Query 042895
Match_columns 150
No_of_seqs 180 out of 1251
Neff 9.3
Searched_HMMs 46136
Date Fri Mar 29 10:42:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042895.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042895hhsearch_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 4.4E-27 9.6E-32 178.3 -1.9 113 8-148 275-389 (468)
2 KOG1701 Focal adhesion adaptor 99.9 5.7E-25 1.2E-29 166.9 -0.2 117 5-149 332-460 (468)
3 KOG4577 Transcription factor L 99.9 2.9E-25 6.4E-30 161.1 -4.8 117 6-150 32-152 (383)
4 KOG2272 Focal adhesion protein 99.9 4.3E-24 9.2E-29 152.6 -2.1 116 6-149 194-310 (332)
5 KOG1700 Regulatory protein MLP 99.8 7.8E-21 1.7E-25 135.4 2.6 149 1-149 1-164 (200)
6 KOG1703 Adaptor protein Enigma 99.8 4.2E-20 9.1E-25 147.3 3.5 117 6-149 302-418 (479)
7 KOG1703 Adaptor protein Enigma 99.8 2.9E-20 6.3E-25 148.2 2.1 117 5-149 361-479 (479)
8 KOG2272 Focal adhesion protein 99.8 3.3E-21 7E-26 137.9 -3.1 114 8-148 13-127 (332)
9 KOG1044 Actin-binding LIM Zn-f 99.8 1.4E-19 3E-24 142.1 5.2 141 8-150 17-189 (670)
10 KOG1044 Actin-binding LIM Zn-f 99.8 5.6E-20 1.2E-24 144.3 1.6 114 6-147 132-246 (670)
11 PF00412 LIM: LIM domain; Int 99.6 8.4E-16 1.8E-20 88.9 4.2 57 10-66 1-58 (58)
12 PF00412 LIM: LIM domain; Int 99.6 7.2E-16 1.6E-20 89.2 1.3 53 97-149 1-55 (58)
13 smart00132 LIM Zinc-binding do 98.9 1.7E-09 3.7E-14 56.9 2.5 36 96-131 1-38 (39)
14 smart00132 LIM Zinc-binding do 98.8 2.5E-09 5.5E-14 56.3 2.6 37 9-45 1-38 (39)
15 KOG4577 Transcription factor L 98.7 4.5E-10 9.7E-15 82.5 -3.6 55 93-148 32-87 (383)
16 KOG1700 Regulatory protein MLP 98.5 2E-08 4.3E-13 71.8 0.8 74 4-77 105-178 (200)
17 KOG1702 Nebulin repeat protein 98.3 5.2E-08 1.1E-12 68.6 -1.6 55 95-149 5-60 (264)
18 KOG1702 Nebulin repeat protein 98.1 2.2E-07 4.8E-12 65.5 -2.2 60 8-67 5-64 (264)
19 KOG0490 Transcription factor, 97.9 9E-07 2E-11 64.4 -1.7 108 13-149 2-117 (235)
20 KOG0490 Transcription factor, 92.1 0.033 7.1E-07 40.4 -0.6 49 100-149 2-53 (235)
21 PF09943 DUF2175: Uncharacteri 89.7 0.12 2.6E-06 32.8 0.4 32 9-40 4-36 (101)
22 PF14446 Prok-RING_1: Prokaryo 88.6 0.34 7.5E-06 27.1 1.7 29 7-35 5-36 (54)
23 PF10367 Vps39_2: Vacuolar sor 87.0 0.48 1E-05 29.9 1.9 29 7-35 78-107 (109)
24 PF14835 zf-RING_6: zf-RING of 85.6 1 2.3E-05 26.2 2.6 33 35-67 8-40 (65)
25 PF08394 Arc_trans_TRASH: Arch 84.7 0.57 1.2E-05 24.1 1.1 29 10-42 1-31 (37)
26 PF02069 Metallothio_Pro: Prok 83.7 0.63 1.4E-05 25.9 1.1 23 123-145 10-32 (52)
27 PRK14890 putative Zn-ribbon RN 83.5 1.1 2.3E-05 25.6 2.0 30 5-43 5-34 (59)
28 PF09943 DUF2175: Uncharacteri 83.2 0.38 8.2E-06 30.6 0.1 31 95-125 3-35 (101)
29 PF13240 zinc_ribbon_2: zinc-r 83.0 0.64 1.4E-05 21.2 0.8 10 10-19 2-11 (23)
30 PF11781 RRN7: RNA polymerase 81.8 0.72 1.6E-05 23.6 0.8 22 122-147 10-31 (36)
31 COG2888 Predicted Zn-ribbon RN 79.8 1.9 4.2E-05 24.6 2.1 45 94-147 9-56 (61)
32 PF00645 zf-PARP: Poly(ADP-rib 79.2 1 2.2E-05 27.3 1.0 16 6-21 6-21 (82)
33 PF13719 zinc_ribbon_5: zinc-r 78.0 1.1 2.3E-05 23.0 0.7 31 95-130 3-35 (37)
34 PF13717 zinc_ribbon_4: zinc-r 77.9 0.98 2.1E-05 23.0 0.5 30 96-130 4-35 (36)
35 PF10367 Vps39_2: Vacuolar sor 77.8 1.8 3.8E-05 27.3 1.9 29 94-122 78-108 (109)
36 COG2191 Formylmethanofuran deh 77.8 1.2 2.6E-05 31.9 1.1 29 121-149 173-201 (206)
37 COG4847 Uncharacterized protei 77.3 0.81 1.8E-05 28.6 0.1 36 9-44 8-44 (103)
38 PF01258 zf-dskA_traR: Prokary 76.3 0.28 6E-06 25.0 -1.8 12 97-108 6-17 (36)
39 COG1645 Uncharacterized Zn-fin 76.0 1.7 3.7E-05 29.0 1.4 23 36-63 30-52 (131)
40 PF14471 DUF4428: Domain of un 75.9 1.5 3.2E-05 24.3 1.0 29 36-65 1-30 (51)
41 PF10235 Cript: Microtubule-as 74.7 1.7 3.6E-05 27.1 1.0 29 30-64 40-68 (90)
42 PF12773 DZR: Double zinc ribb 74.5 2.4 5.1E-05 22.9 1.6 8 37-44 15-22 (50)
43 KOG0320 Predicted E3 ubiquitin 72.5 2.2 4.8E-05 30.0 1.3 36 32-67 129-165 (187)
44 COG2191 Formylmethanofuran deh 72.4 1.7 3.7E-05 31.2 0.8 31 35-65 173-203 (206)
45 KOG4443 Putative transcription 72.1 2.8 6.1E-05 35.2 2.0 23 110-132 105-127 (694)
46 smart00504 Ubox Modified RING 71.9 5.2 0.00011 22.4 2.7 32 35-67 2-33 (63)
47 PF06677 Auto_anti-p27: Sjogre 71.6 2.6 5.6E-05 22.2 1.2 10 138-147 31-40 (41)
48 TIGR02098 MJ0042_CXXC MJ0042 f 69.2 2.4 5.2E-05 21.5 0.7 30 96-130 4-35 (38)
49 PF13834 DUF4193: Domain of un 66.4 2.3 5E-05 26.9 0.4 29 119-147 69-98 (99)
50 PF10886 DUF2685: Protein of u 66.2 4.5 9.8E-05 22.6 1.5 25 8-32 2-26 (54)
51 PF09723 Zn-ribbon_8: Zinc rib 64.9 2.8 6.2E-05 22.0 0.5 8 95-102 6-13 (42)
52 PRK00807 50S ribosomal protein 64.0 6 0.00013 21.9 1.7 32 8-42 2-36 (52)
53 COG4357 Zinc finger domain con 63.6 1.1 2.5E-05 28.1 -1.3 36 113-148 55-90 (105)
54 PF04810 zf-Sec23_Sec24: Sec23 63.2 6.7 0.00014 20.3 1.7 31 7-42 2-32 (40)
55 PF13923 zf-C3HC4_2: Zinc fing 62.5 7.5 0.00016 19.7 1.9 31 37-67 1-31 (39)
56 PF06750 DiS_P_DiS: Bacterial 62.4 3.4 7.3E-05 25.8 0.6 43 2-46 28-70 (92)
57 KOG2462 C2H2-type Zn-finger pr 62.4 4.4 9.6E-05 30.5 1.3 16 33-48 129-144 (279)
58 cd02249 ZZ Zinc finger, ZZ typ 61.3 4 8.8E-05 21.8 0.7 7 96-102 2-8 (46)
59 PRK00420 hypothetical protein; 60.2 5.5 0.00012 25.9 1.3 9 95-103 24-32 (112)
60 PF10083 DUF2321: Uncharacteri 58.9 6 0.00013 27.2 1.3 35 95-130 40-78 (158)
61 smart00291 ZnF_ZZ Zinc-binding 58.8 4.6 9.9E-05 21.4 0.6 9 95-103 5-13 (44)
62 PLN02195 cellulose synthase A 58.2 10 0.00022 33.6 2.9 34 3-44 2-35 (977)
63 PF12677 DUF3797: Domain of un 57.8 8.7 0.00019 21.0 1.6 26 95-120 14-42 (49)
64 PF14634 zf-RING_5: zinc-RING 57.5 6.8 0.00015 20.5 1.2 17 50-66 17-33 (44)
65 smart00834 CxxC_CXXC_SSSS Puta 56.1 5.2 0.00011 20.4 0.6 9 95-103 6-14 (41)
66 PF07191 zinc-ribbons_6: zinc- 55.1 3.6 7.9E-05 24.4 -0.2 12 121-132 51-62 (70)
67 TIGR02605 CxxC_CxxC_SSSS putat 54.9 5.7 0.00012 21.6 0.6 11 95-105 6-16 (52)
68 PF14569 zf-UDP: Zinc-binding 54.9 11 0.00023 22.9 1.8 12 7-18 9-20 (80)
69 PF06906 DUF1272: Protein of u 54.0 11 0.00023 21.3 1.6 31 37-67 8-41 (57)
70 cd02336 ZZ_RSC8 Zinc finger, Z 52.6 5.9 0.00013 21.3 0.4 10 141-150 23-32 (45)
71 KOG2893 Zn finger protein [Gen 51.6 3.8 8.3E-05 30.3 -0.5 35 95-131 11-45 (341)
72 PF11571 Med27: Mediator compl 49.7 5.2 0.00011 24.8 -0.1 10 95-104 55-64 (90)
73 smart00659 RPOLCX RNA polymera 48.3 12 0.00026 20.0 1.2 10 121-130 20-29 (44)
74 PF08209 Sgf11: Sgf11 (transcr 48.3 4.9 0.00011 20.1 -0.3 17 121-137 5-21 (33)
75 cd00472 Ribosomal_L24e_L24 Rib 46.5 15 0.00033 20.5 1.5 24 8-31 4-30 (54)
76 PF00096 zf-C2H2: Zinc finger, 45.9 9.8 0.00021 16.5 0.6 12 121-132 1-12 (23)
77 KOG3002 Zn finger protein [Gen 45.8 11 0.00025 28.8 1.2 69 34-130 48-120 (299)
78 COG4068 Uncharacterized protei 45.7 13 0.00028 21.2 1.1 15 7-21 8-22 (64)
79 cd00162 RING RING-finger (Real 45.7 11 0.00023 18.9 0.8 26 97-122 2-28 (45)
80 PF13920 zf-C3HC4_3: Zinc fing 45.5 30 0.00064 18.5 2.6 31 36-67 4-35 (50)
81 PLN03208 E3 ubiquitin-protein 44.1 35 0.00076 24.4 3.3 31 34-65 18-48 (193)
82 PF02591 DUF164: Putative zinc 44.1 7.3 0.00016 21.7 -0.1 26 122-147 24-52 (56)
83 PF06827 zf-FPG_IleRS: Zinc fi 44.0 8.9 0.00019 18.3 0.2 12 95-106 2-13 (30)
84 PF14255 Cys_rich_CPXG: Cystei 43.9 13 0.00029 20.6 1.0 30 9-38 2-31 (52)
85 PF00130 C1_1: Phorbol esters/ 43.9 17 0.00037 19.6 1.4 13 5-17 9-21 (53)
86 COG2075 RPL24A Ribosomal prote 43.4 20 0.00044 20.9 1.7 22 36-57 5-29 (66)
87 PF00097 zf-C3HC4: Zinc finger 42.5 25 0.00054 17.7 1.9 31 37-67 1-31 (41)
88 PRK14891 50S ribosomal protein 42.4 17 0.00036 24.2 1.4 25 7-31 4-31 (131)
89 smart00531 TFIIE Transcription 42.2 8.2 0.00018 26.2 -0.1 34 9-45 101-134 (147)
90 PF05502 Dynactin_p62: Dynacti 41.4 17 0.00036 29.8 1.6 37 95-131 27-63 (483)
91 PF12674 Zn_ribbon_2: Putative 41.0 12 0.00026 22.8 0.6 27 123-149 3-34 (81)
92 cd02340 ZZ_NBR1_like Zinc fing 41.0 17 0.00037 19.1 1.1 11 96-106 2-12 (43)
93 PF01286 XPA_N: XPA protein N- 40.2 18 0.00038 18.2 1.0 11 8-18 4-14 (34)
94 PF13639 zf-RING_2: Ring finge 40.1 6.2 0.00013 20.6 -0.7 27 96-122 2-31 (44)
95 PRK12495 hypothetical protein; 40.0 16 0.00034 26.7 1.1 27 95-131 43-69 (226)
96 PF01246 Ribosomal_L24e: Ribos 39.9 20 0.00044 21.3 1.4 25 7-31 3-30 (71)
97 PRK00398 rpoP DNA-directed RNA 39.9 16 0.00035 19.4 0.9 27 95-130 4-31 (46)
98 PF01927 Mut7-C: Mut7-C RNAse 38.8 26 0.00056 23.7 2.0 39 6-44 90-134 (147)
99 PHA00626 hypothetical protein 38.6 27 0.00059 19.7 1.7 38 96-138 2-41 (59)
100 PF07754 DUF1610: Domain of un 38.0 23 0.00051 16.3 1.1 9 10-18 1-9 (24)
101 PLN02638 cellulose synthase A 37.8 29 0.00063 31.3 2.6 29 8-44 18-46 (1079)
102 PF08790 zf-LYAR: LYAR-type C2 37.8 11 0.00025 18.1 0.1 17 121-137 1-17 (28)
103 KOG0823 Predicted E3 ubiquitin 36.1 42 0.00092 24.7 2.8 37 30-67 43-79 (230)
104 PLN02189 cellulose synthase 35.9 32 0.00069 31.0 2.5 8 56-63 62-69 (1040)
105 PF13894 zf-C2H2_4: C2H2-type 35.4 19 0.0004 15.3 0.6 12 121-132 1-12 (24)
106 PRK04023 DNA polymerase II lar 34.7 45 0.00098 30.0 3.2 13 95-107 664-677 (1121)
107 PLN02436 cellulose synthase A 34.6 34 0.00074 30.9 2.5 9 9-17 38-46 (1094)
108 KOG2114 Vacuolar assembly/sort 34.4 17 0.00037 31.8 0.6 36 95-130 841-882 (933)
109 PF08271 TF_Zn_Ribbon: TFIIB z 34.4 19 0.00041 18.8 0.6 14 118-131 17-30 (43)
110 PF12855 Ecl1: Life-span regul 34.3 14 0.00031 19.6 0.1 19 123-145 9-27 (43)
111 PF12874 zf-met: Zinc-finger o 34.0 19 0.00042 15.9 0.6 13 121-133 1-13 (25)
112 PF07649 C1_3: C1-like domain; 33.7 19 0.00042 17.1 0.5 12 121-132 1-12 (30)
113 cd02344 ZZ_HERC2 Zinc finger, 33.4 28 0.00061 18.6 1.2 13 96-108 2-15 (45)
114 PRK03564 formate dehydrogenase 33.3 1.3E+02 0.0028 23.3 5.2 10 7-16 187-196 (309)
115 cd02341 ZZ_ZZZ3 Zinc finger, Z 32.2 22 0.00048 19.3 0.7 12 96-107 2-14 (48)
116 PF04570 DUF581: Protein of un 32.2 28 0.0006 19.8 1.1 24 36-59 18-43 (58)
117 cd02342 ZZ_UBA_plant Zinc fing 32.1 29 0.00062 18.5 1.0 13 96-108 2-15 (43)
118 PF13912 zf-C2H2_6: C2H2-type 32.0 22 0.00047 16.1 0.6 13 121-133 2-14 (27)
119 COG5152 Uncharacterized conser 31.8 18 0.00039 26.1 0.3 33 34-67 196-228 (259)
120 KOG2932 E3 ubiquitin ligase in 31.1 16 0.00035 28.2 -0.0 29 36-64 92-120 (389)
121 PF12171 zf-C2H2_jaz: Zinc-fin 31.0 37 0.00081 15.5 1.3 13 121-133 2-14 (27)
122 KOG1813 Predicted E3 ubiquitin 30.9 31 0.00068 26.4 1.5 33 34-67 241-273 (313)
123 PRK14714 DNA polymerase II lar 30.8 50 0.0011 30.5 2.9 7 96-102 711-717 (1337)
124 PF00628 PHD: PHD-finger; Int 30.5 46 0.001 17.6 1.8 26 97-122 2-30 (51)
125 TIGR00570 cdk7 CDK-activating 30.0 57 0.0012 25.2 2.7 16 52-67 25-40 (309)
126 PF04216 FdhE: Protein involve 29.9 30 0.00064 26.2 1.3 11 8-18 173-183 (290)
127 COG0068 HypF Hydrogenase matur 29.7 26 0.00057 30.1 1.0 32 95-130 152-183 (750)
128 PRK00085 recO DNA repair prote 29.6 26 0.00056 25.6 0.8 8 95-102 150-157 (247)
129 PF10122 Mu-like_Com: Mu-like 29.5 18 0.0004 20.0 0.0 8 95-102 5-12 (51)
130 PRK12775 putative trifunctiona 29.4 53 0.0012 29.6 2.9 54 3-61 792-847 (1006)
131 cd02335 ZZ_ADA2 Zinc finger, Z 29.3 32 0.0007 18.5 1.0 12 96-107 2-14 (49)
132 PF13248 zf-ribbon_3: zinc-rib 28.7 28 0.0006 16.0 0.6 10 9-18 4-13 (26)
133 PRK14559 putative protein seri 28.6 42 0.00091 28.7 2.0 10 9-18 3-12 (645)
134 COG1656 Uncharacterized conser 28.5 24 0.00053 24.5 0.5 40 4-43 94-139 (165)
135 PF08746 zf-RING-like: RING-li 28.5 13 0.00029 19.6 -0.6 26 97-122 1-29 (43)
136 KOG0978 E3 ubiquitin ligase in 28.4 17 0.00036 31.2 -0.3 33 34-67 643-675 (698)
137 smart00249 PHD PHD zinc finger 28.3 36 0.00079 17.1 1.1 26 10-35 2-29 (47)
138 COG1381 RecO Recombinational D 28.2 28 0.00062 25.8 0.9 8 95-102 155-162 (251)
139 PRK05978 hypothetical protein; 27.6 44 0.00096 22.9 1.7 30 95-132 34-64 (148)
140 KOG3579 Predicted E3 ubiquitin 27.6 28 0.0006 26.6 0.7 33 35-67 269-304 (352)
141 PF09889 DUF2116: Uncharacteri 27.5 28 0.00061 19.8 0.6 10 9-18 5-14 (59)
142 PHA00080 DksA-like zinc finger 27.4 14 0.0003 22.0 -0.7 31 95-130 32-62 (72)
143 PLN02915 cellulose synthase A 26.9 56 0.0012 29.5 2.5 30 7-44 15-44 (1044)
144 cd02338 ZZ_PCMF_like Zinc fing 26.6 25 0.00055 19.0 0.3 13 96-108 2-15 (49)
145 TIGR01206 lysW lysine biosynth 25.7 52 0.0011 18.4 1.4 29 95-130 3-32 (54)
146 KOG2186 Cell growth-regulating 25.6 16 0.00035 27.3 -0.8 41 96-136 5-45 (276)
147 KOG1829 Uncharacterized conser 25.3 32 0.0007 28.9 0.8 32 118-149 338-374 (580)
148 PF00569 ZZ: Zinc finger, ZZ t 24.9 20 0.00042 19.1 -0.4 13 95-107 5-18 (46)
149 KOG3476 Microtubule-associated 24.8 7.3 0.00016 24.0 -2.2 23 36-64 56-78 (100)
150 PF10080 DUF2318: Predicted me 24.4 42 0.00091 21.4 1.0 11 121-131 53-63 (102)
151 TIGR00373 conserved hypothetic 24.3 24 0.00051 24.3 -0.1 30 9-46 111-140 (158)
152 smart00746 TRASH metallochaper 24.3 66 0.0014 14.6 1.6 9 10-18 1-9 (39)
153 PF06524 NOA36: NOA36 protein; 24.2 81 0.0018 23.8 2.6 8 95-102 172-179 (314)
154 TIGR02419 C4_traR_proteo phage 24.2 17 0.00037 20.9 -0.7 17 95-111 32-48 (63)
155 PLN02400 cellulose synthase 24.0 55 0.0012 29.7 2.0 9 9-17 38-46 (1085)
156 PRK13715 conjugal transfer pro 23.8 16 0.00034 21.8 -1.0 31 95-130 35-65 (73)
157 COG0266 Nei Formamidopyrimidin 23.7 60 0.0013 24.6 1.9 25 95-119 246-270 (273)
158 cd02339 ZZ_Mind_bomb Zinc fing 23.5 54 0.0012 17.4 1.2 13 96-108 2-15 (45)
159 PF08792 A2L_zn_ribbon: A2L zi 23.2 52 0.0011 16.3 1.0 8 95-102 4-11 (33)
160 PHA02929 N1R/p28-like protein; 22.9 44 0.00095 24.8 1.0 14 7-20 174-187 (238)
