Query 029230
Match_columns 197
No_of_seqs 253 out of 1326
Neff 8.6
Searched_HMMs 46136
Date Fri Mar 29 09:35:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029230.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029230hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701 Focal adhesion adaptor 99.9 1.2E-29 2.5E-34 209.9 -1.2 132 9-180 274-407 (468)
2 KOG2272 Focal adhesion protein 99.9 4.4E-27 9.5E-32 182.9 0.2 175 8-183 11-270 (332)
3 KOG1701 Focal adhesion adaptor 99.9 1.4E-25 3.1E-30 185.7 1.3 124 8-170 333-467 (468)
4 KOG4577 Transcription factor L 99.9 1.1E-24 2.4E-29 172.3 -1.7 125 8-171 32-159 (383)
5 KOG2272 Focal adhesion protein 99.9 8.5E-24 1.9E-28 164.6 -0.4 117 8-164 194-311 (332)
6 KOG1044 Actin-binding LIM Zn-f 99.9 8.9E-23 1.9E-27 174.4 4.2 161 10-183 17-208 (670)
7 KOG1703 Adaptor protein Enigma 99.8 9.5E-22 2.1E-26 171.7 5.3 132 8-178 302-433 (479)
8 KOG1700 Regulatory protein MLP 99.8 3E-21 6.5E-26 150.2 3.7 179 4-182 2-183 (200)
9 KOG1703 Adaptor protein Enigma 99.8 1E-20 2.2E-25 165.3 0.7 117 7-162 361-478 (479)
10 KOG1044 Actin-binding LIM Zn-f 99.7 3.8E-19 8.2E-24 152.4 2.8 115 8-162 132-247 (670)
11 PF00412 LIM: LIM domain; Int 99.7 1.8E-16 3.9E-21 99.6 5.6 57 110-166 1-58 (58)
12 PF00412 LIM: LIM domain; Int 99.6 1.4E-15 3.1E-20 95.5 4.4 57 12-68 1-58 (58)
13 KOG4577 Transcription factor L 99.2 1.6E-12 3.5E-17 103.6 -2.3 74 106-180 32-105 (383)
14 smart00132 LIM Zinc-binding do 98.9 1.1E-09 2.3E-14 62.7 2.7 37 109-145 1-38 (39)
15 smart00132 LIM Zinc-binding do 98.8 4.1E-09 8.8E-14 60.2 2.5 37 11-47 1-38 (39)
16 KOG1700 Regulatory protein MLP 98.7 9E-09 1.9E-13 80.3 2.3 70 106-175 6-76 (200)
17 KOG1702 Nebulin repeat protein 98.2 6E-08 1.3E-12 74.3 -3.1 59 108-166 5-63 (264)
18 KOG0490 Transcription factor, 98.0 9.7E-07 2.1E-11 70.2 -1.1 111 15-165 2-119 (235)
19 KOG1702 Nebulin repeat protein 97.9 9.3E-07 2E-11 67.9 -2.0 61 9-69 4-64 (264)
20 KOG0490 Transcription factor, 93.4 0.025 5.4E-07 44.7 0.3 63 113-176 2-68 (235)
21 PF14446 Prok-RING_1: Prokaryo 92.5 0.088 1.9E-06 32.1 1.7 36 108-143 6-50 (54)
22 PF09943 DUF2175: Uncharacteri 90.0 0.11 2.4E-06 35.9 0.4 31 108-138 3-34 (101)
23 PF14471 DUF4428: Domain of un 86.5 0.61 1.3E-05 28.1 2.1 29 136-165 1-30 (51)
24 PF10367 Vps39_2: Vacuolar sor 86.3 0.57 1.2E-05 32.2 2.1 29 108-136 79-108 (109)
25 smart00504 Ubox Modified RING 84.4 1.4 3.1E-05 27.1 3.1 32 37-69 2-33 (63)
26 COG2888 Predicted Zn-ribbon RN 82.9 0.89 1.9E-05 28.2 1.6 34 4-46 4-37 (61)
27 PF14835 zf-RING_6: zf-RING of 81.7 1.3 2.7E-05 28.1 2.0 33 37-69 8-40 (65)
28 PF01258 zf-dskA_traR: Prokary 81.6 0.29 6.3E-06 27.1 -0.8 28 137-164 6-33 (36)
29 PF08394 Arc_trans_TRASH: Arch 80.7 1.2 2.7E-05 24.9 1.5 28 110-137 1-29 (37)
30 KOG0320 Predicted E3 ubiquitin 79.4 1.3 2.9E-05 33.8 1.8 37 33-69 128-165 (187)
31 PF09943 DUF2175: Uncharacteri 79.3 0.82 1.8E-05 31.6 0.7 29 11-39 4-33 (101)
32 PF11781 RRN7: RNA polymerase 78.6 1.3 2.8E-05 24.6 1.2 23 136-162 10-32 (36)
33 PF10367 Vps39_2: Vacuolar sor 78.0 1.7 3.7E-05 29.8 2.0 29 9-37 78-107 (109)
34 PF13240 zinc_ribbon_2: zinc-r 77.5 1.5 3.2E-05 21.8 1.1 10 110-119 2-11 (23)
35 COG2191 Formylmethanofuran deh 77.3 0.76 1.7E-05 35.8 0.0 31 135-165 173-203 (206)
36 PF10083 DUF2321: Uncharacteri 76.0 2 4.3E-05 32.0 1.9 37 108-145 40-79 (158)
37 PF02069 Metallothio_Pro: Prok 75.0 2 4.3E-05 26.0 1.4 28 137-164 10-38 (52)
38 COG4847 Uncharacterized protei 73.9 1.4 3.1E-05 29.9 0.6 35 108-142 7-42 (103)
39 PF10235 Cript: Microtubule-as 73.1 2 4.4E-05 29.1 1.2 27 32-64 40-66 (90)
40 cd00162 RING RING-finger (Real 70.3 4.7 0.0001 22.2 2.3 31 39-69 2-32 (45)
41 PF14634 zf-RING_5: zinc-RING 69.1 6.8 0.00015 22.4 2.8 37 137-173 2-42 (44)
42 PF13923 zf-C3HC4_2: Zinc fing 68.8 5.7 0.00012 22.0 2.3 31 39-69 1-31 (39)
43 COG2191 Formylmethanofuran deh 66.8 2.2 4.8E-05 33.2 0.4 31 37-67 173-203 (206)
44 PF00645 zf-PARP: Poly(ADP-rib 65.3 4 8.6E-05 26.8 1.4 18 7-24 5-22 (82)
45 PF13920 zf-C3HC4_3: Zinc fing 65.3 6.5 0.00014 23.1 2.2 32 37-69 3-35 (50)
46 PF10886 DUF2685: Protein of u 65.1 3.8 8.2E-05 24.9 1.1 25 108-132 2-26 (54)
47 KOG0978 E3 ubiquitin ligase in 63.7 2.6 5.5E-05 39.0 0.3 51 36-122 643-693 (698)
48 PF14835 zf-RING_6: zf-RING of 63.0 5 0.00011 25.4 1.4 45 136-180 9-53 (65)
49 PF06677 Auto_anti-p27: Sjogre 63.0 5.2 0.00011 22.9 1.4 22 38-63 19-40 (41)
50 COG1645 Uncharacterized Zn-fin 61.7 4.8 0.0001 29.2 1.3 22 38-64 30-51 (131)
51 PF13248 zf-ribbon_3: zinc-rib 61.3 5.3 0.00012 20.2 1.1 12 108-119 3-14 (26)
52 cd02249 ZZ Zinc finger, ZZ typ 60.9 6.9 0.00015 22.7 1.7 12 154-165 22-33 (46)
53 COG0068 HypF Hydrogenase matur 56.7 4.2 9.2E-05 37.6 0.4 89 3-144 95-183 (750)
54 smart00291 ZnF_ZZ Zinc-binding 56.3 10 0.00023 21.7 1.9 9 156-164 28-36 (44)
55 PF07191 zinc-ribbons_6: zinc- 55.7 3.9 8.4E-05 26.3 0.0 32 108-146 31-62 (70)
56 PF12674 Zn_ribbon_2: Putative 55.1 6.3 0.00014 26.1 1.0 28 137-164 3-35 (81)
57 KOG4443 Putative transcription 54.9 6.2 0.00014 36.0 1.2 22 125-146 106-127 (694)
58 KOG0823 Predicted E3 ubiquitin 54.5 17 0.00038 28.9 3.5 40 29-69 40-79 (230)
59 PRK00807 50S ribosomal protein 53.0 12 0.00026 22.6 1.8 25 108-132 2-29 (52)
60 PLN03208 E3 ubiquitin-protein 51.4 18 0.00039 28.1 3.0 33 35-68 17-49 (193)
61 KOG3002 Zn finger protein [Gen 49.4 14 0.00029 30.9 2.3 32 37-68 49-80 (299)
62 PF07754 DUF1610: Domain of un 49.2 14 0.00031 18.5 1.5 12 110-121 1-12 (24)
63 PF00097 zf-C3HC4: Zinc finger 48.9 22 0.00048 19.5 2.5 31 39-69 1-31 (41)
64 PF06689 zf-C4_ClpX: ClpX C4-t 43.8 53 0.0011 18.5 3.5 30 136-165 3-34 (41)
65 PF04810 zf-Sec23_Sec24: Sec23 43.0 20 0.00044 20.1 1.7 30 108-142 3-32 (40)
66 PF00569 ZZ: Zinc finger, ZZ t 42.5 24 0.00052 20.4 2.0 9 156-164 29-37 (46)
67 PRK00420 hypothetical protein; 42.1 15 0.00033 25.9 1.3 25 37-65 24-48 (112)
68 PF12773 DZR: Double zinc ribb 41.7 12 0.00026 21.9 0.6 11 108-118 13-23 (50)
69 PF12855 Ecl1: Life-span regul 41.5 12 0.00026 21.6 0.6 23 137-163 9-32 (43)
70 PRK14890 putative Zn-ribbon RN 40.7 22 0.00048 22.0 1.7 27 108-143 8-34 (59)
71 KOG1813 Predicted E3 ubiquitin 40.6 14 0.00031 30.5 1.1 33 36-69 241-273 (313)
72 KOG3579 Predicted E3 ubiquitin 40.4 18 0.0004 29.8 1.7 30 11-40 270-299 (352)
73 cd02336 ZZ_RSC8 Zinc finger, Z 39.9 26 0.00056 20.4 1.8 30 136-165 2-33 (45)
74 TIGR00570 cdk7 CDK-activating 39.2 30 0.00065 29.0 2.8 15 55-69 26-40 (309)
75 PRK14559 putative protein seri 38.8 18 0.00039 33.5 1.6 10 108-117 42-51 (645)
76 PF08746 zf-RING-like: RING-li 38.7 11 0.00025 21.6 0.2 26 110-135 1-28 (43)
77 TIGR02098 MJ0042_CXXC MJ0042 f 38.0 12 0.00025 20.6 0.2 32 10-46 3-35 (38)
78 COG5152 Uncharacterized conser 37.3 12 0.00026 29.2 0.2 34 35-69 195-228 (259)
79 PF00628 PHD: PHD-finger; Int 37.1 19 0.00041 20.9 1.0 47 110-163 2-50 (51)
80 cd02340 ZZ_NBR1_like Zinc fing 37.0 32 0.0007 19.7 1.9 10 109-118 2-11 (43)
81 PRK04023 DNA polymerase II lar 36.7 29 0.00063 33.7 2.6 14 108-121 664-677 (1121)
82 PF13834 DUF4193: Domain of un 36.6 9.4 0.0002 26.3 -0.4 29 133-161 69-98 (99)
83 PF06906 DUF1272: Protein of u 36.4 75 0.0016 19.5 3.5 41 137-177 8-51 (57)
84 PF06750 DiS_P_DiS: Bacterial 35.4 17 0.00037 24.6 0.7 37 108-146 34-70 (92)
85 cd02341 ZZ_ZZZ3 Zinc finger, Z 34.8 36 0.00077 20.1 1.9 10 156-165 27-36 (48)
86 PF01844 HNH: HNH endonuclease 34.2 31 0.00067 19.4 1.6 43 110-165 1-44 (47)
87 PF14255 Cys_rich_CPXG: Cystei 34.0 23 0.0005 21.4 1.0 34 11-47 2-35 (52)
88 PF01927 Mut7-C: Mut7-C RNAse 33.6 31 0.00068 25.3 1.9 37 108-144 92-134 (147)
89 PF07503 zf-HYPF: HypF finger; 32.5 12 0.00027 20.5 -0.3 31 12-47 2-32 (35)
90 COG5152 Uncharacterized conser 32.1 20 0.00044 28.0 0.7 42 134-176 196-239 (259)
91 PRK00398 rpoP DNA-directed RNA 32.0 30 0.00066 19.9 1.3 29 108-145 4-32 (46)
92 PF09862 DUF2089: Protein of u 31.9 20 0.00044 25.3 0.6 24 110-146 1-24 (113)
93 PF00320 GATA: GATA zinc finge 31.8 54 0.0012 17.9 2.2 27 137-163 1-28 (36)
94 KOG4739 Uncharacterized protei 31.7 23 0.00049 28.4 0.9 42 39-118 6-48 (233)
95 cd02342 ZZ_UBA_plant Zinc fing 31.7 47 0.001 19.2 2.0 9 156-164 25-33 (43)
96 PF00096 zf-C2H2: Zinc finger, 31.6 19 0.00042 16.9 0.4 12 37-48 1-12 (23)
97 smart00834 CxxC_CXXC_SSSS Puta 31.6 18 0.00039 20.0 0.2 10 37-46 6-15 (41)
98 PF06827 zf-FPG_IleRS: Zinc fi 31.2 18 0.00039 18.7 0.2 11 108-118 2-12 (30)
99 TIGR02605 CxxC_CxxC_SSSS putat 31.1 19 0.00041 21.2 0.3 28 37-64 6-33 (52)
100 PF09723 Zn-ribbon_8: Zinc rib 31.1 18 0.0004 20.5 0.2 28 37-64 6-33 (42)
101 PF01286 XPA_N: XPA protein N- 30.8 29 0.00062 19.0 0.9 11 10-20 4-14 (34)
102 PF00130 C1_1: Phorbol esters/ 30.3 41 0.00089 19.7 1.7 11 108-118 12-22 (53)
103 COG4357 Zinc finger domain con 30.0 6.3 0.00014 26.9 -2.1 32 29-60 55-86 (105)
104 COG4306 Uncharacterized protei 29.7 39 0.00084 24.4 1.7 37 108-145 40-79 (160)
105 smart00659 RPOLCX RNA polymera 29.4 19 0.00042 20.8 0.1 11 108-118 3-13 (44)
106 PF13639 zf-RING_2: Ring finge 29.3 17 0.00037 20.5 -0.1 13 154-166 22-34 (44)
107 TIGR00373 conserved hypothetic 29.1 15 0.00032 27.5 -0.5 29 11-47 111-139 (158)
108 COG4357 Zinc finger domain con 29.0 4.3 9.3E-05 27.7 -3.0 51 109-159 37-87 (105)
109 smart00249 PHD PHD zinc finger 28.6 43 0.00094 18.3 1.6 26 110-135 2-29 (47)
110 COG2075 RPL24A Ribosomal prote 28.6 47 0.001 21.0 1.8 31 38-69 5-41 (66)
111 PF04570 DUF581: Protein of un 28.3 36 0.00078 21.0 1.2 28 136-163 18-48 (58)
112 smart00531 TFIIE Transcription 28.1 17 0.00038 26.7 -0.3 35 10-47 100-134 (147)
113 TIGR00270 conserved hypothetic 27.6 62 0.0013 24.1 2.6 30 137-168 3-35 (154)
114 PF05502 Dynactin_p62: Dynacti 27.5 31 0.00067 30.8 1.1 38 108-146 27-64 (483)
115 PRK06266 transcription initiat 27.4 20 0.00043 27.5 -0.1 30 11-48 119-148 (178)
116 PF07649 C1_3: C1-like domain; 27.4 35 0.00076 17.6 0.9 12 135-146 1-12 (30)
117 PRK14891 50S ribosomal protein 27.2 36 0.00077 24.6 1.2 24 108-131 5-31 (131)
118 PF13717 zinc_ribbon_4: zinc-r 26.9 47 0.001 18.2 1.4 31 108-143 3-34 (36)
119 COG4068 Uncharacterized protei 26.6 30 0.00065 21.4 0.6 15 108-122 9-23 (64)
120 cd02338 ZZ_PCMF_like Zinc fing 26.5 46 0.001 19.6 1.4 10 156-165 25-34 (49)
121 KOG3896 Dynactin, subunit p62 26.4 25 0.00054 29.8 0.3 37 108-146 46-82 (449)
122 KOG3579 Predicted E3 ubiquitin 25.9 29 0.00063 28.7 0.6 48 108-160 269-316 (352)
123 PRK14714 DNA polymerase II lar 25.7 52 0.0011 32.9 2.3 10 109-118 694-703 (1337)
124 PRK12495 hypothetical protein; 25.5 38 0.00082 26.9 1.2 23 37-64 43-65 (226)
125 COG0266 Nei Formamidopyrimidin 25.3 51 0.0011 27.1 1.9 26 106-134 244-271 (273)
126 COG1381 RecO Recombinational D 25.2 39 0.00084 27.3 1.2 30 133-162 153-182 (251)
127 PF13894 zf-C2H2_4: C2H2-type 25.2 28 0.0006 16.1 0.3 12 135-146 1-12 (24)
128 cd00472 Ribosomal_L24e_L24 Rib 25.2 45 0.00098 20.2 1.2 24 108-131 4-30 (54)
129 PF04564 U-box: U-box domain; 25.1 1.2E+02 0.0025 19.3 3.3 34 35-69 3-36 (73)
130 PF13719 zinc_ribbon_5: zinc-r 24.8 50 0.0011 18.1 1.3 31 108-143 3-34 (37)
131 COG1997 RPL43A Ribosomal prote 24.8 86 0.0019 21.1 2.6 35 108-151 36-70 (89)
132 PF10122 Mu-like_Com: Mu-like 24.8 23 0.0005 21.3 -0.1 26 37-64 5-31 (51)
133 cd02335 ZZ_ADA2 Zinc finger, Z 24.5 76 0.0016 18.5 2.1 10 156-165 25-34 (49)
134 PF12677 DUF3797: Domain of un 24.3 76 0.0016 18.9 2.0 27 108-134 14-42 (49)
135 PHA02929 N1R/p28-like protein; 24.2 50 0.0011 26.6 1.6 38 108-145 175-227 (238)
136 PRK00085 recO DNA repair prote 23.9 39 0.00084 26.8 1.0 32 33-64 146-177 (247)
137 PF11571 Med27: Mediator compl 23.8 19 0.0004 24.2 -0.7 17 98-117 48-64 (90)
138 PLN02195 cellulose synthase A 23.6 80 0.0017 30.7 3.1 30 7-44 4-33 (977)
139 PRK00085 recO DNA repair prote 23.6 35 0.00076 27.0 0.7 29 134-162 149-177 (247)
140 PF08271 TF_Zn_Ribbon: TFIIB z 23.3 45 0.00097 18.9 0.9 11 37-47 20-30 (43)
141 COG1656 Uncharacterized conser 22.8 40 0.00087 25.5 0.8 37 108-144 98-140 (165)
142 COG1381 RecO Recombinational D 22.8 42 0.0009 27.1 1.0 31 34-64 152-182 (251)
143 PF10080 DUF2318: Predicted me 22.6 60 0.0013 22.5 1.6 35 30-68 29-63 (102)
144 PLN02436 cellulose synthase A 22.4 73 0.0016 31.3 2.6 9 11-19 38-46 (1094)
145 PF13912 zf-C2H2_6: C2H2-type 22.3 36 0.00078 16.7 0.4 12 37-48 2-13 (27)
146 PLN02638 cellulose synthase A 22.3 74 0.0016 31.3 2.6 29 10-46 18-46 (1079)
147 PF14570 zf-RING_4: RING/Ubox 21.9 51 0.0011 19.5 1.0 12 58-69 23-34 (48)
148 cd02344 ZZ_HERC2 Zinc finger, 21.8 73 0.0016 18.5 1.6 10 155-164 24-33 (45)
149 PF02591 DUF164: Putative zinc 21.8 22 0.00048 21.4 -0.6 14 108-121 23-36 (56)
150 PF12171 zf-C2H2_jaz: Zinc-fin 21.7 58 0.0013 16.2 1.1 12 135-146 2-13 (27)
151 TIGR03826 YvyF flagellar opero 21.5 77 0.0017 23.2 2.1 23 135-165 82-104 (137)
152 KOG2893 Zn finger protein [Gen 21.3 25 0.00055 28.3 -0.5 10 39-48 13-22 (341)
153 PLN02189 cellulose synthase 21.1 81 0.0018 30.9 2.6 9 57-65 61-69 (1040)
154 cd02345 ZZ_dah Zinc finger, ZZ 21.0 64 0.0014 18.9 1.3 9 157-165 26-34 (49)
155 PF01246 Ribosomal_L24e: Ribos 21.0 51 0.0011 21.2 0.9 15 108-122 4-18 (71)
156 PF12874 zf-met: Zinc-finger o 20.9 40 0.00087 16.2 0.4 12 37-48 1-12 (25)
157 PF08209 Sgf11: Sgf11 (transcr 20.5 22 0.00047 19.3 -0.7 16 135-150 5-20 (33)
158 PRK13715 conjugal transfer pro 20.3 28 0.0006 22.5 -0.4 10 109-118 36-45 (73)
159 KOG2462 C2H2-type Zn-finger pr 20.3 53 0.0012 27.0 1.1 38 108-146 188-227 (279)
160 PF14447 Prok-RING_4: Prokaryo 20.2 69 0.0015 19.6 1.3 14 108-121 40-53 (55)
161 PF04641 Rtf2: Rtf2 RING-finge 20.1 1.3E+02 0.0027 24.4 3.3 36 32-67 109-147 (260)
No 1
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.95 E-value=1.2e-29 Score=209.90 Aligned_cols=132 Identities=22% Similarity=0.495 Sum_probs=120.6
Q ss_pred Cccccccccceeccee-EEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCcccCC
Q 029230 9 QQKCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKP 87 (197)
Q Consensus 9 ~~~C~~C~~~I~~~~~-~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 87 (197)
..+|.+|+|.|....- +.|+++.||..||+|..|++.|.++.||.+|+++||+.||++..
