Query psy17880
Match_columns 120
No_of_seqs 182 out of 1302
Neff 9.2
Searched_HMMs 46136
Date Fri Aug 16 16:31:14 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17880.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17880hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701|consensus 99.9 2.9E-28 6.4E-33 175.7 -2.3 117 3-120 274-393 (468)
2 KOG1701|consensus 99.9 2E-26 4.4E-31 166.3 2.2 116 4-119 335-462 (468)
3 KOG2272|consensus 99.9 1.8E-26 4E-31 157.2 -2.3 118 1-118 193-311 (332)
4 KOG4577|consensus 99.9 1.8E-25 3.8E-30 154.8 -4.3 115 3-118 33-152 (383)
5 KOG2272|consensus 99.9 1.9E-24 4E-29 147.4 -3.5 114 4-118 138-251 (332)
6 KOG1703|consensus 99.9 9.9E-23 2.1E-27 153.3 3.8 117 3-119 303-420 (479)
7 KOG1703|consensus 99.9 6E-23 1.3E-27 154.5 2.3 115 2-116 362-478 (479)
8 KOG1044|consensus 99.8 1E-21 2.2E-26 146.4 2.3 108 3-111 133-242 (670)
9 KOG1044|consensus 99.7 5.7E-18 1.2E-22 126.5 3.1 113 7-120 69-191 (670)
10 PF00412 LIM: LIM domain; Int 99.7 3.4E-17 7.5E-22 90.3 2.2 56 65-120 1-58 (58)
11 PF00412 LIM: LIM domain; Int 99.6 3.4E-16 7.3E-21 86.3 4.6 56 6-61 1-58 (58)
12 KOG1700|consensus 99.5 2.4E-15 5.2E-20 101.9 -0.1 117 3-119 7-166 (200)
13 smart00132 LIM Zinc-binding do 99.0 2.7E-10 5.9E-15 57.3 2.9 36 64-99 1-38 (39)
14 smart00132 LIM Zinc-binding do 98.9 1.3E-09 2.8E-14 54.8 2.4 36 5-40 1-38 (39)
15 KOG4577|consensus 98.4 4.8E-09 1E-13 73.6 -5.9 58 62-120 33-91 (383)
16 KOG0490|consensus 98.0 4.6E-07 9.9E-12 62.4 -2.5 108 9-117 2-117 (235)
17 KOG1700|consensus 97.8 4.1E-06 8.8E-11 57.0 -0.5 55 63-117 8-64 (200)
18 KOG1702|consensus 97.5 6.1E-06 1.3E-10 55.7 -2.3 55 64-118 6-61 (264)
19 KOG1702|consensus 97.4 8E-06 1.7E-10 55.2 -2.8 60 2-61 3-63 (264)
20 PF14446 Prok-RING_1: Prokaryo 93.3 0.079 1.7E-06 28.4 2.0 37 62-98 5-51 (54)
21 KOG0490|consensus 92.0 0.03 6.6E-07 38.4 -0.8 50 68-118 2-54 (235)
22 PF08394 Arc_trans_TRASH: Arch 91.8 0.13 2.8E-06 25.4 1.5 31 65-98 1-33 (37)
23 PF14835 zf-RING_6: zf-RING of 90.9 0.16 3.4E-06 28.3 1.4 45 30-74 8-52 (65)
24 PF10083 DUF2321: Uncharacteri 90.6 0.28 6E-06 32.1 2.6 50 49-100 27-80 (158)
25 PF09943 DUF2175: Uncharacteri 87.9 0.19 4.1E-06 30.5 0.3 28 64-91 4-33 (101)
26 PF10367 Vps39_2: Vacuolar sor 87.2 0.47 1E-05 28.5 1.9 27 63-89 79-107 (109)
27 smart00504 Ubox Modified RING 87.1 1.5 3.1E-05 23.6 3.7 43 30-73 2-46 (63)
28 PF02069 Metallothio_Pro: Prok 86.5 0.43 9.4E-06 25.4 1.2 25 90-114 9-33 (52)
29 PF11781 RRN7: RNA polymerase 86.1 0.62 1.3E-05 22.8 1.6 25 90-118 10-34 (36)
30 PF07191 zinc-ribbons_6: zinc- 85.8 0.26 5.5E-06 27.9 0.1 48 49-102 16-64 (70)
31 PF01258 zf-dskA_traR: Prokary 85.4 0.18 3.9E-06 24.6 -0.6 28 32-59 6-33 (36)
32 PF13920 zf-C3HC4_3: Zinc fing 84.9 2.4 5.2E-05 21.9 3.6 42 31-73 4-48 (50)
33 COG1645 Uncharacterized Zn-fin 84.8 0.77 1.7E-05 29.2 1.9 23 90-117 30-52 (131)
34 PRK14890 putative Zn-ribbon RN 83.6 0.95 2.1E-05 24.7 1.7 50 2-69 6-55 (59)
35 PF13248 zf-ribbon_3: zinc-rib 81.5 0.97 2.1E-05 20.3 1.1 12 3-14 2-13 (26)
36 COG2191 Formylmethanofuran deh 80.2 0.99 2.1E-05 30.9 1.2 31 89-119 173-203 (206)
37 COG4847 Uncharacterized protei 80.0 0.77 1.7E-05 27.5 0.6 30 64-93 8-39 (103)
38 PF14634 zf-RING_5: zinc-RING 79.7 2.8 6E-05 21.1 2.6 39 32-70 2-44 (44)
39 PF10367 Vps39_2: Vacuolar sor 78.9 2.7 5.8E-05 25.1 2.8 29 90-118 80-109 (109)
40 PF13717 zinc_ribbon_4: zinc-r 78.6 0.54 1.2E-05 23.0 -0.3 32 2-38 1-34 (36)
41 PF06677 Auto_anti-p27: Sjogre 78.3 1.1 2.3E-05 22.7 0.7 22 31-56 19-40 (41)
42 PF04570 DUF581: Protein of un 78.3 1.4 3E-05 24.0 1.2 28 90-117 18-47 (58)
43 cd00162 RING RING-finger (Real 77.3 3.4 7.3E-05 19.9 2.5 24 48-71 18-44 (45)
44 COG2888 Predicted Zn-ribbon RN 77.3 2.6 5.6E-05 23.1 2.1 10 4-13 10-19 (61)
45 PF10235 Cript: Microtubule-as 75.4 1.9 4.2E-05 25.6 1.4 42 25-74 40-81 (90)
46 PF13240 zinc_ribbon_2: zinc-r 74.8 2 4.3E-05 18.7 1.0 6 67-72 4-9 (23)
47 PF14471 DUF4428: Domain of un 74.4 3.3 7.2E-05 21.8 2.0 29 31-60 1-30 (51)
48 KOG0320|consensus 72.7 3.4 7.3E-05 27.8 2.1 48 27-74 129-179 (187)
49 PF13923 zf-C3HC4_2: Zinc fing 72.4 4.6 9.9E-05 19.6 2.2 30 32-61 1-30 (39)
50 COG5152 Uncharacterized conser 72.2 1.4 3.1E-05 30.1 0.4 47 29-76 196-244 (259)
51 PRK00420 hypothetical protein; 72.1 3.1 6.7E-05 25.8 1.8 11 62-72 23-33 (112)
52 PLN03208 E3 ubiquitin-protein 71.7 11 0.00023 25.8 4.4 50 28-78 17-85 (193)
53 COG2191 Formylmethanofuran deh 69.7 1.4 3.1E-05 30.1 -0.1 31 30-60 173-203 (206)
54 PF10886 DUF2685: Protein of u 69.3 3.4 7.3E-05 22.1 1.3 24 63-86 2-26 (54)
55 PF00645 zf-PARP: Poly(ADP-rib 69.3 2.1 4.5E-05 24.6 0.6 12 3-14 7-18 (82)
56 KOG1813|consensus 68.0 2.9 6.2E-05 30.3 1.1 46 29-75 241-288 (313)
57 PF12674 Zn_ribbon_2: Putative 67.7 2.9 6.4E-05 24.3 1.0 28 32-59 3-35 (81)
58 PF13719 zinc_ribbon_5: zinc-r 66.3 1.9 4.1E-05 21.1 -0.0 32 2-38 1-34 (37)
59 TIGR02098 MJ0042_CXXC MJ0042 f 64.9 1.9 4.1E-05 20.9 -0.2 12 2-13 1-12 (38)
60 PF06827 zf-FPG_IleRS: Zinc fi 64.2 1.3 2.9E-05 20.4 -0.8 12 63-74 2-13 (30)
61 PF12773 DZR: Double zinc ribb 63.7 6.9 0.00015 20.0 1.9 7 65-71 32-38 (50)
62 PF06906 DUF1272: Protein of u 63.7 17 0.00036 19.7 3.3 23 51-73 30-52 (57)
63 KOG0978|consensus 62.6 3.4 7.3E-05 33.4 0.7 44 29-73 643-689 (698)
64 KOG3002|consensus 61.5 8.6 0.00019 28.0 2.6 45 28-73 47-91 (299)
65 cd02340 ZZ_NBR1_like Zinc fing 61.1 7.6 0.00017 19.6 1.7 13 64-76 2-14 (43)
66 smart00659 RPOLCX RNA polymera 61.1 6 0.00013 20.2 1.3 9 90-98 4-12 (44)
67 smart00291 ZnF_ZZ Zinc-binding 60.5 8.4 0.00018 19.4 1.8 9 51-59 28-36 (44)
68 PLN03208 E3 ubiquitin-protein 60.3 7.7 0.00017 26.4 2.0 41 63-103 19-83 (193)
69 PF11571 Med27: Mediator compl 57.3 4.4 9.5E-05 23.9 0.4 17 56-72 48-64 (90)
70 PF10080 DUF2318: Predicted me 56.1 12 0.00027 22.7 2.3 26 90-119 37-62 (102)
71 PRK14559 putative protein seri 55.6 8 0.00017 31.2 1.7 48 4-72 2-51 (645)
72 cd02249 ZZ Zinc finger, ZZ typ 55.4 10 0.00023 19.2 1.6 8 52-59 25-32 (46)
73 PF02591 DUF164: Putative zinc 55.1 2.7 5.9E-05 22.4 -0.7 28 90-117 24-54 (56)
74 PF09723 Zn-ribbon_8: Zinc rib 50.7 5.8 0.00013 19.9 0.2 9 90-98 7-15 (42)
75 COG4306 Uncharacterized protei 50.5 19 0.00041 22.9 2.5 48 51-100 29-80 (160)
76 COG0266 Nei Formamidopyrimidin 50.3 8.9 0.00019 27.6 1.1 27 62-88 245-271 (273)
77 KOG4443|consensus 50.2 8 0.00017 31.1 1.0 22 79-100 106-127 (694)
78 COG2075 RPL24A Ribosomal prote 48.7 19 0.00042 20.1 2.1 21 90-110 5-28 (66)
79 PF00569 ZZ: Zinc finger, ZZ t 48.2 16 0.00034 18.6 1.6 10 50-59 28-37 (46)
80 COG4357 Zinc finger domain con 47.6 1.3 2.8E-05 26.7 -2.9 32 82-113 56-87 (105)
81 PF12677 DUF3797: Domain of un 47.0 21 0.00045 18.7 1.9 26 63-88 14-42 (49)
82 PF12855 Ecl1: Life-span regul 46.2 7 0.00015 19.9 0.1 20 91-114 9-28 (43)
83 cd02336 ZZ_RSC8 Zinc finger, Z 45.9 18 0.0004 18.5 1.6 30 31-60 2-33 (45)
84 PRK00807 50S ribosomal protein 45.4 21 0.00045 18.8 1.8 9 64-72 3-11 (52)
85 PF14569 zf-UDP: Zinc-binding 45.3 24 0.00052 20.4 2.2 24 49-72 35-61 (80)
86 PF00097 zf-C3HC4: Zinc finger 45.0 28 0.00061 16.7 2.3 30 32-61 1-30 (41)
87 PF07503 zf-HYPF: HypF finger; 44.9 5.5 0.00012 19.3 -0.4 30 6-39 2-31 (35)
88 PHA02929 N1R/p28-like protein; 44.8 12 0.00025 26.4 1.0 37 63-99 175-227 (238)
89 PF00096 zf-C2H2: Zinc finger, 44.7 7.6 0.00016 16.2 0.1 13 89-101 1-13 (23)
90 PRK00398 rpoP DNA-directed RNA 44.1 11 0.00024 19.1 0.7 27 64-98 5-31 (46)
91 smart00184 RING Ring finger. E 42.5 12 0.00026 17.0 0.6 24 66-89 2-25 (39)
92 smart00834 CxxC_CXXC_SSSS Puta 42.3 9.8 0.00021 18.4 0.3 9 64-72 7-15 (41)
93 PF12156 ATPase-cat_bd: Putati 41.4 14 0.00031 21.7 0.9 30 64-96 2-34 (88)
94 PF01286 XPA_N: XPA protein N- 41.3 12 0.00026 18.0 0.5 10 32-41 6-15 (34)
95 KOG0978|consensus 41.1 5.4 0.00012 32.3 -1.2 43 63-105 644-695 (698)
96 PRK11595 DNA utilization prote 38.6 30 0.00065 23.9 2.3 21 52-72 22-44 (227)
97 PF13894 zf-C2H2_4: C2H2-type 37.5 14 0.0003 15.0 0.3 12 89-100 1-12 (24)
98 KOG2114|consensus 37.1 18 0.0004 30.1 1.2 33 64-96 842-880 (933)
99 COG4393 Predicted membrane pro 37.0 21 0.00045 26.6 1.3 26 91-120 337-362 (405)
100 PF08271 TF_Zn_Ribbon: TFIIB z 36.9 29 0.00064 17.2 1.6 12 89-100 20-31 (43)
101 PF07649 C1_3: C1-like domain; 36.8 20 0.00044 16.3 0.9 11 90-100 2-12 (30)
102 TIGR02605 CxxC_CxxC_SSSS putat 36.5 14 0.00031 19.0 0.4 10 64-73 7-16 (52)
103 PF04641 Rtf2: Rtf2 RING-finge 36.1 76 0.0016 22.5 4.0 55 26-80 110-169 (260)
104 PHA02610 uvsY.-2 hypothetical 36.0 29 0.00063 18.4 1.4 13 4-16 2-14 (53)
105 PF08209 Sgf11: Sgf11 (transcr 35.8 8.4 0.00018 18.4 -0.6 16 89-104 5-20 (33)
106 TIGR00570 cdk7 CDK-activating 35.3 59 0.0013 23.9 3.4 26 48-73 26-54 (309)
107 PF12171 zf-C2H2_jaz: Zinc-fin 35.0 17 0.00038 15.9 0.5 14 89-102 2-15 (27)
108 cd02342 ZZ_UBA_plant Zinc fing 35.0 38 0.00082 17.3 1.7 8 52-59 26-33 (43)
109 PF00130 C1_1: Phorbol esters/ 35.0 47 0.001 16.9 2.2 12 3-14 11-22 (53)
110 KOG4739|consensus 34.3 24 0.00053 24.8 1.3 33 42-74 16-49 (233)
111 PF01873 eIF-5_eIF-2B: Domain 34.0 61 0.0013 20.4 2.9 32 57-91 89-120 (125)
112 PF07754 DUF1610: Domain of un 33.9 47 0.001 14.6 1.7 9 65-73 1-9 (24)
113 PF12874 zf-met: Zinc-finger o 33.5 15 0.00032 15.6 0.1 13 89-101 1-13 (25)
114 PF13834 DUF4193: Domain of un 33.4 15 0.00032 22.3 0.1 30 27-56 68-98 (99)
115 KOG2462|consensus 33.2 17 0.00037 26.2 0.4 16 27-42 128-143 (279)
116 PRK00085 recO DNA repair prote 32.9 26 0.00056 24.2 1.3 28 89-116 150-177 (247)
117 PF00628 PHD: PHD-finger; Int 32.8 42 0.00092 16.9 1.8 27 5-31 1-30 (51)
118 PF07975 C1_4: TFIIH C1-like d 32.3 21 0.00045 18.9 0.6 9 65-73 2-10 (51)
119 PRK01103 formamidopyrimidine/5 32.0 24 0.00052 25.2 1.0 12 62-73 245-256 (274)
120 PF13912 zf-C2H2_6: C2H2-type 31.9 16 0.00035 15.8 0.1 13 89-101 2-14 (27)
121 PRK14810 formamidopyrimidine-D 31.9 24 0.00052 25.2 1.0 13 62-74 244-256 (272)
122 PRK14873 primosome assembly pr 31.0 24 0.00052 28.6 1.0 37 32-71 395-431 (665)
123 PRK10445 endonuclease VIII; Pr 30.8 27 0.00058 24.8 1.0 12 62-73 235-246 (263)
124 COG0846 SIR2 NAD-dependent pro 30.5 87 0.0019 22.2 3.6 48 16-77 112-162 (250)
125 cd02335 ZZ_ADA2 Zinc finger, Z 30.4 51 0.0011 16.9 1.9 8 52-59 26-33 (49)
126 KOG2932|consensus 30.4 27 0.00058 25.8 1.0 42 31-72 92-133 (389)
127 TIGR00577 fpg formamidopyrimid 30.3 27 0.00059 24.9 1.0 26 62-87 245-270 (272)
128 COG1996 RPC10 DNA-directed RNA 29.8 21 0.00045 18.7 0.3 9 90-98 8-16 (49)
129 PRK14811 formamidopyrimidine-D 29.8 27 0.00059 24.9 1.0 13 62-74 235-247 (269)
130 PF14803 Nudix_N_2: Nudix N-te 29.4 14 0.0003 17.8 -0.4 10 5-14 2-11 (34)
131 PHA00080 DksA-like zinc finger 29.3 21 0.00045 20.2 0.3 28 31-58 33-60 (72)
132 PF11331 DUF3133: Protein of u 29.3 38 0.00083 17.5 1.2 6 65-70 34-39 (46)
133 COG1381 RecO Recombinational D 29.1 32 0.0007 24.2 1.2 26 90-115 156-181 (251)
134 PF10122 Mu-like_Com: Mu-like 28.8 18 0.00038 19.2 -0.1 10 63-72 5-14 (51)
135 PRK14891 50S ribosomal protein 28.6 36 0.00077 21.7 1.2 23 63-85 5-31 (131)
136 PRK13945 formamidopyrimidine-D 28.6 30 0.00064 24.9 1.0 13 62-74 254-266 (282)
137 TIGR00599 rad18 DNA repair pro 28.3 24 0.00052 26.8 0.5 44 29-73 26-71 (397)
138 PF00320 GATA: GATA zinc finge 28.2 71 0.0015 15.2 2.1 28 32-59 1-29 (36)
139 smart00746 TRASH metallochaper 28.0 57 0.0012 14.1 1.7 9 65-73 1-9 (39)
140 PRK13715 conjugal transfer pro 27.5 22 0.00047 20.2 0.1 29 30-58 35-63 (73)
141 cd02344 ZZ_HERC2 Zinc finger, 27.1 54 0.0012 16.8 1.6 8 52-59 26-33 (45)
142 COG1997 RPL43A Ribosomal prote 26.6 74 0.0016 18.9 2.2 37 2-46 34-70 (89)
143 KOG2186|consensus 26.3 15 0.00032 26.2 -0.8 44 1-44 1-44 (276)
144 KOG3816|consensus 26.0 25 0.00054 26.8 0.2 49 52-100 429-486 (526)
145 PF04981 NMD3: NMD3 family ; 25.9 48 0.001 23.1 1.6 24 32-61 1-24 (236)
146 PF10892 DUF2688: Protein of u 25.7 20 0.00042 19.4 -0.3 37 31-72 12-48 (60)
147 PF04810 zf-Sec23_Sec24: Sec23 25.7 53 0.0011 16.1 1.4 29 4-37 3-32 (40)
148 PRK00241 nudC NADH pyrophospha 25.3 46 0.001 23.6 1.5 9 64-72 101-109 (256)
149 PF05502 Dynactin_p62: Dynacti 25.3 44 0.00095 26.1 1.4 13 87-99 51-63 (483)
150 PF03604 DNA_RNApol_7kD: DNA d 25.1 39 0.00085 15.9 0.7 8 91-98 3-10 (32)
151 TIGR02419 C4_traR_proteo phage 25.1 19 0.00041 19.8 -0.4 27 31-57 33-59 (63)
152 PF03854 zf-P11: P-11 zinc fin 24.8 43 0.00094 17.5 0.9 26 49-74 20-47 (50)
153 cd02339 ZZ_Mind_bomb Zinc fing 24.7 66 0.0014 16.3 1.6 13 64-76 2-15 (45)
154 KOG2114|consensus 24.5 31 0.00067 28.9 0.5 46 22-70 835-880 (933)
155 PRK12495 hypothetical protein; 24.4 53 0.0012 22.9 1.6 28 63-100 43-70 (226)
156 PHA02768 hypothetical protein; 24.4 12 0.00026 20.2 -1.3 12 88-99 31-42 (55)
157 PF15121 TMEM71: TMEM71 protei 24.3 85 0.0018 20.2 2.3 30 88-117 55-84 (149)
158 PF08792 A2L_zn_ribbon: A2L zi 24.1 44 0.00096 15.8 0.8 10 46-55 17-26 (33)
159 PRK04023 DNA polymerase II lar 23.6 61 0.0013 27.9 2.0 36 30-73 639-674 (1121)
160 cd01412 SIRT5_Af1_CobB SIRT5_A 23.5 1.5E+02 0.0033 20.2 3.8 47 16-77 99-145 (224)
161 smart00355 ZnF_C2H2 zinc finge 23.4 44 0.00096 13.4 0.8 13 89-101 1-13 (26)
162 PF13771 zf-HC5HC2H: PHD-like 23.4 1.1E+02 0.0025 17.3 2.7 54 58-115 32-89 (90)
163 PF03107 C1_2: C1 domain; Int 22.7 76 0.0016 14.4 1.5 12 90-101 2-13 (30)
164 cd02341 ZZ_ZZZ3 Zinc finger, Z 22.6 61 0.0013 16.7 1.3 13 64-76 2-15 (48)
165 PF05864 Chordopox_RPO7: Chord 22.5 20 0.00042 19.5 -0.6 17 89-105 5-21 (63)
166 PRK03564 formate dehydrogenase 22.5 2.3E+02 0.0049 20.9 4.5 10 3-12 187-196 (309)
167 KOG3039|consensus 22.5 1.7E+02 0.0036 21.1 3.7 51 25-75 217-272 (303)
168 PF13832 zf-HC5HC2H_2: PHD-zin 22.1 69 0.0015 19.1 1.7 29 60-89 53-85 (110)
169 PRK11019 hypothetical protein; 21.9 34 0.00073 20.3 0.2 29 30-58 37-65 (88)
170 PF09889 DUF2116: Uncharacteri 21.9 49 0.0011 18.0 0.8 12 63-74 4-15 (59)
171 cd01407 SIR2-fam SIR2 family o 21.9 89 0.0019 21.3 2.3 17 62-78 133-149 (218)
172 PF11077 DUF2616: Protein of u 21.8 31 0.00067 23.1 0.0 35 27-61 137-171 (173)
173 KOG2879|consensus 21.6 1.2E+02 0.0025 22.1 2.8 43 30-73 240-287 (298)
174 PF07750 GcrA: GcrA cell cycle 21.5 17 0.00036 24.0 -1.3 28 93-120 117-152 (162)
175 cd01411 SIR2H SIR2H: Uncharact 21.3 1.9E+02 0.0041 20.0 3.8 17 62-78 136-152 (225)
176 KOG3970|consensus 21.3 82 0.0018 22.3 2.0 49 22-73 46-105 (299)
177 PF04945 YHS: YHS domain; Int 21.3 11 0.00024 19.1 -1.7 30 66-98 4-36 (47)
178 PHA03082 DNA-dependent RNA pol 21.1 21 0.00046 19.4 -0.7 16 89-104 5-20 (63)
179 PLN03123 poly [ADP-ribose] pol 20.8 69 0.0015 27.5 1.8 30 3-32 17-58 (981)
180 PF13639 zf-RING_2: Ring finge 20.7 1.2E+02 0.0027 14.6 2.6 9 49-57 22-30 (44)
181 KOG0823|consensus 20.6 1.6E+02 0.0035 20.7 3.3 55 26-81 44-104 (230)
182 smart00249 PHD PHD zinc finger 20.6 79 0.0017 14.9 1.5 25 6-30 2-29 (47)
183 smart00653 eIF2B_5 domain pres 20.4 1.1E+02 0.0025 18.7 2.4 24 63-88 81-104 (110)
184 PF05290 Baculo_IE-1: Baculovi 20.3 76 0.0017 20.4 1.6 43 30-72 81-131 (140)
185 PF14255 Cys_rich_CPXG: Cystei 20.1 40 0.00088 17.8 0.3 10 5-14 2-11 (52)
186 PF14570 zf-RING_4: RING/Ubox 20.0 93 0.002 16.2 1.6 20 52-71 24-46 (48)
No 1
>KOG1701|consensus
Probab=99.93 E-value=2.9e-28 Score=175.69 Aligned_cols=117 Identities=32% Similarity=0.709 Sum_probs=109.1
Q ss_pred Cccccccccccccc--eEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcccCcEEEEe
Q psy17880 3 KAYCTSCKKKCSGE--VLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTAL 80 (120)
Q Consensus 3 ~~~C~~C~~~i~~~--~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~~~~~~~ 80 (120)
..+|.+|++.|.++ .+.++++.||..||+|..|++.|.++.||..|+++||+.||.... .+|..|+++|++++|.|.