161 PRK14873 primosome assembly pr 22.9 55 0.0012 28.1 1.7 14 51-64 406-419 (665)
162 cd02334 ZZ_dystrophin Zinc fin 22.8 51 0.0011 17.9 1.0 13 96-108 2-15 (49)
163 PRK06266 transcription initiat 22.6 34 0.00074 24.0 0.4 30 9-46 119-148 (178)
164 PF13901 DUF4206: Domain of un 22.6 61 0.0013 23.2 1.7 10 113-122 179-188 (202)
165 TIGR02420 dksA RNA polymerase- 22.2 19 0.00042 23.1 -0.9 20 93-112 79-98 (110)
166 PF00320 GATA: GATA zinc finge 22.2 56 0.0012 16.3 1.1 28 37-64 1-29 (36)
167 COG5540 RING-finger-containing 21.9 47 0.001 25.7 1.0 40 92-131 321-372 (374)
168 PF06689 zf-C4_ClpX: ClpX C4-t 21.6 84 0.0018 16.2 1.7 29 36-64 3-33 (41)
169 PF09862 DUF2089: Protein of u 21.4 47 0.001 21.7 0.8 12 121-132 13-24 (113)
170 PF03107 C1_2: C1 domain; Int 21.3 57 0.0012 15.5 0.9 12 121-132 1-12 (30)
171 COG1571 Predicted DNA-binding 20.6 81 0.0018 25.5 2.1 38 90-136 346-383 (421)
172 smart00355 ZnF_C2H2 zinc finge 20.4 55 0.0012 13.8 0.8 12 121-132 1-12 (26)
173 PF13465 zf-H2C2_2: Zinc-finge 20.3 51 0.0011 15.0 0.6 10 121-130 15-24 (26)
No 1
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.92 E-value=4.4e-27 Score=178.32 Aligned_cols=113 Identities=21% Similarity=0.479 Sum_probs=105.0
Q ss_pred ccccccCceeeccc-eEEeCCcccccCCcccccccccCCCCCccccCCeeecCchhhhhhccccccCCCCCCCCCCCccc
Q 042895 8 QKCKVCEKTVCPVE-QLSTDGVVYHKSCFKCSRCKGTLKLSNYSSLEGVFYCKPHFEQLLKESSNFNKNFQLPAKSPSKV 86 (150)
Q Consensus 8 ~~C~~C~~~I~~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (150)
.+|++|+|.|...+ .+.++++.||..||+|..|++.|....|+.+++++||+.||++.+
T Consensus 275 ~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl-------------------- 334 (468)
T KOG1701|consen 275 GICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL-------------------- 334 (468)
T ss_pred hhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH--------------------
Confidence 48999999998555 579999999999999999999999999999999999999999877
Q ss_pred cccCCCCCCcCCcccceeccceeeeCCccccccccccccCCcccCCCCcccc-CCcccccccc
Q 042895 87 ASMFSGPNKNVLLAVKQCPWEKVAAESQASHKTCFKCSYAGYSISPSNYAAL-EGILYCKHNF 148 (150)
Q Consensus 87 ~~~~~~~~~~C~~C~~i~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~-~g~~yC~~cy 148 (150)
++|..|+++|....|.|+|+.||+.||+|..|++-|++..|+.. ++++||..||
T Consensus 335 --------ekC~~Cg~~I~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~df 389 (468)
T KOG1701|consen 335 --------EKCNKCGEPIMDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDF 389 (468)
T ss_pred --------HHHhhhhhHHHHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhh
Confidence 68999999777778999999999999999999999999999985 9999999998
No 2
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.89 E-value=5.7e-25 Score=166.92 Aligned_cols=117 Identities=26% Similarity=0.550 Sum_probs=104.0
Q ss_pred CCcccccccCceeeccceEEeCCcccccCCcccccccccCCCCCccc-cCCeeecCchhhhhhccccccCCCCCCCCCCC
Q 042895 5 GTQQKCKVCEKTVCPVEQLSTDGVVYHKSCFKCSRCKGTLKLSNYSS-LEGVFYCKPHFEQLLKESSNFNKNFQLPAKSP 83 (150)
Q Consensus 5 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~-~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~ 83 (150)
.+..+|..|++.|+ ..++.++|+.||+.||+|..|++.|++..|.. .++++||-.||.+.|+
T Consensus 332 ~tlekC~~Cg~~I~-d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfA---------------- 394 (468)
T KOG1701|consen 332 DTLEKCNKCGEPIM-DRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFA---------------- 394 (468)
T ss_pred HHHHHHhhhhhHHH-HHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcC----------------
Confidence 34568999999997 56789999999999999999999999988875 6899999999999999
Q ss_pred ccccccCCCCCCcCCcccc-eeccc------eeeeCCccccccccccccCCcccCC----CCccccCCccccccccC
Q 042895 84 SKVASMFSGPNKNVLLAVK-QCPWE------KVAAESQASHKTCFKCSYAGYSISP----SNYAALEGILYCKHNFS 149 (150)
Q Consensus 84 ~~~~~~~~~~~~~C~~C~~-i~~~~------~v~~~~~~~H~~Cf~C~~C~~~l~~----~~~~~~~g~~yC~~cy~ 149 (150)
++|+.|++ |++.+ +|.++|+.||.+|++|++|+.+|++ ..-+-.||.++|+.|..
T Consensus 395 -----------PrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch~ 460 (468)
T KOG1701|consen 395 -----------PRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCHL 460 (468)
T ss_pred -----------cchhhccCCccCCCCCcceEEEEEccccccccceehhhcCccccccCCCCcceeccCceeechhhh
Confidence 99999999 87754 5889999999999999999999963 34677899999999974
No 3
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.88 E-value=2.9e-25 Score=161.13 Aligned_cols=117 Identities=24% Similarity=0.432 Sum_probs=105.9
Q ss_pred CcccccccCceeeccceEEeCCcccccCCcccccccccCCCCCccccCCeeecCchhhhhhccccccCCCCCCCCCCCcc
Q 042895 6 TQQKCKVCEKTVCPVEQLSTDGVVYHKSCFKCSRCKGTLKLSNYSSLEGVFYCKPHFEQLLKESSNFNKNFQLPAKSPSK 85 (150)
Q Consensus 6 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 85 (150)
+.++|+.|.+.|.+..++.++++.||..|++|+.|...|.. ..+.++|.+||+.+|.++|+
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfG------------------ 92 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFG------------------ 92 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhC------------------
Confidence 67899999999987778899999999999999999999965 67788999999999999998
Q ss_pred ccccCCCCCCcCCcccc-eecccee-eeCCccccccccccccCCccc-CCCCccc-cCCccccccccCC
Q 042895 86 VASMFSGPNKNVLLAVK-QCPWEKV-AAESQASHKTCFKCSYAGYSI-SPSNYAA-LEGILYCKHNFSQ 150 (150)
Q Consensus 86 ~~~~~~~~~~~C~~C~~-i~~~~~v-~~~~~~~H~~Cf~C~~C~~~l-~~~~~~~-~~g~~yC~~cy~~ 150 (150)
++|.+|.+ |.+.++| .|.+.+||..||.|..|+++| .+..|+. .|+++.|+++|++
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 99999999 8787776 688999999999999999999 6777875 5999999999964
No 4
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.87 E-value=4.3e-24 Score=152.64 Aligned_cols=116 Identities=19% Similarity=0.417 Sum_probs=108.4
Q ss_pred CcccccccCceeeccceEEeCCcccccCCcccccccccCCCCCccccCCeeecCchhhhhhccccccCCCCCCCCCCCcc
Q 042895 6 TQQKCKVCEKTVCPVEQLSTDGVVYHKSCFKCSRCKGTLKLSNYSSLEGVFYCKPHFEQLLKESSNFNKNFQLPAKSPSK 85 (150)
Q Consensus 6 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 85 (150)
+.++|+.|.++|. ..++.++|+.||.+.|+|+.|.+|+-+.+.+++.|..||+.+|.++|+
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 5689999999996 668899999999999999999999988889999999999999999998
Q ss_pred ccccCCCCCCcCCcccceeccceeeeCCccccccccccccCCcccC-CCCccccCCccccccccC
Q 042895 86 VASMFSGPNKNVLLAVKQCPWEKVAAESQASHKTCFKCSYAGYSIS-PSNYAALEGILYCKHNFS 149 (150)
Q Consensus 86 ~~~~~~~~~~~C~~C~~i~~~~~v~~~~~~~H~~Cf~C~~C~~~l~-~~~~~~~~g~~yC~~cy~ 149 (150)
..|..|+.++.++++.|+++.|-++||+|+.|.+.|. -..|++.|..|.|++||.
T Consensus 255 ---------~~CF~C~~~i~G~vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~ 310 (332)
T KOG2272|consen 255 ---------NLCFICNRVIGGDVVSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYD 310 (332)
T ss_pred ---------hhheecCCccCccHHHHhhhhhccccccccccccccccccceeeeccchHHHHHHh
Confidence 8999999999999999999999999999999999995 446888899999999985
No 5
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.81 E-value=7.8e-21 Score=135.35 Aligned_cols=149 Identities=46% Similarity=0.831 Sum_probs=125.0
Q ss_pred CCCCCCcccccccCceeeccceEEeCCcccccCCcccccccccCCCCCccccCCeeecCchhhhhhcccc-ccCCCCCCC
Q 042895 1 MSFIGTQQKCKVCEKTVCPVEQLSTDGVVYHKSCFKCSRCKGTLKLSNYSSLEGVFYCKPHFEQLLKESS-NFNKNFQLP 79 (150)
Q Consensus 1 ~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~~-~~~~~~~~~ 79 (150)
|++.+...+|..|++.|+..+.+...+..||..||.|..|.+.|....+...++.+||+.+|..++.+.+ ++.+.+...
T Consensus 1 ~~~~~~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~ 80 (200)
T KOG1700|consen 1 SSFTGTTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKA 80 (200)
T ss_pred CCcccccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCccccccccccccc
Confidence 6788888899999999998888888899999999999999999999999999999999998888888765 333332211
Q ss_pred C------C-------CCccccccCCCCCCcCCcccc-eeccceeeeCCccccccccccccCCcccCCCCccccCCccccc
Q 042895 80 A------K-------SPSKVASMFSGPNKNVLLAVK-QCPWEKVAAESQASHKTCFKCSYAGYSISPSNYAALEGILYCK 145 (150)
Q Consensus 80 ~------~-------~~~~~~~~~~~~~~~C~~C~~-i~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~ 145 (150)
. . .+......+.+....|.+|.+ +++.+.+...+..||+.||+|+.|+..|+...+...+|.+||.
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~ 160 (200)
T KOG1700|consen 81 GGLGKDGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCK 160 (200)
T ss_pred CCCCcccccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccc
Confidence 0 0 112234456777799999999 9999999999999999999999999999999999999999998
Q ss_pred cccC
Q 042895 146 HNFS 149 (150)
Q Consensus 146 ~cy~ 149 (150)
.++.
T Consensus 161 ~~~~ 164 (200)
T KOG1700|consen 161 HHFA 164 (200)
T ss_pred hhhh
Confidence 8764
No 6
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.79 E-value=4.2e-20 Score=147.26 Aligned_cols=117 Identities=22% Similarity=0.451 Sum_probs=108.9
Q ss_pred CcccccccCceeeccceEEeCCcccccCCcccccccccCCCCCccccCCeeecCchhhhhhccccccCCCCCCCCCCCcc
Q 042895 6 TQQKCKVCEKTVCPVEQLSTDGVVYHKSCFKCSRCKGTLKLSNYSSLEGVFYCKPHFEQLLKESSNFNKNFQLPAKSPSK 85 (150)
Q Consensus 6 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 85 (150)
..++|..|++.|.....+.++++.||+.+|.|..|...+..+.+...+|++||..|+.+.+.
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 34789999999974378899999999999999999999999889899999999999999998
Q ss_pred ccccCCCCCCcCCcccceeccceeeeCCccccccccccccCCcccCCCCccccCCccccccccC
Q 042895 86 VASMFSGPNKNVLLAVKQCPWEKVAAESQASHKTCFKCSYAGYSISPSNYAALEGILYCKHNFS 149 (150)
Q Consensus 86 ~~~~~~~~~~~C~~C~~i~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~cy~ 149 (150)
+.|.+|++.|.++.|.++++.||++||.|..|++.|.+..|++.+|.|||+.||.
T Consensus 364 ---------p~C~~C~~~i~~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~ 418 (479)
T KOG1703|consen 364 ---------PNCKRCLLPILEEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYK 418 (479)
T ss_pred ---------ccccccCCchHHhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHh
Confidence 8999999977888899999999999999999999999999999999999999985
No 7
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.79 E-value=2.9e-20 Score=148.16 Aligned_cols=117 Identities=22% Similarity=0.493 Sum_probs=106.3
Q ss_pred CCcccccccCceeeccceEEeCCcccccCCcccccccccCCCCCccccCCeeecCchhhhhhccccccCCCCCCCCCCCc
Q 042895 5 GTQQKCKVCEKTVCPVEQLSTDGVVYHKSCFKCSRCKGTLKLSNYSSLEGVFYCKPHFEQLLKESSNFNKNFQLPAKSPS 84 (150)
Q Consensus 5 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~ 84 (150)
...++|.+|+++|. ++.|.+.+..||++||.|..|+++|....|+..+|.+||+.||.+++.
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 35678999999996 777888899999999999999999999999999999999999999997
Q ss_pred cccccCCCCCCcCCcccc-eec-cceeeeCCccccccccccccCCcccCCCCccccCCccccccccC
Q 042895 85 KVASMFSGPNKNVLLAVK-QCP-WEKVAAESQASHKTCFKCSYAGYSISPSNYAALEGILYCKHNFS 149 (150)
Q Consensus 85 ~~~~~~~~~~~~C~~C~~-i~~-~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~cy~ 149 (150)
.+|..|.+ +.. +..+.+++..||..||+|..|.+.|.++.|+...++|+|..|+.
T Consensus 423 ----------~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~~~~~~~~~~~p~c~~~~~ 479 (479)
T KOG1703|consen 423 ----------TKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKKLTKKTFFETLDKPLCQKHFP 479 (479)
T ss_pred ----------ccchhccchhHhhhhHhhccCccccccceehhhhhccccCCceeecCCccccccCCC
Confidence 78999998 443 34589999999999999999999999999999999999999874
No 8
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.78 E-value=3.3e-21 Score=137.94 Aligned_cols=114 Identities=20% Similarity=0.471 Sum_probs=104.1
Q ss_pred ccccccCceeeccc-eEEeCCcccccCCcccccccccCCCCCccccCCeeecCchhhhhhccccccCCCCCCCCCCCccc
Q 042895 8 QKCKVCEKTVCPVE-QLSTDGVVYHKSCFKCSRCKGTLKLSNYSSLEGVFYCKPHFEQLLKESSNFNKNFQLPAKSPSKV 86 (150)
Q Consensus 8 ~~C~~C~~~I~~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (150)
..|.+|.....+.+ +++.++..||..||.|+.|-.++.++.|+..+|+.||+.++..+|+
T Consensus 13 ~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~Lfa------------------- 73 (332)
T KOG2272|consen 13 MVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFA------------------- 73 (332)
T ss_pred HHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhc-------------------
Confidence 46899999988888 5688899999999999999999999999999999999999999998
Q ss_pred cccCCCCCCcCCcccceeccceeeeCCccccccccccccCCcccCCCCccccCCcccccccc
Q 042895 87 ASMFSGPNKNVLLAVKQCPWEKVAAESQASHKTCFKCSYAGYSISPSNYAALEGILYCKHNF 148 (150)
Q Consensus 87 ~~~~~~~~~~C~~C~~i~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~cy 148 (150)
|.|..|++.|-+.+|.+++..||+.||+|..|++.|....|+--.|..+|..|-
T Consensus 74 --------PcC~kC~EFiiGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn 127 (332)
T KOG2272|consen 74 --------PCCGKCGEFIIGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECN 127 (332)
T ss_pred --------hhhcccccchhhHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhh
Confidence 899999996667789999999999999999999999877888888999988774
No 9
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.78 E-value=1.4e-19 Score=142.11 Aligned_cols=141 Identities=19% Similarity=0.385 Sum_probs=103.5
Q ss_pred ccccccCceeeccceEEeCCcccccCCcccccccccCCCCCccccC-CeeecCchhhhhhcc------------ccc---
Q 042895 8 QKCKVCEKTVCPVEQLSTDGVVYHKSCFKCSRCKGTLKLSNYSSLE-GVFYCKPHFEQLLKE------------SSN--- 71 (150)
Q Consensus 8 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~-g~~yC~~c~~~~~~~------------~~~--- 71 (150)
..|.+|.+.-. ++++.+.++.||..||+|..|+..|..+.|+.++ ..+|+.......... ++.
