=+|..|+....-.+++ + .=|.|..||..|.
T Consensus 117 ~Y~Cp~C~~rytf~eA~---~-----~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAM---E-----YGFRCPQCGEMLE 147 (178)
T ss_pred EEECCCCCcEEeHHHHh---h-----cCCcCCCCCCCCe
Confidence 44688888766554332 2 2488888988885
No 125
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.22 E-value=27 Score=27.73 Aligned_cols=29 Identities=24% Similarity=0.474 Sum_probs=17.0
Q ss_pred CCccccccceeccccc-ccccccccccccC
Q psy7479 65 ANLILCKRDYLRLFGT-TGYCAACTKVIPA 93 (170)
Q Consensus 65 ~~~~yC~~c~~~~~~~-~~~C~~C~~~i~~ 93 (170)
=|..+|..|..+.+.. .+.|..|+.++..
T Consensus 26 CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 26 CGHTLCESCVDLLFVRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence 4556677776654421 1267778777644
No 126
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=28.46 E-value=37 Score=22.27 Aligned_cols=26 Identities=19% Similarity=0.461 Sum_probs=20.2
Q ss_pred ccccCCcccccCCeEEEeCCeeccHHhHHHH
Q psy7479 111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEER 141 (170)
Q Consensus 111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~ 141 (170)
.|..| .+..|+..++.+.|..|-.+.
T Consensus 37 aCeiC-----~~~GY~q~g~~lvC~~C~~~~ 62 (102)
T PF10080_consen 37 ACEIC-----GPKGYYQEGDQLVCKNCGVRF 62 (102)
T ss_pred ecccc-----CCCceEEECCEEEEecCCCEE
Confidence 58888 345799999999999996543
No 127
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=27.41 E-value=78 Score=30.20 Aligned_cols=54 Identities=17% Similarity=0.306 Sum_probs=33.8
Q ss_pred CccccccccccccCCCeeEEeCCccccccceecccccccccccccccccCCceEEecCCcccccCccccccCCcccc
Q psy7479 44 CLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFC 120 (170)
Q Consensus 44 Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 120 (170)
-++|..|+.... ..+|..|-...-.. ..|..|+..+..++.. . -.|..|+.++.
T Consensus 667 ~rkCPkCG~~t~-----------~~fCP~CGs~te~v-y~CPsCGaev~~des~-----a------~~CP~CGtplv 720 (1337)
T PRK14714 667 RRRCPSCGTETY-----------ENRCPDCGTHTEPV-YVCPDCGAEVPPDESG-----R------VECPRCDVELT 720 (1337)
T ss_pred EEECCCCCCccc-----------cccCcccCCcCCCc-eeCccCCCccCCCccc-----c------ccCCCCCCccc
Confidence 478888887642 11788886654322 2799999877653211 1 13888898883
No 128
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=27.12 E-value=20 Score=28.20 Aligned_cols=44 Identities=27% Similarity=0.651 Sum_probs=28.6
Q ss_pred ccccccccccccCCCeeEEeCCccccccceecccccccccccccccc
Q psy7479 45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVI 91 (170)
Q Consensus 45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i 91 (170)
++|..|...|. -.+...=|.-||.-|..+..+.++.|..|....
T Consensus 26 lrC~IC~~~i~---ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~ 69 (391)
T COG5432 26 LRCRICDCRIS---IPCETTCGHTFCSLCIRRHLGTQPFCPVCREDP 69 (391)
T ss_pred HHhhhhhheee---cceecccccchhHHHHHHHhcCCCCCccccccH
Confidence 45666666664 234455566777777777777667888887644
No 129
>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=26.84 E-value=28 Score=15.14 Aligned_cols=10 Identities=40% Similarity=1.182 Sum_probs=5.8
Q ss_pred cccccCCccc
Q psy7479 110 FACQQCNHRF 119 (170)
Q Consensus 110 f~C~~C~~~l 119 (170)
|.|..|+..+
T Consensus 1 ~~C~~C~~~~ 10 (24)
T PF13894_consen 1 FQCPICGKSF 10 (24)
T ss_dssp EE-SSTS-EE
T ss_pred CCCcCCCCcC
Confidence 5677787776
No 130
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=26.72 E-value=56 Score=17.78 Aligned_cols=27 Identities=19% Similarity=0.710 Sum_probs=12.1
Q ss_pred ccccccccccceeEEeC--CccccccCcc
Q psy7479 20 CASCGKRITERFLLKAL--DLFWHEDCLK 46 (170)
Q Consensus 20 C~~C~~~I~~~~~~~~~--~~~~H~~Cf~ 46 (170)
|..|++.-.++.+|.-. ++.||..|..