T Consensus 274 ~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl------------------- 334 (468)
T KOG1701|consen 274 FGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL------------------- 334 (468)
T ss_pred hhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH-------------------
Confidence 3589999999985433 79999999999999999999999999999999999999998876
Q ss_pred CCcccccCccccccccCCCCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeee-CCeeecHHHHHhHh
Q 029230 88 EKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAH-EGKLYCKHHHIQLF 166 (197)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~-dg~~yC~~cy~~~~ 166 (197)
.+|..|+++|.+. .|.|+|+.||+.||+|..|++.|++..|.+. ++++||..||.++|
T Consensus 335 --------------------ekC~~Cg~~I~d~-iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kf 393 (468)
T KOG1701|consen 335 --------------------EKCNKCGEPIMDR-ILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKF 393 (468)
T ss_pred --------------------HHHhhhhhHHHHH-HHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhc
Confidence 7899999999642 3679999999999999999999999889764 79999999999999
Q ss_pred cCCCCCCCCCCchh
Q 029230 167 REKGNYSQLESDLE 180 (197)
Q Consensus 167 ~~k~~~~~~~~~~~ 180 (197)
++||+.|.+.+.++
T Consensus 394 APrCs~C~~PI~P~ 407 (468)
T KOG1701|consen 394 APRCSVCGNPILPR 407 (468)
T ss_pred CcchhhccCCccCC
Confidence 99999999998876
No 2
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.92 E-value=4.4e-27 Score=182.86 Aligned_cols=175 Identities=19% Similarity=0.283 Sum_probs=145.7
Q ss_pred CCccccccccceeccee-EEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCcccC
Q 029230 8 TQQKCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVK 86 (197)
Q Consensus 8 ~~~~C~~C~~~I~~~~~-~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~ 86 (197)
....|.+|.....+.+. +...|..||..||.|++|-.+|.++.|++.+|+.||+.+|+.+|+|-+..+..|+....+.+
T Consensus 11 ~~~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFiiGrVika 90 (332)
T KOG2272|consen 11 ANMVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFIIGRVIKA 90 (332)
T ss_pred HHHHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhchhhcccccchhhHHHHh
Confidence 34679999998877665 68889999999999999999999999999999999999999999999988888888888877
Q ss_pred CCCcccccCc-------------------------------------------------------------c--------
Q 029230 87 PEKLVENENA-------------------------------------------------------------Q-------- 97 (197)
Q Consensus 87 ~~~~~~~~~~-------------------------------------------------------------~-------- 97 (197)
.+.+||+.+- .
T Consensus 91 mnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C~ 170 (332)
T KOG2272|consen 91 MNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTCG 170 (332)
T ss_pred hccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccceeccccc
Confidence 7777764310 0
Q ss_pred ---------------ccccccCCCCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHH
Q 029230 98 ---------------KVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHH 162 (197)
Q Consensus 98 ---------------~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy 162 (197)
+....-..+.|+|..|.+||. ...|.++|+.||.++|+|+.|.+|+-+...+++.|.+||+.+|
T Consensus 171 keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIe-ervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~ 249 (332)
T KOG2272|consen 171 KELTSDAREVKGELYCLRCHDKMGIPICGACRRPIE-ERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 249 (332)
T ss_pred ccccchhhhhccceeccccccccCCcccccccCchH-HHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHH
Confidence 000000134589999999996 3446799999999999999999999999999999999999999
Q ss_pred HhHhcCCCCCCCCCCchhhhc
Q 029230 163 IQLFREKGNYSQLESDLEKSQ 183 (197)
Q Consensus 163 ~~~~~~k~~~~~~~~~~~~~~ 183 (197)
.++||.-|..|...+.-.+-.
T Consensus 250 ~qLfG~~CF~C~~~i~G~vv~ 270 (332)
T KOG2272|consen 250 HQLFGNLCFICNRVIGGDVVS 270 (332)
T ss_pred HHHhhhhheecCCccCccHHH
Confidence 999999999888776655443
No 3
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.91 E-value=1.4e-25 Score=185.74 Aligned_cols=124 Identities=27% Similarity=0.647 Sum_probs=111.6
Q ss_pred CCccccccccceecceeEEeCCccccccccccccccccccCCCeee-cCCeeeccccHHHHhhccCCcccccCCCCcccC
Q 029230 8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNS-FEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVK 86 (197)
Q Consensus 8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~-~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~ 86 (197)
...+|..|++.|+ +..|.|+|+.||+.||+|..|++.|++..|.. .++++||..||++.|+
T Consensus 333 tlekC~~Cg~~I~-d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfA----------------- 394 (468)
T KOG1701|consen 333 TLEKCNKCGEPIM-DRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFA----------------- 394 (468)
T ss_pred HHHHHhhhhhHHH-HHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcC-----------------
Confidence 3468999999998 78899999999999999999999999999965 4789999999999998
Q ss_pred CCCcccccCccccccccCCCCCCCCCCCceeecCc------eeeecCccccccccccCcCCCCCC----CCCeeeeCCee
Q 029230 87 PEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTE------KVSVNGAAYHRSCFKCSHGGCTIS----PSNYIAHEGKL 156 (197)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e------~v~~~g~~~H~~CF~C~~C~~~l~----~~~~~~~dg~~ 156 (197)
++|+.|+++|.+.+ +|++|++.||.+|++|..|+..|+ +...|..||.+
T Consensus 395 ---------------------PrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~Hl 453 (468)
T KOG1701|consen 395 ---------------------PRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHL 453 (468)
T ss_pred ---------------------cchhhccCCccCCCCCcceEEEEEccccccccceehhhcCccccccCCCCcceeccCce
Confidence 99999999998764 478999999999999999999998 34689999999
Q ss_pred ecHHHHHhHhcCCC
Q 029230 157 YCKHHHIQLFREKG 170 (197)
Q Consensus 157 yC~~cy~~~~~~k~ 170 (197)
+|+.|..++....+
T Consensus 454 lCk~Ch~~Rl~~~~ 467 (468)
T KOG1701|consen 454 LCKTCHLKRLQAGS 467 (468)
T ss_pred eechhhhhhhcccC
Confidence 99999998876543
No 4
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.88 E-value=1.1e-24 Score=172.26 Aligned_cols=125 Identities=26% Similarity=0.567 Sum_probs=112.6
Q ss_pred CCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCcccCC
Q 029230 8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKP 87 (197)
Q Consensus 8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 87 (197)
..++|++|++.|.+..++.++++.||..|++|+.|...|.+..|. ++|.+||+.+|.++|+
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCFs-R~~s~yCkedFfKrfG------------------ 92 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCFS-REGSVYCKEDFFKRFG------------------ 92 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHhh-cCCceeehHHHHHHhC------------------
Confidence 679999999999977778999999999999999999999976655 8999999999999998
Q ss_pred CCcccccCccccccccCCCCCCCCCCCceeecCceee-ecCccccccccccCcCCCCCCC-CCee-eeCCeeecHHHHHh
Q 029230 88 EKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVS-VNGAAYHRSCFKCSHGGCTISP-SNYI-AHEGKLYCKHHHIQ 164 (197)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~-~~g~~~H~~CF~C~~C~~~l~~-~~~~-~~dg~~yC~~cy~~ 164 (197)
.+|..|...|.+.+.|. |.+.+||..||.|..|+++|.. +.|+ +.|+++.|+.+|++
T Consensus 93 --------------------TKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~ 152 (383)
T KOG4577|consen 93 --------------------TKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYET 152 (383)
T ss_pred --------------------CcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHH
Confidence 89999999999998774 9999999999999999999985 4555 57899999999999
Q ss_pred HhcCCCC
Q 029230 165 LFREKGN 171 (197)
Q Consensus 165 ~~~~k~~ 171 (197)
.-...|.
T Consensus 153 Ak~k~~~ 159 (383)
T KOG4577|consen 153 AKQKHCN 159 (383)
T ss_pred HHhcccc
Confidence 8776664
No 5
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.87 E-value=8.5e-24 Score=164.58 Aligned_cols=117 Identities=24% Similarity=0.490 Sum_probs=109.9
Q ss_pred CCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCcccCC
Q 029230 8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKP 87 (197)
Q Consensus 8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 87 (197)
+.++|..|.++|. +.++.++|+.||.+.|+|+.|.+|+-+...|++.|.+||+.+|.++|+
T Consensus 194 gipiCgaC~rpIe-ervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG------------------ 254 (332)
T KOG2272|consen 194 GIPICGACRRPIE-ERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFG------------------ 254 (332)
T ss_pred CCcccccccCchH-HHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhh------------------
Confidence 4689999999997 788999999999999999999999998899999999999999999998
Q ss_pred CCcccccCccccccccCCCCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCC-CCeeeeCCeeecHHHHHh
Q 029230 88 EKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISP-SNYIAHEGKLYCKHHHIQ 164 (197)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~-~~~~~~dg~~yC~~cy~~ 164 (197)
..|..|+++|. ++.|.++++.|.++||.|+.|++.|.. .+|++.|-+|.|+.||.+
T Consensus 255 --------------------~~CF~C~~~i~-G~vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~r 311 (332)
T KOG2272|consen 255 --------------------NLCFICNRVIG-GDVVSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDR 311 (332)
T ss_pred --------------------hhheecCCccC-ccHHHHhhhhhccccccccccccccccccceeeeccchHHHHHHhh
Confidence 89999999996 677899999999999999999999986 689999999999999974
No 6
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.86 E-value=8.9e-23 Score=174.43 Aligned_cols=161 Identities=21% Similarity=0.367 Sum_probs=122.8
Q ss_pred ccccccccceecceeEEeCCccccccccccccccccccCCCeeecCC-eeeccccHHHHhhccCCcccccCCCCcccCCC
Q 029230 10 QKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEG-VLYCRPHFDQLFKRTGSLEKSFEGTPKIVKPE 88 (197)
Q Consensus 10 ~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g-~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~ 88 (197)
..|.+|.+.-. ++++.+.++.||..||+|..|+..|..+.|+.+++ ++|+..... .++....+.++.
T Consensus 17 i~c~~c~~kc~-gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~-----------~~~~gevvsa~g 84 (670)
T KOG1044|consen 17 IKCDKCRKKCS-GEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCR-----------AFVEGEVVSTLG 84 (670)
T ss_pred eehhhhCCccc-cceeEeeccccceeeeeccccCCCcccccceecccceeecccchh-----------hhccceeEeccc
Confidence 46999999987 99999999999999999999999999999888765 567663322 122222222222
Q ss_pred CcccccC------------------------------ccccccccCCCCCCCCCCCceeecCceeeecCccccccccccC
Q 029230 89 KLVENEN------------------------------AQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCS 138 (197)
Q Consensus 89 ~~~~~~~------------------------------~~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~ 138 (197)
+..|..+ +.........+...|++|++.|..++.+.|+++.||+.||+|.
T Consensus 85 ktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~ 164 (670)
T KOG1044|consen 85 KTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCK 164 (670)
T ss_pred ceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeeeeeehh
Confidence 2222110 0111111112457899999999999989999999999999999
Q ss_pred cCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCCCCCCCchhhhc
Q 029230 139 HGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLEKSQ 183 (197)
Q Consensus 139 ~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~~~~~~~~~~~~ 183 (197)
.|...|.+ .|+.+||.|||+.+|.+.||.||.+|..++..-|-+
T Consensus 165 ~c~~vL~g-ey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvLq 208 (670)
T KOG1044|consen 165 SCSAVLNG-EYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVLQ 208 (670)
T ss_pred hhcccccc-eeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhhh
Confidence 99999887 899999999999999999999999999887655443
No 7
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.84 E-value=9.5e-22 Score=171.72 Aligned_cols=132 Identities=24% Similarity=0.585 Sum_probs=121.9
Q ss_pred CCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCcccCC
Q 029230 8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKP 87 (197)
Q Consensus 8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 87 (197)
..+.|..|+..|.....+.++++.||+.+|.|..|...|....|...+|.+||..||.+.++
T Consensus 302 ~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~------------------ 363 (479)
T KOG1703|consen 302 TRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFR------------------ 363 (479)
T ss_pred ccccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhC------------------
Confidence 45899999999984489999999999999999999999999999999999999999999987
Q ss_pred CCcccccCccccccccCCCCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhc
Q 029230 88 EKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR 167 (197)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~ 167 (197)
+.|.+|+++|. ++.|.+.++.||++||.|..|+++|....|+..||.|||+.||.++++
T Consensus 364 --------------------p~C~~C~~~i~-~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~ 422 (479)
T KOG1703|consen 364 --------------------PNCKRCLLPIL-EEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFT 422 (479)
T ss_pred --------------------ccccccCCchH-HhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhcc
Confidence 99999999998 556888899999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCc
Q 029230 168 EKGNYSQLESD 178 (197)
Q Consensus 168 ~k~~~~~~~~~ 178 (197)
++|.+|.....