T Consensus 17 i~c~~c~~kc~-gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~~~~gevvsa~gktyh~~cf~cs 95 (670)
T KOG1044|consen 17 IKCDKCRKKCS-GEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRAFVEGEVVSTLGKTYHPKCFSCS 95 (670)
T ss_pred eehhhhCCccc-cceeEeeccccceeeeeccccCCCcccccceecccceeecccchhhhccceeEecccceeccccceec
Confidence 36999999997 9999999999999999999999999999988764 467776333322111 000
Q ss_pred -cCCCC--CCCC------------CCCccccccCCCCCCcCCcccc-eeccceeeeCCccccccccccccCCcccCCCCc
Q 042895 72 -FNKNF--QLPA------------KSPSKVASMFSGPNKNVLLAVK-QCPWEKVAAESQASHKTCFKCSYAGYSISPSNY 135 (150)
Q Consensus 72 -~~~~~--~~~~------------~~~~~~~~~~~~~~~~C~~C~~-i~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~ 135 (150)
....+ +++. .+++.....-..+...|++|++ +..++.+.|+++.||..||+|..|...|. +.|
T Consensus 96 ~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~-gey 174 (670)
T KOG1044|consen 96 TCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLN-GEY 174 (670)
T ss_pred ccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeeeeeehhhhccccc-cee
Confidence 00011 0000 0122222222234578999999 99999999999999999999999999994 589
Q ss_pred cccCCccccccccCC
Q 042895 136 AALEGILYCKHNFSQ 150 (150)
Q Consensus 136 ~~~~g~~yC~~cy~~ 150 (150)
+.+||.|||++||.+
T Consensus 175 ~skdg~pyce~dy~~ 189 (670)
T KOG1044|consen 175 MSKDGVPYCEKDYQA 189 (670)
T ss_pred eccCCCcchhhhhhh
Confidence 999999999999853
No 10
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.77 E-value=5.6e-20 Score=144.25 Aligned_cols=114 Identities=22% Similarity=0.382 Sum_probs=102.7
Q ss_pred CcccccccCceeeccceEEeCCcccccCCcccccccccCCCCCccccCCeeecCchhhhhhccccccCCCCCCCCCCCcc
Q 042895 6 TQQKCKVCEKTVCPVEQLSTDGVVYHKSCFKCSRCKGTLKLSNYSSLEGVFYCKPHFEQLLKESSNFNKNFQLPAKSPSK 85 (150)
Q Consensus 6 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 85 (150)
+...|++|++.|..+..+.++++.||..||+|..|...| .+.|..++|.+||+.||++.|+
T Consensus 132 ~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL-~gey~skdg~pyce~dy~~~fg------------------ 192 (670)
T KOG1044|consen 132 GPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVL-NGEYMSKDGVPYCEKDYQAKFG------------------ 192 (670)
T ss_pred CCccccchhhhhhccceeeeeccceeeeeeehhhhcccc-cceeeccCCCcchhhhhhhhcC------------------
Confidence 567899999999989999999999999999999999988 5689999999999999999998
Q ss_pred ccccCCCCCCcCCcccceeccceeeeCCccccccccccccCCccc-CCCCccccCCccccccc
Q 042895 86 VASMFSGPNKNVLLAVKQCPWEKVAAESQASHKTCFKCSYAGYSI-SPSNYAALEGILYCKHN 147 (150)
Q Consensus 86 ~~~~~~~~~~~C~~C~~i~~~~~v~~~~~~~H~~Cf~C~~C~~~l-~~~~~~~~~g~~yC~~c 147 (150)
.+|..|.+.|.+.+|.|.|++||+.|-+|+.|+..+ ++++.++....+|-..|
T Consensus 193 ---------vkc~~c~~fisgkvLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C 246 (670)
T KOG1044|consen 193 ---------VKCEECEKFISGKVLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDC 246 (670)
T ss_pred ---------eehHHhhhhhhhhhhhccCcccCcchhhhhhhccccccchheeeccccccCCcc
Confidence 899999998888899999999999999999999999 56677776667665554
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=99.60 E-value=8.4e-16 Score=88.86 Aligned_cols=57 Identities=30% Similarity=0.729 Sum_probs=52.6
Q ss_pred ccccCceeeccceE-EeCCcccccCCcccccccccCCCCCccccCCeeecCchhhhhh
Q 042895 10 CKVCEKTVCPVEQL-STDGVVYHKSCFKCSRCKGTLKLSNYSSLEGVFYCKPHFEQLL 66 (150)
Q Consensus 10 C~~C~~~I~~~~~~-~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~ 66 (150)
|.+|+++|.+++.+ .++++.||++||+|..|+++|..+.++..+|++||+.||.++|
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 78999999977755 7999999999999999999999988999999999999998875
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=99.56 E-value=7.2e-16 Score=89.15 Aligned_cols=53 Identities=28% Similarity=0.456 Sum_probs=47.4
Q ss_pred CCcccc-eecccee-eeCCccccccccccccCCcccCCCCccccCCccccccccC
Q 042895 97 VLLAVK-QCPWEKV-AAESQASHKTCFKCSYAGYSISPSNYAALEGILYCKHNFS 149 (150)
Q Consensus 97 C~~C~~-i~~~~~v-~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~cy~ 149 (150)
|.+|++ |.+.+.+ .++|+.||++||+|..|+++|..+.+++.+|++||+.||.
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~ 55 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQ 55 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHH
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHh
Confidence 789999 6666665 6999999999999999999998888999999999999985
No 13
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.86 E-value=1.7e-09 Score=56.90 Aligned_cols=36 Identities=25% Similarity=0.262 Sum_probs=31.0
Q ss_pred cCCcccc-eecc-ceeeeCCccccccccccccCCcccC
Q 042895 96 NVLLAVK-QCPW-EKVAAESQASHKTCFKCSYAGYSIS 131 (150)
Q Consensus 96 ~C~~C~~-i~~~-~~v~~~~~~~H~~Cf~C~~C~~~l~ 131 (150)
+|.+|++ |.+. ..+.+.++.||++||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 4889999 5555 5678999999999999999999984
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=98.83 E-value=2.5e-09 Score=56.25 Aligned_cols=37 Identities=41% Similarity=0.770 Sum_probs=33.2
Q ss_pred cccccCceeecc-ceEEeCCcccccCCcccccccccCC
Q 042895 9 KCKVCEKTVCPV-EQLSTDGVVYHKSCFKCSRCKGTLK 45 (150)
Q Consensus 9 ~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~ 45 (150)
+|.+|+++|.+. ..+.+.++.||..||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 589999999876 5678899999999999999999885
No 15
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.72 E-value=4.5e-10 Score=82.51 Aligned_cols=55 Identities=20% Similarity=0.278 Sum_probs=50.0
Q ss_pred CCCcCCcccc-eeccceeeeCCccccccccccccCCcccCCCCccccCCcccccccc
Q 042895 93 PNKNVLLAVK-QCPWEKVAAESQASHKTCFKCSYAGYSISPSNYAALEGILYCKHNF 148 (150)
Q Consensus 93 ~~~~C~~C~~-i~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~cy 148 (150)
..++|++|.+ |+....+.++++.||..|++|+.|+.+| ....+.++|.+||+++|
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL-~drCFsR~~s~yCkedF 87 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQL-ADRCFSREGSVYCKEDF 87 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHH-HHHHhhcCCceeehHHH
Confidence 3489999999 8888888999999999999999999999 55778899999999987
No 16
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.54 E-value=2e-08 Score=71.81 Aligned_cols=74 Identities=47% Similarity=1.038 Sum_probs=64.8
Q ss_pred CCCcccccccCceeeccceEEeCCcccccCCcccccccccCCCCCccccCCeeecCchhhhhhccccccCCCCC
Q 042895 4 IGTQQKCKVCEKTVCPVEQLSTDGVVYHKSCFKCSRCKGTLKLSNYSSLEGVFYCKPHFEQLLKESSNFNKNFQ 77 (150)
Q Consensus 4 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~ 77 (150)
.++...|..|.+.+++.+.+...+..||..||+|+.|+..|..+.+....|.+||...+..++-+.++++...+
T Consensus 105 ~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~~~~~~~~~~~~ 178 (200)
T KOG1700|consen 105 AGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLFKGKGNYNEGFG 178 (200)
T ss_pred hccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheeecCCCcccccch
Confidence 45677899999999999999999999999999999999999999999999999999888887776666655443
No 17
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=98.32 E-value=5.2e-08 Score=68.62 Aligned_cols=55 Identities=29% Similarity=0.521 Sum_probs=51.1
Q ss_pred CcCCcccc-eeccceeeeCCccccccccccccCCcccCCCCccccCCccccccccC
Q 042895 95 KNVLLAVK-QCPWEKVAAESQASHKTCFKCSYAGYSISPSNYAALEGILYCKHNFS 149 (150)
Q Consensus 95 ~~C~~C~~-i~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~cy~ 149 (150)
..|..|++ +++.|.|..+++.||..||+|+.|+.+|.-.++...+.+|||..+|.
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYp 60 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYP 60 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccc
Confidence 56888999 99999999999999999999999999998888888999999999984
No 18
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=98.10 E-value=2.2e-07 Score=65.51 Aligned_cols=60 Identities=38% Similarity=0.773 Sum_probs=54.5
Q ss_pred ccccccCceeeccceEEeCCcccccCCcccccccccCCCCCccccCCeeecCchhhhhhc
Q 042895 8 QKCKVCEKTVCPVEQLSTDGVVYHKSCFKCSRCKGTLKLSNYSSLEGVFYCKPHFEQLLK 67 (150)
Q Consensus 8 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~ 67 (150)
..|..|++.+++.+.+.-+++.||..||.|..|+.+|...++...+.++||..+|.+..+
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVA 64 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccccee
Confidence 457899999999999999999999999999999999988888889999999999977654
No 19
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.94 E-value=9e-07 Score=64.44 Aligned_cols=108 Identities=19% Similarity=0.362 Sum_probs=82.5
Q ss_pred cCceeeccceEEeCCcccccCCcccccccccCC--CCCccccCCeeecCchhhh--hhccccccCCCCCCCCCCCccccc
Q 042895 13 CEKTVCPVEQLSTDGVVYHKSCFKCSRCKGTLK--LSNYSSLEGVFYCKPHFEQ--LLKESSNFNKNFQLPAKSPSKVAS 88 (150)
Q Consensus 13 C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~g~~yC~~c~~~--~~~~~~~~~~~~~~~~~~~~~~~~ 88 (150)
|+..|.+...+...+..||..|..|..|...|. ...+.. +|..||..+|.+ .+.
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~--------------------- 59 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFS--------------------- 59 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcc---------------------
Confidence 667776555567779999999999999999997 444555 999999999987 444
Q ss_pred cCCCCCCcCCcccc-eecccee-eeCCccccccccccccCCccc-CCCCccccCC-ccccccccC
Q 042895 89 MFSGPNKNVLLAVK-QCPWEKV-AAESQASHKTCFKCSYAGYSI-SPSNYAALEG-ILYCKHNFS 149 (150)
Q Consensus 89 ~~~~~~~~C~~C~~-i~~~~~v-~~~~~~~H~~Cf~C~~C~~~l-~~~~~~~~~g-~~yC~~cy~ 149 (150)
.+|.+|.. +...+.| .+..+. |.-||.|..|...+ ....+.+.+. +.+|.+++.
T Consensus 60 ------~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~ 117 (235)
T KOG0490|consen 60 ------KRCARCKFTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRK 117 (235)
T ss_pred ------ccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhh
Confidence 78999999 6555444 566666 99999999999876 5556666544 777776653
No 20
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=92.10 E-value=0.033 Score=40.39 Aligned_cols=49 Identities=16% Similarity=0.454 Sum_probs=38.2
Q ss_pred ccc-eeccceeeeCCccccccccccccCCcccC--CCCccccCCccccccccC
Q 042895 100 AVK-QCPWEKVAAESQASHKTCFKCSYAGYSIS--PSNYAALEGILYCKHNFS 149 (150)
Q Consensus 100 C~~-i~~~~~v~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~g~~yC~~cy~ 149 (150)
|+. +.+...+.+.+..||..|..|..|...+. ...|.. +|..||..+|.
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~ 53 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQ 53 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccch
Confidence 444 44444567779999999999999999996 445555 99999998874
No 21
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=89.70 E-value=0.12 Score=32.78 Aligned_cols=32 Identities=22% Similarity=0.464 Sum_probs=24.7
Q ss_pred cccccCceeeccceEEeCC-cccccCCcccccc
Q 042895 9 KCKVCEKTVCPVEQLSTDG-VVYHKSCFKCSRC 40 (150)
Q Consensus 9 ~C~~C~~~I~~~~~~~~~~-~~~H~~Cf~C~~C 40 (150)
+|..|+++|..++.+.+.. ...|-.||+-..-
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~~ 36 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKAS 36 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHHHh
Confidence 6899999999888876644 4679899876543
No 22
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=88.64 E-value=0.34 Score=27.14 Aligned_cols=29 Identities=31% Similarity=0.668 Sum_probs=21.2
Q ss_pred cccccccCceeeccc-eE--EeCCcccccCCc
Q 042895 7 QQKCKVCEKTVCPVE-QL--STDGVVYHKSCF 35 (150)
Q Consensus 7 ~~~C~~C~~~I~~~~-~~--~~~~~~~H~~Cf 35 (150)
..+|..|+++|.+++ .+ ..=+..||.+|.
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 457999999996544 33 445678999887
No 23
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=87.05 E-value=0.48 Score=29.93 Aligned_cols=29 Identities=34% Similarity=0.543 Sum_probs=16.2
Q ss_pred cccccccCceeeccceE-EeCCcccccCCc
Q 042895 7 QQKCKVCEKTVCPVEQL-STDGVVYHKSCF 35 (150)
Q Consensus 7 ~~~C~~C~~~I~~~~~~-~~~~~~~H~~Cf 35 (150)
...|..|+++|.....+ -..|..+|..|+
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 44577777777543322 334455666664
No 24
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=85.55 E-value=1 Score=26.17 Aligned_cols=33 Identities=18% Similarity=0.337 Sum_probs=15.6
Q ss_pred cccccccccCCCCCccccCCeeecCchhhhhhc
Q 042895 35 FKCSRCKGTLKLSNYSSLEGVFYCKPHFEQLLK 67 (150)
Q Consensus 35 f~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~ 67 (150)
++|+.|..-|...-....=+..||..|-.+.++
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 578888777654333445567889999877766
No 25
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=84.73 E-value=0.57 Score=24.15 Aligned_cols=29 Identities=24% Similarity=0.533 Sum_probs=19.8
Q ss_pred ccccCceeeccc--eEEeCCcccccCCcccccccc
Q 042895 10 CKVCEKTVCPVE--QLSTDGVVYHKSCFKCSRCKG 42 (150)
Q Consensus 10 C~~C~~~I~~~~--~~~~~~~~~H~~Cf~C~~C~~ 42 (150)
|.-|+++|. ++ ++...++.||. -|..|..
T Consensus 1 Cd~CG~~I~-~eP~~~k~~~~~y~f---CC~tC~~ 31 (37)
T PF08394_consen 1 CDYCGGEIT-GEPIVVKIGNKVYYF---CCPTCLS 31 (37)
T ss_pred CCccCCccc-CCEEEEEECCeEEEE---ECHHHHH
Confidence 677899996 44 55788888884 4444543
No 26
>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=83.72 E-value=0.63 Score=25.90 Aligned_cols=23 Identities=22% Similarity=0.531 Sum_probs=11.9
Q ss_pred cccCCcccCCCCccccCCccccc
Q 042895 123 CSYAGYSISPSNYAALEGILYCK 145 (150)
Q Consensus 123 C~~C~~~l~~~~~~~~~g~~yC~ 145 (150)
|..|...++...-+++||+.||.
T Consensus 10 C~~C~C~V~~~~Ai~~dGk~YCS 32 (52)
T PF02069_consen 10 CPSCSCVVSEEEAIQKDGKYYCS 32 (52)
T ss_dssp STT----B-TTTSEESSS-EESS
T ss_pred CCCCEeEECchHhHHhCCEeeec
Confidence 56677777666677778888874
No 27
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=83.50 E-value=1.1 Score=25.62 Aligned_cols=30 Identities=27% Similarity=0.613 Sum_probs=18.4
Q ss_pred CCcccccccCceeeccceEEeCCcccccCCccccccccc
Q 042895 5 GTQQKCKVCEKTVCPVEQLSTDGVVYHKSCFKCSRCKGT 43 (150)
Q Consensus 5 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~ 43 (150)
...++|..|+..|.+.+. ..-|.|..|+..
T Consensus 5 ~~~~~CtSCg~~i~~~~~---------~~~F~CPnCG~~ 34 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREK---------AVKFLCPNCGEV 34 (59)
T ss_pred ccCccccCCCCcccCCCc---------cCEeeCCCCCCe
Confidence 345578888888765541 112667777765
No 28
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=83.23 E-value=0.38 Score=30.57 Aligned_cols=31 Identities=13% Similarity=0.108 Sum_probs=24.3
Q ss_pred CcCCcccc-eeccceeeeC-Ccccccccccccc
Q 042895 95 KNVLLAVK-QCPWEKVAAE-SQASHKTCFKCSY 125 (150)
Q Consensus 95 ~~C~~C~~-i~~~~~v~~~-~~~~H~~Cf~C~~ 125 (150)
-+|..|++ |+.++..++. +..-|.+||+=..