T Consensus 2 C~vC~~~~~~~~~i~C~~C~~~~H~~C~~ 30 (51)
T PF00628_consen 2 CPVCGQSDDDGDMIQCDSCNRWYHQECVG 30 (51)
T ss_dssp BTTTTSSCTTSSEEEBSTTSCEEETTTST
T ss_pred CcCCCCcCCCCCeEEcCCCChhhCcccCC
Confidence 55555533333333222 3456666643
No 131
>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=25.82 E-value=22 Score=19.77 Aligned_cols=9 Identities=33% Similarity=0.840 Sum_probs=4.6
Q ss_pred ccccccccc
Q psy7479 83 YCAACTKVI 91 (170)
Q Consensus 83 ~C~~C~~~i 91 (170)
+|..|+..+
T Consensus 7 ~C~~Cg~~f 15 (52)
T TIGR02605 7 RCTACGHRF 15 (52)
T ss_pred EeCCCCCEe
Confidence 455555433
No 132
>PRK04023 DNA polymerase II large subunit; Validated
Probab=25.82 E-value=60 Score=30.18 Aligned_cols=37 Identities=16% Similarity=0.391 Sum_probs=19.0
Q ss_pred ccccccccccccCCCeeEEeCCccccccceecccccccccccccccccC
Q psy7479 45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 93 (170)
Q Consensus 45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~ 93 (170)
|+|..|+..-. ...+|..|-...... .|..|+..+.+
T Consensus 639 frCP~CG~~Te----------~i~fCP~CG~~~~~y--~CPKCG~El~~ 675 (1121)
T PRK04023 639 RRCPFCGTHTE----------PVYRCPRCGIEVEED--ECEKCGREPTP 675 (1121)
T ss_pred ccCCCCCCCCC----------cceeCccccCcCCCC--cCCCCCCCCCc
Confidence 56666766521 122466664433333 56666665544
No 133
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=25.65 E-value=28 Score=18.96 Aligned_cols=27 Identities=26% Similarity=0.524 Sum_probs=16.0
Q ss_pred ccccccccccCCceEEecCCcccccCccccccCCccc
Q psy7479 83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRF 119 (170)
Q Consensus 83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 119 (170)
+|..|+..+...+.. . -++|..|+.++
T Consensus 5 ~C~~CG~~~~~~~~~-----~-----~~~Cp~CG~~~ 31 (46)
T PRK00398 5 KCARCGREVELDEYG-----T-----GVRCPYCGYRI 31 (46)
T ss_pred ECCCCCCEEEECCCC-----C-----ceECCCCCCeE
Confidence 688888766331111 1 25688887766
No 134
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=25.41 E-value=57 Score=22.65 Aligned_cols=24 Identities=25% Similarity=0.663 Sum_probs=19.0
Q ss_pred cccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479 110 FACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ 142 (170)
Q Consensus 110 f~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~ 142 (170)
+.|..||.++..|. ||..|...+.
