Query psy8111
Match_columns 135
No_of_seqs 221 out of 1382
Neff 9.1
Searched_HMMs 46136
Date Fri Aug 16 18:53:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8111.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8111hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701|consensus 100.0 9.6E-35 2.1E-39 216.9 0.2 129 3-135 275-406 (468)
2 KOG1701|consensus 99.9 9.6E-28 2.1E-32 179.6 3.1 122 4-126 336-467 (468)
3 KOG2272|consensus 99.9 5.2E-26 1.1E-30 160.6 1.4 127 4-134 139-265 (332)
4 KOG2272|consensus 99.9 2.6E-26 5.6E-31 162.2 -0.4 115 3-120 196-311 (332)
5 KOG1703|consensus 99.9 4.2E-25 9.1E-30 172.8 3.8 129 3-134 304-433 (479)
6 KOG4577|consensus 99.9 9E-26 1.9E-30 161.9 -2.7 123 2-126 33-158 (383)
7 KOG1703|consensus 99.8 3.1E-22 6.6E-27 156.8 1.7 116 2-118 363-478 (479)
8 KOG1044|consensus 99.8 2.3E-21 5E-26 150.0 2.3 113 3-119 134-248 (670)
9 KOG1044|consensus 99.8 3E-21 6.5E-26 149.3 2.8 126 6-134 69-203 (670)
10 PF00412 LIM: LIM domain; Int 99.7 2.4E-17 5.2E-22 94.1 4.0 58 65-122 1-58 (58)
11 PF00412 LIM: LIM domain; Int 99.6 1.3E-16 2.8E-21 91.1 3.5 56 5-61 1-58 (58)
12 KOG1700|consensus 99.5 3.6E-15 7.8E-20 104.8 1.3 119 2-122 7-167 (200)
13 KOG4577|consensus 99.5 2.5E-15 5.4E-20 108.4 -2.2 78 56-135 27-104 (383)
14 smart00132 LIM Zinc-binding do 99.0 2.7E-10 5.9E-15 59.3 2.0 38 64-101 1-38 (39)
15 smart00132 LIM Zinc-binding do 98.9 7.6E-10 1.6E-14 57.6 2.3 36 4-40 1-38 (39)
16 KOG0490|consensus 98.3 1.5E-07 3.2E-12 67.4 -0.4 112 7-120 1-118 (235)
17 KOG1700|consensus 98.1 1.2E-06 2.6E-11 61.8 1.0 63 62-125 7-69 (200)
18 KOG1702|consensus 97.8 2.7E-06 5.8E-11 59.5 -1.5 61 63-124 5-65 (264)
19 KOG1702|consensus 97.2 3E-05 6.5E-10 54.3 -2.0 59 3-62 5-64 (264)
20 KOG0490|consensus 96.2 0.0016 3.4E-08 46.5 0.5 65 68-134 2-70 (235)
21 PF14835 zf-RING_6: zf-RING of 93.0 0.067 1.5E-06 30.8 1.6 43 91-133 8-50 (65)
22 PF14835 zf-RING_6: zf-RING of 91.3 0.19 4.2E-06 28.9 2.1 47 30-76 8-54 (65)
23 PF14634 zf-RING_5: zinc-RING 90.8 0.38 8.2E-06 25.3 2.8 39 93-131 2-44 (44)
24 PF14446 Prok-RING_1: Prokaryo 90.8 0.18 3.8E-06 28.0 1.6 30 62-91 5-36 (54)
25 PF10367 Vps39_2: Vacuolar sor 89.3 0.2 4.4E-06 31.2 1.2 29 63-91 79-107 (109)
26 PF08394 Arc_trans_TRASH: Arch 89.0 0.18 3.9E-06 25.8 0.6 26 65-90 1-26 (37)
27 PRK14890 putative Zn-ribbon RN 87.8 0.53 1.1E-05 26.6 2.1 49 62-130 7-55 (59)
28 COG2888 Predicted Zn-ribbon RN 83.5 0.99 2.1E-05 25.5 1.8 29 62-100 9-37 (61)
29 PF06677 Auto_anti-p27: Sjogre 83.3 1 2.2E-05 23.5 1.7 22 31-56 19-40 (41)
30 smart00504 Ubox Modified RING 82.9 1.8 3.8E-05 24.1 2.8 43 91-134 2-46 (63)
31 COG2191 Formylmethanofuran deh 82.8 0.6 1.3E-05 33.0 0.9 31 30-60 173-203 (206)
32 COG2191 Formylmethanofuran deh 81.2 0.57 1.2E-05 33.1 0.4 31 91-121 173-203 (206)
33 cd00162 RING RING-finger (Real 80.3 1.6 3.5E-05 21.9 1.9 40 93-133 2-45 (45)
34 PF13920 zf-C3HC4_3: Zinc fing 80.2 1 2.2E-05 24.1 1.1 42 92-134 4-48 (50)
35 PF11781 RRN7: RNA polymerase 80.1 1.1 2.5E-05 22.6 1.2 25 30-58 9-33 (36)
36 PF13240 zinc_ribbon_2: zinc-r 79.7 1.6 3.6E-05 19.7 1.5 8 65-72 2-9 (23)
37 PF07191 zinc-ribbons_6: zinc- 78.7 1.1 2.4E-05 26.2 1.0 60 31-103 3-63 (70)
38 PF01258 zf-dskA_traR: Prokary 78.6 0.3 6.5E-06 24.6 -1.3 26 93-118 6-31 (36)
39 PF10367 Vps39_2: Vacuolar sor 77.7 1.5 3.2E-05 27.2 1.4 28 92-119 80-108 (109)
40 PF06906 DUF1272: Protein of u 77.2 4.8 0.0001 22.5 3.2 42 93-134 8-52 (57)
41 PF09943 DUF2175: Uncharacteri 75.7 0.82 1.8E-05 28.7 -0.1 28 64-92 4-32 (101)
42 COG1645 Uncharacterized Zn-fin 75.4 2.3 5E-05 28.0 1.9 23 31-58 30-52 (131)
43 COG4357 Zinc finger domain con 75.2 0.5 1.1E-05 29.3 -1.2 59 64-127 37-95 (105)
44 PF10235 Cript: Microtubule-as 74.0 2 4.3E-05 26.5 1.2 42 23-73 39-80 (90)
45 KOG4739|consensus 72.2 2.9 6.3E-05 30.3 1.9 40 95-134 8-48 (233)
46 PF14471 DUF4428: Domain of un 71.9 3.1 6.8E-05 22.7 1.6 29 92-121 1-30 (51)
47 PF13248 zf-ribbon_3: zinc-rib 71.3 2.4 5.2E-05 19.6 0.9 13 1-13 1-13 (26)
48 KOG0320|consensus 71.3 3.2 7E-05 28.8 1.9 47 88-134 129-178 (187)
49 PF02069 Metallothio_Pro: Prok 69.8 3.1 6.7E-05 22.9 1.3 27 32-58 10-37 (52)
50 PF11571 Med27: Mediator compl 69.8 1.9 4E-05 26.5 0.4 16 57-72 49-64 (90)
51 PF12773 DZR: Double zinc ribb 68.3 6.5 0.00014 20.9 2.4 23 93-119 15-37 (50)
52 PF00645 zf-PARP: Poly(ADP-rib 66.8 1.3 2.8E-05 26.4 -0.7 31 62-92 7-47 (82)
53 PRK14559 putative protein seri 66.6 5.6 0.00012 33.2 2.7 9 64-72 29-37 (645)
54 PF10083 DUF2321: Uncharacteri 65.9 4.9 0.00011 27.3 1.9 11 5-15 42-52 (158)
55 PF12674 Zn_ribbon_2: Putative 63.5 3.7 8E-05 24.7 0.9 28 93-120 3-35 (81)
56 KOG2682|consensus 63.4 2.6 5.6E-05 30.9 0.2 50 75-135 140-189 (314)
57 PF07754 DUF1610: Domain of un 62.5 5.6 0.00012 18.2 1.2 10 5-14 1-10 (24)
58 cd02249 ZZ Zinc finger, ZZ typ 62.5 6.7 0.00015 20.6 1.7 10 111-120 23-32 (46)
59 PRK00420 hypothetical protein; 62.5 5.5 0.00012 25.6 1.6 25 30-58 24-48 (112)
60 TIGR02098 MJ0042_CXXC MJ0042 f 62.2 3.9 8.4E-05 20.5 0.7 13 1-13 1-13 (38)
61 PF04570 DUF581: Protein of un 61.9 5.6 0.00012 22.4 1.4 27 31-57 18-47 (58)
62 PF07503 zf-HYPF: HypF finger; 61.5 3.1 6.7E-05 20.9 0.2 22 18-40 11-32 (35)
63 KOG1813|consensus 61.4 4.8 0.0001 30.2 1.3 43 91-134 242-286 (313)
64 KOG3002|consensus 59.4 8.3 0.00018 29.1 2.3 43 91-134 49-91 (299)
65 smart00291 ZnF_ZZ Zinc-binding 58.5 9.6 0.00021 19.9 1.9 11 110-120 26-36 (44)
66 PLN03208 E3 ubiquitin-protein 57.7 12 0.00026 26.4 2.7 44 90-134 18-79 (193)
67 PF13923 zf-C3HC4_2: Zinc fing 57.4 4.5 9.8E-05 20.3 0.5 37 93-129 1-39 (39)
68 KOG0978|consensus 57.0 3.3 7.2E-05 34.7 -0.2 44 91-135 644-690 (698)
69 PF06827 zf-FPG_IleRS: Zinc fi 56.9 3 6.6E-05 19.8 -0.3 11 63-73 2-12 (30)
70 PF13717 zinc_ribbon_4: zinc-r 56.3 5.1 0.00011 20.1 0.5 7 92-98 27-33 (36)
71 COG5152 Uncharacterized conser 55.8 4.9 0.00011 28.5 0.5 41 91-132 197-239 (259)
72 PF00569 ZZ: Zinc finger, ZZ t 55.8 4.5 9.7E-05 21.4 0.3 30 30-59 5-37 (46)
73 PF13719 zinc_ribbon_5: zinc-r 54.8 6.6 0.00014 19.8 0.8 13 1-13 1-13 (37)
74 PF09943 DUF2175: Uncharacteri 54.7 8.5 0.00018 24.2 1.4 33 91-123 3-36 (101)
75 KOG2462|consensus 54.2 2 4.4E-05 31.8 -1.6 35 5-40 133-172 (279)
76 PF01286 XPA_N: XPA protein N- 52.5 5.6 0.00012 19.9 0.3 10 63-72 4-13 (34)
77 COG0068 HypF Hydrogenase matur 52.4 9.6 0.00021 32.1 1.8 81 4-100 103-183 (750)
78 KOG4739|consensus 52.0 9.8 0.00021 27.6 1.6 42 32-73 6-48 (233)
79 PF10886 DUF2685: Protein of u 51.5 8.3 0.00018 21.3 0.9 25 63-88 2-26 (54)
80 PRK14873 primosome assembly pr 50.6 13 0.00028 31.2 2.3 57 14-71 369-431 (665)
81 cd02341 ZZ_ZZZ3 Zinc finger, Z 48.5 18 0.00039 19.4 1.9 11 111-121 26-36 (48)
82 PF09723 Zn-ribbon_8: Zinc rib 48.3 6.5 0.00014 20.4 0.2 12 30-41 6-17 (42)
83 PRK14714 DNA polymerase II lar 48.3 22 0.00048 32.1 3.4 11 93-103 712-722 (1337)
84 TIGR00570 cdk7 CDK-activating 47.3 24 0.00051 26.8 3.0 26 109-134 26-54 (309)
85 PF13834 DUF4193: Domain of un 47.1 5.4 0.00012 25.0 -0.3 28 90-117 70-98 (99)
86 cd02336 ZZ_RSC8 Zinc finger, Z 47.0 19 0.00041 19.1 1.8 29 92-120 2-32 (45)
87 PF00096 zf-C2H2: Zinc finger, 46.2 8.7 0.00019 16.5 0.4 12 30-41 1-12 (23)
88 smart00834 CxxC_CXXC_SSSS Puta 45.2 8.3 0.00018 19.4 0.3 11 30-40 6-16 (41)
89 smart00659 RPOLCX RNA polymera 44.8 16 0.00034 19.2 1.3 11 30-40 3-13 (44)
90 TIGR02605 CxxC_CxxC_SSSS putat 44.8 9 0.0002 20.5 0.4 12 30-41 6-17 (52)
91 PF07649 C1_3: C1-like domain; 44.8 14 0.00031 17.4 1.1 12 30-41 1-12 (30)
92 KOG1813|consensus 43.8 11 0.00025 28.3 0.9 50 21-73 235-286 (313)
93 PF13695 zf-3CxxC: Zinc-bindin 43.7 28 0.00062 21.5 2.6 9 85-93 36-44 (98)
94 cd02340 ZZ_NBR1_like Zinc fing 43.0 22 0.00047 18.5 1.7 9 64-72 2-10 (43)
95 PF14353 CpXC: CpXC protein 41.3 32 0.00069 22.2 2.6 38 3-41 2-50 (128)
96 PF13894 zf-C2H2_4: C2H2-type 40.5 14 0.00031 15.5 0.7 11 30-40 1-11 (24)
97 PF15135 UPF0515: Uncharacteri 39.6 34 0.00073 25.3 2.7 36 62-102 132-167 (278)
98 PRK00807 50S ribosomal protein 39.3 28 0.00061 19.0 1.8 22 31-52 3-27 (52)
99 COG4847 Uncharacterized protei 38.9 9.5 0.00021 23.7 -0.1 29 64-93 8-37 (103)
100 KOG3002|consensus 37.9 22 0.00047 26.9 1.6 44 29-73 48-91 (299)
101 PF02591 DUF164: Putative zinc 36.1 9.9 0.00021 20.9 -0.3 26 31-56 24-52 (56)
102 PF00097 zf-C3HC4: Zinc finger 35.9 16 0.00034 18.2 0.5 30 93-122 1-30 (41)
103 PF08209 Sgf11: Sgf11 (transcr 35.7 4.5 9.7E-05 20.1 -1.6 16 91-106 5-20 (33)
104 cd02335 ZZ_ADA2 Zinc finger, Z 35.6 14 0.00031 19.7 0.2 12 30-41 1-12 (49)
105 PRK04023 DNA polymerase II lar 35.5 37 0.00081 30.1 2.7 23 51-73 652-674 (1121)
106 KOG2932|consensus 34.7 20 0.00044 27.3 1.0 40 93-132 93-132 (389)
107 COG2075 RPL24A Ribosomal prote 34.6 40 0.00087 19.5 2.0 22 31-52 5-29 (66)
108 KOG2893|consensus 34.3 12 0.00027 27.4 -0.2 35 5-42 13-47 (341)
109 cd02338 ZZ_PCMF_like Zinc fing 34.3 37 0.00079 18.1 1.8 10 112-121 25-34 (49)
110 PF12874 zf-met: Zinc-finger o 34.2 17 0.00038 15.9 0.4 12 30-41 1-12 (25)
111 PF06524 NOA36: NOA36 protein; 33.8 59 0.0013 24.2 3.2 92 29-133 113-219 (314)
112 PF11077 DUF2616: Protein of u 33.8 20 0.00043 24.9 0.8 32 92-123 138-172 (173)
113 PRK13796 GTPase YqeH; Provisio 33.7 19 0.0004 27.8 0.7 28 31-58 2-42 (365)
114 PF13912 zf-C2H2_6: C2H2-type 33.5 18 0.00039 16.2 0.4 12 30-41 2-13 (27)
115 smart00184 RING Ring finger. E 32.6 49 0.0011 15.3 2.0 13 109-121 16-28 (39)
116 PF08792 A2L_zn_ribbon: A2L zi 32.5 50 0.0011 16.2 1.9 23 31-56 5-27 (33)
117 COG4306 Uncharacterized protei 32.1 42 0.00092 22.1 2.0 10 5-14 42-51 (160)
118 PF08271 TF_Zn_Ribbon: TFIIB z 32.0 21 0.00045 18.4 0.5 14 4-17 21-34 (43)
119 PF06689 zf-C4_ClpX: ClpX C4-t 31.1 47 0.001 17.0 1.8 29 92-120 3-33 (41)
120 cd01407 SIR2-fam SIR2 family o 30.1 33 0.00071 24.3 1.4 14 122-135 132-145 (218)
121 COG1198 PriA Primosomal protei 29.4 41 0.00089 28.7 2.1 55 15-71 422-484 (730)
122 COG0266 Nei Formamidopyrimidin 29.2 24 0.00052 26.3 0.6 27 62-90 245-271 (273)
123 PRK12495 hypothetical protein; 28.8 32 0.00069 24.8 1.2 25 29-58 42-66 (226)
124 KOG1734|consensus 28.5 37 0.0008 25.4 1.5 45 43-92 210-262 (328)
125 PF12855 Ecl1: Life-span regul 28.1 23 0.0005 18.6 0.3 19 93-115 9-27 (43)
126 PRK00398 rpoP DNA-directed RNA 28.1 32 0.00069 17.9 0.8 11 30-40 4-14 (46)
127 PF05864 Chordopox_RPO7: Chord 27.9 14 0.00031 20.7 -0.6 16 30-45 5-20 (63)
128 PF14569 zf-UDP: Zinc-binding 27.9 28 0.00061 20.8 0.6 43 30-72 10-61 (80)
129 PF10080 DUF2318: Predicted me 27.7 66 0.0014 20.2 2.3 36 19-59 26-61 (102)
130 smart00531 TFIIE Transcription 27.5 27 0.00059 23.2 0.6 10 30-39 100-109 (147)
131 PHA03082 DNA-dependent RNA pol 27.4 14 0.0003 20.7 -0.6 16 30-45 5-20 (63)
132 PF05502 Dynactin_p62: Dynacti 26.9 43 0.00093 27.1 1.7 52 48-101 3-63 (483)
133 PF14447 Prok-RING_4: Prokaryo 26.5 37 0.0008 18.9 0.9 27 109-135 25-51 (55)
134 PF10764 Gin: Inhibitor of sig 26.0 69 0.0015 17.0 1.9 10 91-100 19-28 (46)
135 PF12156 ATPase-cat_bd: Putati 26.0 34 0.00075 20.7 0.8 10 4-13 2-11 (88)
136 PF13639 zf-RING_2: Ring finge 25.9 22 0.00047 18.2 -0.1 9 110-118 22-30 (44)
137 PHA02610 uvsY.-2 hypothetical 25.7 53 0.0012 18.0 1.4 25 3-27 2-27 (53)
138 PF12171 zf-C2H2_jaz: Zinc-fin 25.5 45 0.00098 15.0 1.0 13 91-103 2-14 (27)
139 PF14255 Cys_rich_CPXG: Cystei 24.9 25 0.00054 19.3 0.1 8 65-72 3-10 (52)
140 PF03107 C1_2: C1 domain; Int 24.7 58 0.0012 15.3 1.3 13 30-42 1-13 (30)
141 cd02334 ZZ_dystrophin Zinc fin 24.6 76 0.0016 17.0 1.9 10 112-121 25-34 (49)
142 cd02342 ZZ_UBA_plant Zinc fing 24.3 73 0.0016 16.8 1.7 9 112-120 25-33 (43)
143 PF00130 C1_1: Phorbol esters/ 24.3 42 0.00091 17.8 0.9 11 63-73 12-22 (53)
144 COG1381 RecO Recombinational D 24.2 45 0.00098 24.3 1.3 31 88-118 152-182 (251)
145 KOG4443|consensus 24.2 46 0.00099 28.0 1.4 21 82-102 107-127 (694)
146 TIGR00595 priA primosomal prot 24.1 97 0.0021 25.1 3.2 56 15-71 200-262 (505)
147 TIGR03597 GTPase_YqeH ribosome 23.3 32 0.00069 26.5 0.4 27 32-58 1-36 (360)
148 cd01412 SIRT5_Af1_CobB SIRT5_A 23.2 1.1E+02 0.0024 21.6 3.2 13 123-135 130-142 (224)
149 PRK14873 primosome assembly pr 23.2 50 0.0011 27.9 1.5 37 93-132 395-431 (665)
150 PF00628 PHD: PHD-finger; Int 23.1 70 0.0015 16.6 1.7 7 84-90 22-28 (51)
151 cd02344 ZZ_HERC2 Zinc finger, 23.0 75 0.0016 16.8 1.7 10 111-120 24-33 (45)
152 PLN03123 poly [ADP-ribose] pol 22.9 45 0.00097 29.5 1.2 35 58-92 13-57 (981)
153 TIGR00143 hypF [NiFe] hydrogen 22.7 52 0.0011 28.0 1.5 81 4-100 70-150 (711)
154 PRK00085 recO DNA repair prote 22.7 48 0.001 23.7 1.2 33 24-57 145-177 (247)
155 PF14570 zf-RING_4: RING/Ubox 22.6 47 0.001 17.9 0.8 23 110-132 21-46 (48)
156 PF04641 Rtf2: Rtf2 RING-finge 22.5 80 0.0017 23.1 2.3 49 24-73 109-161 (260)
157 smart00355 ZnF_C2H2 zinc finge 22.5 44 0.00094 14.0 0.6 10 31-40 2-11 (26)
158 COG3813 Uncharacterized protei 22.4 57 0.0012 19.3 1.2 42 93-134 8-52 (84)
159 PF07975 C1_4: TFIIH C1-like d 22.2 45 0.00097 18.2 0.7 10 32-41 2-11 (51)
160 PF05290 Baculo_IE-1: Baculovi 22.2 55 0.0012 21.8 1.2 47 87-133 77-131 (140)
161 PF14149 YhfH: YhfH-like prote 21.9 18 0.0004 18.4 -0.8 15 119-133 9-23 (37)
162 cd00472 Ribosomal_L24e_L24 Rib 21.8 81 0.0017 17.4 1.7 22 31-52 5-29 (54)
163 PRK11595 DNA utilization prote 21.7 53 0.0012 23.4 1.2 21 52-72 22-44 (227)
164 KOG0823|consensus 21.7 88 0.0019 22.8 2.3 54 25-81 44-102 (230)
165 cd02345 ZZ_dah Zinc finger, ZZ 21.3 78 0.0017 16.8 1.6 9 64-72 2-11 (49)
166 PF10170 C6_DPF: Cysteine-rich 21.1 97 0.0021 19.4 2.1 28 93-120 52-80 (97)
167 PF13465 zf-H2C2_2: Zinc-finge 20.6 42 0.00092 15.1 0.4 11 29-39 14-24 (26)
No 1
>KOG1701|consensus
Probab=100.00 E-value=9.6e-35 Score=216.94 Aligned_cols=129 Identities=25% Similarity=0.552 Sum_probs=121.9
Q ss_pred ccccccCcccccc--ceeeCCCcccCCCCeeccccCCccCCCceEeECCeeeccCchhhhcCCchhhcCCccccCcccce
Q psy8111 3 SAVKHQDKSFRED--YNKLGGKDRGSGQHFCCWQCDESLTGQRYVLRDDHPYCIKCYESVFANSCEECSKIIGIDSKDLS 80 (135)
Q Consensus 3 ~~C~~C~~~i~~~--~i~a~~~~~H~~~cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~~~~~~~~ 80 (135)
.+|.+|+|.|.++ .+.||++.||.. ||+|.+|++.|.++.||..|+++||+.||... ..+|..|+++|+ +++++
T Consensus 275 ~iC~~C~K~V~g~~~ac~Am~~~fHv~-CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~t-lekC~~Cg~~I~--d~iLr 350 (468)
T KOG1701|consen 275 GICAFCHKTVSGQGLAVEAMDQLFHVQ-CFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDT-LEKCNKCGEPIM--DRILR 350 (468)
T ss_pred hhhhhcCCcccCcchHHHHhhhhhccc-ceehHhhhhhhccccccccCCcccchHHHHHH-HHHHhhhhhHHH--HHHHH
Confidence 4799999999964 589999999999 99999999999999999999999999999876 479999999995 88999
Q ss_pred eCCccccccccccccccccCCCCCeeee-CCcccCHHhHhhhcCCCcccCCCCCCC
Q psy8111 81 YKDKHWHEACFSCSKCRQSLVDKQFGSK-SEKIYCGNCYDAQFASRCDGCSEIFKA 135 (135)
Q Consensus 81 ~~~~~~H~~Cf~C~~C~~~l~~~~~~~~-~~~~~C~~c~~~~~~~~C~~C~~~I~~ 135 (135)
|.|+.||+.||+|..|.+.|++..|.+. ++++||..+|.++|++||+.|++||+|
T Consensus 351 A~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P 406 (468)
T KOG1701|consen 351 ALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILP 406 (468)
T ss_pred hcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccC
Confidence 9999999999999999999999988876 799999999999999999999999987
No 2
>KOG1701|consensus
Probab=99.94 E-value=9.6e-28 Score=179.59 Aligned_cols=122 Identities=19% Similarity=0.452 Sum_probs=111.2
Q ss_pred cccccCccccccceeeCCCcccCCCCeeccccCCccCCCceEe-ECCeeeccCchhhhcCCchhhcCCccccC-----cc
Q psy8111 4 AVKHQDKSFREDYNKLGGKDRGSGQHFCCWQCDESLTGQRYVL-RDDHPYCIKCYESVFANSCEECSKIIGID-----SK 77 (135)
Q Consensus 4 ~C~~C~~~i~~~~i~a~~~~~H~~~cf~C~~C~~~l~~~~~~~-~~~~~~C~~c~~~~~~~~C~~C~~~I~~~-----~~ 77 (135)
.|..|+++|.+++|.|+|+.||+. ||+|..|++.|++..|.. .++++||.+||+++|+++|+.|+++|++. ..