T Consensus 423 ~~~~~~~~p~~ 433 (479)
T KOG1703|consen 423 TKCDYCKKPVE 433 (479)
T ss_pred ccchhccchhH
Confidence 99988866543
No 8
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.82 E-value=3e-21 Score=150.20 Aligned_cols=179 Identities=44% Similarity=0.840 Sum_probs=143.1
Q ss_pred CCCCCCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCC-cccccCCCC
Q 029230 4 PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGS-LEKSFEGTP 82 (197)
Q Consensus 4 ~~~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~-~~~~~~~~~ 82 (197)
++......|..|++.|+..+.+...|..||..||+|..|.+.|....+..+++.+||+.+|...+++.+. ..+.++...
T Consensus 2 ~~~~~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~ 81 (200)
T KOG1700|consen 2 SFTGTTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAG 81 (200)
T ss_pred CcccccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccC
Confidence 4556678999999999998999999999999999999999999999999999999999988888887653 233333222
Q ss_pred cccCCCCcccccCc--cccccccCCCCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHH
Q 029230 83 KIVKPEKLVENENA--QKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKH 160 (197)
Q Consensus 83 ~~~~~~~~~~~~~~--~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~ 160 (197)
.+.....+....+. ......+.++...|.+|.+.+++.|.+...+..||..||+|+.|+..|+.+.+....|.+||..
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~ 161 (200)
T KOG1700|consen 82 GLGKDGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKH 161 (200)
T ss_pred CCCcccccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccch
Confidence 22122222222222 2344556777899999999999999999999999999999999999999999999999999999
Q ss_pred HHHhHhcCCCCCCCCCCchhhh
Q 029230 161 HHIQLFREKGNYSQLESDLEKS 182 (197)
Q Consensus 161 cy~~~~~~k~~~~~~~~~~~~~ 182 (197)
++.+++..+..+-.+.......
T Consensus 162 ~~~~~~~~~~~~~~~~~~~~~~ 183 (200)
T KOG1700|consen 162 HFAQLFKGKGNYNEGFGARENK 183 (200)
T ss_pred hhheeecCCCcccccchhhhhh
Confidence 9999888888877776655533
No 9
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.79 E-value=1e-20 Score=165.28 Aligned_cols=117 Identities=26% Similarity=0.645 Sum_probs=108.8
Q ss_pred CCCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCcccC
Q 029230 7 GTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVK 86 (197)
Q Consensus 7 ~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~ 86 (197)
...++|.+|.++|. ++.|.+.++.||++||.|..|+++|....|+..++.+||+.||.++++
T Consensus 361 ~~~p~C~~C~~~i~-~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~----------------- 422 (479)
T KOG1703|consen 361 PFRPNCKRCLLPIL-EEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFT----------------- 422 (479)
T ss_pred hhCccccccCCchH-HhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhcc-----------------
Confidence 35689999999998 888999999999999999999999999999999999999999999986
Q ss_pred CCCcccccCccccccccCCCCCCCCCCCceeecCce-eeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHH
Q 029230 87 PEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEK-VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHH 162 (197)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~-v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy 162 (197)
++|..|.++|..+.. |.+++..||..||+|..|.+.|.++.|+...++|+|..|+
T Consensus 423 ---------------------~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~~~~~~~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 423 ---------------------TKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKKLTKKTFFETLDKPLCQKHF 478 (479)
T ss_pred ---------------------ccchhccchhHhhhhHhhccCccccccceehhhhhccccCCceeecCCccccccCC
Confidence 789999999876654 7899999999999999999999999999999999999875
No 10
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.75 E-value=3.8e-19 Score=152.39 Aligned_cols=115 Identities=21% Similarity=0.564 Sum_probs=105.3
Q ss_pred CCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCcccCC
Q 029230 8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKP 87 (197)
Q Consensus 8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 87 (197)
+...|++|++.|..++.+.|+++.||..||+|..|...|. +.|..++|.+||+.||++.|+
T Consensus 132 ~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~-gey~skdg~pyce~dy~~~fg------------------ 192 (670)
T KOG1044|consen 132 GPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLN-GEYMSKDGVPYCEKDYQAKFG------------------ 192 (670)
T ss_pred CCccccchhhhhhccceeeeeccceeeeeeehhhhccccc-ceeeccCCCcchhhhhhhhcC------------------
Confidence 5578999999999999999999999999999999999997 578899999999999999998
Q ss_pred CCcccccCccccccccCCCCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCC-CCeeeeCCeeecHHHH
Q 029230 88 EKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISP-SNYIAHEGKLYCKHHH 162 (197)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~-~~~~~~dg~~yC~~cy 162 (197)
.+|..|.+-|. +..|.|.|++||+.|-+|..|+..++. ++.++.+..+|-..|-
T Consensus 193 --------------------vkc~~c~~fis-gkvLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~ 247 (670)
T KOG1044|consen 193 --------------------VKCEECEKFIS-GKVLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCK 247 (670)
T ss_pred --------------------eehHHhhhhhh-hhhhhccCcccCcchhhhhhhccccccchheeeccccccCCccc
Confidence 89999999997 556789999999999999999999984 6788888888888885
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=99.66 E-value=1.8e-16 Score=99.63 Aligned_cols=57 Identities=35% Similarity=0.792 Sum_probs=53.4
Q ss_pred CCCCCceeecCcee-eecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHh
Q 029230 110 CVGCDRTVYPTEKV-SVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLF 166 (197)
Q Consensus 110 C~~C~~~I~~~e~v-~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~ 166 (197)
|++|+++|.+.+.+ .++|+.||++||+|..|+++|.++.|+..+|++||+.||.++|
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 78999999988875 5999999999999999999999988999999999999999986
No 12
>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=99.59 E-value=1.4e-15 Score=95.54 Aligned_cols=57 Identities=28% Similarity=0.773 Sum_probs=53.0
Q ss_pred ccccccceecceeE-EeCCccccccccccccccccccCCCeeecCCeeeccccHHHHh
Q 029230 12 CMACDKTVYLVDKL-TADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLF 68 (197)
Q Consensus 12 C~~C~~~I~~~~~~-~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~ 68 (197)
|.+|+++|..++.+ .++|+.||++||+|..|+++|.++.|+..+|++||+.||.++|
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 78999999977765 7999999999999999999999988999999999999998875
No 13
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.17 E-value=1.6e-12 Score=103.57 Aligned_cols=74 Identities=26% Similarity=0.475 Sum_probs=65.3
Q ss_pred CCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCCCCCCCchh
Q 029230 106 TRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLE 180 (197)
Q Consensus 106 ~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~~~~~~~~~ 180 (197)
..++|++|++.|.+.-.+.++++.||..|++|+.|+.+|.. ..+.++|.+||+++|-++||.||+.|+.-+++-
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPt 105 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPT 105 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChH
Confidence 34899999999986544579999999999999999999987 789999999999999999999999888766543
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=98.90 E-value=1.1e-09 Score=62.65 Aligned_cols=37 Identities=32% Similarity=0.769 Sum_probs=33.2
Q ss_pred CCCCCCceeecC-ceeeecCccccccccccCcCCCCCC
Q 029230 109 KCVGCDRTVYPT-EKVSVNGAAYHRSCFKCSHGGCTIS 145 (197)
Q Consensus 109 ~C~~C~~~I~~~-e~v~~~g~~~H~~CF~C~~C~~~l~ 145 (197)
+|.+|+++|.+. ..+.+.++.||++||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 589999999987 5577999999999999999999985
No 15
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.78 E-value=4.1e-09 Score=60.19 Aligned_cols=37 Identities=35% Similarity=0.729 Sum_probs=33.6
Q ss_pred cccccccceecc-eeEEeCCcccccccccccccccccc
Q 029230 11 KCMACDKTVYLV-DKLTADNRVYHKACFRCHHCKGTLK 47 (197)
Q Consensus 11 ~C~~C~~~I~~~-~~~~~~g~~~H~~CF~C~~C~~~L~ 47 (197)
+|.+|+++|.+. ..+.+.++.||+.||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 589999999976 6788999999999999999999985
No 16
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.68 E-value=9e-09 Score=80.33 Aligned_cols=70 Identities=43% Similarity=0.842 Sum_probs=63.1
Q ss_pred CCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCC-CCCC
Q 029230 106 TRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGN-YSQL 175 (197)
Q Consensus 106 ~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~-~~~~ 175 (197)
...+|.+|++.|+..+.+...|..||+.||+|..|.+.|..+.+...++.+||+.||...++++.. +..+
T Consensus 6 ~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~ 76 (200)
T KOG1700|consen 6 TTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKG 76 (200)
T ss_pred ccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCccccccccc
Confidence 346999999999999988899999999999999999999999999999999999999999998885 4444
No 17
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=98.23 E-value=6e-08 Score=74.32 Aligned_cols=59 Identities=34% Similarity=0.660 Sum_probs=54.9
Q ss_pred CCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHh
Q 029230 108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLF 166 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~ 166 (197)
..|..|++.+++.|.|.-+++.||..||+|..|+.+|.-..+...|.+|||..+|.+..
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~ 63 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQV 63 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccce
Confidence 56889999999999999999999999999999999999888888999999999998765
No 18
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.97 E-value=9.7e-07 Score=70.17 Aligned_cols=111 Identities=18% Similarity=0.478 Sum_probs=88.5
Q ss_pred cccceecceeEEeCCcccccccccccccccccc--CCCeeecCCeeeccccHHH--HhhccCCcccccCCCCcccCCCCc
Q 029230 15 CDKTVYLVDKLTADNRVYHKACFRCHHCKGTLK--LSNFNSFEGVLYCRPHFDQ--LFKRTGSLEKSFEGTPKIVKPEKL 90 (197)
Q Consensus 15 C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~--~~~f~~~~g~~yC~~c~~~--~~~~~~~~~~~~~~~~~~~~~~~~ 90 (197)
|+..|.+...+.+.+..||..|..|..|...|. ...|.. +|..||..+|.+ .+.
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~--------------------- 59 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFS--------------------- 59 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcc---------------------
Confidence 667777656677779999999999999999998 555666 999999999987 333
Q ss_pred ccccCccccccccCCCCCCCCCCCceeecCceee-ecCccccccccccCcCCCCCC-CCCeeeeCC-eeecHHHHHhH
Q 029230 91 VENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVS-VNGAAYHRSCFKCSHGGCTIS-PSNYIAHEG-KLYCKHHHIQL 165 (197)
Q Consensus 91 ~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~-~~g~~~H~~CF~C~~C~~~l~-~~~~~~~dg-~~yC~~cy~~~ 165 (197)
.+|.+|...+...+.|. +..+. |..||.|..|...+. +..+.+.+. +.+|..++.+.
T Consensus 60 -----------------~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 60 -----------------KRCARCKFTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred -----------------ccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 78999999997666664 66666 999999999988665 456666554 99999888654
No 19
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=97.91 E-value=9.3e-07 Score=67.86 Aligned_cols=61 Identities=33% Similarity=0.802 Sum_probs=55.1
Q ss_pred CccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230 9 QQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK 69 (197)
Q Consensus 9 ~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~ 69 (197)
...|..|++.+++.+.+..+++.||..||.|..|+.+|.-..|--.+.++||..+|....+
T Consensus 4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVA 64 (264)
T ss_pred cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccccee
Confidence 4678899999999999999999999999999999999998888888999999999965443
No 20
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=93.43 E-value=0.025 Score=44.71 Aligned_cols=63 Identities=21% Similarity=0.514 Sum_probs=49.6
Q ss_pred CCceeecCceeeecCccccccccccCcCCCCCC--CCCeeeeCCeeecHHHHHh--HhcCCCCCCCCC
Q 029230 113 CDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTIS--PSNYIAHEGKLYCKHHHIQ--LFREKGNYSQLE 176 (197)
Q Consensus 113 C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~--~~~~~~~dg~~yC~~cy~~--~~~~k~~~~~~~ 176 (197)
|+..|.+...+.+.+..||..|..|..|...|. ...|.. +|..||...|.. .+..+|.-+...
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~ 68 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFT 68 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCC
Confidence 666776555566779999999999999999997 445556 999999999998 777777644443
No 21
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=92.52 E-value=0.088 Score=32.08 Aligned_cols=36 Identities=33% Similarity=0.696 Sum_probs=26.2
Q ss_pred CCCCCCCceeecCce-ee--ecCcccccccc----ccCc--CCCC
Q 029230 108 DKCVGCDRTVYPTEK-VS--VNGAAYHRSCF----KCSH--GGCT 143 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~-v~--~~g~~~H~~CF----~C~~--C~~~ 143 (197)
.+|..|+++|.+++- |. .-+..||++|. .|.. |+.+
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~ 50 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTG 50 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCC
Confidence 789999999985543 43 56788999988 4655 5544
No 22
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=89.98 E-value=0.11 Score=35.86 Aligned_cols=31 Identities=23% Similarity=0.548 Sum_probs=21.9
Q ss_pred CCCCCCCceeecCceee-ecCccccccccccC
Q 029230 108 DKCVGCDRTVYPTEKVS-VNGAAYHRSCFKCS 138 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~v~-~~g~~~H~~CF~C~ 138 (197)
-+|..|+++|+.++..+ ..+..-|.+||+=.
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~ 34 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREK 34 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHH
Confidence 35888888888887755 44467788888644
No 23
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=86.54 E-value=0.61 Score=28.10 Aligned_cols=29 Identities=28% Similarity=0.515 Sum_probs=23.6
Q ss_pred ccCcCCCCCCC-CCeeeeCCeeecHHHHHhH
Q 029230 136 KCSHGGCTISP-SNYIAHEGKLYCKHHHIQL 165 (197)
Q Consensus 136 ~C~~C~~~l~~-~~~~~~dg~~yC~~cy~~~ 165 (197)
.|..|+..+.. ..+...|| ..|..|+.++
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 48889998875 34777888 6999999997
No 24
>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=86.31 E-value=0.57 Score=32.23 Aligned_cols=29 Identities=31% Similarity=0.482 Sum_probs=21.7
Q ss_pred CCCCCCCceeecCcee-eecCccccccccc
Q 029230 108 DKCVGCDRTVYPTEKV-SVNGAAYHRSCFK 136 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~v-~~~g~~~H~~CF~ 136 (197)
..|+.|+++|.....+ ...|..+|..|++
T Consensus 79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 6799999999765443 3667778888863
No 25
>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=84.36 E-value=1.4 Score=27.07 Aligned_cols=32 Identities=19% Similarity=0.199 Sum_probs=25.8
Q ss_pred cccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230 37 FRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK 69 (197)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~ 69 (197)
|.|..|+..+.+ ......|..||+.|..+.+.
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~ 33 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLL 33 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHH
Confidence 578899988876 45567799999999988775
No 26
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=82.94 E-value=0.89 Score=28.17 Aligned_cols=34 Identities=15% Similarity=0.337 Sum_probs=22.9
Q ss_pred CCCCCCccccccccceecceeEEeCCccccccccccccccccc
Q 029230 4 PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTL 46 (197)
Q Consensus 4 ~~~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L 46 (197)
++....+.|..|+..|..++.... |.|-.|+..+
T Consensus 4 ~~~~~~~~CtSCg~~i~p~e~~v~---------F~CPnCGe~~ 37 (61)
T COG2888 4 MEMKDPPVCTSCGREIAPGETAVK---------FPCPNCGEVE 37 (61)
T ss_pred ccccCCceeccCCCEeccCCceeE---------eeCCCCCcee
Confidence 344457899999999966655433 7777777443
No 27
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=81.69 E-value=1.3 Score=28.08 Aligned_cols=33 Identities=18% Similarity=0.304 Sum_probs=15.2
Q ss_pred cccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230 37 FRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK 69 (197)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~ 69 (197)
++|+.|...|...--...=.+.+|..|-.+.++
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~ 40 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIG 40 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTT
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcC
Confidence 578888887764322334457889888866665
No 28
>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=81.61 E-value=0.29 Score=27.10 Aligned_cols=28 Identities=21% Similarity=0.418 Sum_probs=13.0
Q ss_pred cCcCCCCCCCCCeeeeCCeeecHHHHHh
Q 029230 137 CSHGGCTISPSNYIAHEGKLYCKHHHIQ 164 (197)
Q Consensus 137 C~~C~~~l~~~~~~~~dg~~yC~~cy~~ 164 (197)
|..|+.+|.........+..+|..|+.+
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 4444544444444444555556555543
No 29
>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=80.66 E-value=1.2 Score=24.90 Aligned_cols=28 Identities=21% Similarity=0.488 Sum_probs=17.3
Q ss_pred CCCCCceeecCce-eeecCcccccccccc
Q 029230 110 CVGCDRTVYPTEK-VSVNGAAYHRSCFKC 137 (197)
Q Consensus 110 C~~C~~~I~~~e~-v~~~g~~~H~~CF~C 137 (197)
|.-|+++|.+... +...++.||.-|-.|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC 29 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTC 29 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHH
Confidence 5677888874433 347777777544444
No 30
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.39 E-value=1.3 Score=33.76 Aligned_cols=37 Identities=14% Similarity=0.449 Sum_probs=28.8
Q ss_pred cccccccccccccccCCC-eeecCCeeeccccHHHHhh
Q 029230 33 HKACFRCHHCKGTLKLSN-FNSFEGVLYCRPHFDQLFK 69 (197)
Q Consensus 33 H~~CF~C~~C~~~L~~~~-f~~~~g~~yC~~c~~~~~~ 69 (197)
-..++.|-.|-....... +..+=|+++|..|......