T Consensus 82 ~~CE~CG~~I~~Gr---------~C~~C~~~l~ 105 (137)
T TIGR03826 82 YPCERCGTSIREGR---------LCDSCAGELK 105 (137)
T ss_pred CcccccCCcCCCCC---------ccHHHHHHHH
Confidence 56999999995553 8999987664
No 135
>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=25.39 E-value=19 Score=18.73 Aligned_cols=9 Identities=22% Similarity=0.792 Sum_probs=5.3
Q ss_pred ccccccccc
Q psy7479 83 YCAACTKVI 91 (170)
Q Consensus 83 ~C~~C~~~i 91 (170)
+|..|+..+
T Consensus 7 ~C~~Cg~~f 15 (41)
T smart00834 7 RCEDCGHTF 15 (41)
T ss_pred EcCCCCCEE
Confidence 566666544
No 136
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=25.02 E-value=30 Score=18.89 Aligned_cols=9 Identities=22% Similarity=0.730 Sum_probs=4.3
Q ss_pred ccccccccc
Q psy7479 83 YCAACTKVI 91 (170)
Q Consensus 83 ~C~~C~~~i 91 (170)
+|..|+..+
T Consensus 4 ~C~~Cg~~~ 12 (44)
T smart00659 4 ICGECGREN 12 (44)
T ss_pred ECCCCCCEe
Confidence 455555443
No 137
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=24.72 E-value=6.8 Score=25.36 Aligned_cols=50 Identities=12% Similarity=0.355 Sum_probs=30.0
Q ss_pred ccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeecc
Q psy7479 83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILC 134 (170)
Q Consensus 83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C 134 (170)
.|..|...+.. .......-..+++.+..|..|.+.| .-.+|.....=++|
T Consensus 37 aCy~CHdel~~-Hpf~p~~~~~~~~~~iiCGvC~~~L-T~~EY~~~~~Cp~C 86 (105)
T COG4357 37 ACYHCHDELED-HPFEPWGLQEFNPKAIICGVCRKLL-TRAEYGMCGSCPYC 86 (105)
T ss_pred hHHHHHhHHhc-CCCccCChhhcCCccEEhhhhhhhh-hHHHHhhcCCCCCc
Confidence 46667666643 2233444466788888888888877 44555555544444
No 138
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=24.63 E-value=53 Score=18.06 Aligned_cols=11 Identities=18% Similarity=0.419 Sum_probs=7.9
Q ss_pred CeeccHHhHHH
Q psy7479 130 NKILCEYDYEE 140 (170)
Q Consensus 130 ~~~~C~~c~~~ 140 (170)
+.-+|..||..
T Consensus 23 dyDLC~~Cf~~ 33 (45)
T cd02344 23 DFDFCENCFKT 33 (45)
T ss_pred CccchHHhhCC
Confidence 34479999875
No 139
>PRK12495 hypothetical protein; Provisional
Probab=24.53 E-value=28 Score=26.18 Aligned_cols=10 Identities=30% Similarity=0.610 Sum_probs=6.1
Q ss_pred cccccccccc
Q psy7479 83 YCAACTKVIP 92 (170)
Q Consensus 83 ~C~~C~~~i~ 92 (170)
.|..|+.||.
T Consensus 44 hC~~CG~PIp 53 (226)
T PRK12495 44 HCDECGDPIF 53 (226)
T ss_pred hcccccCccc
Confidence 4666666663
No 140
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=24.33 E-value=53 Score=24.81 Aligned_cols=25 Identities=28% Similarity=0.465 Sum_probs=14.3
Q ss_pred ccccccccccCCCeeEEeCCccccccceecccc
Q psy7479 47 CGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 79 (170)
Q Consensus 47 C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~ 79 (170)
|..||.+... . . .-+|.+||.+.+.
