Query 046210
Match_columns 186
No_of_seqs 205 out of 1308
Neff 8.6
Searched_HMMs 46136
Date Fri Mar 29 09:48:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046210.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046210hhsearch_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 4.2E-27 9.1E-32 193.1 -1.3 123 9-169 276-401 (468)
2 KOG4577 Transcription factor L 99.9 1.7E-25 3.7E-30 175.4 -2.2 141 6-185 32-176 (383)
3 KOG1701 Focal adhesion adaptor 99.9 1.2E-24 2.6E-29 178.7 0.3 123 5-164 332-466 (468)
4 KOG2272 Focal adhesion protein 99.9 6.1E-24 1.3E-28 164.0 -1.7 159 6-166 72-258 (332)
5 KOG1700 Regulatory protein MLP 99.9 1.8E-22 3.9E-27 155.5 2.9 178 1-178 1-184 (200)
6 KOG2272 Focal adhesion protein 99.8 2.1E-22 4.5E-27 155.6 -0.2 116 6-159 194-311 (332)
7 KOG1703 Adaptor protein Enigma 99.8 6.4E-21 1.4E-25 164.7 5.3 128 6-170 302-430 (479)
8 KOG1044 Actin-binding LIM Zn-f 99.8 1.4E-19 2.9E-24 153.7 5.5 162 7-170 16-200 (670)
9 KOG1703 Adaptor protein Enigma 99.8 5.8E-20 1.3E-24 158.8 1.3 116 5-157 361-478 (479)
10 KOG1044 Actin-binding LIM Zn-f 99.7 1.4E-18 3E-23 147.7 1.3 115 6-158 132-248 (670)
11 PF00412 LIM: LIM domain; Int 99.6 2.8E-16 6.1E-21 97.9 4.0 57 10-66 1-58 (58)
12 PF00412 LIM: LIM domain; Int 99.6 3.9E-15 8.6E-20 92.6 4.2 56 106-161 1-58 (58)
13 KOG4577 Transcription factor L 99.0 2.9E-11 6.3E-16 95.7 -1.4 67 102-169 32-99 (383)
14 smart00132 LIM Zinc-binding do 98.9 1E-09 2.2E-14 62.2 2.8 37 9-45 1-38 (39)
15 KOG1700 Regulatory protein MLP 98.6 9.2E-09 2E-13 79.5 0.8 75 3-77 104-178 (200)
16 smart00132 LIM Zinc-binding do 98.5 8.2E-08 1.8E-12 54.2 2.0 36 105-140 1-38 (39)
17 KOG1702 Nebulin repeat protein 98.2 1.7E-07 3.6E-12 71.3 -1.8 62 7-68 4-65 (264)
18 KOG1702 Nebulin repeat protein 98.0 5.3E-07 1.2E-11 68.6 -2.7 61 105-165 6-67 (264)
19 KOG0490 Transcription factor, 97.7 8.3E-06 1.8E-10 64.1 -0.3 113 12-160 1-119 (235)
20 KOG0490 Transcription factor, 92.5 0.031 6.8E-07 43.7 -0.4 54 111-165 5-62 (235)
21 PF08394 Arc_trans_TRASH: Arch 89.6 0.14 3.1E-06 28.4 0.6 31 10-44 1-33 (37)
22 PF14446 Prok-RING_1: Prokaryo 88.6 0.31 6.8E-06 29.4 1.6 39 6-44 4-51 (54)
23 COG2888 Predicted Zn-ribbon RN 86.7 0.58 1.2E-05 28.8 2.0 48 5-61 7-56 (61)
24 PRK14890 putative Zn-ribbon RN 86.6 0.52 1.1E-05 29.0 1.8 32 3-43 3-34 (59)
25 PF02069 Metallothio_Pro: Prok 86.4 0.6 1.3E-05 28.0 1.9 29 131-159 9-38 (52)
26 PF01258 zf-dskA_traR: Prokary 85.0 0.24 5.1E-06 27.2 -0.3 29 132-160 6-34 (36)
27 PF09943 DUF2175: Uncharacteri 84.9 0.34 7.3E-06 33.2 0.4 32 9-40 4-36 (101)
28 PF10367 Vps39_2: Vacuolar sor 84.2 0.82 1.8E-05 31.1 2.1 31 5-35 76-107 (109)
29 PF14471 DUF4428: Domain of un 83.1 0.96 2.1E-05 27.0 1.8 29 131-160 1-30 (51)
30 PF00645 zf-PARP: Poly(ADP-rib 80.9 0.83 1.8E-05 29.8 1.1 18 5-22 5-22 (82)
31 PF11781 RRN7: RNA polymerase 80.3 0.81 1.8E-05 25.2 0.7 25 130-158 9-33 (36)
32 PF13240 zinc_ribbon_2: zinc-r 78.4 1.2 2.6E-05 21.9 0.9 8 10-17 2-9 (23)
33 COG2191 Formylmethanofuran deh 78.3 0.77 1.7E-05 35.4 0.3 31 130-160 173-203 (206)
34 PF10367 Vps39_2: Vacuolar sor 76.0 1.6 3.4E-05 29.6 1.4 28 36-63 80-108 (109)
35 COG2191 Formylmethanofuran deh 75.4 1.3 2.8E-05 34.2 0.8 32 35-66 173-204 (206)
36 smart00504 Ubox Modified RING 71.6 4.2 9.2E-05 24.6 2.4 32 35-67 2-33 (63)
37 COG1645 Uncharacterized Zn-fin 70.3 1.8 3.8E-05 31.2 0.5 22 132-158 31-52 (131)
38 PRK00807 50S ribosomal protein 70.2 2.3 4.9E-05 25.5 0.9 34 8-44 2-38 (52)
39 PF06677 Auto_anti-p27: Sjogre 69.4 2 4.3E-05 24.5 0.5 22 131-156 19-40 (41)
40 PF09943 DUF2175: Uncharacteri 62.6 7.1 0.00015 26.8 2.2 40 130-169 3-43 (101)
41 COG1813 Predicted transcriptio 62.0 10 0.00022 28.4 3.2 43 132-176 6-50 (165)
42 PF07754 DUF1610: Domain of un 61.8 5 0.00011 20.0 1.0 9 10-18 1-9 (24)
43 cd02249 ZZ Zinc finger, ZZ typ 61.3 6.2 0.00013 22.7 1.6 31 130-160 1-33 (46)
44 PF06750 DiS_P_DiS: Bacterial 60.5 4 8.6E-05 27.5 0.7 43 2-46 28-70 (92)
45 smart00291 ZnF_ZZ Zinc-binding 59.3 7.8 0.00017 22.1 1.7 29 131-159 6-36 (44)
46 KOG4443 Putative transcription 58.6 4.3 9.4E-05 36.7 0.8 39 120-158 106-144 (694)
47 PRK00420 hypothetical protein; 55.4 4.8 0.00011 28.2 0.5 24 131-158 25-48 (112)
48 PF12855 Ecl1: Life-span regul 54.1 6.4 0.00014 22.6 0.8 24 132-159 9-33 (43)
49 TIGR00270 conserved hypothetic 52.9 24 0.00052 26.1 3.8 32 131-164 2-36 (154)
50 PF10886 DUF2685: Protein of u 50.6 10 0.00023 22.8 1.3 24 9-32 3-26 (54)
51 PF13923 zf-C3HC4_2: Zinc fing 49.9 15 0.00032 20.1 1.8 32 132-163 1-32 (39)
52 cd00162 RING RING-finger (Real 48.1 9.4 0.0002 20.7 0.8 8 10-17 2-9 (45)
53 PF14835 zf-RING_6: zf-RING of 47.0 22 0.00048 22.3 2.4 34 35-68 8-41 (65)
54 PF00569 ZZ: Zinc finger, ZZ t 46.9 17 0.00037 20.9 1.8 30 130-159 5-37 (46)
55 PF07191 zinc-ribbons_6: zinc- 46.7 10 0.00023 24.2 0.9 39 8-65 2-40 (70)
56 PF13248 zf-ribbon_3: zinc-rib 45.6 14 0.0003 18.5 1.1 9 9-17 4-12 (26)
57 KOG0320 Predicted E3 ubiquitin 44.8 12 0.00026 28.4 1.2 38 31-68 128-166 (187)
58 TIGR00373 conserved hypothetic 44.7 6.5 0.00014 29.2 -0.3 30 9-46 111-140 (158)
59 PRK06266 transcription initiat 44.5 7.9 0.00017 29.4 0.2 30 9-46 119-148 (178)
60 PRK00398 rpoP DNA-directed RNA 44.5 11 0.00024 21.6 0.8 9 9-17 5-13 (46)
61 smart00531 TFIIE Transcription 44.5 7.2 0.00016 28.5 -0.0 35 9-46 101-135 (147)
62 cd02341 ZZ_ZZZ3 Zinc finger, Z 43.8 19 0.00041 21.1 1.7 31 130-160 1-36 (48)
63 smart00249 PHD PHD zinc finger 42.8 31 0.00068 18.8 2.6 27 9-35 1-29 (47)
64 cd02340 ZZ_NBR1_like Zinc fing 41.8 20 0.00043 20.4 1.5 30 131-160 2-33 (43)
65 PF12773 DZR: Double zinc ribb 41.8 21 0.00046 20.5 1.7 9 37-45 15-23 (50)
66 PF00130 C1_1: Phorbol esters/ 41.4 19 0.00041 21.0 1.5 13 5-17 9-21 (53)
67 PF02591 DUF164: Putative zinc 40.9 5.6 0.00012 23.9 -0.9 26 36-61 24-52 (56)
68 PF12674 Zn_ribbon_2: Putative 40.6 16 0.00035 23.9 1.2 29 131-159 2-35 (81)
69 COG4847 Uncharacterized protei 39.6 20 0.00044 24.3 1.5 30 130-159 7-37 (103)
70 PF00320 GATA: GATA zinc finge 39.4 25 0.00054 19.1 1.7 28 132-159 1-29 (36)
71 PF13834 DUF4193: Domain of un 39.3 9.7 0.00021 26.0 -0.1 29 128-156 69-98 (99)
72 cd02336 ZZ_RSC8 Zinc finger, Z 38.3 25 0.00053 20.3 1.6 29 131-159 2-32 (45)
73 PF01286 XPA_N: XPA protein N- 38.2 15 0.00032 20.0 0.6 26 131-156 5-30 (34)
74 PF14255 Cys_rich_CPXG: Cystei 37.3 18 0.00039 21.7 0.9 34 9-45 2-35 (52)
75 PF09723 Zn-ribbon_8: Zinc rib 37.1 10 0.00022 21.4 -0.2 28 130-157 6-33 (42)
76 PF00096 zf-C2H2: Zinc finger, 36.5 16 0.00034 17.1 0.5 13 130-142 1-13 (23)
77 PF04570 DUF581: Protein of un 36.3 18 0.00038 22.2 0.8 28 36-63 18-48 (58)
78 PF10122 Mu-like_Com: Mu-like 36.3 13 0.00027 22.2 0.1 26 35-62 5-31 (51)
79 PF10764 Gin: Inhibitor of sig 36.2 33 0.00072 19.9 1.9 30 132-163 2-31 (46)
80 PF00628 PHD: PHD-finger; Int 36.0 22 0.00049 20.4 1.2 28 9-36 1-30 (51)
81 PF04945 YHS: YHS domain; Int 35.8 9.5 0.00021 21.9 -0.5 33 10-46 3-38 (47)
82 PF08209 Sgf11: Sgf11 (transcr 35.4 8.5 0.00018 20.8 -0.7 17 35-51 5-21 (33)