T Consensus 336 kC~~Cg~~I~d~iLrA~GkayHp~-CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etv 414 (468)
T KOG1701|consen 336 KCNKCGEPIMDRILRALGKAYHPG-CFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETV 414 (468)
T ss_pred HHhhhhhHHHHHHHHhcccccCCC-ceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcceE
Confidence 599999999999999999999999 999999999999999986 78999999999999999999999999764 24
Q ss_pred cceeCCccccccccccccccccCCC----CCeeeeCCcccCHHhHhhhcCCCc
Q psy8111 78 DLSYKDKHWHEACFSCSKCRQSLVD----KQFGSKSEKIYCGNCYDAQFASRC 126 (135)
Q Consensus 78 ~~~~~~~~~H~~Cf~C~~C~~~l~~----~~~~~~~~~~~C~~c~~~~~~~~C 126 (135)
.|.++++.||.+|++|..|+.+|+. ...|..||.++|+.|..++....+
T Consensus 415 Rvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch~~Rl~~~~ 467 (468)
T KOG1701|consen 415 RVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCHLKRLQAGS 467 (468)
T ss_pred EEEEccccccccceehhhcCccccccCCCCcceeccCceeechhhhhhhcccC
Confidence 4788999999999999999999972 368899999999999988876554
No 3
>KOG2272|consensus
Probab=99.91 E-value=5.2e-26 Score=160.59 Aligned_cols=127 Identities=23% Similarity=0.513 Sum_probs=119.7
Q ss_pred cccccCccccccceeeCCCcccCCCCeeccccCCccCCCceEeECCeeeccCchhhhcCCchhhcCCccccCcccceeCC
Q psy8111 4 AVKHQDKSFREDYNKLGGKDRGSGQHFCCWQCDESLTGQRYVLRDDHPYCIKCYESVFANSCEECSKIIGIDSKDLSYKD 83 (135)
Q Consensus 4 ~C~~C~~~i~~~~i~a~~~~~H~~~cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~ 83 (135)
.|.+|+..|+++.|+..|..||+. +|+|..|++.|++. -.+..|.+||.+|+.+.-.|.|..|.+|| ++.+|.++|
T Consensus 139 vC~KCh~~iD~~~l~fr~d~yH~y-HFkCt~C~keL~sd-aRevk~eLyClrChD~mgipiCgaC~rpI--eervi~amg 214 (332)
T KOG2272|consen 139 VCQKCHAHIDEQPLTFRGDPYHPY-HFKCTTCGKELTSD-AREVKGELYCLRCHDKMGIPICGACRRPI--EERVIFAMG 214 (332)
T ss_pred ehhhhhhhcccccccccCCCCCcc-ceecccccccccch-hhhhccceeccccccccCCcccccccCch--HHHHHHHhc
Confidence 489999999999999999999999 99999999999875 55677899999999998889999999999 588999999
Q ss_pred ccccccccccccccccCCCCCeeeeCCcccCHHhHhhhcCCCcccCCCCCC
Q psy8111 84 KHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFASRCDGCSEIFK 134 (135)
Q Consensus 84 ~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~ 134 (135)
+.||.++|+|+.|.+|+-+-..|++.|.+||+.+|.++|+..|..|+++|.
T Consensus 215 KhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~ 265 (332)
T KOG2272|consen 215 KHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIG 265 (332)
T ss_pred cccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccC
Confidence 999999999999999999989999999999999999999999999999884
No 4
>KOG2272|consensus
Probab=99.91 E-value=2.6e-26 Score=162.16 Aligned_cols=115 Identities=30% Similarity=0.603 Sum_probs=109.4
Q ss_pred ccccccCccccccceeeCCCcccCCCCeeccccCCccCCCceEeECCeeeccCchhhhcCCchhhcCCccccCcccceeC
Q psy8111 3 SAVKHQDKSFREDYNKLGGKDRGSGQHFCCWQCDESLTGQRYVLRDDHPYCIKCYESVFANSCEECSKIIGIDSKDLSYK 82 (135)
Q Consensus 3 ~~C~~C~~~i~~~~i~a~~~~~H~~~cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~~~~~~~~~~ 82 (135)
..|..|.+||++++|.|+|+.||.+ +|+|+.|.+|+-+.+.|++.|.+||+.+|.++++..|..|+.+| .+.++.++
T Consensus 196 piCgaC~rpIeervi~amgKhWHve-HFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i--~G~vv~al 272 (332)
T KOG2272|consen 196 PICGACRRPIEERVIFAMGKHWHVE-HFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVI--GGDVVSAL 272 (332)
T ss_pred cccccccCchHHHHHHHhccccchh-heeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCcc--CccHHHHh
Confidence 4699999999999999999999999 99999999999999999999999999999999999999999999 57799999
Q ss_pred CccccccccccccccccCCCC-CeeeeCCcccCHHhHhh
Q psy8111 83 DKHWHEACFSCSKCRQSLVDK-QFGSKSEKIYCGNCYDA 120 (135)
Q Consensus 83 ~~~~H~~Cf~C~~C~~~l~~~-~~~~~~~~~~C~~c~~~ 120 (135)
++.|-++||+|+.|++.|... .|++.|-+|.|+.||.+
T Consensus 273 ~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~r 311 (332)
T KOG2272|consen 273 NKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDR 311 (332)
T ss_pred hhhhccccccccccccccccccceeeeccchHHHHHHhh
Confidence 999999999999999999854 79999999999999974
No 5
>KOG1703|consensus
Probab=99.91 E-value=4.2e-25 Score=172.84 Aligned_cols=129 Identities=22% Similarity=0.520 Sum_probs=123.4
Q ss_pred ccccccCccccc-cceeeCCCcccCCCCeeccccCCccCCCceEeECCeeeccCchhhhcCCchhhcCCccccCccccee
Q psy8111 3 SAVKHQDKSFRE-DYNKLGGKDRGSGQHFCCWQCDESLTGQRYVLRDDHPYCIKCYESVFANSCEECSKIIGIDSKDLSY 81 (135)
Q Consensus 3 ~~C~~C~~~i~~-~~i~a~~~~~H~~~cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~~~~~~~~~ 81 (135)
..|..|+++|.+ +++.++++.||++ +|.|+.|+..+....+...+|++||.+|+.+.+++.|.+|+++|. +..|.+
T Consensus 304 p~c~~c~~~i~~~~~i~~~~~~~h~~-~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~--~~~v~a 380 (479)
T KOG1703|consen 304 PLCLSCNQKIRSVKVIVALGKEWHPE-HFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPIL--EEGVCA 380 (479)
T ss_pred ccccccccCcccceeEeecccccccc-ceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchH--HhHhhh
Confidence 579999999999 9999999999999 999999999999888899999999999999999999999999995 778999
Q ss_pred CCccccccccccccccccCCCCCeeeeCCcccCHHhHhhhcCCCcccCCCCCC
Q psy8111 82 KDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFASRCDGCSEIFK 134 (135)
Q Consensus 82 ~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~ 134 (135)
.+..||++||+|..|+++|.+..|+..++.|||+.||.++++++|..|.++|.
T Consensus 381 ~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~ 433 (479)
T KOG1703|consen 381 LGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVE 433 (479)
T ss_pred ccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccchhH
Confidence 99999999999999999999999999999999999999999999999998875
No 6
>KOG4577|consensus
Probab=99.90 E-value=9e-26 Score=161.93 Aligned_cols=123 Identities=20% Similarity=0.436 Sum_probs=109.4
Q ss_pred cccccccCccccccc-eeeCCCcccCCCCeeccccCCccCCCceEeECCeeeccCchhhhcCCchhhcCCccccCcccce
Q psy8111 2 ESAVKHQDKSFREDY-NKLGGKDRGSGQHFCCWQCDESLTGQRYVLRDDHPYCIKCYESVFANSCEECSKIIGIDSKDLS 80 (135)
Q Consensus 2 ~~~C~~C~~~i~~~~-i~a~~~~~H~~~cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~~~~~~~~ 80 (135)
+..|+.|++.|.+++ +.++++.||.. |++|+.|..+|... +|.++|.+||+++|.++|+.+|++|...|.|+..+..
T Consensus 33 ip~CagC~q~IlDrFilKvl~R~wHs~-CLkCs~C~~qL~dr-CFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRk 110 (383)
T KOG4577|consen 33 IPICAGCDQHILDRFILKVLDRHWHSS-CLKCSDCHDQLADR-CFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRK 110 (383)
T ss_pred cccccchHHHHHHHHHHHHHhhhhhhh-hcchhhhhhHHHHH-HhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHH
Confidence 356999999999998 57899999999 99999999999864 9999999999999999999999999999998777778
Q ss_pred eCCccccccccccccccccCCCC-Ceee-eCCcccCHHhHhhhcCCCc
Q psy8111 81 YKDKHWHEACFSCSKCRQSLVDK-QFGS-KSEKIYCGNCYDAQFASRC 126 (135)
Q Consensus 81 ~~~~~~H~~Cf~C~~C~~~l~~~-~~~~-~~~~~~C~~c~~~~~~~~C 126 (135)
|.+..||..||.|..|+++|..+ .||+ .|.+++|++.|+..-+.-|
T Consensus 111 Aqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~ 158 (383)
T KOG4577|consen 111 AQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHC 158 (383)
T ss_pred hhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccc
Confidence 89999999999999999999743 5555 5899999999987654433
No 7
>KOG1703|consensus
Probab=99.84 E-value=3.1e-22 Score=156.78 Aligned_cols=116 Identities=23% Similarity=0.523 Sum_probs=110.2
Q ss_pred cccccccCccccccceeeCCCcccCCCCeeccccCCccCCCceEeECCeeeccCchhhhcCCchhhcCCccccCccccee
Q psy8111 2 ESAVKHQDKSFREDYNKLGGKDRGSGQHFCCWQCDESLTGQRYVLRDDHPYCIKCYESVFANSCEECSKIIGIDSKDLSY 81 (135)
Q Consensus 2 ~~~C~~C~~~i~~~~i~a~~~~~H~~~cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~~~~~~~~~ 81 (135)
...|.+|+++|.++.|.|+++.||++ ||.|..|+++|.+..|+..+|.+||+.||.+++.++|..|.+++...+..+.+
T Consensus 363 ~p~C~~C~~~i~~~~v~a~~~~wH~~-cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~~~ie~ 441 (479)
T KOG1703|consen 363 RPNCKRCLLPILEEGVCALGRLWHPE-CFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGSRQIEA 441 (479)
T ss_pred CccccccCCchHHhHhhhccCeechh-ceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccchhHhhhhHhhc
Confidence 35699999999999999999999999 99999999999999999999999999999999999999999998666788999
Q ss_pred CCccccccccccccccccCCCCCeeeeCCcccCHHhH
Q psy8111 82 KDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCY 118 (135)
Q Consensus 82 ~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~ 118 (135)
++..||..||+|..|.+.|.++.|+...++|+|..|+
T Consensus 442 ~~~~~h~~~F~c~~c~~~l~~~~~~~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 442 DGSPFHGDCFRCANCMKKLTKKTFFETLDKPLCQKHF 478 (479)
T ss_pred cCccccccceehhhhhccccCCceeecCCccccccCC
Confidence 9999999999999999999999999999999998875
No 8
>KOG1044|consensus
Probab=99.82 E-value=2.3e-21 Score=149.96 Aligned_cols=113 Identities=30% Similarity=0.594 Sum_probs=103.6
Q ss_pred ccccccCcccc-ccceeeCCCcccCCCCeeccccCCccCCCceEeECCeeeccCchhhhcCCchhhcCCccccCccccee
Q psy8111 3 SAVKHQDKSFR-EDYNKLGGKDRGSGQHFCCWQCDESLTGQRYVLRDDHPYCIKCYESVFANSCEECSKIIGIDSKDLSY 81 (135)
Q Consensus 3 ~~C~~C~~~i~-~~~i~a~~~~~H~~~cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~~~~~~~~~ 81 (135)
+.|++|++.|. |+.+.|+++.||.. ||+|..|...|.++ |+.++|.|||++||.+.|+.+|..|.+.| .+.++.|
T Consensus 134 s~cagc~~~lk~gq~llald~qwhv~-cfkc~~c~~vL~ge-y~skdg~pyce~dy~~~fgvkc~~c~~fi--sgkvLqa 209 (670)
T KOG1044|consen 134 STCAGCGEELKNGQALLALDKQWHVS-CFKCKSCSAVLNGE-YMSKDGVPYCEKDYQAKFGVKCEECEKFI--SGKVLQA 209 (670)
T ss_pred ccccchhhhhhccceeeeeccceeee-eeehhhhcccccce-eeccCCCcchhhhhhhhcCeehHHhhhhh--hhhhhhc
Confidence 57999999885 89999999999999 99999999999986 99999999999999999999999999999 4889999
Q ss_pred CCccccccccccccccccCCC-CCeeeeCCcccCHHhHh
Q psy8111 82 KDKHWHEACFSCSKCRQSLVD-KQFGSKSEKIYCGNCYD 119 (135)
Q Consensus 82 ~~~~~H~~Cf~C~~C~~~l~~-~~~~~~~~~~~C~~c~~ 119 (135)
.|++|||.|-+|+.|+..+++ +..|+.+..++-..|-+
T Consensus 210 g~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~q 248 (670)
T KOG1044|consen 210 GDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCKQ 248 (670)
T ss_pred cCcccCcchhhhhhhccccccchheeeccccccCCcccc
Confidence 999999999999999999985 57888888888777743
No 9
>KOG1044|consensus
Probab=99.82 E-value=3e-21 Score=149.31 Aligned_cols=126 Identities=23% Similarity=0.552 Sum_probs=109.7
Q ss_pred cccCccccccceeeCCCcccCCCCeeccccCCccCCCceE-eECCeeeccCchhhh--------cCCchhhcCCccccCc
Q psy8111 6 KHQDKSFREDYNKLGGKDRGSGQHFCCWQCDESLTGQRYV-LRDDHPYCIKCYESV--------FANSCEECSKIIGIDS 76 (135)
Q Consensus 6 ~~C~~~i~~~~i~a~~~~~H~~~cf~C~~C~~~l~~~~~~-~~~~~~~C~~c~~~~--------~~~~C~~C~~~I~~~~ 76 (135)
..|...|.+++|.++|++||++ ||.|+.|+.++....-+ .......|+.|..-. ....|++|++.|. .+
T Consensus 69 ~~c~~~~~gevvsa~gktyh~~-cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk-~g 146 (670)
T KOG1044|consen 69 DDCRAFVEGEVVSTLGKTYHPK-CFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELK-NG 146 (670)
T ss_pred cchhhhccceeEecccceeccc-cceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhh-cc
Confidence 5788899999999999999999 99999999999876444 445557788876531 2357999999997 67
Q ss_pred ccceeCCccccccccccccccccCCCCCeeeeCCcccCHHhHhhhcCCCcccCCCCCC
Q psy8111 77 KDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFASRCDGCSEIFK 134 (135)
Q Consensus 77 ~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~ 134 (135)
+.+.|+++.||..||+|..|+..|.++ |+..+|.|||+.+|.++|+.+|..|.+.|.