T Consensus 1 C~~CG~~~~~-~-----~--~~lC~~C~~~~~~ 25 (236)
T PF04981_consen 1 CPRCGREIEP-L-----I--DGLCPDCYLKRFD 25 (236)
T ss_pred CCCCCCCCCC-c-----c--cccChHHhcccCC
Confidence 5567776541 0 1 1268888876654
No 141
>PRK11595 DNA utilization protein GntX; Provisional
Probab=24.03 E-value=45 Score=24.98 Aligned_cols=23 Identities=17% Similarity=0.273 Sum_probs=11.0
Q ss_pred ccccceecccccccccccccccc
Q psy7479 69 LCKRDYLRLFGTTGYCAACTKVI 91 (170)
Q Consensus 69 yC~~c~~~~~~~~~~C~~C~~~i 91 (170)
+|..|........+.|..|++++
T Consensus 22 lC~~C~~~l~~~~~~C~~Cg~~~ 44 (227)
T PRK11595 22 ICSVCSRALRTLKTCCPQCGLPA 44 (227)
T ss_pred ccHHHHhhCCcccCcCccCCCcC
Confidence 46655443211112577776554
No 142
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=23.87 E-value=44 Score=25.58 Aligned_cols=28 Identities=18% Similarity=0.267 Sum_probs=21.8
Q ss_pred cccccCCcccccCCeEEEeCCeeccHHhH
Q psy7479 110 FACQQCNHRFCVGDRFYLCDNKILCEYDY 138 (170)
Q Consensus 110 f~C~~C~~~l~~~~~~~~~~~~~~C~~c~ 138 (170)
-.|..|+.+. ....|+...+...|..|+
T Consensus 155 ~~Ca~cg~~~-~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 155 TSCARCGTPV-DPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred HHHhCcCCcC-CCcceeeccCcccchhcc
Confidence 4688888887 445677788888888886
No 143
>PRK13796 GTPase YqeH; Provisional
Probab=23.72 E-value=38 Score=27.40 Aligned_cols=10 Identities=10% Similarity=0.630 Sum_probs=6.7
Q ss_pred CeeccHHhHH
Q psy7479 130 NKILCEYDYE 139 (170)
Q Consensus 130 ~~~~C~~c~~ 139 (170)
+.++|..||.
T Consensus 33 ~~~~C~RC~~ 42 (365)
T PRK13796 33 EEVYCQRCFR 42 (365)
T ss_pred CCeEchhhhh
Confidence 4567777774
No 144
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=23.50 E-value=45 Score=15.42 Aligned_cols=6 Identities=50% Similarity=1.104 Sum_probs=2.8
Q ss_pred cccccc
Q psy7479 83 YCAACT 88 (170)
Q Consensus 83 ~C~~C~ 88 (170)
.|..|+
T Consensus 18 ~C~~C~ 23 (26)
T smart00547 18 KCFACG 23 (26)
T ss_pred cccccC
Confidence 444444
No 145
>PHA02929 N1R/p28-like protein; Provisional
Probab=23.10 E-value=60 Score=24.79 Aligned_cols=28 Identities=14% Similarity=0.250 Sum_probs=16.8
Q ss_pred CccccccceecccccccccccccccccC
Q psy7479 66 NLILCKRDYLRLFGTTGYCAACTKVIPA 93 (170)
Q Consensus 66 ~~~yC~~c~~~~~~~~~~C~~C~~~i~~ 93 (170)
+..||..|..+-....+.|+.|..++..
T Consensus 201 ~H~FC~~CI~~Wl~~~~tCPlCR~~~~~ 228 (238)
T PHA02929 201 NHVFCIECIDIWKKEKNTCPVCRTPFIS 228 (238)
T ss_pred CCcccHHHHHHHHhcCCCCCCCCCEeeE
Confidence 4566666664433333378888877753
No 146
>KOG3476|consensus
Probab=23.07 E-value=9 Score=24.27 Aligned_cols=37 Identities=27% Similarity=0.521 Sum_probs=25.7
Q ss_pred ccccccccccccCCCeeEEeCCccccccceecccccccccccccccccC
Q psy7479 45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 93 (170)
Q Consensus 45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~ 93 (170)
-+|..|...+.+ .|.-||..|..+. +.|+-|++.|..