83 TIGR02098 MJ0042_CXXC MJ0042 f 34.9 15 0.00032 19.9 0.3 32 9-45 4-36 (38)
84 PF05502 Dynactin_p62: Dynacti 34.6 27 0.00059 30.8 2.0 14 127-140 50-63 (483)
85 PF10083 DUF2321: Uncharacteri 33.9 29 0.00063 25.7 1.7 37 8-46 40-80 (158)
86 PF13920 zf-C3HC4_3: Zinc fing 33.9 46 0.001 19.1 2.3 32 35-67 3-35 (50)
87 PF06689 zf-C4_ClpX: ClpX C4-t 33.3 57 0.0012 18.2 2.5 30 131-160 3-34 (41)
88 smart00659 RPOLCX RNA polymera 33.2 18 0.0004 20.7 0.5 27 130-160 3-29 (44)
89 PF11023 DUF2614: Protein of u 33.1 16 0.00035 25.5 0.3 33 3-46 65-97 (114)
90 PRK08359 transcription factor; 32.9 75 0.0016 24.1 3.8 32 131-163 8-42 (176)
91 cd02342 ZZ_UBA_plant Zinc fing 32.7 40 0.00087 19.3 1.8 36 131-167 2-40 (43)
92 smart00834 CxxC_CXXC_SSSS Puta 32.6 14 0.0003 20.3 -0.1 10 130-139 6-15 (41)
93 cd02338 ZZ_PCMF_like Zinc fing 32.5 30 0.00064 20.2 1.3 30 131-160 2-34 (49)
94 PF04810 zf-Sec23_Sec24: Sec23 32.3 35 0.00075 19.0 1.5 10 8-17 3-12 (40)
95 PRK02935 hypothetical protein; 32.2 22 0.00047 24.6 0.8 30 6-46 69-98 (110)
96 COG5152 Uncharacterized conser 32.1 16 0.00034 28.4 0.1 34 34-68 196-229 (259)
97 TIGR02420 dksA RNA polymerase- 31.9 11 0.00023 26.2 -0.8 20 5-25 78-97 (110)
98 PF12677 DUF3797: Domain of un 31.5 35 0.00077 20.1 1.5 28 7-34 13-42 (49)
99 PF13639 zf-RING_2: Ring finge 31.4 12 0.00027 20.9 -0.5 10 9-18 2-11 (44)
100 PF14634 zf-RING_5: zinc-RING 31.4 46 0.001 18.6 2.0 30 132-161 2-33 (44)
101 cd02335 ZZ_ADA2 Zinc finger, Z 31.4 40 0.00088 19.6 1.8 31 130-160 1-34 (49)
102 PF08746 zf-RING-like: RING-li 31.1 13 0.00027 21.2 -0.5 26 10-35 1-28 (43)
103 PF10571 UPF0547: Uncharacteri 30.3 37 0.00079 17.1 1.2 9 9-17 2-10 (26)
104 TIGR02605 CxxC_CxxC_SSSS putat 30.2 21 0.00045 20.8 0.4 28 35-62 6-33 (52)
105 PF08271 TF_Zn_Ribbon: TFIIB z 30.1 32 0.0007 19.3 1.2 9 53-61 17-25 (43)
106 COG2075 RPL24A Ribosomal prote 29.8 35 0.00076 21.5 1.3 33 131-164 5-43 (66)
107 PF13894 zf-C2H2_4: C2H2-type 28.5 28 0.00061 15.9 0.6 12 130-141 1-12 (24)
108 PRK12495 hypothetical protein; 28.3 36 0.00077 26.8 1.5 23 35-62 43-65 (226)
109 smart00746 TRASH metallochaper 28.1 46 0.001 16.5 1.6 22 10-31 1-25 (39)
110 PF07649 C1_3: C1-like domain; 27.9 28 0.00061 17.9 0.6 12 130-141 1-12 (30)
111 PF05502 Dynactin_p62: Dynacti 27.8 40 0.00087 29.8 1.9 39 8-47 27-65 (483)
112 COG1381 RecO Recombinational D 27.8 31 0.00067 27.5 1.1 33 125-157 150-182 (251)
113 cd02344 ZZ_HERC2 Zinc finger, 27.5 46 0.00099 19.2 1.5 29 131-159 2-33 (45)
114 PF12874 zf-met: Zinc-finger o 27.5 27 0.00059 16.7 0.5 13 130-142 1-13 (25)
115 PF00097 zf-C3HC4: Zinc finger 27.5 54 0.0012 17.7 1.8 32 132-163 1-32 (41)
116 PF01927 Mut7-C: Mut7-C RNAse 27.5 38 0.00082 24.6 1.4 38 7-44 91-134 (147)
117 cd00472 Ribosomal_L24e_L24 Rib 27.0 42 0.00091 20.2 1.3 24 8-31 4-30 (54)
118 PRK00085 recO DNA repair prote 26.8 26 0.00057 27.5 0.5 32 126-157 146-177 (247)
119 PF10080 DUF2318: Predicted me 26.4 29 0.00064 23.8 0.6 35 123-161 29-63 (102)
120 PF12156 ATPase-cat_bd: Putati 26.2 45 0.00098 22.1 1.5 31 9-42 2-34 (88)
121 PF06906 DUF1272: Protein of u 26.2 1.2E+02 0.0026 18.5 3.1 41 131-171 7-51 (57)
122 PRK00085 recO DNA repair prote 25.8 31 0.00067 27.1 0.8 32 31-62 146-177 (247)
123 PHA00080 DksA-like zinc finger 25.1 32 0.00069 22.0 0.6 28 131-158 33-60 (72)
124 KOG3579 Predicted E3 ubiquitin 24.8 61 0.0013 26.6 2.2 34 35-68 269-305 (352)
125 KOG1813 Predicted E3 ubiquitin 24.3 44 0.00094 27.5 1.3 33 35-68 242-274 (313)
126 PF13912 zf-C2H2_6: C2H2-type 24.2 34 0.00074 16.7 0.5 13 130-142 2-14 (27)
127 PF12171 zf-C2H2_jaz: Zinc-fin 23.9 37 0.0008 16.8 0.6 13 130-142 2-14 (27)
128 PRK14891 50S ribosomal protein 23.9 27 0.00057 25.1 0.0 32 8-42 5-39 (131)
129 cd02345 ZZ_dah Zinc finger, ZZ 23.9 51 0.0011 19.2 1.3 30 131-160 2-34 (49)
130 TIGR01053 LSD1 zinc finger dom 23.5 54 0.0012 17.3 1.2 9 9-17 3-11 (31)
131 COG4068 Uncharacterized protei 23.5 35 0.00076 21.0 0.5 16 7-22 8-23 (64)
132 TIGR03826 YvyF flagellar opero 23.2 61 0.0013 23.5 1.8 24 130-161 82-105 (137)
133 PRK13715 conjugal transfer pro 23.0 35 0.00075 21.9 0.4 28 131-158 36-63 (73)
134 PF06827 zf-FPG_IleRS: Zinc fi 22.8 27 0.00059 17.9 -0.1 10 8-17 2-11 (30)
135 PF10235 Cript: Microtubule-as 22.7 67 0.0015 21.6 1.8 10 8-17 45-54 (90)
136 KOG0978 E3 ubiquitin ligase in 22.6 26 0.00057 32.3 -0.2 36 33-69 642-677 (698)
137 PTZ00218 40S ribosomal protein 22.4 62 0.0013 19.5 1.4 28 130-160 17-44 (54)
138 KOG2186 Cell growth-regulating 22.1 20 0.00043 28.8 -0.9 42 9-51 5-46 (276)
139 cd02334 ZZ_dystrophin Zinc fin 21.9 73 0.0016 18.7 1.7 30 131-160 2-34 (49)
140 TIGR02419 C4_traR_proteo phage 21.7 31 0.00067 21.4 0.0 26 131-156 33-58 (63)
141 PF01246 Ribosomal_L24e: Ribos 21.2 49 0.0011 21.1 0.9 24 8-31 4-30 (71)
142 COG1381 RecO Recombinational D 21.1 43 0.00092 26.7 0.7 31 32-62 152-182 (251)
143 PF09862 DUF2089: Protein of u 21.0 41 0.00088 23.6 0.5 24 10-46 1-24 (113)
144 PF03966 Trm112p: Trm112p-like 21.0 63 0.0014 20.1 1.4 14 49-62 47-60 (68)
145 PF12760 Zn_Tnp_IS1595: Transp 20.2 1.5E+02 0.0032 16.8 2.7 8 8-15 19-26 (46)
146 KOG3579 Predicted E3 ubiquitin 20.1 46 0.001 27.3 0.7 47 8-59 269-315 (352)
147 PF15227 zf-C3HC4_4: zinc fing 20.1 1.5E+02 0.0033 16.4 2.7 33 132-165 1-33 (42)
No 1
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.92 E-value=4.2e-27 Score=193.08 Aligned_cols=123 Identities=21% Similarity=0.437 Sum_probs=111.6
Q ss_pred CcccCCceeccCce-EEeCCccccccccccccccccccCCCccccCCeeecCcchhhhhcccCCCCccCCCCchhhhhhh
Q 046210 9 KCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYFKPHFEQLFKESGNFNKNFQSPAKLIEKLT 87 (186)
Q Consensus 9 ~C~~C~~~I~~~~~-i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~ 87 (186)
+|.+|+|.|+..+. +.|+++.||..||+|..|++.|.+..|+..++++||+.||....
T Consensus 276 iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl--------------------- 334 (468)
T KOG1701|consen 276 ICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL--------------------- 334 (468)
T ss_pred hhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH---------------------
Confidence 89999999965543 79999999999999999999999999999999999999998764
Q ss_pred cccccCCCCcccCCCCCCCCC-CceeecccceecccccccccceeccccccccCCCCcee-cCCccccHHHHhhhhcCCC
Q 046210 88 RQDRLAKLPACYLGPKNMCFL-HKIVCPSEKVAMESQAHHKSCFKCSHGGYSISPSNYAA-LEGIWYCKHHFSKLFKEKD 165 (186)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~C~~-~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~~~~-~~g~~yC~~cy~k~~~~k~ 165 (186)
.+|.. +.+|.+ ..|.+.|+.||+.||+|..|.+.|++..|++ .++++||..||+++|+++|
T Consensus 335 ----------------ekC~~Cg~~I~d-~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrC 397 (468)
T KOG1701|consen 335 ----------------EKCNKCGEPIMD-RILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRC 397 (468)
T ss_pred ----------------HHHhhhhhHHHH-HHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcch
Confidence 47999 999954 4588999999999999999999999999986 6899999999999999999
Q ss_pred CCCc
Q 046210 166 SYNH 169 (186)
Q Consensus 166 ~~~~ 169 (186)
+-+.