T Consensus 274 ~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl-ekC~~Cg~~I~d~iLrA~ 352 (468)
T KOG1701|consen 274 FGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL-EKCNKCGEPIMDRILRAL 352 (468)
T ss_pred hhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH-HHHhhhhhHHHHHHHHhc
Confidence 34899999999765 678999999999999999999999999999999999999999887 899999999999999999
Q ss_pred CccccccccccccCCCcCCCCceeee-CCeeeeccCCCcCC
Q psy17880 81 GKTYHQKCFTCARCRFSKKREIYNWL-GGRAYENRLGGRAY 120 (120)
Q Consensus 81 ~~~~H~~Cf~C~~C~~~l~~~~~~~~-~g~~yC~~~~~~~~ 120 (120)
|+.||+.||+|..|++.|++..|.+. ++++||-.|+-+.|
T Consensus 353 GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kf 393 (468)
T KOG1701|consen 353 GKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKF 393 (468)
T ss_pred ccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhc
Confidence 99999999999999999999998876 79999999987765
No 2
>KOG1701|consensus
Probab=99.92 E-value=2e-26 Score=166.26 Aligned_cols=116 Identities=27% Similarity=0.624 Sum_probs=104.2
Q ss_pred ccccccccccccceEEECCcccccccccccccccccCCCCee-ecCCeeccHhHHHhHhCCCCCCCCCccc---C--c--
Q psy17880 4 AYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYF-NKDGAYYCTSDYQKKFGTKCAQCGEYVE---G--E-- 75 (120)
Q Consensus 4 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~-~~~~~~~C~~c~~~~~~~~C~~C~~~i~---~--~-- 75 (120)
.+|..|+++|.+.+|.+.|+.||+.||+|..|.+.|++-.|. ..++++||..||.++|+++|+.|+++|. | +
T Consensus 335 ekC~~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 335 EKCNKCGEPIMDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETV 414 (468)
T ss_pred HHHhhhhhHHHHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcceE
Confidence 468999999999999999999999999999999999987776 4678999999999999999999999994 2 2
Q ss_pred EEEEeCccccccccccccCCCcCCC----CceeeeCCeeeeccCCCcC
Q psy17880 76 VVTALGKTYHQKCFTCARCRFSKKR----EIYNWLGGRAYENRLGGRA 119 (120)
Q Consensus 76 ~~~~~~~~~H~~Cf~C~~C~~~l~~----~~~~~~~g~~yC~~~~~~~ 119 (120)
.|+++++.||.+|++|..|+.+|+. ..-|-+||.++|+.+..++
T Consensus 415 Rvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch~~R 462 (468)
T KOG1701|consen 415 RVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCHLKR 462 (468)
T ss_pred EEEEccccccccceehhhcCccccccCCCCcceeccCceeechhhhhh
Confidence 6789999999999999999999982 3588899999999987553
No 3
>KOG2272|consensus
Probab=99.91 E-value=1.8e-26 Score=157.15 Aligned_cols=118 Identities=25% Similarity=0.592 Sum_probs=111.2
Q ss_pred CCCccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcccCcEEEEe
Q psy17880 1 MIKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTAL 80 (120)
Q Consensus 1 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~~~~~~~ 80 (120)
|.-++|..|.+||+++++.++|+.||.++|+|+.|.+|+-+...|++.|.+||+.+|.++++..|..|+.+|.|+++.+.
T Consensus 193 mgipiCgaC~rpIeervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~vv~al 272 (332)
T KOG2272|consen 193 MGIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGGDVVSAL 272 (332)
T ss_pred cCCcccccccCchHHHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCccHHHHh
Confidence 34578999999999999999999999999999999999988899999999999999999999999999999999999999
Q ss_pred CccccccccccccCCCcCC-CCceeeeCCeeeeccCCCc
Q psy17880 81 GKTYHQKCFTCARCRFSKK-REIYNWLGGRAYENRLGGR 118 (120)
Q Consensus 81 ~~~~H~~Cf~C~~C~~~l~-~~~~~~~~g~~yC~~~~~~ 118 (120)
+++|.++||.|+.|++.|. ...|++.|-+|.|++++.|
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 9999999999999999996 5579999999999998864
No 4
>KOG4577|consensus
Probab=99.89 E-value=1.8e-25 Score=154.77 Aligned_cols=115 Identities=30% Similarity=0.668 Sum_probs=102.3
Q ss_pred Cccccccccccccc-eEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcccC-cEE-EE
Q psy17880 3 KAYCTSCKKKCSGE-VLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEG-EVV-TA 79 (120)
Q Consensus 3 ~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~-~~~-~~ 79 (120)
-++|+.|.+.|.++ ++.++++.||..|++|+.|..+|.+ .+|.+++.+||+++|.++|+.+|..|.+.|+. .+| .|
T Consensus 33 ip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRkA 111 (383)
T KOG4577|consen 33 IPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRKA 111 (383)
T ss_pred cccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHHh
Confidence 47899999999877 6788999999999999999999986 69999999999999999999999999999975 444 68
Q ss_pred eCccccccccccccCCCcCCCC-cee-eeCCeeeeccCCCc
Q psy17880 80 LGKTYHQKCFTCARCRFSKKRE-IYN-WLGGRAYENRLGGR 118 (120)
Q Consensus 80 ~~~~~H~~Cf~C~~C~~~l~~~-~~~-~~~g~~yC~~~~~~ 118 (120)
.+..||.+||.|..|+++|..+ +|| +.|+++.|+.++..
T Consensus 112 qd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~ 152 (383)
T KOG4577|consen 112 QDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYET 152 (383)
T ss_pred hcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHH
Confidence 8999999999999999999655 566 45899999998854
No 5
>KOG2272|consensus
Probab=99.87 E-value=1.9e-24 Score=147.41 Aligned_cols=114 Identities=24% Similarity=0.417 Sum_probs=105.9
Q ss_pred ccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcccCcEEEEeCcc
Q psy17880 4 AYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALGKT 83 (120)
Q Consensus 4 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~~~~~~~~~~ 83 (120)
-+|.+|+..|+++.+...+..||+.+|.|..|++.|.+ ...+..+.+||.+|+.+.-.|+|..|.+||++++|.++|+.
T Consensus 138 YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C~keL~s-daRevk~eLyClrChD~mgipiCgaC~rpIeervi~amgKh 216 (332)
T KOG2272|consen 138 YVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTCGKELTS-DAREVKGELYCLRCHDKMGIPICGACRRPIEERVIFAMGKH 216 (332)
T ss_pred eehhhhhhhcccccccccCCCCCccceecccccccccc-hhhhhccceeccccccccCCcccccccCchHHHHHHHhccc
Confidence 46899999999899999999999999999999999976 45667789999999999888999999999999999999999
Q ss_pred ccccccccccCCCcCCCCceeeeCCeeeeccCCCc
Q psy17880 84 YHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGR 118 (120)
Q Consensus 84 ~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~ 118 (120)
||.++|+|+.|.+|+-+...++.+|.+||+.++.+
T Consensus 217 WHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~q 251 (332)
T KOG2272|consen 217 WHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQ 251 (332)
T ss_pred cchhheeehhcCCcccchhhhhhcCchhHHHHHHH
Confidence 99999999999999999999999999999998755
No 6
>KOG1703|consensus
Probab=99.86 E-value=9.9e-23 Score=153.33 Aligned_cols=117 Identities=28% Similarity=0.554 Sum_probs=111.2
Q ss_pred Ccccccccccccc-ceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcccCcEEEEeC
Q psy17880 3 KAYCTSCKKKCSG-EVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALG 81 (120)
Q Consensus 3 ~~~C~~C~~~i~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~~~~~~~~ 81 (120)
.+.|..|++.|.+ +++.++++.||+.+|.|..|...+....+...+|.+||..|+...+.+.|.+|+++|.++.|.+.+
T Consensus 303 ~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a~~ 382 (479)
T KOG1703|consen 303 RPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVCALG 382 (479)
T ss_pred cccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhHhhhcc
Confidence 4789999999998 899999999999999999999999888888999999999999999999999999999999999999
Q ss_pred ccccccccccccCCCcCCCCceeeeCCeeeeccCCCcC
Q psy17880 82 KTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRA 119 (120)
Q Consensus 82 ~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~ 119 (120)
+.||++||.|..|+++|.+..|++.||.+||+.++...
T Consensus 383 ~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~ 420 (479)
T KOG1703|consen 383 RLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKL 420 (479)
T ss_pred CeechhceeeecccCCCCCCcccccCCccchhhhHhhh
Confidence 99999999999999999999999999999999988543
No 7
>KOG1703|consensus
Probab=99.86 E-value=6e-23 Score=154.51 Aligned_cols=115 Identities=27% Similarity=0.590 Sum_probs=109.7
Q ss_pred CCccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCccc--CcEEEE
Q psy17880 2 IKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVE--GEVVTA 79 (120)
Q Consensus 2 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~--~~~~~~ 79 (120)
..+.|.+|+++|.++.|.+.+..||++||.|..|++++....|+..++.+||+.||.++++.+|..|.++++ +..+.+
T Consensus 362 ~~p~C~~C~~~i~~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~~~ie~ 441 (479)
T KOG1703|consen 362 FRPNCKRCLLPILEEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGSRQIEA 441 (479)
T ss_pred hCccccccCCchHHhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccchhHhhhhHhhc
Confidence 357899999999999999999999999999999999999999999999999999999999999999999986 678999
Q ss_pred eCccccccccccccCCCcCCCCceeeeCCeeeeccCC
Q psy17880 80 LGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLG 116 (120)
Q Consensus 80 ~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~ 116 (120)
.+..||..||+|+.|.+.|.++.|+...++++|+.++
T Consensus 442 ~~~~~h~~~F~c~~c~~~l~~~~~~~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 442 DGSPFHGDCFRCANCMKKLTKKTFFETLDKPLCQKHF 478 (479)
T ss_pred cCccccccceehhhhhccccCCceeecCCccccccCC
Confidence 9999999999999999999999999999999999986
No 8
>KOG1044|consensus
Probab=99.83 E-value=1e-21 Score=146.38 Aligned_cols=108 Identities=34% Similarity=0.807 Sum_probs=97.6
Q ss_pred Ccccccccccc-ccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcccCcEEEEeC
Q psy17880 3 KAYCTSCKKKC-SGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVVTALG 81 (120)
Q Consensus 3 ~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~~~~~~~~ 81 (120)
...|++|++.| .|+.+.++++.||..||+|..|+..|.+ .+..+|+.+||+.+|.+.|+.+|..|.+.|.|.++.+.|
T Consensus 133 ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~g-ey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvLqag~ 211 (670)
T KOG1044|consen 133 PSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNG-EYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVLQAGD 211 (670)
T ss_pred Cccccchhhhhhccceeeeeccceeeeeeehhhhcccccc-eeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhhhccC
Confidence 35799999988 7889999999999999999999999976 699999999999999999999999999999999999999
Q ss_pred ccccccccccccCCCcCCCCc-eeeeCCeee
Q psy17880 82 KTYHQKCFTCARCRFSKKREI-YNWLGGRAY 111 (120)
Q Consensus 82 ~~~H~~Cf~C~~C~~~l~~~~-~~~~~g~~y 111 (120)
++||+.|-+|++|+..+..++ .|+-+..+|
T Consensus 212 kh~HPtCARCsRCgqmF~eGEEMYlQGs~iW 242 (670)
T KOG1044|consen 212 KHFHPTCARCSRCGQMFGEGEEMYLQGSEIW 242 (670)
T ss_pred cccCcchhhhhhhccccccchheeecccccc
Confidence 999999999999999998665 554454444
No 9
>KOG1044|consensus
Probab=99.70 E-value=5.7e-18 Score=126.55 Aligned_cols=113 Identities=28% Similarity=0.563 Sum_probs=94.6
Q ss_pred cccccccccceEEECCcccccccccccccccccCCC-CeeecCCeeccHhHHHhHh--------CCCCCCCCCcc-cCcE
Q psy17880 7 TSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQG-GYFNKDGAYYCTSDYQKKF--------GTKCAQCGEYV-EGEV 76 (120)
Q Consensus 7 ~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~~~~~~C~~c~~~~~--------~~~C~~C~~~i-~~~~ 76 (120)
..|..-|.++++.++|++||++||.|+.|..+...+ ....-+....|+.|....- ...|++|++.| .|..
T Consensus 69 ~~c~~~~~gevvsa~gktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~ 148 (670)
T KOG1044|consen 69 DDCRAFVEGEVVSTLGKTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQA 148 (670)
T ss_pred cchhhhccceeEecccceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccce
Confidence 456677889999999999999999999999998766 4445555678888875321 24799999999 6789
Q ss_pred EEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880 77 VTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY 120 (120)
Q Consensus 77 ~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~ 120 (120)
+.|.++.||..||+|..|...|. ++|+..||.|||++++...|
T Consensus 149 llald~qwhv~cfkc~~c~~vL~-gey~skdg~pyce~dy~~~f 191 (670)
T KOG1044|consen 149 LLALDKQWHVSCFKCKSCSAVLN-GEYMSKDGVPYCEKDYQAKF 191 (670)
T ss_pred eeeeccceeeeeeehhhhccccc-ceeeccCCCcchhhhhhhhc
Confidence 99999999999999999999884 55788999999999998765
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=99.66 E-value=3.4e-17 Score=90.29 Aligned_cols=56 Identities=29% Similarity=0.698 Sum_probs=50.6
Q ss_pred CCCCCCcccCc--EEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880 65 CAQCGEYVEGE--VVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY 120 (120)
Q Consensus 65 C~~C~~~i~~~--~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~ 120 (120)
|..|+++|.+. ++.+.|+.||++||+|+.|+++|.++.++..||++||+.++.++|
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 78999999753 346999999999999999999999999999999999999998776
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=3.4e-16 Score=86.30 Aligned_cols=56 Identities=39% Similarity=1.002 Sum_probs=50.6
Q ss_pred ccccccccccc-e-EEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHh
Q psy17880 6 CTSCKKKCSGE-V-LRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF 61 (120)
Q Consensus 6 C~~C~~~i~~~-~-~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~ 61 (120)
|.+|+++|.+. . +.+.|+.||++||+|+.|+++|.++.++..++++||+.||.++|
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 78999999755 3 36999999999999999999999888999999999999999875
No 12
>KOG1700|consensus
Probab=99.50 E-value=2.4e-15 Score=101.85 Aligned_cols=117 Identities=32% Similarity=0.625 Sum_probs=99.8
Q ss_pred Cccccccccccc-cceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCC------------------
Q psy17880 3 KAYCTSCKKKCS-GEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGT------------------ 63 (120)
Q Consensus 3 ~~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~------------------ 63 (120)
...|.+|++.+. .+.+...|..||..||.|..|.+.|....+..+++.+||+.+|...+++
T Consensus 7 ~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (200)
T KOG1700|consen 7 TDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGKD 86 (200)
T ss_pred cchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCcc
Confidence 347999999883 3344477889999999999999999988899999999999977666544
Q ss_pred -----------------------CCCCCCCccc-CcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcC
Q psy17880 64 -----------------------KCAQCGEYVE-GEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRA 119 (120)
Q Consensus 64 -----------------------~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~ 119 (120)
.|..|.+.+- .+-+...+..||..||+|+.|+..|+...+...+|.+||..++.+.