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~ 35 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREKA 35 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHHH
Confidence 46999999 9999987655 4567999998443
No 29
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=83.00 E-value=0.64 Score=21.24 Aligned_cols=10 Identities=20% Similarity=0.610 Sum_probs=6.0
Q ss_pred ccccCceeec
Q 042895 10 CKVCEKTVCP 19 (150)
Q Consensus 10 C~~C~~~I~~ 19 (150)
|..|+..|.+
T Consensus 2 Cp~CG~~~~~ 11 (23)
T PF13240_consen 2 CPNCGAEIED 11 (23)
T ss_pred CcccCCCCCC
Confidence 5666666653
No 30
>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=81.76 E-value=0.72 Score=23.58 Aligned_cols=22 Identities=23% Similarity=0.614 Sum_probs=14.3
Q ss_pred ccccCCcccCCCCccccCCccccccc
Q 042895 122 KCSYAGYSISPSNYAALEGILYCKHN 147 (150)
Q Consensus 122 ~C~~C~~~l~~~~~~~~~g~~yC~~c 147 (150)
.|..|+.. .|...||..||..|
T Consensus 10 ~C~~C~~~----~~~~~dG~~yC~~c 31 (36)
T PF11781_consen 10 PCPVCGSR----WFYSDDGFYYCDRC 31 (36)
T ss_pred cCCCCCCe----EeEccCCEEEhhhC
Confidence 36666653 45667888888665
No 31
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=79.80 E-value=1.9 Score=24.57 Aligned_cols=45 Identities=18% Similarity=0.169 Sum_probs=24.0
Q ss_pred CCcCCcccc-eeccceeeeCCccccccccccccCCccc-CCCCccccCCccc-cccc
Q 042895 94 NKNVLLAVK-QCPWEKVAAESQASHKTCFKCSYAGYSI-SPSNYAALEGILY-CKHN 147 (150)
Q Consensus 94 ~~~C~~C~~-i~~~~~v~~~~~~~H~~Cf~C~~C~~~l-~~~~~~~~~g~~y-C~~c 147 (150)
.+.|..|+. |.+++... -|.|..|+..+ ..-.---+.|.+| |.+|
T Consensus 9 ~~~CtSCg~~i~p~e~~v---------~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~C 56 (61)
T COG2888 9 PPVCTSCGREIAPGETAV---------KFPCPNCGEVEIYRCAKCRKLGNPYRCPKC 56 (61)
T ss_pred CceeccCCCEeccCCcee---------EeeCCCCCceeeehhhhHHHcCCceECCCc
Confidence 378999999 43555322 26677777433 2222222344554 5554
No 32
>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=79.23 E-value=1 Score=27.29 Aligned_cols=16 Identities=38% Similarity=0.711 Sum_probs=12.2
Q ss_pred CcccccccCceeeccc
Q 042895 6 TQQKCKVCEKTVCPVE 21 (150)
Q Consensus 6 ~~~~C~~C~~~I~~~~ 21 (150)
+-.+|..|++.|..++
T Consensus 6 ~Ra~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 6 GRAKCKGCKKKIAKGE 21 (82)
T ss_dssp STEBETTTSCBE-TTS
T ss_pred CCccCcccCCcCCCCC
Confidence 4568999999998665
No 33
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=78.00 E-value=1.1 Score=22.99 Aligned_cols=31 Identities=16% Similarity=0.267 Sum_probs=18.4
Q ss_pred CcCCcccc--eeccceeeeCCccccccccccccCCccc
Q 042895 95 KNVLLAVK--QCPWEKVAAESQASHKTCFKCSYAGYSI 130 (150)
Q Consensus 95 ~~C~~C~~--i~~~~~v~~~~~~~H~~Cf~C~~C~~~l 130 (150)
..|+.|+. -++.+.|...+.. .+|..|+..+
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~-----vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRK-----VRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcE-----EECCCCCcEe
Confidence 35777877 5555555555543 5666666544
No 34
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=77.86 E-value=0.98 Score=23.03 Aligned_cols=30 Identities=17% Similarity=0.235 Sum_probs=17.6
Q ss_pred cCCcccc--eeccceeeeCCccccccccccccCCccc
Q 042895 96 NVLLAVK--QCPWEKVAAESQASHKTCFKCSYAGYSI 130 (150)
Q Consensus 96 ~C~~C~~--i~~~~~v~~~~~~~H~~Cf~C~~C~~~l 130 (150)
.|+.|+. -++.+.|...+.. ++|..|+..+
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~-----v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRK-----VRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcE-----EECCCCCCEe
Confidence 4777777 4555555555544 5666666543
No 35
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=77.81 E-value=1.8 Score=27.27 Aligned_cols=29 Identities=17% Similarity=0.107 Sum_probs=18.5
Q ss_pred CCcCCcccc-eeccce-eeeCCccccccccc
Q 042895 94 NKNVLLAVK-QCPWEK-VAAESQASHKTCFK 122 (150)
Q Consensus 94 ~~~C~~C~~-i~~~~~-v~~~~~~~H~~Cf~ 122 (150)
...|+.|++ +..... +...|..+|..|++
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 367999999 444333 33446778888864
No 36
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=77.81 E-value=1.2 Score=31.95 Aligned_cols=29 Identities=24% Similarity=0.348 Sum_probs=23.7
Q ss_pred cccccCCcccCCCCccccCCccccccccC
Q 042895 121 FKCSYAGYSISPSNYAALEGILYCKHNFS 149 (150)
Q Consensus 121 f~C~~C~~~l~~~~~~~~~g~~yC~~cy~ 149 (150)
-+|+.|+..+-...-...+|++.|..||.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~ 201 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAE 201 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccc
Confidence 57888888886666677899999999985
No 37
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=77.29 E-value=0.81 Score=28.63 Aligned_cols=36 Identities=25% Similarity=0.377 Sum_probs=27.6
Q ss_pred cccccCceeeccceEEeCCc-ccccCCcccccccccC
Q 042895 9 KCKVCEKTVCPVEQLSTDGV-VYHKSCFKCSRCKGTL 44 (150)
Q Consensus 9 ~C~~C~~~I~~~~~~~~~~~-~~H~~Cf~C~~C~~~l 44 (150)
+|..|+++|..++.+.+-.+ ..|-+||.-+.-+++-
T Consensus 8 kC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~k~~ 44 (103)
T COG4847 8 KCYVCGGTIIEGQKFTFTKKGSVHYECLAESKRKKPG 44 (103)
T ss_pred eEeeeCCEeeeccEEEEeeCCcchHHHHHHHHhcCcC
Confidence 69999999998888766544 6898998776655543
No 38
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=76.26 E-value=0.28 Score=24.98 Aligned_cols=12 Identities=17% Similarity=0.000 Sum_probs=5.1
Q ss_pred CCcccceeccce
Q 042895 97 VLLAVKQCPWEK 108 (150)
Q Consensus 97 C~~C~~i~~~~~ 108 (150)
|..|++.|+.++
T Consensus 6 C~~CGe~I~~~R 17 (36)
T PF01258_consen 6 CEDCGEPIPEER 17 (36)
T ss_dssp -TTTSSBEEHHH
T ss_pred ccccCChHHHHH
Confidence 555555434333
No 39
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=75.99 E-value=1.7 Score=29.02 Aligned_cols=23 Identities=22% Similarity=0.522 Sum_probs=18.1
Q ss_pred ccccccccCCCCCccccCCeeecCchhh
Q 042895 36 KCSRCKGTLKLSNYSSLEGVFYCKPHFE 63 (150)
Q Consensus 36 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~ 63 (150)
.|..|+.+| |.++|.+||+.|-.
T Consensus 30 hCp~Cg~PL-----F~KdG~v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTPL-----FRKDGEVFCPVCGY 52 (131)
T ss_pred hCcccCCcc-----eeeCCeEECCCCCc
Confidence 367888877 34999999999963
No 40
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=75.94 E-value=1.5 Score=24.27 Aligned_cols=29 Identities=28% Similarity=0.723 Sum_probs=20.8
Q ss_pred ccccccccCCCCC-ccccCCeeecCchhhhh
Q 042895 36 KCSRCKGTLKLSN-YSSLEGVFYCKPHFEQL 65 (150)
Q Consensus 36 ~C~~C~~~l~~~~-~~~~~g~~yC~~c~~~~ 65 (150)
.|..|+..++-.. +-..|| ..|..|+.++
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 3777888775544 446677 6899998876
No 41
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=74.70 E-value=1.7 Score=27.11 Aligned_cols=29 Identities=28% Similarity=0.549 Sum_probs=18.5
Q ss_pred cccCCcccccccccCCCCCccccCCeeecCchhhh
Q 042895 30 YHKSCFKCSRCKGTLKLSNYSSLEGVFYCKPHFEQ 64 (150)
Q Consensus 30 ~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~ 64 (150)
|-+.--.|..|...+.. .|..||..|..+
T Consensus 40 y~~~~~~C~~CK~~v~q------~g~~YCq~CAYk 68 (90)
T PF10235_consen 40 YAPYSSKCKICKTKVHQ------PGAKYCQTCAYK 68 (90)
T ss_pred ccccCcccccccccccc------CCCccChhhhcc
Confidence 44433467777776633 356789999655
No 42
>PF12773 DZR: Double zinc ribbon
Probab=74.52 E-value=2.4 Score=22.95 Aligned_cols=8 Identities=38% Similarity=1.078 Sum_probs=3.5
Q ss_pred cccccccC
Q 042895 37 CSRCKGTL 44 (150)
Q Consensus 37 C~~C~~~l 44 (150)
|..|+..|
T Consensus 15 C~~CG~~l 22 (50)
T PF12773_consen 15 CPHCGTPL 22 (50)
T ss_pred ChhhcCCh
Confidence 34444444
No 43
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.54 E-value=2.2 Score=30.01 Aligned_cols=36 Identities=22% Similarity=0.495 Sum_probs=27.9
Q ss_pred cCCcccccccccCCCCC-ccccCCeeecCchhhhhhc
Q 042895 32 KSCFKCSRCKGTLKLSN-YSSLEGVFYCKPHFEQLLK 67 (150)
Q Consensus 32 ~~Cf~C~~C~~~l~~~~-~~~~~g~~yC~~c~~~~~~ 67 (150)
..++.|..|-.+..... +..+=|.+||..|......
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk 165 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALK 165 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHH
Confidence 35788888877765555 5578899999999988765
No 44
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=72.41 E-value=1.7 Score=31.15 Aligned_cols=31 Identities=29% Similarity=0.521 Sum_probs=26.1
Q ss_pred cccccccccCCCCCccccCCeeecCchhhhh
Q 042895 35 FKCSRCKGTLKLSNYSSLEGVFYCKPHFEQL 65 (150)
Q Consensus 35 f~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~ 65 (150)
-+|+.|+.......-...+|+++|..|+.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 5899999988776777889999999998753
No 45
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=72.10 E-value=2.8 Score=35.20 Aligned_cols=23 Identities=13% Similarity=0.299 Sum_probs=16.2
Q ss_pred eeCCccccccccccccCCcccCC
Q 042895 110 AAESQASHKTCFKCSYAGYSISP 132 (150)
Q Consensus 110 ~~~~~~~H~~Cf~C~~C~~~l~~ 132 (150)
...+...-++|++|..|..+|.+
T Consensus 105 v~sg~~~ckk~~~c~qc~~~lpg 127 (694)
T KOG4443|consen 105 VPSGPWLCKKCTRCRQCDSTLPG 127 (694)
T ss_pred ccCcccccHHHHhhhhccccccc
Confidence 34455567888888888887755
No 46
>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=71.89 E-value=5.2 Score=22.43 Aligned_cols=32 Identities=22% Similarity=0.227 Sum_probs=24.0
Q ss_pred cccccccccCCCCCccccCCeeecCchhhhhhc
Q 042895 35 FKCSRCKGTLKLSNYSSLEGVFYCKPHFEQLLK 67 (150)
Q Consensus 35 f~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~ 67 (150)
|.|..|+..+.. ......|..||+.+..+.+.
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~ 33 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLL 33 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHH
Confidence 567778877755 45567889999999887765
No 47
>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=71.62 E-value=2.6 Score=22.20 Aligned_cols=10 Identities=30% Similarity=0.783 Sum_probs=5.7
Q ss_pred cCCccccccc
Q 042895 138 LEGILYCKHN 147 (150)
Q Consensus 138 ~~g~~yC~~c 147 (150)
++|+.||..|
T Consensus 31 k~g~~~Cv~C 40 (41)
T PF06677_consen 31 KDGKIYCVSC 40 (41)
T ss_pred cCCCEECCCC
Confidence 4556666554
No 48
>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=69.19 E-value=2.4 Score=21.54 Aligned_cols=30 Identities=10% Similarity=0.085 Sum_probs=16.8
Q ss_pred cCCcccc--eeccceeeeCCccccccccccccCCccc
Q 042895 96 NVLLAVK--QCPWEKVAAESQASHKTCFKCSYAGYSI 130 (150)
Q Consensus 96 ~C~~C~~--i~~~~~v~~~~~~~H~~Cf~C~~C~~~l 130 (150)
.|+.|+. -++.+.+...+. -++|..|+..|
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~-----~v~C~~C~~~~ 35 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGG-----KVRCGKCGHVW 35 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCC-----EEECCCCCCEE
Confidence 5888887 233333333332 26677777766
No 49
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=66.35 E-value=2.3 Score=26.88 Aligned_cols=29 Identities=24% Similarity=0.315 Sum_probs=20.4
Q ss_pred cccccccCCcccCCCCcc-ccCCccccccc
Q 042895 119 TCFKCSYAGYSISPSNYA-ALEGILYCKHN 147 (150)
Q Consensus 119 ~Cf~C~~C~~~l~~~~~~-~~~g~~yC~~c 147 (150)
+=|+|+.|-..-..+... ..+|+++|..|
T Consensus 69 DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 69 DEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CceeeeeeeeEechhhhccccCCCEecccc
Confidence 448888887665444444 46899999987
No 50
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=66.18 E-value=4.5 Score=22.62 Aligned_cols=25 Identities=20% Similarity=0.387 Sum_probs=15.4
Q ss_pred ccccccCceeeccceEEeCCccccc
Q 042895 8 QKCKVCEKTVCPVEQLSTDGVVYHK 32 (150)
Q Consensus 8 ~~C~~C~~~I~~~~~~~~~~~~~H~ 32 (150)
.+|..|+++|.+...+.-.+...|+
T Consensus 2 ~~CvVCKqpi~~a~~v~T~~G~VH~ 26 (54)
T PF10886_consen 2 EICVVCKQPIDDALVVETESGPVHP 26 (54)
T ss_pred CeeeeeCCccCcceEEEcCCCccCc
Confidence 3677788888655555544445554
No 51
>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=64.89 E-value=2.8 Score=22.01 Aligned_cols=8 Identities=0% Similarity=-0.396 Sum_probs=4.2
Q ss_pred CcCCcccc
Q 042895 95 KNVLLAVK 102 (150)
Q Consensus 95 ~~C~~C~~ 102 (150)
.+|..|+.
T Consensus 6 y~C~~Cg~ 13 (42)
T PF09723_consen 6 YRCEECGH 13 (42)
T ss_pred EEeCCCCC
Confidence 34555554
No 52
>PRK00807 50S ribosomal protein L24e; Validated
Probab=63.99 E-value=6 Score=21.93 Aligned_cols=32 Identities=28% Similarity=0.674 Sum_probs=20.7
Q ss_pred ccccccCceeeccc---eEEeCCcccccCCcccccccc
Q 042895 8 QKCKVCEKTVCPVE---QLSTDGVVYHKSCFKCSRCKG 42 (150)
Q Consensus 8 ~~C~~C~~~I~~~~---~~~~~~~~~H~~Cf~C~~C~~ 42 (150)
..|..|+..|.++. .+..+|+.|. |-+..|..
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~---Fcs~KC~~ 36 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILY---FCSSKCEK 36 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEE---EeCHHHHH
Confidence 46888888888776 2456777775 44444433
No 53
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=63.57 E-value=1.1 Score=28.06 Aligned_cols=36 Identities=17% Similarity=0.357 Sum_probs=23.5
Q ss_pred CccccccccccccCCcccCCCCccccCCcccccccc
Q 042895 113 SQASHKTCFKCSYAGYSISPSNYAALEGILYCKHNF 148 (150)
Q Consensus 113 ~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~cy 148 (150)
-..++..+.-|-.|.+.|+...|.+-..=|||..-|
T Consensus 55 ~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~spF 90 (105)
T COG4357 55 LQEFNPKAIICGVCRKLLTRAEYGMCGSCPYCQSPF 90 (105)
T ss_pred hhhcCCccEEhhhhhhhhhHHHHhhcCCCCCcCCCC
Confidence 345677777777777777666666666666665544
No 54
>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=63.18 E-value=6.7 Score=20.33 Aligned_cols=31 Identities=23% Similarity=0.626 Sum_probs=14.6
Q ss_pred cccccccCceeeccceEEeCCcccccCCcccccccc
Q 042895 7 QQKCKVCEKTVCPVEQLSTDGVVYHKSCFKCSRCKG 42 (150)
Q Consensus 7 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~ 42 (150)
..+|..|+-.|.+--.+...++.| +|..|+.
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w-----~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTW-----ICNFCGT 32 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEE-----EETTT--
T ss_pred ccccCCCCCEECCcceEcCCCCEE-----ECcCCCC
Confidence 457888887776544555555555 5666654
No 55
>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=62.52 E-value=7.5 Score=19.73 Aligned_cols=31 Identities=26% Similarity=0.485 Sum_probs=19.7
Q ss_pred cccccccCCCCCccccCCeeecCchhhhhhc
Q 042895 37 CSRCKGTLKLSNYSSLEGVFYCKPHFEQLLK 67 (150)
Q Consensus 37 C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~ 67 (150)
|..|...+........=|..||..|..+.+.
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 3445555544224567788899999888765
No 56
>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=62.42 E-value=3.4 Score=25.81 Aligned_cols=43 Identities=14% Similarity=0.262 Sum_probs=28.4
Q ss_pred CCCCCcccccccCceeeccceEEeCCcccccCCcccccccccCCC
Q 042895 2 SFIGTQQKCKVCEKTVCPVEQLSTDGVVYHKSCFKCSRCKGTLKL 46 (150)
Q Consensus 2 ~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~ 46 (150)
++....+.|..|++++..-+.+.+.+-.+. --+|..|+.+++.
T Consensus 28 ~i~~~rS~C~~C~~~L~~~~lIPi~S~l~l--rGrCr~C~~~I~~ 70 (92)
T PF06750_consen 28 SIIFPRSHCPHCGHPLSWWDLIPILSYLLL--RGRCRYCGAPIPP 70 (92)
T ss_pred CccCCCCcCcCCCCcCcccccchHHHHHHh--CCCCcccCCCCCh
Confidence 445556789999999976665554443332 3467778888754
No 57
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=62.36 E-value=4.4 Score=30.46 Aligned_cols=16 Identities=25% Similarity=0.657 Sum_probs=10.8
Q ss_pred CCcccccccccCCCCC
Q 042895 33 SCFKCSRCKGTLKLSN 48 (150)
Q Consensus 33 ~Cf~C~~C~~~l~~~~ 48 (150)
..++|..|++.+....