T Consensus 398 s~C~ 401 (468)
T KOG1701|consen 398 SVCG 401 (468)
T ss_pred hhcc
Confidence 6554
No 2
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.89 E-value=1.7e-25 Score=175.39 Aligned_cols=141 Identities=23% Similarity=0.374 Sum_probs=123.2
Q ss_pred CCCCcccCCceeccCceEEeCCccccccccccccccccccCCCccccCCeeecCcchhhhhcccCCCCccCCCCchhhhh
Q 046210 6 TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYFKPHFEQLFKESGNFNKNFQSPAKLIEK 85 (186)
Q Consensus 6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~ 85 (186)
+.++|++|.+.|.+.-++.++++.||..|++|+.|+.+|.. ..+.++|.+||+.+|.++|++
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGT----------------- 93 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGT----------------- 93 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCC-----------------
Confidence 77899999999977677899999999999999999999988 667899999999999999977
Q ss_pred hhcccccCCCCcccCCCCCCCCC-Cceeeccccee-cccccccccceecccccccc-CCCCcee-cCCccccHHHHhhhh
Q 046210 86 LTRQDRLAKLPACYLGPKNMCFL-HKIVCPSEKVA-MESQAHHKSCFKCSHGGYSI-SPSNYAA-LEGIWYCKHHFSKLF 161 (186)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~~C~~-~~~I~~~~~v~-~~g~~~H~~CF~C~~C~~~L-~~~~~~~-~~g~~yC~~cy~k~~ 161 (186)
+|.. ...|.+.+.|. +.+.+||..||.|..|+++| .+..||. .|+++.|+.+|+..-
T Consensus 94 -------------------KCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak 154 (383)
T KOG4577|consen 94 -------------------KCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAK 154 (383)
T ss_pred -------------------cchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHH
Confidence 7888 78887787664 78899999999999999999 4557775 689999999999865
Q ss_pred cCCCCCCcccccccccccCCCCCC
Q 046210 162 KEKDSYNHLIKFASMKRVVASVPE 185 (186)
Q Consensus 162 ~~k~~~~~~~~~~~~~~~~~~~~~ 185 (186)
..-+ +++++..+.||++.++.|
T Consensus 155 ~k~~--~~l~gd~~nKRPRTTItA 176 (383)
T KOG4577|consen 155 QKHC--NELEGDASNKRPRTTITA 176 (383)
T ss_pred hccc--cccccccccCCCcceeeH
Confidence 5444 389999999999988754
No 3
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.89 E-value=1.2e-24 Score=178.67 Aligned_cols=123 Identities=26% Similarity=0.542 Sum_probs=107.6
Q ss_pred CCCCCcccCCceeccCceEEeCCccccccccccccccccccCCCccc-cCCeeecCcchhhhhcccCCCCccCCCCchhh
Q 046210 5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSS-MEGVLYFKPHFEQLFKESGNFNKNFQSPAKLI 83 (186)
Q Consensus 5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~-~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~ 83 (186)
-+..+|..|++.| ...+|.|+|+.||+.||+|-.|++.|++..|.+ .++++||..||+++|++
T Consensus 332 ~tlekC~~Cg~~I-~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAP--------------- 395 (468)
T KOG1701|consen 332 DTLEKCNKCGEPI-MDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAP--------------- 395 (468)
T ss_pred HHHHHHhhhhhHH-HHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCc---------------
Confidence 3456899999999 466789999999999999999999999999975 49999999999999977
Q ss_pred hhhhcccccCCCCcccCCCCCCCCC-Cceeeccc------ceecccccccccceeccccccccC----CCCceecCCccc
Q 046210 84 EKLTRQDRLAKLPACYLGPKNMCFL-HKIVCPSE------KVAMESQAHHKSCFKCSHGGYSIS----PSNYAALEGIWY 152 (186)
Q Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~C~~-~~~I~~~~------~v~~~g~~~H~~CF~C~~C~~~L~----~~~~~~~~g~~y 152 (186)
+|+. +++|++.+ +|+++++.||.+|++|.+|+.+|+ +...|-.||.++
T Consensus 396 ---------------------rCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~Hll 454 (468)
T KOG1701|consen 396 ---------------------RCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLL 454 (468)
T ss_pred ---------------------chhhccCCccCCCCCcceEEEEEccccccccceehhhcCccccccCCCCcceeccCcee
Confidence 7777 77887644 588999999999999999999996 346889999999
Q ss_pred cHHHHhhhhcCC
Q 046210 153 CKHHFSKLFKEK 164 (186)
Q Consensus 153 C~~cy~k~~~~k 164 (186)
|+.|..++....
T Consensus 455 Ck~Ch~~Rl~~~ 466 (468)
T KOG1701|consen 455 CKTCHLKRLQAG 466 (468)
T ss_pred echhhhhhhccc
Confidence 999998887653
No 4
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.87 E-value=6.1e-24 Score=164.05 Aligned_cols=159 Identities=16% Similarity=0.279 Sum_probs=118.4
Q ss_pred CCCCcccCCceeccCceEEeCCccccccccccccccccccCCCccccCCeeecCcchhhhhccc-CCC---------Ccc
Q 046210 6 TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYFKPHFEQLFKES-GNF---------NKN 75 (186)
Q Consensus 6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~-~~~---------~~~ 75 (186)
.+|-|+.|++.| .|.+|.+++.+||+.||+|..|++.|.+..|+-..|..+|..|.++.-+.. +-| ++.
T Consensus 72 faPcC~kC~EFi-iGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~ 150 (332)
T KOG2272|consen 72 FAPCCGKCGEFI-IGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQ 150 (332)
T ss_pred hchhhcccccch-hhHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccc
Confidence 468999999999 799999999999999999999999999999999999999999988743221 111 110
Q ss_pred ---CCCCch------h-h-hhhhcccccCCCCccc------CCCCCCCCC-Cceeecccceecccccccccceecccccc
Q 046210 76 ---FQSPAK------L-I-EKLTRQDRLAKLPACY------LGPKNMCFL-HKIVCPSEKVAMESQAHHKSCFKCSHGGY 137 (186)
Q Consensus 76 ---~~~~~~------~-~-~~~~~~~~~~~~~~~~------~~~~~~C~~-~~~I~~~~~v~~~g~~~H~~CF~C~~C~~ 137 (186)
+...|- . . .+.......+-..+++ .-..++|.. .+|| +...|.++|+.||.++|+|+.|.+
T Consensus 151 ~l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpI-eervi~amgKhWHveHFvCa~Cek 229 (332)
T KOG2272|consen 151 PLTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPI-EERVIFAMGKHWHVEHFVCAKCEK 229 (332)
T ss_pred cccccCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCch-HHHHHHHhccccchhheeehhcCC
Confidence 000000 0 0 0000001111111111 123579999 9999 677788999999999999999999
Q ss_pred ccCCCCceecCCccccHHHHhhhhcCCCC
Q 046210 138 SISPSNYAALEGIWYCKHHFSKLFKEKDS 166 (186)
Q Consensus 138 ~L~~~~~~~~~g~~yC~~cy~k~~~~k~~ 166 (186)
++-+...|++.|.+||+.||.++||--|.
T Consensus 230 PFlGHrHYEkkGlaYCe~h~~qLfG~~CF 258 (332)
T KOG2272|consen 230 PFLGHRHYEKKGLAYCETHYHQLFGNLCF 258 (332)
T ss_pred cccchhhhhhcCchhHHHHHHHHhhhhhe
Confidence 99999999999999999999999998773
No 5
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.85 E-value=1.8e-22 Score=155.51 Aligned_cols=178 Identities=45% Similarity=0.761 Sum_probs=149.2
Q ss_pred CCCCCCCCCcccCCceeccCceEEeCCccccccccccccccccccCCCccccCCeeecCcchhhhhcccC-CCCccCCCC
Q 046210 1 MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYFKPHFEQLFKESG-NFNKNFQSP 79 (186)
Q Consensus 1 ~~~~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~~-~~~~~~~~~ 79 (186)
|++.+....|.+|++.|+..+.+...|..||+.||+|..|.+.|....+..+++.+||..+|...++++. ++.++++..
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 7788889999999999999999999999999999999999999999999999999999998888888765 345555442
Q ss_pred chh--h--hhhhcccccCCCCcccCCCCCCCCC-CceeecccceecccccccccceeccccccccCCCCceecCCccccH
Q 046210 80 AKL--I--EKLTRQDRLAKLPACYLGPKNMCFL-HKIVCPSEKVAMESQAHHKSCFKCSHGGYSISPSNYAALEGIWYCK 154 (186)
Q Consensus 80 ~~~--~--~~~~~~~~~~~~~~~~~~~~~~C~~-~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~ 154 (186)
... . .....+..+......+.+....|.+ .+.+++.+.+...+..||+.||+|+.|+..|+...+...+|.+||.
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 111 1 2222233344455566777889999 9999999999999999999999999999999999999999999999
Q ss_pred HHHhhhhcCCCCCCcccccccccc
Q 046210 155 HHFSKLFKEKDSYNHLIKFASMKR 178 (186)
Q Consensus 155 ~cy~k~~~~k~~~~~~~~~~~~~~ 178 (186)
.++..+|-.+..|..+.+-+..++
T Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~ 184 (200)
T KOG1700|consen 161 HHFAQLFKGKGNYNEGFGARENKE 184 (200)
T ss_pred hhhheeecCCCcccccchhhhhhh
Confidence 999999999999998877665544
No 6
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.84 E-value=2.1e-22 Score=155.63 Aligned_cols=116 Identities=21% Similarity=0.513 Sum_probs=106.9
Q ss_pred CCCCcccCCceeccCceEEeCCccccccccccccccccccCCCccccCCeeecCcchhhhhcccCCCCccCCCCchhhhh
Q 046210 6 TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYFKPHFEQLFKESGNFNKNFQSPAKLIEK 85 (186)
Q Consensus 6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~ 85 (186)
+.++|..|.++| ...+|.++|+.||.++|+|+.|-+|+-+..-+++.|.+||+.+|.++|+.
T Consensus 194 gipiCgaC~rpI-eervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~----------------- 255 (332)
T KOG2272|consen 194 GIPICGACRRPI-EERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGN----------------- 255 (332)
T ss_pred CCcccccccCch-HHHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhh-----------------
Confidence 568999999999 56778999999999999999999999888889999999999999999965
Q ss_pred hhcccccCCCCcccCCCCCCCCC-CceeecccceecccccccccceeccccccccCCC-CceecCCccccHHHHhh
Q 046210 86 LTRQDRLAKLPACYLGPKNMCFL-HKIVCPSEKVAMESQAHHKSCFKCSHGGYSISPS-NYAALEGIWYCKHHFSK 159 (186)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~~C~~-~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~cy~k 159 (186)
.|.. +.+| .++.+.++++.|.++||.|+.|++.|... .|++.|-+|.|+.||.+
T Consensus 256 -------------------~CF~C~~~i-~G~vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~r 311 (332)
T KOG2272|consen 256 -------------------LCFICNRVI-GGDVVSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDR 311 (332)
T ss_pred -------------------hheecCCcc-CccHHHHhhhhhccccccccccccccccccceeeeccchHHHHHHhh
Confidence 8999 8999 78889999999999999999999999654 68899999999999974
No 7
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.82 E-value=6.4e-21 Score=164.73 Aligned_cols=128 Identities=24% Similarity=0.473 Sum_probs=116.6
Q ss_pred CCCCcccCCceeccCceEEeCCccccccccccccccccccCCCccccCCeeecCcchhhhhcccCCCCccCCCCchhhhh
Q 046210 6 TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYFKPHFEQLFKESGNFNKNFQSPAKLIEK 85 (186)
Q Consensus 6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~ 85 (186)
..+.|..|++.|...+.+.++++.||+.+|.|..|...|....+...+|++||..||...+.+
T Consensus 302 ~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p----------------- 364 (479)
T KOG1703|consen 302 TRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRP----------------- 364 (479)
T ss_pred ccccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCc-----------------
Confidence 458999999999433889999999999999999999999999998999999999999999965
Q ss_pred hhcccccCCCCcccCCCCCCCCC-CceeecccceecccccccccceeccccccccCCCCceecCCccccHHHHhhhhcCC
Q 046210 86 LTRQDRLAKLPACYLGPKNMCFL-HKIVCPSEKVAMESQAHHKSCFKCSHGGYSISPSNYAALEGIWYCKHHFSKLFKEK 164 (186)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~~C~~-~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~k~~~~k 164 (186)
.|.+ +.+| .++.|.+.++.||++||+|..|++.|.+..|++.||.+||+.||+++|+++
T Consensus 365 -------------------~C~~C~~~i-~~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~ 424 (479)
T KOG1703|consen 365 -------------------NCKRCLLPI-LEEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTK 424 (479)
T ss_pred -------------------cccccCCch-HHhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhcccc
Confidence 8999 8999 567788999999999999999999999999999999999999999999999
Q ss_pred CCCCcc
Q 046210 165 DSYNHL 170 (186)
Q Consensus 165 ~~~~~~ 170 (186)
+.++..
T Consensus 425 ~~~~~~ 430 (479)
T KOG1703|consen 425 CDYCKK 430 (479)
T ss_pred chhccc
Confidence 866533
No 8
>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=153.71 Aligned_cols=162 Identities=19% Similarity=0.321 Sum_probs=115.1
Q ss_pred CCCcccCCceeccCceEEeCCccccccccccccccccccCCCccccCC-eeecCcchhhh------------hcccCCCC
Q 046210 7 QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEG-VLYFKPHFEQL------------FKESGNFN 73 (186)
Q Consensus 7 ~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g-~~yC~~cy~~~------------~~~~~~~~ 73 (186)
...|..|++.- .+|++.+.++.||..||.|..|+..|..+.|+.+++ .+|+......- |.++|.+.