T Consensus 55 ~kC~iCk~~vHQ--------~GshYC~tCAY~K----giCAMCGKki~n 91 (100)
T KOG3476|consen 55 AKCRICKQLVHQ--------PGSHYCQTCAYKK----GICAMCGKKILN 91 (100)
T ss_pred chhHHHHHHhcC--------CcchhHhHhhhhh----hHHHHhhhHhhc
Confidence 466677666542 3566899986543 389999999865
No 147
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=22.64 E-value=82 Score=17.60 Aligned_cols=11 Identities=18% Similarity=0.202 Sum_probs=8.2
Q ss_pred eeccHHhHHHH
Q psy7479 131 KILCEYDYEER 141 (170)
Q Consensus 131 ~~~C~~c~~~~ 141 (170)
.-+|..||...
T Consensus 24 ~DLC~~Cf~~g 34 (49)
T cd02334 24 YDLCQSCFFSG 34 (49)
T ss_pred cCchHHHHhCC
Confidence 34899999764
No 148
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=22.61 E-value=19 Score=19.50 Aligned_cols=11 Identities=27% Similarity=0.851 Sum_probs=4.2
Q ss_pred ccccccccccc
Q psy7479 20 CASCGKRITER 30 (170)
Q Consensus 20 C~~C~~~I~~~ 30 (170)
|..|++.+.-+
T Consensus 1 C~~C~~iv~~G 11 (43)
T PF08746_consen 1 CEACKEIVTQG 11 (43)
T ss_dssp -TTT-SB-SSS
T ss_pred CcccchhHeee
Confidence 44555555544
No 149
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=22.55 E-value=48 Score=25.87 Aligned_cols=25 Identities=20% Similarity=0.557 Sum_probs=16.9
Q ss_pred ccccccccccCCceEEecCCcccccCc
Q psy7479 83 YCAACTKVIPAFEMVMRAKNNVYHLEC 109 (170)
Q Consensus 83 ~C~~C~~~i~~~~~~~~~~~~~~H~~C 109 (170)
-|..|+.+|. ...+.-++..|.+.|
T Consensus 247 pC~~CGt~I~--k~~~~gR~t~~CP~C 271 (273)
T COG0266 247 PCRRCGTPIE--KIKLGGRSTFYCPVC 271 (273)
T ss_pred CCCccCCEeE--EEEEcCCcCEeCCCC
Confidence 6999999993 245555566665554
No 150
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=22.39 E-value=97 Score=22.27 Aligned_cols=36 Identities=11% Similarity=0.115 Sum_probs=20.6
Q ss_pred cccCCcccccCCeEEEeCC--eeccHHhHHHHhhhccccCC
Q psy7479 112 CQQCNHRFCVGDRFYLCDN--KILCEYDYEERQVFANIAYN 150 (170)
Q Consensus 112 C~~C~~~l~~~~~~~~~~~--~~~C~~c~~~~~~~~~~~~~ 150 (170)
|..|++.+..+ .-...+| .-.|..|+ +|.......+
T Consensus 6 CEiCG~~i~~~-~~v~vegsel~VC~~Ca--k~G~~~~~~~ 43 (165)
T COG1813 6 CELCGREIDKP-IKVKVEGAELTVCDDCA--KFGTAAKTAS 43 (165)
T ss_pred eeccccccCCC-eeEEeecceeehhHHHH--HhccCccccC
Confidence 89999998422 2222343 34599998 5443333333
No 151
>PRK05580 primosome assembly protein PriA; Validated
Probab=22.07 E-value=1.1e+02 Score=27.15 Aligned_cols=58 Identities=17% Similarity=0.195 Sum_probs=31.3
Q ss_pred eeEEeCCccccccCccccccccccc----cCCCeeEEeCCccccccceecc-ccccccccccccc
Q psy7479 31 FLLKALDLFWHEDCLKCGCCDCRLG----EVGSTLYQKANLILCKRDYLRL-FGTTGYCAACTKV 90 (170)
Q Consensus 31 ~~~~~~~~~~H~~Cf~C~~C~~~l~----~~~~~~~~~~~~~yC~~c~~~~-~~~~~~C~~C~~~ 90 (170)
.++...++.-+..-+.|..|+..+. +....+....+.+.|..|-... ... .|..|+..