T Consensus 87 ~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~ 166 (200)
T KOG1700|consen 87 GKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQL 166 (200)
T ss_pred cccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhhee
Confidence 6999998884 4667888999999999999999999999999999999999887553
No 13
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=99.02 E-value=2.7e-10 Score=57.30 Aligned_cols=36 Identities=44% Similarity=1.019 Sum_probs=32.5
Q ss_pred CCCCCCCcccC--cEEEEeCccccccccccccCCCcCC
Q psy17880 64 KCAQCGEYVEG--EVVTALGKTYHQKCFTCARCRFSKK 99 (120)
Q Consensus 64 ~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~l~ 99 (120)
+|..|+++|.+ ..+.+.++.||++||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 58899999976 6778999999999999999999985
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=98.88 E-value=1.3e-09 Score=54.76 Aligned_cols=36 Identities=42% Similarity=0.867 Sum_probs=32.1
Q ss_pred ccccccccccc--ceEEECCcccccccccccccccccC
Q psy17880 5 YCTSCKKKCSG--EVLRVQDKYFHITCFQCSVCKNSLA 40 (120)
Q Consensus 5 ~C~~C~~~i~~--~~~~~~~~~~H~~Cf~C~~C~~~l~ 40 (120)
+|.+|+++|.+ ..+.+.++.||++||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 48899999976 5778889999999999999999985
No 15
>KOG4577|consensus
Probab=98.36 E-value=4.8e-09 Score=73.64 Aligned_cols=58 Identities=17% Similarity=0.430 Sum_probs=49.4
Q ss_pred CCCCCCCCCcccCc-EEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880 62 GTKCAQCGEYVEGE-VVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGRAY 120 (120)
Q Consensus 62 ~~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~ 120 (120)
.++|+.|.+.|.++ ++.+.+++||..|++|+.|..+|...=| ..+|.+||+.++-.+|
T Consensus 33 ip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCF-sR~~s~yCkedFfKrf 91 (383)
T KOG4577|consen 33 IPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCF-SREGSVYCKEDFFKRF 91 (383)
T ss_pred cccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHh-hcCCceeehHHHHHHh
Confidence 48999999999887 4579999999999999999999966544 4789999999875544
No 16
>KOG0490|consensus
Probab=97.98 E-value=4.6e-07 Score=62.41 Aligned_cols=108 Identities=31% Similarity=0.695 Sum_probs=82.4
Q ss_pred cccccccc-eEEECCcccccccccccccccccC-CCCeeecCCeeccHhHHHh--HhCCCCCCCCCccc--CcEEEEeCc
Q psy17880 9 CKKKCSGE-VLRVQDKYFHITCFQCSVCKNSLA-QGGYFNKDGAYYCTSDYQK--KFGTKCAQCGEYVE--GEVVTALGK 82 (120)
Q Consensus 9 C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~-~~~~~~~~~~~~C~~c~~~--~~~~~C~~C~~~i~--~~~~~~~~~ 82 (120)
|+..|.+. .+.+.+..||..|..|..|...+. ....+..++..||..+|.. .+..+|.+|...+. +++..+..+
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f~~ 81 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAFEK 81 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchhhhhccccccCCCCCcCHHHHHHHhhcC
Confidence 56667655 355568899999999999999997 2245555999999999998 77789999999984 345566677
Q ss_pred cccccccccccCCCcCCC-CceeeeCC-eeeeccCCC
Q psy17880 83 TYHQKCFTCARCRFSKKR-EIYNWLGG-RAYENRLGG 117 (120)
Q Consensus 83 ~~H~~Cf~C~~C~~~l~~-~~~~~~~g-~~yC~~~~~ 117 (120)
. |..||.|..|...+.+ ..+.+.+. +.++.++..
T Consensus 82 ~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~ 117 (235)
T KOG0490|consen 82 V-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRK 117 (235)
T ss_pred C-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhh
Confidence 7 9999999999886644 44555544 777777654
No 17
>KOG1700|consensus
Probab=97.77 E-value=4.1e-06 Score=56.98 Aligned_cols=55 Identities=29% Similarity=0.565 Sum_probs=47.8
Q ss_pred CCCCCCCCccc-CcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeecc-CCC
Q psy17880 63 TKCAQCGEYVE-GEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENR-LGG 117 (120)
Q Consensus 63 ~~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~-~~~ 117 (120)
..|..|++.+. .+.+...|..||..||+|..|.+.|+...+...++.+||+. ++.
T Consensus 8 ~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~ 64 (200)
T KOG1700|consen 8 DKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVA 64 (200)
T ss_pred chhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHh
Confidence 58999999883 45556889999999999999999999999999999999999 443
No 18
>KOG1702|consensus
Probab=97.54 E-value=6.1e-06 Score=55.73 Aligned_cols=55 Identities=27% Similarity=0.528 Sum_probs=46.2
Q ss_pred CCCCCCCccc-CcEEEEeCccccccccccccCCCcCCCCceeeeCCeeeeccCCCc
Q psy17880 64 KCAQCGEYVE-GEVVTALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRLGGR 118 (120)
Q Consensus 64 ~C~~C~~~i~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~~ 118 (120)
.|..|++.+- -+.|.-.++.||..||+|..|+.+|.-..+.-.|.++||+.++..
T Consensus 6 n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpk 61 (264)
T KOG1702|consen 6 NREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPK 61 (264)
T ss_pred hhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccc
Confidence 4556777663 356777899999999999999999999998889999999999864
No 19
>KOG1702|consensus
Probab=97.44 E-value=8e-06 Score=55.18 Aligned_cols=60 Identities=32% Similarity=0.616 Sum_probs=50.5
Q ss_pred CCcccccccccc-ccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHh
Q psy17880 2 IKAYCTSCKKKC-SGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF 61 (120)
Q Consensus 2 ~~~~C~~C~~~i-~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~ 61 (120)
++..|..|++.+ +-+.+..+++.||..||.|..|+.+|.-.++-..+.++||..+|.+..
T Consensus 3 ~k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~ 63 (264)
T KOG1702|consen 3 KKCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQV 63 (264)
T ss_pred ccchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccce
Confidence 456678888876 445677889999999999999999998878888899999999997654
No 20
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=93.27 E-value=0.079 Score=28.45 Aligned_cols=37 Identities=32% Similarity=0.886 Sum_probs=25.8
Q ss_pred CCCCCCCCCccc--CcEEE--EeCcccccccc----cccc--CCCcC
Q psy17880 62 GTKCAQCGEYVE--GEVVT--ALGKTYHQKCF----TCAR--CRFSK 98 (120)
Q Consensus 62 ~~~C~~C~~~i~--~~~~~--~~~~~~H~~Cf----~C~~--C~~~l 98 (120)
+.+|..|+++|. +++|+ .-+..||.+|. .|.. |+.++
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence 478999999994 44553 45778999998 4655 55544
No 21
>KOG0490|consensus
Probab=92.03 E-value=0.03 Score=38.38 Aligned_cols=50 Identities=24% Similarity=0.547 Sum_probs=39.9
Q ss_pred CCCcccCc-EEEEeCccccccccccccCCCcCC--CCceeeeCCeeeeccCCCc
Q psy17880 68 CGEYVEGE-VVTALGKTYHQKCFTCARCRFSKK--REIYNWLGGRAYENRLGGR 118 (120)
Q Consensus 68 C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~g~~yC~~~~~~ 118 (120)
|+.+|.+. .+.+.+..||..|..|..|...+. ...|.. +|..||..++.+
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~ 54 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQR 54 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchh
Confidence 56667654 345568999999999999999997 555666 999999998865
No 22
>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=91.84 E-value=0.13 Score=25.43 Aligned_cols=31 Identities=39% Similarity=0.749 Sum_probs=22.3
Q ss_pred CCCCCCcccCc--EEEEeCccccccccccccCCCcC
Q psy17880 65 CAQCGEYVEGE--VVTALGKTYHQKCFTCARCRFSK 98 (120)
Q Consensus 65 C~~C~~~i~~~--~~~~~~~~~H~~Cf~C~~C~~~l 98 (120)
|..|+++|.++ ++...++.|+ |.|..|.+.|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~f 33 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQF 33 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE---EECHHHHHHH
Confidence 67899999775 5678888888 5556665544
No 23
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=90.94 E-value=0.16 Score=28.30 Aligned_cols=45 Identities=20% Similarity=0.438 Sum_probs=23.1
Q ss_pred ccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcccC
Q psy17880 30 FQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEG 74 (120)
Q Consensus 30 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~ 74 (120)
++|+.|...|...-....=+.++|..|-.+.++..|..|..|-..
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~ 52 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWI 52 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHH
Confidence 578888888765433455568899999988888889999988743
No 24
>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=90.62 E-value=0.28 Score=32.06 Aligned_cols=50 Identities=24% Similarity=0.523 Sum_probs=37.5
Q ss_pred CeeccHhHHHhHhCCCCCCCCCcccCcE----EEEeCccccccccccccCCCcCCC
Q psy17880 49 GAYYCTSDYQKKFGTKCAQCGEYVEGEV----VTALGKTYHQKCFTCARCRFSKKR 100 (120)
Q Consensus 49 ~~~~C~~c~~~~~~~~C~~C~~~i~~~~----~~~~~~~~H~~Cf~C~~C~~~l~~ 100 (120)
..-||..|-.+.. ..|..|+.+|.|.+ +...+..|+.-- -|..|+++++.
T Consensus 27 ~~~fC~kCG~~tI-~~Cp~C~~~IrG~y~v~gv~~~g~~~~~Ps-YC~~CGkpyPW 80 (158)
T PF10083_consen 27 REKFCSKCGAKTI-TSCPNCSTPIRGDYHVEGVFGLGGHYEAPS-YCHNCGKPYPW 80 (158)
T ss_pred HHHHHHHhhHHHH-HHCcCCCCCCCCceecCCeeeeCCCCCCCh-hHHhCCCCCch
Confidence 4558999988877 89999999998852 334466676543 48999998864
No 25
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=87.93 E-value=0.19 Score=30.52 Aligned_cols=28 Identities=36% Similarity=0.717 Sum_probs=20.6
Q ss_pred CCCCCCCcc-cCcEEEEe-Ccccccccccc
Q psy17880 64 KCAQCGEYV-EGEVVTAL-GKTYHQKCFTC 91 (120)
Q Consensus 64 ~C~~C~~~i-~~~~~~~~-~~~~H~~Cf~C 91 (120)
+|..|+++| .|+..++. +..-|.+||.=
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~ 33 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFRE 33 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHH
Confidence 588899998 57776654 45779888863
No 26
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=87.24 E-value=0.47 Score=28.46 Aligned_cols=27 Identities=33% Similarity=0.698 Sum_probs=15.9
Q ss_pred CCCCCCCCcccCc-EEEEe-Ccccccccc
Q psy17880 63 TKCAQCGEYVEGE-VVTAL-GKTYHQKCF 89 (120)
Q Consensus 63 ~~C~~C~~~i~~~-~~~~~-~~~~H~~Cf 89 (120)
..|..|+++|... ++.+. |..+|..|+
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 4688888877543 33333 445676664
No 27
>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=87.12 E-value=1.5 Score=23.61 Aligned_cols=43 Identities=14% Similarity=0.217 Sum_probs=31.7
Q ss_pred ccccccccccCCCCeeecCCeeccHhHHHhHh--CCCCCCCCCccc
Q psy17880 30 FQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF--GTKCAQCGEYVE 73 (120)
Q Consensus 30 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~--~~~C~~C~~~i~ 73 (120)
|.|..|+..+.. ......|..||..+..+.+ ...|..|++++.
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence 567888888765 4666778999998887654 356888877774
No 28
>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=86.45 E-value=0.43 Score=25.40 Aligned_cols=25 Identities=20% Similarity=0.333 Sum_probs=15.3
Q ss_pred ccccCCCcCCCCceeeeCCeeeecc
Q psy17880 90 TCARCRFSKKREIYNWLGGRAYENR 114 (120)
Q Consensus 90 ~C~~C~~~l~~~~~~~~~g~~yC~~ 114 (120)
.|..|...++...-+..||+.||..
T Consensus 9 aC~~C~C~V~~~~Ai~~dGk~YCS~ 33 (52)
T PF02069_consen 9 ACPSCSCVVSEEEAIQKDGKYYCSE 33 (52)
T ss_dssp SSTT----B-TTTSEESSS-EESSH
T ss_pred cCCCCEeEECchHhHHhCCEeeecH
Confidence 3678888888788888999999964
No 29
>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=86.14 E-value=0.62 Score=22.81 Aligned_cols=25 Identities=24% Similarity=0.404 Sum_probs=17.9
Q ss_pred ccccCCCcCCCCceeeeCCeeeeccCCCc
Q psy17880 90 TCARCRFSKKREIYNWLGGRAYENRLGGR 118 (120)
Q Consensus 90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~~~ 118 (120)
.|..|+.. .|...||..||..++-+
T Consensus 10 ~C~~C~~~----~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 10 PCPVCGSR----WFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred cCCCCCCe----EeEccCCEEEhhhCceE
Confidence 47777554 57778999999877643
No 30
>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=85.81 E-value=0.26 Score=27.92 Aligned_cols=48 Identities=25% Similarity=0.522 Sum_probs=20.5
Q ss_pred CeeccHhHHHhHh-CCCCCCCCCcccCcEEEEeCccccccccccccCCCcCCCCc
Q psy17880 49 GAYYCTSDYQKKF-GTKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKREI 102 (120)
Q Consensus 49 ~~~~C~~c~~~~~-~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~ 102 (120)
+..+|..|..... ...|..|++++. ++.+-|.. =|.|..|+..++..+
T Consensus 16 ~~~~C~~C~~~~~~~a~CPdC~~~Le--~LkACGAv----dYFC~~c~gLiSKkr 64 (70)
T PF07191_consen 16 GHYHCEACQKDYKKEAFCPDCGQPLE--VLKACGAV----DYFCNHCHGLISKKR 64 (70)
T ss_dssp TEEEETTT--EEEEEEE-TTT-SB-E--EEEETTEE----EEE-TTTT-EE-TTT
T ss_pred CEEECccccccceecccCCCcccHHH--HHHHhccc----ceeeccCCceeecce
Confidence 4444554443211 156777777763 45555431 145677777776654
No 31
>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=85.39 E-value=0.18 Score=24.56 Aligned_cols=28 Identities=18% Similarity=0.468 Sum_probs=18.4
Q ss_pred ccccccccCCCCeeecCCeeccHhHHHh
Q psy17880 32 CSVCKNSLAQGGYFNKDGAYYCTSDYQK 59 (120)
Q Consensus 32 C~~C~~~l~~~~~~~~~~~~~C~~c~~~ 59 (120)
|..|+.++.........+..+|..|..+
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQER 33 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHhCc
Confidence 6777777766666666777778777654
No 32
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=84.86 E-value=2.4 Score=21.88 Aligned_cols=42 Identities=19% Similarity=0.515 Sum_probs=28.3
Q ss_pred cccccccccCCCCeeecCCee-ccHhHHHhHh--CCCCCCCCCccc
Q psy17880 31 QCSVCKNSLAQGGYFNKDGAY-YCTSDYQKKF--GTKCAQCGEYVE 73 (120)
Q Consensus 31 ~C~~C~~~l~~~~~~~~~~~~-~C~~c~~~~~--~~~C~~C~~~i~ 73 (120)
.|..|...... ..+..=|.. +|..|..+.. ...|..|.++|.
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 344556777 9999998874 478999998885
No 33
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=84.76 E-value=0.77 Score=29.22 Aligned_cols=23 Identities=17% Similarity=0.459 Sum_probs=15.4
Q ss_pred ccccCCCcCCCCceeeeCCeeeeccCCC
Q psy17880 90 TCARCRFSKKREIYNWLGGRAYENRLGG 117 (120)
Q Consensus 90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~~ 117 (120)
.|..|+.|| |. ++|.+||..|+.
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 367777776 33 777777777764
No 34
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=83.56 E-value=0.95 Score=24.71 Aligned_cols=50 Identities=22% Similarity=0.487 Sum_probs=28.3
Q ss_pred CCccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCC
Q psy17880 2 IKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCG 69 (120)
Q Consensus 2 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~ 69 (120)
+.++|.+|+.+|.+.- +.--|.|..|+..+.. -|..|-.....-+|..|+
T Consensus 6 ~~~~CtSCg~~i~~~~--------~~~~F~CPnCG~~~I~----------RC~~CRk~~~~Y~CP~CG 55 (59)
T PRK14890 6 EPPKCTSCGIEIAPRE--------KAVKFLCPNCGEVIIY----------RCEKCRKQSNPYTCPKCG 55 (59)
T ss_pred cCccccCCCCcccCCC--------ccCEeeCCCCCCeeEe----------echhHHhcCCceECCCCC
Confidence 4567888888875321 1112677788776322 166665554444566665
No 35
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=81.47 E-value=0.97 Score=20.27 Aligned_cols=12 Identities=17% Similarity=0.797 Sum_probs=6.5
Q ss_pred Cccccccccccc
Q psy17880 3 KAYCTSCKKKCS 14 (120)
Q Consensus 3 ~~~C~~C~~~i~ 14 (120)
...|..|+..|.
T Consensus 2 ~~~Cp~Cg~~~~ 13 (26)
T PF13248_consen 2 EMFCPNCGAEID 13 (26)
T ss_pred cCCCcccCCcCC
Confidence 345666666543
No 36
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=80.18 E-value=0.99 Score=30.85 Aligned_cols=31 Identities=13% Similarity=0.172 Sum_probs=27.5
Q ss_pred cccccCCCcCCCCceeeeCCeeeeccCCCcC
Q psy17880 89 FTCARCRFSKKREIYNWLGGRAYENRLGGRA 119 (120)
Q Consensus 89 f~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~ 119 (120)
-+|+.|+..+....-...||++.|..|+...
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 6899999999888888999999999998754
No 37
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=80.03 E-value=0.77 Score=27.49 Aligned_cols=30 Identities=30% Similarity=0.637 Sum_probs=20.9
Q ss_pred CCCCCCCcc-cCcEEEEe-Ccccccccccccc
Q psy17880 64 KCAQCGEYV-EGEVVTAL-GKTYHQKCFTCAR 93 (120)
Q Consensus 64 ~C~~C~~~i-~~~~~~~~-~~~~H~~Cf~C~~ 93 (120)
+|+.|+++| +|+..++. ...-|-+||.=+.
T Consensus 8 kC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~ 39 (103)
T COG4847 8 KCYVCGGTIIEGQKFTFTKKGSVHYECLAESK 39 (103)
T ss_pred eEeeeCCEeeeccEEEEeeCCcchHHHHHHHH
Confidence 688898888 67766543 4467888885443
No 38
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=79.68 E-value=2.8 Score=21.08 Aligned_cols=39 Identities=21% Similarity=0.562 Sum_probs=24.0
Q ss_pred ccccccccCCC--CeeecCCeeccHhHHHhHh--CCCCCCCCC
Q psy17880 32 CSVCKNSLAQG--GYFNKDGAYYCTSDYQKKF--GTKCAQCGE 70 (120)
Q Consensus 32 C~~C~~~l~~~--~~~~~~~~~~C~~c~~~~~--~~~C~~C~~ 70 (120)
|..|.....+. .+...=|.++|..|..+.. ...|..|++
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 44555555221 2334557888888888776 567777753
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=78.91 E-value=2.7 Score=25.06 Aligned_cols=29 Identities=14% Similarity=0.250 Sum_probs=22.0
Q ss_pred ccccCCCcCCCCceeee-CCeeeeccCCCc
Q psy17880 90 TCARCRFSKKREIYNWL-GGRAYENRLGGR 118 (120)
Q Consensus 90 ~C~~C~~~l~~~~~~~~-~g~~yC~~~~~~ 118 (120)
.|..|+++|..+.|... +|..+=..|..|
T Consensus 80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~~r 109 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFPCGHVVHYSCIKR 109 (109)
T ss_pred CccCcCCcCCCceEEEeCCCeEEecccccC
Confidence 58999999998877654 788776666544
No 40
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=78.61 E-value=0.54 Score=22.97 Aligned_cols=32 Identities=22% Similarity=0.562 Sum_probs=18.0
Q ss_pred CCccccccccc--cccceEEECCcccccccccccccccc
Q psy17880 2 IKAYCTSCKKK--CSGEVLRVQDKYFHITCFQCSVCKNS 38 (120)
Q Consensus 2 ~~~~C~~C~~~--i~~~~~~~~~~~~H~~Cf~C~~C~~~ 38 (120)
|...|.+|+.. |+++.+...+.. ++|+.|+..