T Consensus 129 ~r~~c~eCgk~ysT~s 144 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSS 144 (279)
T ss_pred Cceecccccccccccc
Confidence 4667888887765544
No 58
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=61.28 E-value=4 Score=21.78 Aligned_cols=7 Identities=14% Similarity=-0.092 Sum_probs=3.9
Q ss_pred cCCcccc
Q 042895 96 NVLLAVK 102 (150)
Q Consensus 96 ~C~~C~~ 102 (150)
.|..|++
T Consensus 2 ~C~~C~~ 8 (46)
T cd02249 2 SCDGCLK 8 (46)
T ss_pred CCcCCCC
Confidence 3556665
No 59
>PRK00420 hypothetical protein; Validated
Probab=60.17 E-value=5.5 Score=25.88 Aligned_cols=9 Identities=11% Similarity=-0.042 Sum_probs=6.1
Q ss_pred CcCCcccce
Q 042895 95 KNVLLAVKQ 103 (150)
Q Consensus 95 ~~C~~C~~i 103 (150)
..|+.|+.+
T Consensus 24 ~~CP~Cg~p 32 (112)
T PRK00420 24 KHCPVCGLP 32 (112)
T ss_pred CCCCCCCCc
Confidence 567777763
No 60
>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=58.86 E-value=6 Score=27.18 Aligned_cols=35 Identities=9% Similarity=-0.017 Sum_probs=23.2
Q ss_pred CcCCcccceeccce----eeeCCccccccccccccCCccc
Q 042895 95 KNVLLAVKQCPWEK----VAAESQASHKTCFKCSYAGYSI 130 (150)
Q Consensus 95 ~~C~~C~~i~~~~~----v~~~~~~~H~~Cf~C~~C~~~l 130 (150)
..|+.|+..|.|++ |...+..|+.-- -|..|+++.
T Consensus 40 ~~Cp~C~~~IrG~y~v~gv~~~g~~~~~Ps-YC~~CGkpy 78 (158)
T PF10083_consen 40 TSCPNCSTPIRGDYHVEGVFGLGGHYEAPS-YCHNCGKPY 78 (158)
T ss_pred HHCcCCCCCCCCceecCCeeeeCCCCCCCh-hHHhCCCCC
Confidence 57999999666654 344556666332 378888876
No 61
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=58.81 E-value=4.6 Score=21.37 Aligned_cols=9 Identities=11% Similarity=-0.230 Sum_probs=5.6
Q ss_pred CcCCcccce
Q 042895 95 KNVLLAVKQ 103 (150)
Q Consensus 95 ~~C~~C~~i 103 (150)
..|..|+.+
T Consensus 5 ~~C~~C~~~ 13 (44)
T smart00291 5 YSCDTCGKP 13 (44)
T ss_pred cCCCCCCCC
Confidence 457777663
No 62
>PLN02195 cellulose synthase A
Probab=58.21 E-value=10 Score=33.64 Aligned_cols=34 Identities=21% Similarity=0.579 Sum_probs=22.4
Q ss_pred CCCCcccccccCceeeccceEEeCCcccccCCcccccccccC
Q 042895 3 FIGTQQKCKVCEKTVCPVEQLSTDGVVYHKSCFKCSRCKGTL 44 (150)
Q Consensus 3 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l 44 (150)
++++...|..|+..|. +..+|..| -.|..|+-++
T Consensus 2 ~~~~~~~c~~cgd~~~----~~~~g~~f----vaC~eC~~pv 35 (977)
T PLN02195 2 MESGAPICATCGEEVG----VDSNGEAF----VACHECSYPL 35 (977)
T ss_pred CcCCCccceecccccC----cCCCCCeE----EEeccCCCcc
Confidence 4567778999998885 34556655 3456666554
No 63
>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=57.75 E-value=8.7 Score=20.97 Aligned_cols=26 Identities=15% Similarity=0.087 Sum_probs=20.1
Q ss_pred CcCCcccc--eeccce-eeeCCccccccc
Q 042895 95 KNVLLAVK--QCPWEK-VAAESQASHKTC 120 (150)
Q Consensus 95 ~~C~~C~~--i~~~~~-v~~~~~~~H~~C 120 (150)
..|+.|+. +-.+|- |.+.+..|++.|
T Consensus 14 ~~Cp~CGN~~vGngEG~liV~edtfkRtC 42 (49)
T PF12677_consen 14 CKCPKCGNDKVGNGEGTLIVEEDTFKRTC 42 (49)
T ss_pred ccCcccCCcEeecCcceEEEeccceeeee
Confidence 46999998 555553 788899999887
No 64
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=57.46 E-value=6.8 Score=20.54 Aligned_cols=17 Identities=18% Similarity=0.440 Sum_probs=11.1
Q ss_pred cccCCeeecCchhhhhh
Q 042895 50 SSLEGVFYCKPHFEQLL 66 (150)
Q Consensus 50 ~~~~g~~yC~~c~~~~~ 66 (150)
...=|..+|..|..+..
T Consensus 17 l~~CgH~~C~~C~~~~~ 33 (44)
T PF14634_consen 17 LTSCGHIFCEKCLKKLK 33 (44)
T ss_pred EcccCCHHHHHHHHhhc
Confidence 34456677777776655
No 65
>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=56.10 E-value=5.2 Score=20.40 Aligned_cols=9 Identities=0% Similarity=-0.396 Sum_probs=5.9
Q ss_pred CcCCcccce
Q 042895 95 KNVLLAVKQ 103 (150)
Q Consensus 95 ~~C~~C~~i 103 (150)
.+|..|+.+
T Consensus 6 y~C~~Cg~~ 14 (41)
T smart00834 6 YRCEDCGHT 14 (41)
T ss_pred EEcCCCCCE
Confidence 467777773
No 66
>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=55.12 E-value=3.6 Score=24.35 Aligned_cols=12 Identities=25% Similarity=0.296 Sum_probs=4.9
Q ss_pred cccccCCcccCC
Q 042895 121 FKCSYAGYSISP 132 (150)
Q Consensus 121 f~C~~C~~~l~~ 132 (150)
|-|..|+..++.
T Consensus 51 YFC~~c~gLiSK 62 (70)
T PF07191_consen 51 YFCNHCHGLISK 62 (70)
T ss_dssp EE-TTTT-EE-T
T ss_pred eeeccCCceeec
Confidence 346666666543
No 67
>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=54.95 E-value=5.7 Score=21.60 Aligned_cols=11 Identities=0% Similarity=-0.188 Sum_probs=7.3
Q ss_pred CcCCcccceec
Q 042895 95 KNVLLAVKQCP 105 (150)
Q Consensus 95 ~~C~~C~~i~~ 105 (150)
.+|..|+....
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 56888887433
No 68
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=54.88 E-value=11 Score=22.87 Aligned_cols=12 Identities=33% Similarity=0.786 Sum_probs=3.9
Q ss_pred cccccccCceee
Q 042895 7 QQKCKVCEKTVC 18 (150)
Q Consensus 7 ~~~C~~C~~~I~ 18 (150)
..+|..|+..|.
T Consensus 9 ~qiCqiCGD~VG 20 (80)
T PF14569_consen 9 GQICQICGDDVG 20 (80)
T ss_dssp S-B-SSS--B--
T ss_pred CcccccccCccc
Confidence 446777776664
No 69
>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=54.02 E-value=11 Score=21.32 Aligned_cols=31 Identities=23% Similarity=0.464 Sum_probs=16.0
Q ss_pred cccccccCCCCC---ccccCCeeecCchhhhhhc
Q 042895 37 CSRCKGTLKLSN---YSSLEGVFYCKPHFEQLLK 67 (150)
Q Consensus 37 C~~C~~~l~~~~---~~~~~g~~yC~~c~~~~~~ 67 (150)
|..|++.|.+.. +.-.-.=.||.+|....+.
T Consensus 8 CE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~ 41 (57)
T PF06906_consen 8 CECCDKDLPPDSPEAYICSFECTFCADCAETMLN 41 (57)
T ss_pred ccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc
Confidence 445555554433 1112233467777777665
No 70
>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=52.60 E-value=5.9 Score=21.28 Aligned_cols=10 Identities=10% Similarity=0.374 Sum_probs=6.1
Q ss_pred ccccccccCC
Q 042895 141 ILYCKHNFSQ 150 (150)
Q Consensus 141 ~~yC~~cy~~ 150 (150)
.-+|..||.|
T Consensus 23 ~dLC~~CF~~ 32 (45)
T cd02336 23 YDLCPSCYQE 32 (45)
T ss_pred cccChHHHhC
Confidence 4567777653
No 71
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=51.63 E-value=3.8 Score=30.26 Aligned_cols=35 Identities=17% Similarity=0.193 Sum_probs=25.5
Q ss_pred CcCCcccceeccceeeeCCccccccccccccCCcccC
Q 042895 95 KNVLLAVKQCPWEKVAAESQASHKTCFKCSYAGYSIS 131 (150)
Q Consensus 95 ~~C~~C~~i~~~~~v~~~~~~~H~~Cf~C~~C~~~l~ 131 (150)
+-|+-|+.-++.|.|.+.-+ -..+|+|..|++.|-
T Consensus 11 pwcwycnrefddekiliqhq--kakhfkchichkkl~ 45 (341)
T KOG2893|consen 11 PWCWYCNREFDDEKILIQHQ--KAKHFKCHICHKKLF 45 (341)
T ss_pred ceeeecccccchhhhhhhhh--hhccceeeeehhhhc
Confidence 66889988666776555432 356799999999983
No 72
>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=49.74 E-value=5.2 Score=24.78 Aligned_cols=10 Identities=10% Similarity=-0.253 Sum_probs=8.5
Q ss_pred CcCCccccee
Q 042895 95 KNVLLAVKQC 104 (150)
Q Consensus 95 ~~C~~C~~i~ 104 (150)
..|..|++++
T Consensus 55 ~pC~~C~klL 64 (90)
T PF11571_consen 55 TPCKKCGKLL 64 (90)
T ss_pred chhhHHHhHh
Confidence 7899999955
No 73
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=48.33 E-value=12 Score=19.95 Aligned_cols=10 Identities=40% Similarity=1.002 Sum_probs=6.1
Q ss_pred cccccCCccc
Q 042895 121 FKCSYAGYSI 130 (150)
Q Consensus 121 f~C~~C~~~l 130 (150)
.+|..|+..+
T Consensus 20 irC~~CG~rI 29 (44)
T smart00659 20 VRCRECGYRI 29 (44)
T ss_pred eECCCCCceE
Confidence 5666666554
No 74
>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=48.32 E-value=4.9 Score=20.11 Aligned_cols=17 Identities=24% Similarity=0.634 Sum_probs=11.5
Q ss_pred cccccCCcccCCCCccc
Q 042895 121 FKCSYAGYSISPSNYAA 137 (150)
Q Consensus 121 f~C~~C~~~l~~~~~~~ 137 (150)
|.|..|++++....|..
T Consensus 5 ~~C~nC~R~v~a~RfA~ 21 (33)
T PF08209_consen 5 VECPNCGRPVAASRFAP 21 (33)
T ss_dssp EE-TTTSSEEEGGGHHH
T ss_pred EECCCCcCCcchhhhHH
Confidence 56778888887766654
No 75
>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=46.47 E-value=15 Score=20.52 Aligned_cols=24 Identities=29% Similarity=0.718 Sum_probs=16.3
Q ss_pred ccccccCceeeccc---eEEeCCcccc
Q 042895 8 QKCKVCEKTVCPVE---QLSTDGVVYH 31 (150)
Q Consensus 8 ~~C~~C~~~I~~~~---~~~~~~~~~H 31 (150)
..|.-|+..|+++. .+..+|+.++
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~ 30 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFR 30 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEE
Confidence 46888888888776 3455666554
No 76
>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=45.95 E-value=9.8 Score=16.55 Aligned_cols=12 Identities=42% Similarity=0.841 Sum_probs=9.1
Q ss_pred cccccCCcccCC
Q 042895 121 FKCSYAGYSISP 132 (150)
Q Consensus 121 f~C~~C~~~l~~ 132 (150)
|+|..|++.+..
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 578888888744
No 77
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=45.79 E-value=11 Score=28.79 Aligned_cols=69 Identities=12% Similarity=0.152 Sum_probs=44.8
Q ss_pred CcccccccccCCCCCccccCCeeecCchhhhhhccccccCCCCCCCCCCCccccccCCCCCCcCCcccceeccceeeeCC
Q 042895 34 CFKCSRCKGTLKLSNYSSLEGVFYCKPHFEQLLKESSNFNKNFQLPAKSPSKVASMFSGPNKNVLLAVKQCPWEKVAAES 113 (150)
Q Consensus 34 Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~i~~~~~v~~~~ 113 (150)
=+-|..|-..|...-+.-.+|.+.|..|-.++. .+|+.|...+..-+=.++.
T Consensus 48 lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~----------------------------~~CP~Cr~~~g~~R~~amE 99 (299)
T KOG3002|consen 48 LLDCPVCFNPLSPPIFQCDNGHLACSSCRTKVS----------------------------NKCPTCRLPIGNIRCRAME 99 (299)
T ss_pred hccCchhhccCcccceecCCCcEehhhhhhhhc----------------------------ccCCccccccccHHHHHHH
Confidence 356778888887777888899999999976554 5788888855433333444
Q ss_pred ccccccccccc----cCCccc
Q 042895 114 QASHKTCFKCS----YAGYSI 130 (150)
Q Consensus 114 ~~~H~~Cf~C~----~C~~~l 130 (150)
+.--.-.+.|. .|.+.+
T Consensus 100 kV~e~~~vpC~~~~~GC~~~~ 120 (299)
T KOG3002|consen 100 KVAEAVLVPCKNAKLGCTKSF 120 (299)
T ss_pred HHHHhceecccccccCCceee
Confidence 44334444453 455555
No 78
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=45.68 E-value=13 Score=21.18 Aligned_cols=15 Identities=40% Similarity=0.873 Sum_probs=9.0
Q ss_pred cccccccCceeeccc
Q 042895 7 QQKCKVCEKTVCPVE 21 (150)
Q Consensus 7 ~~~C~~C~~~I~~~~ 21 (150)
-..|..|+++|.+++
T Consensus 8 H~HC~VCg~aIp~de 22 (64)
T COG4068 8 HRHCVVCGKAIPPDE 22 (64)
T ss_pred CccccccCCcCCCcc
Confidence 345666666665554
No 79
>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=45.65 E-value=11 Score=18.92 Aligned_cols=26 Identities=4% Similarity=0.133 Sum_probs=12.4
Q ss_pred CCcccceeccce-eeeCCccccccccc
Q 042895 97 VLLAVKQCPWEK-VAAESQASHKTCFK 122 (150)
Q Consensus 97 C~~C~~i~~~~~-v~~~~~~~H~~Cf~ 122 (150)
|+.|...+.... +..-+..||..|+.
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~ 28 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCID 28 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHH
Confidence 556666322222 22245666666653
No 80
>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=45.49 E-value=30 Score=18.48 Aligned_cols=31 Identities=26% Similarity=0.418 Sum_probs=18.5
Q ss_pred ccccccccCCCCCccccCCee-ecCchhhhhhc
Q 042895 36 KCSRCKGTLKLSNYSSLEGVF-YCKPHFEQLLK 67 (150)
Q Consensus 36 ~C~~C~~~l~~~~~~~~~g~~-yC~~c~~~~~~ 67 (150)
.|..|...... ..+..=|.. +|..|..+...
T Consensus 4 ~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~ 35 (50)
T PF13920_consen 4 ECPICFENPRD-VVLLPCGHLCFCEECAERLLK 35 (50)
T ss_dssp B-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHH
T ss_pred CCccCCccCCc-eEEeCCCChHHHHHHhHHhcc
Confidence 35555554322 233456677 89999988764
No 81
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=44.10 E-value=35 Score=24.44 Aligned_cols=31 Identities=23% Similarity=0.560 Sum_probs=19.6
Q ss_pred CcccccccccCCCCCccccCCeeecCchhhhh
Q 042895 34 CFKCSRCKGTLKLSNYSSLEGVFYCKPHFEQL 65 (150)
Q Consensus 34 Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~ 65 (150)
-|.|..|...+.. .....=|..||..|..+.
T Consensus 18 ~~~CpICld~~~d-PVvT~CGH~FC~~CI~~w 48 (193)
T PLN03208 18 DFDCNICLDQVRD-PVVTLCGHLFCWPCIHKW 48 (193)
T ss_pred ccCCccCCCcCCC-cEEcCCCchhHHHHHHHH
Confidence 4667777665533 344556778888887654
No 82
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=44.07 E-value=7.3 Score=21.70 Aligned_cols=26 Identities=19% Similarity=0.503 Sum_probs=11.1
Q ss_pred ccccCCcccCCCCccc---cCCccccccc
Q 042895 122 KCSYAGYSISPSNYAA---LEGILYCKHN 147 (150)
Q Consensus 122 ~C~~C~~~l~~~~~~~---~~g~~yC~~c 147 (150)
+|..|+..|+.+.+.. .+..++|+.|
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~C 52 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNC 52 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCC
Confidence 3455555554333322 1334555544
No 83
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=43.95 E-value=8.9 Score=18.32 Aligned_cols=12 Identities=0% Similarity=-0.338 Sum_probs=5.0
Q ss_pred CcCCcccceecc
Q 042895 95 KNVLLAVKQCPW 106 (150)
Q Consensus 95 ~~C~~C~~i~~~ 106 (150)
..|.+|..++..
T Consensus 2 ~~C~rC~~~~~~ 13 (30)
T PF06827_consen 2 EKCPRCWNYIED 13 (30)
T ss_dssp SB-TTT--BBEE
T ss_pred CcCccCCCcceE
Confidence 457777774443
No 84
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=43.92 E-value=13 Score=20.60 Aligned_cols=30 Identities=20% Similarity=0.492 Sum_probs=20.2
Q ss_pred cccccCceeeccceEEeCCcccccCCcccc
Q 042895 9 KCKVCEKTVCPVEQLSTDGVVYHKSCFKCS 38 (150)
Q Consensus 9 ~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~ 38 (150)
.|+.|+++|...--.+..++.|-..|-.|.
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC 31 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCC 31 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcC
Confidence 589999998632223555677888886654
No 85
>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=43.87 E-value=17 Score=19.63 Aligned_cols=13 Identities=31% Similarity=0.728 Sum_probs=9.4
Q ss_pred CCcccccccCcee
Q 042895 5 GTQQKCKVCEKTV 17 (150)
Q Consensus 5 ~~~~~C~~C~~~I 17 (150)
..+..|..|++.|
T Consensus 9 ~~~~~C~~C~~~i 21 (53)
T PF00130_consen 9 SKPTYCDVCGKFI 21 (53)
T ss_dssp SSTEB-TTSSSBE
T ss_pred CCCCCCcccCccc
Confidence 4556899999998
No 86
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=43.39 E-value=20 Score=20.91 Aligned_cols=22 Identities=23% Similarity=0.487 Sum_probs=14.0
Q ss_pred ccccccccCCCCC---ccccCCeee
Q 042895 36 KCSRCKGTLKLSN---YSSLEGVFY 57 (150)
Q Consensus 36 ~C~~C~~~l~~~~---~~~~~g~~y 57 (150)
+|+-|+..+.++. |+..||.++
T Consensus 5 ~CsFcG~~I~PGtG~m~Vr~Dg~v~ 29 (66)
T COG2075 5 VCSFCGKKIEPGTGIMYVRNDGKVL 29 (66)
T ss_pred EecCcCCccCCCceEEEEecCCeEE
Confidence 4677777776665 455677644
No 87
>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=42.53 E-value=25 Score=17.70 Aligned_cols=31 Identities=16% Similarity=0.355 Sum_probs=19.3
Q ss_pred cccccccCCCCCccccCCeeecCchhhhhhc
Q 042895 37 CSRCKGTLKLSNYSSLEGVFYCKPHFEQLLK 67 (150)
Q Consensus 37 C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~ 67 (150)
|..|...+........=|..||..|..+.+.