T Consensus 368 qvll~~nrrGy~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~--~Cp~Cg~~ 430 (679)
T PRK05580 368 QVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPK--ACPECGST 430 (679)
T ss_pred eEEEEEcCCCCCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCC--CCCCCcCC
Confidence 3444444443344455555554442 1112244456778899986554 333 89999764
No 152
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=21.90 E-value=45 Score=25.05 Aligned_cols=32 Identities=16% Similarity=0.124 Sum_probs=22.8
Q ss_pred ccCccccccCCcccccCCeEEEeCCeeccHHhH
Q psy7479 106 HLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138 (170)
Q Consensus 106 H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~ 138 (170)
=++=..|..|++++ ....|...+|.++|..|.
T Consensus 146 ~p~l~~C~~Cg~~~-~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 146 GLDLDHCAVCGAPG-DHRYFSPKEGGAVCSECG 177 (247)
T ss_pred ccchhhHhcCCCCC-CceEEecccCCccccccc
Confidence 33444789999887 334455678999999885
No 153
>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=21.73 E-value=39 Score=15.63 Aligned_cols=10 Identities=40% Similarity=1.345 Sum_probs=7.9
Q ss_pred cccccCCccc
Q psy7479 110 FACQQCNHRF 119 (170)
Q Consensus 110 f~C~~C~~~l 119 (170)
|.|..|++.+
T Consensus 2 ~~C~~C~~~F 11 (27)
T PF13912_consen 2 FECDECGKTF 11 (27)
T ss_dssp EEETTTTEEE
T ss_pred CCCCccCCcc
Confidence 5688888887
No 154
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=21.68 E-value=1e+02 Score=17.25 Aligned_cols=12 Identities=17% Similarity=0.152 Sum_probs=8.4
Q ss_pred eeccHHhHHHHh
Q psy7479 131 KILCEYDYEERQ 142 (170)
Q Consensus 131 ~~~C~~c~~~~~ 142 (170)
--+|..||..-.
T Consensus 23 ~DlC~~Cf~~g~ 34 (48)
T cd02343 23 MDLCKTCFLGGV 34 (48)
T ss_pred chhHHHHHhCCc
Confidence 347999987653
No 155
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=21.42 E-value=51 Score=27.93 Aligned_cols=36 Identities=31% Similarity=0.748 Sum_probs=21.9
Q ss_pred ccccccccccCCceEEecCCcccccCccccccCCcccc
Q psy7479 83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFC 120 (170)
Q Consensus 83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 120 (170)
.|..|-..+...+ +.+.+..--.+||.|..|...|.
T Consensus 28 yCp~CL~~~p~~e--~~~~~nrC~r~Cf~CP~C~~~L~ 63 (483)
T PF05502_consen 28 YCPNCLFEVPSSE--ARSEKNRCSRNCFDCPICFSPLS 63 (483)
T ss_pred ECccccccCChhh--heeccceeccccccCCCCCCcce
Confidence 5666665554322 22333333449999999999884
No 156
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=21.01 E-value=41 Score=15.18 Aligned_cols=10 Identities=50% Similarity=1.265 Sum_probs=7.5
Q ss_pred cccccCCccc
Q psy7479 110 FACQQCNHRF 119 (170)
Q Consensus 110 f~C~~C~~~l 119 (170)
|.|..|++.+
T Consensus 1 ~~C~~C~~~f 10 (25)
T PF12874_consen 1 FYCDICNKSF 10 (25)
T ss_dssp EEETTTTEEE
T ss_pred CCCCCCCCCc
Confidence 5688888877
No 157
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=20.95 E-value=55 Score=24.26 Aligned_cols=11 Identities=18% Similarity=0.449 Sum_probs=6.7
Q ss_pred ccccccccccc
Q psy7479 45 LKCGCCDCRLG 55 (170)
Q Consensus 45 f~C~~C~~~l~ 55 (170)
++|..|+.+.+
T Consensus 1 miCIeCg~~v~ 11 (208)
T PF04161_consen 1 MICIECGHPVK 11 (208)
T ss_pred CEeccCCCcch
Confidence 35666776653
No 158
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=20.90 E-value=40 Score=24.92 Aligned_cols=6 Identities=33% Similarity=1.220 Sum_probs=3.6
Q ss_pred cccccc
Q psy7479 83 YCAACT 88 (170)
Q Consensus 83 ~C~~C~ 88 (170)
.|..|+
T Consensus 154 iCe~C~ 159 (202)
T PF13901_consen 154 ICEICN 159 (202)
T ss_pred CCccCC
Confidence 566665
No 159
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=20.54 E-value=47 Score=16.09 Aligned_cols=12 Identities=8% Similarity=0.215 Sum_probs=5.5
Q ss_pred eCCcccccccee
Q psy7479 64 KANLILCKRDYL 75 (170)
Q Consensus 64 ~~~~~yC~~c~~ 75 (170)
.=|..+|..|..