T Consensus 147 q~llald~qwhv~cfkc~~c~~vL~ge-y~skdg~pyce~dy~~~fgvkc~~c~~fis 203 (670)
T KOG1044|consen 147 QALLALDKQWHVSCFKCKSCSAVLNGE-YMSKDGVPYCEKDYQAKFGVKCEECEKFIS 203 (670)
T ss_pred ceeeeeccceeeeeeehhhhcccccce-eeccCCCcchhhhhhhhcCeehHHhhhhhh
Confidence 889999999999999999999999876 889999999999999999999999998874
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=99.69 E-value=2.4e-17 Score=94.14 Aligned_cols=58 Identities=40% Similarity=0.844 Sum_probs=53.1
Q ss_pred hhhcCCccccCcccceeCCccccccccccccccccCCCCCeeeeCCcccCHHhHhhhc
Q psy8111 65 CEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQF 122 (135)
Q Consensus 65 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~ 122 (135)
|++|+++|.+.+.++.+.|+.||++||+|+.|+++|.++.++..+++|||+.||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 7889999986666667999999999999999999999888999999999999999876
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=99.64 E-value=1.3e-16 Score=91.08 Aligned_cols=56 Identities=27% Similarity=0.504 Sum_probs=51.2
Q ss_pred ccccCccccccce--eeCCCcccCCCCeeccccCCccCCCceEeECCeeeccCchhhhc
Q psy8111 5 VKHQDKSFREDYN--KLGGKDRGSGQHFCCWQCDESLTGQRYVLRDDHPYCIKCYESVF 61 (135)
Q Consensus 5 C~~C~~~i~~~~i--~a~~~~~H~~~cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~ 61 (135)
|.+|+++|.+..+ .++|+.||++ ||+|+.|+++|.+..|+..+|++||++||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~-Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPE-CFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETT-TSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEcc-ccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 7899999997553 5999999999 999999999999988999999999999998764
No 12
>KOG1700|consensus
Probab=99.51 E-value=3.6e-15 Score=104.83 Aligned_cols=119 Identities=23% Similarity=0.531 Sum_probs=102.5
Q ss_pred cccccccCccccc-cceeeCCCcccCCCCeeccccCCccCCCceEeECCeeeccCchhhhcC------------------
Q psy8111 2 ESAVKHQDKSFRE-DYNKLGGKDRGSGQHFCCWQCDESLTGQRYVLRDDHPYCIKCYESVFA------------------ 62 (135)
Q Consensus 2 ~~~C~~C~~~i~~-~~i~a~~~~~H~~~cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~------------------ 62 (135)
-..|.+|++.+.- +.+...|..||.. ||+|..|+..|+...+..+++.+||..+|...++
T Consensus 7 ~~kc~~c~k~vy~~e~~~~~g~~~hk~-c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (200)
T KOG1700|consen 7 TDKCNACGKTVYFVEKVQKDGVDFHKE-CFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGK 85 (200)
T ss_pred cchhhhccCcchHHHHHhccCcchhhh-HHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCc
Confidence 3569999999984 5567899999999 9999999999999889999999999996554433
Q ss_pred -----------------------CchhhcCCccccCcccceeCCccccccccccccccccCCCCCeeeeCCcccCHHhHh
Q psy8111 63 -----------------------NSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYD 119 (135)
Q Consensus 63 -----------------------~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~ 119 (135)
..|.+|++.+++ .+.+...+..||..||+|+.|+..|....+....+.+||..++.
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~-~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~ 164 (200)
T KOG1700|consen 86 DGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYP-LEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFA 164 (200)
T ss_pred ccccccccccccchhHHhhhccccccccccceeee-hHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhh
Confidence 479999999985 44577789999999999999999999999999999999988876
Q ss_pred hhc
Q psy8111 120 AQF 122 (135)
Q Consensus 120 ~~~ 122 (135)
.++
T Consensus 165 ~~~ 167 (200)
T KOG1700|consen 165 QLF 167 (200)
T ss_pred eee
Confidence 654
No 13
>KOG4577|consensus
Probab=99.46 E-value=2.5e-15 Score=108.44 Aligned_cols=78 Identities=29% Similarity=0.689 Sum_probs=69.7
Q ss_pred chhhhcCCchhhcCCccccCcccceeCCccccccccccccccccCCCCCeeeeCCcccCHHhHhhhcCCCcccCCCCCCC
Q psy8111 56 CYESVFANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFASRCDGCSEIFKA 135 (135)
Q Consensus 56 c~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~~ 135 (135)
++...-.++|++|.+.|. +..++.++++.||..|++|+.|..+|.+. .+.+++.+||+++|.++|++||+.|+++|.|
T Consensus 27 df~~~eip~CagC~q~Il-DrFilKvl~R~wHs~CLkCs~C~~qL~dr-CFsR~~s~yCkedFfKrfGTKCsaC~~GIpP 104 (383)
T KOG4577|consen 27 DFSNVEIPICAGCDQHIL-DRFILKVLDRHWHSSCLKCSDCHDQLADR-CFSREGSVYCKEDFFKRFGTKCSACQEGIPP 104 (383)
T ss_pred cccccccccccchHHHHH-HHHHHHHHhhhhhhhhcchhhhhhHHHHH-HhhcCCceeehHHHHHHhCCcchhhcCCCCh
Confidence 344445689999999997 67778999999999999999999999775 6689999999999999999999999999986
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=98.98 E-value=2.7e-10 Score=59.30 Aligned_cols=38 Identities=39% Similarity=0.756 Sum_probs=33.5
Q ss_pred chhhcCCccccCcccceeCCccccccccccccccccCC
Q psy8111 64 SCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLV 101 (135)
Q Consensus 64 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 101 (135)
+|.+|+++|.+.+..+.+.++.||++||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 58899999975447788999999999999999999985
No 15
>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=98.91 E-value=7.6e-10 Score=57.57 Aligned_cols=36 Identities=22% Similarity=0.235 Sum_probs=32.8
Q ss_pred cccccCccccc--cceeeCCCcccCCCCeeccccCCccC
Q psy8111 4 AVKHQDKSFRE--DYNKLGGKDRGSGQHFCCWQCDESLT 40 (135)
Q Consensus 4 ~C~~C~~~i~~--~~i~a~~~~~H~~~cf~C~~C~~~l~ 40 (135)
.|.+|+++|.+ ..+.++++.||++ ||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~-Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPE-CFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCcccccc-CCCCcccCCcCc
Confidence 48899999997 5688999999999 999999999986
No 16
>KOG0490|consensus
Probab=98.26 E-value=1.5e-07 Score=67.37 Aligned_cols=112 Identities=20% Similarity=0.385 Sum_probs=91.1
Q ss_pred ccCccccccc-eeeCCCcccCCCCeeccccCCccC-CCceEeECCeeeccCchhh--hcCCchhhcCCccccCcccceeC
Q psy8111 7 HQDKSFREDY-NKLGGKDRGSGQHFCCWQCDESLT-GQRYVLRDDHPYCIKCYES--VFANSCEECSKIIGIDSKDLSYK 82 (135)
Q Consensus 7 ~C~~~i~~~~-i~a~~~~~H~~~cf~C~~C~~~l~-~~~~~~~~~~~~C~~c~~~--~~~~~C~~C~~~I~~~~~~~~~~ 82 (135)
.|+..|.|++ +.+.+..||.. |..|..|...|. ....+.++|..||..+|.. .+..+|.+|...+...+++..+.
T Consensus 1 ~~~~~~~~~~~l~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f 79 (235)
T KOG0490|consen 1 GCGRQILDRYLLRVLDRYWHAS-CLKCAECDNPLGVGDTCFSKDGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAF 79 (235)
T ss_pred CCCccccchHHhhcccHHHHHH-HHhhhhhcchhccCCCcccCCCcccccccchhhhhccccccCCCCCcCHHHHHHHhh
Confidence 3778888876 67789999999 999999999997 2244444999999999998 77889999999997778888888
Q ss_pred CccccccccccccccccCCC-CCeeeeC-CcccCHHhHhh
Q psy8111 83 DKHWHEACFSCSKCRQSLVD-KQFGSKS-EKIYCGNCYDA 120 (135)
Q Consensus 83 ~~~~H~~Cf~C~~C~~~l~~-~~~~~~~-~~~~C~~c~~~ 120 (135)
.+. |..||.|..|...+.+ ..+.+.+ -+..+.+.+.+
T Consensus 80 ~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 80 EKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred cCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhh
Confidence 888 9999999999887754 3555554 48888877754
No 17
>KOG1700|consensus
Probab=98.07 E-value=1.2e-06 Score=61.78 Aligned_cols=63 Identities=27% Similarity=0.704 Sum_probs=54.1
Q ss_pred CCchhhcCCccccCcccceeCCccccccccccccccccCCCCCeeeeCCcccCHHhHhhhcCCC
Q psy8111 62 ANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFASR 125 (135)
Q Consensus 62 ~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~ 125 (135)
..+|.+|++.++..+ .+...|..||+.||+|..|...|....+...++.+||+.++..+++++
T Consensus 7 ~~kc~~c~k~vy~~e-~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~ 69 (200)
T KOG1700|consen 7 TDKCNACGKTVYFVE-KVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPK 69 (200)
T ss_pred cchhhhccCcchHHH-HHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcc
Confidence 468999999997544 455889999999999999999999888989999999999877777653
No 18
>KOG1702|consensus
Probab=97.77 E-value=2.7e-06 Score=59.45 Aligned_cols=61 Identities=31% Similarity=0.647 Sum_probs=52.4
Q ss_pred CchhhcCCccccCcccceeCCccccccccccccccccCCCCCeeeeCCcccCHHhHhhhcCC
Q psy8111 63 NSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFAS 124 (135)
Q Consensus 63 ~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~ 124 (135)
+.+..|++.++|.+ .+..+++.||..||+|..|+.+|.-..+...+.+|||..+|.++.++
T Consensus 5 ~n~~~cgk~vYPvE-~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~at 65 (264)
T KOG1702|consen 5 CNREDCGKTVYPVE-EVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVAT 65 (264)
T ss_pred chhhhhccccccHH-HHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccceee
Confidence 45677889888654 57788999999999999999999988888899999999999887653
No 19
>KOG1702|consensus
Probab=97.23 E-value=3e-05 Score=54.32 Aligned_cols=59 Identities=24% Similarity=0.284 Sum_probs=50.7
Q ss_pred ccccccCccccc-cceeeCCCcccCCCCeeccccCCccCCCceEeECCeeeccCchhhhcC
Q psy8111 3 SAVKHQDKSFRE-DYNKLGGKDRGSGQHFCCWQCDESLTGQRYVLRDDHPYCIKCYESVFA 62 (135)
Q Consensus 3 ~~C~~C~~~i~~-~~i~a~~~~~H~~~cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~ 62 (135)
-.+..|++.+.. +-+.-+++.||.. ||+|..|+.+|.-..+-..+.++||..+|.+..+
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~-cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQ-CFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVA 64 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHH-hheeeeccCChhhhhccccccCCCcCccccccee
Confidence 357889999884 6688899999999 9999999999987778889999999999976543
No 20
>KOG0490|consensus
Probab=96.19 E-value=0.0016 Score=46.51 Aligned_cols=65 Identities=32% Similarity=0.759 Sum_probs=53.1
Q ss_pred cCCccccCcccceeCCccccccccccccccccCC--CCCeeeeCCcccCHHhHhh--hcCCCcccCCCCCC
Q psy8111 68 CSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLV--DKQFGSKSEKIYCGNCYDA--QFASRCDGCSEIFK 134 (135)
Q Consensus 68 C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~~~~~C~~c~~~--~~~~~C~~C~~~I~ 134 (135)
|+..|. +...+.+.+..||..|..|..|...+. ...|.. +|..||...+.+ .+..+|.+|...|.
T Consensus 2 ~~~~~~-~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ 70 (235)
T KOG0490|consen 2 CGRQIL-DRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTIS 70 (235)
T ss_pred CCcccc-chHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcC
Confidence 556664 445566779999999999999999997 445655 999999999998 88899999987763
No 21
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=93.05 E-value=0.067 Score=30.77 Aligned_cols=43 Identities=26% Similarity=0.541 Sum_probs=21.6
Q ss_pred cccccccccCCCCCeeeeCCcccCHHhHhhhcCCCcccCCCCC
Q psy8111 91 FSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFASRCDGCSEIF 133 (135)
Q Consensus 91 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I 133 (135)
.+|+.|...|...--...=+..||..|..+.++..|..|+.|-
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Pa 50 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPA 50 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChH
Confidence 5677887776543222334788999999998899999998764
No 22
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=91.26 E-value=0.19 Score=28.91 Aligned_cols=47 Identities=19% Similarity=0.438 Sum_probs=24.5
Q ss_pred eeccccCCccCCCceEeECCeeeccCchhhhcCCchhhcCCccccCc
Q psy8111 30 FCCWQCDESLTGQRYVLRDDHPYCIKCYESVFANSCEECSKIIGIDS 76 (135)
Q Consensus 30 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~~~~ 76 (135)
++|+.|...|........=+..||..|....++..|+.|..|-+..+
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD 54 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQD 54 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-SS
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHHH
Confidence 67888988887643445557889999998888889999999986433
No 23
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=90.77 E-value=0.38 Score=25.26 Aligned_cols=39 Identities=18% Similarity=0.584 Sum_probs=28.0
Q ss_pred cccccccCC-CCCeeee-CCcccCHHhHhhhc--CCCcccCCC
Q psy8111 93 CSKCRQSLV-DKQFGSK-SEKIYCGNCYDAQF--ASRCDGCSE 131 (135)
Q Consensus 93 C~~C~~~l~-~~~~~~~-~~~~~C~~c~~~~~--~~~C~~C~~ 131 (135)
|..|...+. ...+.+. =|..+|..|..+.. ..+|..|++
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 566777773 2334444 49999999998888 678888864
No 24
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=90.76 E-value=0.18 Score=28.03 Aligned_cols=30 Identities=17% Similarity=0.398 Sum_probs=19.9
Q ss_pred CCchhhcCCccccCccccee--CCcccccccc
Q psy8111 62 ANSCEECSKIIGIDSKDLSY--KDKHWHEACF 91 (135)
Q Consensus 62 ~~~C~~C~~~I~~~~~~~~~--~~~~~H~~Cf 91 (135)
+.+|..|+++|.+.+.+|.- =+..||.+|+
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 46888888888644444442 3567777776
No 25
>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=89.30 E-value=0.2 Score=31.19 Aligned_cols=29 Identities=21% Similarity=0.334 Sum_probs=15.8
Q ss_pred CchhhcCCccccCcccceeCCcccccccc
Q psy8111 63 NSCEECSKIIGIDSKDLSYKDKHWHEACF 91 (135)
Q Consensus 63 ~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf 91 (135)
..|+.|+++|.....++...|..+|..|+
T Consensus 79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 46777777775333233334555666664
No 26
>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=88.96 E-value=0.18 Score=25.76 Aligned_cols=26 Identities=19% Similarity=0.381 Sum_probs=15.6
Q ss_pred hhhcCCccccCcccceeCCccccccc
Q psy8111 65 CEECSKIIGIDSKDLSYKDKHWHEAC 90 (135)
Q Consensus 65 C~~C~~~I~~~~~~~~~~~~~~H~~C 90 (135)
|.-|+++|.....++...++.|+.-|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC 26 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCC 26 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEEC
Confidence 45677777544445566777776433
No 27
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=87.79 E-value=0.53 Score=26.57 Aligned_cols=49 Identities=22% Similarity=0.666 Sum_probs=26.3
Q ss_pred CCchhhcCCccccCcccceeCCccccccccccccccccCCCCCeeeeCCcccCHHhHhhhcCCCcccCC
Q psy8111 62 ANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFASRCDGCS 130 (135)
Q Consensus 62 ~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~ 130 (135)
.++|..|+..|.+.+..+. |.|..|+..+... |..|-.....-+|..|+
T Consensus 7 ~~~CtSCg~~i~~~~~~~~----------F~CPnCG~~~I~R----------C~~CRk~~~~Y~CP~CG 55 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVK----------FLCPNCGEVIIYR----------CEKCRKQSNPYTCPKCG 55 (59)
T ss_pred CccccCCCCcccCCCccCE----------eeCCCCCCeeEee----------chhHHhcCCceECCCCC
Confidence 3567778777754332221 6677776653221 55554443344566654
No 28
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=83.48 E-value=0.99 Score=25.51 Aligned_cols=29 Identities=21% Similarity=0.625 Sum_probs=18.0
Q ss_pred CCchhhcCCccccCcccceeCCccccccccccccccccC
Q psy8111 62 ANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSL 100 (135)
Q Consensus 62 ~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 100 (135)
.+.|.+|+..|.+.+..+. |.|..|+..+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~----------F~CPnCGe~~ 37 (61)
T COG2888 9 PPVCTSCGREIAPGETAVK----------FPCPNCGEVE 37 (61)
T ss_pred CceeccCCCEeccCCceeE----------eeCCCCCcee
Confidence 4678888888755444332 6677777443
No 29
>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=83.26 E-value=1 Score=23.53 Aligned_cols=22 Identities=32% Similarity=0.832 Sum_probs=15.4
Q ss_pred eccccCCccCCCceEeECCeeeccCc
Q psy8111 31 CCWQCDESLTGQRYVLRDDHPYCIKC 56 (135)
Q Consensus 31 ~C~~C~~~l~~~~~~~~~~~~~C~~c 56 (135)
.|..|+.||- -.++|+.||..|
T Consensus 19 ~Cp~C~~PL~----~~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPLM----RDKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCeeE----EecCCCEECCCC
Confidence 4667777763 357888888766
No 30
>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=82.88 E-value=1.8 Score=24.10 Aligned_cols=43 Identities=12% Similarity=0.102 Sum_probs=27.9
Q ss_pred cccccccccCCCCCeeeeCCcccCHHhHhhhc--CCCcccCCCCCC
Q psy8111 91 FSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQF--ASRCDGCSEIFK 134 (135)
Q Consensus 91 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~--~~~C~~C~~~I~ 134 (135)
|.|..|+..+.+ ......|..||+.+..+.+ ...|..|++++.