T Consensus 1 M~i~Cp~C~~~y~i~d~~ip~~g~~-----v~C~~C~~~ 34 (36)
T PF13717_consen 1 MIITCPNCQAKYEIDDEKIPPKGRK-----VRCSKCGHV 34 (36)
T ss_pred CEEECCCCCCEEeCCHHHCCCCCcE-----EECCCCCCE
Confidence 45678888875 345444443433 466666543
No 41
>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=78.27 E-value=1.1 Score=22.68 Aligned_cols=22 Identities=41% Similarity=0.848 Sum_probs=13.8
Q ss_pred cccccccccCCCCeeecCCeeccHhH
Q psy17880 31 QCSVCKNSLAQGGYFNKDGAYYCTSD 56 (120)
Q Consensus 31 ~C~~C~~~l~~~~~~~~~~~~~C~~c 56 (120)
.|..|+.|| +..++++.+|..|
T Consensus 19 ~Cp~C~~PL----~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPL----MRDKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCee----EEecCCCEECCCC
Confidence 456677766 3356777777554
No 42
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=78.26 E-value=1.4 Score=24.05 Aligned_cols=28 Identities=21% Similarity=0.442 Sum_probs=19.6
Q ss_pred ccccCCCcCCC--CceeeeCCeeeeccCCC
Q psy17880 90 TCARCRFSKKR--EIYNWLGGRAYENRLGG 117 (120)
Q Consensus 90 ~C~~C~~~l~~--~~~~~~~g~~yC~~~~~ 117 (120)
.|..|++.|.. +.|+..+.++||...-|
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS~ECR 47 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCSEECR 47 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccccHHHH
Confidence 37788888873 34667788888876543
No 43
>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=77.32 E-value=3.4 Score=19.90 Aligned_cols=24 Identities=25% Similarity=0.498 Sum_probs=12.6
Q ss_pred CCeeccHhHHHhHh---CCCCCCCCCc
Q psy17880 48 DGAYYCTSDYQKKF---GTKCAQCGEY 71 (120)
Q Consensus 48 ~~~~~C~~c~~~~~---~~~C~~C~~~ 71 (120)
=+..+|..|..+.+ ...|..|+..
T Consensus 18 C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 18 CGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 45556666665433 2356666543
No 44
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=77.25 E-value=2.6 Score=23.05 Aligned_cols=10 Identities=40% Similarity=0.953 Sum_probs=7.3
Q ss_pred cccccccccc
Q psy17880 4 AYCTSCKKKC 13 (120)
Q Consensus 4 ~~C~~C~~~i 13 (120)
++|.+|+..|
T Consensus 10 ~~CtSCg~~i 19 (61)
T COG2888 10 PVCTSCGREI 19 (61)
T ss_pred ceeccCCCEe
Confidence 5677777777
No 45
>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=75.38 E-value=1.9 Score=25.64 Aligned_cols=42 Identities=33% Similarity=0.682 Sum_probs=26.7
Q ss_pred cccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcccC
Q psy17880 25 FHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEG 74 (120)
Q Consensus 25 ~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~ 74 (120)
|-+.=-.|..|...+.. .|.-||..|-.+. .+|+.|++.|.+
T Consensus 40 y~~~~~~C~~CK~~v~q------~g~~YCq~CAYkk--GiCamCGKki~d 81 (90)
T PF10235_consen 40 YAPYSSKCKICKTKVHQ------PGAKYCQTCAYKK--GICAMCGKKILD 81 (90)
T ss_pred ccccCcccccccccccc------CCCccChhhhccc--CcccccCCeecc
Confidence 44434466777665543 2456888886654 588888888843
No 46
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=74.80 E-value=2 Score=18.74 Aligned_cols=6 Identities=33% Similarity=1.066 Sum_probs=2.2
Q ss_pred CCCCcc
Q psy17880 67 QCGEYV 72 (120)
Q Consensus 67 ~C~~~i 72 (120)
.|+..|
T Consensus 4 ~CG~~~ 9 (23)
T PF13240_consen 4 NCGAEI 9 (23)
T ss_pred ccCCCC
Confidence 333333
No 47
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=74.39 E-value=3.3 Score=21.85 Aligned_cols=29 Identities=28% Similarity=0.645 Sum_probs=20.6
Q ss_pred cccccccccCCC-CeeecCCeeccHhHHHhH
Q psy17880 31 QCSVCKNSLAQG-GYFNKDGAYYCTSDYQKK 60 (120)
Q Consensus 31 ~C~~C~~~l~~~-~~~~~~~~~~C~~c~~~~ 60 (120)
.|+.|++.++-- .+-..|| ..|.+|+.+.
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 477888887543 2446777 6899998775
No 48
>KOG0320|consensus
Probab=72.68 E-value=3.4 Score=27.78 Aligned_cols=48 Identities=19% Similarity=0.530 Sum_probs=36.9
Q ss_pred cccccccccccccCCCC-eeecCCeeccHhHHHhHh--CCCCCCCCCcccC
Q psy17880 27 ITCFQCSVCKNSLAQGG-YFNKDGAYYCTSDYQKKF--GTKCAQCGEYVEG 74 (120)
Q Consensus 27 ~~Cf~C~~C~~~l~~~~-~~~~~~~~~C~~c~~~~~--~~~C~~C~~~i~~ 74 (120)
..++.|-.|-.+..... +..+=|.++|..|-.... +.+|..|++.|..
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 35788888877776553 557889999999997654 4789999998854
No 49
>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=72.37 E-value=4.6 Score=19.62 Aligned_cols=30 Identities=20% Similarity=0.485 Sum_probs=18.0
Q ss_pred ccccccccCCCCeeecCCeeccHhHHHhHh
Q psy17880 32 CSVCKNSLAQGGYFNKDGAYYCTSDYQKKF 61 (120)
Q Consensus 32 C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~ 61 (120)
|..|...+.+......=|..||.+|..+..
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~ 30 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYL 30 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHH
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHH
Confidence 345655554422456667888888877654
No 50
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=72.21 E-value=1.4 Score=30.09 Aligned_cols=47 Identities=26% Similarity=0.658 Sum_probs=35.9
Q ss_pred cccccccccccCCCCeeecCCeeccHhHHHhHh--CCCCCCCCCcccCcE
Q psy17880 29 CFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF--GTKCAQCGEYVEGEV 76 (120)
Q Consensus 29 Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~--~~~C~~C~~~i~~~~ 76 (120)
-|.|..|.+...+ .....-|..+|..|+.+.+ ++.|..|++...|..
T Consensus 196 PF~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~f 244 (259)
T COG5152 196 PFLCGICKKDYES-PVVTECGHSFCSLCAIRKYQKGDECGVCGKATYGRF 244 (259)
T ss_pred ceeehhchhhccc-hhhhhcchhHHHHHHHHHhccCCcceecchhhccce
Confidence 4788888877654 4666778889999998766 478999998877654
No 51
>PRK00420 hypothetical protein; Validated
Probab=72.11 E-value=3.1 Score=25.80 Aligned_cols=11 Identities=27% Similarity=0.770 Sum_probs=6.4
Q ss_pred CCCCCCCCCcc
Q psy17880 62 GTKCAQCGEYV 72 (120)
Q Consensus 62 ~~~C~~C~~~i 72 (120)
+..|..|+.|+
T Consensus 23 ~~~CP~Cg~pL 33 (112)
T PRK00420 23 SKHCPVCGLPL 33 (112)
T ss_pred cCCCCCCCCcc
Confidence 34566666555
No 52
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=71.74 E-value=11 Score=25.78 Aligned_cols=50 Identities=22% Similarity=0.451 Sum_probs=35.6
Q ss_pred ccccccccccccCCCCeeecCCeeccHhHHHhHh------------------CCCCCCCCCcccC-cEEE
Q psy17880 28 TCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF------------------GTKCAQCGEYVEG-EVVT 78 (120)
Q Consensus 28 ~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~------------------~~~C~~C~~~i~~-~~~~ 78 (120)
+-|.|..|...+.+ .....=|..||..|..+-. .+.|..|..+|.. ..+.
T Consensus 17 ~~~~CpICld~~~d-PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvP 85 (193)
T PLN03208 17 GDFDCNICLDQVRD-PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVP 85 (193)
T ss_pred CccCCccCCCcCCC-cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEE
Confidence 34788899887754 4566788999999986532 2579999999854 3443
No 53
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=69.74 E-value=1.4 Score=30.09 Aligned_cols=31 Identities=23% Similarity=0.385 Sum_probs=26.6
Q ss_pred ccccccccccCCCCeeecCCeeccHhHHHhH
Q psy17880 30 FQCSVCKNSLAQGGYFNKDGAYYCTSDYQKK 60 (120)
Q Consensus 30 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~ 60 (120)
.+|+.|+.......-...+|++.|..|+.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 6899999998877778899999999998753
No 54
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=69.33 E-value=3.4 Score=22.14 Aligned_cols=24 Identities=21% Similarity=0.398 Sum_probs=18.3
Q ss_pred CCCCCCCCcccC-cEEEEeCccccc
Q psy17880 63 TKCAQCGEYVEG-EVVTALGKTYHQ 86 (120)
Q Consensus 63 ~~C~~C~~~i~~-~~~~~~~~~~H~ 86 (120)
.+|..|++||.. ..+...+..-|+
T Consensus 2 ~~CvVCKqpi~~a~~v~T~~G~VH~ 26 (54)
T PF10886_consen 2 EICVVCKQPIDDALVVETESGPVHP 26 (54)
T ss_pred CeeeeeCCccCcceEEEcCCCccCc
Confidence 479999999965 566667777777
No 55
>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=69.27 E-value=2.1 Score=24.59 Aligned_cols=12 Identities=50% Similarity=1.002 Sum_probs=9.4
Q ss_pred Cccccccccccc
Q psy17880 3 KAYCTSCKKKCS 14 (120)
Q Consensus 3 ~~~C~~C~~~i~ 14 (120)
...|..|++.|.
T Consensus 7 Ra~Ck~C~~~I~ 18 (82)
T PF00645_consen 7 RAKCKGCKKKIA 18 (82)
T ss_dssp TEBETTTSCBE-
T ss_pred CccCcccCCcCC
Confidence 457999999995
No 56
>KOG1813|consensus
Probab=68.04 E-value=2.9 Score=30.31 Aligned_cols=46 Identities=26% Similarity=0.640 Sum_probs=34.5
Q ss_pred cccccccccccCCCCeeecCCeeccHhHHHhHhC--CCCCCCCCcccCc
Q psy17880 29 CFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG--TKCAQCGEYVEGE 75 (120)
Q Consensus 29 Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~--~~C~~C~~~i~~~ 75 (120)
-|.|..|+++... .....-+..+|+.|..+.+. ++|..|++.+.|.
T Consensus 241 Pf~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~ 288 (313)
T KOG1813|consen 241 PFKCFICRKYFYR-PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGS 288 (313)
T ss_pred Ccccccccccccc-chhhcCCceeehhhhccccccCCcceecccccccc
Confidence 4677788887754 46677788889999877653 6899999888653
No 57
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=67.73 E-value=2.9 Score=24.31 Aligned_cols=28 Identities=36% Similarity=0.778 Sum_probs=15.9
Q ss_pred ccccccccCCCCee--ecCC---eeccHhHHHh
Q psy17880 32 CSVCKNSLAQGGYF--NKDG---AYYCTSDYQK 59 (120)
Q Consensus 32 C~~C~~~l~~~~~~--~~~~---~~~C~~c~~~ 59 (120)
|..|+.||.....+ ..|| .-||..||..
T Consensus 3 CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 3 CQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred CCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 66677777654422 1222 4488888764
No 58
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=66.33 E-value=1.9 Score=21.07 Aligned_cols=32 Identities=16% Similarity=0.542 Sum_probs=16.9
Q ss_pred CCcccccccccc--ccceEEECCcccccccccccccccc
Q psy17880 2 IKAYCTSCKKKC--SGEVLRVQDKYFHITCFQCSVCKNS 38 (120)
Q Consensus 2 ~~~~C~~C~~~i--~~~~~~~~~~~~H~~Cf~C~~C~~~ 38 (120)
|...|.+|+... +++.+...+.. .+|+.|+..
T Consensus 1 M~i~CP~C~~~f~v~~~~l~~~~~~-----vrC~~C~~~ 34 (37)
T PF13719_consen 1 MIITCPNCQTRFRVPDDKLPAGGRK-----VRCPKCGHV 34 (37)
T ss_pred CEEECCCCCceEEcCHHHcccCCcE-----EECCCCCcE
Confidence 456777887753 44444333332 456666543
No 59
>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=64.90 E-value=1.9 Score=20.93 Aligned_cols=12 Identities=25% Similarity=0.813 Sum_probs=7.5
Q ss_pred CCcccccccccc
Q psy17880 2 IKAYCTSCKKKC 13 (120)
Q Consensus 2 ~~~~C~~C~~~i 13 (120)
|+..|..|+..+
T Consensus 1 M~~~CP~C~~~~ 12 (38)
T TIGR02098 1 MRIQCPNCKTSF 12 (38)
T ss_pred CEEECCCCCCEE
Confidence 345677777754
No 60
>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=64.19 E-value=1.3 Score=20.41 Aligned_cols=12 Identities=42% Similarity=1.093 Sum_probs=5.4
Q ss_pred CCCCCCCCcccC
Q psy17880 63 TKCAQCGEYVEG 74 (120)
Q Consensus 63 ~~C~~C~~~i~~ 74 (120)
.+|..|...|..
T Consensus 2 ~~C~rC~~~~~~ 13 (30)
T PF06827_consen 2 EKCPRCWNYIED 13 (30)
T ss_dssp SB-TTT--BBEE
T ss_pred CcCccCCCcceE
Confidence 457777777643
No 61
>PF12773 DZR: Double zinc ribbon
Probab=63.73 E-value=6.9 Score=20.04 Aligned_cols=7 Identities=43% Similarity=1.327 Sum_probs=3.0
Q ss_pred CCCCCCc
Q psy17880 65 CAQCGEY 71 (120)
Q Consensus 65 C~~C~~~ 71 (120)
|..|+..
T Consensus 32 C~~Cg~~ 38 (50)
T PF12773_consen 32 CPNCGAE 38 (50)
T ss_pred CcCCcCC
Confidence 4444443
No 62
>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=63.69 E-value=17 Score=19.68 Aligned_cols=23 Identities=17% Similarity=0.543 Sum_probs=17.9
Q ss_pred eccHhHHHhHhCCCCCCCCCccc
Q psy17880 51 YYCTSDYQKKFGTKCAQCGEYVE 73 (120)
Q Consensus 51 ~~C~~c~~~~~~~~C~~C~~~i~ 73 (120)
.+|.+|....+...|.-|+..+.
T Consensus 30 TFC~~C~e~~l~~~CPNCgGelv 52 (57)
T PF06906_consen 30 TFCADCAETMLNGVCPNCGGELV 52 (57)
T ss_pred cccHHHHHHHhcCcCcCCCCccc
Confidence 37888888887888888887653
No 63
>KOG0978|consensus
Probab=62.56 E-value=3.4 Score=33.45 Aligned_cols=44 Identities=25% Similarity=0.641 Sum_probs=29.3
Q ss_pred cccccccccccCCCCeeecCCeeccHhHHHhHhC---CCCCCCCCccc
Q psy17880 29 CFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG---TKCAQCGEYVE 73 (120)
Q Consensus 29 Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~---~~C~~C~~~i~ 73 (120)
=++|+.|+....+ ....+=+.++|..|...++. .+|+.|+.+..
T Consensus 643 ~LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFg 689 (698)
T KOG0978|consen 643 LLKCSVCNTRWKD-AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFG 689 (698)
T ss_pred ceeCCCccCchhh-HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCC
Confidence 3577778755543 34456677888888877665 57777777663
No 64
>KOG3002|consensus
Probab=61.51 E-value=8.6 Score=28.00 Aligned_cols=45 Identities=27% Similarity=0.491 Sum_probs=36.7
Q ss_pred ccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCccc
Q psy17880 28 TCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVE 73 (120)
Q Consensus 28 ~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~ 73 (120)
+=+.|..|...|....+.=.+|.+.|..|-.++. .+|..|.++|.
T Consensus 47 ~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~-~~CP~Cr~~~g 91 (299)
T KOG3002|consen 47 DLLDCPVCFNPLSPPIFQCDNGHLACSSCRTKVS-NKCPTCRLPIG 91 (299)
T ss_pred hhccCchhhccCcccceecCCCcEehhhhhhhhc-ccCCccccccc
Confidence 3467888888887766777889999999987665 89999999884
No 65
>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=61.14 E-value=7.6 Score=19.60 Aligned_cols=13 Identities=23% Similarity=0.478 Sum_probs=9.4
Q ss_pred CCCCCCCcccCcE
Q psy17880 64 KCAQCGEYVEGEV 76 (120)
Q Consensus 64 ~C~~C~~~i~~~~ 76 (120)
.|..|+++|.|..
T Consensus 2 ~Cd~C~~~i~G~r 14 (43)
T cd02340 2 ICDGCQGPIVGVR 14 (43)
T ss_pred CCCCCCCcCcCCe
Confidence 5778888877654
No 66
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=61.10 E-value=6 Score=20.18 Aligned_cols=9 Identities=22% Similarity=0.744 Sum_probs=4.2
Q ss_pred ccccCCCcC
Q psy17880 90 TCARCRFSK 98 (120)
Q Consensus 90 ~C~~C~~~l 98 (120)
.|..|+..+
T Consensus 4 ~C~~Cg~~~ 12 (44)
T smart00659 4 ICGECGREN 12 (44)
T ss_pred ECCCCCCEe
Confidence 445554443
No 67
>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=60.52 E-value=8.4 Score=19.41 Aligned_cols=9 Identities=33% Similarity=0.586 Sum_probs=6.0
Q ss_pred eccHhHHHh
Q psy17880 51 YYCTSDYQK 59 (120)
Q Consensus 51 ~~C~~c~~~ 59 (120)
-+|.+||.+
T Consensus 28 dlC~~Cf~~ 36 (44)
T smart00291 28 DLCQSCFAK 36 (44)
T ss_pred cchHHHHhC
Confidence 367777764
No 68
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=60.33 E-value=7.7 Score=26.43 Aligned_cols=41 Identities=24% Similarity=0.526 Sum_probs=27.8
Q ss_pred CCCCCCCCcccCcEEEEeCcccccccc------------------------ccccCCCcCCCCce
Q psy17880 63 TKCAQCGEYVEGEVVTALGKTYHQKCF------------------------TCARCRFSKKREIY 103 (120)
Q Consensus 63 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf------------------------~C~~C~~~l~~~~~ 103 (120)
..|..|...+.+.+++.-|..|+..|+ +|-.|...++....
T Consensus 19 ~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~L 83 (193)
T PLN03208 19 FDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATL 83 (193)
T ss_pred cCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcE
Confidence 457777777666666666766666555 57888888866543
No 69
>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=57.27 E-value=4.4 Score=23.93 Aligned_cols=17 Identities=35% Similarity=1.009 Sum_probs=14.2
Q ss_pred HHHhHhCCCCCCCCCcc
Q psy17880 56 DYQKKFGTKCAQCGEYV 72 (120)
Q Consensus 56 c~~~~~~~~C~~C~~~i 72 (120)
-|..+|...|.+|++.+
T Consensus 48 sY~~lfs~pC~~C~klL 64 (90)
T PF11571_consen 48 SYRNLFSTPCKKCGKLL 64 (90)
T ss_pred HHhhhccchhhHHHhHh
Confidence 46777888999999988
No 70
>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=56.07 E-value=12 Score=22.71 Aligned_cols=26 Identities=23% Similarity=0.322 Sum_probs=20.7
Q ss_pred ccccCCCcCCCCceeeeCCeeeeccCCCcC
Q psy17880 90 TCARCRFSKKREIYNWLGGRAYENRLGGRA 119 (120)
Q Consensus 90 ~C~~C~~~l~~~~~~~~~g~~yC~~~~~~~ 119 (120)
.|..| .+..|+..++.+.|+.|+.|.