T Consensus 16 ~i~c~~c~~kc-~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~~~~gevvsa~gktyh~~cf~c 94 (670)
T KOG1044|consen 16 GIKCDKCRKKC-SGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRAFVEGEVVSTLGKTYHPKCFSC 94 (670)
T ss_pred ceehhhhCCcc-ccceeEeeccccceeeeeccccCCCcccccceecccceeecccchhhhccceeEecccceecccccee
Confidence 34799999999 799999999999999999999999999999988744 67776333221 11111100
Q ss_pred ----ccCCCCchhh--hhh---hcccccCCCCcccCCCCCCCCC-CceeecccceecccccccccceeccccccccCCCC
Q 046210 74 ----KNFQSPAKLI--EKL---TRQDRLAKLPACYLGPKNMCFL-HKIVCPSEKVAMESQAHHKSCFKCSHGGYSISPSN 143 (186)
Q Consensus 74 ----~~~~~~~~~~--~~~---~~~~~~~~~~~~~~~~~~~C~~-~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~ 143 (186)
..+-...++. .+- .....++.+..........|++ +..|..++.+.++++.||..||+|..|+..|.++
T Consensus 95 s~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~ge- 173 (670)
T KOG1044|consen 95 STCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNGE- 173 (670)
T ss_pred cccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccce-
Confidence 0000000100 000 0011111111111223458999 8888899999999999999999999999999765
Q ss_pred ceecCCccccHHHHhhhhcCCCCCCcc
Q 046210 144 YAALEGIWYCKHHFSKLFKEKDSYNHL 170 (186)
Q Consensus 144 ~~~~~g~~yC~~cy~k~~~~k~~~~~~ 170 (186)
|+.+||.|||+.||.+.|+.||.+++.
T Consensus 174 y~skdg~pyce~dy~~~fgvkc~~c~~ 200 (670)
T KOG1044|consen 174 YMSKDGVPYCEKDYQAKFGVKCEECEK 200 (670)
T ss_pred eeccCCCcchhhhhhhhcCeehHHhhh
Confidence 999999999999999999999977654
No 9
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.77 E-value=5.8e-20 Score=158.79 Aligned_cols=116 Identities=26% Similarity=0.544 Sum_probs=104.6
Q ss_pred CCCCCcccCCceeccCceEEeCCccccccccccccccccccCCCccccCCeeecCcchhhhhcccCCCCccCCCCchhhh
Q 046210 5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYFKPHFEQLFKESGNFNKNFQSPAKLIE 84 (186)
Q Consensus 5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~ 84 (186)
...+.|.+|+++| .++.|.+.+..||++||.|..|+++|....|+..+|.+||+.||.+++.+
T Consensus 361 ~~~p~C~~C~~~i-~~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~---------------- 423 (479)
T KOG1703|consen 361 PFRPNCKRCLLPI-LEEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTT---------------- 423 (479)
T ss_pred hhCccccccCCch-HHhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccc----------------
Confidence 3468999999999 78889999999999999999999999999999999999999999999964
Q ss_pred hhhcccccCCCCcccCCCCCCCCC-Cceeec-ccceecccccccccceeccccccccCCCCceecCCccccHHHH
Q 046210 85 KLTRQDRLAKLPACYLGPKNMCFL-HKIVCP-SEKVAMESQAHHKSCFKCSHGGYSISPSNYAALEGIWYCKHHF 157 (186)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~~C~~-~~~I~~-~~~v~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy 157 (186)
+|.. .++|.. ...+.+++..||..||+|..|.+.|.++.|+...++|+|..|+
T Consensus 424 --------------------~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~~~~~~~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 424 --------------------KCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKKLTKKTFFETLDKPLCQKHF 478 (479)
T ss_pred --------------------cchhccchhHhhhhHhhccCccccccceehhhhhccccCCceeecCCccccccCC
Confidence 6776 666632 3458899999999999999999999999999999999999886
No 10
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.71 E-value=1.4e-18 Score=147.65 Aligned_cols=115 Identities=22% Similarity=0.406 Sum_probs=103.5
Q ss_pred CCCCcccCCceeccCceEEeCCccccccccccccccccccCCCccccCCeeecCcchhhhhcccCCCCccCCCCchhhhh
Q 046210 6 TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYFKPHFEQLFKESGNFNKNFQSPAKLIEK 85 (186)
Q Consensus 6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~ 85 (186)
+...|++|++.|..+..+.|+++.||..||+|..|...|.+ .|..++|.+||+.||++.|+.
T Consensus 132 ~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~g-ey~skdg~pyce~dy~~~fgv----------------- 193 (670)
T KOG1044|consen 132 GPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNG-EYMSKDGVPYCEKDYQAKFGV----------------- 193 (670)
T ss_pred CCccccchhhhhhccceeeeeccceeeeeeehhhhcccccc-eeeccCCCcchhhhhhhhcCe-----------------
Confidence 56789999999999999999999999999999999999976 899999999999999999966
Q ss_pred hhcccccCCCCcccCCCCCCCCC-Cceeecccceecccccccccceecccccccc-CCCCceecCCccccHHHHh
Q 046210 86 LTRQDRLAKLPACYLGPKNMCFL-HKIVCPSEKVAMESQAHHKSCFKCSHGGYSI-SPSNYAALEGIWYCKHHFS 158 (186)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~~C~~-~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L-~~~~~~~~~g~~yC~~cy~ 158 (186)
+|.. .+.| .+..|.+.|++||+.|-+|+.|+..+ +++..|.....++-..|-.
T Consensus 194 -------------------kc~~c~~fi-sgkvLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~q 248 (670)
T KOG1044|consen 194 -------------------KCEECEKFI-SGKVLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCKQ 248 (670)
T ss_pred -------------------ehHHhhhhh-hhhhhhccCcccCcchhhhhhhccccccchheeeccccccCCcccc
Confidence 7888 7888 67788999999999999999999999 6778888888887777743
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=99.63 E-value=2.8e-16 Score=97.86 Aligned_cols=57 Identities=33% Similarity=0.743 Sum_probs=53.2
Q ss_pred cccCCceeccCceE-EeCCccccccccccccccccccCCCccccCCeeecCcchhhhh
Q 046210 10 CKVCEKTVYPVEQL-SADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYFKPHFEQLF 66 (186)
Q Consensus 10 C~~C~~~I~~~~~i-~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~ 66 (186)
|.+|+++|...+.+ .+.|+.||++||+|+.|+++|.+..|+..+|++||..||.++|
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 88999999877765 7999999999999999999999999999999999999999876
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=99.55 E-value=3.9e-15 Score=92.63 Aligned_cols=56 Identities=30% Similarity=0.580 Sum_probs=50.4
Q ss_pred CCC-Cceeecccce-ecccccccccceeccccccccCCCCceecCCccccHHHHhhhh
Q 046210 106 CFL-HKIVCPSEKV-AMESQAHHKSCFKCSHGGYSISPSNYAALEGIWYCKHHFSKLF 161 (186)
Q Consensus 106 C~~-~~~I~~~~~v-~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~k~~ 161 (186)
|.+ +++|.+.+.+ .+.|+.||++||+|..|+++|....|+..||++||+.||.++|
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 567 7889777765 5999999999999999999998888999999999999999987
No 13
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.01 E-value=2.9e-11 Score=95.69 Aligned_cols=67 Identities=25% Similarity=0.354 Sum_probs=60.7
Q ss_pred CCCCCCC-CceeecccceecccccccccceeccccccccCCCCceecCCccccHHHHhhhhcCCCCCCc
Q 046210 102 PKNMCFL-HKIVCPSEKVAMESQAHHKSCFKCSHGGYSISPSNYAALEGIWYCKHHFSKLFKEKDSYNH 169 (186)
Q Consensus 102 ~~~~C~~-~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~k~~~~k~~~~~ 169 (186)
..++|++ .+.|.+.-.+.++++.||-.|++|+.|+.+|.. ..+.++|.+||+++|.|+||+||+-++
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~ 99 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQ 99 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhc
Confidence 4679999 999988888899999999999999999999954 588999999999999999999995554
No 14
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.90 E-value=1e-09 Score=62.20 Aligned_cols=37 Identities=43% Similarity=0.767 Sum_probs=33.4
Q ss_pred CcccCCceeccC-ceEEeCCcccccccccccccccccc
Q 046210 9 KCKVCEKTVYPV-EQLSADGIVYHKSCFKCSHCKGTLK 45 (186)
Q Consensus 9 ~C~~C~~~I~~~-~~i~~~g~~~H~~CF~C~~C~~~L~ 45 (186)
+|.+|+++|... ..+.+.++.||++||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 589999999776 5688999999999999999999985
No 15
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.62 E-value=9.2e-09 Score=79.48 Aligned_cols=75 Identities=52% Similarity=1.126 Sum_probs=66.1
Q ss_pred CCCCCCCcccCCceeccCceEEeCCccccccccccccccccccCCCccccCCeeecCcchhhhhcccCCCCccCC
Q 046210 3 FIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYFKPHFEQLFKESGNFNKNFQ 77 (186)
Q Consensus 3 ~~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~~~~~~~~~ 77 (186)
+.+....|.+|.+.+++.|.+...+..||..||+|+.|+..|....+...+|.+||...+..++-...+++...+
T Consensus 104 ~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~~~~~~~~~~~~ 178 (200)
T KOG1700|consen 104 FAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLFKGKGNYNEGFG 178 (200)
T ss_pred hhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheeecCCCcccccch
Confidence 357788999999999999999999999999999999999999999999999999999998888766666554443
No 16
>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=98.47 E-value=8.2e-08 Score=54.16 Aligned_cols=36 Identities=25% Similarity=0.412 Sum_probs=30.3
Q ss_pred CCCC-Cceeecc-cceecccccccccceeccccccccC
Q 046210 105 MCFL-HKIVCPS-EKVAMESQAHHKSCFKCSHGGYSIS 140 (186)
Q Consensus 105 ~C~~-~~~I~~~-~~v~~~g~~~H~~CF~C~~C~~~L~ 140 (186)
+|.+ +++|.+. ..+.+.++.||++||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 3677 7888665 5677899999999999999999985
No 17
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=98.17 E-value=1.7e-07 Score=71.30 Aligned_cols=62 Identities=37% Similarity=0.735 Sum_probs=56.4
Q ss_pred CCCcccCCceeccCceEEeCCccccccccccccccccccCCCccccCCeeecCcchhhhhcc
Q 046210 7 QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYFKPHFEQLFKE 68 (186)
Q Consensus 7 ~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~ 68 (186)
...|..|++.+++.|.+.-+++.||..||+|..|+-+|.-.+|-..+.++||..+|.+..++
T Consensus 4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~at 65 (264)
T KOG1702|consen 4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVAT 65 (264)
T ss_pred cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccceee
Confidence 35688999999999999999999999999999999999999998899999999999876543
No 18
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=97.96 E-value=5.3e-07 Score=68.62 Aligned_cols=61 Identities=30% Similarity=0.466 Sum_probs=53.4
Q ss_pred CCCC-CceeecccceecccccccccceeccccccccCCCCceecCCccccHHHHhhhhcCCC
Q 046210 105 MCFL-HKIVCPSEKVAMESQAHHKSCFKCSHGGYSISPSNYAALEGIWYCKHHFSKLFKEKD 165 (186)
Q Consensus 105 ~C~~-~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~k~~~~k~ 165 (186)
.|.. ++.+++.+.|..+++.||..||.|..|+.+|.-.+|.-.|-++||..+|.+..++-.
T Consensus 6 n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~at~~ 67 (264)
T KOG1702|consen 6 NREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVATVM 67 (264)
T ss_pred hhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccceeeee
Confidence 4555 888899999999999999999999999999988888889999999999988654433
No 19
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.67 E-value=8.3e-06 Score=64.06 Aligned_cols=113 Identities=18% Similarity=0.335 Sum_probs=84.5
Q ss_pred cCCceeccCceEEeCCcccccccccccccccccc--CCCccccCCeeecCcchhhhhcccCCCCccCCCCchhhhhhhcc
Q 046210 12 VCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLK--LSNYSSMEGVLYFKPHFEQLFKESGNFNKNFQSPAKLIEKLTRQ 89 (186)
Q Consensus 12 ~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~--~~~~~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (186)
.|+..|.+...+.+.+..||..|..|..|...|. ...|.. +|..||..+|...+..