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence 456777777655 3555667888888876543 356777777663
No 31
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=82.76 E-value=0.6 Score=32.99 Aligned_cols=31 Identities=29% Similarity=0.604 Sum_probs=26.6
Q ss_pred eeccccCCccCCCceEeECCeeeccCchhhh
Q psy8111 30 FCCWQCDESLTGQRYVLRDDHPYCIKCYESV 60 (135)
Q Consensus 30 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~ 60 (135)
-+|+.|+..+....-...+|+++|..|+.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 4789999999887777899999999998754
No 32
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=81.24 E-value=0.57 Score=33.12 Aligned_cols=31 Identities=23% Similarity=0.513 Sum_probs=27.1
Q ss_pred cccccccccCCCCCeeeeCCcccCHHhHhhh
Q psy8111 91 FSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQ 121 (135)
Q Consensus 91 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~ 121 (135)
-+|+.|+..+....-...||+++|..|+.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 5799999999887788889999999999754
No 33
>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=80.25 E-value=1.6 Score=21.90 Aligned_cols=40 Identities=18% Similarity=0.553 Sum_probs=22.0
Q ss_pred cccccccCCCCCeeee-CCcccCHHhHhhhc---CCCcccCCCCC
Q psy8111 93 CSKCRQSLVDKQFGSK-SEKIYCGNCYDAQF---ASRCDGCSEIF 133 (135)
Q Consensus 93 C~~C~~~l~~~~~~~~-~~~~~C~~c~~~~~---~~~C~~C~~~I 133 (135)
|..|...+.. .+... =+..+|..|..+.+ ..+|..|+..+
T Consensus 2 C~iC~~~~~~-~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 2 CPICLEEFRE-PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCcCchhhhC-ceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 4455555522 22222 46677777775443 34688887653
No 34
>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=80.22 E-value=1 Score=24.15 Aligned_cols=42 Identities=17% Similarity=0.478 Sum_probs=27.5
Q ss_pred ccccccccCCCCCeeeeCCcc-cCHHhHhhh--cCCCcccCCCCCC
Q psy8111 92 SCSKCRQSLVDKQFGSKSEKI-YCGNCYDAQ--FASRCDGCSEIFK 134 (135)
Q Consensus 92 ~C~~C~~~l~~~~~~~~~~~~-~C~~c~~~~--~~~~C~~C~~~I~ 134 (135)
.|..|.....+ .....=|.. +|..|+.+. ...+|..|.++|.
T Consensus 4 ~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 4 ECPICFENPRD-VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp B-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred CCccCCccCCc-eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 45666665433 233334667 999999876 4689999999885
No 35
>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=80.05 E-value=1.1 Score=22.61 Aligned_cols=25 Identities=24% Similarity=0.498 Sum_probs=18.7
Q ss_pred eeccccCCccCCCceEeECCeeeccCchh
Q psy8111 30 FCCWQCDESLTGQRYVLRDDHPYCIKCYE 58 (135)
Q Consensus 30 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~ 58 (135)
+.|..|+.. .|...+|..||.+|..
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEhhhCce
Confidence 447888665 4778999999987754
No 36
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=79.69 E-value=1.6 Score=19.67 Aligned_cols=8 Identities=38% Similarity=1.028 Sum_probs=3.3
Q ss_pred hhhcCCcc
Q psy8111 65 CEECSKII 72 (135)
Q Consensus 65 C~~C~~~I 72 (135)
|..|+..|
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 33444444
No 37
>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=78.73 E-value=1.1 Score=26.20 Aligned_cols=60 Identities=20% Similarity=0.461 Sum_probs=25.6
Q ss_pred eccccCCccCCCceEeECCeeeccCchhh-hcCCchhhcCCccccCcccceeCCccccccccccccccccCCCC
Q psy8111 31 CCWQCDESLTGQRYVLRDDHPYCIKCYES-VFANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDK 103 (135)
Q Consensus 31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~-~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~ 103 (135)
.|..|..+|+. .++..+|..|... ...+.|+.|++++. ++.|=|.. =|.|..|+..++.+
T Consensus 3 ~CP~C~~~L~~-----~~~~~~C~~C~~~~~~~a~CPdC~~~Le----~LkACGAv----dYFC~~c~gLiSKk 63 (70)
T PF07191_consen 3 TCPKCQQELEW-----QGGHYHCEACQKDYKKEAFCPDCGQPLE----VLKACGAV----DYFCNHCHGLISKK 63 (70)
T ss_dssp B-SSS-SBEEE-----ETTEEEETTT--EEEEEEE-TTT-SB-E----EEEETTEE----EEE-TTTT-EE-TT
T ss_pred cCCCCCCccEE-----eCCEEECccccccceecccCCCcccHHH----HHHHhccc----ceeeccCCceeecc
Confidence 35555555532 2356666655432 12357777888773 45554421 14466666666544
No 38
>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=78.56 E-value=0.3 Score=24.57 Aligned_cols=26 Identities=15% Similarity=0.601 Sum_probs=10.0
Q ss_pred cccccccCCCCCeeeeCCcccCHHhH
Q psy8111 93 CSKCRQSLVDKQFGSKSEKIYCGNCY 118 (135)
Q Consensus 93 C~~C~~~l~~~~~~~~~~~~~C~~c~ 118 (135)
|..|+.++.........+..+|..|.
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~ 31 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQ 31 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHh
Confidence 34444444333333334444444443
No 39
>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=77.67 E-value=1.5 Score=27.18 Aligned_cols=28 Identities=21% Similarity=0.408 Sum_probs=21.9
Q ss_pred ccccccccCCCCCeeee-CCcccCHHhHh
Q psy8111 92 SCSKCRQSLVDKQFGSK-SEKIYCGNCYD 119 (135)
Q Consensus 92 ~C~~C~~~l~~~~~~~~-~~~~~C~~c~~ 119 (135)
.|..|+++|+.+.|... +|.++...|..
T Consensus 80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 49999999998877665 67887777753
No 40
>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=77.19 E-value=4.8 Score=22.48 Aligned_cols=42 Identities=19% Similarity=0.580 Sum_probs=28.0
Q ss_pred cccccccCCCC---CeeeeCCcccCHHhHhhhcCCCcccCCCCCC
Q psy8111 93 CSKCRQSLVDK---QFGSKSEKIYCGNCYDAQFASRCDGCSEIFK 134 (135)
Q Consensus 93 C~~C~~~l~~~---~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~ 134 (135)
|..|++.|... .+.-.-.=-||.+|.+..+...|..|+..+.
T Consensus 8 CE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCgGelv 52 (57)
T PF06906_consen 8 CECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCGGELV 52 (57)
T ss_pred ccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCCCccc
Confidence 55666666533 2222334567889988888889999987654
No 41
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=75.74 E-value=0.82 Score=28.72 Aligned_cols=28 Identities=29% Similarity=0.577 Sum_probs=15.4
Q ss_pred chhhcCCccccCccccee-CCccccccccc
Q psy8111 64 SCEECSKIIGIDSKDLSY-KDKHWHEACFS 92 (135)
Q Consensus 64 ~C~~C~~~I~~~~~~~~~-~~~~~H~~Cf~ 92 (135)
+|..|+++|. .++..++ .+..-|-.||+
T Consensus 4 kC~iCg~~I~-~gqlFTF~~kG~VH~~C~~ 32 (101)
T PF09943_consen 4 KCYICGKPIY-EGQLFTFTKKGPVHYECFR 32 (101)
T ss_pred EEEecCCeee-ecceEEEecCCcEeHHHHH
Confidence 5666777765 3334333 33455666665
No 42
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=75.40 E-value=2.3 Score=28.02 Aligned_cols=23 Identities=26% Similarity=0.709 Sum_probs=18.0
Q ss_pred eccccCCccCCCceEeECCeeeccCchh
Q psy8111 31 CCWQCDESLTGQRYVLRDDHPYCIKCYE 58 (135)
Q Consensus 31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~ 58 (135)
.|..|+.|| |- ++|.+||.-|-.
T Consensus 30 hCp~Cg~PL----F~-KdG~v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTPL----FR-KDGEVFCPVCGY 52 (131)
T ss_pred hCcccCCcc----ee-eCCeEECCCCCc
Confidence 467888877 44 999999998864
No 43
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=75.18 E-value=0.5 Score=29.33 Aligned_cols=59 Identities=20% Similarity=0.541 Sum_probs=36.5
Q ss_pred chhhcCCccccCcccceeCCccccccccccccccccCCCCCeeeeCCcccCHHhHhhhcCCCcc
Q psy8111 64 SCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFASRCD 127 (135)
Q Consensus 64 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~ 127 (135)
.|..|...+. +.......-..+++.+.-|..|.+.|.-..|...+.=||| +..|.|+|.
T Consensus 37 aCy~CHdel~-~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C----~spFNp~Ck 95 (105)
T COG4357 37 ACYHCHDELE-DHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYC----QSPFNPGCK 95 (105)
T ss_pred hHHHHHhHHh-cCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCc----CCCCCcccc
Confidence 4555665553 2233444446678888888888888876667666665555 345555553
No 44
>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=74.02 E-value=2 Score=26.47 Aligned_cols=42 Identities=21% Similarity=0.385 Sum_probs=27.5
Q ss_pred cccCCCCeeccccCCccCCCceEeECCeeeccCchhhhcCCchhhcCCccc
Q psy8111 23 DRGSGQHFCCWQCDESLTGQRYVLRDDHPYCIKCYESVFANSCEECSKIIG 73 (135)
Q Consensus 23 ~~H~~~cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~ 73 (135)
.|-+. --.|..|+..+.. .|.-||+.|..+. ..|+-|++.|.
T Consensus 39 Py~~~-~~~C~~CK~~v~q------~g~~YCq~CAYkk--GiCamCGKki~ 80 (90)
T PF10235_consen 39 PYAPY-SSKCKICKTKVHQ------PGAKYCQTCAYKK--GICAMCGKKIL 80 (90)
T ss_pred ccccc-Ccccccccccccc------CCCccChhhhccc--CcccccCCeec
Confidence 34443 3456677655532 3677898887664 48888888884
No 45
>KOG4739|consensus
Probab=72.21 E-value=2.9 Score=30.30 Aligned_cols=40 Identities=20% Similarity=0.498 Sum_probs=27.0
Q ss_pred cccccCCCCCeeeeC-CcccCHHhHhhhcCCCcccCCCCCC
Q psy8111 95 KCRQSLVDKQFGSKS-EKIYCGNCYDAQFASRCDGCSEIFK 134 (135)
Q Consensus 95 ~C~~~l~~~~~~~~~-~~~~C~~c~~~~~~~~C~~C~~~I~ 134 (135)
.|.+.=....|++.. ..++|..|.....++.|.-|+++|.
T Consensus 8 ~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir 48 (233)
T KOG4739|consen 8 KCFRFPSQDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIR 48 (233)
T ss_pred cccccCCCCceeeeechhhhhhhhcccCCccccccccceee
Confidence 333333344565554 7888888887777778888888764
No 46
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=71.87 E-value=3.1 Score=22.71 Aligned_cols=29 Identities=21% Similarity=0.513 Sum_probs=19.3
Q ss_pred ccccccccCCCC-CeeeeCCcccCHHhHhhh
Q psy8111 92 SCSKCRQSLVDK-QFGSKSEKIYCGNCYDAQ 121 (135)
Q Consensus 92 ~C~~C~~~l~~~-~~~~~~~~~~C~~c~~~~ 121 (135)
.|..|+..++-- .+-..|| ..|.+|+.+.
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 367777777643 3556677 5788888665
No 47
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=71.32 E-value=2.4 Score=19.59 Aligned_cols=13 Identities=15% Similarity=0.079 Sum_probs=7.9
Q ss_pred CcccccccCcccc
Q psy8111 1 MESAVKHQDKSFR 13 (135)
Q Consensus 1 ~~~~C~~C~~~i~ 13 (135)
|+..|..|+..|.
T Consensus 1 m~~~Cp~Cg~~~~ 13 (26)
T PF13248_consen 1 MEMFCPNCGAEID 13 (26)
T ss_pred CcCCCcccCCcCC
Confidence 4566666666554
No 48
>KOG0320|consensus
Probab=71.27 E-value=3.2 Score=28.85 Aligned_cols=47 Identities=21% Similarity=0.685 Sum_probs=36.5
Q ss_pred ccccccccccccCCCC-CeeeeCCcccCHHhHhhh--cCCCcccCCCCCC
Q psy8111 88 EACFSCSKCRQSLVDK-QFGSKSEKIYCGNCYDAQ--FASRCDGCSEIFK 134 (135)
Q Consensus 88 ~~Cf~C~~C~~~l~~~-~~~~~~~~~~C~~c~~~~--~~~~C~~C~~~I~ 134 (135)
..+|+|..|-...... .+...=|.+||+.|.... .+.+|..|.+-|.
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 4678888887777654 355677999999999764 4679999998775
No 49
>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=69.78 E-value=3.1 Score=22.90 Aligned_cols=27 Identities=22% Similarity=0.629 Sum_probs=15.3
Q ss_pred ccccCCccCCCceEeECCeeecc-Cchh
Q psy8111 32 CWQCDESLTGQRYVLRDDHPYCI-KCYE 58 (135)
Q Consensus 32 C~~C~~~l~~~~~~~~~~~~~C~-~c~~ 58 (135)
|..|...++...-+.+||+.||. .|..
T Consensus 10 C~~C~C~V~~~~Ai~~dGk~YCS~aCA~ 37 (52)
T PF02069_consen 10 CPSCSCVVSEEEAIQKDGKYYCSEACAN 37 (52)
T ss_dssp STT----B-TTTSEESSS-EESSHHHHH
T ss_pred CCCCEeEECchHhHHhCCEeeecHHHhc
Confidence 56777777766788999999985 4543
No 50
>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=69.78 E-value=1.9 Score=26.46 Aligned_cols=16 Identities=31% Similarity=1.134 Sum_probs=12.9
Q ss_pred hhhhcCCchhhcCCcc
Q psy8111 57 YESVFANSCEECSKII 72 (135)
Q Consensus 57 ~~~~~~~~C~~C~~~I 72 (135)
|..+|...|..|++.+
T Consensus 49 Y~~lfs~pC~~C~klL 64 (90)
T PF11571_consen 49 YRNLFSTPCKKCGKLL 64 (90)
T ss_pred HhhhccchhhHHHhHh
Confidence 4567778999999988
No 51
>PF12773 DZR: Double zinc ribbon
Probab=68.32 E-value=6.5 Score=20.86 Aligned_cols=23 Identities=30% Similarity=0.676 Sum_probs=12.2
Q ss_pred cccccccCCCCCeeeeCCcccCHHhHh
Q psy8111 93 CSKCRQSLVDKQFGSKSEKIYCGNCYD 119 (135)
Q Consensus 93 C~~C~~~l~~~~~~~~~~~~~C~~c~~ 119 (135)
|..|+.+|. .......+|..|-.
T Consensus 15 C~~CG~~l~----~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 15 CPHCGTPLP----PPDQSKKICPNCGA 37 (50)
T ss_pred ChhhcCChh----hccCCCCCCcCCcC
Confidence 667777776 12223445555543
No 52
>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=66.79 E-value=1.3 Score=26.39 Aligned_cols=31 Identities=26% Similarity=0.540 Sum_probs=17.8
Q ss_pred CCchhhcCCccccCccccee-----CC-----ccccccccc
Q psy8111 62 ANSCEECSKIIGIDSKDLSY-----KD-----KHWHEACFS 92 (135)
Q Consensus 62 ~~~C~~C~~~I~~~~~~~~~-----~~-----~~~H~~Cf~ 92 (135)
..+|..|++.|..++..|.. .+ .-||..||.
T Consensus 7 Ra~Ck~C~~~I~kg~lRiG~~~~~~~~~~~~~~W~H~~C~~ 47 (82)
T PF00645_consen 7 RAKCKGCKKKIAKGELRIGKIVPSPEGDGDIPKWYHWDCFF 47 (82)
T ss_dssp TEBETTTSCBE-TTSEEEEEEEEETTSSCEEEEEEEHHHHH
T ss_pred CccCcccCCcCCCCCEEEEEEecccccCCCCCceECccccc
Confidence 45788899988644332221 11 346888876
No 53
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=66.59 E-value=5.6 Score=33.23 Aligned_cols=9 Identities=22% Similarity=0.944 Sum_probs=4.0
Q ss_pred chhhcCCcc
Q psy8111 64 SCEECSKII 72 (135)
Q Consensus 64 ~C~~C~~~I 72 (135)
.|..|+..+
T Consensus 29 ~Cp~CG~~~ 37 (645)
T PRK14559 29 PCPQCGTEV 37 (645)
T ss_pred cCCCCCCCC
Confidence 344444443
No 54
>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=65.95 E-value=4.9 Score=27.28 Aligned_cols=11 Identities=18% Similarity=0.268 Sum_probs=5.6
Q ss_pred ccccCcccccc
Q psy8111 5 VKHQDKSFRED 15 (135)
Q Consensus 5 C~~C~~~i~~~ 15 (135)
|..|+-+|.|.
T Consensus 42 Cp~C~~~IrG~ 52 (158)
T PF10083_consen 42 CPNCSTPIRGD 52 (158)
T ss_pred CcCCCCCCCCc
Confidence 45555555543
No 55
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=63.51 E-value=3.7 Score=24.72 Aligned_cols=28 Identities=32% Similarity=0.952 Sum_probs=17.4
Q ss_pred cccccccCCCCC-eeee-C---CcccCHHhHhh
Q psy8111 93 CSKCRQSLVDKQ-FGSK-S---EKIYCGNCYDA 120 (135)
Q Consensus 93 C~~C~~~l~~~~-~~~~-~---~~~~C~~c~~~ 120 (135)
|.+|+.||.... +... | +.-||.-||..
T Consensus 3 CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 3 CQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred CCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 677888886554 2222 2 45688888753
No 56
>KOG2682|consensus
Probab=63.45 E-value=2.6 Score=30.87 Aligned_cols=50 Identities=16% Similarity=0.338 Sum_probs=35.6
Q ss_pred CcccceeCCccccccccccccccccCCCCCeeeeCCcccCHHhHhhhcCCCcccCCCCCCC
Q psy8111 75 DSKDLSYKDKHWHEACFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFASRCDGCSEIFKA 135 (135)
Q Consensus 75 ~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~~ 135 (135)
++..|+|.|...|..|.. .|++....+-+ +.+....-.|||..|+..|.|
T Consensus 140 d~~lvEAHGtFa~s~Ci~--~C~~~yp~e~~---------ka~i~~~~vpkC~vC~~lVKP 189 (314)
T KOG2682|consen 140 DEDLVEAHGTFATSHCIS--SCRHEYPLEWM---------KAKIMSEVVPKCEVCQGLVKP 189 (314)
T ss_pred HHHHHHhccceeeeeehh--hhcCcCCHHHH---------HHHHHhccCCCCchhhccccc
Confidence 456788888888887764 57777765522 444555566899999988876
No 57
>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=62.51 E-value=5.6 Score=18.23 Aligned_cols=10 Identities=0% Similarity=0.023 Sum_probs=4.6
Q ss_pred ccccCccccc
Q psy8111 5 VKHQDKSFRE 14 (135)
Q Consensus 5 C~~C~~~i~~ 14 (135)
|..|+.+|.+
T Consensus 1 C~sC~~~i~~ 10 (24)
T PF07754_consen 1 CTSCGRPIAP 10 (24)
T ss_pred CccCCCcccC
Confidence 3445555443
No 58
>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=62.49 E-value=6.7 Score=20.64 Aligned_cols=10 Identities=30% Similarity=0.810 Sum_probs=5.5
Q ss_pred cccCHHhHhh
Q psy8111 111 KIYCGNCYDA 120 (135)
Q Consensus 111 ~~~C~~c~~~ 120 (135)
--+|.+||..
T Consensus 23 ~dLC~~Cf~~ 32 (46)
T cd02249 23 FDLCSSCYAK 32 (46)
T ss_pred CcCHHHHHCc
Confidence 3456666653
No 59
>PRK00420 hypothetical protein; Validated
Probab=62.45 E-value=5.5 Score=25.57 Aligned_cols=25 Identities=24% Similarity=0.387 Sum_probs=17.1
Q ss_pred eeccccCCccCCCceEeECCeeeccCchh
Q psy8111 30 FCCWQCDESLTGQRYVLRDDHPYCIKCYE 58 (135)
Q Consensus 30 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~ 58 (135)
-.|..|+.+| |-.++|+.||..|-.
T Consensus 24 ~~CP~Cg~pL----f~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPL----FELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcc----eecCCCceECCCCCC
Confidence 3567787776 334788888887744
No 60
>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=62.18 E-value=3.9 Score=20.49 Aligned_cols=13 Identities=31% Similarity=0.396 Sum_probs=6.7
Q ss_pred CcccccccCcccc
Q psy8111 1 MESAVKHQDKSFR 13 (135)
Q Consensus 1 ~~~~C~~C~~~i~ 13 (135)
|...|..|+..+.