T Consensus 37 aCeiC----~~~GY~q~g~~lvC~~C~~~~ 62 (102)
T PF10080_consen 37 ACEIC----GPKGYYQEGDQLVCKNCGVRF 62 (102)
T ss_pred ecccc----CCCceEEECCEEEEecCCCEE
Confidence 47777 566788999999999998764
No 71
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=55.56 E-value=8 Score=31.18 Aligned_cols=48 Identities=21% Similarity=0.452 Sum_probs=25.4
Q ss_pred ccccccccccccceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHh--CCCCCCCCCcc
Q psy17880 4 AYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF--GTKCAQCGEYV 72 (120)
Q Consensus 4 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~--~~~C~~C~~~i 72 (120)
.+|..|+..+.+.. --|..||.+|.. ..|..|-.... ...|..|+.++
T Consensus 2 ~~Cp~Cg~~n~~~a------------kFC~~CG~~l~~---------~~Cp~CG~~~~~~~~fC~~CG~~~ 51 (645)
T PRK14559 2 LICPQCQFENPNNN------------RFCQKCGTSLTH---------KPCPQCGTEVPVDEAHCPNCGAET 51 (645)
T ss_pred CcCCCCCCcCCCCC------------ccccccCCCCCC---------CcCCCCCCCCCcccccccccCCcc
Confidence 57888888765321 125556666632 12444443321 24677777665
No 72
>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=55.44 E-value=10 Score=19.21 Aligned_cols=8 Identities=50% Similarity=0.949 Sum_probs=4.6
Q ss_pred ccHhHHHh
Q psy17880 52 YCTSDYQK 59 (120)
Q Consensus 52 ~C~~c~~~ 59 (120)
+|..||..
T Consensus 25 LC~~Cf~~ 32 (46)
T cd02249 25 LCSSCYAK 32 (46)
T ss_pred CHHHHHCc
Confidence 56666653
No 73
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=55.11 E-value=2.7 Score=22.40 Aligned_cols=28 Identities=18% Similarity=0.338 Sum_probs=18.2
Q ss_pred ccccCCCcCCCCceeee---CCeeeeccCCC
Q psy17880 90 TCARCRFSKKREIYNWL---GGRAYENRLGG 117 (120)
Q Consensus 90 ~C~~C~~~l~~~~~~~~---~g~~yC~~~~~ 117 (120)
+|+.|...|+++.+... ++..+|+.+++
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNCGR 54 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCCCc
Confidence 67778777776654332 45677777764
No 74
>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=50.65 E-value=5.8 Score=19.87 Aligned_cols=9 Identities=22% Similarity=0.704 Sum_probs=3.8
Q ss_pred ccccCCCcC
Q psy17880 90 TCARCRFSK 98 (120)
Q Consensus 90 ~C~~C~~~l 98 (120)
+|..|+..+
T Consensus 7 ~C~~Cg~~f 15 (42)
T PF09723_consen 7 RCEECGHEF 15 (42)
T ss_pred EeCCCCCEE
Confidence 344444333
No 75
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.49 E-value=19 Score=22.91 Aligned_cols=48 Identities=25% Similarity=0.585 Sum_probs=31.9
Q ss_pred eccHhHHHhHhCCCCCCCCCcccCc----EEEEeCccccccccccccCCCcCCC
Q psy17880 51 YYCTSDYQKKFGTKCAQCGEYVEGE----VVTALGKTYHQKCFTCARCRFSKKR 100 (120)
Q Consensus 51 ~~C~~c~~~~~~~~C~~C~~~i~~~----~~~~~~~~~H~~Cf~C~~C~~~l~~ 100 (120)
.+|..|-.... ..|..|+.+|.|+ -|...|.-|-+--| |..|++++..
T Consensus 29 afcskcgeati-~qcp~csasirgd~~vegvlglg~dye~psf-chncgs~fpw 80 (160)
T COG4306 29 AFCSKCGEATI-TQCPICSASIRGDYYVEGVLGLGGDYEPPSF-CHNCGSRFPW 80 (160)
T ss_pred HHHhhhchHHH-hcCCccCCcccccceeeeeeccCCCCCCcch-hhcCCCCCCc
Confidence 46777666554 6789999999874 23345666666543 7788887754
No 76
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=50.29 E-value=8.9 Score=27.57 Aligned_cols=27 Identities=26% Similarity=0.591 Sum_probs=18.3
Q ss_pred CCCCCCCCCcccCcEEEEeCccccccc
Q psy17880 62 GTKCAQCGEYVEGEVVTALGKTYHQKC 88 (120)
Q Consensus 62 ~~~C~~C~~~i~~~~~~~~~~~~H~~C 88 (120)
+..|..|+.+|....+.-.+..|.+.|
T Consensus 245 GepC~~CGt~I~k~~~~gR~t~~CP~C 271 (273)
T COG0266 245 GEPCRRCGTPIEKIKLGGRSTFYCPVC 271 (273)
T ss_pred CCCCCccCCEeEEEEEcCCcCEeCCCC
Confidence 468999999997555555555555544
No 77
>KOG4443|consensus
Probab=50.19 E-value=8 Score=31.09 Aligned_cols=22 Identities=23% Similarity=0.483 Sum_probs=17.2
Q ss_pred EeCccccccccccccCCCcCCC
Q psy17880 79 ALGKTYHQKCFTCARCRFSKKR 100 (120)
Q Consensus 79 ~~~~~~H~~Cf~C~~C~~~l~~ 100 (120)
..+..+.++|+.|..|+..+.+
T Consensus 106 ~sg~~~ckk~~~c~qc~~~lpg 127 (694)
T KOG4443|consen 106 PSGPWLCKKCTRCRQCDSTLPG 127 (694)
T ss_pred cCcccccHHHHhhhhccccccc
Confidence 3466678888999999888876
No 78
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=48.71 E-value=19 Score=20.07 Aligned_cols=21 Identities=19% Similarity=0.382 Sum_probs=10.2
Q ss_pred ccccCCCcCCCCc---eeeeCCee
Q psy17880 90 TCARCRFSKKREI---YNWLGGRA 110 (120)
Q Consensus 90 ~C~~C~~~l~~~~---~~~~~g~~ 110 (120)
+|+-|+..|.++. |+..||.+
T Consensus 5 ~CsFcG~~I~PGtG~m~Vr~Dg~v 28 (66)
T COG2075 5 VCSFCGKKIEPGTGIMYVRNDGKV 28 (66)
T ss_pred EecCcCCccCCCceEEEEecCCeE
Confidence 3566666664331 33345553
No 79
>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=48.23 E-value=16 Score=18.59 Aligned_cols=10 Identities=20% Similarity=0.408 Sum_probs=7.1
Q ss_pred eeccHhHHHh
Q psy17880 50 AYYCTSDYQK 59 (120)
Q Consensus 50 ~~~C~~c~~~ 59 (120)
--+|..||.+
T Consensus 28 ~dLC~~C~~~ 37 (46)
T PF00569_consen 28 YDLCEDCFSK 37 (46)
T ss_dssp -EEEHHHHHH
T ss_pred CchhhHHHhC
Confidence 3478999876
No 80
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=47.55 E-value=1.3 Score=26.65 Aligned_cols=32 Identities=25% Similarity=0.508 Sum_probs=15.5
Q ss_pred ccccccccccccCCCcCCCCceeeeCCeeeec
Q psy17880 82 KTYHQKCFTCARCRFSKKREIYNWLGGRAYEN 113 (120)
Q Consensus 82 ~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~ 113 (120)
..+++.+..|..|.+.|+..+|.+.+--|||+
T Consensus 56 ~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~ 87 (105)
T COG4357 56 QEFNPKAIICGVCRKLLTRAEYGMCGSCPYCQ 87 (105)
T ss_pred hhcCCccEEhhhhhhhhhHHHHhhcCCCCCcC
Confidence 34455555555555555544444444444443
No 81
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=47.01 E-value=21 Score=18.70 Aligned_cols=26 Identities=31% Similarity=0.747 Sum_probs=19.6
Q ss_pred CCCCCCCCcccC--c-EEEEeCccccccc
Q psy17880 63 TKCAQCGEYVEG--E-VVTALGKTYHQKC 88 (120)
Q Consensus 63 ~~C~~C~~~i~~--~-~~~~~~~~~H~~C 88 (120)
..|..|+.-..+ + .+.+.+.+|+..|
T Consensus 14 ~~Cp~CGN~~vGngEG~liV~edtfkRtC 42 (49)
T PF12677_consen 14 CKCPKCGNDKVGNGEGTLIVEEDTFKRTC 42 (49)
T ss_pred ccCcccCCcEeecCcceEEEeccceeeee
Confidence 478889887643 2 5688888998876
No 82
>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=46.16 E-value=7 Score=19.91 Aligned_cols=20 Identities=20% Similarity=0.280 Sum_probs=12.8
Q ss_pred cccCCCcCCCCceeeeCCeeeecc
Q psy17880 91 CARCRFSKKREIYNWLGGRAYENR 114 (120)
Q Consensus 91 C~~C~~~l~~~~~~~~~g~~yC~~ 114 (120)
|..|.+++.. ..++.+||..
T Consensus 9 C~~Cdk~~~~----~~~~~lYCSe 28 (43)
T PF12855_consen 9 CIVCDKQIDP----PDDGSLYCSE 28 (43)
T ss_pred HHHhhccccC----CCCCccccCH
Confidence 5666667644 3577788764
No 83
>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=45.92 E-value=18 Score=18.48 Aligned_cols=30 Identities=27% Similarity=0.454 Sum_probs=16.6
Q ss_pred cccccccccCCCCee-e-cCCeeccHhHHHhH
Q psy17880 31 QCSVCKNSLAQGGYF-N-KDGAYYCTSDYQKK 60 (120)
Q Consensus 31 ~C~~C~~~l~~~~~~-~-~~~~~~C~~c~~~~ 60 (120)
.|..|+..+..-.|. . ..+..+|..||.+.
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~G 33 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQEG 33 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhCc
Confidence 456666666532222 1 12355888888763
No 84
>PRK00807 50S ribosomal protein L24e; Validated
Probab=45.40 E-value=21 Score=18.85 Aligned_cols=9 Identities=33% Similarity=1.103 Sum_probs=4.5
Q ss_pred CCCCCCCcc
Q psy17880 64 KCAQCGEYV 72 (120)
Q Consensus 64 ~C~~C~~~i 72 (120)
.|+.|+..|
T Consensus 3 ~C~fcG~~I 11 (52)
T PRK00807 3 TCSFCGKEI 11 (52)
T ss_pred ccCCCCCeE
Confidence 345555555
No 85
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=45.35 E-value=24 Score=20.42 Aligned_cols=24 Identities=29% Similarity=0.501 Sum_probs=9.2
Q ss_pred CeeccHhHHHh--HhC-CCCCCCCCcc
Q psy17880 49 GAYYCTSDYQK--KFG-TKCAQCGEYV 72 (120)
Q Consensus 49 ~~~~C~~c~~~--~~~-~~C~~C~~~i 72 (120)
+-+.|..||+- +-+ ..|..|+.+-
T Consensus 35 ~fPvCr~CyEYErkeg~q~CpqCkt~y 61 (80)
T PF14569_consen 35 AFPVCRPCYEYERKEGNQVCPQCKTRY 61 (80)
T ss_dssp -----HHHHHHHHHTS-SB-TTT--B-
T ss_pred CCccchhHHHHHhhcCcccccccCCCc
Confidence 34568888852 222 5677777543
No 86
>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=45.02 E-value=28 Score=16.65 Aligned_cols=30 Identities=17% Similarity=0.434 Sum_probs=17.1
Q ss_pred ccccccccCCCCeeecCCeeccHhHHHhHh
Q psy17880 32 CSVCKNSLAQGGYFNKDGAYYCTSDYQKKF 61 (120)
Q Consensus 32 C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~ 61 (120)
|..|...+........=+..+|..|..+..
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 345555554433344556778888776654
No 87
>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=44.90 E-value=5.5 Score=19.31 Aligned_cols=30 Identities=23% Similarity=0.628 Sum_probs=17.5
Q ss_pred ccccccccccceEEECCccccccccccccccccc
Q psy17880 6 CTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSL 39 (120)
Q Consensus 6 C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l 39 (120)
|..|.+.+. ...++.||..=..|..||-.+
T Consensus 2 C~~C~~Ey~----~p~~RR~~~~~isC~~CGPr~ 31 (35)
T PF07503_consen 2 CDDCLKEYF----DPSNRRFHYQFISCTNCGPRY 31 (35)
T ss_dssp -HHHHHHHC----STTSTTTT-TT--BTTCC-SC
T ss_pred CHHHHHHHc----CCCCCcccCcCccCCCCCCCE
Confidence 555666543 235788999999999998765
No 88
>PHA02929 N1R/p28-like protein; Provisional
Probab=44.84 E-value=12 Score=26.41 Aligned_cols=37 Identities=27% Similarity=0.607 Sum_probs=24.9
Q ss_pred CCCCCCCCcccCc--------EEEEeCcccccccc--------ccccCCCcCC
Q psy17880 63 TKCAQCGEYVEGE--------VVTALGKTYHQKCF--------TCARCRFSKK 99 (120)
Q Consensus 63 ~~C~~C~~~i~~~--------~~~~~~~~~H~~Cf--------~C~~C~~~l~ 99 (120)
..|+.|...+.+. ++..-++.||.+|+ .|..|..++.
T Consensus 175 ~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 175 KECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred CCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 5688888876431 22345777888887 5888877664
No 89
>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=44.68 E-value=7.6 Score=16.16 Aligned_cols=13 Identities=23% Similarity=0.559 Sum_probs=9.2
Q ss_pred cccccCCCcCCCC
Q psy17880 89 FTCARCRFSKKRE 101 (120)
Q Consensus 89 f~C~~C~~~l~~~ 101 (120)
|.|..|++.+...
T Consensus 1 y~C~~C~~~f~~~ 13 (23)
T PF00096_consen 1 YKCPICGKSFSSK 13 (23)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCCCCCccCCH
Confidence 5678888877554
No 90
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=44.08 E-value=11 Score=19.06 Aligned_cols=27 Identities=33% Similarity=0.704 Sum_probs=14.6
Q ss_pred CCCCCCCcccCcEEEEeCccccccccccccCCCcC
Q psy17880 64 KCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSK 98 (120)
Q Consensus 64 ~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l 98 (120)
+|..|+..+.-+ ... .-++|..|+.++
T Consensus 5 ~C~~CG~~~~~~-----~~~---~~~~Cp~CG~~~ 31 (46)
T PRK00398 5 KCARCGREVELD-----EYG---TGVRCPYCGYRI 31 (46)
T ss_pred ECCCCCCEEEEC-----CCC---CceECCCCCCeE
Confidence 577777766311 110 025677777655
No 91
>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=42.52 E-value=12 Score=16.99 Aligned_cols=24 Identities=29% Similarity=0.569 Sum_probs=11.2
Q ss_pred CCCCCcccCcEEEEeCcccccccc
Q psy17880 66 AQCGEYVEGEVVTALGKTYHQKCF 89 (120)
Q Consensus 66 ~~C~~~i~~~~~~~~~~~~H~~Cf 89 (120)
..|........+..-+..||.+|+
T Consensus 2 ~iC~~~~~~~~~~~C~H~~c~~C~ 25 (39)
T smart00184 2 PICLEELKDPVVLPCGHTFCRSCI 25 (39)
T ss_pred CcCccCCCCcEEecCCChHHHHHH
Confidence 344444333344445555655554
No 92
>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=42.30 E-value=9.8 Score=18.42 Aligned_cols=9 Identities=33% Similarity=1.176 Sum_probs=5.0
Q ss_pred CCCCCCCcc
Q psy17880 64 KCAQCGEYV 72 (120)
Q Consensus 64 ~C~~C~~~i 72 (120)
+|..|+...
T Consensus 7 ~C~~Cg~~f 15 (41)
T smart00834 7 RCEDCGHTF 15 (41)
T ss_pred EcCCCCCEE
Confidence 456666544
No 93
>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=41.43 E-value=14 Score=21.65 Aligned_cols=30 Identities=37% Similarity=0.769 Sum_probs=18.4
Q ss_pred CCCCCCCccc-Cc--EEEEeCccccccccccccCCC
Q psy17880 64 KCAQCGEYVE-GE--VVTALGKTYHQKCFTCARCRF 96 (120)
Q Consensus 64 ~C~~C~~~i~-~~--~~~~~~~~~H~~Cf~C~~C~~ 96 (120)
.|.+|+++|+ +. .+.+.|.. .=|.|..|..
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~---~~FCC~GC~~ 34 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEE---RPFCCPGCQA 34 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCc---cccccHHHHH
Confidence 5889999995 32 33445543 2266777754
No 94
>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=41.30 E-value=12 Score=18.04 Aligned_cols=10 Identities=20% Similarity=0.796 Sum_probs=2.7
Q ss_pred ccccccccCC
Q psy17880 32 CSVCKNSLAQ 41 (120)
Q Consensus 32 C~~C~~~l~~ 41 (120)
|..|++++..
T Consensus 6 C~eC~~~f~d 15 (34)
T PF01286_consen 6 CDECGKPFMD 15 (34)
T ss_dssp -TTT--EES-
T ss_pred HhHhCCHHHH
Confidence 3444444443
No 95
>KOG0978|consensus
Probab=41.09 E-value=5.4 Score=32.34 Aligned_cols=43 Identities=21% Similarity=0.544 Sum_probs=30.8
Q ss_pred CCCCCCCCcccCcEEEEeCcccccccc---------ccccCCCcCCCCceee
Q psy17880 63 TKCAQCGEYVEGEVVTALGKTYHQKCF---------TCARCRFSKKREIYNW 105 (120)
Q Consensus 63 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf---------~C~~C~~~l~~~~~~~ 105 (120)
.+|+.|+....+.+|+--++.|..+|. +|..|+.+|+..++..
T Consensus 644 LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~~ 695 (698)
T KOG0978|consen 644 LKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVHR 695 (698)
T ss_pred eeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccccc
Confidence 589999866666666655555555555 6999999998877653
No 96
>PRK11595 DNA utilization protein GntX; Provisional
Probab=38.63 E-value=30 Score=23.87 Aligned_cols=21 Identities=29% Similarity=0.436 Sum_probs=12.5
Q ss_pred ccHhHHHhHh--CCCCCCCCCcc
Q psy17880 52 YCTSDYQKKF--GTKCAQCGEYV 72 (120)
Q Consensus 52 ~C~~c~~~~~--~~~C~~C~~~i 72 (120)
+|..|..... .+.|..|++++
T Consensus 22 lC~~C~~~l~~~~~~C~~Cg~~~ 44 (227)
T PRK11595 22 ICSVCSRALRTLKTCCPQCGLPA 44 (227)
T ss_pred ccHHHHhhCCcccCcCccCCCcC
Confidence 5666665432 25677777664
No 97
>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=37.51 E-value=14 Score=15.02 Aligned_cols=12 Identities=33% Similarity=0.694 Sum_probs=6.5
Q ss_pred cccccCCCcCCC
Q psy17880 89 FTCARCRFSKKR 100 (120)
Q Consensus 89 f~C~~C~~~l~~ 100 (120)
|.|..|+..+..
T Consensus 1 ~~C~~C~~~~~~ 12 (24)
T PF13894_consen 1 FQCPICGKSFRS 12 (24)
T ss_dssp EE-SSTS-EESS
T ss_pred CCCcCCCCcCCc
Confidence 467778776654
No 98
>KOG2114|consensus
Probab=37.06 E-value=18 Score=30.11 Aligned_cols=33 Identities=33% Similarity=0.837 Sum_probs=22.8
Q ss_pred CCCCCCCcccCcEEE-EeCccccccccc-----cccCCC
Q psy17880 64 KCAQCGEYVEGEVVT-ALGKTYHQKCFT-----CARCRF 96 (120)
Q Consensus 64 ~C~~C~~~i~~~~~~-~~~~~~H~~Cf~-----C~~C~~ 96 (120)
+|..|..++.-..|. .-+..||..||. |..|..