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 3445555544333556677888888877765
No 88
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=42.43 E-value=17 Score=24.22 Aligned_cols=25 Identities=24% Similarity=0.486 Sum_probs=19.1
Q ss_pred cccccccCceeeccc---eEEeCCcccc
Q 042895 7 QQKCKVCEKTVCPVE---QLSTDGVVYH 31 (150)
Q Consensus 7 ~~~C~~C~~~I~~~~---~~~~~~~~~H 31 (150)
..+|..|+.+|+|+. +|...|++|+
T Consensus 4 ~e~CsFcG~kIyPG~G~~fVR~DGkvf~ 31 (131)
T PRK14891 4 TRTCDYTGEEIEPGTGTMFVRKDGTVLH 31 (131)
T ss_pred eeeecCcCCcccCCCCcEEEecCCCEEE
Confidence 347999999999987 4566677776
No 89
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=42.19 E-value=8.2 Score=26.16 Aligned_cols=34 Identities=26% Similarity=0.564 Sum_probs=22.2
Q ss_pred cccccCceeeccceEEeCCcccccCCcccccccccCC
Q 042895 9 KCKVCEKTVCPVEQLSTDGVVYHKSCFKCSRCKGTLK 45 (150)
Q Consensus 9 ~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~ 45 (150)
.|+.|+......+.+...+. ..-|.|..|+..|.
T Consensus 101 ~Cp~C~~~y~~~ea~~~~d~---~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 101 KCPNCQSKYTFLEANQLLDM---DGTFTCPRCGEELE 134 (147)
T ss_pred ECcCCCCEeeHHHHHHhcCC---CCcEECCCCCCEEE
Confidence 68899888775554433231 23388999988874
No 90
>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=41.37 E-value=17 Score=29.85 Aligned_cols=37 Identities=16% Similarity=0.309 Sum_probs=17.8
Q ss_pred CcCCcccceeccceeeeCCccccccccccccCCcccC
Q 042895 95 KNVLLAVKQCPWEKVAAESQASHKTCFKCSYAGYSIS 131 (150)
Q Consensus 95 ~~C~~C~~i~~~~~v~~~~~~~H~~Cf~C~~C~~~l~ 131 (150)
..|+.|-..++.--+...+..--++||.|..|...|.
T Consensus 27 ~yCp~CL~~~p~~e~~~~~nrC~r~Cf~CP~C~~~L~ 63 (483)
T PF05502_consen 27 YYCPNCLFEVPSSEARSEKNRCSRNCFDCPICFSPLS 63 (483)
T ss_pred eECccccccCChhhheeccceeccccccCCCCCCcce
Confidence 3455554422222233344444456666666666663
No 91
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=41.04 E-value=12 Score=22.77 Aligned_cols=27 Identities=19% Similarity=0.549 Sum_probs=13.8
Q ss_pred cccCCcccCCCC-cc-ccC---CccccccccC
Q 042895 123 CSYAGYSISPSN-YA-ALE---GILYCKHNFS 149 (150)
Q Consensus 123 C~~C~~~l~~~~-~~-~~~---g~~yC~~cy~ 149 (150)
|..|+.+|.... +. ..| +.-||.-||.
T Consensus 3 CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~ 34 (81)
T PF12674_consen 3 CQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQ 34 (81)
T ss_pred CCcCcCccCCccccccccCCCCchhHHHHHhc
Confidence 566666664433 21 122 3447777764
No 92
>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=41.03 E-value=17 Score=19.14 Aligned_cols=11 Identities=0% Similarity=-0.614 Sum_probs=5.9
Q ss_pred cCCcccceecc
Q 042895 96 NVLLAVKQCPW 106 (150)
Q Consensus 96 ~C~~C~~i~~~ 106 (150)
.|.+|++++.+
T Consensus 2 ~Cd~C~~~i~G 12 (43)
T cd02340 2 ICDGCQGPIVG 12 (43)
T ss_pred CCCCCCCcCcC
Confidence 36666663333
No 93
>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=40.18 E-value=18 Score=18.23 Aligned_cols=11 Identities=36% Similarity=0.797 Sum_probs=4.6
Q ss_pred ccccccCceee
Q 042895 8 QKCKVCEKTVC 18 (150)
Q Consensus 8 ~~C~~C~~~I~ 18 (150)
++|..|+++..
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 45666666654
No 94
>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=40.12 E-value=6.2 Score=20.58 Aligned_cols=27 Identities=22% Similarity=0.329 Sum_probs=15.9
Q ss_pred cCCcccc-eeccceeeeC--Cccccccccc
Q 042895 96 NVLLAVK-QCPWEKVAAE--SQASHKTCFK 122 (150)
Q Consensus 96 ~C~~C~~-i~~~~~v~~~--~~~~H~~Cf~ 122 (150)
.|+.|.. +..++.+... +..||.+|+.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~ 31 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIK 31 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHH
Confidence 4777777 4344443333 6677877754
No 95
>PRK12495 hypothetical protein; Provisional
Probab=40.01 E-value=16 Score=26.69 Aligned_cols=27 Identities=7% Similarity=-0.064 Sum_probs=19.3
Q ss_pred CcCCcccceeccceeeeCCccccccccccccCCcccC
Q 042895 95 KNVLLAVKQCPWEKVAAESQASHKTCFKCSYAGYSIS 131 (150)
Q Consensus 95 ~~C~~C~~i~~~~~v~~~~~~~H~~Cf~C~~C~~~l~ 131 (150)
..|..|+.+|+ . ++.+-.|..|+....
T Consensus 43 ~hC~~CG~PIp---------a-~pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 43 AHCDECGDPIF---------R-HDGQEFCPTCQQPVT 69 (226)
T ss_pred hhcccccCccc---------C-CCCeeECCCCCCccc
Confidence 68999999655 1 256677888887763
No 96
>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=39.93 E-value=20 Score=21.27 Aligned_cols=25 Identities=24% Similarity=0.501 Sum_probs=13.4
Q ss_pred cccccccCceeeccc---eEEeCCcccc
Q 042895 7 QQKCKVCEKTVCPVE---QLSTDGVVYH 31 (150)
Q Consensus 7 ~~~C~~C~~~I~~~~---~~~~~~~~~H 31 (150)
..+|.-|+..|+++. +|..+|+.++
T Consensus 3 ~~~C~Fsg~~I~PG~G~~~Vr~DG~v~~ 30 (71)
T PF01246_consen 3 TEKCSFSGYKIYPGHGKMYVRNDGKVFY 30 (71)
T ss_dssp SEE-TTT-SEE-SSSSEEEE-TTS-EEE
T ss_pred eEEecccCCccCCCCCeEEEecCCCeEE
Confidence 356888888888886 3455566654
No 97
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=39.87 E-value=16 Score=19.36 Aligned_cols=27 Identities=22% Similarity=0.263 Sum_probs=17.2
Q ss_pred CcCCcccc-eeccceeeeCCccccccccccccCCccc
Q 042895 95 KNVLLAVK-QCPWEKVAAESQASHKTCFKCSYAGYSI 130 (150)
Q Consensus 95 ~~C~~C~~-i~~~~~v~~~~~~~H~~Cf~C~~C~~~l 130 (150)
.+|..|+. +...+... =++|..|+..+
T Consensus 4 y~C~~CG~~~~~~~~~~---------~~~Cp~CG~~~ 31 (46)
T PRK00398 4 YKCARCGREVELDEYGT---------GVRCPYCGYRI 31 (46)
T ss_pred EECCCCCCEEEECCCCC---------ceECCCCCCeE
Confidence 67999988 32222111 37899998876
No 98
>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=38.76 E-value=26 Score=23.67 Aligned_cols=39 Identities=15% Similarity=0.433 Sum_probs=22.9
Q ss_pred CcccccccCceeeccce--E--EeCCc--ccccCCcccccccccC
Q 042895 6 TQQKCKVCEKTVCPVEQ--L--STDGV--VYHKSCFKCSRCKGTL 44 (150)
Q Consensus 6 ~~~~C~~C~~~I~~~~~--~--~~~~~--~~H~~Cf~C~~C~~~l 44 (150)
...+|..|+.++...+. + .+... ..+..-+.|..|++-.
T Consensus 90 ~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 90 IFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 35689999998754331 1 11112 2355567888887643
No 99
>PHA00626 hypothetical protein
Probab=38.60 E-value=27 Score=19.72 Aligned_cols=38 Identities=11% Similarity=0.141 Sum_probs=22.4
Q ss_pred cCCcccc--eeccceeeeCCccccccccccccCCcccCCCCcccc
Q 042895 96 NVLLAVK--QCPWEKVAAESQASHKTCFKCSYAGYSISPSNYAAL 138 (150)
Q Consensus 96 ~C~~C~~--i~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~ 138 (150)
.|+.|+. |+....+.- |..=|+|..|+-.++.+.|.+.
T Consensus 2 ~CP~CGS~~Ivrcg~cr~-----~snrYkCkdCGY~ft~~~~~~~ 41 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRG-----WSDDYVCCDCGYNDSKDAFGER 41 (59)
T ss_pred CCCCCCCceeeeeceecc-----cCcceEcCCCCCeechhhhhhc
Confidence 3777776 332221111 3344789999988876666554
No 100
>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=38.00 E-value=23 Score=16.28 Aligned_cols=9 Identities=22% Similarity=1.025 Sum_probs=4.0
Q ss_pred ccccCceee
Q 042895 10 CKVCEKTVC 18 (150)
Q Consensus 10 C~~C~~~I~ 18 (150)
|..|+..|.
T Consensus 1 C~sC~~~i~ 9 (24)
T PF07754_consen 1 CTSCGRPIA 9 (24)
T ss_pred CccCCCccc
Confidence 334444444
No 101
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=37.80 E-value=29 Score=31.30 Aligned_cols=29 Identities=28% Similarity=0.688 Sum_probs=18.5
Q ss_pred ccccccCceeeccceEEeCCcccccCCcccccccccC
Q 042895 8 QKCKVCEKTVCPVEQLSTDGVVYHKSCFKCSRCKGTL 44 (150)
Q Consensus 8 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l 44 (150)
.+|..|+..|. +..+|..| -.|..|+-++
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 37888888775 34556655 3456666655
No 102
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=37.78 E-value=11 Score=18.05 Aligned_cols=17 Identities=18% Similarity=0.454 Sum_probs=12.1
Q ss_pred cccccCCcccCCCCccc
Q 042895 121 FKCSYAGYSISPSNYAA 137 (150)
Q Consensus 121 f~C~~C~~~l~~~~~~~ 137 (150)
|.|-.|++.+.+..+..
T Consensus 1 ~sCiDC~~~F~~~~y~~ 17 (28)
T PF08790_consen 1 FSCIDCSKDFDGDSYKS 17 (28)
T ss_dssp EEETTTTEEEEGGGTTT
T ss_pred CeeecCCCCcCcCCcCC
Confidence 57888898886665543
No 103
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=36.12 E-value=42 Score=24.67 Aligned_cols=37 Identities=24% Similarity=0.472 Sum_probs=26.0
Q ss_pred cccCCcccccccccCCCCCccccCCeeecCchhhhhhc
Q 042895 30 YHKSCFKCSRCKGTLKLSNYSSLEGVFYCKPHFEQLLK 67 (150)
Q Consensus 30 ~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~ 67 (150)
--...|-|..|-..- .......=|.+||.+|..+-+.
T Consensus 43 ~~~~~FdCNICLd~a-kdPVvTlCGHLFCWpClyqWl~ 79 (230)
T KOG0823|consen 43 RDGGFFDCNICLDLA-KDPVVTLCGHLFCWPCLYQWLQ 79 (230)
T ss_pred CCCCceeeeeecccc-CCCEEeecccceehHHHHHHHh
Confidence 345678888884432 3356778899999999877554
No 104
>PLN02189 cellulose synthase
Probab=35.95 E-value=32 Score=30.96 Aligned_cols=8 Identities=38% Similarity=1.011 Sum_probs=4.4
Q ss_pred eecCchhh
Q 042895 56 FYCKPHFE 63 (150)
Q Consensus 56 ~yC~~c~~ 63 (150)
+.|.+||+
T Consensus 62 pvCr~Cye 69 (1040)
T PLN02189 62 PVCRPCYE 69 (1040)
T ss_pred ccccchhh
Confidence 44666664
No 105
>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=35.42 E-value=19 Score=15.31 Aligned_cols=12 Identities=33% Similarity=0.780 Sum_probs=6.9
Q ss_pred cccccCCcccCC
Q 042895 121 FKCSYAGYSISP 132 (150)
Q Consensus 121 f~C~~C~~~l~~ 132 (150)
|.|..|+..+..
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 568888887743
No 106
>PRK04023 DNA polymerase II large subunit; Validated
Probab=34.67 E-value=45 Score=30.02 Aligned_cols=13 Identities=8% Similarity=0.197 Sum_probs=7.9
Q ss_pred CcCCcccc-eeccc
Q 042895 95 KNVLLAVK-QCPWE 107 (150)
Q Consensus 95 ~~C~~C~~-i~~~~ 107 (150)
..|+.|+. +.+..
T Consensus 664 y~CPKCG~El~~~s 677 (1121)
T PRK04023 664 DECEKCGREPTPYS 677 (1121)
T ss_pred CcCCCCCCCCCccc
Confidence 56777777 44444
No 107
>PLN02436 cellulose synthase A
Probab=34.61 E-value=34 Score=30.88 Aligned_cols=9 Identities=22% Similarity=1.125 Sum_probs=4.6
Q ss_pred cccccCcee
Q 042895 9 KCKVCEKTV 17 (150)
Q Consensus 9 ~C~~C~~~I 17 (150)
+|..|+..|
T Consensus 38 iCqICGD~V 46 (1094)
T PLN02436 38 TCQICGDEI 46 (1094)
T ss_pred ccccccccc
Confidence 455555444
No 108
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=34.41 E-value=17 Score=31.79 Aligned_cols=36 Identities=11% Similarity=0.135 Sum_probs=28.9
Q ss_pred CcCCcccceeccceeeeC-Cccccccccc-----cccCCccc
Q 042895 95 KNVLLAVKQCPWEKVAAE-SQASHKTCFK-----CSYAGYSI 130 (150)
Q Consensus 95 ~~C~~C~~i~~~~~v~~~-~~~~H~~Cf~-----C~~C~~~l 130 (150)
.+|..|...+.-..|..+ +..||..||. |..|.-.+
T Consensus 841 skCs~C~~~LdlP~VhF~CgHsyHqhC~e~~~~~CP~C~~e~ 882 (933)
T KOG2114|consen 841 SKCSACEGTLDLPFVHFLCGHSYHQHCLEDKEDKCPKCLPEL 882 (933)
T ss_pred eeecccCCccccceeeeecccHHHHHhhccCcccCCccchhh
Confidence 789999986666667766 8889999987 88887644
No 109
>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=34.36 E-value=19 Score=18.79 Aligned_cols=14 Identities=14% Similarity=0.441 Sum_probs=9.3
Q ss_pred ccccccccCCcccC
Q 042895 118 KTCFKCSYAGYSIS 131 (150)
Q Consensus 118 ~~Cf~C~~C~~~l~ 131 (150)
..=+.|..|+..|.
T Consensus 17 ~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 17 RGELVCPNCGLVLE 30 (43)
T ss_dssp TTEEEETTT-BBEE
T ss_pred CCeEECCCCCCEee
Confidence 34468899988884
No 110
>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=34.33 E-value=14 Score=19.58 Aligned_cols=19 Identities=37% Similarity=0.817 Sum_probs=10.1
Q ss_pred cccCCcccCCCCccccCCccccc
Q 042895 123 CSYAGYSISPSNYAALEGILYCK 145 (150)
Q Consensus 123 C~~C~~~l~~~~~~~~~g~~yC~ 145 (150)
|..|.+++.. ..++.+||.
T Consensus 9 C~~Cdk~~~~----~~~~~lYCS 27 (43)
T PF12855_consen 9 CIVCDKQIDP----PDDGSLYCS 27 (43)
T ss_pred HHHhhccccC----CCCCccccC
Confidence 3445555532 346677773
No 111
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=34.05 E-value=19 Score=15.91 Aligned_cols=13 Identities=31% Similarity=0.539 Sum_probs=9.8
Q ss_pred cccccCCcccCCC
Q 042895 121 FKCSYAGYSISPS 133 (150)
Q Consensus 121 f~C~~C~~~l~~~ 133 (150)
|.|..|++.+.+.
T Consensus 1 ~~C~~C~~~f~s~ 13 (25)
T PF12874_consen 1 FYCDICNKSFSSE 13 (25)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCCCCCCcCCH
Confidence 5788999888543
No 112
>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=33.66 E-value=19 Score=17.10 Aligned_cols=12 Identities=33% Similarity=0.772 Sum_probs=3.3
Q ss_pred cccccCCcccCC
Q 042895 121 FKCSYAGYSISP 132 (150)
Q Consensus 121 f~C~~C~~~l~~ 132 (150)
|+|..|++++.+
T Consensus 1 ~~C~~C~~~~~~ 12 (30)
T PF07649_consen 1 FRCDACGKPIDG 12 (30)
T ss_dssp ---TTTS----S
T ss_pred CcCCcCCCcCCC
Confidence 456677776644
No 113
>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=33.37 E-value=28 Score=18.65 Aligned_cols=13 Identities=0% Similarity=-0.363 Sum_probs=7.8
Q ss_pred cCCcccc-eeccce
Q 042895 96 NVLLAVK-QCPWEK 108 (150)
Q Consensus 96 ~C~~C~~-i~~~~~ 108 (150)
.|.+|+. +|.+.+
T Consensus 2 ~Cd~C~~~pI~G~R 15 (45)
T cd02344 2 TCDGCQMFPINGPR 15 (45)
T ss_pred CCCCCCCCCCccCe
Confidence 3677776 655543
No 114
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=33.30 E-value=1.3e+02 Score=23.26 Aligned_cols=10 Identities=40% Similarity=0.846 Sum_probs=7.2
Q ss_pred cccccccCce
Q 042895 7 QQKCKVCEKT 16 (150)
Q Consensus 7 ~~~C~~C~~~ 16 (150)
...|+.|+..
T Consensus 187 ~~~CPvCGs~ 196 (309)
T PRK03564 187 RQFCPVCGSM 196 (309)
T ss_pred CCCCCCCCCc
Confidence 4578888775
No 115
>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=32.22 E-value=22 Score=19.27 Aligned_cols=12 Identities=8% Similarity=-0.219 Sum_probs=7.8
Q ss_pred cCCcccc-eeccc
Q 042895 96 NVLLAVK-QCPWE 107 (150)
Q Consensus 96 ~C~~C~~-i~~~~ 107 (150)
.|..|++ +|.+.