T Consensus 1 M~~~CP~C~~~~~ 13 (38)
T TIGR02098 1 MRIQCPNCKTSFR 13 (38)
T ss_pred CEEECCCCCCEEE
Confidence 4445556655543
No 61
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=61.86 E-value=5.6 Score=22.40 Aligned_cols=27 Identities=30% Similarity=0.907 Sum_probs=20.2
Q ss_pred eccccCCccCC-C-ceEeECCeeecc-Cch
Q psy8111 31 CCWQCDESLTG-Q-RYVLRDDHPYCI-KCY 57 (135)
Q Consensus 31 ~C~~C~~~l~~-~-~~~~~~~~~~C~-~c~ 57 (135)
.|..|++.|.. . .|..++++++|. +|-
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS~ECR 47 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCSEECR 47 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccccHHHH
Confidence 46788999984 3 677888999996 443
No 62
>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=61.52 E-value=3.1 Score=20.89 Aligned_cols=22 Identities=9% Similarity=0.244 Sum_probs=13.8
Q ss_pred eeCCCcccCCCCeeccccCCccC
Q psy8111 18 KLGGKDRGSGQHFCCWQCDESLT 40 (135)
Q Consensus 18 ~a~~~~~H~~~cf~C~~C~~~l~ 40 (135)
...++.||.. =..|..||-.+.
T Consensus 11 ~p~~RR~~~~-~isC~~CGPr~~ 32 (35)
T PF07503_consen 11 DPSNRRFHYQ-FISCTNCGPRYS 32 (35)
T ss_dssp STTSTTTT-T-T--BTTCC-SCC
T ss_pred CCCCCcccCc-CccCCCCCCCEE
Confidence 3457999999 888999987653
No 63
>KOG1813|consensus
Probab=61.36 E-value=4.8 Score=30.23 Aligned_cols=43 Identities=23% Similarity=0.580 Sum_probs=32.6
Q ss_pred cccccccccCCCCCeeeeCCcccCHHhHhhhc--CCCcccCCCCCC
Q psy8111 91 FSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQF--ASRCDGCSEIFK 134 (135)
Q Consensus 91 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~--~~~C~~C~~~I~ 134 (135)
|.|..|.+.+-. .....-+.-+|+.|.-+.| +++|..|++.+.
T Consensus 242 f~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~ 286 (313)
T KOG1813|consen 242 FKCFICRKYFYR-PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTH 286 (313)
T ss_pred cccccccccccc-chhhcCCceeehhhhccccccCCcceecccccc
Confidence 778888888754 3555667888999987766 479999998763
No 64
>KOG3002|consensus
Probab=59.35 E-value=8.3 Score=29.08 Aligned_cols=43 Identities=19% Similarity=0.575 Sum_probs=34.1
Q ss_pred cccccccccCCCCCeeeeCCcccCHHhHhhhcCCCcccCCCCCC
Q psy8111 91 FSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFASRCDGCSEIFK 134 (135)
Q Consensus 91 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~ 134 (135)
+.|..|-..|..-.|.-.+|.+.|..|-. +...+|..|..+|.
T Consensus 49 leCPvC~~~l~~Pi~QC~nGHlaCssC~~-~~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 49 LDCPVCFNPLSPPIFQCDNGHLACSSCRT-KVSNKCPTCRLPIG 91 (299)
T ss_pred ccCchhhccCcccceecCCCcEehhhhhh-hhcccCCccccccc
Confidence 55777778887777888899999999964 44679999998875
No 65
>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=58.50 E-value=9.6 Score=19.87 Aligned_cols=11 Identities=18% Similarity=0.730 Sum_probs=7.0
Q ss_pred CcccCHHhHhh
Q psy8111 110 EKIYCGNCYDA 120 (135)
Q Consensus 110 ~~~~C~~c~~~ 120 (135)
+.-+|..||.+
T Consensus 26 d~dlC~~Cf~~ 36 (44)
T smart00291 26 DYDLCQSCFAK 36 (44)
T ss_pred CccchHHHHhC
Confidence 34468888764
No 66
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=57.73 E-value=12 Score=26.40 Aligned_cols=44 Identities=18% Similarity=0.480 Sum_probs=28.9
Q ss_pred ccccccccccCCCCCeeeeCCcccCHHhHhhh------------------cCCCcccCCCCCC
Q psy8111 90 CFSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQ------------------FASRCDGCSEIFK 134 (135)
Q Consensus 90 Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~------------------~~~~C~~C~~~I~ 134 (135)
-|.|..|...+.+ .....=|..||..|..+- -.++|..|..+|.
T Consensus 18 ~~~CpICld~~~d-PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is 79 (193)
T PLN03208 18 DFDCNICLDQVRD-PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVS 79 (193)
T ss_pred ccCCccCCCcCCC-cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCC
Confidence 3667777766543 244456778888887532 1358999998875
No 67
>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=57.36 E-value=4.5 Score=20.32 Aligned_cols=37 Identities=22% Similarity=0.651 Sum_probs=19.1
Q ss_pred cccccccCCCCCeeeeCCcccCHHhHhhhc--CCCcccC
Q psy8111 93 CSKCRQSLVDKQFGSKSEKIYCGNCYDAQF--ASRCDGC 129 (135)
Q Consensus 93 C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~--~~~C~~C 129 (135)
|..|...+.+......=|..||..|..+.+ ..+|..|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 344555554422334458888888876543 3445433
No 68
>KOG0978|consensus
Probab=56.96 E-value=3.3 Score=34.67 Aligned_cols=44 Identities=25% Similarity=0.745 Sum_probs=26.9
Q ss_pred cccccccccCCCCCeeeeCCcccCHHhHhhhcC---CCcccCCCCCCC
Q psy8111 91 FSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQFA---SRCDGCSEIFKA 135 (135)
Q Consensus 91 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~---~~C~~C~~~I~~ 135 (135)
.+|+.|+..-.+ .....=+.+||..|..+++. .+|.+|+.+..|
T Consensus 644 LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 644 LKCSVCNTRWKD-AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred eeCCCccCchhh-HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 456666633222 12233467788888777765 478888877654
No 69
>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=56.91 E-value=3 Score=19.82 Aligned_cols=11 Identities=27% Similarity=0.724 Sum_probs=5.1
Q ss_pred CchhhcCCccc
Q psy8111 63 NSCEECSKIIG 73 (135)
Q Consensus 63 ~~C~~C~~~I~ 73 (135)
.+|.+|+..|.
T Consensus 2 ~~C~rC~~~~~ 12 (30)
T PF06827_consen 2 EKCPRCWNYIE 12 (30)
T ss_dssp SB-TTT--BBE
T ss_pred CcCccCCCcce
Confidence 46777777773
No 70
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=56.27 E-value=5.1 Score=20.10 Aligned_cols=7 Identities=57% Similarity=1.350 Sum_probs=3.0
Q ss_pred ccccccc
Q psy8111 92 SCSKCRQ 98 (135)
Q Consensus 92 ~C~~C~~ 98 (135)
+|+.|+.
T Consensus 27 ~C~~C~~ 33 (36)
T PF13717_consen 27 RCSKCGH 33 (36)
T ss_pred ECCCCCC
Confidence 4444443
No 71
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=55.82 E-value=4.9 Score=28.52 Aligned_cols=41 Identities=17% Similarity=0.605 Sum_probs=31.9
Q ss_pred cccccccccCCCCCeeeeCCcccCHHhHhhhc--CCCcccCCCC
Q psy8111 91 FSCSKCRQSLVDKQFGSKSEKIYCGNCYDAQF--ASRCDGCSEI 132 (135)
Q Consensus 91 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~--~~~C~~C~~~ 132 (135)
|.|..|++.... ..+..=|.-+|..|+-+.+ ++.|..|++.
T Consensus 197 F~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~ 239 (259)
T COG5152 197 FLCGICKKDYES-PVVTECGHSFCSLCAIRKYQKGDECGVCGKA 239 (259)
T ss_pred eeehhchhhccc-hhhhhcchhHHHHHHHHHhccCCcceecchh
Confidence 788889887754 3555668899999998766 5899999864
No 72
>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=55.77 E-value=4.5 Score=21.41 Aligned_cols=30 Identities=27% Similarity=0.702 Sum_probs=14.3
Q ss_pred eeccccCC-ccCCCceEe--ECCeeeccCchhh
Q psy8111 30 FCCWQCDE-SLTGQRYVL--RDDHPYCIKCYES 59 (135)
Q Consensus 30 f~C~~C~~-~l~~~~~~~--~~~~~~C~~c~~~ 59 (135)
+.|+.|+. ++.+..|.= =.+--+|.+||.+
T Consensus 5 ~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~ 37 (46)
T PF00569_consen 5 YTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSK 37 (46)
T ss_dssp CE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH
T ss_pred eECcCCCCCcCcCCeEECCCCCCCchhhHHHhC
Confidence 56777766 555543321 1234466666654
No 73
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=54.78 E-value=6.6 Score=19.77 Aligned_cols=13 Identities=23% Similarity=0.286 Sum_probs=7.4
Q ss_pred CcccccccCcccc
Q psy8111 1 MESAVKHQDKSFR 13 (135)
Q Consensus 1 ~~~~C~~C~~~i~ 13 (135)
|...|..|+....
T Consensus 1 M~i~CP~C~~~f~ 13 (37)
T PF13719_consen 1 MIITCPNCQTRFR 13 (37)
T ss_pred CEEECCCCCceEE
Confidence 4556666666543
No 74
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=54.68 E-value=8.5 Score=24.22 Aligned_cols=33 Identities=12% Similarity=0.377 Sum_probs=26.3
Q ss_pred cccccccccCC-CCCeeeeCCcccCHHhHhhhcC
Q psy8111 91 FSCSKCRQSLV-DKQFGSKSEKIYCGNCYDAQFA 123 (135)
Q Consensus 91 f~C~~C~~~l~-~~~~~~~~~~~~C~~c~~~~~~ 123 (135)
++|..|+.++- ++.|.+..+-|..-.|+.+..+
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~~ 36 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREKAS 36 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHHHh
Confidence 57999999986 5567777778999999976544
No 75
>KOG2462|consensus
Probab=54.16 E-value=2 Score=31.81 Aligned_cols=35 Identities=20% Similarity=0.282 Sum_probs=17.5
Q ss_pred ccccCccccccceeeCCCccc-----CCCCeeccccCCccC
Q psy8111 5 VKHQDKSFREDYNKLGGKDRG-----SGQHFCCWQCDESLT 40 (135)
Q Consensus 5 C~~C~~~i~~~~i~a~~~~~H-----~~~cf~C~~C~~~l~ 40 (135)
|..|++.....--.+--+..| .. =|.|..|++.-.
T Consensus 133 c~eCgk~ysT~snLsrHkQ~H~~~~s~k-a~~C~~C~K~Yv 172 (279)
T KOG2462|consen 133 CPECGKSYSTSSNLSRHKQTHRSLDSKK-AFSCKYCGKVYV 172 (279)
T ss_pred ccccccccccccccchhhcccccccccc-cccCCCCCceee
Confidence 556666554333222333444 33 466777766543
No 76
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=52.55 E-value=5.6 Score=19.86 Aligned_cols=10 Identities=40% Similarity=1.016 Sum_probs=3.3
Q ss_pred CchhhcCCcc
Q psy8111 63 NSCEECSKII 72 (135)
Q Consensus 63 ~~C~~C~~~I 72 (135)
+.|..|+++.
T Consensus 4 ~~C~eC~~~f 13 (34)
T PF01286_consen 4 PKCDECGKPF 13 (34)
T ss_dssp EE-TTT--EE
T ss_pred chHhHhCCHH
Confidence 3444555544
No 77
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=52.42 E-value=9.6 Score=32.13 Aligned_cols=81 Identities=15% Similarity=0.268 Sum_probs=50.7
Q ss_pred cccccCccccccceeeCCCcccCCCCeeccccCCccCCCceEeECCeeeccCchhhhcCCchhhcCCccccCcccceeCC
Q psy8111 4 AVKHQDKSFREDYNKLGGKDRGSGQHFCCWQCDESLTGQRYVLRDDHPYCIKCYESVFANSCEECSKIIGIDSKDLSYKD 83 (135)
Q Consensus 4 ~C~~C~~~i~~~~i~a~~~~~H~~~cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~ 83 (135)
+|..|-+.|.+. .++.||-- --.|..|+-. |...+..||=..--...--+.|..|.+. +-...+
T Consensus 103 ~C~~Cl~Ei~dp----~~rrY~YP-F~~CT~CGPR-----fTIi~alPYDR~nTsM~~F~lC~~C~~E------Y~dP~n 166 (750)
T COG0068 103 TCEDCLEEIFDP----NSRRYLYP-FINCTNCGPR-----FTIIEALPYDRENTSMADFPLCPFCDKE------YKDPLN 166 (750)
T ss_pred hhHHHHHHhcCC----CCcceecc-ccccCCCCcc-----eeeeccCCCCcccCccccCcCCHHHHHH------hcCccc
Confidence 566676666553 46788888 7789999644 4444444442111111112566666553 234568
Q ss_pred ccccccccccccccccC
Q psy8111 84 KHWHEACFSCSKCRQSL 100 (135)
Q Consensus 84 ~~~H~~Cf~C~~C~~~l 100 (135)
+.||.+=..|..|+-.+
T Consensus 167 RRfHAQp~aCp~CGP~~ 183 (750)
T COG0068 167 RRFHAQPIACPKCGPHL 183 (750)
T ss_pred cccccccccCcccCCCe
Confidence 99999989999998876
No 78
>KOG4739|consensus
Probab=52.00 E-value=9.8 Score=27.64 Aligned_cols=42 Identities=24% Similarity=0.586 Sum_probs=30.9
Q ss_pred ccccCCccCCCceEeEC-CeeeccCchhhhcCCchhhcCCccc
Q psy8111 32 CWQCDESLTGQRYVLRD-DHPYCIKCYESVFANSCEECSKIIG 73 (135)
Q Consensus 32 C~~C~~~l~~~~~~~~~-~~~~C~~c~~~~~~~~C~~C~~~I~ 73 (135)
|..|...=...+|+... ..++|+.|.....++.|.-|+++|.
T Consensus 6 Cn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir 48 (233)
T KOG4739|consen 6 CNKCFRFPSQDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIR 48 (233)
T ss_pred eccccccCCCCceeeeechhhhhhhhcccCCccccccccceee
Confidence 33444444455677654 7899999998888789999999984
No 79
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=51.50 E-value=8.3 Score=21.35 Aligned_cols=25 Identities=16% Similarity=0.199 Sum_probs=15.8
Q ss_pred CchhhcCCccccCcccceeCCccccc
Q psy8111 63 NSCEECSKIIGIDSKDLSYKDKHWHE 88 (135)
Q Consensus 63 ~~C~~C~~~I~~~~~~~~~~~~~~H~ 88 (135)
.+|..|++||.+. ..+...+..-|+
T Consensus 2 ~~CvVCKqpi~~a-~~v~T~~G~VH~ 26 (54)
T PF10886_consen 2 EICVVCKQPIDDA-LVVETESGPVHP 26 (54)
T ss_pred CeeeeeCCccCcc-eEEEcCCCccCc
Confidence 4688888888633 445555556665
No 80
>PRK14873 primosome assembly protein PriA; Provisional
Probab=50.60 E-value=13 Score=31.19 Aligned_cols=57 Identities=12% Similarity=0.171 Sum_probs=36.1
Q ss_pred ccceeeCCCcccCCCCeeccccCCccCCC------ceEeECCeeeccCchhhhcCCchhhcCCc
Q psy8111 14 EDYNKLGGKDRGSGQHFCCWQCDESLTGQ------RYVLRDDHPYCIKCYESVFANSCEECSKI 71 (135)
Q Consensus 14 ~~~i~a~~~~~H~~~cf~C~~C~~~l~~~------~~~~~~~~~~C~~c~~~~~~~~C~~C~~~ 71 (135)
|++|...++.-... -+.|..|+..+.=. .|...++.+.|..|-.......|..|+..
T Consensus 369 gqvll~lnRrGyap-~l~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 369 GPVLVQVPRRGYVP-SLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred CcEEEEecCCCCCC-eeEhhhCcCeeECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 45555556544444 46666666655311 24345678889999776666799999876
No 81
>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=48.47 E-value=18 Score=19.42 Aligned_cols=11 Identities=18% Similarity=0.356 Sum_probs=6.9
Q ss_pred cccCHHhHhhh
Q psy8111 111 KIYCGNCYDAQ 121 (135)
Q Consensus 111 ~~~C~~c~~~~ 121 (135)
--+|..||...
T Consensus 26 ~DlC~~C~~~~ 36 (48)
T cd02341 26 FDLCQDCVVKG 36 (48)
T ss_pred CccCHHHHhCc
Confidence 34577777654
No 82
>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=48.34 E-value=6.5 Score=20.36 Aligned_cols=12 Identities=17% Similarity=0.628 Sum_probs=8.3
Q ss_pred eeccccCCccCC
Q psy8111 30 FCCWQCDESLTG 41 (135)
Q Consensus 30 f~C~~C~~~l~~ 41 (135)
|+|..|+..++.
T Consensus 6 y~C~~Cg~~fe~ 17 (42)
T PF09723_consen 6 YRCEECGHEFEV 17 (42)
T ss_pred EEeCCCCCEEEE
Confidence 778888766653
No 83
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=48.28 E-value=22 Score=32.08 Aligned_cols=11 Identities=27% Similarity=0.779 Sum_probs=5.9
Q ss_pred cccccccCCCC
Q psy8111 93 CSKCRQSLVDK 103 (135)
Q Consensus 93 C~~C~~~l~~~ 103 (135)
|..|+.++...
T Consensus 712 CP~CGtplv~~ 722 (1337)
T PRK14714 712 CPRCDVELTPY 722 (1337)
T ss_pred CCCCCCccccc
Confidence 55566555443
No 84
>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=47.28 E-value=24 Score=26.84 Aligned_cols=26 Identities=23% Similarity=0.699 Sum_probs=18.4
Q ss_pred CCcccCHHhHhhhcC---CCcccCCCCCC
Q psy8111 109 SEKIYCGNCYDAQFA---SRCDGCSEIFK 134 (135)
Q Consensus 109 ~~~~~C~~c~~~~~~---~~C~~C~~~I~ 134 (135)
=|..+|..|..+.|. ..|..|+.++.
T Consensus 26 CGH~~C~sCv~~l~~~~~~~CP~C~~~lr 54 (309)
T TIGR00570 26 CGHTLCESCVDLLFVRGSGSCPECDTPLR 54 (309)
T ss_pred CCCcccHHHHHHHhcCCCCCCCCCCCccc
Confidence 377778888777652 47888887764
No 85
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=47.10 E-value=5.4 Score=24.97 Aligned_cols=28 Identities=29% Similarity=0.615 Sum_probs=18.5
Q ss_pred ccccccccccCCCCCee-eeCCcccCHHh
Q psy8111 90 CFSCSKCRQSLVDKQFG-SKSEKIYCGNC 117 (135)
Q Consensus 90 Cf~C~~C~~~l~~~~~~-~~~~~~~C~~c 117 (135)
=|+|++|--.-..++.. ..+|+++|.+|
T Consensus 70 EFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 70 EFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred ceeeeeeeeEechhhhccccCCCEecccc
Confidence 38888885554433322 45789999887
No 86
>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=47.04 E-value=19 Score=19.07 Aligned_cols=29 Identities=17% Similarity=0.543 Sum_probs=17.0
Q ss_pred ccccccccCCCCCeeee--CCcccCHHhHhh
Q psy8111 92 SCSKCRQSLVDKQFGSK--SEKIYCGNCYDA 120 (135)
Q Consensus 92 ~C~~C~~~l~~~~~~~~--~~~~~C~~c~~~ 120 (135)
.|..|+..+....|... .+.-+|..||.+
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhC
Confidence 45666666654333322 246679999865
No 87
>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=46.18 E-value=8.7 Score=16.54 Aligned_cols=12 Identities=25% Similarity=0.717 Sum_probs=6.9
Q ss_pred eeccccCCccCC
Q psy8111 30 FCCWQCDESLTG 41 (135)
Q Consensus 30 f~C~~C~~~l~~ 41 (135)
|+|..|++.+..