T Consensus 1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~--------------------- 58 (235)
T KOG0490|consen 1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKF--------------------- 58 (235)
T ss_pred CCCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhc---------------------
Confidence 3778886556677889999999999999999998 545555 9999999999982211
Q ss_pred cccCCCCcccCCCCCCCCC-Cceeeccccee-cccccccccceecccccccc-CCCCceecCC-ccccHHHHhhh
Q 046210 90 DRLAKLPACYLGPKNMCFL-HKIVCPSEKVA-MESQAHHKSCFKCSHGGYSI-SPSNYAALEG-IWYCKHHFSKL 160 (186)
Q Consensus 90 ~~~~~~~~~~~~~~~~C~~-~~~I~~~~~v~-~~g~~~H~~CF~C~~C~~~L-~~~~~~~~~g-~~yC~~cy~k~ 160 (186)
..+|.+ ...|...+.|. +..+. |.-||.|..|...+ ....+.+.+. +.+|..++.+.
T Consensus 59 -------------~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 59 -------------SKRCARCKFTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred -------------cccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 236777 66654444444 45555 99999999999876 5556766655 99999888654
No 20
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=92.48 E-value=0.031 Score=43.65 Aligned_cols=54 Identities=19% Similarity=0.485 Sum_probs=41.8
Q ss_pred eeecccceecccccccccceeccccccccC--CCCceecCCccccHHHHhh--hhcCCC
Q 046210 111 IVCPSEKVAMESQAHHKSCFKCSHGGYSIS--PSNYAALEGIWYCKHHFSK--LFKEKD 165 (186)
Q Consensus 111 ~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~--~~~~~~~~g~~yC~~cy~k--~~~~k~ 165 (186)
.|.+...+.+.+..||..|..|..|...|. ...|.. +|..||..+|.. .+..++
T Consensus 5 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr 62 (235)
T KOG0490|consen 5 QILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRC 62 (235)
T ss_pred cccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccc
Confidence 444455566679999999999999999996 444444 999999999998 555555
No 21
>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=89.56 E-value=0.14 Score=28.45 Aligned_cols=31 Identities=26% Similarity=0.629 Sum_probs=22.1
Q ss_pred cccCCceeccCc--eEEeCCccccccccccccccccc
Q 046210 10 CKVCEKTVYPVE--QLSADGIVYHKSCFKCSHCKGTL 44 (186)
Q Consensus 10 C~~C~~~I~~~~--~i~~~g~~~H~~CF~C~~C~~~L 44 (186)
|.-||.+| .++ .+...++.|| |-|..|...|
T Consensus 1 Cd~CG~~I-~~eP~~~k~~~~~y~---fCC~tC~~~f 33 (37)
T PF08394_consen 1 CDYCGGEI-TGEPIVVKIGNKVYY---FCCPTCLSQF 33 (37)
T ss_pred CCccCCcc-cCCEEEEEECCeEEE---EECHHHHHHH
Confidence 67799999 455 3577899999 5566665544
No 22
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=88.58 E-value=0.31 Score=29.45 Aligned_cols=39 Identities=28% Similarity=0.690 Sum_probs=27.5
Q ss_pred CCCCcccCCceeccCce-E--EeCCcccccccc----cccc--ccccc
Q 046210 6 TQQKCKVCEKTVYPVEQ-L--SADGIVYHKSCF----KCSH--CKGTL 44 (186)
Q Consensus 6 ~~~~C~~C~~~I~~~~~-i--~~~g~~~H~~CF----~C~~--C~~~L 44 (186)
...+|..|+++|..++- + ..-+..||++|- .|.. |+.++
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence 35679999999975553 3 346789999997 5655 55443
No 23
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=86.69 E-value=0.58 Score=28.78 Aligned_cols=48 Identities=19% Similarity=0.344 Sum_probs=28.7
Q ss_pred CCCCCcccCCceeccCceEEeCCccccccccccccccccccCCC-ccccCCeee-cCcc
Q 046210 5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSN-YSSMEGVLY-FKPH 61 (186)
Q Consensus 5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~-~~~~~g~~y-C~~c 61 (186)
...+.|..|+..|..+|.-.. |.|-.|++.+-..- ---+.|.+| |.+|
T Consensus 7 ~~~~~CtSCg~~i~p~e~~v~---------F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~C 56 (61)
T COG2888 7 KDPPVCTSCGREIAPGETAVK---------FPCPNCGEVEIYRCAKCRKLGNPYRCPKC 56 (61)
T ss_pred cCCceeccCCCEeccCCceeE---------eeCCCCCceeeehhhhHHHcCCceECCCc
Confidence 346899999999976665433 77888875443211 112234444 6665
No 24
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=86.65 E-value=0.52 Score=28.96 Aligned_cols=32 Identities=25% Similarity=0.558 Sum_probs=22.1
Q ss_pred CCCCCCCcccCCceeccCceEEeCCcccccccccccccccc
Q 046210 3 FIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGT 43 (186)
Q Consensus 3 ~~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~ 43 (186)
-.-..++|..|+..|.+.+.-.. |.|-.|++.
T Consensus 3 ~~~~~~~CtSCg~~i~~~~~~~~---------F~CPnCG~~ 34 (59)
T PRK14890 3 EMMEPPKCTSCGIEIAPREKAVK---------FLCPNCGEV 34 (59)
T ss_pred ccccCccccCCCCcccCCCccCE---------eeCCCCCCe
Confidence 34456789999999965553222 778888776
No 25
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=86.42 E-value=0.6 Score=28.02 Aligned_cols=29 Identities=17% Similarity=0.415 Sum_probs=18.1
Q ss_pred eccccccccCCCCceecCCcccc-HHHHhh
Q 046210 131 KCSHGGYSISPSNYAALEGIWYC-KHHFSK 159 (186)
Q Consensus 131 ~C~~C~~~L~~~~~~~~~g~~yC-~~cy~k 159 (186)
-|..|...++...-+.+||+.|| ++|...
T Consensus 9 aC~~C~C~V~~~~Ai~~dGk~YCS~aCA~g 38 (52)
T PF02069_consen 9 ACPSCSCVVSEEEAIQKDGKYYCSEACANG 38 (52)
T ss_dssp SSTT----B-TTTSEESSS-EESSHHHHHT
T ss_pred cCCCCEeEECchHhHHhCCEeeecHHHhcc
Confidence 37788888887788899999998 667654
No 26
>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=84.97 E-value=0.24 Score=27.24 Aligned_cols=29 Identities=21% Similarity=0.368 Sum_probs=22.3
Q ss_pred ccccccccCCCCceecCCccccHHHHhhh
Q 046210 132 CSHGGYSISPSNYAALEGIWYCKHHFSKL 160 (186)
Q Consensus 132 C~~C~~~L~~~~~~~~~g~~yC~~cy~k~ 160 (186)
|..|+.+|........++..+|..|+.+.
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~~~ 34 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQERR 34 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHHHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHhCcc
Confidence 88899998777777788999999997653
No 27
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=84.89 E-value=0.34 Score=33.19 Aligned_cols=32 Identities=25% Similarity=0.540 Sum_probs=23.2
Q ss_pred CcccCCceeccCceEEe-CCccccccccccccc
Q 046210 9 KCKVCEKTVYPVEQLSA-DGIVYHKSCFKCSHC 40 (186)
Q Consensus 9 ~C~~C~~~I~~~~~i~~-~g~~~H~~CF~C~~C 40 (186)
+|..|+++|+.|+.... .+..-|-.||+=..=
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~~ 36 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKAS 36 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHHHh
Confidence 58889998888887644 446678888875543
No 28
>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=84.22 E-value=0.82 Score=31.08 Aligned_cols=31 Identities=32% Similarity=0.474 Sum_probs=18.0
Q ss_pred CCCCCcccCCceeccCceE-EeCCcccccccc
Q 046210 5 GTQQKCKVCEKTVYPVEQL-SADGIVYHKSCF 35 (186)
Q Consensus 5 ~~~~~C~~C~~~I~~~~~i-~~~g~~~H~~CF 35 (186)
.....|..|+++|.....+ .-.|..+|..|+
T Consensus 76 ~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 76 TESTKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCCCCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 3455677777777443332 334566776665
No 29
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=83.06 E-value=0.96 Score=27.02 Aligned_cols=29 Identities=31% Similarity=0.614 Sum_probs=22.6
Q ss_pred eccccccccCCC-CceecCCccccHHHHhhh
Q 046210 131 KCSHGGYSISPS-NYAALEGIWYCKHHFSKL 160 (186)
Q Consensus 131 ~C~~C~~~L~~~-~~~~~~g~~yC~~cy~k~ 160 (186)
.|..|+..+.-- .+-..|| ..|..|+.++
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 488999988433 3557788 7999999887
No 30
>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=80.93 E-value=0.83 Score=29.81 Aligned_cols=18 Identities=33% Similarity=0.560 Sum_probs=13.5
Q ss_pred CCCCCcccCCceeccCce
Q 046210 5 GTQQKCKVCEKTVYPVEQ 22 (186)
Q Consensus 5 ~~~~~C~~C~~~I~~~~~ 22 (186)
++-..|..|++.|..+++
T Consensus 5 s~Ra~Ck~C~~~I~kg~l 22 (82)
T PF00645_consen 5 SGRAKCKGCKKKIAKGEL 22 (82)
T ss_dssp SSTEBETTTSCBE-TTSE
T ss_pred CCCccCcccCCcCCCCCE
Confidence 455689999999977764
No 31
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=80.29 E-value=0.81 Score=25.24 Aligned_cols=25 Identities=20% Similarity=0.433 Sum_probs=18.6
Q ss_pred eeccccccccCCCCceecCCccccHHHHh
Q 046210 130 FKCSHGGYSISPSNYAALEGIWYCKHHFS 158 (186)
Q Consensus 130 F~C~~C~~~L~~~~~~~~~g~~yC~~cy~ 158 (186)
+.|..|+.. .|...||..||..|-.
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEhhhCce
Confidence 347788774 5777899999977743
No 32
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=78.39 E-value=1.2 Score=21.94 Aligned_cols=8 Identities=25% Similarity=0.916 Sum_probs=5.0
Q ss_pred cccCCcee
Q 046210 10 CKVCEKTV 17 (186)
Q Consensus 10 C~~C~~~I 17 (186)
|..|+..|
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 56666666
No 33
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=78.27 E-value=0.77 Score=35.41 Aligned_cols=31 Identities=26% Similarity=0.317 Sum_probs=26.6
Q ss_pred eeccccccccCCCCceecCCccccHHHHhhh
Q 046210 130 FKCSHGGYSISPSNYAALEGIWYCKHHFSKL 160 (186)
Q Consensus 130 F~C~~C~~~L~~~~~~~~~g~~yC~~cy~k~ 160 (186)
-+|+.|+-.+-...-...||+++|..||.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 6899999988766677889999999999764
No 34
>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=76.00 E-value=1.6 Score=29.63 Aligned_cols=28 Identities=25% Similarity=0.362 Sum_probs=22.8
Q ss_pred ccccccccccCCCcccc-CCeeecCcchh
Q 046210 36 KCSHCKGTLKLSNYSSM-EGVLYFKPHFE 63 (186)
Q Consensus 36 ~C~~C~~~L~~~~~~~~-~g~~yC~~cy~ 63 (186)
.|..|+++|....|... +|.++...|..