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk 165 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALK 165 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHHH
Confidence 346789999977776554 6678899999999987764
No 31
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=79.28 E-value=0.82 Score=31.58 Aligned_cols=29 Identities=34% Similarity=0.637 Sum_probs=16.5
Q ss_pred cccccccceecceeEEeCC-cccccccccc
Q 029230 11 KCMACDKTVYLVDKLTADN-RVYHKACFRC 39 (197)
Q Consensus 11 ~C~~C~~~I~~~~~~~~~g-~~~H~~CF~C 39 (197)
+|..|+++|+.++.+.+.. ...|-.||+=
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~ 33 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFRE 33 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHH
Confidence 5666666666666654433 3456666653
No 32
>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=78.55 E-value=1.3 Score=24.65 Aligned_cols=23 Identities=22% Similarity=0.577 Sum_probs=14.0
Q ss_pred ccCcCCCCCCCCCeeeeCCeeecHHHH
Q 029230 136 KCSHGGCTISPSNYIAHEGKLYCKHHH 162 (197)
Q Consensus 136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy 162 (197)
.|..|+.. .|...||..||..|-
T Consensus 10 ~C~~C~~~----~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 10 PCPVCGSR----WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCCCCe----EeEccCCEEEhhhCc
Confidence 36666532 456677777776653
No 33
>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=78.02 E-value=1.7 Score=29.79 Aligned_cols=29 Identities=24% Similarity=0.413 Sum_probs=14.1
Q ss_pred CccccccccceecceeEE-eCCcccccccc
Q 029230 9 QQKCMACDKTVYLVDKLT-ADNRVYHKACF 37 (197)
Q Consensus 9 ~~~C~~C~~~I~~~~~~~-~~g~~~H~~CF 37 (197)
...|..|+++|.....+. -.|..+|..|+
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 345666666665433322 23344555554
No 34
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=77.49 E-value=1.5 Score=21.77 Aligned_cols=10 Identities=20% Similarity=0.690 Sum_probs=5.9
Q ss_pred CCCCCceeec
Q 029230 110 CVGCDRTVYP 119 (197)
Q Consensus 110 C~~C~~~I~~ 119 (197)
|..|+..|.+
T Consensus 2 Cp~CG~~~~~ 11 (23)
T PF13240_consen 2 CPNCGAEIED 11 (23)
T ss_pred CcccCCCCCC
Confidence 6666666643
No 35
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=77.26 E-value=0.76 Score=35.76 Aligned_cols=31 Identities=23% Similarity=0.343 Sum_probs=26.0
Q ss_pred cccCcCCCCCCCCCeeeeCCeeecHHHHHhH
Q 029230 135 FKCSHGGCTISPSNYIAHEGKLYCKHHHIQL 165 (197)
Q Consensus 135 F~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~ 165 (197)
-+|+.|+-.+....-...+|++.|..||.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 5788899888777778889999999999854
No 36
>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=75.99 E-value=2 Score=32.02 Aligned_cols=37 Identities=19% Similarity=0.365 Sum_probs=26.7
Q ss_pred CCCCCCCceeecCce---eeecCccccccccccCcCCCCCC
Q 029230 108 DKCVGCDRTVYPTEK---VSVNGAAYHRSCFKCSHGGCTIS 145 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~---v~~~g~~~H~~CF~C~~C~~~l~ 145 (197)
..|+.|+-+|..... |...|..|+.-- -|..||++..
T Consensus 40 ~~Cp~C~~~IrG~y~v~gv~~~g~~~~~Ps-YC~~CGkpyP 79 (158)
T PF10083_consen 40 TSCPNCSTPIRGDYHVEGVFGLGGHYEAPS-YCHNCGKPYP 79 (158)
T ss_pred HHCcCCCCCCCCceecCCeeeeCCCCCCCh-hHHhCCCCCc
Confidence 679999999985533 446677777543 3888898875
No 37
>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=75.04 E-value=2 Score=25.97 Aligned_cols=28 Identities=29% Similarity=0.667 Sum_probs=17.2
Q ss_pred cCcCCCCCCCCCeeeeCCeeec-HHHHHh
Q 029230 137 CSHGGCTISPSNYIAHEGKLYC-KHHHIQ 164 (197)
Q Consensus 137 C~~C~~~l~~~~~~~~dg~~yC-~~cy~~ 164 (197)
|..|...++...-+.+||+.|| +.|...
T Consensus 10 C~~C~C~V~~~~Ai~~dGk~YCS~aCA~g 38 (52)
T PF02069_consen 10 CPSCSCVVSEEEAIQKDGKYYCSEACANG 38 (52)
T ss_dssp STT----B-TTTSEESSS-EESSHHHHHT
T ss_pred CCCCEeEECchHhHHhCCEeeecHHHhcc
Confidence 6778888887788899999999 567654
No 38
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=73.88 E-value=1.4 Score=29.94 Aligned_cols=35 Identities=23% Similarity=0.364 Sum_probs=25.7
Q ss_pred CCCCCCCceeecCceee-ecCccccccccccCcCCC
Q 029230 108 DKCVGCDRTVYPTEKVS-VNGAAYHRSCFKCSHGGC 142 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~v~-~~g~~~H~~CF~C~~C~~ 142 (197)
-+|+.|+++|..++..+ .....-|.+||.=+.=++
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~k 42 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECLAESKRKK 42 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHHHHHHhcC
Confidence 57999999998888765 344567888887665443
No 39
>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=73.07 E-value=2 Score=29.05 Aligned_cols=27 Identities=26% Similarity=0.605 Sum_probs=16.9
Q ss_pred ccccccccccccccccCCCeeecCCeeeccccH
Q 029230 32 YHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64 (197)
Q Consensus 32 ~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~ 64 (197)
|-+.=-.|..|...+. ..|.-||..|-
T Consensus 40 y~~~~~~C~~CK~~v~------q~g~~YCq~CA 66 (90)
T PF10235_consen 40 YAPYSSKCKICKTKVH------QPGAKYCQTCA 66 (90)
T ss_pred ccccCccccccccccc------cCCCccChhhh
Confidence 3333335777766553 34678999995
No 40
>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=70.31 E-value=4.7 Score=22.18 Aligned_cols=31 Identities=23% Similarity=0.469 Sum_probs=18.2
Q ss_pred cccccccccCCCeeecCCeeeccccHHHHhh
Q 029230 39 CHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK 69 (197)
Q Consensus 39 C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~ 69 (197)
|..|...+........=|..+|..|....+.
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~ 32 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLK 32 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHH
Confidence 5566666632222223567788888876654
No 41
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=69.05 E-value=6.8 Score=22.40 Aligned_cols=37 Identities=16% Similarity=0.158 Sum_probs=24.2
Q ss_pred cCcCCCCCC-CCCeeeeC-CeeecHHHHHhHh--cCCCCCC
Q 029230 137 CSHGGCTIS-PSNYIAHE-GKLYCKHHHIQLF--REKGNYS 173 (197)
Q Consensus 137 C~~C~~~l~-~~~~~~~d-g~~yC~~cy~~~~--~~k~~~~ 173 (197)
|..|...+. ...+.... |..+|..|..++. ..+|.+|
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C 42 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPIC 42 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCC
Confidence 566666663 23455544 8899999998887 4455444
No 42
>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=68.76 E-value=5.7 Score=22.01 Aligned_cols=31 Identities=16% Similarity=0.426 Sum_probs=21.2
Q ss_pred cccccccccCCCeeecCCeeeccccHHHHhh
Q 029230 39 CHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK 69 (197)
Q Consensus 39 C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~ 69 (197)
|..|...+.+......=|..||..|..+...
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~ 31 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLE 31 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHH
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHH
Confidence 4567666665324556789999999988765
No 43
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=66.78 E-value=2.2 Score=33.24 Aligned_cols=31 Identities=19% Similarity=0.460 Sum_probs=26.5
Q ss_pred cccccccccccCCCeeecCCeeeccccHHHH
Q 029230 37 FRCHHCKGTLKLSNFNSFEGVLYCRPHFDQL 67 (197)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~ 67 (197)
-+|+.|+..+....-...+|++.|..||.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 6899999998877777789999999998643
No 44
>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=65.31 E-value=4 Score=26.78 Aligned_cols=18 Identities=22% Similarity=0.479 Sum_probs=13.1
Q ss_pred CCCccccccccceeccee
Q 029230 7 GTQQKCMACDKTVYLVDK 24 (197)
Q Consensus 7 ~~~~~C~~C~~~I~~~~~ 24 (197)
++...|..|++.|..++.
T Consensus 5 s~Ra~Ck~C~~~I~kg~l 22 (82)
T PF00645_consen 5 SGRAKCKGCKKKIAKGEL 22 (82)
T ss_dssp SSTEBETTTSCBE-TTSE
T ss_pred CCCccCcccCCcCCCCCE
Confidence 456789999999986554
No 45
>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=65.29 E-value=6.5 Score=23.07 Aligned_cols=32 Identities=22% Similarity=0.313 Sum_probs=20.6
Q ss_pred cccccccccccCCCeeecCCee-eccccHHHHhh
Q 029230 37 FRCHHCKGTLKLSNFNSFEGVL-YCRPHFDQLFK 69 (197)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~-yC~~c~~~~~~ 69 (197)
+.|..|...... ..+..=|.. +|..|+.+...
T Consensus 3 ~~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~ 35 (50)
T PF13920_consen 3 EECPICFENPRD-VVLLPCGHLCFCEECAERLLK 35 (50)
T ss_dssp SB-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHH
T ss_pred CCCccCCccCCc-eEEeCCCChHHHHHHhHHhcc
Confidence 356677666543 233345777 99999988864
No 46
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=65.06 E-value=3.8 Score=24.91 Aligned_cols=25 Identities=20% Similarity=0.417 Sum_probs=15.0
Q ss_pred CCCCCCCceeecCceeeecCccccc
Q 029230 108 DKCVGCDRTVYPTEKVSVNGAAYHR 132 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~v~~~g~~~H~ 132 (197)
.+|..|++||.++..|...+..-|+
T Consensus 2 ~~CvVCKqpi~~a~~v~T~~G~VH~ 26 (54)
T PF10886_consen 2 EICVVCKQPIDDALVVETESGPVHP 26 (54)
T ss_pred CeeeeeCCccCcceEEEcCCCccCc
Confidence 4677777777666545544445554
No 47
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=63.74 E-value=2.6 Score=38.96 Aligned_cols=51 Identities=16% Similarity=0.410 Sum_probs=36.9
Q ss_pred ccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCcccCCCCcccccCccccccccCCCCCCCCCCCc
Q 029230 36 CFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDR 115 (197)
Q Consensus 36 CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~ 115 (197)
=++|..|+....+ ....+=++++|..|-..++.++. .+|+.|+.
T Consensus 643 ~LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~etRq-----------------------------------RKCP~Cn~ 686 (698)
T KOG0978|consen 643 LLKCSVCNTRWKD-AVITKCGHVFCEECVQTRYETRQ-----------------------------------RKCPKCNA 686 (698)
T ss_pred ceeCCCccCchhh-HHHHhcchHHHHHHHHHHHHHhc-----------------------------------CCCCCCCC
Confidence 4689999855432 23345578899999988887544 78999999
Q ss_pred eeecCce
Q 029230 116 TVYPTEK 122 (197)
Q Consensus 116 ~I~~~e~ 122 (197)
+..+.+.
T Consensus 687 aFganDv 693 (698)
T KOG0978|consen 687 AFGANDV 693 (698)
T ss_pred CCCcccc
Confidence 8876653
No 48
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=63.02 E-value=5 Score=25.39 Aligned_cols=45 Identities=7% Similarity=0.092 Sum_probs=19.0
Q ss_pred ccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCCCCCCCchh
Q 029230 136 KCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLE 180 (197)
Q Consensus 136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~~~~~~~~~ 180 (197)
+|+.|...|..--....=+..||..|-...++..|..|+.+.-.+
T Consensus 9 rCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~q 53 (65)
T PF14835_consen 9 RCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQ 53 (65)
T ss_dssp S-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-S
T ss_pred CCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHH
Confidence 566666555432122233667888888888888888777665433
No 49
>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=62.99 E-value=5.2 Score=22.92 Aligned_cols=22 Identities=27% Similarity=0.685 Sum_probs=14.5
Q ss_pred ccccccccccCCCeeecCCeeecccc
Q 029230 38 RCHHCKGTLKLSNFNSFEGVLYCRPH 63 (197)
Q Consensus 38 ~C~~C~~~L~~~~f~~~~g~~yC~~c 63 (197)
.|..|+.+|-. .++|+.||..|
T Consensus 19 ~Cp~C~~PL~~----~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPLMR----DKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCeeEE----ecCCCEECCCC
Confidence 35667776642 46788888765
No 50
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=61.71 E-value=4.8 Score=29.21 Aligned_cols=22 Identities=27% Similarity=0.691 Sum_probs=17.6
Q ss_pred ccccccccccCCCeeecCCeeeccccH
Q 029230 38 RCHHCKGTLKLSNFNSFEGVLYCRPHF 64 (197)
Q Consensus 38 ~C~~C~~~L~~~~f~~~~g~~yC~~c~ 64 (197)
.|..|+.+| |- ++|.+||..|-
T Consensus 30 hCp~Cg~PL----F~-KdG~v~CPvC~ 51 (131)
T COG1645 30 HCPKCGTPL----FR-KDGEVFCPVCG 51 (131)
T ss_pred hCcccCCcc----ee-eCCeEECCCCC
Confidence 367888877 33 99999999885
No 51
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=61.25 E-value=5.3 Score=20.23 Aligned_cols=12 Identities=25% Similarity=0.628 Sum_probs=8.0
Q ss_pred CCCCCCCceeec
Q 029230 108 DKCVGCDRTVYP 119 (197)
Q Consensus 108 ~~C~~C~~~I~~ 119 (197)
..|+.|+..|..
T Consensus 3 ~~Cp~Cg~~~~~ 14 (26)
T PF13248_consen 3 MFCPNCGAEIDP 14 (26)
T ss_pred CCCcccCCcCCc
Confidence 468888876643
No 52
>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=60.93 E-value=6.9 Score=22.70 Aligned_cols=12 Identities=8% Similarity=-0.081 Sum_probs=7.9
Q ss_pred CeeecHHHHHhH
Q 029230 154 GKLYCKHHHIQL 165 (197)
Q Consensus 154 g~~yC~~cy~~~ 165 (197)
+--+|..||.+.
T Consensus 22 d~dLC~~Cf~~~ 33 (46)
T cd02249 22 DFDLCSSCYAKG 33 (46)
T ss_pred CCcCHHHHHCcC
Confidence 344688888754
No 53
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=56.71 E-value=4.2 Score=37.57 Aligned_cols=89 Identities=19% Similarity=0.430 Sum_probs=58.3
Q ss_pred CCCCCCCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCC
Q 029230 3 SPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTP 82 (197)
Q Consensus 3 ~~~~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~ 82 (197)
+.......+|..|-+.|. .-.++.||=-=-.|+.|+- .|...+..||=..-..
T Consensus 95 ~~I~pD~a~C~~Cl~Ei~-----dp~~rrY~YPF~~CT~CGP-----RfTIi~alPYDR~nTs----------------- 147 (750)
T COG0068 95 TQIPPDAATCEDCLEEIF-----DPNSRRYLYPFINCTNCGP-----RFTIIEALPYDRENTS----------------- 147 (750)
T ss_pred cccCCchhhhHHHHHHhc-----CCCCcceeccccccCCCCc-----ceeeeccCCCCcccCc-----------------
Confidence 345566778999977776 3455666666567888874 4555566665111100
Q ss_pred cccCCCCcccccCccccccccCCCCCCCCCCCceeecCceeeecCccccccccccCcCCCCC
Q 029230 83 KIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTI 144 (197)
Q Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l 144 (197)
...-+.|..|.+ |+-...++.||-.=..|..|+-.+
T Consensus 148 ---------------------M~~F~lC~~C~~-----EY~dP~nRRfHAQp~aCp~CGP~~ 183 (750)
T COG0068 148 ---------------------MADFPLCPFCDK-----EYKDPLNRRFHAQPIACPKCGPHL 183 (750)
T ss_pred ---------------------cccCcCCHHHHH-----HhcCccccccccccccCcccCCCe
Confidence 000178999975 334678999999999999999765
No 54
>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=56.33 E-value=10 Score=21.73 Aligned_cols=9 Identities=11% Similarity=0.301 Sum_probs=6.4
Q ss_pred eecHHHHHh
Q 029230 156 LYCKHHHIQ 164 (197)
Q Consensus 156 ~yC~~cy~~ 164 (197)
-+|..||.+
T Consensus 28 dlC~~Cf~~ 36 (44)
T smart00291 28 DLCQSCFAK 36 (44)
T ss_pred cchHHHHhC
Confidence 358888875
No 55
>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=55.66 E-value=3.9 Score=26.32 Aligned_cols=32 Identities=25% Similarity=0.439 Sum_probs=13.5
Q ss_pred CCCCCCCceeecCceeeecCccccccccccCcCCCCCCC
Q 029230 108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISP 146 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~ 146 (197)
..|+.|++++. .+.|-|.. =|-|..|+-.++.