T Consensus 1 y~C~~C~~~f~~ 12 (23)
T PF00096_consen 1 YKCPICGKSFSS 12 (23)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCccCC
Confidence 456666665543
No 88
>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=45.21 E-value=8.3 Score=19.37 Aligned_cols=11 Identities=18% Similarity=0.800 Sum_probs=7.2
Q ss_pred eeccccCCccC
Q psy8111 30 FCCWQCDESLT 40 (135)
Q Consensus 30 f~C~~C~~~l~ 40 (135)
|+|..|+..++
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 66777766554
No 89
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=44.85 E-value=16 Score=19.25 Aligned_cols=11 Identities=18% Similarity=0.676 Sum_probs=7.5
Q ss_pred eeccccCCccC
Q psy8111 30 FCCWQCDESLT 40 (135)
Q Consensus 30 f~C~~C~~~l~ 40 (135)
|.|..|+..++
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 56777777654
No 90
>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=44.84 E-value=9 Score=20.51 Aligned_cols=12 Identities=17% Similarity=0.587 Sum_probs=8.6
Q ss_pred eeccccCCccCC
Q psy8111 30 FCCWQCDESLTG 41 (135)
Q Consensus 30 f~C~~C~~~l~~ 41 (135)
|+|..|+..++.
T Consensus 6 y~C~~Cg~~fe~ 17 (52)
T TIGR02605 6 YRCTACGHRFEV 17 (52)
T ss_pred EEeCCCCCEeEE
Confidence 778888776653
No 91
>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=44.80 E-value=14 Score=17.38 Aligned_cols=12 Identities=33% Similarity=0.930 Sum_probs=3.0
Q ss_pred eeccccCCccCC
Q psy8111 30 FCCWQCDESLTG 41 (135)
Q Consensus 30 f~C~~C~~~l~~ 41 (135)
|+|..|++++.+
T Consensus 1 ~~C~~C~~~~~~ 12 (30)
T PF07649_consen 1 FRCDACGKPIDG 12 (30)
T ss_dssp ---TTTS----S
T ss_pred CcCCcCCCcCCC
Confidence 456666666654
No 92
>KOG1813|consensus
Probab=43.80 E-value=11 Score=28.27 Aligned_cols=50 Identities=20% Similarity=0.403 Sum_probs=36.8
Q ss_pred CCcccCCCCeeccccCCccCCCceEeECCeeeccCchhhhc--CCchhhcCCccc
Q psy8111 21 GKDRGSGQHFCCWQCDESLTGQRYVLRDDHPYCIKCYESVF--ANSCEECSKIIG 73 (135)
Q Consensus 21 ~~~~H~~~cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~--~~~C~~C~~~I~ 73 (135)
...|-.. |.|..|++.+... -+..-+..+|+.|..+.+ +++|..|++.+.
T Consensus 235 ~D~~~~P--f~c~icr~~f~~p-Vvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~ 286 (313)
T KOG1813|consen 235 EDIELLP--FKCFICRKYFYRP-VVTKCGHYFCEVCALKPYQKGEKCYVCSQQTH 286 (313)
T ss_pred CCcccCC--ccccccccccccc-hhhcCCceeehhhhccccccCCcceecccccc
Confidence 3456655 8888888888653 556678888999887654 368999998884
No 93
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=43.65 E-value=28 Score=21.48 Aligned_cols=9 Identities=22% Similarity=0.781 Sum_probs=4.6
Q ss_pred ccccccccc
Q psy8111 85 HWHEACFSC 93 (135)
Q Consensus 85 ~~H~~Cf~C 93 (135)
.|+..|-+|
T Consensus 36 v~~Q~C~~C 44 (98)
T PF13695_consen 36 VFGQRCKKC 44 (98)
T ss_pred EECCCCCCC
Confidence 355555544
No 94
>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=43.03 E-value=22 Score=18.54 Aligned_cols=9 Identities=33% Similarity=0.874 Sum_probs=5.4
Q ss_pred chhhcCCcc
Q psy8111 64 SCEECSKII 72 (135)
Q Consensus 64 ~C~~C~~~I 72 (135)
.|.+|+++|
T Consensus 2 ~Cd~C~~~i 10 (43)
T cd02340 2 ICDGCQGPI 10 (43)
T ss_pred CCCCCCCcC
Confidence 466666655
No 95
>PF14353 CpXC: CpXC protein
Probab=41.25 E-value=32 Score=22.15 Aligned_cols=38 Identities=16% Similarity=0.151 Sum_probs=22.0
Q ss_pred ccccccCccccccceeeCCCc-----------ccCCCCeeccccCCccCC
Q psy8111 3 SAVKHQDKSFREDYNKLGGKD-----------RGSGQHFCCWQCDESLTG 41 (135)
Q Consensus 3 ~~C~~C~~~i~~~~i~a~~~~-----------~H~~~cf~C~~C~~~l~~ 41 (135)
.+|.+|+....-++-+..+.. .-.. -|+|..|+....-
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~-~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLF-SFTCPSCGHKFRL 50 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcC-EEECCCCCCceec
Confidence 468888888775543322222 2223 4778888776643
No 96
>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=40.45 E-value=14 Score=15.51 Aligned_cols=11 Identities=36% Similarity=0.788 Sum_probs=5.0
Q ss_pred eeccccCCccC
Q psy8111 30 FCCWQCDESLT 40 (135)
Q Consensus 30 f~C~~C~~~l~ 40 (135)
|.|..|+..+.
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 45666655554
No 97
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=39.65 E-value=34 Score=25.26 Aligned_cols=36 Identities=33% Similarity=0.695 Sum_probs=25.0
Q ss_pred CCchhhcCCccccCcccceeCCccccccccccccccccCCC
Q psy8111 62 ANSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLVD 102 (135)
Q Consensus 62 ~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~ 102 (135)
..+|.+|++.-.| | ..++-|=..=|.|..|+..+.+
T Consensus 132 VSRCr~C~~rYDP----V-P~dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 132 VSRCRKCRKRYDP----V-PCDKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred cccccccccccCC----C-ccccccceeeeecccccccchh
Confidence 4678888886522 1 1456666666889999998865
No 98
>PRK00807 50S ribosomal protein L24e; Validated
Probab=39.35 E-value=28 Score=18.99 Aligned_cols=22 Identities=23% Similarity=0.459 Sum_probs=11.6
Q ss_pred eccccCCccCCC---ceEeECCeee
Q psy8111 31 CCWQCDESLTGQ---RYVLRDDHPY 52 (135)
Q Consensus 31 ~C~~C~~~l~~~---~~~~~~~~~~ 52 (135)
.|+.|+..+... .|+..||++|
T Consensus 3 ~C~fcG~~I~pg~G~~~vr~Dgkv~ 27 (52)
T PRK00807 3 TCSFCGKEIEPGTGKMYVKKDGTIL 27 (52)
T ss_pred ccCCCCCeEcCCCCeEEEEeCCcEE
Confidence 356666666522 3445666654
No 99
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=38.85 E-value=9.5 Score=23.69 Aligned_cols=29 Identities=21% Similarity=0.519 Sum_probs=13.4
Q ss_pred chhhcCCccccCccccee-CCcccccccccc
Q psy8111 64 SCEECSKIIGIDSKDLSY-KDKHWHEACFSC 93 (135)
Q Consensus 64 ~C~~C~~~I~~~~~~~~~-~~~~~H~~Cf~C 93 (135)
+|+.|+++|. .++..++ ...+-|-+||.=
T Consensus 8 kC~VCg~~ii-eGqkFTF~~kGsVH~eCl~~ 37 (103)
T COG4847 8 KCYVCGGTII-EGQKFTFTKKGSVHYECLAE 37 (103)
T ss_pred eEeeeCCEee-eccEEEEeeCCcchHHHHHH
Confidence 4566666654 2333222 233445555543
No 100
>KOG3002|consensus
Probab=37.86 E-value=22 Score=26.87 Aligned_cols=44 Identities=27% Similarity=0.554 Sum_probs=36.5
Q ss_pred CeeccccCCccCCCceEeECCeeeccCchhhhcCCchhhcCCccc
Q psy8111 29 HFCCWQCDESLTGQRYVLRDDHPYCIKCYESVFANSCEECSKIIG 73 (135)
Q Consensus 29 cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~ 73 (135)
=+.|..|-..|....|.=.+|.+.|..|-.++ ..+|..|..+|.
T Consensus 48 lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~-~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 48 LLDCPVCFNPLSPPIFQCDNGHLACSSCRTKV-SNKCPTCRLPIG 91 (299)
T ss_pred hccCchhhccCcccceecCCCcEehhhhhhhh-cccCCccccccc
Confidence 47788898999877666788999999998655 479999999994
No 101
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=36.06 E-value=9.9 Score=20.87 Aligned_cols=26 Identities=27% Similarity=0.591 Sum_probs=14.8
Q ss_pred eccccCCccCCCceEe---ECCeeeccCc
Q psy8111 31 CCWQCDESLTGQRYVL---RDDHPYCIKC 56 (135)
Q Consensus 31 ~C~~C~~~l~~~~~~~---~~~~~~C~~c 56 (135)
+|+.|+..|+.+.+.. .++.++|+.|
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~C 52 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNC 52 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCC
Confidence 5677777777654332 2345566655
No 102
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=35.91 E-value=16 Score=18.23 Aligned_cols=30 Identities=17% Similarity=0.487 Sum_probs=15.7
Q ss_pred cccccccCCCCCeeeeCCcccCHHhHhhhc
Q psy8111 93 CSKCRQSLVDKQFGSKSEKIYCGNCYDAQF 122 (135)
Q Consensus 93 C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~ 122 (135)
|..|...+........=|..||..|..+.+
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~ 30 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRDCLRKWL 30 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHHHHHHHH
T ss_pred CCcCCccccCCCEEecCCCcchHHHHHHHH
Confidence 344555444433233336777888875543
No 103
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=35.67 E-value=4.5 Score=20.06 Aligned_cols=16 Identities=19% Similarity=0.752 Sum_probs=9.9
Q ss_pred cccccccccCCCCCee
Q psy8111 91 FSCSKCRQSLVDKQFG 106 (135)
Q Consensus 91 f~C~~C~~~l~~~~~~ 106 (135)
|.|..|++++....|+
T Consensus 5 ~~C~nC~R~v~a~RfA 20 (33)
T PF08209_consen 5 VECPNCGRPVAASRFA 20 (33)
T ss_dssp EE-TTTSSEEEGGGHH
T ss_pred EECCCCcCCcchhhhH
Confidence 5577777777666554
No 104
>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=35.65 E-value=14 Score=19.74 Aligned_cols=12 Identities=33% Similarity=0.944 Sum_probs=7.1
Q ss_pred eeccccCCccCC
Q psy8111 30 FCCWQCDESLTG 41 (135)
Q Consensus 30 f~C~~C~~~l~~ 41 (135)
++|..|.+.+.+
T Consensus 1 ~~Cd~C~~~~~~ 12 (49)
T cd02335 1 YHCDYCSKDITG 12 (49)
T ss_pred CCCCCcCCCCCC
Confidence 356666666554
No 105
>PRK04023 DNA polymerase II large subunit; Validated
Probab=35.49 E-value=37 Score=30.08 Aligned_cols=23 Identities=26% Similarity=0.553 Sum_probs=13.3
Q ss_pred eeccCchhhhcCCchhhcCCccc
Q psy8111 51 PYCIKCYESVFANSCEECSKIIG 73 (135)
Q Consensus 51 ~~C~~c~~~~~~~~C~~C~~~I~ 73 (135)
..|.+|-.......|..|+..+.
T Consensus 652 ~fCP~CG~~~~~y~CPKCG~El~ 674 (1121)
T PRK04023 652 YRCPRCGIEVEEDECEKCGREPT 674 (1121)
T ss_pred eeCccccCcCCCCcCCCCCCCCC
Confidence 35666655544456666666664
No 106
>KOG2932|consensus
Probab=34.74 E-value=20 Score=27.28 Aligned_cols=40 Identities=15% Similarity=0.443 Sum_probs=18.5
Q ss_pred cccccccCCCCCeeeeCCcccCHHhHhhhcCCCcccCCCC
Q psy8111 93 CSKCRQSLVDKQFGSKSEKIYCGNCYDAQFASRCDGCSEI 132 (135)
Q Consensus 93 C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~ 132 (135)
|..|+.+|.--.-..-=+.+||.+|...--...|..|...
T Consensus 93 Cd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~ 132 (389)
T KOG2932|consen 93 CDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDR 132 (389)
T ss_pred ecccCCcceeeecccccchhhhhhhhhcCccccCcCcccH
Confidence 5555555533222223345555555543333455555543
No 107
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=34.57 E-value=40 Score=19.45 Aligned_cols=22 Identities=23% Similarity=0.452 Sum_probs=14.1
Q ss_pred eccccCCccCCC---ceEeECCeee
Q psy8111 31 CCWQCDESLTGQ---RYVLRDDHPY 52 (135)
Q Consensus 31 ~C~~C~~~l~~~---~~~~~~~~~~ 52 (135)
+|+-|+..+... -|+..||+++
T Consensus 5 ~CsFcG~~I~PGtG~m~Vr~Dg~v~ 29 (66)
T COG2075 5 VCSFCGKKIEPGTGIMYVRNDGKVL 29 (66)
T ss_pred EecCcCCccCCCceEEEEecCCeEE
Confidence 577788877654 3445667654
No 108
>KOG2893|consensus
Probab=34.32 E-value=12 Score=27.36 Aligned_cols=35 Identities=17% Similarity=0.347 Sum_probs=25.1
Q ss_pred ccccCccccccceeeCCCcccCCCCeeccccCCccCCC
Q psy8111 5 VKHQDKSFREDYNKLGGKDRGSGQHFCCWQCDESLTGQ 42 (135)
Q Consensus 5 C~~C~~~i~~~~i~a~~~~~H~~~cf~C~~C~~~l~~~ 42 (135)
|.-|+..+.++.|.+..+ -.. +|+|..|.+.|-+.
T Consensus 13 cwycnrefddekiliqhq--kak-hfkchichkkl~sg 47 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQ--KAK-HFKCHICHKKLFSG 47 (341)
T ss_pred eeecccccchhhhhhhhh--hhc-cceeeeehhhhccC
Confidence 777888888877655322 356 89999998887543
No 109
>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=34.31 E-value=37 Score=18.14 Aligned_cols=10 Identities=40% Similarity=1.149 Sum_probs=5.5
Q ss_pred ccCHHhHhhh
Q psy8111 112 IYCGNCYDAQ 121 (135)
Q Consensus 112 ~~C~~c~~~~ 121 (135)
-+|.+||...
T Consensus 25 dlC~~Cf~~~ 34 (49)
T cd02338 25 DLCADCYDSG 34 (49)
T ss_pred ccchhHHhCC
Confidence 3566666543
No 110
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=34.18 E-value=17 Score=15.89 Aligned_cols=12 Identities=33% Similarity=0.886 Sum_probs=7.3
Q ss_pred eeccccCCccCC
Q psy8111 30 FCCWQCDESLTG 41 (135)
Q Consensus 30 f~C~~C~~~l~~ 41 (135)
|.|..|+..+.+
T Consensus 1 ~~C~~C~~~f~s 12 (25)
T PF12874_consen 1 FYCDICNKSFSS 12 (25)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCCcCC
Confidence 456666666554
No 111
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=33.81 E-value=59 Score=24.23 Aligned_cols=92 Identities=12% Similarity=0.260 Sum_probs=44.0
Q ss_pred CeeccccCCccCCCceEe-------ECCeeeccCchhhhcCCchhhcCCccccCccc-ceeCCccccccccccccccccC
Q psy8111 29 HFCCWQCDESLTGQRYVL-------RDDHPYCIKCYESVFANSCEECSKIIGIDSKD-LSYKDKHWHEACFSCSKCRQSL 100 (135)
Q Consensus 29 cf~C~~C~~~l~~~~~~~-------~~~~~~C~~c~~~~~~~~C~~C~~~I~~~~~~-~~~~~~~~H~~Cf~C~~C~~~l 100 (135)
|++=..|.-||.+....+ +.|++| +|+.|...+-.+++. -.|.=+..-.+=|+|.+|++.=
T Consensus 113 Cl~~HaC~Cpl~da~C~EC~R~vw~hGGrif-----------~CsfC~~flCEDDQFEHQAsCQvLe~E~~KC~SCNrlG 181 (314)
T PF06524_consen 113 CLSTHACTCPLQDAVCIECERGVWDHGGRIF-----------KCSFCDNFLCEDDQFEHQASCQVLESETFKCQSCNRLG 181 (314)
T ss_pred ccccccccCcCCCcEeeeeecccccCCCeEE-----------EeecCCCeeeccchhhhhhhhhhhhccccccccccccc
Confidence 555567777887654433 223322 566666655322221 1122223333446777776542
Q ss_pred CCCCeeeeCCcccCHHhHhhh-------cCCCcccCCCCC
Q psy8111 101 VDKQFGSKSEKIYCGNCYDAQ-------FASRCDGCSEIF 133 (135)
Q Consensus 101 ~~~~~~~~~~~~~C~~c~~~~-------~~~~C~~C~~~I 133 (135)
.-+ -++=..-||.+|..++ -++.|.+|+.+.
T Consensus 182 q~s--CLRCK~cfCddHvrrKg~ky~k~k~~PCPKCg~et 219 (314)
T PF06524_consen 182 QYS--CLRCKICFCDDHVRRKGFKYEKGKPIPCPKCGYET 219 (314)
T ss_pred chh--hhheeeeehhhhhhhcccccccCCCCCCCCCCCcc
Confidence 111 1222344566665432 235677776553
No 112
>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=33.78 E-value=20 Score=24.86 Aligned_cols=32 Identities=25% Similarity=0.616 Sum_probs=22.3
Q ss_pred ccccccccCCC--CC-eeeeCCcccCHHhHhhhcC
Q psy8111 92 SCSKCRQSLVD--KQ-FGSKSEKIYCGNCYDAQFA 123 (135)
Q Consensus 92 ~C~~C~~~l~~--~~-~~~~~~~~~C~~c~~~~~~ 123 (135)
+|-.|+++... .. ++..|-+++|..|+..+|.
T Consensus 138 kC~QC~~~~~~~~~~~~~~F~~~lFC~~ClFPLF~ 172 (173)
T PF11077_consen 138 KCVQCSQKCENVGAKIFTYFNFNLFCKNCLFPLFD 172 (173)
T ss_pred ccCcCCCCcccccceeEEecChhhcccccCccccc
Confidence 45566665432 23 6677999999999988773
No 113
>PRK13796 GTPase YqeH; Provisional
Probab=33.70 E-value=19 Score=27.83 Aligned_cols=28 Identities=21% Similarity=0.786 Sum_probs=17.7
Q ss_pred eccccCCccCCC-----ceEe--------ECCeeeccCchh
Q psy8111 31 CCWQCDESLTGQ-----RYVL--------RDDHPYCIKCYE 58 (135)
Q Consensus 31 ~C~~C~~~l~~~-----~~~~--------~~~~~~C~~c~~ 58 (135)
+|..||..|... .|.. ..+.++|++||.