T Consensus 842 kCs~C~~~LdlP~VhF~CgHsyHqhC~e~~~~~CP~C~~ 880 (933)
T KOG2114|consen 842 KCSACEGTLDLPFVHFLCGHSYHQHCLEDKEDKCPKCLP 880 (933)
T ss_pred eecccCCccccceeeeecccHHHHHhhccCcccCCccch
Confidence 688888777655554 347778888875 767654
No 99
>COG4393 Predicted membrane protein [Function unknown]
Probab=37.02 E-value=21 Score=26.62 Aligned_cols=26 Identities=23% Similarity=0.326 Sum_probs=21.2
Q ss_pred cccCCCcCCCCceeeeCCeeeeccCCCcCC
Q psy17880 91 CARCRFSKKREIYNWLGGRAYENRLGGRAY 120 (120)
Q Consensus 91 C~~C~~~l~~~~~~~~~g~~yC~~~~~~~~ 120 (120)
|..|+. .+|.++|+++.|.+|+.|+|
T Consensus 337 C~iCGd----~GYv~e~dqvICv~C~Vrmf 362 (405)
T COG4393 337 CDICGD----QGYVMEGDQVICVRCDVRMF 362 (405)
T ss_pred HHhccc----cceEeECCEEEEEEccEEEE
Confidence 555643 47999999999999999875
No 100
>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=36.89 E-value=29 Score=17.19 Aligned_cols=12 Identities=17% Similarity=0.697 Sum_probs=6.3
Q ss_pred cccccCCCcCCC
Q psy17880 89 FTCARCRFSKKR 100 (120)
Q Consensus 89 f~C~~C~~~l~~ 100 (120)
+.|..|+..|..
T Consensus 20 ~vC~~CG~Vl~e 31 (43)
T PF08271_consen 20 LVCPNCGLVLEE 31 (43)
T ss_dssp EEETTT-BBEE-
T ss_pred EECCCCCCEeec
Confidence 456777666643
No 101
>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=36.77 E-value=20 Score=16.27 Aligned_cols=11 Identities=18% Similarity=0.468 Sum_probs=2.2
Q ss_pred ccccCCCcCCC
Q psy17880 90 TCARCRFSKKR 100 (120)
Q Consensus 90 ~C~~C~~~l~~ 100 (120)
.|..|++++.+
T Consensus 2 ~C~~C~~~~~~ 12 (30)
T PF07649_consen 2 RCDACGKPIDG 12 (30)
T ss_dssp --TTTS----S
T ss_pred cCCcCCCcCCC
Confidence 34444444433
No 102
>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=36.48 E-value=14 Score=19.00 Aligned_cols=10 Identities=40% Similarity=1.165 Sum_probs=5.9
Q ss_pred CCCCCCCccc
Q psy17880 64 KCAQCGEYVE 73 (120)
Q Consensus 64 ~C~~C~~~i~ 73 (120)
+|..|+...+
T Consensus 7 ~C~~Cg~~fe 16 (52)
T TIGR02605 7 RCTACGHRFE 16 (52)
T ss_pred EeCCCCCEeE
Confidence 5666765443
No 103
>PF04641 Rtf2: Rtf2 RING-finger
Probab=36.07 E-value=76 Score=22.46 Aligned_cols=55 Identities=15% Similarity=0.342 Sum_probs=41.0
Q ss_pred ccccccccccccccCCC-Cee--ecCCeeccHhHHHhHh-CCCCCCCCCcccC-cEEEEe
Q psy17880 26 HITCFQCSVCKNSLAQG-GYF--NKDGAYYCTSDYQKKF-GTKCAQCGEYVEG-EVVTAL 80 (120)
Q Consensus 26 H~~Cf~C~~C~~~l~~~-~~~--~~~~~~~C~~c~~~~~-~~~C~~C~~~i~~-~~~~~~ 80 (120)
...-|.|..-+..+.+. .|. ..-|.++.+....+.- ...|..|+++... ++|...
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k~~~~Cp~c~~~f~~~DiI~Ln 169 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELKKSKKCPVCGKPFTEEDIIPLN 169 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhcccccccccCCccccCCEEEec
Confidence 45678999999999665 333 4578999999888876 5689999999854 465544
No 104
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=36.04 E-value=29 Score=18.38 Aligned_cols=13 Identities=23% Similarity=0.590 Sum_probs=9.3
Q ss_pred ccccccccccccc
Q psy17880 4 AYCTSCKKKCSGE 16 (120)
Q Consensus 4 ~~C~~C~~~i~~~ 16 (120)
.+|..|++||.+.
T Consensus 2 ~iCvvCK~Pi~~a 14 (53)
T PHA02610 2 KICVVCKQPIEKA 14 (53)
T ss_pred ceeeeeCCchhhc
Confidence 4678888888544
No 105
>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=35.78 E-value=8.4 Score=18.44 Aligned_cols=16 Identities=13% Similarity=0.412 Sum_probs=10.5
Q ss_pred cccccCCCcCCCCcee
Q psy17880 89 FTCARCRFSKKREIYN 104 (120)
Q Consensus 89 f~C~~C~~~l~~~~~~ 104 (120)
|.|..|++++....|.
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 5678888887766554
No 106
>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=35.28 E-value=59 Score=23.93 Aligned_cols=26 Identities=23% Similarity=0.430 Sum_probs=18.7
Q ss_pred CCeeccHhHHHhHhC---CCCCCCCCccc
Q psy17880 48 DGAYYCTSDYQKKFG---TKCAQCGEYVE 73 (120)
Q Consensus 48 ~~~~~C~~c~~~~~~---~~C~~C~~~i~ 73 (120)
=|..+|..|....+. ..|..|++++.
T Consensus 26 CGH~~C~sCv~~l~~~~~~~CP~C~~~lr 54 (309)
T TIGR00570 26 CGHTLCESCVDLLFVRGSGSCPECDTPLR 54 (309)
T ss_pred CCCcccHHHHHHHhcCCCCCCCCCCCccc
Confidence 466778888877653 46888888774
No 107
>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=35.04 E-value=17 Score=15.90 Aligned_cols=14 Identities=29% Similarity=0.456 Sum_probs=10.1
Q ss_pred cccccCCCcCCCCc
Q psy17880 89 FTCARCRFSKKREI 102 (120)
Q Consensus 89 f~C~~C~~~l~~~~ 102 (120)
|.|..|++.+.+..
T Consensus 2 ~~C~~C~k~f~~~~ 15 (27)
T PF12171_consen 2 FYCDACDKYFSSEN 15 (27)
T ss_dssp CBBTTTTBBBSSHH
T ss_pred CCcccCCCCcCCHH
Confidence 56888888876653
No 108
>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=34.97 E-value=38 Score=17.25 Aligned_cols=8 Identities=25% Similarity=0.708 Sum_probs=5.0
Q ss_pred ccHhHHHh
Q psy17880 52 YCTSDYQK 59 (120)
Q Consensus 52 ~C~~c~~~ 59 (120)
+|+.||.+
T Consensus 26 LC~~C~~~ 33 (43)
T cd02342 26 LCTICFSR 33 (43)
T ss_pred cHHHHhhh
Confidence 56666654
No 109
>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=34.96 E-value=47 Score=16.94 Aligned_cols=12 Identities=33% Similarity=0.672 Sum_probs=7.4
Q ss_pred Cccccccccccc
Q psy17880 3 KAYCTSCKKKCS 14 (120)
Q Consensus 3 ~~~C~~C~~~i~ 14 (120)
...|..|++.|.
T Consensus 11 ~~~C~~C~~~i~ 22 (53)
T PF00130_consen 11 PTYCDVCGKFIW 22 (53)
T ss_dssp TEB-TTSSSBEC
T ss_pred CCCCcccCcccC
Confidence 456777877773
No 110
>KOG4739|consensus
Probab=34.33 E-value=24 Score=24.78 Aligned_cols=33 Identities=12% Similarity=0.328 Sum_probs=25.4
Q ss_pred CCee-ecCCeeccHhHHHhHhCCCCCCCCCcccC
Q psy17880 42 GGYF-NKDGAYYCTSDYQKKFGTKCAQCGEYVEG 74 (120)
Q Consensus 42 ~~~~-~~~~~~~C~~c~~~~~~~~C~~C~~~i~~ 74 (120)
..|+ .-=..++|..|.....++.|..|+++|..
T Consensus 16 ~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir~ 49 (233)
T KOG4739|consen 16 DPFFLTACRHVFCEPCLKASSPDVCPLCKKSIRI 49 (233)
T ss_pred CceeeeechhhhhhhhcccCCccccccccceeee
Confidence 3455 45578899999888777799999999743
No 111
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=33.98 E-value=61 Score=20.44 Aligned_cols=32 Identities=25% Similarity=0.672 Sum_probs=20.3
Q ss_pred HHhHhCCCCCCCCCcccCcEEEEeCcccccccccc
Q psy17880 57 YQKKFGTKCAQCGEYVEGEVVTALGKTYHQKCFTC 91 (120)
Q Consensus 57 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C 91 (120)
|.+.| ..|..|+.| +..+...++.|-..|-.|
T Consensus 89 fI~~y-VlC~~C~sp--dT~l~k~~r~~~l~C~aC 120 (125)
T PF01873_consen 89 FIKEY-VLCPECGSP--DTELIKEGRLIFLKCKAC 120 (125)
T ss_dssp HHCHH-SSCTSTSSS--SEEEEEETTCCEEEETTT
T ss_pred HHHHE-EEcCCCCCC--ccEEEEcCCEEEEEeccc
Confidence 44444 689999876 345555578777655444
No 112
>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=33.92 E-value=47 Score=14.64 Aligned_cols=9 Identities=33% Similarity=1.139 Sum_probs=4.2
Q ss_pred CCCCCCccc
Q psy17880 65 CAQCGEYVE 73 (120)
Q Consensus 65 C~~C~~~i~ 73 (120)
|.+|+.+|.
T Consensus 1 C~sC~~~i~ 9 (24)
T PF07754_consen 1 CTSCGRPIA 9 (24)
T ss_pred CccCCCccc
Confidence 344555553
No 113
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=33.45 E-value=15 Score=15.60 Aligned_cols=13 Identities=38% Similarity=0.636 Sum_probs=9.3
Q ss_pred cccccCCCcCCCC
Q psy17880 89 FTCARCRFSKKRE 101 (120)
Q Consensus 89 f~C~~C~~~l~~~ 101 (120)
|.|..|++.+.+.
T Consensus 1 ~~C~~C~~~f~s~ 13 (25)
T PF12874_consen 1 FYCDICNKSFSSE 13 (25)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCCCCCCcCCH
Confidence 5688888877654
No 114
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=33.38 E-value=15 Score=22.29 Aligned_cols=30 Identities=27% Similarity=0.329 Sum_probs=18.0
Q ss_pred cccccccccccccCCC-CeeecCCeeccHhH
Q psy17880 27 ITCFQCSVCKNSLAQG-GYFNKDGAYYCTSD 56 (120)
Q Consensus 27 ~~Cf~C~~C~~~l~~~-~~~~~~~~~~C~~c 56 (120)
.+=|+|+.|-..--.+ .-...+|+++|.+|
T Consensus 68 ~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 68 ADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CCceeeeeeeeEechhhhccccCCCEecccc
Confidence 4568888884433222 22356788888776
No 115
>KOG2462|consensus
Probab=33.21 E-value=17 Score=26.18 Aligned_cols=16 Identities=19% Similarity=0.567 Sum_probs=11.7
Q ss_pred cccccccccccccCCC
Q psy17880 27 ITCFQCSVCKNSLAQG 42 (120)
Q Consensus 27 ~~Cf~C~~C~~~l~~~ 42 (120)
...++|..|++.....
T Consensus 128 ~~r~~c~eCgk~ysT~ 143 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTS 143 (279)
T ss_pred CCceeccccccccccc
Confidence 3467888898888654
No 116
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=32.90 E-value=26 Score=24.21 Aligned_cols=28 Identities=21% Similarity=0.285 Sum_probs=17.8
Q ss_pred cccccCCCcCCCCceeeeCCeeeeccCC
Q psy17880 89 FTCARCRFSKKREIYNWLGGRAYENRLG 116 (120)
Q Consensus 89 f~C~~C~~~l~~~~~~~~~g~~yC~~~~ 116 (120)
..|..|++++....|...+|...|..+.
T Consensus 150 ~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 150 DHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred hhHhcCCCCCCceEEecccCCccccccc
Confidence 3567777776644555667777776653
No 117
>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=32.82 E-value=42 Score=16.91 Aligned_cols=27 Identities=22% Similarity=0.894 Sum_probs=14.8
Q ss_pred cccccccccc-cceEEEC--Cccccccccc
Q psy17880 5 YCTSCKKKCS-GEVLRVQ--DKYFHITCFQ 31 (120)
Q Consensus 5 ~C~~C~~~i~-~~~~~~~--~~~~H~~Cf~ 31 (120)
+|..|++.-. +..|.-. +..||..|..
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~ 30 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVG 30 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTST
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCC
Confidence 3666777333 3344433 5667877743
No 118
>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=32.34 E-value=21 Score=18.88 Aligned_cols=9 Identities=22% Similarity=0.608 Sum_probs=4.0
Q ss_pred CCCCCCccc
Q psy17880 65 CAQCGEYVE 73 (120)
Q Consensus 65 C~~C~~~i~ 73 (120)
|.+|.+++.
T Consensus 2 CfgC~~~~~ 10 (51)
T PF07975_consen 2 CFGCQKPFP 10 (51)
T ss_dssp ETTTTEE-T
T ss_pred CccCCCCCC
Confidence 445555553
No 119
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=32.03 E-value=24 Score=25.17 Aligned_cols=12 Identities=42% Similarity=1.107 Sum_probs=8.6
Q ss_pred CCCCCCCCCccc
Q psy17880 62 GTKCAQCGEYVE 73 (120)
Q Consensus 62 ~~~C~~C~~~i~ 73 (120)
+..|..|+.+|.
T Consensus 245 g~pC~~Cg~~I~ 256 (274)
T PRK01103 245 GEPCRRCGTPIE 256 (274)
T ss_pred CCCCCCCCCeeE
Confidence 456888887774
No 120
>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=31.91 E-value=16 Score=15.81 Aligned_cols=13 Identities=23% Similarity=0.539 Sum_probs=9.4
Q ss_pred cccccCCCcCCCC
Q psy17880 89 FTCARCRFSKKRE 101 (120)
Q Consensus 89 f~C~~C~~~l~~~ 101 (120)
|.|..|++.+...
T Consensus 2 ~~C~~C~~~F~~~ 14 (27)
T PF13912_consen 2 FECDECGKTFSSL 14 (27)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCccCCccCCh
Confidence 5688888877654
No 121
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=31.86 E-value=24 Score=25.18 Aligned_cols=13 Identities=23% Similarity=0.682 Sum_probs=9.8
Q ss_pred CCCCCCCCCcccC
Q psy17880 62 GTKCAQCGEYVEG 74 (120)
Q Consensus 62 ~~~C~~C~~~i~~ 74 (120)
+..|..|+.+|..
T Consensus 244 g~pCprCG~~I~~ 256 (272)
T PRK14810 244 GEPCLNCKTPIRR 256 (272)
T ss_pred CCcCCCCCCeeEE
Confidence 4678889888853
No 122
>PRK14873 primosome assembly protein PriA; Provisional
Probab=31.05 E-value=24 Score=28.64 Aligned_cols=37 Identities=22% Similarity=0.461 Sum_probs=23.3
Q ss_pred ccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCc
Q psy17880 32 CSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEY 71 (120)
Q Consensus 32 C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~ 71 (120)
|..|+.+|. +...++.+.|..|-.......|..|+..
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 334444442 3334567788888665556789999875
No 123
>PRK10445 endonuclease VIII; Provisional
Probab=30.79 E-value=27 Score=24.84 Aligned_cols=12 Identities=42% Similarity=1.176 Sum_probs=8.7
Q ss_pred CCCCCCCCCccc
Q psy17880 62 GTKCAQCGEYVE 73 (120)
Q Consensus 62 ~~~C~~C~~~i~ 73 (120)
+..|..|+.+|.
T Consensus 235 g~~Cp~Cg~~I~ 246 (263)
T PRK10445 235 GEACERCGGIIE 246 (263)
T ss_pred CCCCCCCCCEeE
Confidence 467888887774
No 124
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=30.46 E-value=87 Score=22.25 Aligned_cols=48 Identities=25% Similarity=0.589 Sum_probs=26.4
Q ss_pred ceEEECCcccccccccccccccccCCCCee--ecCCeeccHhHHHhHhCCCCCCCCC-cccCcEE
Q psy17880 16 EVLRVQDKYFHITCFQCSVCKNSLAQGGYF--NKDGAYYCTSDYQKKFGTKCAQCGE-YVEGEVV 77 (120)
Q Consensus 16 ~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~--~~~~~~~C~~c~~~~~~~~C~~C~~-~i~~~~~ 77 (120)
.++.+-|..++.. |..|+......... ..++ ..|+|..|+. .|..++|
T Consensus 112 ~Vi~lHGsl~~~~---C~~C~~~~~~~~~~~~~~~~-----------~~p~C~~Cg~~~lrP~VV 162 (250)
T COG0846 112 NVIELHGSLKRVR---CSKCGNQYYDEDVIKFIEDG-----------LIPRCPKCGGPVLRPDVV 162 (250)
T ss_pred cEEEeccceeeeE---eCCCcCccchhhhhhhcccC-----------CCCcCccCCCccccCCEE
Confidence 4666667777754 45676655432211 1111 2378999988 4544443
No 125
>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=30.43 E-value=51 Score=16.90 Aligned_cols=8 Identities=13% Similarity=0.505 Sum_probs=4.9
Q ss_pred ccHhHHHh
Q psy17880 52 YCTSDYQK 59 (120)
Q Consensus 52 ~C~~c~~~ 59 (120)
+|.+||..
T Consensus 26 LC~~Cf~~ 33 (49)
T cd02335 26 LCLECFSA 33 (49)
T ss_pred hhHHhhhC
Confidence 56666654
No 126
>KOG2932|consensus
Probab=30.37 E-value=27 Score=25.81 Aligned_cols=42 Identities=19% Similarity=0.369 Sum_probs=21.2
Q ss_pred cccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcc
Q psy17880 31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYV 72 (120)
Q Consensus 31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i 72 (120)
-|..|+.+|..=.-.+--+.++|.+|-...-...|..|..+|
T Consensus 92 fCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 92 FCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRV 133 (389)
T ss_pred eecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHH
Confidence 355666665321111223455666665544345677776665
No 127
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.28 E-value=27 Score=24.90 Aligned_cols=26 Identities=27% Similarity=0.597 Sum_probs=14.1
Q ss_pred CCCCCCCCCcccCcEEEEeCcccccc
Q psy17880 62 GTKCAQCGEYVEGEVVTALGKTYHQK 87 (120)
Q Consensus 62 ~~~C~~C~~~i~~~~~~~~~~~~H~~ 87 (120)
+..|..|+.+|.-..+.-.+..|.+.
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~ 270 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQ 270 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCC
Confidence 45788888888543333233334433
No 128
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=29.84 E-value=21 Score=18.73 Aligned_cols=9 Identities=44% Similarity=0.907 Sum_probs=4.2
Q ss_pred ccccCCCcC
Q psy17880 90 TCARCRFSK 98 (120)
Q Consensus 90 ~C~~C~~~l 98 (120)
+|+.|++.+
T Consensus 8 ~C~~Cg~~~ 16 (49)
T COG1996 8 KCARCGREV 16 (49)
T ss_pred EhhhcCCee
Confidence 344444444
No 129
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=29.79 E-value=27 Score=24.90 Aligned_cols=13 Identities=38% Similarity=1.020 Sum_probs=10.2
Q ss_pred CCCCCCCCCcccC
Q psy17880 62 GTKCAQCGEYVEG 74 (120)
Q Consensus 62 ~~~C~~C~~~i~~ 74 (120)
+..|..|+.+|.-
T Consensus 235 g~pC~~Cg~~I~~ 247 (269)
T PRK14811 235 GQPCPRCGTPIEK 247 (269)
T ss_pred cCCCCcCCCeeEE
Confidence 4679999998853
No 130
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=29.42 E-value=14 Score=17.77 Aligned_cols=10 Identities=20% Similarity=0.810 Sum_probs=3.2
Q ss_pred cccccccccc
Q psy17880 5 YCTSCKKKCS 14 (120)
Q Consensus 5 ~C~~C~~~i~ 14 (120)
.|..|+.++.
T Consensus 2 fC~~CG~~l~ 11 (34)
T PF14803_consen 2 FCPQCGGPLE 11 (34)
T ss_dssp B-TTT--B-E
T ss_pred ccccccChhh
Confidence 4556666543
No 131
>PHA00080 DksA-like zinc finger domain containing protein
Probab=29.29 E-value=21 Score=20.22 Aligned_cols=28 Identities=18% Similarity=0.403 Sum_probs=17.8
Q ss_pred cccccccccCCCCeeecCCeeccHhHHH
Q psy17880 31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQ 58 (120)
Q Consensus 31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~ 58 (120)
.|..|+.+|+........+-.+|..|..