T Consensus 31 a~CPdC~~~Le---~LkACGAv----dYFC~~c~gLiSK 62 (70)
T PF07191_consen 31 AFCPDCGQPLE---VLKACGAV----DYFCNHCHGLISK 62 (70)
T ss_dssp EE-TTT-SB-E---EEEETTEE----EEE-TTTT-EE-T
T ss_pred ccCCCcccHHH---HHHHhccc----ceeeccCCceeec
Confidence 46777777763 45555531 0235566554443
No 56
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=55.13 E-value=6.3 Score=26.13 Aligned_cols=28 Identities=18% Similarity=0.374 Sum_probs=17.8
Q ss_pred cCcCCCCCCCCCee--eeC---CeeecHHHHHh
Q 029230 137 CSHGGCTISPSNYI--AHE---GKLYCKHHHIQ 164 (197)
Q Consensus 137 C~~C~~~l~~~~~~--~~d---g~~yC~~cy~~ 164 (197)
|..||.||.....+ ..| +.-||.-||..
T Consensus 3 CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 3 CQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred CCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 77788887764422 223 46688888864
No 57
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=54.87 E-value=6.2 Score=36.05 Aligned_cols=22 Identities=18% Similarity=0.466 Sum_probs=17.8
Q ss_pred ecCccccccccccCcCCCCCCC
Q 029230 125 VNGAAYHRSCFKCSHGGCTISP 146 (197)
Q Consensus 125 ~~g~~~H~~CF~C~~C~~~l~~ 146 (197)
..|..+.++||+|..|+.+|.+
T Consensus 106 ~sg~~~ckk~~~c~qc~~~lpg 127 (694)
T KOG4443|consen 106 PSGPWLCKKCTRCRQCDSTLPG 127 (694)
T ss_pred cCcccccHHHHhhhhccccccc
Confidence 4567778889999999988876
No 58
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.48 E-value=17 Score=28.90 Aligned_cols=40 Identities=25% Similarity=0.508 Sum_probs=27.8
Q ss_pred CccccccccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230 29 NRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK 69 (197)
Q Consensus 29 g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~ 69 (197)
+..---..|-|..|-. +.....+..=|++||-.|..+-..
T Consensus 40 ~~~~~~~~FdCNICLd-~akdPVvTlCGHLFCWpClyqWl~ 79 (230)
T KOG0823|consen 40 GRNRDGGFFDCNICLD-LAKDPVVTLCGHLFCWPCLYQWLQ 79 (230)
T ss_pred CccCCCCceeeeeecc-ccCCCEEeecccceehHHHHHHHh
Confidence 3334556788888843 333466777899999999877654
No 59
>PRK00807 50S ribosomal protein L24e; Validated
Probab=53.01 E-value=12 Score=22.57 Aligned_cols=25 Identities=20% Similarity=0.401 Sum_probs=16.3
Q ss_pred CCCCCCCceeecCce---eeecCccccc
Q 029230 108 DKCVGCDRTVYPTEK---VSVNGAAYHR 132 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~---v~~~g~~~H~ 132 (197)
..|..|+..|+++.. |...|+.|.-
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~F 29 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILYF 29 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEEE
Confidence 468888888886653 3455666653
No 60
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=51.35 E-value=18 Score=28.12 Aligned_cols=33 Identities=21% Similarity=0.525 Sum_probs=24.0
Q ss_pred cccccccccccccCCCeeecCCeeeccccHHHHh
Q 029230 35 ACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLF 68 (197)
Q Consensus 35 ~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~ 68 (197)
.-|.|..|...+.+ .....=|+.||..|..+..
T Consensus 17 ~~~~CpICld~~~d-PVvT~CGH~FC~~CI~~wl 49 (193)
T PLN03208 17 GDFDCNICLDQVRD-PVVTLCGHLFCWPCIHKWT 49 (193)
T ss_pred CccCCccCCCcCCC-cEEcCCCchhHHHHHHHHH
Confidence 35888999887754 3445678999999987643
No 61
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=49.45 E-value=14 Score=30.87 Aligned_cols=32 Identities=22% Similarity=0.381 Sum_probs=26.7
Q ss_pred cccccccccccCCCeeecCCeeeccccHHHHh
Q 029230 37 FRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLF 68 (197)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~ 68 (197)
+-|-.|...|....|.=.+|.+.|..|-.++.
T Consensus 49 leCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~ 80 (299)
T KOG3002|consen 49 LDCPVCFNPLSPPIFQCDNGHLACSSCRTKVS 80 (299)
T ss_pred ccCchhhccCcccceecCCCcEehhhhhhhhc
Confidence 66888888998888888899999999986554
No 62
>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=49.22 E-value=14 Score=18.52 Aligned_cols=12 Identities=42% Similarity=1.115 Sum_probs=7.4
Q ss_pred CCCCCceeecCc
Q 029230 110 CVGCDRTVYPTE 121 (197)
Q Consensus 110 C~~C~~~I~~~e 121 (197)
|..|+..|.+.+
T Consensus 1 C~sC~~~i~~r~ 12 (24)
T PF07754_consen 1 CTSCGRPIAPRE 12 (24)
T ss_pred CccCCCcccCcc
Confidence 556777776554
No 63
>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=48.88 E-value=22 Score=19.52 Aligned_cols=31 Identities=16% Similarity=0.334 Sum_probs=21.5
Q ss_pred cccccccccCCCeeecCCeeeccccHHHHhh
Q 029230 39 CHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK 69 (197)
Q Consensus 39 C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~ 69 (197)
|..|...+........=|..||..|..+.+.
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~ 31 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLE 31 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHHHHHHHHH
T ss_pred CCcCCccccCCCEEecCCCcchHHHHHHHHH
Confidence 4566666665443445578899999988775
No 64
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=43.76 E-value=53 Score=18.55 Aligned_cols=30 Identities=27% Similarity=0.376 Sum_probs=17.6
Q ss_pred ccCcCCCCCCCC-CeeeeC-CeeecHHHHHhH
Q 029230 136 KCSHGGCTISPS-NYIAHE-GKLYCKHHHIQL 165 (197)
Q Consensus 136 ~C~~C~~~l~~~-~~~~~d-g~~yC~~cy~~~ 165 (197)
+|+.|+++.... ..+.-. +...|..|-...
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~~ 34 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQA 34 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHHH
Confidence 588888887653 333333 788898887654
No 65
>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=42.95 E-value=20 Score=20.10 Aligned_cols=30 Identities=20% Similarity=0.496 Sum_probs=15.0
Q ss_pred CCCCCCCceeecCceeeecCccccccccccCcCCC
Q 029230 108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGC 142 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~ 142 (197)
.+|..|+--|-+--.+...++.| +|..|+.
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 68999987776544455555564 6777765
No 66
>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=42.47 E-value=24 Score=20.42 Aligned_cols=9 Identities=11% Similarity=0.276 Sum_probs=7.2
Q ss_pred eecHHHHHh
Q 029230 156 LYCKHHHIQ 164 (197)
Q Consensus 156 ~yC~~cy~~ 164 (197)
=+|..||.+
T Consensus 29 dLC~~C~~~ 37 (46)
T PF00569_consen 29 DLCEDCFSK 37 (46)
T ss_dssp EEEHHHHHH
T ss_pred chhhHHHhC
Confidence 469999987
No 67
>PRK00420 hypothetical protein; Validated
Probab=42.14 E-value=15 Score=25.91 Aligned_cols=25 Identities=28% Similarity=0.487 Sum_probs=16.7
Q ss_pred cccccccccccCCCeeecCCeeeccccHH
Q 029230 37 FRCHHCKGTLKLSNFNSFEGVLYCRPHFD 65 (197)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~~ 65 (197)
-.|..|+.+| |-.++|..||..|-.
T Consensus 24 ~~CP~Cg~pL----f~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPL----FELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcc----eecCCCceECCCCCC
Confidence 3567787666 223788888887753
No 68
>PF12773 DZR: Double zinc ribbon
Probab=41.75 E-value=12 Score=21.87 Aligned_cols=11 Identities=18% Similarity=0.476 Sum_probs=6.8
Q ss_pred CCCCCCCceee
Q 029230 108 DKCVGCDRTVY 118 (197)
Q Consensus 108 ~~C~~C~~~I~ 118 (197)
..|..|+.++.
T Consensus 13 ~fC~~CG~~l~ 23 (50)
T PF12773_consen 13 KFCPHCGTPLP 23 (50)
T ss_pred cCChhhcCChh
Confidence 56666666654
No 69
>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=41.45 E-value=12 Score=21.64 Aligned_cols=23 Identities=30% Similarity=0.757 Sum_probs=13.8
Q ss_pred cCcCCCCCCCCCeeeeCCeeec-HHHHH
Q 029230 137 CSHGGCTISPSNYIAHEGKLYC-KHHHI 163 (197)
Q Consensus 137 C~~C~~~l~~~~~~~~dg~~yC-~~cy~ 163 (197)
|..|.+.+.. ..++.+|| +.|-.
T Consensus 9 C~~Cdk~~~~----~~~~~lYCSe~Cr~ 32 (43)
T PF12855_consen 9 CIVCDKQIDP----PDDGSLYCSEECRL 32 (43)
T ss_pred HHHhhccccC----CCCCccccCHHHHh
Confidence 3444566644 45788898 56643
No 70
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=40.72 E-value=22 Score=22.04 Aligned_cols=27 Identities=33% Similarity=0.673 Sum_probs=20.1
Q ss_pred CCCCCCCceeecCceeeecCccccccccccCcCCCC
Q 029230 108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCT 143 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~ 143 (197)
+.|..|+..|.+.+.- -=|.|..|+..
T Consensus 8 ~~CtSCg~~i~~~~~~---------~~F~CPnCG~~ 34 (59)
T PRK14890 8 PKCTSCGIEIAPREKA---------VKFLCPNCGEV 34 (59)
T ss_pred ccccCCCCcccCCCcc---------CEeeCCCCCCe
Confidence 7899999999876621 23778888876
No 71
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.62 E-value=14 Score=30.52 Aligned_cols=33 Identities=15% Similarity=0.354 Sum_probs=23.2
Q ss_pred ccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230 36 CFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK 69 (197)
Q Consensus 36 CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~ 69 (197)
=|.|..|.+.+.. ..+..-+..+|+.|....+.
T Consensus 241 Pf~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~q 273 (313)
T KOG1813|consen 241 PFKCFICRKYFYR-PVVTKCGHYFCEVCALKPYQ 273 (313)
T ss_pred Ccccccccccccc-chhhcCCceeehhhhccccc
Confidence 3677888877763 44556788899999866553
No 72
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.42 E-value=18 Score=29.79 Aligned_cols=30 Identities=23% Similarity=0.496 Sum_probs=15.5
Q ss_pred cccccccceecceeEEeCCccccccccccc
Q 029230 11 KCMACDKTVYLVDKLTADNRVYHKACFRCH 40 (197)
Q Consensus 11 ~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~ 40 (197)
.|..|++.+.+.-.|..-.-.-|.-||-|+
T Consensus 270 cCTLC~ERLEDTHFVQCPSVp~HKFCFPCS 299 (352)
T KOG3579|consen 270 CCTLCHERLEDTHFVQCPSVPSHKFCFPCS 299 (352)
T ss_pred eehhhhhhhccCceeecCCCcccceecccC
Confidence 455555555544444444444555555554
No 73
>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=39.86 E-value=26 Score=20.41 Aligned_cols=30 Identities=13% Similarity=0.120 Sum_probs=17.2
Q ss_pred ccCcCCCCCCCCCeeee--CCeeecHHHHHhH
Q 029230 136 KCSHGGCTISPSNYIAH--EGKLYCKHHHIQL 165 (197)
Q Consensus 136 ~C~~C~~~l~~~~~~~~--dg~~yC~~cy~~~ 165 (197)
.|..|+..++.-.|... .+.-+|..||.+-
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~G 33 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQEG 33 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhCc
Confidence 45566666554233221 2467899999864
No 74
>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=39.23 E-value=30 Score=28.96 Aligned_cols=15 Identities=33% Similarity=0.530 Sum_probs=11.8
Q ss_pred CCeeeccccHHHHhh
Q 029230 55 EGVLYCRPHFDQLFK 69 (197)
Q Consensus 55 ~g~~yC~~c~~~~~~ 69 (197)
=|+.+|..|..++|.
T Consensus 26 CGH~~C~sCv~~l~~ 40 (309)
T TIGR00570 26 CGHTLCESCVDLLFV 40 (309)
T ss_pred CCCcccHHHHHHHhc
Confidence 367889999888874
No 75
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=38.77 E-value=18 Score=33.45 Aligned_cols=10 Identities=20% Similarity=0.710 Sum_probs=5.1
Q ss_pred CCCCCCCcee
Q 029230 108 DKCVGCDRTV 117 (197)
Q Consensus 108 ~~C~~C~~~I 117 (197)
..|..|+.++
T Consensus 42 ~fC~~CG~~~ 51 (645)
T PRK14559 42 AHCPNCGAET 51 (645)
T ss_pred ccccccCCcc
Confidence 3455555544
No 76
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=38.68 E-value=11 Score=21.61 Aligned_cols=26 Identities=27% Similarity=0.623 Sum_probs=10.2
Q ss_pred CCCCCceeecCceee--ecCcccccccc
Q 029230 110 CVGCDRTVYPTEKVS--VNGAAYHRSCF 135 (197)
Q Consensus 110 C~~C~~~I~~~e~v~--~~g~~~H~~CF 135 (197)
|..|++.|+-+.+=. .=+..||..|+
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~ 28 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCF 28 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHH
T ss_pred CcccchhHeeeccCCCCccCchHHHHHH
Confidence 556777666554211 22345777776
No 77
>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=37.98 E-value=12 Score=20.57 Aligned_cols=32 Identities=28% Similarity=0.607 Sum_probs=17.6
Q ss_pred ccccccccceeccee-EEeCCccccccccccccccccc
Q 029230 10 QKCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTL 46 (197)
Q Consensus 10 ~~C~~C~~~I~~~~~-~~~~g~~~H~~CF~C~~C~~~L 46 (197)
-.|..|+..+...+. +...+. -++|..|+..|
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~-----~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGG-----KVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCC-----EEECCCCCCEE
Confidence 357778776653322 222221 36777777665
No 78
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=37.26 E-value=12 Score=29.16 Aligned_cols=34 Identities=18% Similarity=0.279 Sum_probs=23.2
Q ss_pred cccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230 35 ACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK 69 (197)
Q Consensus 35 ~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~ 69 (197)
.=|.|..|.+.... ..+..=|..+|..|+.+.+.
T Consensus 195 IPF~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~ 228 (259)
T COG5152 195 IPFLCGICKKDYES-PVVTECGHSFCSLCAIRKYQ 228 (259)
T ss_pred Cceeehhchhhccc-hhhhhcchhHHHHHHHHHhc
Confidence 34788888776653 34445678888888877664
No 79
>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=37.07 E-value=19 Score=20.94 Aligned_cols=47 Identities=17% Similarity=0.360 Sum_probs=23.7
Q ss_pred CCCCCceeecCceee--ecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHH
Q 029230 110 CVGCDRTVYPTEKVS--VNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHI 163 (197)
Q Consensus 110 C~~C~~~I~~~e~v~--~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~ 163 (197)
|..|++.-..++.|. .=++.||..|.. +.........+.-+|..|-.
T Consensus 2 C~vC~~~~~~~~~i~C~~C~~~~H~~C~~-------~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 2 CPVCGQSDDDGDMIQCDSCNRWYHQECVG-------PPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp BTTTTSSCTTSSEEEBSTTSCEEETTTST-------SSHSHHSHHSSSBSSHHHHH
T ss_pred CcCCCCcCCCCCeEEcCCCChhhCcccCC-------CChhhccCCCCcEECcCCcC
Confidence 566766333334343 334678887752 22222222333677777643
No 80
>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=37.01 E-value=32 Score=19.66 Aligned_cols=10 Identities=30% Similarity=0.886 Sum_probs=6.4
Q ss_pred CCCCCCceee
Q 029230 109 KCVGCDRTVY 118 (197)
Q Consensus 109 ~C~~C~~~I~ 118 (197)
.|.+|+++|.
T Consensus 2 ~Cd~C~~~i~ 11 (43)
T cd02340 2 ICDGCQGPIV 11 (43)
T ss_pred CCCCCCCcCc
Confidence 4677776654
No 81
>PRK04023 DNA polymerase II large subunit; Validated
Probab=36.66 E-value=29 Score=33.71 Aligned_cols=14 Identities=36% Similarity=0.781 Sum_probs=8.1
Q ss_pred CCCCCCCceeecCc
Q 029230 108 DKCVGCDRTVYPTE 121 (197)
Q Consensus 108 ~~C~~C~~~I~~~e 121 (197)
..|..|+..+.+..