T Consensus 2 ~Cd~C~~~pI~G~ 14 (48)
T cd02341 2 KCDSCGIEPIPGT 14 (48)
T ss_pred CCCCCCCCccccc
Confidence 4777777 65554
No 116
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=32.22 E-value=28 Score=19.82 Aligned_cols=24 Identities=25% Similarity=0.494 Sum_probs=16.7
Q ss_pred ccccccccCCCCC--ccccCCeeecC
Q 042895 36 KCSRCKGTLKLSN--YSSLEGVFYCK 59 (150)
Q Consensus 36 ~C~~C~~~l~~~~--~~~~~g~~yC~ 59 (150)
.|..|++.|..+. |.-++.+.+|.
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS 43 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCS 43 (58)
T ss_pred HHHccCCCCCCCCCeeeecccccccc
Confidence 4677889997544 44566778885
No 117
>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=32.13 E-value=29 Score=18.48 Aligned_cols=13 Identities=0% Similarity=-0.386 Sum_probs=8.8
Q ss_pred cCCcccc-eeccce
Q 042895 96 NVLLAVK-QCPWEK 108 (150)
Q Consensus 96 ~C~~C~~-i~~~~~ 108 (150)
.|.+|+. +|.+.+
T Consensus 2 ~CDgCg~~PI~G~R 15 (43)
T cd02342 2 QCDGCGVLPITGPR 15 (43)
T ss_pred CCCCCCCCcccccc
Confidence 4778887 666654
No 118
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=31.99 E-value=22 Score=16.09 Aligned_cols=13 Identities=31% Similarity=0.654 Sum_probs=9.7
Q ss_pred cccccCCcccCCC
Q 042895 121 FKCSYAGYSISPS 133 (150)
Q Consensus 121 f~C~~C~~~l~~~ 133 (150)
|.|..|++.+...
T Consensus 2 ~~C~~C~~~F~~~ 14 (27)
T PF13912_consen 2 FECDECGKTFSSL 14 (27)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCccCCccCCh
Confidence 5788899888543
No 119
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=31.80 E-value=18 Score=26.07 Aligned_cols=33 Identities=18% Similarity=0.279 Sum_probs=24.1
Q ss_pred CcccccccccCCCCCccccCCeeecCchhhhhhc
Q 042895 34 CFKCSRCKGTLKLSNYSSLEGVFYCKPHFEQLLK 67 (150)
Q Consensus 34 Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~ 67 (150)
=|.|..|.+.... ..+..-|..+|..|+.+.+.
T Consensus 196 PF~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~ 228 (259)
T COG5152 196 PFLCGICKKDYES-PVVTECGHSFCSLCAIRKYQ 228 (259)
T ss_pred ceeehhchhhccc-hhhhhcchhHHHHHHHHHhc
Confidence 4788888876633 45556788899999987765
No 120
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=31.13 E-value=16 Score=28.17 Aligned_cols=29 Identities=14% Similarity=0.251 Sum_probs=18.4
Q ss_pred ccccccccCCCCCccccCCeeecCchhhh
Q 042895 36 KCSRCKGTLKLSNYSSLEGVFYCKPHFEQ 64 (150)
Q Consensus 36 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~ 64 (150)
-|..|+.++.--...+.=..++|.+|...
T Consensus 92 fCd~Cd~PI~IYGRmIPCkHvFCl~CAr~ 120 (389)
T KOG2932|consen 92 FCDRCDFPIAIYGRMIPCKHVFCLECARS 120 (389)
T ss_pred eecccCCcceeeecccccchhhhhhhhhc
Confidence 47788887755444455566777777543
No 121
>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=30.99 E-value=37 Score=15.47 Aligned_cols=13 Identities=23% Similarity=0.388 Sum_probs=10.1
Q ss_pred cccccCCcccCCC
Q 042895 121 FKCSYAGYSISPS 133 (150)
Q Consensus 121 f~C~~C~~~l~~~ 133 (150)
|.|..|++.+.+.
T Consensus 2 ~~C~~C~k~f~~~ 14 (27)
T PF12171_consen 2 FYCDACDKYFSSE 14 (27)
T ss_dssp CBBTTTTBBBSSH
T ss_pred CCcccCCCCcCCH
Confidence 6789999988544
No 122
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.94 E-value=31 Score=26.39 Aligned_cols=33 Identities=18% Similarity=0.362 Sum_probs=24.0
Q ss_pred CcccccccccCCCCCccccCCeeecCchhhhhhc
Q 042895 34 CFKCSRCKGTLKLSNYSSLEGVFYCKPHFEQLLK 67 (150)
Q Consensus 34 Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~ 67 (150)
=|.|..|++.... ..+..-+..+|+.|..+.+.
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 3677788877643 45567788899999877664
No 123
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=30.82 E-value=50 Score=30.49 Aligned_cols=7 Identities=0% Similarity=-0.363 Sum_probs=3.8
Q ss_pred cCCcccc
Q 042895 96 NVLLAVK 102 (150)
Q Consensus 96 ~C~~C~~ 102 (150)
.|+.|+.
T Consensus 711 ~CP~CGt 717 (1337)
T PRK14714 711 ECPRCDV 717 (1337)
T ss_pred cCCCCCC
Confidence 4555554
No 124
>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=30.52 E-value=46 Score=17.61 Aligned_cols=26 Identities=8% Similarity=0.174 Sum_probs=13.4
Q ss_pred CCcccc-eeccceeeeC--Cccccccccc
Q 042895 97 VLLAVK-QCPWEKVAAE--SQASHKTCFK 122 (150)
Q Consensus 97 C~~C~~-i~~~~~v~~~--~~~~H~~Cf~ 122 (150)
|..|++ -..++.|.=. ++.||..|..
T Consensus 2 C~vC~~~~~~~~~i~C~~C~~~~H~~C~~ 30 (51)
T PF00628_consen 2 CPVCGQSDDDGDMIQCDSCNRWYHQECVG 30 (51)
T ss_dssp BTTTTSSCTTSSEEEBSTTSCEEETTTST
T ss_pred CcCCCCcCCCCCeEEcCCCChhhCcccCC
Confidence 555555 2233334333 4567887754
No 125
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.99 E-value=57 Score=25.20 Aligned_cols=16 Identities=19% Similarity=0.387 Sum_probs=10.7
Q ss_pred cCCeeecCchhhhhhc
Q 042895 52 LEGVFYCKPHFEQLLK 67 (150)
Q Consensus 52 ~~g~~yC~~c~~~~~~ 67 (150)
.=|..+|..|..+++.
T Consensus 25 ~CGH~~C~sCv~~l~~ 40 (309)
T TIGR00570 25 VCGHTLCESCVDLLFV 40 (309)
T ss_pred CCCCcccHHHHHHHhc
Confidence 3456678888777664
No 126
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=29.90 E-value=30 Score=26.20 Aligned_cols=11 Identities=27% Similarity=0.615 Sum_probs=4.6
Q ss_pred ccccccCceee
Q 042895 8 QKCKVCEKTVC 18 (150)
Q Consensus 8 ~~C~~C~~~I~ 18 (150)
..|+.||..-.
T Consensus 173 g~CPvCGs~P~ 183 (290)
T PF04216_consen 173 GYCPVCGSPPV 183 (290)
T ss_dssp SS-TTT---EE
T ss_pred CcCCCCCCcCc
Confidence 57888877643
No 127
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=29.70 E-value=26 Score=30.12 Aligned_cols=32 Identities=16% Similarity=0.131 Sum_probs=26.3
Q ss_pred CcCCcccceeccceeeeCCccccccccccccCCccc
Q 042895 95 KNVLLAVKQCPWEKVAAESQASHKTCFKCSYAGYSI 130 (150)
Q Consensus 95 ~~C~~C~~i~~~~~v~~~~~~~H~~Cf~C~~C~~~l 130 (150)
+.|..|.+ |+-...++.||..=..|..|+-.+
T Consensus 152 ~lC~~C~~----EY~dP~nRRfHAQp~aCp~CGP~~ 183 (750)
T COG0068 152 PLCPFCDK----EYKDPLNRRFHAQPIACPKCGPHL 183 (750)
T ss_pred cCCHHHHH----HhcCccccccccccccCcccCCCe
Confidence 67888876 455688999999999999999765
No 128
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=29.61 E-value=26 Score=25.59 Aligned_cols=8 Identities=0% Similarity=-0.035 Sum_probs=5.2
Q ss_pred CcCCcccc
Q 042895 95 KNVLLAVK 102 (150)
Q Consensus 95 ~~C~~C~~ 102 (150)
..|..|++
T Consensus 150 ~~C~~Cg~ 157 (247)
T PRK00085 150 DHCAVCGA 157 (247)
T ss_pred hhHhcCCC
Confidence 46667766
No 129
>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=29.46 E-value=18 Score=19.95 Aligned_cols=8 Identities=13% Similarity=-0.272 Sum_probs=6.6
Q ss_pred CcCCcccc
Q 042895 95 KNVLLAVK 102 (150)
Q Consensus 95 ~~C~~C~~ 102 (150)
-+|..|++
T Consensus 5 iRC~~Cnk 12 (51)
T PF10122_consen 5 IRCGHCNK 12 (51)
T ss_pred eeccchhH
Confidence 57888988
No 130
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=29.37 E-value=53 Score=29.60 Aligned_cols=54 Identities=11% Similarity=0.212 Sum_probs=34.4
Q ss_pred CCCCcccccccCceeeccc-eEEeCCcccccCCcccccccccCCCCCccc-cCCeeecCch
Q 042895 3 FIGTQQKCKVCEKTVCPVE-QLSTDGVVYHKSCFKCSRCKGTLKLSNYSS-LEGVFYCKPH 61 (150)
Q Consensus 3 ~~~~~~~C~~C~~~I~~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~-~~g~~yC~~c 61 (150)
|+.+..+|++|+.|+...+ ++-..+.... ++|..|++.... |.. .+--|||-..
T Consensus 792 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~--~~~~~~~~~~~~~~ 847 (1006)
T PRK12775 792 AETGVATCPKCHRPLEGDEEYVCCATSELQ---WRCDDCGKVSEG--FAFPYGMCPACGGK 847 (1006)
T ss_pred ccCCCccCcccCCCCCCCceeEEecCccee---eehhhhcccccc--ccCCcCcCcccccc
Confidence 5667789999999998655 5654444433 478899886432 333 3444555544
No 131
>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=29.27 E-value=32 Score=18.53 Aligned_cols=12 Identities=8% Similarity=-0.282 Sum_probs=7.1
Q ss_pred cCCcccc-eeccc
Q 042895 96 NVLLAVK-QCPWE 107 (150)
Q Consensus 96 ~C~~C~~-i~~~~ 107 (150)
.|..|.+ ++.+.
T Consensus 2 ~Cd~C~~~~~~g~ 14 (49)
T cd02335 2 HCDYCSKDITGTI 14 (49)
T ss_pred CCCCcCCCCCCCc
Confidence 4777777 54443
No 132
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=28.70 E-value=28 Score=16.04 Aligned_cols=10 Identities=20% Similarity=0.517 Sum_probs=6.3
Q ss_pred cccccCceee
Q 042895 9 KCKVCEKTVC 18 (150)
Q Consensus 9 ~C~~C~~~I~ 18 (150)
.|..|+..|.
T Consensus 4 ~Cp~Cg~~~~ 13 (26)
T PF13248_consen 4 FCPNCGAEID 13 (26)
T ss_pred CCcccCCcCC
Confidence 4667776554
No 133
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=28.55 E-value=42 Score=28.68 Aligned_cols=10 Identities=20% Similarity=0.394 Sum_probs=6.6
Q ss_pred cccccCceee
Q 042895 9 KCKVCEKTVC 18 (150)
Q Consensus 9 ~C~~C~~~I~ 18 (150)
+|+.|+..+.
T Consensus 3 ~Cp~Cg~~n~ 12 (645)
T PRK14559 3 ICPQCQFENP 12 (645)
T ss_pred cCCCCCCcCC
Confidence 5777776664
No 134
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=28.53 E-value=24 Score=24.54 Aligned_cols=40 Identities=13% Similarity=0.348 Sum_probs=24.3
Q ss_pred CCCcccccccCceeeccc---eE-EeCC--cccccCCccccccccc
Q 042895 4 IGTQQKCKVCEKTVCPVE---QL-STDG--VVYHKSCFKCSRCKGT 43 (150)
Q Consensus 4 ~~~~~~C~~C~~~I~~~~---~~-~~~~--~~~H~~Cf~C~~C~~~ 43 (150)
.....+|+.|+.++.... +. .+.. ...+.+..+|..|++-
T Consensus 94 ~~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~Cgki 139 (165)
T COG1656 94 FPEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKI 139 (165)
T ss_pred ccccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccc
Confidence 345678999999886432 11 1111 2346677788888764
No 135
>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=28.46 E-value=13 Score=19.55 Aligned_cols=26 Identities=15% Similarity=0.218 Sum_probs=9.6
Q ss_pred CCcccc-eeccceee--eCCccccccccc
Q 042895 97 VLLAVK-QCPWEKVA--AESQASHKTCFK 122 (150)
Q Consensus 97 C~~C~~-i~~~~~v~--~~~~~~H~~Cf~ 122 (150)
|..|++ ++-+.+=. .=+..||..|+.
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~ 29 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFK 29 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHH
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHH
Confidence 455666 33333211 123458888864
No 136
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=28.40 E-value=17 Score=31.18 Aligned_cols=33 Identities=21% Similarity=0.401 Sum_probs=23.0
Q ss_pred CcccccccccCCCCCccccCCeeecCchhhhhhc
Q 042895 34 CFKCSRCKGTLKLSNYSSLEGVFYCKPHFEQLLK 67 (150)
Q Consensus 34 Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~ 67 (150)
=++|+.|+....+ ....+=+..||..|-..++.
T Consensus 643 ~LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~e 675 (698)
T KOG0978|consen 643 LLKCSVCNTRWKD-AVITKCGHVFCEECVQTRYE 675 (698)
T ss_pred ceeCCCccCchhh-HHHHhcchHHHHHHHHHHHH
Confidence 3578888865432 23456778899999887765
No 137
>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 COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=28.17 E-value=28 Score=25.79 Aligned_cols=8 Identities=0% Similarity=-0.209 Sum_probs=4.5
Q ss_pred CcCCcccc
Q 042895 95 KNVLLAVK 102 (150)
Q Consensus 95 ~~C~~C~~ 102 (150)
..|+.|+.
T Consensus 155 ~~Ca~cg~ 162 (251)
T COG1381 155 TSCARCGT 162 (251)
T ss_pred HHHhCcCC
Confidence 45555555
No 139
>PRK05978 hypothetical protein; Provisional
Probab=27.64 E-value=44 Score=22.85 Aligned_cols=30 Identities=10% Similarity=0.039 Sum_probs=19.7
Q ss_pred CcCCcccc-eeccceeeeCCccccccccccccCCcccCC
Q 042895 95 KNVLLAVK-QCPWEKVAAESQASHKTCFKCSYAGYSISP 132 (150)
Q Consensus 95 ~~C~~C~~-i~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~ 132 (150)
-+|++|++ -+-..++ +---+|+.|+..+..
T Consensus 34 grCP~CG~G~LF~g~L--------kv~~~C~~CG~~~~~ 64 (148)
T PRK05978 34 GRCPACGEGKLFRAFL--------KPVDHCAACGEDFTH 64 (148)
T ss_pred CcCCCCCCCccccccc--------ccCCCccccCCcccc
Confidence 68999999 4443333 333458888888743
No 140
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.55 E-value=28 Score=26.58 Aligned_cols=33 Identities=21% Similarity=0.511 Sum_probs=17.8
Q ss_pred cccccccccCCCCCcc---ccCCeeecCchhhhhhc
Q 042895 35 FKCSRCKGTLKLSNYS---SLEGVFYCKPHFEQLLK 67 (150)
Q Consensus 35 f~C~~C~~~l~~~~~~---~~~g~~yC~~c~~~~~~ 67 (150)
+.|..|+..|++..|+ ......||-+|..+.+.
T Consensus 269 LcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK 304 (352)
T KOG3579|consen 269 LCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIK 304 (352)
T ss_pred eeehhhhhhhccCceeecCCCcccceecccCHHHHH
Confidence 5566666666665554 34455556555544443
No 141
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=27.52 E-value=28 Score=19.85 Aligned_cols=10 Identities=40% Similarity=0.962 Sum_probs=5.4
Q ss_pred cccccCceee
Q 042895 9 KCKVCEKTVC 18 (150)
Q Consensus 9 ~C~~C~~~I~ 18 (150)
.|..||++|.
T Consensus 5 HC~~CG~~Ip 14 (59)
T PF09889_consen 5 HCPVCGKPIP 14 (59)
T ss_pred cCCcCCCcCC
Confidence 3555555554
No 142
>PHA00080 DksA-like zinc finger domain containing protein
Probab=27.43 E-value=14 Score=21.97 Aligned_cols=31 Identities=13% Similarity=0.107 Sum_probs=19.3
Q ss_pred CcCCcccceeccceeeeCCccccccccccccCCccc
Q 042895 95 KNVLLAVKQCPWEKVAAESQASHKTCFKCSYAGYSI 130 (150)
Q Consensus 95 ~~C~~C~~i~~~~~v~~~~~~~H~~Cf~C~~C~~~l 130 (150)
..|..|++.|+..++.+. +.+-.|..|....
T Consensus 32 ~~C~~Cg~~Ip~~Rl~a~-----P~~~~Cv~Cq~~~ 62 (72)
T PHA00080 32 THCEECGDPIPEARREAV-----PGCRTCVSCQEIL 62 (72)
T ss_pred CEecCCCCcCcHHHHHhC-----CCccCcHHHHHHH
Confidence 579999997676665443 3344566665544
No 143
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=26.92 E-value=56 Score=29.53 Aligned_cols=30 Identities=27% Similarity=0.695 Sum_probs=18.3
Q ss_pred cccccccCceeeccceEEeCCcccccCCcccccccccC
Q 042895 7 QQKCKVCEKTVCPVEQLSTDGVVYHKSCFKCSRCKGTL 44 (150)
Q Consensus 7 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l 44 (150)
...|..|+..|. +..+|..| -.|..|+-++
T Consensus 15 ~~~c~iCGd~vg----~~~~Ge~F----VAC~eC~fpv 44 (1044)
T PLN02915 15 AKTCRVCGDEVG----VKEDGQPF----VACHVCGFPV 44 (1044)
T ss_pred cchhhccccccC----cCCCCCEE----EEeccCCCcc
Confidence 346888887774 34556655 3456666555
No 144
>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=26.59 E-value=25 Score=19.00 Aligned_cols=13 Identities=8% Similarity=-0.202 Sum_probs=8.1
Q ss_pred cCCcccc-eeccce
Q 042895 96 NVLLAVK-QCPWEK 108 (150)
Q Consensus 96 ~C~~C~~-i~~~~~ 108 (150)
.|..|++ +|.+.+
T Consensus 2 ~C~~C~~~~i~g~R 15 (49)
T cd02338 2 SCDGCGKSNFTGRR 15 (49)
T ss_pred CCCCCcCCCcEEee
Confidence 4788885 555543
No 145
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=25.74 E-value=52 Score=18.37 Aligned_cols=29 Identities=7% Similarity=-0.117 Sum_probs=17.4
Q ss_pred CcCCcccc-eeccceeeeCCccccccccccccCCccc
Q 042895 95 KNVLLAVK-QCPWEKVAAESQASHKTCFKCSYAGYSI 130 (150)
Q Consensus 95 ~~C~~C~~-i~~~~~v~~~~~~~H~~Cf~C~~C~~~l 130 (150)
..|+.|+. +-..+.+. |. -..|..|+..|
T Consensus 3 ~~CP~CG~~iev~~~~~--Ge-----iV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPEL--GE-----LVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCcc--CC-----EEeCCCCCCEE
Confidence 47999998 42222211 32 34788888877
No 146
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=25.56 E-value=16 Score=27.25 Aligned_cols=41 Identities=12% Similarity=0.214 Sum_probs=25.7
Q ss_pred cCCcccceeccceeeeCCccccccccccccCCcccCCCCcc
Q 042895 96 NVLLAVKQCPWEKVAAESQASHKTCFKCSYAGYSISPSNYA 136 (150)
Q Consensus 96 ~C~~C~~i~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~ 136 (150)
.|..|+..+.-..|.---...|..+|.|-+|++.+.+..|.