T Consensus 80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 58999999999888654 77888888764
No 35
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=75.36 E-value=1.3 Score=34.22 Aligned_cols=32 Identities=22% Similarity=0.411 Sum_probs=27.6
Q ss_pred cccccccccccCCCccccCCeeecCcchhhhh
Q 046210 35 FKCSHCKGTLKLSNYSSMEGVLYFKPHFEQLF 66 (186)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~ 66 (186)
-+|+.|+..+....-...+|++.|..||.+.+
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~~ 204 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKKY 204 (206)
T ss_pred eeccccCcccccchhhhcCCceeccccccccc
Confidence 68999999998877778899999999997643
No 36
>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=71.60 E-value=4.2 Score=24.61 Aligned_cols=32 Identities=19% Similarity=0.207 Sum_probs=25.7
Q ss_pred cccccccccccCCCccccCCeeecCcchhhhhc
Q 046210 35 FKCSHCKGTLKLSNYSSMEGVLYFKPHFEQLFK 67 (186)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~ 67 (186)
|.|..|+..+.. ......|..||..|..+.+.
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~ 33 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLL 33 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHH
Confidence 678899998877 45566889999999988764
No 37
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=70.26 E-value=1.8 Score=31.19 Aligned_cols=22 Identities=18% Similarity=0.462 Sum_probs=18.6
Q ss_pred ccccccccCCCCceecCCccccHHHHh
Q 046210 132 CSHGGYSISPSNYAALEGIWYCKHHFS 158 (186)
Q Consensus 132 C~~C~~~L~~~~~~~~~g~~yC~~cy~ 158 (186)
|..|+.+| |- +||.+||..|-.
T Consensus 31 Cp~Cg~PL----F~-KdG~v~CPvC~~ 52 (131)
T COG1645 31 CPKCGTPL----FR-KDGEVFCPVCGY 52 (131)
T ss_pred CcccCCcc----ee-eCCeEECCCCCc
Confidence 89999987 44 999999999964
No 38
>PRK00807 50S ribosomal protein L24e; Validated
Probab=70.20 E-value=2.3 Score=25.51 Aligned_cols=34 Identities=26% Similarity=0.618 Sum_probs=24.2
Q ss_pred CCcccCCceeccCce---EEeCCccccccccccccccccc
Q 046210 8 QKCKVCEKTVYPVEQ---LSADGIVYHKSCFKCSHCKGTL 44 (186)
Q Consensus 8 ~~C~~C~~~I~~~~~---i~~~g~~~H~~CF~C~~C~~~L 44 (186)
..|.-|+..|++++- +...|+.|. |-+..|.+.+
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~---Fcs~KC~~~f 38 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILY---FCSSKCEKNY 38 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEE---EeCHHHHHHH
Confidence 468999999986653 557788888 6666665543
No 39
>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=69.35 E-value=2 Score=24.45 Aligned_cols=22 Identities=23% Similarity=0.545 Sum_probs=14.9
Q ss_pred eccccccccCCCCceecCCccccHHH
Q 046210 131 KCSHGGYSISPSNYAALEGIWYCKHH 156 (186)
Q Consensus 131 ~C~~C~~~L~~~~~~~~~g~~yC~~c 156 (186)
.|..|+.+|- ..++|+.||-.|
T Consensus 19 ~Cp~C~~PL~----~~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPLM----RDKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCeeE----EecCCCEECCCC
Confidence 4667777762 247888888665
No 40
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=62.57 E-value=7.1 Score=26.79 Aligned_cols=40 Identities=15% Similarity=0.024 Sum_probs=26.8
Q ss_pred eecccccccc-CCCCceecCCccccHHHHhhhhcCCCCCCc
Q 046210 130 FKCSHGGYSI-SPSNYAALEGIWYCKHHFSKLFKEKDSYNH 169 (186)
Q Consensus 130 F~C~~C~~~L-~~~~~~~~~g~~yC~~cy~k~~~~k~~~~~ 169 (186)
.+|..|+..+ .++.|+...+-|.--.||.+...++...+.
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~~~k~~~~~ 43 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREKASKKLYGDV 43 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHHHhhhcccCh
Confidence 3677777777 566676666677777888776666654433
No 41
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=62.04 E-value=10 Score=28.42 Aligned_cols=43 Identities=16% Similarity=0.134 Sum_probs=29.3
Q ss_pred ccccccccCCCCceecCC--ccccHHHHhhhhcCCCCCCcccccccc
Q 046210 132 CSHGGYSISPSNYAALEG--IWYCKHHFSKLFKEKDSYNHLIKFASM 176 (186)
Q Consensus 132 C~~C~~~L~~~~~~~~~g--~~yC~~cy~k~~~~k~~~~~~~~~~~~ 176 (186)
|..|++.+....-...+| .-.|..|+ .||++..+.........
T Consensus 6 CEiCG~~i~~~~~v~vegsel~VC~~Ca--k~G~~~~~~~~~~~~~~ 50 (165)
T COG1813 6 CELCGREIDKPIKVKVEGAELTVCDDCA--KFGTAAKTASGDPRKEP 50 (165)
T ss_pred eeccccccCCCeeEEeecceeehhHHHH--HhccCccccCCCccccc
Confidence 999999998333334566 34599999 89977766555444433
No 42
>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=61.77 E-value=5 Score=20.04 Aligned_cols=9 Identities=22% Similarity=0.925 Sum_probs=4.5
Q ss_pred cccCCceec
Q 046210 10 CKVCEKTVY 18 (186)
Q Consensus 10 C~~C~~~I~ 18 (186)
|..|+..|.
T Consensus 1 C~sC~~~i~ 9 (24)
T PF07754_consen 1 CTSCGRPIA 9 (24)
T ss_pred CccCCCccc
Confidence 445555553
No 43
>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=61.35 E-value=6.2 Score=22.71 Aligned_cols=31 Identities=19% Similarity=0.313 Sum_probs=20.2
Q ss_pred eeccccccccCCCCcee--cCCccccHHHHhhh
Q 046210 130 FKCSHGGYSISPSNYAA--LEGIWYCKHHFSKL 160 (186)
Q Consensus 130 F~C~~C~~~L~~~~~~~--~~g~~yC~~cy~k~ 160 (186)
|.|..|+++|.+..|.- =.+--+|..||.+.
T Consensus 1 ~~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~ 33 (46)
T cd02249 1 YSCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKG 33 (46)
T ss_pred CCCcCCCCCCcCCEEECCCCCCCcCHHHHHCcC
Confidence 45777888776543332 24567899999864
No 44
>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=60.51 E-value=4 Score=27.49 Aligned_cols=43 Identities=14% Similarity=0.283 Sum_probs=31.6
Q ss_pred CCCCCCCCcccCCceeccCceEEeCCccccccccccccccccccC
Q 046210 2 SFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKL 46 (186)
Q Consensus 2 ~~~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~ 46 (186)
++....+.|..|++++..-|.|-+.+=.+.+ -+|..|+.++..
T Consensus 28 ~i~~~rS~C~~C~~~L~~~~lIPi~S~l~lr--GrCr~C~~~I~~ 70 (92)
T PF06750_consen 28 SIIFPRSHCPHCGHPLSWWDLIPILSYLLLR--GRCRYCGAPIPP 70 (92)
T ss_pred CccCCCCcCcCCCCcCcccccchHHHHHHhC--CCCcccCCCCCh
Confidence 4556678999999999777777665544443 467888888865
No 45
>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=59.35 E-value=7.8 Score=22.08 Aligned_cols=29 Identities=24% Similarity=0.437 Sum_probs=18.8
Q ss_pred eccccccccCCCCcee--cCCccccHHHHhh
Q 046210 131 KCSHGGYSISPSNYAA--LEGIWYCKHHFSK 159 (186)
Q Consensus 131 ~C~~C~~~L~~~~~~~--~~g~~yC~~cy~k 159 (186)
.|..|+++|.+..|.- =.+--+|..||.+
T Consensus 6 ~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~ 36 (44)
T smart00291 6 SCDTCGKPIVGVRYHCLVCPDYDLCQSCFAK 36 (44)
T ss_pred CCCCCCCCCcCCEEECCCCCCccchHHHHhC
Confidence 4667777666555432 2456689999976
No 46
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=58.59 E-value=4.3 Score=36.69 Aligned_cols=39 Identities=18% Similarity=0.255 Sum_probs=25.2
Q ss_pred cccccccccceeccccccccCCCCceecCCccccHHHHh
Q 046210 120 MESQAHHKSCFKCSHGGYSISPSNYAALEGIWYCKHHFS 158 (186)
Q Consensus 120 ~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~ 158 (186)
..|....++|++|..|+..|.+...-+.+|.+-|-.|..
T Consensus 106 ~sg~~~ckk~~~c~qc~~~lpg~s~~~~~~~~~~~~c~s 144 (694)
T KOG4443|consen 106 PSGPWLCKKCTRCRQCDSTLPGLSLDLQEGYLQCAPCAS 144 (694)
T ss_pred cCcccccHHHHhhhhccccccccchhhhccCcccccccc
Confidence 455667888999999999887632222335555555544
No 47
>PRK00420 hypothetical protein; Validated
Probab=55.41 E-value=4.8 Score=28.18 Aligned_cols=24 Identities=21% Similarity=0.457 Sum_probs=16.1
Q ss_pred eccccccccCCCCceecCCccccHHHHh
Q 046210 131 KCSHGGYSISPSNYAALEGIWYCKHHFS 158 (186)
Q Consensus 131 ~C~~C~~~L~~~~~~~~~g~~yC~~cy~ 158 (186)
.|..|+.+| |..++|+.||..|-.
T Consensus 25 ~CP~Cg~pL----f~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 25 HCPVCGLPL----FELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCcc----eecCCCceECCCCCC
Confidence 477777765 334778888887754
No 48
>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=54.14 E-value=6.4 Score=22.60 Aligned_cols=24 Identities=29% Similarity=0.509 Sum_probs=16.1
Q ss_pred ccccccccCCCCceecCCcccc-HHHHhh
Q 046210 132 CSHGGYSISPSNYAALEGIWYC-KHHFSK 159 (186)
Q Consensus 132 C~~C~~~L~~~~~~~~~g~~yC-~~cy~k 159 (186)
|..|.+++.. ..++.+|| ++|-.+
T Consensus 9 C~~Cdk~~~~----~~~~~lYCSe~Cr~~ 33 (43)
T PF12855_consen 9 CIVCDKQIDP----PDDGSLYCSEECRLK 33 (43)
T ss_pred HHHhhccccC----CCCCccccCHHHHhH
Confidence 5566777754 46788999 666443
No 49
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=52.94 E-value=24 Score=26.12 Aligned_cols=32 Identities=22% Similarity=0.454 Sum_probs=24.6
Q ss_pred eccccccccCCCCcee-cCC--ccccHHHHhhhhcCC
Q 046210 131 KCSHGGYSISPSNYAA-LEG--IWYCKHHFSKLFKEK 164 (186)
Q Consensus 131 ~C~~C~~~L~~~~~~~-~~g--~~yC~~cy~k~~~~k 164 (186)
.|..|++.+.+..+.+ .+| .-.|..|+ +||+.
T Consensus 2 ~CEiCG~~i~~~~~~v~iega~l~vC~~C~--k~G~~ 36 (154)
T TIGR00270 2 NCEICGRKIKGKGFKIVIEGSEMTVCGECR--KFGKE 36 (154)
T ss_pred ccccCCCccCCCCeEEEEcCeEEehhhhHH--hcCCc
Confidence 3999999998775654 577 34599999 78874
No 50
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=50.63 E-value=10 Score=22.84 Aligned_cols=24 Identities=17% Similarity=0.342 Sum_probs=12.1
Q ss_pred CcccCCceeccCceEEeCCccccc
Q 046210 9 KCKVCEKTVYPVEQLSADGIVYHK 32 (186)
Q Consensus 9 ~C~~C~~~I~~~~~i~~~g~~~H~ 32 (186)
+|..|.++|.....+...+..-|+
T Consensus 3 ~CvVCKqpi~~a~~v~T~~G~VH~ 26 (54)
T PF10886_consen 3 ICVVCKQPIDDALVVETESGPVHP 26 (54)
T ss_pred eeeeeCCccCcceEEEcCCCccCc
Confidence 466666666444444444444443
No 51
>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=49.90 E-value=15 Score=20.08 Aligned_cols=32 Identities=16% Similarity=0.251 Sum_probs=21.4
Q ss_pred ccccccccCCCCceecCCccccHHHHhhhhcC
Q 046210 132 CSHGGYSISPSNYAALEGIWYCKHHFSKLFKE 163 (186)
Q Consensus 132 C~~C~~~L~~~~~~~~~g~~yC~~cy~k~~~~ 163 (186)
|..|...+........=|..||..|..+.+..