T Consensus 664 y~CPKCG~El~~~s 677 (1121)
T PRK04023 664 DECEKCGREPTPYS 677 (1121)
T ss_pred CcCCCCCCCCCccc
Confidence 45666666665444
No 82
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=36.60 E-value=9.4 Score=26.27 Aligned_cols=29 Identities=21% Similarity=0.301 Sum_probs=18.8
Q ss_pred cccccCcCCCCCCCCC-eeeeCCeeecHHH
Q 029230 133 SCFKCSHGGCTISPSN-YIAHEGKLYCKHH 161 (197)
Q Consensus 133 ~CF~C~~C~~~l~~~~-~~~~dg~~yC~~c 161 (197)
+=|+|..|-..-.-+. -...+|.+||..|
T Consensus 69 DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 69 DEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CceeeeeeeeEechhhhccccCCCEecccc
Confidence 3478888865433222 2356899999887
No 83
>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=36.37 E-value=75 Score=19.51 Aligned_cols=41 Identities=15% Similarity=0.216 Sum_probs=24.4
Q ss_pred cCcCCCCCCCC---CeeeeCCeeecHHHHHhHhcCCCCCCCCCC
Q 029230 137 CSHGGCTISPS---NYIAHEGKLYCKHHHIQLFREKGNYSQLES 177 (197)
Q Consensus 137 C~~C~~~l~~~---~~~~~dg~~yC~~cy~~~~~~k~~~~~~~~ 177 (197)
|..|++.|..+ .++-.-.=-||..|...++...|-.|.+..
T Consensus 8 CE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCgGel 51 (57)
T PF06906_consen 8 CECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCGGEL 51 (57)
T ss_pred ccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCCCcc
Confidence 44455555432 233333445788888888877777776644
No 84
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=35.42 E-value=17 Score=24.62 Aligned_cols=37 Identities=19% Similarity=0.370 Sum_probs=25.3
Q ss_pred CCCCCCCceeecCceeeecCccccccccccCcCCCCCCC
Q 029230 108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISP 146 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~ 146 (197)
..|..|++++..-|.|=..+-.+.+ -+|..|+.+|+.
T Consensus 34 S~C~~C~~~L~~~~lIPi~S~l~lr--GrCr~C~~~I~~ 70 (92)
T PF06750_consen 34 SHCPHCGHPLSWWDLIPILSYLLLR--GRCRYCGAPIPP 70 (92)
T ss_pred CcCcCCCCcCcccccchHHHHHHhC--CCCcccCCCCCh
Confidence 7899999999877754333322222 468888888875
No 85
>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=34.77 E-value=36 Score=20.09 Aligned_cols=10 Identities=10% Similarity=0.212 Sum_probs=7.3
Q ss_pred eecHHHHHhH
Q 029230 156 LYCKHHHIQL 165 (197)
Q Consensus 156 ~yC~~cy~~~ 165 (197)
=+|..||...
T Consensus 27 DlC~~C~~~~ 36 (48)
T cd02341 27 DLCQDCVVKG 36 (48)
T ss_pred ccCHHHHhCc
Confidence 4688888764
No 86
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=34.22 E-value=31 Score=19.42 Aligned_cols=43 Identities=16% Similarity=0.171 Sum_probs=20.8
Q ss_pred CCCCCceeecCceeeecCccccccccccCcCCCCCC-CCCeeeeCCeeecHHHHHhH
Q 029230 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTIS-PSNYIAHEGKLYCKHHHIQL 165 (197)
Q Consensus 110 C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~-~~~~~~~dg~~yC~~cy~~~ 165 (197)
|..|++++... ..|+.++.. ++. ++.....+-.+.|..|..++
T Consensus 1 C~~C~~~~~~~-------~~~~v~Hi~------~~~~gg~~~~~Nl~~lC~~Ch~~k 44 (47)
T PF01844_consen 1 CQYCGKPGSDN-------ESLHVHHII------PRSKGGKNDLENLILLCPSCHRKK 44 (47)
T ss_dssp -TTT--B--GG--------GEEEEESS-------TTTT---STTTEEEEEHHHHHHH
T ss_pred CCCCCCcCccC-------cceEeECcC------chhcCCCCCHHHHHHHhHHHHHHh
Confidence 67788877543 233333332 222 44566777899999998765
No 87
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=34.01 E-value=23 Score=21.35 Aligned_cols=34 Identities=18% Similarity=0.508 Sum_probs=23.2
Q ss_pred cccccccceecceeEEeCCcccccccccccccccccc
Q 029230 11 KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLK 47 (197)
Q Consensus 11 ~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~ 47 (197)
.|..|+..|...--....++.|=..|-.| -+++.
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vC---C~PI~ 35 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVC---CRPIE 35 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhc---CCccE
Confidence 58899999874333566677888888655 45553
No 88
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=33.62 E-value=31 Score=25.32 Aligned_cols=37 Identities=19% Similarity=0.386 Sum_probs=24.1
Q ss_pred CCCCCCCceeecCceeee------cCccccccccccCcCCCCC
Q 029230 108 DKCVGCDRTVYPTEKVSV------NGAAYHRSCFKCSHGGCTI 144 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~v~~------~g~~~H~~CF~C~~C~~~l 144 (197)
.+|..|+.++...+.-.+ .-...+..-+.|..|++..
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 799999998865532111 1123455677899999864
No 89
>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=32.50 E-value=12 Score=20.53 Aligned_cols=31 Identities=26% Similarity=0.645 Sum_probs=18.6
Q ss_pred ccccccceecceeEEeCCcccccccccccccccccc
Q 029230 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLK 47 (197)
Q Consensus 12 C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~ 47 (197)
|..|.+.+. ...++.||-.=..|..||-.+.
T Consensus 2 C~~C~~Ey~-----~p~~RR~~~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 2 CDDCLKEYF-----DPSNRRFHYQFISCTNCGPRYS 32 (35)
T ss_dssp -HHHHHHHC-----STTSTTTT-TT--BTTCC-SCC
T ss_pred CHHHHHHHc-----CCCCCcccCcCccCCCCCCCEE
Confidence 555655443 4568899999999999987664
No 90
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=32.11 E-value=20 Score=27.99 Aligned_cols=42 Identities=12% Similarity=0.225 Sum_probs=27.7
Q ss_pred ccccCcCCCCCCCCCeeeeCCeeecHHHHHhHh--cCCCCCCCCC
Q 029230 134 CFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLF--REKGNYSQLE 176 (197)
Q Consensus 134 CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~--~~k~~~~~~~ 176 (197)
=|.|..|.+.... ...-.=|.-+|..|+.+.+ ++.|..|+..
T Consensus 196 PF~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~ 239 (259)
T COG5152 196 PFLCGICKKDYES-PVVTECGHSFCSLCAIRKYQKGDECGVCGKA 239 (259)
T ss_pred ceeehhchhhccc-hhhhhcchhHHHHHHHHHhccCCcceecchh
Confidence 3677777776544 3333457788888888776 5677766543
No 91
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=31.96 E-value=30 Score=19.88 Aligned_cols=29 Identities=31% Similarity=0.479 Sum_probs=17.4
Q ss_pred CCCCCCCceeecCceeeecCccccccccccCcCCCCCC
Q 029230 108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTIS 145 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~ 145 (197)
.+|..|+..+...+... =++|..|+.++.
T Consensus 4 y~C~~CG~~~~~~~~~~---------~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELDEYGT---------GVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEEECCCCC---------ceECCCCCCeEE
Confidence 46888887765332111 367788876553
No 92
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=31.93 E-value=20 Score=25.33 Aligned_cols=24 Identities=25% Similarity=0.537 Sum_probs=16.3
Q ss_pred CCCCCceeecCceeeecCccccccccccCcCCCCCCC
Q 029230 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISP 146 (197)
Q Consensus 110 C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~ 146 (197)
|+.|+..+.. .-++|..|+..+.|
T Consensus 1 CPvCg~~l~v-------------t~l~C~~C~t~i~G 24 (113)
T PF09862_consen 1 CPVCGGELVV-------------TRLKCPSCGTEIEG 24 (113)
T ss_pred CCCCCCceEE-------------EEEEcCCCCCEEEe
Confidence 6777766542 23578888888776
No 93
>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=31.83 E-value=54 Score=17.87 Aligned_cols=27 Identities=26% Similarity=0.463 Sum_probs=14.3
Q ss_pred cCcCCCCCCCCCeeeeCCee-ecHHHHH
Q 029230 137 CSHGGCTISPSNYIAHEGKL-YCKHHHI 163 (197)
Q Consensus 137 C~~C~~~l~~~~~~~~dg~~-yC~~cy~ 163 (197)
|..|+..-+..-....+|.. +|..|..
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~ 28 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGL 28 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHH
Confidence 56677655443333446777 9999964
No 94
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=31.72 E-value=23 Score=28.39 Aligned_cols=42 Identities=19% Similarity=0.464 Sum_probs=0.0
Q ss_pred cccccccccCCCeeecC-CeeeccccHHHHhhccCCcccccCCCCcccCCCCcccccCccccccccCCCCCCCCCCCcee
Q 029230 39 CHHCKGTLKLSNFNSFE-GVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTV 117 (197)
Q Consensus 39 C~~C~~~L~~~~f~~~~-g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I 117 (197)
|-.|+..-....|+... .+++|+.|...-.+ +.|.-|+++|
T Consensus 6 Cn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~--------------------------------------~~C~lCkk~i 47 (233)
T KOG4739|consen 6 CNKCFRFPSQDPFFLTACRHVFCEPCLKASSP--------------------------------------DVCPLCKKSI 47 (233)
T ss_pred eccccccCCCCceeeeechhhhhhhhcccCCc--------------------------------------ccccccccee
Q ss_pred e
Q 029230 118 Y 118 (197)
Q Consensus 118 ~ 118 (197)
.
T Consensus 48 r 48 (233)
T KOG4739|consen 48 R 48 (233)
T ss_pred e
No 95
>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=31.70 E-value=47 Score=19.22 Aligned_cols=9 Identities=11% Similarity=0.139 Sum_probs=6.0
Q ss_pred eecHHHHHh
Q 029230 156 LYCKHHHIQ 164 (197)
Q Consensus 156 ~yC~~cy~~ 164 (197)
=+|..||.+
T Consensus 25 DLC~~C~~~ 33 (43)
T cd02342 25 DLCTICFSR 33 (43)
T ss_pred ccHHHHhhh
Confidence 357777765
No 96
>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=31.61 E-value=19 Score=16.95 Aligned_cols=12 Identities=17% Similarity=0.744 Sum_probs=8.6
Q ss_pred cccccccccccC
Q 029230 37 FRCHHCKGTLKL 48 (197)
Q Consensus 37 F~C~~C~~~L~~ 48 (197)
|+|..|++.+..
T Consensus 1 y~C~~C~~~f~~ 12 (23)
T PF00096_consen 1 YKCPICGKSFSS 12 (23)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCccCC
Confidence 568888877654
No 97
>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=31.56 E-value=18 Score=19.95 Aligned_cols=10 Identities=40% Similarity=1.185 Sum_probs=4.8
Q ss_pred cccccccccc
Q 029230 37 FRCHHCKGTL 46 (197)
Q Consensus 37 F~C~~C~~~L 46 (197)
|+|..|+..+
T Consensus 6 y~C~~Cg~~f 15 (41)
T smart00834 6 YRCEDCGHTF 15 (41)
T ss_pred EEcCCCCCEE
Confidence 3455555444
No 98
>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=31.21 E-value=18 Score=18.73 Aligned_cols=11 Identities=27% Similarity=0.598 Sum_probs=6.3
Q ss_pred CCCCCCCceee
Q 029230 108 DKCVGCDRTVY 118 (197)
Q Consensus 108 ~~C~~C~~~I~ 118 (197)
.+|.+|...|.
T Consensus 2 ~~C~rC~~~~~ 12 (30)
T PF06827_consen 2 EKCPRCWNYIE 12 (30)
T ss_dssp SB-TTT--BBE
T ss_pred CcCccCCCcce
Confidence 57999998875
No 99
>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=31.15 E-value=19 Score=21.20 Aligned_cols=28 Identities=18% Similarity=0.337 Sum_probs=13.0
Q ss_pred cccccccccccCCCeeecCCeeeccccH
Q 029230 37 FRCHHCKGTLKLSNFNSFEGVLYCRPHF 64 (197)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~ 64 (197)
|+|..|+..+....-...+..+-|..|-
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg 33 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSDDPLATCPECG 33 (52)
T ss_pred EEeCCCCCEeEEEEecCCCCCCCCCCCC
Confidence 5666676655432111113344565553
No 100
>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=31.11 E-value=18 Score=20.52 Aligned_cols=28 Identities=18% Similarity=0.365 Sum_probs=13.2
Q ss_pred cccccccccccCCCeeecCCeeeccccH
Q 029230 37 FRCHHCKGTLKLSNFNSFEGVLYCRPHF 64 (197)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~ 64 (197)
|+|..|+..+....-...+..+-|..|-
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg 33 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECG 33 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCC
Confidence 5666666555432111113455555553
No 101
>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=30.75 E-value=29 Score=19.01 Aligned_cols=11 Identities=36% Similarity=0.797 Sum_probs=4.3
Q ss_pred cccccccccee
Q 029230 10 QKCMACDKTVY 20 (197)
Q Consensus 10 ~~C~~C~~~I~ 20 (197)
+.|..|++++.
T Consensus 4 ~~C~eC~~~f~ 14 (34)
T PF01286_consen 4 PKCDECGKPFM 14 (34)
T ss_dssp EE-TTT--EES
T ss_pred chHhHhCCHHH
Confidence 45555655554
No 102
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=30.32 E-value=41 Score=19.66 Aligned_cols=11 Identities=18% Similarity=0.682 Sum_probs=8.6
Q ss_pred CCCCCCCceee
Q 029230 108 DKCVGCDRTVY 118 (197)
Q Consensus 108 ~~C~~C~~~I~ 118 (197)
..|..|++.|.
T Consensus 12 ~~C~~C~~~i~ 22 (53)
T PF00130_consen 12 TYCDVCGKFIW 22 (53)
T ss_dssp EB-TTSSSBEC
T ss_pred CCCcccCcccC
Confidence 68999999993
No 103
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=30.00 E-value=6.3 Score=26.95 Aligned_cols=32 Identities=16% Similarity=0.466 Sum_probs=16.3
Q ss_pred CccccccccccccccccccCCCeeecCCeeec
Q 029230 29 NRVYHKACFRCHHCKGTLKLSNFNSFEGVLYC 60 (197)
Q Consensus 29 g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC 60 (197)
-..+++.+..|-.|.+.|.-..|...+.-+||
T Consensus 55 ~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C 86 (105)
T COG4357 55 LQEFNPKAIICGVCRKLLTRAEYGMCGSCPYC 86 (105)
T ss_pred hhhcCCccEEhhhhhhhhhHHHHhhcCCCCCc
Confidence 34455666666666666554444443333333
No 104
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.72 E-value=39 Score=24.39 Aligned_cols=37 Identities=22% Similarity=0.447 Sum_probs=26.9
Q ss_pred CCCCCCCceeecCce---eeecCccccccccccCcCCCCCC
Q 029230 108 DKCVGCDRTVYPTEK---VSVNGAAYHRSCFKCSHGGCTIS 145 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~---v~~~g~~~H~~CF~C~~C~~~l~ 145 (197)
..|+.|+.+|..... |..+|..|-+-=| |..|++.+.
T Consensus 40 ~qcp~csasirgd~~vegvlglg~dye~psf-chncgs~fp 79 (160)
T COG4306 40 TQCPICSASIRGDYYVEGVLGLGGDYEPPSF-CHNCGSRFP 79 (160)
T ss_pred hcCCccCCcccccceeeeeeccCCCCCCcch-hhcCCCCCC
Confidence 569999999986544 4466777777655 788888765
No 105
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=29.39 E-value=19 Score=20.81 Aligned_cols=11 Identities=27% Similarity=0.419 Sum_probs=6.1
Q ss_pred CCCCCCCceee
Q 029230 108 DKCVGCDRTVY 118 (197)
Q Consensus 108 ~~C~~C~~~I~ 118 (197)
-+|..|+..+.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 35666665543
No 106
>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=29.27 E-value=17 Score=20.51 Aligned_cols=13 Identities=8% Similarity=0.327 Sum_probs=6.5
Q ss_pred CeeecHHHHHhHh
Q 029230 154 GKLYCKHHHIQLF 166 (197)
Q Consensus 154 g~~yC~~cy~~~~ 166 (197)
|..||..|..+.+
T Consensus 22 ~H~fh~~Ci~~~~ 34 (44)
T PF13639_consen 22 GHVFHRSCIKEWL 34 (44)
T ss_dssp SEEEEHHHHHHHH
T ss_pred CCeeCHHHHHHHH
Confidence 4555555544433
No 107
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=29.11 E-value=15 Score=27.53 Aligned_cols=29 Identities=17% Similarity=0.384 Sum_probs=21.7
Q ss_pred cccccccceecceeEEeCCcccccccccccccccccc
Q 029230 11 KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLK 47 (197)
Q Consensus 11 ~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~ 47 (197)
.|..|+..+...+.+. .=|+|..|+..|.