T Consensus 2 ~C~GCG~~lq~~~~~~~Gy~p~~~~~~~~~~~~~~C~RC~~ 42 (365)
T PRK13796 2 RCIGCGAAIQTEDKNKPGYAPASALKKGLETEEVYCQRCFR 42 (365)
T ss_pred cccCCCceeEcCCCCCCCCCCHHHhhcccccCCeEchhhhh
Confidence 577788777422 3443 235678998884
No 114
>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=33.53 E-value=18 Score=16.20 Aligned_cols=12 Identities=25% Similarity=0.839 Sum_probs=7.2
Q ss_pred eeccccCCccCC
Q psy8111 30 FCCWQCDESLTG 41 (135)
Q Consensus 30 f~C~~C~~~l~~ 41 (135)
|+|..|++.+..
T Consensus 2 ~~C~~C~~~F~~ 13 (27)
T PF13912_consen 2 FECDECGKTFSS 13 (27)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCccCCccCC
Confidence 566666666543
No 115
>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=32.57 E-value=49 Score=15.28 Aligned_cols=13 Identities=15% Similarity=0.595 Sum_probs=7.3
Q ss_pred CCcccCHHhHhhh
Q psy8111 109 SEKIYCGNCYDAQ 121 (135)
Q Consensus 109 ~~~~~C~~c~~~~ 121 (135)
=+..+|..|..+.
T Consensus 16 C~H~~c~~C~~~~ 28 (39)
T smart00184 16 CGHTFCRSCIRKW 28 (39)
T ss_pred CCChHHHHHHHHH
Confidence 4555666666543
No 116
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=32.54 E-value=50 Score=16.16 Aligned_cols=23 Identities=30% Similarity=0.550 Sum_probs=12.7
Q ss_pred eccccCCccCCCceEeECCeeeccCc
Q psy8111 31 CCWQCDESLTGQRYVLRDDHPYCIKC 56 (135)
Q Consensus 31 ~C~~C~~~l~~~~~~~~~~~~~C~~c 56 (135)
+|..|+..+. +...++..+|..|
T Consensus 5 ~C~~C~~~~i---~~~~~~~~~C~~C 27 (33)
T PF08792_consen 5 KCSKCGGNGI---VNKEDDYEVCIFC 27 (33)
T ss_pred EcCCCCCCeE---EEecCCeEEcccC
Confidence 4555655542 3355666666665
No 117
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.10 E-value=42 Score=22.08 Aligned_cols=10 Identities=20% Similarity=0.069 Sum_probs=4.3
Q ss_pred ccccCccccc
Q psy8111 5 VKHQDKSFRE 14 (135)
Q Consensus 5 C~~C~~~i~~ 14 (135)
|..|+-+|+|
T Consensus 42 cp~csasirg 51 (160)
T COG4306 42 CPICSASIRG 51 (160)
T ss_pred CCccCCcccc
Confidence 3344444444
No 118
>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=31.98 E-value=21 Score=18.39 Aligned_cols=14 Identities=7% Similarity=0.003 Sum_probs=8.1
Q ss_pred cccccCccccccce
Q psy8111 4 AVKHQDKSFREDYN 17 (135)
Q Consensus 4 ~C~~C~~~i~~~~i 17 (135)
.|..||.+|.+..+
T Consensus 21 vC~~CG~Vl~e~~i 34 (43)
T PF08271_consen 21 VCPNCGLVLEENII 34 (43)
T ss_dssp EETTT-BBEE-TTB
T ss_pred ECCCCCCEeecccc
Confidence 57777777766554
No 119
>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=31.08 E-value=47 Score=17.02 Aligned_cols=29 Identities=21% Similarity=0.468 Sum_probs=13.9
Q ss_pred ccccccccCCCCC-eeeeC-CcccCHHhHhh
Q psy8111 92 SCSKCRQSLVDKQ-FGSKS-EKIYCGNCYDA 120 (135)
Q Consensus 92 ~C~~C~~~l~~~~-~~~~~-~~~~C~~c~~~ 120 (135)
+|+-|+++-.... ..... +...|..|...
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQ 33 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHH
Confidence 4667777765443 22222 55667777654
No 120
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=30.05 E-value=33 Score=24.31 Aligned_cols=14 Identities=21% Similarity=0.712 Sum_probs=9.6
Q ss_pred cCCCcccCCCCCCC
Q psy8111 122 FASRCDGCSEIFKA 135 (135)
Q Consensus 122 ~~~~C~~C~~~I~~ 135 (135)
..|+|..|+.++.|
T Consensus 132 ~~p~C~~Cg~~lrP 145 (218)
T cd01407 132 EVPRCPKCGGLLRP 145 (218)
T ss_pred CCCcCCCCCCccCC
Confidence 35777778777665
No 121
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=29.44 E-value=41 Score=28.72 Aligned_cols=55 Identities=15% Similarity=0.219 Sum_probs=34.5
Q ss_pred cceeeCCC-cccCCCCeeccccCCccCCC------ceEeECCeeeccCchhh-hcCCchhhcCCc
Q psy8111 15 DYNKLGGK-DRGSGQHFCCWQCDESLTGQ------RYVLRDDHPYCIKCYES-VFANSCEECSKI 71 (135)
Q Consensus 15 ~~i~a~~~-~~H~~~cf~C~~C~~~l~~~------~~~~~~~~~~C~~c~~~-~~~~~C~~C~~~ 71 (135)
+.|...++ -|.+. .-|..|+..+.-. .|....+.+.|..|-.+ .....|..|+..
T Consensus 422 Q~llflnRRGys~~--l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 422 QVLLFLNRRGYAPL--LLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred eEEEEEccCCccce--eecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 34444444 55544 5555555544311 35556789999998776 455689999887
No 122
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=29.24 E-value=24 Score=26.32 Aligned_cols=27 Identities=19% Similarity=0.528 Sum_probs=18.4
Q ss_pred CCchhhcCCccccCcccceeCCccccccc
Q psy8111 62 ANSCEECSKIIGIDSKDLSYKDKHWHEAC 90 (135)
Q Consensus 62 ~~~C~~C~~~I~~~~~~~~~~~~~~H~~C 90 (135)
+..|..|+.+|. ...+.-++..|.|.|
T Consensus 245 GepC~~CGt~I~--k~~~~gR~t~~CP~C 271 (273)
T COG0266 245 GEPCRRCGTPIE--KIKLGGRSTFYCPVC 271 (273)
T ss_pred CCCCCccCCEeE--EEEEcCCcCEeCCCC
Confidence 568999999994 444555566665655
No 123
>PRK12495 hypothetical protein; Provisional
Probab=28.79 E-value=32 Score=24.83 Aligned_cols=25 Identities=20% Similarity=0.672 Sum_probs=17.1
Q ss_pred CeeccccCCccCCCceEeECCeeeccCchh
Q psy8111 29 HFCCWQCDESLTGQRYVLRDDHPYCIKCYE 58 (135)
Q Consensus 29 cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~ 58 (135)
=+.|..|+.+|. ...|..+|..|-.
T Consensus 42 a~hC~~CG~PIp-----a~pG~~~Cp~CQ~ 66 (226)
T PRK12495 42 NAHCDECGDPIF-----RHDGQEFCPTCQQ 66 (226)
T ss_pred hhhcccccCccc-----CCCCeeECCCCCC
Confidence 467778888885 3467777776643
No 124
>KOG1734|consensus
Probab=28.51 E-value=37 Score=25.43 Aligned_cols=45 Identities=16% Similarity=0.355 Sum_probs=27.1
Q ss_pred ceEeECCeeeccCchhhhcCCchhhcCCccccCc---ccc-----eeCCccccccccc
Q psy8111 43 RYVLRDDHPYCIKCYESVFANSCEECSKIIGIDS---KDL-----SYKDKHWHEACFS 92 (135)
Q Consensus 43 ~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~~~~---~~~-----~~~~~~~H~~Cf~ 92 (135)
.|+..+|.|- ..+....|+.|++.|..+. .++ -.-|..||+.|.+
T Consensus 210 GfYs~~glPt-----khl~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIr 262 (328)
T KOG1734|consen 210 GFYSPSGLPT-----KHLSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIR 262 (328)
T ss_pred cccCCCCCCC-----CCCCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhh
Confidence 5777777762 2334578999999984221 111 1235677877754
No 125
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=28.12 E-value=23 Score=18.59 Aligned_cols=19 Identities=21% Similarity=0.760 Sum_probs=10.9
Q ss_pred cccccccCCCCCeeeeCCcccCH
Q psy8111 93 CSKCRQSLVDKQFGSKSEKIYCG 115 (135)
Q Consensus 93 C~~C~~~l~~~~~~~~~~~~~C~ 115 (135)
|..|.+.+.. ..++.+||.
T Consensus 9 C~~Cdk~~~~----~~~~~lYCS 27 (43)
T PF12855_consen 9 CIVCDKQIDP----PDDGSLYCS 27 (43)
T ss_pred HHHhhccccC----CCCCccccC
Confidence 4455666533 446777874
No 126
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=28.11 E-value=32 Score=17.94 Aligned_cols=11 Identities=18% Similarity=0.776 Sum_probs=6.4
Q ss_pred eeccccCCccC
Q psy8111 30 FCCWQCDESLT 40 (135)
Q Consensus 30 f~C~~C~~~l~ 40 (135)
|+|..|+..+.
T Consensus 4 y~C~~CG~~~~ 14 (46)
T PRK00398 4 YKCARCGREVE 14 (46)
T ss_pred EECCCCCCEEE
Confidence 55666665553
No 127
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=27.94 E-value=14 Score=20.72 Aligned_cols=16 Identities=31% Similarity=0.825 Sum_probs=11.7
Q ss_pred eeccccCCccCCCceE
Q psy8111 30 FCCWQCDESLTGQRYV 45 (135)
Q Consensus 30 f~C~~C~~~l~~~~~~ 45 (135)
+.|++||+.|+..+|.
T Consensus 5 lvCSTCGrDlSeeRy~ 20 (63)
T PF05864_consen 5 LVCSTCGRDLSEERYR 20 (63)
T ss_pred eeecccCCcchHHHHH
Confidence 5688888888776553
No 128
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=27.87 E-value=28 Score=20.84 Aligned_cols=43 Identities=26% Similarity=0.618 Sum_probs=14.1
Q ss_pred eeccccCCccC----CCceEeEC--CeeeccCchhhh---cCCchhhcCCcc
Q psy8111 30 FCCWQCDESLT----GQRYVLRD--DHPYCIKCYESV---FANSCEECSKII 72 (135)
Q Consensus 30 f~C~~C~~~l~----~~~~~~~~--~~~~C~~c~~~~---~~~~C~~C~~~I 72 (135)
-.|..|+..+. +..|+.-+ +-|.|..||+-. -...|.+|+.+-
T Consensus 10 qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~y 61 (80)
T PF14569_consen 10 QICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRY 61 (80)
T ss_dssp -B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B-
T ss_pred cccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCc
Confidence 45777776653 34555433 567788888632 234667776543
No 129
>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=27.65 E-value=66 Score=20.23 Aligned_cols=36 Identities=17% Similarity=0.249 Sum_probs=25.5
Q ss_pred eCCCcccCCCCeeccccCCccCCCceEeECCeeeccCchhh
Q psy8111 19 LGGKDRGSGQHFCCWQCDESLTGQRYVLRDDHPYCIKCYES 59 (135)
Q Consensus 19 a~~~~~H~~~cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~ 59 (135)
..+..+... ==-|..| .+..|++.++.+.|..|-.+
T Consensus 26 ~~dg~~~va-~daCeiC----~~~GY~q~g~~lvC~~C~~~ 61 (102)
T PF10080_consen 26 KPDGSYRVA-FDACEIC----GPKGYYQEGDQLVCKNCGVR 61 (102)
T ss_pred CCCCCEEEE-EEecccc----CCCceEEECCEEEEecCCCE
Confidence 345556655 4456777 55679999999999988654
No 130
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=27.47 E-value=27 Score=23.24 Aligned_cols=10 Identities=20% Similarity=0.740 Sum_probs=5.0
Q ss_pred eeccccCCcc
Q psy8111 30 FCCWQCDESL 39 (135)
Q Consensus 30 f~C~~C~~~l 39 (135)
|.|..|+..+
T Consensus 100 Y~Cp~C~~~y 109 (147)
T smart00531 100 YKCPNCQSKY 109 (147)
T ss_pred EECcCCCCEe
Confidence 5555555443
No 131
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=27.40 E-value=14 Score=20.72 Aligned_cols=16 Identities=31% Similarity=0.825 Sum_probs=11.6
Q ss_pred eeccccCCccCCCceE
Q psy8111 30 FCCWQCDESLTGQRYV 45 (135)
Q Consensus 30 f~C~~C~~~l~~~~~~ 45 (135)
+.|++||+.|+..+|.
T Consensus 5 lVCsTCGrDlSeeRy~ 20 (63)
T PHA03082 5 LVCSTCGRDLSEERYR 20 (63)
T ss_pred eeecccCcchhHHHHH
Confidence 5688888888766543
No 132
>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=26.90 E-value=43 Score=27.06 Aligned_cols=52 Identities=19% Similarity=0.513 Sum_probs=0.0
Q ss_pred CCeeeccCchhhhcC---------CchhhcCCccccCcccceeCCccccccccccccccccCC
Q psy8111 48 DDHPYCIKCYESVFA---------NSCEECSKIIGIDSKDLSYKDKHWHEACFSCSKCRQSLV 101 (135)
Q Consensus 48 ~~~~~C~~c~~~~~~---------~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 101 (135)
....||+.|..-+-. --|..|-..+ ....+...+..--.+||.|..|..+|.
T Consensus 3 ~~L~fC~~C~~irc~~c~~~Ei~~~yCp~CL~~~--p~~e~~~~~nrC~r~Cf~CP~C~~~L~ 63 (483)
T PF05502_consen 3 EELYFCEHCHKIRCPRCVSEEIDSYYCPNCLFEV--PSSEARSEKNRCSRNCFDCPICFSPLS 63 (483)
T ss_pred ccceecccccccCChhhcccccceeECccccccC--ChhhheeccceeccccccCCCCCCcce
No 133
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=26.52 E-value=37 Score=18.90 Aligned_cols=27 Identities=22% Similarity=0.626 Sum_probs=17.7
Q ss_pred CCcccCHHhHhhhcCCCcccCCCCCCC
Q psy8111 109 SEKIYCGNCYDAQFASRCDGCSEIFKA 135 (135)
Q Consensus 109 ~~~~~C~~c~~~~~~~~C~~C~~~I~~ 135 (135)
=+.+.|..||...-..-|.-|+.+|.+
T Consensus 25 CgH~I~~~~f~~~rYngCPfC~~~~~~ 51 (55)
T PF14447_consen 25 CGHLICDNCFPGERYNGCPFCGTPFEF 51 (55)
T ss_pred ccceeeccccChhhccCCCCCCCcccC
Confidence 356677777765555667777777653
No 134
>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=26.04 E-value=69 Score=16.99 Aligned_cols=10 Identities=40% Similarity=1.192 Sum_probs=4.5
Q ss_pred cccccccccC
Q psy8111 91 FSCSKCRQSL 100 (135)
Q Consensus 91 f~C~~C~~~l 100 (135)
|-|..|.+.|
T Consensus 19 fIC~~CE~~i 28 (46)
T PF10764_consen 19 FICSDCEKEI 28 (46)
T ss_pred EehHHHHHHh
Confidence 4444444443
No 135
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=25.96 E-value=34 Score=20.73 Aligned_cols=10 Identities=10% Similarity=-0.041 Sum_probs=6.6
Q ss_pred cccccCcccc
Q psy8111 4 AVKHQDKSFR 13 (135)
Q Consensus 4 ~C~~C~~~i~ 13 (135)
.|.+|+.+|.
T Consensus 2 ~C~HCg~~~p 11 (88)
T PF12156_consen 2 KCYHCGLPVP 11 (88)
T ss_pred CCCCCCCCCC
Confidence 4667777774
No 136
>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=25.87 E-value=22 Score=18.16 Aligned_cols=9 Identities=11% Similarity=0.645 Sum_probs=3.9
Q ss_pred CcccCHHhH
Q psy8111 110 EKIYCGNCY 118 (135)
Q Consensus 110 ~~~~C~~c~ 118 (135)
+..|+..|.
T Consensus 22 ~H~fh~~Ci 30 (44)
T PF13639_consen 22 GHVFHRSCI 30 (44)
T ss_dssp SEEEEHHHH
T ss_pred CCeeCHHHH
Confidence 344444443
No 137
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=25.65 E-value=53 Score=18.00 Aligned_cols=25 Identities=4% Similarity=-0.057 Sum_probs=13.6
Q ss_pred ccccccCccccccc-eeeCCCcccCC
Q psy8111 3 SAVKHQDKSFREDY-NKLGGKDRGSG 27 (135)
Q Consensus 3 ~~C~~C~~~i~~~~-i~a~~~~~H~~ 27 (135)
..|-.|++||.+.. +.-....-|+.
T Consensus 2 ~iCvvCK~Pi~~al~v~T~~Gpvh~g 27 (53)
T PHA02610 2 KICVVCKQPIEKALVVETEKGPVHPG 27 (53)
T ss_pred ceeeeeCCchhhceEEecCCCCCCCh
Confidence 45667777775543 33344455554
No 138
>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=25.48 E-value=45 Score=15.00 Aligned_cols=13 Identities=23% Similarity=0.774 Sum_probs=9.8
Q ss_pred cccccccccCCCC
Q psy8111 91 FSCSKCRQSLVDK 103 (135)
Q Consensus 91 f~C~~C~~~l~~~ 103 (135)
|.|..|++.+.++
T Consensus 2 ~~C~~C~k~f~~~ 14 (27)
T PF12171_consen 2 FYCDACDKYFSSE 14 (27)
T ss_dssp CBBTTTTBBBSSH
T ss_pred CCcccCCCCcCCH
Confidence 5688888888765
No 139
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=24.90 E-value=25 Score=19.28 Aligned_cols=8 Identities=38% Similarity=0.949 Sum_probs=3.8
Q ss_pred hhhcCCcc
Q psy8111 65 CEECSKII 72 (135)
Q Consensus 65 C~~C~~~I 72 (135)
|+.|+.+|
T Consensus 3 CPyCge~~ 10 (52)
T PF14255_consen 3 CPYCGEPI 10 (52)
T ss_pred CCCCCCee
Confidence 44445444
No 140
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=24.74 E-value=58 Score=15.31 Aligned_cols=13 Identities=31% Similarity=0.751 Sum_probs=8.6
Q ss_pred eeccccCCccCCC
Q psy8111 30 FCCWQCDESLTGQ 42 (135)
Q Consensus 30 f~C~~C~~~l~~~ 42 (135)
|.|..|++.+++.
T Consensus 1 ~~C~~C~~~~~~~ 13 (30)
T PF03107_consen 1 FWCDVCRRKIDGF 13 (30)
T ss_pred CCCCCCCCCcCCC
Confidence 4677777777654
No 141
>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=24.61 E-value=76 Score=17.05 Aligned_cols=10 Identities=20% Similarity=0.660 Sum_probs=5.9
Q ss_pred ccCHHhHhhh
Q psy8111 112 IYCGNCYDAQ 121 (135)
Q Consensus 112 ~~C~~c~~~~ 121 (135)
-+|..||...
T Consensus 25 DLC~~Cf~~g 34 (49)
T cd02334 25 DLCQSCFFSG 34 (49)
T ss_pred CchHHHHhCC
Confidence 3577776543
No 142
>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=24.30 E-value=73 Score=16.76 Aligned_cols=9 Identities=22% Similarity=0.752 Sum_probs=4.8
Q ss_pred ccCHHhHhh
Q psy8111 112 IYCGNCYDA 120 (135)
Q Consensus 112 ~~C~~c~~~ 120 (135)
-+|..||.+
T Consensus 25 DLC~~C~~~ 33 (43)
T cd02342 25 DLCTICFSR 33 (43)
T ss_pred ccHHHHhhh
Confidence 346666543
No 143
>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=24.25 E-value=42 Score=17.75 Aligned_cols=11 Identities=36% Similarity=0.818 Sum_probs=6.8
Q ss_pred CchhhcCCccc
Q psy8111 63 NSCEECSKIIG 73 (135)
Q Consensus 63 ~~C~~C~~~I~ 73 (135)
..|..|++.|.