T Consensus 33 ~C~~Cg~~Ip~~Rl~a~P~~~~Cv~Cq~ 60 (72)
T PHA00080 33 HCEECGDPIPEARREAVPGCRTCVSCQE 60 (72)
T ss_pred EecCCCCcCcHHHHHhCCCccCcHHHHH
Confidence 5777788776654444555666766654
No 132
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=29.25 E-value=38 Score=17.48 Aligned_cols=6 Identities=50% Similarity=1.514 Sum_probs=2.5
Q ss_pred CCCCCC
Q psy17880 65 CAQCGE 70 (120)
Q Consensus 65 C~~C~~ 70 (120)
|..|++
T Consensus 34 CGaCs~ 39 (46)
T PF11331_consen 34 CGACSE 39 (46)
T ss_pred CCCCce
Confidence 444443
No 133
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=29.05 E-value=32 Score=24.20 Aligned_cols=26 Identities=19% Similarity=0.332 Sum_probs=16.4
Q ss_pred ccccCCCcCCCCceeeeCCeeeeccC
Q psy17880 90 TCARCRFSKKREIYNWLGGRAYENRL 115 (120)
Q Consensus 90 ~C~~C~~~l~~~~~~~~~g~~yC~~~ 115 (120)
.|+.|+++.+...++...|...|.++
T Consensus 156 ~Ca~cg~~~~~~~~s~~~~~~~C~~~ 181 (251)
T COG1381 156 SCARCGTPVDPVYFSPKSGGFLCSKC 181 (251)
T ss_pred HHhCcCCcCCCcceeeccCcccchhc
Confidence 46666666666666666666666554
No 134
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=28.80 E-value=18 Score=19.17 Aligned_cols=10 Identities=20% Similarity=1.006 Sum_probs=7.5
Q ss_pred CCCCCCCCcc
Q psy17880 63 TKCAQCGEYV 72 (120)
Q Consensus 63 ~~C~~C~~~i 72 (120)
.+|..|++.+
T Consensus 5 iRC~~CnklL 14 (51)
T PF10122_consen 5 IRCGHCNKLL 14 (51)
T ss_pred eeccchhHHH
Confidence 4688888777
No 135
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=28.63 E-value=36 Score=21.68 Aligned_cols=23 Identities=30% Similarity=0.511 Sum_probs=16.7
Q ss_pred CCCCCCCCcc-cC---cEEEEeCcccc
Q psy17880 63 TKCAQCGEYV-EG---EVVTALGKTYH 85 (120)
Q Consensus 63 ~~C~~C~~~i-~~---~~~~~~~~~~H 85 (120)
..|..|+.+| +| .+|...|+.|+
T Consensus 5 e~CsFcG~kIyPG~G~~fVR~DGkvf~ 31 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMFVRKDGTVLH 31 (131)
T ss_pred eeecCcCCcccCCCCcEEEecCCCEEE
Confidence 4688999999 44 36667777776
No 136
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=28.56 E-value=30 Score=24.86 Aligned_cols=13 Identities=38% Similarity=1.002 Sum_probs=9.2
Q ss_pred CCCCCCCCCcccC
Q psy17880 62 GTKCAQCGEYVEG 74 (120)
Q Consensus 62 ~~~C~~C~~~i~~ 74 (120)
+..|..|+.+|.-
T Consensus 254 g~pC~~Cg~~I~~ 266 (282)
T PRK13945 254 GKPCRKCGTPIER 266 (282)
T ss_pred cCCCCcCCCeeEE
Confidence 4678888888753
No 137
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.31 E-value=24 Score=26.83 Aligned_cols=44 Identities=16% Similarity=0.476 Sum_probs=29.1
Q ss_pred cccccccccccCCCCeeecCCeeccHhHHHhHhC--CCCCCCCCccc
Q psy17880 29 CFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFG--TKCAQCGEYVE 73 (120)
Q Consensus 29 Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~--~~C~~C~~~i~ 73 (120)
-+.|..|...+.. .....=+..||..|....+. ..|..|..++.
T Consensus 26 ~l~C~IC~d~~~~-PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~ 71 (397)
T TIGR00599 26 SLRCHICKDFFDV-PVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQ 71 (397)
T ss_pred ccCCCcCchhhhC-ccCCCCCCchhHHHHHHHHhCCCCCCCCCCccc
Confidence 4678888777754 33455577888888775443 35777777663
No 138
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=28.24 E-value=71 Score=15.20 Aligned_cols=28 Identities=18% Similarity=0.242 Sum_probs=12.6
Q ss_pred ccccccccCCCCeeecCCee-ccHhHHHh
Q psy17880 32 CSVCKNSLAQGGYFNKDGAY-YCTSDYQK 59 (120)
Q Consensus 32 C~~C~~~l~~~~~~~~~~~~-~C~~c~~~ 59 (120)
|+.|+..-...-....++.. +|..|...
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~ 29 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLY 29 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHH
Confidence 44555544332222335555 89888753
No 139
>smart00746 TRASH metallochaperone-like domain.
Probab=27.96 E-value=57 Score=14.08 Aligned_cols=9 Identities=33% Similarity=0.995 Sum_probs=5.1
Q ss_pred CCCCCCccc
Q psy17880 65 CAQCGEYVE 73 (120)
Q Consensus 65 C~~C~~~i~ 73 (120)
|..|+..|.
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 455666663
No 140
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=27.52 E-value=22 Score=20.22 Aligned_cols=29 Identities=17% Similarity=0.388 Sum_probs=18.7
Q ss_pred ccccccccccCCCCeeecCCeeccHhHHH
Q psy17880 30 FQCSVCKNSLAQGGYFNKDGAYYCTSDYQ 58 (120)
Q Consensus 30 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~ 58 (120)
+-|..|+.+|+........+-.+|..|..
T Consensus 35 ~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~ 63 (73)
T PRK13715 35 YLCEACGNPIPEARRKIFPGVTLCVECQA 63 (73)
T ss_pred ccHhhcCCcCCHHHHhcCCCcCCCHHHHH
Confidence 35777888887655555556666766654
No 141
>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=27.15 E-value=54 Score=16.76 Aligned_cols=8 Identities=13% Similarity=0.870 Sum_probs=5.1
Q ss_pred ccHhHHHh
Q psy17880 52 YCTSDYQK 59 (120)
Q Consensus 52 ~C~~c~~~ 59 (120)
+|+.||..
T Consensus 26 LC~~Cf~~ 33 (45)
T cd02344 26 FCENCFKT 33 (45)
T ss_pred chHHhhCC
Confidence 57777654
No 142
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=26.57 E-value=74 Score=18.87 Aligned_cols=37 Identities=24% Similarity=0.584 Sum_probs=23.7
Q ss_pred CCccccccccccccceEEECCcccccccccccccccccCCCCeee
Q psy17880 2 IKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGYFN 46 (120)
Q Consensus 2 ~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~ 46 (120)
++..|..|+.+.- -.+....| .|..|+..+.+..|..
T Consensus 34 ~~~~Cp~C~~~~V---kR~a~GIW-----~C~kCg~~fAGgay~P 70 (89)
T COG1997 34 AKHVCPFCGRTTV---KRIATGIW-----KCRKCGAKFAGGAYTP 70 (89)
T ss_pred cCCcCCCCCCcce---eeeccCeE-----EcCCCCCeeccccccc
Confidence 3567888888742 22334455 6888888887765543
No 143
>KOG2186|consensus
Probab=26.26 E-value=15 Score=26.21 Aligned_cols=44 Identities=16% Similarity=0.371 Sum_probs=28.0
Q ss_pred CCCccccccccccccceEEECCcccccccccccccccccCCCCe
Q psy17880 1 MIKAYCTSCKKKCSGEVLRVQDKYFHITCFQCSVCKNSLAQGGY 44 (120)
Q Consensus 1 ~~~~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~ 44 (120)
|+.-.|..|++.|...-+.---..-|...|.|-+|++.+.+..|
T Consensus 1 MV~FtCnvCgEsvKKp~vekH~srCrn~~fSCIDC~k~F~~~sY 44 (276)
T KOG2186|consen 1 MVFFTCNVCGESVKKPQVEKHMSRCRNAYFSCIDCGKTFERVSY 44 (276)
T ss_pred CeEEehhhhhhhccccchHHHHHhccCCeeEEeecccccccchh
Confidence 55668999999885432211111235578999999998866443
No 144
>KOG3816|consensus
Probab=26.00 E-value=25 Score=26.78 Aligned_cols=49 Identities=16% Similarity=0.295 Sum_probs=31.8
Q ss_pred ccHhHHHhHhCCCCCCCCCcccCcEEEEe---------CccccccccccccCCCcCCC
Q psy17880 52 YCTSDYQKKFGTKCAQCGEYVEGEVVTAL---------GKTYHQKCFTCARCRFSKKR 100 (120)
Q Consensus 52 ~C~~c~~~~~~~~C~~C~~~i~~~~~~~~---------~~~~H~~Cf~C~~C~~~l~~ 100 (120)
.|.+|-.......|..|+++..|...+.. ...-.+.=|+|..|.++|..
T Consensus 429 vC~~CL~g~~sI~C~~Ck~~wDGss~vLGTmY~YDI~aa~pCC~~R~~C~~C~k~l~~ 486 (526)
T KOG3816|consen 429 VCARCLWGDWSIICKNCKKDWDGSSFVLGTMYYYDIVAAGPCCPVRLVCQSCRKSLGV 486 (526)
T ss_pred HHHHHhcccchHHHhhcCCCCCCcceeechhhhhhhhhcCCcchhhhhhhhhcccccc
Confidence 46677776666789999999876422211 11224455789999998864
No 145
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=25.92 E-value=48 Score=23.06 Aligned_cols=24 Identities=25% Similarity=0.564 Sum_probs=15.0
Q ss_pred ccccccccCCCCeeecCCeeccHhHHHhHh
Q psy17880 32 CSVCKNSLAQGGYFNKDGAYYCTSDYQKKF 61 (120)
Q Consensus 32 C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~ 61 (120)
|..||.+.... . .-+|.+||.+.+
T Consensus 1 C~~CG~~~~~~----~--~~lC~~C~~~~~ 24 (236)
T PF04981_consen 1 CPRCGREIEPL----I--DGLCPDCYLKRF 24 (236)
T ss_pred CCCCCCCCCCc----c--cccChHHhcccC
Confidence 56677755431 1 137999998765
No 146
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=25.71 E-value=20 Score=19.40 Aligned_cols=37 Identities=22% Similarity=0.383 Sum_probs=22.3
Q ss_pred cccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcc
Q psy17880 31 QCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYV 72 (120)
Q Consensus 31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i 72 (120)
.|..|+++|...+.. ++=.+.-...++.+|..|-.|-
T Consensus 12 ~CrRCGk~i~tl~~S-----L~Gad~lr~klG~IC~~CitpE 48 (60)
T PF10892_consen 12 PCRRCGKSIRTLSRS-----LIGADDLRVKLGGICGDCITPE 48 (60)
T ss_pred hhhhhCccHHHHHHH-----hhChHHHHHHHcchhhccCCHH
Confidence 467788877543221 2223455667788888886553
No 147
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=25.70 E-value=53 Score=16.08 Aligned_cols=29 Identities=17% Similarity=0.435 Sum_probs=10.7
Q ss_pred ccccccccccccc-eEEECCccccccccccccccc
Q psy17880 4 AYCTSCKKKCSGE-VLRVQDKYFHITCFQCSVCKN 37 (120)
Q Consensus 4 ~~C~~C~~~i~~~-~~~~~~~~~H~~Cf~C~~C~~ 37 (120)
.+|..|+--|..- .+...++.| +|..|+.
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w-----~C~~C~~ 32 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTW-----ICNFCGT 32 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEE-----EETTT--
T ss_pred cccCCCCCEECCcceEcCCCCEE-----ECcCCCC
Confidence 4566676666543 222233443 5555544
No 148
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=25.31 E-value=46 Score=23.56 Aligned_cols=9 Identities=33% Similarity=0.888 Sum_probs=4.6
Q ss_pred CCCCCCCcc
Q psy17880 64 KCAQCGEYV 72 (120)
Q Consensus 64 ~C~~C~~~i 72 (120)
.|..|+.++
T Consensus 101 fC~~CG~~~ 109 (256)
T PRK00241 101 FCGYCGHPM 109 (256)
T ss_pred cccccCCCC
Confidence 455555544
No 149
>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=25.31 E-value=44 Score=26.10 Aligned_cols=13 Identities=31% Similarity=0.835 Sum_probs=7.3
Q ss_pred cccccccCCCcCC
Q psy17880 87 KCFTCARCRFSKK 99 (120)
Q Consensus 87 ~Cf~C~~C~~~l~ 99 (120)
+||.|-.|..+|.
T Consensus 51 ~Cf~CP~C~~~L~ 63 (483)
T PF05502_consen 51 NCFDCPICFSPLS 63 (483)
T ss_pred ccccCCCCCCcce
Confidence 5555555555553
No 150
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=25.09 E-value=39 Score=15.93 Aligned_cols=8 Identities=25% Similarity=0.796 Sum_probs=3.8
Q ss_pred cccCCCcC
Q psy17880 91 CARCRFSK 98 (120)
Q Consensus 91 C~~C~~~l 98 (120)
|..|+...
T Consensus 3 C~~Cg~~~ 10 (32)
T PF03604_consen 3 CGECGAEV 10 (32)
T ss_dssp ESSSSSSE
T ss_pred CCcCCCee
Confidence 44554443
No 151
>TIGR02419 C4_traR_proteo phage/conjugal plasmid C-4 type zinc finger protein, TraR family. Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA.
Probab=25.08 E-value=19 Score=19.78 Aligned_cols=27 Identities=19% Similarity=0.365 Sum_probs=14.5
Q ss_pred cccccccccCCCCeeecCCeeccHhHH
Q psy17880 31 QCSVCKNSLAQGGYFNKDGAYYCTSDY 57 (120)
Q Consensus 31 ~C~~C~~~l~~~~~~~~~~~~~C~~c~ 57 (120)
.|..|+.+|+........+-.+|..|.
T Consensus 33 ~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq 59 (63)
T TIGR02419 33 ECEDCGEPIPEARREALPGVTRCVSCQ 59 (63)
T ss_pred eeccCCCcChHHHHhhcCCcCCcHHHH
Confidence 466677776654433444445555553
No 152
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 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 RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=24.78 E-value=43 Score=17.50 Aligned_cols=26 Identities=19% Similarity=0.551 Sum_probs=13.9
Q ss_pred CeeccHhHHHhHhC--CCCCCCCCcccC
Q psy17880 49 GAYYCTSDYQKKFG--TKCAQCGEYVEG 74 (120)
Q Consensus 49 ~~~~C~~c~~~~~~--~~C~~C~~~i~~ 74 (120)
+..+|..|-..+.+ ..|..|+++++.
T Consensus 20 dHYLCl~CLt~ml~~s~~C~iC~~~LPt 47 (50)
T PF03854_consen 20 DHYLCLNCLTLMLSRSDRCPICGKPLPT 47 (50)
T ss_dssp S-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred chhHHHHHHHHHhccccCCCcccCcCcc
Confidence 34456666555443 678888888753
No 153
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=24.68 E-value=66 Score=16.34 Aligned_cols=13 Identities=23% Similarity=0.503 Sum_probs=8.3
Q ss_pred CCCCCC-CcccCcE
Q psy17880 64 KCAQCG-EYVEGEV 76 (120)
Q Consensus 64 ~C~~C~-~~i~~~~ 76 (120)
.|..|+ .+|.|..
T Consensus 2 ~Cd~C~~~~i~G~R 15 (45)
T cd02339 2 ICDTCRKQGIIGIR 15 (45)
T ss_pred CCCCCCCCCcccCe
Confidence 477787 4666644
No 154
>KOG2114|consensus
Probab=24.51 E-value=31 Score=28.88 Aligned_cols=46 Identities=24% Similarity=0.431 Sum_probs=26.6
Q ss_pred CcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCC
Q psy17880 22 DKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGE 70 (120)
Q Consensus 22 ~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~ 70 (120)
.+.+|. .+|+.|+..|+-......=+..|...|..+. ...|..|.-
T Consensus 835 a~i~q~--skCs~C~~~LdlP~VhF~CgHsyHqhC~e~~-~~~CP~C~~ 880 (933)
T KOG2114|consen 835 AQIFQV--SKCSACEGTLDLPFVHFLCGHSYHQHCLEDK-EDKCPKCLP 880 (933)
T ss_pred cceeee--eeecccCCccccceeeeecccHHHHHhhccC-cccCCccch
Confidence 344444 5677777777654444555666666666632 256666654
No 155
>PRK12495 hypothetical protein; Provisional
Probab=24.36 E-value=53 Score=22.95 Aligned_cols=28 Identities=21% Similarity=0.587 Sum_probs=19.0
Q ss_pred CCCCCCCCcccCcEEEEeCccccccccccccCCCcCCC
Q psy17880 63 TKCAQCGEYVEGEVVTALGKTYHQKCFTCARCRFSKKR 100 (120)
Q Consensus 63 ~~C~~C~~~i~~~~~~~~~~~~H~~Cf~C~~C~~~l~~ 100 (120)
..|..|+.||. . ++.+-.|..|+.....
T Consensus 43 ~hC~~CG~PIp---------a-~pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 43 AHCDECGDPIF---------R-HDGQEFCPTCQQPVTE 70 (226)
T ss_pred hhcccccCccc---------C-CCCeeECCCCCCcccc
Confidence 47889999996 1 1445567888776543
No 156
>PHA02768 hypothetical protein; Provisional
Probab=24.35 E-value=12 Score=20.17 Aligned_cols=12 Identities=8% Similarity=0.207 Sum_probs=6.2
Q ss_pred ccccccCCCcCC
Q psy17880 88 CFTCARCRFSKK 99 (120)
Q Consensus 88 Cf~C~~C~~~l~ 99 (120)
=++|..|++.+.
T Consensus 31 ~~kc~~C~k~f~ 42 (55)
T PHA02768 31 NLKLSNCKRISL 42 (55)
T ss_pred cccCCcccceec
Confidence 345555555543
No 157
>PF15121 TMEM71: TMEM71 protein family
Probab=24.26 E-value=85 Score=20.21 Aligned_cols=30 Identities=20% Similarity=0.268 Sum_probs=24.8
Q ss_pred ccccccCCCcCCCCceeeeCCeeeeccCCC
Q psy17880 88 CFTCARCRFSKKREIYNWLGGRAYENRLGG 117 (120)
Q Consensus 88 Cf~C~~C~~~l~~~~~~~~~g~~yC~~~~~ 117 (120)
.+.|-+=.+.|.++.|.+.++...|.++|.
T Consensus 55 ~~~CRRSPRLLtNGYYi~TEDSFl~D~dGN 84 (149)
T PF15121_consen 55 HCTCRRSPRLLTNGYYIWTEDSFLCDEDGN 84 (149)
T ss_pred ccccccCchhhcCccEEEeccceeecCCCC
Confidence 466777778889999999999999988874
No 158
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=24.07 E-value=44 Score=15.81 Aligned_cols=10 Identities=20% Similarity=0.298 Sum_probs=4.2
Q ss_pred ecCCeeccHh
Q psy17880 46 NKDGAYYCTS 55 (120)
Q Consensus 46 ~~~~~~~C~~ 55 (120)
..++..+|..
T Consensus 17 ~~~~~~~C~~ 26 (33)
T PF08792_consen 17 KEDDYEVCIF 26 (33)
T ss_pred ecCCeEEccc
Confidence 3444444443
No 159
>PRK04023 DNA polymerase II large subunit; Validated
Probab=23.57 E-value=61 Score=27.91 Aligned_cols=36 Identities=19% Similarity=0.483 Sum_probs=19.9
Q ss_pred ccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCccc
Q psy17880 30 FQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVE 73 (120)
Q Consensus 30 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~ 73 (120)
|.|..|+..- .....|..|-.......|..|+..+.