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLEK 32 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHHC
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHHC
Confidence 55676666442234567999999999887655
No 52
>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=48.06 E-value=9.4 Score=20.67 Aligned_cols=8 Identities=25% Similarity=0.995 Sum_probs=4.9
Q ss_pred cccCCcee
Q 046210 10 CKVCEKTV 17 (186)
Q Consensus 10 C~~C~~~I 17 (186)
|..|...+
T Consensus 2 C~iC~~~~ 9 (45)
T cd00162 2 CPICLEEF 9 (45)
T ss_pred CCcCchhh
Confidence 56666665
No 53
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=47.02 E-value=22 Score=22.30 Aligned_cols=34 Identities=15% Similarity=0.219 Sum_probs=16.9
Q ss_pred cccccccccccCCCccccCCeeecCcchhhhhcc
Q 046210 35 FKCSHCKGTLKLSNYSSMEGVLYFKPHFEQLFKE 68 (186)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~ 68 (186)
++|+.|...|...--...=..+||..|....++.
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~ 41 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGS 41 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTT
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCC
Confidence 5788888888764334556678999998777654
No 54
>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=46.92 E-value=17 Score=20.90 Aligned_cols=30 Identities=27% Similarity=0.475 Sum_probs=16.1
Q ss_pred eecccccc-ccCCCCcee--cCCccccHHHHhh
Q 046210 130 FKCSHGGY-SISPSNYAA--LEGIWYCKHHFSK 159 (186)
Q Consensus 130 F~C~~C~~-~L~~~~~~~--~~g~~yC~~cy~k 159 (186)
+.|..|+. +|.+..|.- -.+--+|..||.+
T Consensus 5 ~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~ 37 (46)
T PF00569_consen 5 YTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSK 37 (46)
T ss_dssp CE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH
T ss_pred eECcCCCCCcCcCCeEECCCCCCCchhhHHHhC
Confidence 35666666 444444432 1345689999987
No 55
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=46.68 E-value=10 Score=24.17 Aligned_cols=39 Identities=15% Similarity=0.475 Sum_probs=19.9
Q ss_pred CCcccCCceeccCceEEeCCccccccccccccccccccCCCccccCCeeecCcchhhh
Q 046210 8 QKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYFKPHFEQL 65 (186)
Q Consensus 8 ~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~ 65 (186)
..|+.|..++. |-..-+.|..|++.+.. ..+|.+|...+
T Consensus 2 ~~CP~C~~~L~-----------~~~~~~~C~~C~~~~~~--------~a~CPdC~~~L 40 (70)
T PF07191_consen 2 NTCPKCQQELE-----------WQGGHYHCEACQKDYKK--------EAFCPDCGQPL 40 (70)
T ss_dssp -B-SSS-SBEE-----------EETTEEEETTT--EEEE--------EEE-TTT-SB-
T ss_pred CcCCCCCCccE-----------EeCCEEECcccccccee--------cccCCCcccHH
Confidence 36888888773 22244668888775433 67888887665
No 56
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=45.58 E-value=14 Score=18.52 Aligned_cols=9 Identities=22% Similarity=0.693 Sum_probs=5.4
Q ss_pred CcccCCcee
Q 046210 9 KCKVCEKTV 17 (186)
Q Consensus 9 ~C~~C~~~I 17 (186)
.|..|+..|
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 466666655
No 57
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=44.84 E-value=12 Score=28.41 Aligned_cols=38 Identities=16% Similarity=0.380 Sum_probs=29.5
Q ss_pred cccccccccccccccCCC-ccccCCeeecCcchhhhhcc
Q 046210 31 HKSCFKCSHCKGTLKLSN-YSSMEGVLYFKPHFEQLFKE 68 (186)
Q Consensus 31 H~~CF~C~~C~~~L~~~~-~~~~~g~~yC~~cy~~~~~~ 68 (186)
-..++.|-.|-....... +..+=|.+||..|.......
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~ 166 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKN 166 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHHHh
Confidence 457899999977776554 55788999999999887643
No 58
>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=44.70 E-value=6.5 Score=29.19 Aligned_cols=30 Identities=20% Similarity=0.343 Sum_probs=23.6
Q ss_pred CcccCCceeccCceEEeCCccccccccccccccccccC
Q 046210 9 KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKL 46 (186)
Q Consensus 9 ~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~ 46 (186)
.|..|+......+.+.. =|.|..|+..|..
T Consensus 111 ~Cp~c~~r~tf~eA~~~--------~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 111 ICPNMCVRFTFNEAMEL--------NFTCPRCGAMLDY 140 (158)
T ss_pred ECCCCCcEeeHHHHHHc--------CCcCCCCCCEeee
Confidence 59999988876676642 3999999999864
No 59
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=44.50 E-value=7.9 Score=29.37 Aligned_cols=30 Identities=23% Similarity=0.477 Sum_probs=23.4
Q ss_pred CcccCCceeccCceEEeCCccccccccccccccccccC
Q 046210 9 KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKL 46 (186)
Q Consensus 9 ~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~ 46 (186)
.|..|+......+.+.. =|.|..|+..|..
T Consensus 119 ~Cp~C~~rytf~eA~~~--------~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 119 FCPNCHIRFTFDEAMEY--------GFRCPQCGEMLEE 148 (178)
T ss_pred ECCCCCcEEeHHHHhhc--------CCcCCCCCCCCee
Confidence 59999988866666532 4999999999865
No 60
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=44.49 E-value=11 Score=21.59 Aligned_cols=9 Identities=44% Similarity=1.073 Sum_probs=5.7
Q ss_pred CcccCCcee
Q 046210 9 KCKVCEKTV 17 (186)
Q Consensus 9 ~C~~C~~~I 17 (186)
+|..|+..+
T Consensus 5 ~C~~CG~~~ 13 (46)
T PRK00398 5 KCARCGREV 13 (46)
T ss_pred ECCCCCCEE
Confidence 466666665
No 61
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=44.45 E-value=7.2 Score=28.48 Aligned_cols=35 Identities=23% Similarity=0.479 Sum_probs=24.7
Q ss_pred CcccCCceeccCceEEeCCccccccccccccccccccC
Q 046210 9 KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKL 46 (186)
Q Consensus 9 ~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~ 46 (186)
.|+.|+......+.+...+. ..=|+|..|+..|..
T Consensus 101 ~Cp~C~~~y~~~ea~~~~d~---~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 101 KCPNCQSKYTFLEANQLLDM---DGTFTCPRCGEELEE 135 (147)
T ss_pred ECcCCCCEeeHHHHHHhcCC---CCcEECCCCCCEEEE
Confidence 59999988866665544332 334999999998854
No 62
>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=43.84 E-value=19 Score=21.10 Aligned_cols=31 Identities=26% Similarity=0.484 Sum_probs=18.4
Q ss_pred eecccccc-ccCCCCceec--C--CccccHHHHhhh
Q 046210 130 FKCSHGGY-SISPSNYAAL--E--GIWYCKHHFSKL 160 (186)
Q Consensus 130 F~C~~C~~-~L~~~~~~~~--~--g~~yC~~cy~k~ 160 (186)
|+|..|+. +|.+..|.-. . +-=+|..||...
T Consensus 1 y~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~ 36 (48)
T cd02341 1 FKCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKG 36 (48)
T ss_pred CCCCCCCCCccccceEECCCCCCCCCccCHHHHhCc
Confidence 35666665 5555444321 2 456899998764
No 63
>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 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=41.84 E-value=20 Score=20.41 Aligned_cols=30 Identities=20% Similarity=0.173 Sum_probs=18.7
Q ss_pred eccccccccCCCCceec--CCccccHHHHhhh
Q 046210 131 KCSHGGYSISPSNYAAL--EGIWYCKHHFSKL 160 (186)
Q Consensus 131 ~C~~C~~~L~~~~~~~~--~g~~yC~~cy~k~ 160 (186)
.|..|+.+|.+..|.-. .+--+|..||...
T Consensus 2 ~Cd~C~~~i~G~ry~C~~C~d~dLC~~C~~~~ 33 (43)
T cd02340 2 ICDGCQGPIVGVRYKCLVCPDYDLCESCEAKG 33 (43)
T ss_pred CCCCCCCcCcCCeEECCCCCCccchHHhhCcC
Confidence 46677776665544422 3456789998753
No 65
>PF12773 DZR: Double zinc ribbon
Probab=41.81 E-value=21 Score=20.55 Aligned_cols=9 Identities=44% Similarity=1.136 Sum_probs=3.9
Q ss_pred ccccccccc
Q 046210 37 CSHCKGTLK 45 (186)
Q Consensus 37 C~~C~~~L~ 45 (186)
|..|+..|.
T Consensus 15 C~~CG~~l~ 23 (50)
T PF12773_consen 15 CPHCGTPLP 23 (50)
T ss_pred ChhhcCChh
Confidence 444444443
No 66
>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=41.41 E-value=19 Score=20.99 Aligned_cols=13 Identities=31% Similarity=0.728 Sum_probs=9.5
Q ss_pred CCCCCcccCCcee
Q 046210 5 GTQQKCKVCEKTV 17 (186)
Q Consensus 5 ~~~~~C~~C~~~I 17 (186)
.....|..|++.|
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 4566899999998
No 67
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=40.91 E-value=5.6 Score=23.93 Aligned_cols=26 Identities=15% Similarity=0.450 Sum_probs=12.0
Q ss_pred ccccccccccCCCcccc---CCeeecCcc
Q 046210 36 KCSHCKGTLKLSNYSSM---EGVLYFKPH 61 (186)
Q Consensus 36 ~C~~C~~~L~~~~~~~~---~g~~yC~~c 61 (186)
+|..|+-.|....+... ++.++|+.|
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~C 52 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNC 52 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCC
Confidence 45555555555443211 234555554
No 68
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=40.61 E-value=16 Score=23.92 Aligned_cols=29 Identities=21% Similarity=0.536 Sum_probs=20.8
Q ss_pred eccccccccCCCC-ce-ecCC---ccccHHHHhh
Q 046210 131 KCSHGGYSISPSN-YA-ALEG---IWYCKHHFSK 159 (186)
Q Consensus 131 ~C~~C~~~L~~~~-~~-~~~g---~~yC~~cy~k 159 (186)
.|..|+.||.... +. ..|| .-||.-||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 4889999997665 32 3454 5699999965
No 69
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=39.61 E-value=20 Score=24.26 Aligned_cols=30 Identities=13% Similarity=0.151 Sum_probs=14.3
Q ss_pred eecccccccc-CCCCceecCCccccHHHHhh
Q 046210 130 FKCSHGGYSI-SPSNYAALEGIWYCKHHFSK 159 (186)
Q Consensus 130 F~C~~C~~~L-~~~~~~~~~g~~yC~~cy~k 159 (186)
|.|.+|+.++ .++.|....--+.--+||..
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl~~ 37 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECLAE 37 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHHHH
Confidence 4455555554 44455443333444445544
No 70
>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=39.40 E-value=25 Score=19.07 Aligned_cols=28 Identities=21% Similarity=0.261 Sum_probs=15.6
Q ss_pred ccccccccCCCCceecCCcc-ccHHHHhh
Q 046210 132 CSHGGYSISPSNYAALEGIW-YCKHHFSK 159 (186)
Q Consensus 132 C~~C~~~L~~~~~~~~~g~~-yC~~cy~k 159 (186)
|..|+..-+..-....+|.. +|.+|...