T Consensus 111 ~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 111 ICPNMCVRFTFNEAME--------LNFTCPRCGAMLD 139 (158)
T ss_pred ECCCCCcEeeHHHHHH--------cCCcCCCCCCEee
Confidence 5888887776555554 2499999999885
No 108
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=28.98 E-value=4.3 Score=27.73 Aligned_cols=51 Identities=12% Similarity=0.236 Sum_probs=33.4
Q ss_pred CCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecH
Q 029230 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCK 159 (197)
Q Consensus 109 ~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~ 159 (197)
.|..|+..+..-..+.+.-..++..+..|-+|.+.|+-..|.+...=|||.
T Consensus 37 aCy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~ 87 (105)
T COG4357 37 ACYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYCQ 87 (105)
T ss_pred hHHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCcC
Confidence 377777666544334455567788888888888888766666665555553
No 109
>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 COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=28.58 E-value=47 Score=21.05 Aligned_cols=31 Identities=23% Similarity=0.543 Sum_probs=20.4
Q ss_pred ccccccccccCCC---eeecCCeee--cc-ccHHHHhh
Q 029230 38 RCHHCKGTLKLSN---FNSFEGVLY--CR-PHFDQLFK 69 (197)
Q Consensus 38 ~C~~C~~~L~~~~---f~~~~g~~y--C~-~c~~~~~~ 69 (197)
+|+-|+..|.++. |+..||.++ |. .|.. +++
T Consensus 5 ~CsFcG~~I~PGtG~m~Vr~Dg~v~~FcssKc~k-~~~ 41 (66)
T COG2075 5 VCSFCGKKIEPGTGIMYVRNDGKVLRFCSSKCEK-LFK 41 (66)
T ss_pred EecCcCCccCCCceEEEEecCCeEEEEechhHHH-HHH
Confidence 5788888887663 666788764 64 4544 544
No 111
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=28.31 E-value=36 Score=21.04 Aligned_cols=28 Identities=18% Similarity=0.393 Sum_probs=18.5
Q ss_pred ccCcCCCCCCC--CCeeeeCCeeec-HHHHH
Q 029230 136 KCSHGGCTISP--SNYIAHEGKLYC-KHHHI 163 (197)
Q Consensus 136 ~C~~C~~~l~~--~~~~~~dg~~yC-~~cy~ 163 (197)
.|..|++.|.. ..|+..+.+.+| .+|-.
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS~ECR~ 48 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCSEECRS 48 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccccHHHHH
Confidence 36677788873 345667788888 45643
No 112
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=28.09 E-value=17 Score=26.71 Aligned_cols=35 Identities=20% Similarity=0.489 Sum_probs=23.6
Q ss_pred ccccccccceecceeEEeCCcccccccccccccccccc
Q 029230 10 QKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLK 47 (197)
Q Consensus 10 ~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~ 47 (197)
=.|..|+..+...+.+...+. ..=|+|..|+..|.
T Consensus 100 Y~Cp~C~~~y~~~ea~~~~d~---~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 100 YKCPNCQSKYTFLEANQLLDM---DGTFTCPRCGEELE 134 (147)
T ss_pred EECcCCCCEeeHHHHHHhcCC---CCcEECCCCCCEEE
Confidence 468889887765555444332 33399999998885
No 113
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=27.62 E-value=62 Score=24.14 Aligned_cols=30 Identities=23% Similarity=0.418 Sum_probs=21.9
Q ss_pred cCcCCCCCCCCCee-eeCC--eeecHHHHHhHhcC
Q 029230 137 CSHGGCTISPSNYI-AHEG--KLYCKHHHIQLFRE 168 (197)
Q Consensus 137 C~~C~~~l~~~~~~-~~dg--~~yC~~cy~~~~~~ 168 (197)
|..||+.+.+..+. ..+| .-.|..|+ +||.
T Consensus 3 CEiCG~~i~~~~~~v~iega~l~vC~~C~--k~G~ 35 (154)
T TIGR00270 3 CEICGRKIKGKGFKIVIEGSEMTVCGECR--KFGK 35 (154)
T ss_pred cccCCCccCCCCeEEEEcCeEEehhhhHH--hcCC
Confidence 88899999876453 4454 45699999 6765
No 114
>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=27.54 E-value=31 Score=30.78 Aligned_cols=38 Identities=24% Similarity=0.377 Sum_probs=22.9
Q ss_pred CCCCCCCceeecCceeeecCccccccccccCcCCCCCCC
Q 029230 108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISP 146 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~ 146 (197)
.-|+.|-..+...+ +...+..--++||.|..|..+|..
T Consensus 27 ~yCp~CL~~~p~~e-~~~~~nrC~r~Cf~CP~C~~~L~~ 64 (483)
T PF05502_consen 27 YYCPNCLFEVPSSE-ARSEKNRCSRNCFDCPICFSPLSV 64 (483)
T ss_pred eECccccccCChhh-heeccceeccccccCCCCCCccee
Confidence 45777766554443 333444444578888888877764
No 115
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=27.44 E-value=20 Score=27.47 Aligned_cols=30 Identities=23% Similarity=0.533 Sum_probs=21.8
Q ss_pred cccccccceecceeEEeCCccccccccccccccccccC
Q 029230 11 KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKL 48 (197)
Q Consensus 11 ~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~ 48 (197)
.|..|+..+...+.+. .=|+|..|+..|..
T Consensus 119 ~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 119 FCPNCHIRFTFDEAME--------YGFRCPQCGEMLEE 148 (178)
T ss_pred ECCCCCcEEeHHHHhh--------cCCcCCCCCCCCee
Confidence 5888887776555443 25999999999864
No 116
>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=27.35 E-value=35 Score=17.63 Aligned_cols=12 Identities=33% Similarity=0.714 Sum_probs=2.7
Q ss_pred cccCcCCCCCCC
Q 029230 135 FKCSHGGCTISP 146 (197)
Q Consensus 135 F~C~~C~~~l~~ 146 (197)
|+|..|++++.+
T Consensus 1 ~~C~~C~~~~~~ 12 (30)
T PF07649_consen 1 FRCDACGKPIDG 12 (30)
T ss_dssp ---TTTS----S
T ss_pred CcCCcCCCcCCC
Confidence 345555555544
No 117
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=27.22 E-value=36 Score=24.62 Aligned_cols=24 Identities=21% Similarity=0.376 Sum_probs=15.8
Q ss_pred CCCCCCCceeecCce---eeecCcccc
Q 029230 108 DKCVGCDRTVYPTEK---VSVNGAAYH 131 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~---v~~~g~~~H 131 (197)
.+|..|+.+|+|+.. |...|+.|+
T Consensus 5 e~CsFcG~kIyPG~G~~fVR~DGkvf~ 31 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMFVRKDGTVLH 31 (131)
T ss_pred eeecCcCCcccCCCCcEEEecCCCEEE
Confidence 579999999988853 334444443
No 118
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=26.86 E-value=47 Score=18.16 Aligned_cols=31 Identities=19% Similarity=0.477 Sum_probs=16.0
Q ss_pred CCCCCCCceeecCce-eeecCccccccccccCcCCCC
Q 029230 108 DKCVGCDRTVYPTEK-VSVNGAAYHRSCFKCSHGGCT 143 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~-v~~~g~~~H~~CF~C~~C~~~ 143 (197)
..|..|+......+. |...|.. ++|..|+..
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~-----v~C~~C~~~ 34 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRK-----VRCSKCGHV 34 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcE-----EECCCCCCE
Confidence 347777765543332 3343333 456666654
No 119
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=26.59 E-value=30 Score=21.43 Aligned_cols=15 Identities=33% Similarity=0.877 Sum_probs=12.5
Q ss_pred CCCCCCCceeecCce
Q 029230 108 DKCVGCDRTVYPTEK 122 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~ 122 (197)
..|..|+++|.++|.
T Consensus 9 ~HC~VCg~aIp~de~ 23 (64)
T COG4068 9 RHCVVCGKAIPPDEQ 23 (64)
T ss_pred ccccccCCcCCCccc
Confidence 579999999988774
No 120
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=26.47 E-value=46 Score=19.56 Aligned_cols=10 Identities=10% Similarity=-0.130 Sum_probs=6.9
Q ss_pred eecHHHHHhH
Q 029230 156 LYCKHHHIQL 165 (197)
Q Consensus 156 ~yC~~cy~~~ 165 (197)
-+|..||...
T Consensus 25 dlC~~Cf~~~ 34 (49)
T cd02338 25 DLCADCYDSG 34 (49)
T ss_pred ccchhHHhCC
Confidence 3588888754
No 121
>KOG3896 consensus Dynactin, subunit p62 [Cell motility]
Probab=26.37 E-value=25 Score=29.77 Aligned_cols=37 Identities=22% Similarity=0.379 Sum_probs=26.5
Q ss_pred CCCCCCCceeecCceeeecCccccccccccCcCCCCCCC
Q 029230 108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISP 146 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~ 146 (197)
..|+.|-+.+...| .-..+.-..+||-|..|...|+.
T Consensus 46 hfCp~CLEn~ps~E--ArlKKn~CAnCfDCP~C~htLSa 82 (449)
T KOG3896|consen 46 HFCPRCLENSPSPE--ARLKKNKCANCFDCPKCAHTLSA 82 (449)
T ss_pred ccchhhccCCCchH--HHhhhccccccccCcchhhhhhh
Confidence 67888888876554 23345566789999999888864
No 122
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=25.86 E-value=29 Score=28.67 Aligned_cols=48 Identities=27% Similarity=0.536 Sum_probs=33.9
Q ss_pred CCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHH
Q 029230 108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKH 160 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~ 160 (197)
-.|.-|++.+.+...|.--.-.-|+-||-|+. ..|. -....|.+||..
T Consensus 269 LcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSR--esIK---~Qg~sgevYCPS 316 (352)
T KOG3579|consen 269 LCCTLCHERLEDTHFVQCPSVPSHKFCFPCSR--ESIK---QQGASGEVYCPS 316 (352)
T ss_pred eeehhhhhhhccCceeecCCCcccceecccCH--HHHH---hhcCCCceeCCC
Confidence 47888999998888787777888999999974 1121 122346788853
No 123
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=25.71 E-value=52 Score=32.85 Aligned_cols=10 Identities=30% Similarity=0.644 Sum_probs=5.1
Q ss_pred CCCCCCceee
Q 029230 109 KCVGCDRTVY 118 (197)
Q Consensus 109 ~C~~C~~~I~ 118 (197)
.|..|+..+.
T Consensus 694 ~CPsCGaev~ 703 (1337)
T PRK14714 694 VCPDCGAEVP 703 (1337)
T ss_pred eCccCCCccC
Confidence 4555555443
No 124
>PRK12495 hypothetical protein; Provisional
Probab=25.55 E-value=38 Score=26.89 Aligned_cols=23 Identities=17% Similarity=0.541 Sum_probs=13.7
Q ss_pred cccccccccccCCCeeecCCeeeccccH
Q 029230 37 FRCHHCKGTLKLSNFNSFEGVLYCRPHF 64 (197)
Q Consensus 37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~ 64 (197)
+.|..|+.+|- ...|..+|..|-
T Consensus 43 ~hC~~CG~PIp-----a~pG~~~Cp~CQ 65 (226)
T PRK12495 43 AHCDECGDPIF-----RHDGQEFCPTCQ 65 (226)
T ss_pred hhcccccCccc-----CCCCeeECCCCC
Confidence 45666666664 236666666664
No 125
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=25.34 E-value=51 Score=27.14 Aligned_cols=26 Identities=23% Similarity=0.663 Sum_probs=16.2
Q ss_pred CCCCCCCCCceeecCceeeecC--ccccccc
Q 029230 106 TRDKCVGCDRTVYPTEKVSVNG--AAYHRSC 134 (197)
Q Consensus 106 ~~~~C~~C~~~I~~~e~v~~~g--~~~H~~C 134 (197)
....|.+|+.+|. .+...+ ..|.+.|
T Consensus 244 ~GepC~~CGt~I~---k~~~~gR~t~~CP~C 271 (273)
T COG0266 244 AGEPCRRCGTPIE---KIKLGGRSTFYCPVC 271 (273)
T ss_pred CCCCCCccCCEeE---EEEEcCCcCEeCCCC
Confidence 4478999999995 344444 4454443
No 126
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=25.25 E-value=39 Score=27.26 Aligned_cols=30 Identities=17% Similarity=0.506 Sum_probs=22.6
Q ss_pred cccccCcCCCCCCCCCeeeeCCeeecHHHH
Q 029230 133 SCFKCSHGGCTISPSNYIAHEGKLYCKHHH 162 (197)
Q Consensus 133 ~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy 162 (197)
+=-.|+.|+.+.+...|+...|...|..|+
T Consensus 153 ~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 153 NLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred chHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 334678888887776778888888888877
No 127
>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=25.23 E-value=28 Score=16.08 Aligned_cols=12 Identities=25% Similarity=0.631 Sum_probs=6.2
Q ss_pred cccCcCCCCCCC
Q 029230 135 FKCSHGGCTISP 146 (197)
Q Consensus 135 F~C~~C~~~l~~ 146 (197)
|.|..|+..+..
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 567777766543
No 128
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=25.23 E-value=45 Score=20.25 Aligned_cols=24 Identities=29% Similarity=0.736 Sum_probs=15.9
Q ss_pred CCCCCCCceeecCce---eeecCcccc
Q 029230 108 DKCVGCDRTVYPTEK---VSVNGAAYH 131 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~---v~~~g~~~H 131 (197)
..|.-|+..|+++.. |..+|+.++
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~ 30 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFR 30 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEE
Confidence 568888888888753 344555544
No 129
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=25.12 E-value=1.2e+02 Score=19.27 Aligned_cols=34 Identities=15% Similarity=0.181 Sum_probs=24.0
Q ss_pred cccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230 35 ACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK 69 (197)
Q Consensus 35 ~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~ 69 (197)
.=|.|..++..+.+ .....+|..|...+..+-+.
T Consensus 3 ~~f~CpIt~~lM~d-PVi~~~G~tyer~~I~~~l~ 36 (73)
T PF04564_consen 3 DEFLCPITGELMRD-PVILPSGHTYERSAIERWLE 36 (73)
T ss_dssp GGGB-TTTSSB-SS-EEEETTSEEEEHHHHHHHHC
T ss_pred cccCCcCcCcHhhC-ceeCCcCCEEcHHHHHHHHH
Confidence 44788888887764 45567889999988877765
No 130
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=24.80 E-value=50 Score=18.13 Aligned_cols=31 Identities=19% Similarity=0.515 Sum_probs=15.7
Q ss_pred CCCCCCCceeecCc-eeeecCccccccccccCcCCCC
Q 029230 108 DKCVGCDRTVYPTE-KVSVNGAAYHRSCFKCSHGGCT 143 (197)
Q Consensus 108 ~~C~~C~~~I~~~e-~v~~~g~~~H~~CF~C~~C~~~ 143 (197)
..|+.|+......+ .|...+.. .+|..|+..
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~-----vrC~~C~~~ 34 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRK-----VRCPKCGHV 34 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcE-----EECCCCCcE
Confidence 45777876554332 23333332 456666544
No 131
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=24.79 E-value=86 Score=21.10 Aligned_cols=35 Identities=23% Similarity=0.532 Sum_probs=25.6
Q ss_pred CCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeee
Q 029230 108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIA 151 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~ 151 (197)
..|+.|++... . ......| .|..|+..+.++.|..
T Consensus 36 ~~Cp~C~~~~V--k--R~a~GIW-----~C~kCg~~fAGgay~P 70 (89)
T COG1997 36 HVCPFCGRTTV--K--RIATGIW-----KCRKCGAKFAGGAYTP 70 (89)
T ss_pred CcCCCCCCcce--e--eeccCeE-----EcCCCCCeeccccccc
Confidence 78999999853 1 2333455 6899999999887765
No 132
>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=24.79 E-value=23 Score=21.26 Aligned_cols=26 Identities=27% Similarity=0.448 Sum_probs=15.9
Q ss_pred cccccccccccC-CCeeecCCeeeccccH
Q 029230 37 FRCHHCKGTLKL-SNFNSFEGVLYCRPHF 64 (197)
Q Consensus 37 F~C~~C~~~L~~-~~f~~~~g~~yC~~c~ 64 (197)
++|..|++.|.. +.+. ..++-|..|-
T Consensus 5 iRC~~CnklLa~~g~~~--~leIKCpRC~ 31 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVI--ELEIKCPRCK 31 (51)
T ss_pred eeccchhHHHhhhcCcc--EEEEECCCCC
Confidence 577788887765 3333 3456676663
No 133
>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=24.54 E-value=76 Score=18.54 Aligned_cols=10 Identities=10% Similarity=-0.064 Sum_probs=6.6
Q ss_pred eecHHHHHhH
Q 029230 156 LYCKHHHIQL 165 (197)
Q Consensus 156 ~yC~~cy~~~ 165 (197)
-+|..||...