T Consensus 5 tCnvCgEsvKKp~vekH~srCrn~~fSCIDC~k~F~~~sYk 45 (276)
T KOG2186|consen 5 TCNVCGESVKKPQVEKHMSRCRNAYFSCIDCGKTFERVSYK 45 (276)
T ss_pred ehhhhhhhccccchHHHHHhccCCeeEEeecccccccchhh
Confidence 47888874333222211122467899999999999765554
No 147
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=25.29 E-value=32 Score=28.89 Aligned_cols=32 Identities=22% Similarity=0.498 Sum_probs=22.5
Q ss_pred ccccccccCCcccCCCC-----ccccCCccccccccC
Q 042895 118 KTCFKCSYAGYSISPSN-----YAALEGILYCKHNFS 149 (150)
Q Consensus 118 ~~Cf~C~~C~~~l~~~~-----~~~~~g~~yC~~cy~ 149 (150)
..-|+|+.|+++|+... +-...|..||..|..
T Consensus 338 aQ~~~CAgC~~~i~~~~~~~~R~C~y~G~y~C~~Ch~ 374 (580)
T KOG1829|consen 338 AQNFRCAGCGHTIGPDLEQRPRLCRYLGKYFCDCCHQ 374 (580)
T ss_pred ccCceecccCCCcccccccchhHhhhhhhhhCchhcc
Confidence 35588999999986432 224578888888763
No 148
>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=24.93 E-value=20 Score=19.11 Aligned_cols=13 Identities=0% Similarity=-0.572 Sum_probs=7.1
Q ss_pred CcCCcccc-eeccc
Q 042895 95 KNVLLAVK-QCPWE 107 (150)
Q Consensus 95 ~~C~~C~~-i~~~~ 107 (150)
..|..|+. ++.+.
T Consensus 5 ~~C~~C~~~~i~g~ 18 (46)
T PF00569_consen 5 YTCDGCGTDPIIGV 18 (46)
T ss_dssp CE-SSS-SSSEESS
T ss_pred eECcCCCCCcCcCC
Confidence 56888887 55543
No 149
>KOG3476 consensus Microtubule-associated protein CRIPT [Cytoskeleton]
Probab=24.84 E-value=7.3 Score=24.00 Aligned_cols=23 Identities=30% Similarity=0.661 Sum_probs=13.9
Q ss_pred ccccccccCCCCCccccCCeeecCchhhh
Q 042895 36 KCSRCKGTLKLSNYSSLEGVFYCKPHFEQ 64 (150)
Q Consensus 36 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~ 64 (150)
.|..|...+ ...|.-||..|..+
T Consensus 56 kC~iCk~~v------HQ~GshYC~tCAY~ 78 (100)
T KOG3476|consen 56 KCRICKQLV------HQPGSHYCQTCAYK 78 (100)
T ss_pred hhHHHHHHh------cCCcchhHhHhhhh
Confidence 455555433 34667788888655
No 150
>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=24.44 E-value=42 Score=21.41 Aligned_cols=11 Identities=18% Similarity=0.552 Sum_probs=5.8
Q ss_pred cccccCCcccC
Q 042895 121 FKCSYAGYSIS 131 (150)
Q Consensus 121 f~C~~C~~~l~ 131 (150)
..|..|+..+.
T Consensus 53 lvC~~C~~~~~ 63 (102)
T PF10080_consen 53 LVCKNCGVRFN 63 (102)
T ss_pred EEEecCCCEEe
Confidence 34555665553
No 151
>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=24.35 E-value=24 Score=24.29 Aligned_cols=30 Identities=23% Similarity=0.394 Sum_probs=21.9
Q ss_pred cccccCceeeccceEEeCCcccccCCcccccccccCCC
Q 042895 9 KCKVCEKTVCPVEQLSTDGVVYHKSCFKCSRCKGTLKL 46 (150)
Q Consensus 9 ~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~ 46 (150)
.|+.|+......+.+. .=|.|..|+..|..
T Consensus 111 ~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 111 ICPNMCVRFTFNEAME--------LNFTCPRCGAMLDY 140 (158)
T ss_pred ECCCCCcEeeHHHHHH--------cCCcCCCCCCEeee
Confidence 5899988776555443 24999999998743
No 152
>smart00746 TRASH metallochaperone-like domain.
Probab=24.31 E-value=66 Score=14.58 Aligned_cols=9 Identities=33% Similarity=1.043 Sum_probs=6.0
Q ss_pred ccccCceee
Q 042895 10 CKVCEKTVC 18 (150)
Q Consensus 10 C~~C~~~I~ 18 (150)
|..|+..|.
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 566777775
No 153
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=24.18 E-value=81 Score=23.85 Aligned_cols=8 Identities=0% Similarity=-0.213 Sum_probs=4.1
Q ss_pred CcCCcccc
Q 042895 95 KNVLLAVK 102 (150)
Q Consensus 95 ~~C~~C~~ 102 (150)
.+|..|++
T Consensus 172 ~KC~SCNr 179 (314)
T PF06524_consen 172 FKCQSCNR 179 (314)
T ss_pred cccccccc
Confidence 44555554
No 154
>TIGR02419 C4_traR_proteo phage/conjugal plasmid C-4 type zinc finger protein, TraR family. Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA.
Probab=24.15 E-value=17 Score=20.90 Aligned_cols=17 Identities=12% Similarity=0.009 Sum_probs=11.5
Q ss_pred CcCCcccceeccceeee
Q 042895 95 KNVLLAVKQCPWEKVAA 111 (150)
Q Consensus 95 ~~C~~C~~i~~~~~v~~ 111 (150)
..|..|+..|+..++.+
T Consensus 32 g~C~~Cg~~Ip~~Rl~a 48 (63)
T TIGR02419 32 RECEDCGEPIPEARREA 48 (63)
T ss_pred CeeccCCCcChHHHHhh
Confidence 57888888666655444
No 155
>PLN02400 cellulose synthase
Probab=24.03 E-value=55 Score=29.69 Aligned_cols=9 Identities=33% Similarity=1.058 Sum_probs=4.8
Q ss_pred cccccCcee
Q 042895 9 KCKVCEKTV 17 (150)
Q Consensus 9 ~C~~C~~~I 17 (150)
+|..|+..|
T Consensus 38 iCqICGD~V 46 (1085)
T PLN02400 38 ICQICGDDV 46 (1085)
T ss_pred eeeeccccc
Confidence 455555554
No 156
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=23.79 E-value=16 Score=21.79 Aligned_cols=31 Identities=6% Similarity=-0.192 Sum_probs=19.2
Q ss_pred CcCCcccceeccceeeeCCccccccccccccCCccc
Q 042895 95 KNVLLAVKQCPWEKVAAESQASHKTCFKCSYAGYSI 130 (150)
Q Consensus 95 ~~C~~C~~i~~~~~v~~~~~~~H~~Cf~C~~C~~~l 130 (150)
..|-.|+++|+..++.+. +.+..|..|...+
T Consensus 35 ~~C~~Cg~~Ip~~Rl~a~-----p~~~~Cv~Cq~~~ 65 (73)
T PRK13715 35 YLCEACGNPIPEARRKIF-----PGVTLCVECQAYQ 65 (73)
T ss_pred ccHhhcCCcCCHHHHhcC-----CCcCCCHHHHHHH
Confidence 478888887777666554 2345566665443
No 157
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=23.73 E-value=60 Score=24.62 Aligned_cols=25 Identities=8% Similarity=-0.161 Sum_probs=11.5
Q ss_pred CcCCcccceeccceeeeCCcccccc
Q 042895 95 KNVLLAVKQCPWEKVAAESQASHKT 119 (150)
Q Consensus 95 ~~C~~C~~i~~~~~v~~~~~~~H~~ 119 (150)
.-|.+|+.+|....+.-.+..|.+.
T Consensus 246 epC~~CGt~I~k~~~~gR~t~~CP~ 270 (273)
T COG0266 246 EPCRRCGTPIEKIKLGGRSTFYCPV 270 (273)
T ss_pred CCCCccCCEeEEEEEcCCcCEeCCC
Confidence 4466666544443334444444333
No 158
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=23.48 E-value=54 Score=17.44 Aligned_cols=13 Identities=8% Similarity=-0.383 Sum_probs=8.0
Q ss_pred cCCcccc-eeccce
Q 042895 96 NVLLAVK-QCPWEK 108 (150)
Q Consensus 96 ~C~~C~~-i~~~~~ 108 (150)
.|.+|++ +|.+.+
T Consensus 2 ~Cd~C~~~~i~G~R 15 (45)
T cd02339 2 ICDTCRKQGIIGIR 15 (45)
T ss_pred CCCCCCCCCcccCe
Confidence 3777776 655544
No 159
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=23.22 E-value=52 Score=16.29 Aligned_cols=8 Identities=13% Similarity=-0.168 Sum_probs=4.0
Q ss_pred CcCCcccc
Q 042895 95 KNVLLAVK 102 (150)
Q Consensus 95 ~~C~~C~~ 102 (150)
.+|..|+.
T Consensus 4 ~~C~~C~~ 11 (33)
T PF08792_consen 4 KKCSKCGG 11 (33)
T ss_pred eEcCCCCC
Confidence 34555554
No 160
>PHA02929 N1R/p28-like protein; Provisional
Probab=22.94 E-value=44 Score=24.78 Aligned_cols=14 Identities=21% Similarity=0.693 Sum_probs=10.2
Q ss_pred cccccccCceeecc
Q 042895 7 QQKCKVCEKTVCPV 20 (150)
Q Consensus 7 ~~~C~~C~~~I~~~ 20 (150)
...|+.|...+...
T Consensus 174 ~~eC~ICle~~~~~ 187 (238)
T PHA02929 174 DKECAICMEKVYDK 187 (238)
T ss_pred CCCCccCCcccccC
Confidence 45799998887643
No 161
>PRK14873 primosome assembly protein PriA; Provisional
Probab=22.89 E-value=55 Score=28.07 Aligned_cols=14 Identities=21% Similarity=0.100 Sum_probs=8.8
Q ss_pred ccCCeeecCchhhh
Q 042895 51 SLEGVFYCKPHFEQ 64 (150)
Q Consensus 51 ~~~g~~yC~~c~~~ 64 (150)
...+.+.|..|-..
T Consensus 406 ~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 406 SAGGTPRCRWCGRA 419 (665)
T ss_pred cCCCeeECCCCcCC
Confidence 34567778877543
No 162
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=22.78 E-value=51 Score=17.92 Aligned_cols=13 Identities=0% Similarity=-0.146 Sum_probs=8.2
Q ss_pred cCCcccc-eeccce
Q 042895 96 NVLLAVK-QCPWEK 108 (150)
Q Consensus 96 ~C~~C~~-i~~~~~ 108 (150)
.|..|++ +|.+.+
T Consensus 2 ~Cd~C~~~pi~g~R 15 (49)
T cd02334 2 KCNICKEFPITGFR 15 (49)
T ss_pred CCCCCCCCCceeee
Confidence 4777777 666543
No 163
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=22.64 E-value=34 Score=24.05 Aligned_cols=30 Identities=23% Similarity=0.500 Sum_probs=22.0
Q ss_pred cccccCceeeccceEEeCCcccccCCcccccccccCCC
Q 042895 9 KCKVCEKTVCPVEQLSTDGVVYHKSCFKCSRCKGTLKL 46 (150)
Q Consensus 9 ~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~ 46 (150)
.|+.|+......+.+. .=|.|..|+..|..
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 6999988876555432 25999999998854
No 164
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=22.62 E-value=61 Score=23.21 Aligned_cols=10 Identities=40% Similarity=0.982 Sum_probs=6.1
Q ss_pred Cccccccccc
Q 042895 113 SQASHKTCFK 122 (150)
Q Consensus 113 ~~~~H~~Cf~ 122 (150)
+..||..||.
T Consensus 179 ~~v~H~~C~~ 188 (202)
T PF13901_consen 179 KSVFHKSCFR 188 (202)
T ss_pred ccccchhhcC
Confidence 3456777765
No 165
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=22.22 E-value=19 Score=23.06 Aligned_cols=20 Identities=5% Similarity=-0.090 Sum_probs=14.2
Q ss_pred CCCcCCcccceeccceeeeC
Q 042895 93 PNKNVLLAVKQCPWEKVAAE 112 (150)
Q Consensus 93 ~~~~C~~C~~i~~~~~v~~~ 112 (150)
.-..|-.|+++|+.+++.|.
T Consensus 79 ~yG~C~~Cge~I~~~RL~a~ 98 (110)
T TIGR02420 79 EYGYCEECGEEIGLRRLEAR 98 (110)
T ss_pred CCCchhccCCcccHHHHhhC
Confidence 33678888887777776554
No 166
>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=22.19 E-value=56 Score=16.32 Aligned_cols=28 Identities=21% Similarity=0.207 Sum_probs=13.6
Q ss_pred cccccccCCCCCccccCCee-ecCchhhh
Q 042895 37 CSRCKGTLKLSNYSSLEGVF-YCKPHFEQ 64 (150)
Q Consensus 37 C~~C~~~l~~~~~~~~~g~~-yC~~c~~~ 64 (150)
|..|+..-.+.-....+|.. +|..|...
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~ 29 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLY 29 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHH
Confidence 44555544333334456666 88888654
No 167
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.85 E-value=47 Score=25.69 Aligned_cols=40 Identities=13% Similarity=0.244 Sum_probs=30.3
Q ss_pred CCCCcCCcccc-eeccceeeeC--Ccccccccc---------ccccCCcccC
Q 042895 92 GPNKNVLLAVK-QCPWEKVAAE--SQASHKTCF---------KCSYAGYSIS 131 (150)
Q Consensus 92 ~~~~~C~~C~~-i~~~~~v~~~--~~~~H~~Cf---------~C~~C~~~l~ 131 (150)
+..--|+.|-. .+.++.+.+. +..||..|. +|.+|+..+.
T Consensus 321 ~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iP 372 (374)
T COG5540 321 DKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372 (374)
T ss_pred CCCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCC
Confidence 33467999998 8777775554 788999995 5888888763
No 168
>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=21.64 E-value=84 Score=16.24 Aligned_cols=29 Identities=24% Similarity=0.457 Sum_probs=14.9
Q ss_pred ccccccccCCCCCc-c-ccCCeeecCchhhh
Q 042895 36 KCSRCKGTLKLSNY-S-SLEGVFYCKPHFEQ 64 (150)
Q Consensus 36 ~C~~C~~~l~~~~~-~-~~~g~~yC~~c~~~ 64 (150)
+|+-|+++...... . ..++-..|..|...
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQ 33 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHH
Confidence 57778877655542 2 23356667777654
No 169
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=21.43 E-value=47 Score=21.65 Aligned_cols=12 Identities=33% Similarity=0.645 Sum_probs=8.3
Q ss_pred cccccCCcccCC
Q 042895 121 FKCSYAGYSISP 132 (150)
Q Consensus 121 f~C~~C~~~l~~ 132 (150)
++|..|+..+.+
T Consensus 13 l~C~~C~t~i~G 24 (113)
T PF09862_consen 13 LKCPSCGTEIEG 24 (113)
T ss_pred EEcCCCCCEEEe
Confidence 667777777743
No 170
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=21.34 E-value=57 Score=15.49 Aligned_cols=12 Identities=25% Similarity=0.421 Sum_probs=6.8
Q ss_pred cccccCCcccCC
Q 042895 121 FKCSYAGYSISP 132 (150)
Q Consensus 121 f~C~~C~~~l~~ 132 (150)
|.|..|.+.+++
T Consensus 1 ~~C~~C~~~~~~ 12 (30)
T PF03107_consen 1 FWCDVCRRKIDG 12 (30)
T ss_pred CCCCCCCCCcCC
Confidence 456666666544
No 171
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=20.57 E-value=81 Score=25.49 Aligned_cols=38 Identities=11% Similarity=0.176 Sum_probs=25.0
Q ss_pred CCCCCCcCCcccceeccceeeeCCccccccccccccCCcccCCCCcc
Q 042895 90 FSGPNKNVLLAVKQCPWEKVAAESQASHKTCFKCSYAGYSISPSNYA 136 (150)
Q Consensus 90 ~~~~~~~C~~C~~i~~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~ 136 (150)
+....++|+.|+. .+...|+. =|+|..|+..+......
T Consensus 346 ~~~~~p~Cp~Cg~-----~m~S~G~~----g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 346 YERVNPVCPRCGG-----RMKSAGRN----GFRCKKCGTRARETLIK 383 (421)
T ss_pred eEEcCCCCCccCC-----chhhcCCC----CcccccccccCCccccc
Confidence 3444589999987 23344443 48999999988654443
No 172
>smart00355 ZnF_C2H2 zinc finger.
Probab=20.45 E-value=55 Score=13.78 Aligned_cols=12 Identities=17% Similarity=0.625 Sum_probs=8.3
Q ss_pred cccccCCcccCC
Q 042895 121 FKCSYAGYSISP 132 (150)
Q Consensus 121 f~C~~C~~~l~~ 132 (150)
+.|..|++.+..
T Consensus 1 ~~C~~C~~~f~~ 12 (26)
T smart00355 1 YRCPECGKVFKS 12 (26)
T ss_pred CCCCCCcchhCC
Confidence 467788877743
No 173
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=20.30 E-value=51 Score=14.99 Aligned_cols=10 Identities=50% Similarity=1.205 Sum_probs=5.0
Q ss_pred cccccCCccc
Q 042895 121 FKCSYAGYSI 130 (150)
Q Consensus 121 f~C~~C~~~l 130 (150)
|.|..|++.+
T Consensus 15 ~~C~~C~k~F 24 (26)
T PF13465_consen 15 YKCPYCGKSF 24 (26)
T ss_dssp EEESSSSEEE
T ss_pred CCCCCCcCee
Confidence 4455555543
Done!