T Consensus 639 frCP~CG~~T--------e~i~fCP~CG~~~~~y~CPKCG~El~ 674 (1121)
T PRK04023 639 RRCPFCGTHT--------EPVYRCPRCGIEVEEDECEKCGREPT 674 (1121)
T ss_pred ccCCCCCCCC--------CcceeCccccCcCCCCcCCCCCCCCC
Confidence 5566665541 11235666655544456777777664
No 160
>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=23.54 E-value=1.5e+02 Score=20.19 Aligned_cols=47 Identities=21% Similarity=0.523 Sum_probs=25.9
Q ss_pred ceEEECCcccccccccccccccccCCCCeeecCCeeccHhHHHhHhCCCCCCCCCcccCcEE
Q psy17880 16 EVLRVQDKYFHITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKFGTKCAQCGEYVEGEVV 77 (120)
Q Consensus 16 ~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~~~~C~~C~~~i~~~~~ 77 (120)
+++.+-|...+..| ..|+....... -......|.|..|+..+...++
T Consensus 99 ~v~e~HG~~~~~~C---~~C~~~~~~~~------------~~~~~~~p~C~~Cgg~lrp~Vv 145 (224)
T cd01412 99 NVIELHGSLFRVRC---SSCGYVGENNE------------EIPEEELPRCPKCGGLLRPGVV 145 (224)
T ss_pred ceEeeCCCcCcccc---CCCCCCCCcch------------hhhccCCCCCCCCCCccCCceE
Confidence 45666677666555 45655443220 0111124788888887766554
No 161
>smart00355 ZnF_C2H2 zinc finger.
Probab=23.45 E-value=44 Score=13.43 Aligned_cols=13 Identities=23% Similarity=0.621 Sum_probs=8.2
Q ss_pred cccccCCCcCCCC
Q psy17880 89 FTCARCRFSKKRE 101 (120)
Q Consensus 89 f~C~~C~~~l~~~ 101 (120)
+.|..|++.+...
T Consensus 1 ~~C~~C~~~f~~~ 13 (26)
T smart00355 1 YRCPECGKVFKSK 13 (26)
T ss_pred CCCCCCcchhCCH
Confidence 4577777776543
No 162
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=23.43 E-value=1.1e+02 Score=17.31 Aligned_cols=54 Identities=17% Similarity=0.332 Sum_probs=29.2
Q ss_pred HhHhCCCCCCCCCcccCcEEE----EeCccccccccccccCCCcCCCCceeeeCCeeeeccC
Q psy17880 58 QKKFGTKCAQCGEYVEGEVVT----ALGKTYHQKCFTCARCRFSKKREIYNWLGGRAYENRL 115 (120)
Q Consensus 58 ~~~~~~~C~~C~~~i~~~~~~----~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~~ 115 (120)
.+.....|..|+++ .|-.|. --...||+.|-.=+.+...+.. ....-.+||++|
T Consensus 32 ~~~~~~~C~~C~~~-~Ga~i~C~~~~C~~~fH~~CA~~~~~~~~~~~---~~~~~~~~C~~H 89 (90)
T PF13771_consen 32 KRRRKLKCSICKKK-GGACIGCSHPGCSRSFHVPCARKAGCFIEFDE---DNGKFRIFCPKH 89 (90)
T ss_pred HHHhCCCCcCCCCC-CCeEEEEeCCCCCcEEChHHHccCCeEEEEcc---CCCceEEEChhc
Confidence 34455789999877 343332 2256788877543333222221 111346788776
No 163
>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=22.69 E-value=76 Score=14.36 Aligned_cols=12 Identities=25% Similarity=0.343 Sum_probs=6.1
Q ss_pred ccccCCCcCCCC
Q psy17880 90 TCARCRFSKKRE 101 (120)
Q Consensus 90 ~C~~C~~~l~~~ 101 (120)
.|..|.+.+++.
T Consensus 2 ~C~~C~~~~~~~ 13 (30)
T PF03107_consen 2 WCDVCRRKIDGF 13 (30)
T ss_pred CCCCCCCCcCCC
Confidence 455555555443
No 164
>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=22.64 E-value=61 Score=16.74 Aligned_cols=13 Identities=38% Similarity=0.871 Sum_probs=7.6
Q ss_pred CCCCCCC-cccCcE
Q psy17880 64 KCAQCGE-YVEGEV 76 (120)
Q Consensus 64 ~C~~C~~-~i~~~~ 76 (120)
.|..|+. ||.|..
T Consensus 2 ~Cd~C~~~pI~G~R 15 (48)
T cd02341 2 KCDSCGIEPIPGTR 15 (48)
T ss_pred CCCCCCCCccccce
Confidence 4667766 665443
No 165
>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=22.52 E-value=20 Score=19.50 Aligned_cols=17 Identities=24% Similarity=0.573 Sum_probs=12.2
Q ss_pred cccccCCCcCCCCceee
Q psy17880 89 FTCARCRFSKKREIYNW 105 (120)
Q Consensus 89 f~C~~C~~~l~~~~~~~ 105 (120)
..|+.|++-|+.+.|..
T Consensus 5 lvCSTCGrDlSeeRy~L 21 (63)
T PF05864_consen 5 LVCSTCGRDLSEERYRL 21 (63)
T ss_pred eeecccCCcchHHHHHH
Confidence 35888888888776543
No 166
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=22.48 E-value=2.3e+02 Score=20.94 Aligned_cols=10 Identities=20% Similarity=0.909 Sum_probs=5.8
Q ss_pred Cccccccccc
Q psy17880 3 KAYCTSCKKK 12 (120)
Q Consensus 3 ~~~C~~C~~~ 12 (120)
++.|..|+..
T Consensus 187 ~~~CPvCGs~ 196 (309)
T PRK03564 187 RQFCPVCGSM 196 (309)
T ss_pred CCCCCCCCCc
Confidence 3566666653
No 167
>KOG3039|consensus
Probab=22.47 E-value=1.7e+02 Score=21.10 Aligned_cols=51 Identities=10% Similarity=0.116 Sum_probs=39.7
Q ss_pred cccccccccccccccCCC-C--eeecCCeeccHhHHHhHhC--CCCCCCCCcccCc
Q psy17880 25 FHITCFQCSVCKNSLAQG-G--YFNKDGAYYCTSDYQKKFG--TKCAQCGEYVEGE 75 (120)
Q Consensus 25 ~H~~Cf~C~~C~~~l~~~-~--~~~~~~~~~C~~c~~~~~~--~~C~~C~~~i~~~ 75 (120)
-|..-+.|..+...|... . +....|.+++.+|.+++.. ..+..+++++.++
T Consensus 217 a~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdr 272 (303)
T KOG3039|consen 217 AASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDR 272 (303)
T ss_pred hhccceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCccc
Confidence 455778999999999765 2 3356789999999998764 5799999999664
No 168
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=22.12 E-value=69 Score=19.14 Aligned_cols=29 Identities=28% Similarity=0.780 Sum_probs=18.3
Q ss_pred HhCCCCCCCCCcccCcEEEE----eCcccccccc
Q psy17880 60 KFGTKCAQCGEYVEGEVVTA----LGKTYHQKCF 89 (120)
Q Consensus 60 ~~~~~C~~C~~~i~~~~~~~----~~~~~H~~Cf 89 (120)
++..+|..|++. .|-.|.= -...||+.|-
T Consensus 53 ~~~~~C~iC~~~-~G~~i~C~~~~C~~~fH~~CA 85 (110)
T PF13832_consen 53 RFKLKCSICGKS-GGACIKCSHPGCSTAFHPTCA 85 (110)
T ss_pred hcCCcCcCCCCC-CceeEEcCCCCCCcCCCHHHH
Confidence 456789999887 3333321 2467888764
No 169
>PRK11019 hypothetical protein; Provisional
Probab=21.92 E-value=34 Score=20.26 Aligned_cols=29 Identities=17% Similarity=0.374 Sum_probs=19.0
Q ss_pred ccccccccccCCCCeeecCCeeccHhHHH
Q psy17880 30 FQCSVCKNSLAQGGYFNKDGAYYCTSDYQ 58 (120)
Q Consensus 30 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~ 58 (120)
..|..|+.+|+........+-.+|.+|-.
T Consensus 37 g~C~~CG~~Ip~~Rl~A~P~a~~Cv~Cq~ 65 (88)
T PRK11019 37 TECEECGEPIPEARRKAIPGVRLCVACQQ 65 (88)
T ss_pred CeeCcCCCcCcHHHHhhcCCccccHHHHH
Confidence 36788888887654445556667776654
No 170
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=21.88 E-value=49 Score=18.02 Aligned_cols=12 Identities=25% Similarity=0.783 Sum_probs=8.7
Q ss_pred CCCCCCCCcccC
Q psy17880 63 TKCAQCGEYVEG 74 (120)
Q Consensus 63 ~~C~~C~~~i~~ 74 (120)
..|..|++||+.
T Consensus 4 kHC~~CG~~Ip~ 15 (59)
T PF09889_consen 4 KHCPVCGKPIPP 15 (59)
T ss_pred CcCCcCCCcCCc
Confidence 468888888864
No 171
>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=21.86 E-value=89 Score=21.33 Aligned_cols=17 Identities=29% Similarity=0.745 Sum_probs=12.7
Q ss_pred CCCCCCCCCcccCcEEE
Q psy17880 62 GTKCAQCGEYVEGEVVT 78 (120)
Q Consensus 62 ~~~C~~C~~~i~~~~~~ 78 (120)
.|.|..|+.++...++-
T Consensus 133 ~p~C~~Cg~~lrP~Vv~ 149 (218)
T cd01407 133 VPRCPKCGGLLRPDVVF 149 (218)
T ss_pred CCcCCCCCCccCCCeEE
Confidence 47899998888766553
No 172
>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=21.79 E-value=31 Score=23.13 Aligned_cols=35 Identities=17% Similarity=0.254 Sum_probs=19.4
Q ss_pred cccccccccccccCCCCeeecCCeeccHhHHHhHh
Q psy17880 27 ITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF 61 (120)
Q Consensus 27 ~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~ 61 (120)
..|++|+.=....+...++..+.+++|..|...+|
T Consensus 137 ~kC~QC~~~~~~~~~~~~~~F~~~lFC~~ClFPLF 171 (173)
T PF11077_consen 137 DKCVQCSQKCENVGAKIFTYFNFNLFCKNCLFPLF 171 (173)
T ss_pred cccCcCCCCcccccceeEEecChhhcccccCcccc
Confidence 34555554322332223666777778877765544
No 173
>KOG2879|consensus
Probab=21.57 E-value=1.2e+02 Score=22.15 Aligned_cols=43 Identities=30% Similarity=0.498 Sum_probs=23.4
Q ss_pred ccccccccccCCCCee-ecCCeeccHhHHHhHhC----CCCCCCCCccc
Q psy17880 30 FQCSVCKNSLAQGGYF-NKDGAYYCTSDYQKKFG----TKCAQCGEYVE 73 (120)
Q Consensus 30 f~C~~C~~~l~~~~~~-~~~~~~~C~~c~~~~~~----~~C~~C~~~i~ 73 (120)
..|..|+.+-.. .+. ..=+.+||-.|-..... -.|..|+.+..
T Consensus 240 ~~C~~Cg~~Pti-P~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 240 TECPVCGEPPTI-PHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred ceeeccCCCCCC-CeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 345566654433 233 22456777777665543 36777766553
No 174
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=21.48 E-value=17 Score=24.03 Aligned_cols=28 Identities=21% Similarity=0.417 Sum_probs=18.3
Q ss_pred cCCCcCCC---Cceee-----eCCeeeeccCCCcCC
Q psy17880 93 RCRFSKKR---EIYNW-----LGGRAYENRLGGRAY 120 (120)
Q Consensus 93 ~C~~~l~~---~~~~~-----~~g~~yC~~~~~~~~ 120 (120)
.|.=+|++ .+|.+ .+|.+||..|.+.+|
T Consensus 117 ~CrwPiGdp~~~~f~FCG~~~~~g~~YC~~H~~~ay 152 (162)
T PF07750_consen 117 TCRWPIGDPGEPDFHFCGAPTQPGSPYCAAHARIAY 152 (162)
T ss_pred CccCcCCCCCCCCccccCCcCCCCCchhHHHHHHhc
Confidence 45556642 23443 458899999988776
No 175
>cd01411 SIR2H SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; 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.
Probab=21.33 E-value=1.9e+02 Score=19.95 Aligned_cols=17 Identities=24% Similarity=0.530 Sum_probs=12.5
Q ss_pred CCCCCCCCCcccCcEEE
Q psy17880 62 GTKCAQCGEYVEGEVVT 78 (120)
Q Consensus 62 ~~~C~~C~~~i~~~~~~ 78 (120)
.|.|..|+.++...++-
T Consensus 136 ~p~C~~Cgg~lrP~vv~ 152 (225)
T cd01411 136 SPYHAKCGGVIRPDIVL 152 (225)
T ss_pred CCCCCCCCCEeCCCEEE
Confidence 37888898888666553
No 176
>KOG3970|consensus
Probab=21.28 E-value=82 Score=22.26 Aligned_cols=49 Identities=16% Similarity=0.329 Sum_probs=30.3
Q ss_pred CcccccccccccccccccCCCCee-ecCCeeccHhHHHhHhC----------CCCCCCCCccc
Q psy17880 22 DKYFHITCFQCSVCKNSLAQGGYF-NKDGAYYCTSDYQKKFG----------TKCAQCGEYVE 73 (120)
Q Consensus 22 ~~~~H~~Cf~C~~C~~~l~~~~~~-~~~~~~~C~~c~~~~~~----------~~C~~C~~~i~ 73 (120)
+.-|.++ |..|+.+|.++... ..--.++.-.|..++-+ -.|..|+.+|.
T Consensus 46 DsDY~pN---C~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiF 105 (299)
T KOG3970|consen 46 DSDYNPN---CRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIF 105 (299)
T ss_pred hcCCCCC---CceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccC
Confidence 4456655 47788999876432 22223455566665532 37999999884
No 177
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=21.27 E-value=11 Score=19.11 Aligned_cols=30 Identities=30% Similarity=0.453 Sum_probs=15.3
Q ss_pred CCCCCccc---CcEEEEeCccccccccccccCCCcC
Q psy17880 66 AQCGEYVE---GEVVTALGKTYHQKCFTCARCRFSK 98 (120)
Q Consensus 66 ~~C~~~i~---~~~~~~~~~~~H~~Cf~C~~C~~~l 98 (120)
..|+..|. ...++..|+.|+ |.+..|...+
T Consensus 4 Pvcg~~v~~~~~~~~~y~G~~Y~---FCS~~C~~~F 36 (47)
T PF04945_consen 4 PVCGMKVPGNAAYSVEYNGRTYY---FCSEGCKEKF 36 (47)
T ss_dssp -GGG-BE-----EEEEETTEEEE---ESSHHHHHHH
T ss_pred CCCCCEEccCccEEEEECCEEEE---EcCHHHHHHH
Confidence 34566662 235567777776 5555555444
No 178
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=21.07 E-value=21 Score=19.37 Aligned_cols=16 Identities=25% Similarity=0.623 Sum_probs=11.7
Q ss_pred cccccCCCcCCCCcee
Q psy17880 89 FTCARCRFSKKREIYN 104 (120)
Q Consensus 89 f~C~~C~~~l~~~~~~ 104 (120)
..|+.|++-|+.+.|.
T Consensus 5 lVCsTCGrDlSeeRy~ 20 (63)
T PHA03082 5 LVCSTCGRDLSEERYR 20 (63)
T ss_pred eeecccCcchhHHHHH
Confidence 3588888888776654
No 179
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=20.79 E-value=69 Score=27.46 Aligned_cols=30 Identities=23% Similarity=0.603 Sum_probs=19.8
Q ss_pred CccccccccccccceEEE---------CC---cccccccccc
Q psy17880 3 KAYCTSCKKKCSGEVLRV---------QD---KYFHITCFQC 32 (120)
Q Consensus 3 ~~~C~~C~~~i~~~~~~~---------~~---~~~H~~Cf~C 32 (120)
...|..|+++|....+.+ .| ..||..||.=
T Consensus 17 Rs~Ck~C~~~I~K~~lRi~~~v~~~~~dg~~~~W~H~~Cf~~ 58 (981)
T PLN03123 17 RSSCKTCKSPIDKDELRLGKMVQSTQFDGFMPMWNHASCILK 58 (981)
T ss_pred CccccccCCcccCCCeEEEEeecccccCCCCCeeeccccccc
Confidence 467999999996433222 12 3579999863
No 180
>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=20.71 E-value=1.2e+02 Score=14.63 Aligned_cols=9 Identities=22% Similarity=0.246 Sum_probs=3.7
Q ss_pred CeeccHhHH
Q psy17880 49 GAYYCTSDY 57 (120)
Q Consensus 49 ~~~~C~~c~ 57 (120)
+..++..|.
T Consensus 22 ~H~fh~~Ci 30 (44)
T PF13639_consen 22 GHVFHRSCI 30 (44)
T ss_dssp SEEEEHHHH
T ss_pred CCeeCHHHH
Confidence 334444443
No 181
>KOG0823|consensus
Probab=20.64 E-value=1.6e+02 Score=20.72 Aligned_cols=55 Identities=20% Similarity=0.397 Sum_probs=38.3
Q ss_pred ccccccccccccccCCCCeeecCCeeccHhHHHhHh-----CCCCCCCCCcccC-cEEEEeC
Q psy17880 26 HITCFQCSVCKNSLAQGGYFNKDGAYYCTSDYQKKF-----GTKCAQCGEYVEG-EVVTALG 81 (120)
Q Consensus 26 H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~~-----~~~C~~C~~~i~~-~~~~~~~ 81 (120)
-...|.|..|-..- .+.....=|.+||..|..+-. ...|.+|+-.|.. ++|-.-|
T Consensus 44 ~~~~FdCNICLd~a-kdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlYG 104 (230)
T KOG0823|consen 44 DGGFFDCNICLDLA-KDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLYG 104 (230)
T ss_pred CCCceeeeeecccc-CCCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEeeec
Confidence 34568888885544 336888889999999987643 2468999998865 4554433
No 182
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=20.45 E-value=1.1e+02 Score=18.74 Aligned_cols=24 Identities=21% Similarity=0.551 Sum_probs=13.3
Q ss_pred CCCCCCCCcccCcEEEEeCccccccc
Q psy17880 63 TKCAQCGEYVEGEVVTALGKTYHQKC 88 (120)
Q Consensus 63 ~~C~~C~~~i~~~~~~~~~~~~H~~C 88 (120)
..|..|+.|= ..+...++.|=..|
T Consensus 81 VlC~~C~spd--T~l~k~~r~~~l~C 104 (110)
T smart00653 81 VLCPECGSPD--TELIKENRLFFLKC 104 (110)
T ss_pred EECCCCCCCC--cEEEEeCCeEEEEc
Confidence 5788888772 23333355554444
No 184
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=20.28 E-value=76 Score=20.42 Aligned_cols=43 Identities=21% Similarity=0.673 Sum_probs=27.2
Q ss_pred ccccccccccCCCCeeecC---CeeccHhHHHhHhC-----CCCCCCCCcc
Q psy17880 30 FQCSVCKNSLAQGGYFNKD---GAYYCTSDYQKKFG-----TKCAQCGEYV 72 (120)
Q Consensus 30 f~C~~C~~~l~~~~~~~~~---~~~~C~~c~~~~~~-----~~C~~C~~~i 72 (120)
..|..|.....++.|.-.+ |--.|..||..++. |.|..|+...
T Consensus 81 YeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSF 131 (140)
T PF05290_consen 81 YECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSF 131 (140)
T ss_pred eeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccc
Confidence 4778887766655444222 45579999988762 5666665443
No 185
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=20.06 E-value=40 Score=17.82 Aligned_cols=10 Identities=20% Similarity=0.604 Sum_probs=6.0
Q ss_pred cccccccccc
Q psy17880 5 YCTSCKKKCS 14 (120)
Q Consensus 5 ~C~~C~~~i~ 14 (120)
.|..|+++|.
T Consensus 2 ~CPyCge~~~ 11 (52)
T PF14255_consen 2 QCPYCGEPIE 11 (52)
T ss_pred CCCCCCCeeE
Confidence 4666666654
No 186
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=20.03 E-value=93 Score=16.20 Aligned_cols=20 Identities=30% Similarity=0.733 Sum_probs=10.6
Q ss_pred ccHhHHHhHh---CCCCCCCCCc
Q psy17880 52 YCTSDYQKKF---GTKCAQCGEY 71 (120)
Q Consensus 52 ~C~~c~~~~~---~~~C~~C~~~ 71 (120)
+|..||.+.. +.+|..|.++
T Consensus 24 IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 24 ICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp --HHHHHHHTTSS-SB-TTT--B
T ss_pred HHHHHHHHHHhccCCCCCCCCCC
Confidence 5888887765 3688888765
Done!