T Consensus 25 dLC~~Cf~~g 34 (49)
T cd02335 25 DLCLECFSAG 34 (49)
T ss_pred chhHHhhhCc
Confidence 3577887753
No 134
>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=24.26 E-value=76 Score=18.85 Aligned_cols=27 Identities=26% Similarity=0.561 Sum_probs=19.7
Q ss_pred CCCCCCCceee-cCce-eeecCccccccc
Q 029230 108 DKCVGCDRTVY-PTEK-VSVNGAAYHRSC 134 (197)
Q Consensus 108 ~~C~~C~~~I~-~~e~-v~~~g~~~H~~C 134 (197)
..|+.|+--.. .+|. |.+.+..|++.|
T Consensus 14 ~~Cp~CGN~~vGngEG~liV~edtfkRtC 42 (49)
T PF12677_consen 14 CKCPKCGNDKVGNGEGTLIVEEDTFKRTC 42 (49)
T ss_pred ccCcccCCcEeecCcceEEEeccceeeee
Confidence 57999976543 3443 778889999877
No 135
>PHA02929 N1R/p28-like protein; Provisional
Probab=24.18 E-value=50 Score=26.60 Aligned_cols=38 Identities=21% Similarity=0.435 Sum_probs=23.7
Q ss_pred CCCCCCCceeecCc-------eeeecCcccccccc--------ccCcCCCCCC
Q 029230 108 DKCVGCDRTVYPTE-------KVSVNGAAYHRSCF--------KCSHGGCTIS 145 (197)
Q Consensus 108 ~~C~~C~~~I~~~e-------~v~~~g~~~H~~CF--------~C~~C~~~l~ 145 (197)
..|+.|...+...+ .+..-+..||..|+ .|..|..++.
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 67888888776433 12234667777777 4666666554
No 136
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=23.93 E-value=39 Score=26.81 Aligned_cols=32 Identities=19% Similarity=0.179 Sum_probs=23.6
Q ss_pred cccccccccccccccCCCeeecCCeeeccccH
Q 029230 33 HKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64 (197)
Q Consensus 33 H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~ 64 (197)
=++=..|..|+.++....|...+|.++|..|.
T Consensus 146 ~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 146 GLDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred ccchhhHhcCCCCCCceEEecccCCccccccc
Confidence 33445788888887755566788899998885
No 137
>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=23.79 E-value=19 Score=24.25 Aligned_cols=17 Identities=24% Similarity=0.577 Sum_probs=12.9
Q ss_pred ccccccCCCCCCCCCCCcee
Q 029230 98 KVSNKFVGTRDKCVGCDRTV 117 (197)
Q Consensus 98 ~~~~~~~~~~~~C~~C~~~I 117 (197)
.|...|. ..|..|++.+
T Consensus 48 sY~~lfs---~pC~~C~klL 64 (90)
T PF11571_consen 48 SYRNLFS---TPCKKCGKLL 64 (90)
T ss_pred HHhhhcc---chhhHHHhHh
Confidence 3455555 7899999988
No 138
>PLN02195 cellulose synthase A
Probab=23.64 E-value=80 Score=30.73 Aligned_cols=30 Identities=20% Similarity=0.627 Sum_probs=18.7
Q ss_pred CCCccccccccceecceeEEeCCccccccccccccccc
Q 029230 7 GTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKG 44 (197)
Q Consensus 7 ~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~ 44 (197)
+..++|..|+..|. +..+|..| --|..|+-
T Consensus 4 ~~~~~c~~cgd~~~----~~~~g~~f----vaC~eC~~ 33 (977)
T PLN02195 4 SGAPICATCGEEVG----VDSNGEAF----VACHECSY 33 (977)
T ss_pred CCCccceecccccC----cCCCCCeE----EEeccCCC
Confidence 34578999988775 34556655 34556643
No 139
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=23.56 E-value=35 Score=27.04 Aligned_cols=29 Identities=17% Similarity=0.277 Sum_probs=19.4
Q ss_pred ccccCcCCCCCCCCCeeeeCCeeecHHHH
Q 029230 134 CFKCSHGGCTISPSNYIAHEGKLYCKHHH 162 (197)
Q Consensus 134 CF~C~~C~~~l~~~~~~~~dg~~yC~~cy 162 (197)
=..|..|+.++....|...+|.++|..|.
T Consensus 149 l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 149 LDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred hhhHhcCCCCCCceEEecccCCccccccc
Confidence 34677777776644455677777887775
No 140
>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=23.31 E-value=45 Score=18.86 Aligned_cols=11 Identities=27% Similarity=0.691 Sum_probs=5.3
Q ss_pred ccccccccccc
Q 029230 37 FRCHHCKGTLK 47 (197)
Q Consensus 37 F~C~~C~~~L~ 47 (197)
+.|..|+..|.
T Consensus 20 ~vC~~CG~Vl~ 30 (43)
T PF08271_consen 20 LVCPNCGLVLE 30 (43)
T ss_dssp EEETTT-BBEE
T ss_pred EECCCCCCEee
Confidence 45555555554
No 141
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=22.80 E-value=40 Score=25.48 Aligned_cols=37 Identities=14% Similarity=0.357 Sum_probs=24.8
Q ss_pred CCCCCCCceeecCceeeec------CccccccccccCcCCCCC
Q 029230 108 DKCVGCDRTVYPTEKVSVN------GAAYHRSCFKCSHGGCTI 144 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~v~~~------g~~~H~~CF~C~~C~~~l 144 (197)
.+|+.|+.++.....-.+. -...|.+..+|..|++..
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 7899999998643221122 123567788899999864
No 142
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=22.76 E-value=42 Score=27.08 Aligned_cols=31 Identities=16% Similarity=0.336 Sum_probs=25.5
Q ss_pred ccccccccccccccCCCeeecCCeeeccccH
Q 029230 34 KACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64 (197)
Q Consensus 34 ~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~ 64 (197)
++=..|..|+.+.....|+...+...|.+|+
T Consensus 152 ~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 152 PNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred cchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 3445788999999888888889999998887
No 143
>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=22.60 E-value=60 Score=22.49 Aligned_cols=35 Identities=17% Similarity=0.235 Sum_probs=24.8
Q ss_pred ccccccccccccccccccCCCeeecCCeeeccccHHHHh
Q 029230 30 RVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLF 68 (197)
Q Consensus 30 ~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~ 68 (197)
..+...==.|..| .+..|+..++.+.|..|-.+.+
T Consensus 29 g~~~va~daCeiC----~~~GY~q~g~~lvC~~C~~~~~ 63 (102)
T PF10080_consen 29 GSYRVAFDACEIC----GPKGYYQEGDQLVCKNCGVRFN 63 (102)
T ss_pred CCEEEEEEecccc----CCCceEEECCEEEEecCCCEEe
Confidence 3444444457777 5578999999999999965443
No 144
>PLN02436 cellulose synthase A
Probab=22.40 E-value=73 Score=31.32 Aligned_cols=9 Identities=22% Similarity=0.922 Sum_probs=4.6
Q ss_pred cccccccce
Q 029230 11 KCMACDKTV 19 (197)
Q Consensus 11 ~C~~C~~~I 19 (197)
+|..|+..|
T Consensus 38 iCqICGD~V 46 (1094)
T PLN02436 38 TCQICGDEI 46 (1094)
T ss_pred ccccccccc
Confidence 555555444
No 145
>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=22.34 E-value=36 Score=16.72 Aligned_cols=12 Identities=33% Similarity=0.874 Sum_probs=8.9
Q ss_pred cccccccccccC
Q 029230 37 FRCHHCKGTLKL 48 (197)
Q Consensus 37 F~C~~C~~~L~~ 48 (197)
|+|..|++.+..
T Consensus 2 ~~C~~C~~~F~~ 13 (27)
T PF13912_consen 2 FECDECGKTFSS 13 (27)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCccCCccCC
Confidence 578888877764
No 146
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=22.29 E-value=74 Score=31.27 Aligned_cols=29 Identities=28% Similarity=0.566 Sum_probs=18.2
Q ss_pred ccccccccceecceeEEeCCccccccccccccccccc
Q 029230 10 QKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTL 46 (197)
Q Consensus 10 ~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L 46 (197)
.+|..|+..|. +.++|..| --|..|+-++
T Consensus 18 qiCqICGD~vg----~~~~Ge~F----VAC~eC~FPV 46 (1079)
T PLN02638 18 QVCQICGDNVG----KTVDGEPF----VACDVCAFPV 46 (1079)
T ss_pred ceeeecccccC----cCCCCCEE----EEeccCCCcc
Confidence 48888887765 34666666 4456665444
No 147
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=21.91 E-value=51 Score=19.53 Aligned_cols=12 Identities=17% Similarity=0.589 Sum_probs=6.8
Q ss_pred eeccccHHHHhh
Q 029230 58 LYCRPHFDQLFK 69 (197)
Q Consensus 58 ~yC~~c~~~~~~ 69 (197)
-+|..||.+...
T Consensus 23 ~IC~~C~~~i~~ 34 (48)
T PF14570_consen 23 QICRFCYHDILE 34 (48)
T ss_dssp ---HHHHHHHTT
T ss_pred cHHHHHHHHHHh
Confidence 468888887764
No 148
>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=21.84 E-value=73 Score=18.52 Aligned_cols=10 Identities=10% Similarity=0.275 Sum_probs=7.1
Q ss_pred eeecHHHHHh
Q 029230 155 KLYCKHHHIQ 164 (197)
Q Consensus 155 ~~yC~~cy~~ 164 (197)
--+|..||..
T Consensus 24 yDLC~~Cf~~ 33 (45)
T cd02344 24 FDFCENCFKT 33 (45)
T ss_pred ccchHHhhCC
Confidence 3468888876
No 149
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=21.80 E-value=22 Score=21.43 Aligned_cols=14 Identities=36% Similarity=0.888 Sum_probs=10.3
Q ss_pred CCCCCCCceeecCc
Q 029230 108 DKCVGCDRTVYPTE 121 (197)
Q Consensus 108 ~~C~~C~~~I~~~e 121 (197)
..|.+|+-.|.+..
T Consensus 23 ~~C~gC~~~l~~~~ 36 (56)
T PF02591_consen 23 GTCSGCHMELPPQE 36 (56)
T ss_pred CccCCCCEEcCHHH
Confidence 57888888877654
No 150
>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=21.68 E-value=58 Score=16.15 Aligned_cols=12 Identities=25% Similarity=0.365 Sum_probs=9.2
Q ss_pred cccCcCCCCCCC
Q 029230 135 FKCSHGGCTISP 146 (197)
Q Consensus 135 F~C~~C~~~l~~ 146 (197)
|.|..|++.+.+
T Consensus 2 ~~C~~C~k~f~~ 13 (27)
T PF12171_consen 2 FYCDACDKYFSS 13 (27)
T ss_dssp CBBTTTTBBBSS
T ss_pred CCcccCCCCcCC
Confidence 568888887765
No 151
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=21.54 E-value=77 Score=23.22 Aligned_cols=23 Identities=22% Similarity=0.541 Sum_probs=16.5
Q ss_pred cccCcCCCCCCCCCeeeeCCeeecHHHHHhH
Q 029230 135 FKCSHGGCTISPSNYIAHEGKLYCKHHHIQL 165 (197)
Q Consensus 135 F~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~ 165 (197)
..|..||.+|..+. ||..|..++
T Consensus 82 ~~CE~CG~~I~~Gr--------~C~~C~~~l 104 (137)
T TIGR03826 82 YPCERCGTSIREGR--------LCDSCAGEL 104 (137)
T ss_pred CcccccCCcCCCCC--------ccHHHHHHH
Confidence 46788888877654 688887665
No 152
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=21.26 E-value=25 Score=28.29 Aligned_cols=10 Identities=20% Similarity=0.607 Sum_probs=4.6
Q ss_pred cccccccccC
Q 029230 39 CHHCKGTLKL 48 (197)
Q Consensus 39 C~~C~~~L~~ 48 (197)
|..|++.+++
T Consensus 13 cwycnrefdd 22 (341)
T KOG2893|consen 13 CWYCNREFDD 22 (341)
T ss_pred eeecccccch
Confidence 3444554443
No 153
>PLN02189 cellulose synthase
Probab=21.07 E-value=81 Score=30.91 Aligned_cols=9 Identities=33% Similarity=0.999 Sum_probs=5.1
Q ss_pred eeeccccHH
Q 029230 57 VLYCRPHFD 65 (197)
Q Consensus 57 ~~yC~~c~~ 65 (197)
-+.|..||+
T Consensus 61 fpvCr~Cye 69 (1040)
T PLN02189 61 FPVCRPCYE 69 (1040)
T ss_pred Cccccchhh
Confidence 345666664
No 154
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=21.02 E-value=64 Score=18.94 Aligned_cols=9 Identities=11% Similarity=0.039 Sum_probs=6.5
Q ss_pred ecHHHHHhH
Q 029230 157 YCKHHHIQL 165 (197)
Q Consensus 157 yC~~cy~~~ 165 (197)
+|..||...
T Consensus 26 LC~~Cf~~~ 34 (49)
T cd02345 26 LCLGCYTKG 34 (49)
T ss_pred chHHHHhCC
Confidence 588888754
No 155
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=21.00 E-value=51 Score=21.24 Aligned_cols=15 Identities=27% Similarity=0.587 Sum_probs=9.3
Q ss_pred CCCCCCCceeecCce
Q 029230 108 DKCVGCDRTVYPTEK 122 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~ 122 (197)
..|.-|+..|+++..
T Consensus 4 ~~C~Fsg~~I~PG~G 18 (71)
T PF01246_consen 4 EKCSFSGYKIYPGHG 18 (71)
T ss_dssp EE-TTT-SEE-SSSS
T ss_pred EEecccCCccCCCCC
Confidence 568889999988853
No 156
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=20.88 E-value=40 Score=16.16 Aligned_cols=12 Identities=25% Similarity=0.766 Sum_probs=8.4
Q ss_pred cccccccccccC
Q 029230 37 FRCHHCKGTLKL 48 (197)
Q Consensus 37 F~C~~C~~~L~~ 48 (197)
|.|..|+..+.+
T Consensus 1 ~~C~~C~~~f~s 12 (25)
T PF12874_consen 1 FYCDICNKSFSS 12 (25)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCCcCC
Confidence 567888777654
No 157
>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=20.50 E-value=22 Score=19.31 Aligned_cols=16 Identities=19% Similarity=0.588 Sum_probs=8.5
Q ss_pred cccCcCCCCCCCCCee
Q 029230 135 FKCSHGGCTISPSNYI 150 (197)
Q Consensus 135 F~C~~C~~~l~~~~~~ 150 (197)
|.|..|++++..+.|.
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 4566666666555543
No 158
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=20.30 E-value=28 Score=22.55 Aligned_cols=10 Identities=20% Similarity=0.667 Sum_probs=5.5
Q ss_pred CCCCCCceee
Q 029230 109 KCVGCDRTVY 118 (197)
Q Consensus 109 ~C~~C~~~I~ 118 (197)
.|-.|+++|.
T Consensus 36 ~C~~Cg~~Ip 45 (73)
T PRK13715 36 LCEACGNPIP 45 (73)
T ss_pred cHhhcCCcCC
Confidence 4555555553
No 159
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=20.29 E-value=53 Score=26.96 Aligned_cols=38 Identities=18% Similarity=0.323 Sum_probs=19.5
Q ss_pred CCCCCCCceeecCceeeecCcccc--ccccccCcCCCCCCC
Q 029230 108 DKCVGCDRTVYPTEKVSVNGAAYH--RSCFKCSHGGCTISP 146 (197)
Q Consensus 108 ~~C~~C~~~I~~~e~v~~~g~~~H--~~CF~C~~C~~~l~~ 146 (197)
-.|..|+|... .-++.-.--.-| ..=|.|..|++.+.+
T Consensus 188 c~C~iCGKaFS-RPWLLQGHiRTHTGEKPF~C~hC~kAFAD 227 (279)
T KOG2462|consen 188 CECGICGKAFS-RPWLLQGHIRTHTGEKPFSCPHCGKAFAD 227 (279)
T ss_pred ccccccccccc-chHHhhcccccccCCCCccCCcccchhcc
Confidence 46777877653 111111111122 134778888887765
No 160
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=20.16 E-value=69 Score=19.58 Aligned_cols=14 Identities=14% Similarity=0.320 Sum_probs=10.8
Q ss_pred CCCCCCCceeecCc
Q 029230 108 DKCVGCDRTVYPTE 121 (197)
Q Consensus 108 ~~C~~C~~~I~~~e 121 (197)
.-|+-|+++|..++
T Consensus 40 ngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 40 NGCPFCGTPFEFDD 53 (55)
T ss_pred cCCCCCCCcccCCC
Confidence 56999999987553
No 161
>PF04641 Rtf2: Rtf2 RING-finger
Probab=20.06 E-value=1.3e+02 Score=24.42 Aligned_cols=36 Identities=14% Similarity=0.242 Sum_probs=25.7
Q ss_pred ccccccccccccccccCC-Cee--ecCCeeeccccHHHH
Q 029230 32 YHKACFRCHHCKGTLKLS-NFN--SFEGVLYCRPHFDQL 67 (197)
Q Consensus 32 ~H~~CF~C~~C~~~L~~~-~f~--~~~g~~yC~~c~~~~ 67 (197)
....-|.|-..+..|.+. .|+ ..-|.+|++....++
T Consensus 109 ~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~ 147 (260)
T PF04641_consen 109 NSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL 147 (260)
T ss_pred cCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh
Confidence 456788999999999654 343 346788888777665
Done!