T Consensus 15 ~C~H~~c~~C~~ 26 (39)
T smart00184 15 PCGHTFCRSCIR 26 (39)
T ss_pred cCCChHHHHHHH
Confidence 334445555544
No 160
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=20.45 E-value=15 Score=20.96 Aligned_cols=10 Identities=30% Similarity=0.793 Sum_probs=5.4
Q ss_pred cccccccccc
Q psy7479 46 KCGCCDCRLG 55 (170)
Q Consensus 46 ~C~~C~~~l~ 55 (170)
+|..|+..|.
T Consensus 24 ~C~gC~~~l~ 33 (56)
T PF02591_consen 24 TCSGCHMELP 33 (56)
T ss_pred ccCCCCEEcC
Confidence 4555555554
No 161
>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=20.30 E-value=47 Score=17.74 Aligned_cols=7 Identities=43% Similarity=1.094 Sum_probs=3.1
Q ss_pred ccccccc
Q psy7479 46 KCGCCDC 52 (170)
Q Consensus 46 ~C~~C~~ 52 (170)
+|..|+.
T Consensus 2 ~Cp~Cg~ 8 (43)
T PF08271_consen 2 KCPNCGS 8 (43)
T ss_dssp SBTTTSS
T ss_pred CCcCCcC
Confidence 3444443
No 162
>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=20.25 E-value=62 Score=15.11 Aligned_cols=10 Identities=40% Similarity=1.215 Sum_probs=8.0
Q ss_pred cccccCCccc
Q psy7479 110 FACQQCNHRF 119 (170)
Q Consensus 110 f~C~~C~~~l 119 (170)
|.|..|++.+
T Consensus 2 ~~C~~C~k~f 11 (27)
T PF12171_consen 2 FYCDACDKYF 11 (27)
T ss_dssp CBBTTTTBBB
T ss_pred CCcccCCCCc
Confidence 5688888887
No 163
>PRK08359 transcription factor; Validated
Probab=20.02 E-value=1.2e+02 Score=22.12 Aligned_cols=27 Identities=22% Similarity=0.672 Sum_probs=19.1
Q ss_pred cccCCcccccCCeEEE-eCCe--eccHHhHH
Q psy7479 112 CQQCNHRFCVGDRFYL-CDNK--ILCEYDYE 139 (170)
Q Consensus 112 C~~C~~~l~~~~~~~~-~~~~--~~C~~c~~ 139 (170)
|..||+.+ .+..+.+ .+|. ..|..|+.
T Consensus 9 CEiCG~~i-~g~~~~v~ieGael~VC~~Ca~ 38 (176)
T PRK08359 9 CEICGAEI-RGPGHRIRIEGAELLVCDRCYE 38 (176)
T ss_pred eecCCCcc-CCCCeEEEEcCeEEehHHHHHH
Confidence 89999998 5665554 4543 45999984
Done!