T Consensus 12 ~~C~~C~~~i~ 22 (53)
T PF00130_consen 12 TYCDVCGKFIW 22 (53)
T ss_dssp EB-TTSSSBEC
T ss_pred CCCcccCcccC
Confidence 46777777773
No 144
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=24.19 E-value=45 Score=24.33 Aligned_cols=31 Identities=26% Similarity=0.570 Sum_probs=22.9
Q ss_pred ccccccccccccCCCCCeeeeCCcccCHHhH
Q psy8111 88 EACFSCSKCRQSLVDKQFGSKSEKIYCGNCY 118 (135)
Q Consensus 88 ~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~ 118 (135)
++=..|..|+++.....++...+...|..|+
T Consensus 152 ~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 152 PNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred cchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 3434688888888777777778888887775
No 145
>KOG4443|consensus
Probab=24.18 E-value=46 Score=27.97 Aligned_cols=21 Identities=19% Similarity=0.551 Sum_probs=17.2
Q ss_pred CCccccccccccccccccCCC
Q psy8111 82 KDKHWHEACFSCSKCRQSLVD 102 (135)
Q Consensus 82 ~~~~~H~~Cf~C~~C~~~l~~ 102 (135)
.+..+-++|++|..|+..+.+
T Consensus 107 sg~~~ckk~~~c~qc~~~lpg 127 (694)
T KOG4443|consen 107 SGPWLCKKCTRCRQCDSTLPG 127 (694)
T ss_pred CcccccHHHHhhhhccccccc
Confidence 356678899999999998876
No 146
>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=24.11 E-value=97 Score=25.15 Aligned_cols=56 Identities=16% Similarity=0.304 Sum_probs=35.0
Q ss_pred cceeeCCCcccCCCCeeccccCCccCC------CceEeECCeeeccCchhh-hcCCchhhcCCc
Q psy8111 15 DYNKLGGKDRGSGQHFCCWQCDESLTG------QRYVLRDDHPYCIKCYES-VFANSCEECSKI 71 (135)
Q Consensus 15 ~~i~a~~~~~H~~~cf~C~~C~~~l~~------~~~~~~~~~~~C~~c~~~-~~~~~C~~C~~~ 71 (135)
+++...++.-... -..|..|+..+.= ..|...++.+.|..|-.+ .....|..|+..
T Consensus 200 qvLvflnrrGya~-~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 200 QSILFLNRRGYSK-NLLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred cEEEEEeCCcCCC-eeEhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 4555555543333 3666666665531 135556788999999765 345689999875
No 147
>TIGR03597 GTPase_YqeH ribosome biogenesis GTPase YqeH. This family describes YqeH, a member of a larger family of GTPases involved in ribosome biogenesis. Like YqlF, it shows a cyclical permutation relative to GTPases EngA (in which the GTPase domain is duplicated), Era, and others. Members of this protein family are found in a relatively small number of bacterial species, including Bacillus subtilis but not Escherichia coli.
Probab=23.30 E-value=32 Score=26.49 Aligned_cols=27 Identities=22% Similarity=0.854 Sum_probs=16.8
Q ss_pred ccccCCccCCC-----ceEeE----CCeeeccCchh
Q psy8111 32 CWQCDESLTGQ-----RYVLR----DDHPYCIKCYE 58 (135)
Q Consensus 32 C~~C~~~l~~~-----~~~~~----~~~~~C~~c~~ 58 (135)
|..||..|... .|... .+.++|++||.
T Consensus 1 C~GCG~~lq~~d~~~~Gy~p~~~~~~~~~~C~RC~~ 36 (360)
T TIGR03597 1 CIGCGAAIQTTDPKKPGYTPKSALEKEEVYCQRCFR 36 (360)
T ss_pred CCCCCceeEcCCCCCCCCCchHHcCcCCeeecchhh
Confidence 56777777321 34432 25788888887
No 148
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=23.24 E-value=1.1e+02 Score=21.61 Aligned_cols=13 Identities=23% Similarity=0.833 Sum_probs=9.1
Q ss_pred CCCcccCCCCCCC
Q psy8111 123 ASRCDGCSEIFKA 135 (135)
Q Consensus 123 ~~~C~~C~~~I~~ 135 (135)
.|+|..|+..+.|
T Consensus 130 ~p~C~~Cgg~lrp 142 (224)
T cd01412 130 LPRCPKCGGLLRP 142 (224)
T ss_pred CCCCCCCCCccCC
Confidence 4777778776654
No 149
>PRK14873 primosome assembly protein PriA; Provisional
Probab=23.24 E-value=50 Score=27.86 Aligned_cols=37 Identities=27% Similarity=0.474 Sum_probs=23.4
Q ss_pred cccccccCCCCCeeeeCCcccCHHhHhhhcCCCcccCCCC
Q psy8111 93 CSKCRQSLVDKQFGSKSEKIYCGNCYDAQFASRCDGCSEI 132 (135)
Q Consensus 93 C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~ 132 (135)
|..|+.+|. |....+.+.|.-|-......+|..|+..
T Consensus 395 C~~C~~~L~---~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 395 CRHCTGPLG---LPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred CCCCCCcee---EecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 444444442 3234567889888665566789999754
No 150
>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=23.09 E-value=70 Score=16.64 Aligned_cols=7 Identities=29% Similarity=1.199 Sum_probs=3.4
Q ss_pred ccccccc
Q psy8111 84 KHWHEAC 90 (135)
Q Consensus 84 ~~~H~~C 90 (135)
+.||..|
T Consensus 22 ~~~H~~C 28 (51)
T PF00628_consen 22 RWYHQEC 28 (51)
T ss_dssp CEEETTT
T ss_pred hhhCccc
Confidence 3455554
No 151
>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=22.97 E-value=75 Score=16.79 Aligned_cols=10 Identities=30% Similarity=1.006 Sum_probs=6.0
Q ss_pred cccCHHhHhh
Q psy8111 111 KIYCGNCYDA 120 (135)
Q Consensus 111 ~~~C~~c~~~ 120 (135)
--+|+.||..
T Consensus 24 yDLC~~Cf~~ 33 (45)
T cd02344 24 FDFCENCFKT 33 (45)
T ss_pred ccchHHhhCC
Confidence 3457777654
No 152
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=22.90 E-value=45 Score=29.51 Aligned_cols=35 Identities=23% Similarity=0.379 Sum_probs=20.6
Q ss_pred hhhcCCchhhcCCccccCccccee-------CC---ccccccccc
Q psy8111 58 ESVFANSCEECSKIIGIDSKDLSY-------KD---KHWHEACFS 92 (135)
Q Consensus 58 ~~~~~~~C~~C~~~I~~~~~~~~~-------~~---~~~H~~Cf~ 92 (135)
.+.....|.+|++.|.-++..|.. .| ..||..||.
T Consensus 13 AkS~Rs~Ck~C~~~I~K~~lRi~~~v~~~~~dg~~~~W~H~~Cf~ 57 (981)
T PLN03123 13 AKSSRSSCKTCKSPIDKDELRLGKMVQSTQFDGFMPMWNHASCIL 57 (981)
T ss_pred ecCCCccccccCCcccCCCeEEEEeecccccCCCCCeeecccccc
Confidence 333346788888888644333311 12 356899986
No 153
>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=22.73 E-value=52 Score=28.00 Aligned_cols=81 Identities=15% Similarity=0.325 Sum_probs=46.1
Q ss_pred cccccCccccccceeeCCCcccCCCCeeccccCCccCCCceEeECCeeeccCchhhhcCCchhhcCCccccCcccceeCC
Q psy8111 4 AVKHQDKSFREDYNKLGGKDRGSGQHFCCWQCDESLTGQRYVLRDDHPYCIKCYESVFANSCEECSKIIGIDSKDLSYKD 83 (135)
Q Consensus 4 ~C~~C~~~i~~~~i~a~~~~~H~~~cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~~~~~~~~~~~ 83 (135)
+|..|-+.|.+ -.++.|+-- --.|..||-. |......||=..--.-..-+.|..|.+... ...+
T Consensus 70 ~C~~Cl~E~~d----p~~Rry~Yp-F~nCt~CGPr-----~~i~~~lpydr~~t~m~~f~~C~~C~~ey~------~p~~ 133 (711)
T TIGR00143 70 TCSDCLEEMLD----KNDRRYLYP-FISCTHCGPR-----FTIIEALPYDRENTSMADFPLCPDCAKEYK------DPLD 133 (711)
T ss_pred hHHHHHHHhcC----CCcccccCC-cccccCCCCC-----eEEeecCCCCCCCcCCCCCcCCHHHHHHhc------CCcc
Confidence 45555555543 346788877 7788999654 333333333111000011246666666552 2357
Q ss_pred ccccccccccccccccC
Q psy8111 84 KHWHEACFSCSKCRQSL 100 (135)
Q Consensus 84 ~~~H~~Cf~C~~C~~~l 100 (135)
+.||-.=-.|..|+-.|
T Consensus 134 rr~h~~~~~C~~Cgp~l 150 (711)
T TIGR00143 134 RRFHAQPIACPRCGPQL 150 (711)
T ss_pred ccCCCCCccCCCCCcEE
Confidence 88887777788888777
No 154
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=22.66 E-value=48 Score=23.73 Aligned_cols=33 Identities=15% Similarity=0.314 Sum_probs=24.7
Q ss_pred ccCCCCeeccccCCccCCCceEeECCeeeccCch
Q psy8111 24 RGSGQHFCCWQCDESLTGQRYVLRDDHPYCIKCY 57 (135)
Q Consensus 24 ~H~~~cf~C~~C~~~l~~~~~~~~~~~~~C~~c~ 57 (135)
|=++ -..|..|+++++...|...+|..+|..|.
T Consensus 145 ~~p~-l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 145 YGLD-LDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred Cccc-hhhHhcCCCCCCceEEecccCCccccccc
Confidence 4455 45788999998754555788999998885
No 155
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=22.56 E-value=47 Score=17.89 Aligned_cols=23 Identities=35% Similarity=0.804 Sum_probs=11.6
Q ss_pred CcccCHHhHhhhc---CCCcccCCCC
Q psy8111 110 EKIYCGNCYDAQF---ASRCDGCSEI 132 (135)
Q Consensus 110 ~~~~C~~c~~~~~---~~~C~~C~~~ 132 (135)
+--+|..||.+.. +-+|.+|.++
T Consensus 21 gf~IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 21 GFQICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp S----HHHHHHHTTSS-SB-TTT--B
T ss_pred CCcHHHHHHHHHHhccCCCCCCCCCC
Confidence 4456899987655 4689999876
No 156
>PF04641 Rtf2: Rtf2 RING-finger
Probab=22.52 E-value=80 Score=23.14 Aligned_cols=49 Identities=18% Similarity=0.438 Sum_probs=37.6
Q ss_pred ccCCCCeeccccCCccCCC-ceEe--ECCeeeccCchhhhc-CCchhhcCCccc
Q psy8111 24 RGSGQHFCCWQCDESLTGQ-RYVL--RDDHPYCIKCYESVF-ANSCEECSKIIG 73 (135)
Q Consensus 24 ~H~~~cf~C~~C~~~l~~~-~~~~--~~~~~~C~~c~~~~~-~~~C~~C~~~I~ 73 (135)
.... -|.|..-+..|.+. .|+. .-|.++.++...+.- ...|..|+++..
T Consensus 109 ~~~~-~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 109 NSEG-RFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELKKSKKCPVCGKPFT 161 (260)
T ss_pred cCCc-eeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhcccccccccCCccc
Confidence 4566 79999999999775 4543 468899888887765 457899999886
No 157
>smart00355 ZnF_C2H2 zinc finger.
Probab=22.49 E-value=44 Score=13.97 Aligned_cols=10 Identities=20% Similarity=0.664 Sum_probs=5.0
Q ss_pred eccccCCccC
Q psy8111 31 CCWQCDESLT 40 (135)
Q Consensus 31 ~C~~C~~~l~ 40 (135)
.|..|+..+.
T Consensus 2 ~C~~C~~~f~ 11 (26)
T smart00355 2 RCPECGKVFK 11 (26)
T ss_pred CCCCCcchhC
Confidence 4555555443
No 158
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.45 E-value=57 Score=19.27 Aligned_cols=42 Identities=19% Similarity=0.525 Sum_probs=26.2
Q ss_pred cccccccCCCCC---eeeeCCcccCHHhHhhhcCCCcccCCCCCC
Q psy8111 93 CSKCRQSLVDKQ---FGSKSEKIYCGNCYDAQFASRCDGCSEIFK 134 (135)
Q Consensus 93 C~~C~~~l~~~~---~~~~~~~~~C~~c~~~~~~~~C~~C~~~I~ 134 (135)
|.-|++.|...+ ..-.-.--||.+|.+.++.-.|..|+..++
T Consensus 8 CECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~g~CPnCGGelv 52 (84)
T COG3813 8 CECCDRDLPPDSTDARICTFECTFCADCAENRLHGLCPNCGGELV 52 (84)
T ss_pred CcccCCCCCCCCCceeEEEEeeehhHhHHHHhhcCcCCCCCchhh
Confidence 455666665331 111124457888888888888888876543
No 159
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=22.18 E-value=45 Score=18.22 Aligned_cols=10 Identities=20% Similarity=1.009 Sum_probs=4.1
Q ss_pred ccccCCccCC
Q psy8111 32 CWQCDESLTG 41 (135)
Q Consensus 32 C~~C~~~l~~ 41 (135)
|..|.++|..
T Consensus 2 CfgC~~~~~~ 11 (51)
T PF07975_consen 2 CFGCQKPFPD 11 (51)
T ss_dssp ETTTTEE-TT
T ss_pred CccCCCCCCC
Confidence 3344555544
No 160
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=22.16 E-value=55 Score=21.78 Aligned_cols=47 Identities=19% Similarity=0.601 Sum_probs=34.5
Q ss_pred cccccccccccccCCCCCeeeeC---CcccCHHhHhhhc-----CCCcccCCCCC
Q psy8111 87 HEACFSCSKCRQSLVDKQFGSKS---EKIYCGNCYDAQF-----ASRCDGCSEIF 133 (135)
Q Consensus 87 H~~Cf~C~~C~~~l~~~~~~~~~---~~~~C~~c~~~~~-----~~~C~~C~~~I 133 (135)
-+.=+.|..|+..-.++.|.-.+ |--.|..||..+. .|+|.+|+...
T Consensus 77 d~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSF 131 (140)
T PF05290_consen 77 DPKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSF 131 (140)
T ss_pred CCCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccc
Confidence 34456799998887777666554 7788999997653 48999997654
No 161
>PF14149 YhfH: YhfH-like protein
Probab=21.94 E-value=18 Score=18.37 Aligned_cols=15 Identities=13% Similarity=0.428 Sum_probs=8.9
Q ss_pred hhhcCCCcccCCCCC
Q psy8111 119 DAQFASRCDGCSEIF 133 (135)
Q Consensus 119 ~~~~~~~C~~C~~~I 133 (135)
+.+-...|..|++.|
T Consensus 9 rnLp~K~C~~CG~~i 23 (37)
T PF14149_consen 9 RNLPPKKCTECGKEI 23 (37)
T ss_pred HhCCCcccHHHHHHH
Confidence 334455677777665
No 162
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=21.83 E-value=81 Score=17.40 Aligned_cols=22 Identities=23% Similarity=0.401 Sum_probs=12.2
Q ss_pred eccccCCccCCC---ceEeECCeee
Q psy8111 31 CCWQCDESLTGQ---RYVLRDDHPY 52 (135)
Q Consensus 31 ~C~~C~~~l~~~---~~~~~~~~~~ 52 (135)
.|+-|+..+... .|+..||+++
T Consensus 5 ~C~f~g~~I~PG~G~~~Vr~Dgkv~ 29 (54)
T cd00472 5 KCSFCGYKIYPGHGKMYVRNDGKVF 29 (54)
T ss_pred EecCcCCeecCCCccEEEecCCCEE
Confidence 456666666432 4555666654
No 163
>PRK11595 DNA utilization protein GntX; Provisional
Probab=21.69 E-value=53 Score=23.45 Aligned_cols=21 Identities=19% Similarity=0.659 Sum_probs=11.1
Q ss_pred eccCchhhh--cCCchhhcCCcc
Q psy8111 52 YCIKCYESV--FANSCEECSKII 72 (135)
Q Consensus 52 ~C~~c~~~~--~~~~C~~C~~~I 72 (135)
+|..|.... ..+.|..|++++
T Consensus 22 lC~~C~~~l~~~~~~C~~Cg~~~ 44 (227)
T PRK11595 22 ICSVCSRALRTLKTCCPQCGLPA 44 (227)
T ss_pred ccHHHHhhCCcccCcCccCCCcC
Confidence 566665442 124566666654
No 164
>KOG0823|consensus
Probab=21.66 E-value=88 Score=22.76 Aligned_cols=54 Identities=20% Similarity=0.418 Sum_probs=36.3
Q ss_pred cCCCCeeccccCCccCCCceEeECCeeeccCchhh-----hcCCchhhcCCccccCccccee
Q psy8111 25 GSGQHFCCWQCDESLTGQRYVLRDDHPYCIKCYES-----VFANSCEECSKIIGIDSKDLSY 81 (135)
Q Consensus 25 H~~~cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~-----~~~~~C~~C~~~I~~~~~~~~~ 81 (135)
--. .|.|..|=. +...+-+.-=|.+||=.|..+ .....|..|+-.|. .+.+|-.
T Consensus 44 ~~~-~FdCNICLd-~akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs-~~~vvPl 102 (230)
T KOG0823|consen 44 DGG-FFDCNICLD-LAKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVS-IDTVVPL 102 (230)
T ss_pred CCC-ceeeeeecc-ccCCCEEeecccceehHHHHHHHhhcCCCeeCCccccccc-cceEEee
Confidence 345 799999833 333355667799999999876 23356799999886 3444443
No 165
>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=21.31 E-value=78 Score=16.84 Aligned_cols=9 Identities=56% Similarity=1.058 Sum_probs=5.4
Q ss_pred chhhcCC-cc
Q psy8111 64 SCEECSK-II 72 (135)
Q Consensus 64 ~C~~C~~-~I 72 (135)
.|.+|.+ +|
T Consensus 2 ~C~~C~~~~i 11 (49)
T cd02345 2 SCSACRKQDI 11 (49)
T ss_pred cCCCCCCCCc
Confidence 4566666 55
No 166
>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=21.09 E-value=97 Score=19.37 Aligned_cols=28 Identities=21% Similarity=0.511 Sum_probs=15.0
Q ss_pred cccccccCC-CCCeeeeCCcccCHHhHhh
Q psy8111 93 CSKCRQSLV-DKQFGSKSEKIYCGNCYDA 120 (135)
Q Consensus 93 C~~C~~~l~-~~~~~~~~~~~~C~~c~~~ 120 (135)
|+.|+++.= +....+.-.+-+|..|..+
T Consensus 52 CS~C~~~VC~~~~CSlFYtkrFC~pC~~~ 80 (97)
T PF10170_consen 52 CSICGKPVCVGQDCSLFYTKRFCLPCVKR 80 (97)
T ss_pred ccccCCceEcCCCccEEeeCceeHHHHHH
Confidence 666776653 2233333445567777543
No 167
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=20.56 E-value=42 Score=15.12 Aligned_cols=11 Identities=27% Similarity=0.697 Sum_probs=7.5
Q ss_pred CeeccccCCcc
Q psy8111 29 HFCCWQCDESL 39 (135)
Q Consensus 29 cf~C~~C~~~l 39 (135)
=|.|..|++.+
T Consensus 14 ~~~C~~C~k~F 24 (26)
T PF13465_consen 14 PYKCPYCGKSF 24 (26)
T ss_dssp SEEESSSSEEE
T ss_pred CCCCCCCcCee
Confidence 37788887654
Done!