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 56676665444333457777 99999754
No 71
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=39.29 E-value=9.7 Score=25.99 Aligned_cols=29 Identities=21% Similarity=0.227 Sum_probs=18.3
Q ss_pred cceeccccccccCCCC-ceecCCccccHHH
Q 046210 128 SCFKCSHGGYSISPSN-YAALEGIWYCKHH 156 (186)
Q Consensus 128 ~CF~C~~C~~~L~~~~-~~~~~g~~yC~~c 156 (186)
+=|+|+.|=..--... -...+|++||..|
T Consensus 69 DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 69 DEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CceeeeeeeeEechhhhccccCCCEecccc
Confidence 3488888844332221 2257899999987
No 72
>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=38.35 E-value=25 Score=20.34 Aligned_cols=29 Identities=14% Similarity=0.313 Sum_probs=20.0
Q ss_pred eccccccccCCCCcee--cCCccccHHHHhh
Q 046210 131 KCSHGGYSISPSNYAA--LEGIWYCKHHFSK 159 (186)
Q Consensus 131 ~C~~C~~~L~~~~~~~--~~g~~yC~~cy~k 159 (186)
.|..|+..+..-.|.. ..+.-+|..||.+
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhC
Confidence 5777888886544432 2357789999987
No 73
>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=38.20 E-value=15 Score=19.98 Aligned_cols=26 Identities=19% Similarity=0.231 Sum_probs=10.5
Q ss_pred eccccccccCCCCceecCCccccHHH
Q 046210 131 KCSHGGYSISPSNYAALEGIWYCKHH 156 (186)
Q Consensus 131 ~C~~C~~~L~~~~~~~~~g~~yC~~c 156 (186)
.|..|++++..+.....=+.+.|..|
T Consensus 5 ~C~eC~~~f~dSyL~~~F~~~VCD~C 30 (34)
T PF01286_consen 5 KCDECGKPFMDSYLLNNFDLPVCDKC 30 (34)
T ss_dssp E-TTT--EES-SSCCCCTS-S--TTT
T ss_pred hHhHhCCHHHHHHHHHhCCccccccc
Confidence 46667777655444444555666555
No 74
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=37.33 E-value=18 Score=21.66 Aligned_cols=34 Identities=21% Similarity=0.453 Sum_probs=22.6
Q ss_pred CcccCCceeccCceEEeCCcccccccccccccccccc
Q 046210 9 KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLK 45 (186)
Q Consensus 9 ~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~ 45 (186)
.|+-||+.|...--.+..++.|=.+|-. |-+|+.
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~v---CC~PI~ 35 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQV---CCRPIE 35 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhh---cCCccE
Confidence 5899999994322245567788888854 455654
No 75
>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=37.13 E-value=10 Score=21.44 Aligned_cols=28 Identities=11% Similarity=0.185 Sum_probs=14.9
Q ss_pred eeccccccccCCCCceecCCccccHHHH
Q 046210 130 FKCSHGGYSISPSNYAALEGIWYCKHHF 157 (186)
Q Consensus 130 F~C~~C~~~L~~~~~~~~~g~~yC~~cy 157 (186)
|+|..|+..+....-...+..+-|..|-
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg 33 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECG 33 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCC
Confidence 5677777666433212224556666653
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=36.51 E-value=16 Score=17.15 Aligned_cols=13 Identities=38% Similarity=0.677 Sum_probs=9.8
Q ss_pred eeccccccccCCC
Q 046210 130 FKCSHGGYSISPS 142 (186)
Q Consensus 130 F~C~~C~~~L~~~ 142 (186)
|+|..|++.+...
T Consensus 1 y~C~~C~~~f~~~ 13 (23)
T PF00096_consen 1 YKCPICGKSFSSK 13 (23)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCCCCCccCCH
Confidence 6788999887543
No 77
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=36.34 E-value=18 Score=22.24 Aligned_cols=28 Identities=18% Similarity=0.201 Sum_probs=19.6
Q ss_pred ccccccccccCC--CccccCCeeecC-cchh
Q 046210 36 KCSHCKGTLKLS--NYSSMEGVLYFK-PHFE 63 (186)
Q Consensus 36 ~C~~C~~~L~~~--~~~~~~g~~yC~-~cy~ 63 (186)
.|..|++.|..+ .|..+..+.+|. .|-.
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS~ECR~ 48 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCSEECRS 48 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccccHHHHH
Confidence 578899999853 455667788986 4443
No 78
>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=36.32 E-value=13 Score=22.20 Aligned_cols=26 Identities=19% Similarity=0.299 Sum_probs=16.7
Q ss_pred cccccccccccCC-CccccCCeeecCcch
Q 046210 35 FKCSHCKGTLKLS-NYSSMEGVLYFKPHF 62 (186)
Q Consensus 35 F~C~~C~~~L~~~-~~~~~~g~~yC~~cy 62 (186)
++|..|++.|... .+. +.++-|..|-
T Consensus 5 iRC~~CnklLa~~g~~~--~leIKCpRC~ 31 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVI--ELEIKCPRCK 31 (51)
T ss_pred eeccchhHHHhhhcCcc--EEEEECCCCC
Confidence 5788888888662 332 4456677774
No 79
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=36.22 E-value=33 Score=19.90 Aligned_cols=30 Identities=13% Similarity=0.288 Sum_probs=20.0
Q ss_pred ccccccccCCCCceecCCccccHHHHhhhhcC
Q 046210 132 CSHGGYSISPSNYAALEGIWYCKHHFSKLFKE 163 (186)
Q Consensus 132 C~~C~~~L~~~~~~~~~g~~yC~~cy~k~~~~ 163 (186)
|..|++....+ ....|...|..|-.++...
T Consensus 2 CiiC~~~~~~G--I~I~~~fIC~~CE~~iv~~ 31 (46)
T PF10764_consen 2 CIICGKEKEEG--IHIYGKFICSDCEKEIVNT 31 (46)
T ss_pred eEeCCCcCCCC--EEEECeEehHHHHHHhccC
Confidence 66677766442 4467788888887776544
No 80
>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=35.96 E-value=22 Score=20.42 Aligned_cols=28 Identities=21% Similarity=0.472 Sum_probs=16.7
Q ss_pred CcccCCceeccCceEEe--CCccccccccc
Q 046210 9 KCKVCEKTVYPVEQLSA--DGIVYHKSCFK 36 (186)
Q Consensus 9 ~C~~C~~~I~~~~~i~~--~g~~~H~~CF~ 36 (186)
+|..|++.-..+++|.= =++.||..|..
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~ 30 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVG 30 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTST
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCC
Confidence 37778884434445533 35778877743
No 81
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=35.79 E-value=9.5 Score=21.93 Aligned_cols=33 Identities=27% Similarity=0.493 Sum_probs=20.7
Q ss_pred cccCCceeccCc---eEEeCCccccccccccccccccccC
Q 046210 10 CKVCEKTVYPVE---QLSADGIVYHKSCFKCSHCKGTLKL 46 (186)
Q Consensus 10 C~~C~~~I~~~~---~i~~~g~~~H~~CF~C~~C~~~L~~ 46 (186)
...|+..| .+. .+...|+.|| |.+..|...+..
T Consensus 3 DPvcg~~v-~~~~~~~~~y~G~~Y~---FCS~~C~~~F~~ 38 (47)
T PF04945_consen 3 DPVCGMKV-PGNAAYSVEYNGRTYY---FCSEGCKEKFEA 38 (47)
T ss_dssp B-GGG-BE------EEEEETTEEEE---ESSHHHHHHHHC
T ss_pred CCCCCCEE-ccCccEEEEECCEEEE---EcCHHHHHHHHH
Confidence 46788888 442 3678899998 777777665543
No 82
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=35.42 E-value=8.5 Score=20.77 Aligned_cols=17 Identities=18% Similarity=0.651 Sum_probs=11.8
Q ss_pred cccccccccccCCCccc
Q 046210 35 FKCSHCKGTLKLSNYSS 51 (186)
Q Consensus 35 F~C~~C~~~L~~~~~~~ 51 (186)
|.|..|++++....|+.
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 67888888887777653
No 83
>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=34.93 E-value=15 Score=19.94 Aligned_cols=32 Identities=28% Similarity=0.621 Sum_probs=18.3
Q ss_pred CcccCCceeccCc-eEEeCCcccccccccccccccccc
Q 046210 9 KCKVCEKTVYPVE-QLSADGIVYHKSCFKCSHCKGTLK 45 (186)
Q Consensus 9 ~C~~C~~~I~~~~-~i~~~g~~~H~~CF~C~~C~~~L~ 45 (186)
.|..|+..+...+ .+...+. -++|..|+..|.
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~-----~v~C~~C~~~~~ 36 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGG-----KVRCGKCGHVWY 36 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCC-----EEECCCCCCEEE
Confidence 5888888764333 2332221 367788877653
No 84
>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=34.56 E-value=27 Score=30.81 Aligned_cols=14 Identities=29% Similarity=0.681 Sum_probs=8.1
Q ss_pred ccceeccccccccC
Q 046210 127 KSCFKCSHGGYSIS 140 (186)
Q Consensus 127 ~~CF~C~~C~~~L~ 140 (186)
+.||.|..|...|.
T Consensus 50 r~Cf~CP~C~~~L~ 63 (483)
T PF05502_consen 50 RNCFDCPICFSPLS 63 (483)
T ss_pred cccccCCCCCCcce
Confidence 35666666665553
No 85
>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=33.93 E-value=29 Score=25.75 Aligned_cols=37 Identities=16% Similarity=0.389 Sum_probs=21.7
Q ss_pred CCcccCCceeccCce----EEeCCccccccccccccccccccC
Q 046210 8 QKCKVCEKTVYPVEQ----LSADGIVYHKSCFKCSHCKGTLKL 46 (186)
Q Consensus 8 ~~C~~C~~~I~~~~~----i~~~g~~~H~~CF~C~~C~~~L~~ 46 (186)
..|..|+-+| .|+. +...|..|+.-- -|+.|+++...
T Consensus 40 ~~Cp~C~~~I-rG~y~v~gv~~~g~~~~~Ps-YC~~CGkpyPW 80 (158)
T PF10083_consen 40 TSCPNCSTPI-RGDYHVEGVFGLGGHYEAPS-YCHNCGKPYPW 80 (158)
T ss_pred HHCcCCCCCC-CCceecCCeeeeCCCCCCCh-hHHhCCCCCch
Confidence 3577888888 3432 344456666432 36777776543
No 86
>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=33.90 E-value=46 Score=19.10 Aligned_cols=32 Identities=22% Similarity=0.238 Sum_probs=20.8
Q ss_pred cccccccccccCCCccccCCee-ecCcchhhhhc
Q 046210 35 FKCSHCKGTLKLSNYSSMEGVL-YFKPHFEQLFK 67 (186)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~-yC~~cy~~~~~ 67 (186)
+.|..|...... ..+..=|.. +|..|..+...
T Consensus 3 ~~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~ 35 (50)
T PF13920_consen 3 EECPICFENPRD-VVLLPCGHLCFCEECAERLLK 35 (50)
T ss_dssp SB-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHH
T ss_pred CCCccCCccCCc-eEEeCCCChHHHHHHhHHhcc
Confidence 356677666544 334456777 99999988864
No 87
>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=33.31 E-value=57 Score=18.25 Aligned_cols=30 Identities=20% Similarity=0.377 Sum_probs=17.6
Q ss_pred eccccccccCCCCc-eec-CCccccHHHHhhh
Q 046210 131 KCSHGGYSISPSNY-AAL-EGIWYCKHHFSKL 160 (186)
Q Consensus 131 ~C~~C~~~L~~~~~-~~~-~g~~yC~~cy~k~ 160 (186)
+|+.|+++.+.... ..- ++...|..|-...
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~~ 34 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQA 34 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHHH
Confidence 68999998854433 333 3778899997654
No 88
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=33.24 E-value=18 Score=20.74 Aligned_cols=27 Identities=11% Similarity=0.283 Sum_probs=18.0
Q ss_pred eeccccccccCCCCceecCCccccHHHHhhh
Q 046210 130 FKCSHGGYSISPSNYAALEGIWYCKHHFSKL 160 (186)
Q Consensus 130 F~C~~C~~~L~~~~~~~~~g~~yC~~cy~k~ 160 (186)
+.|..|+..++.. ..+.+.|..|-.+.
T Consensus 3 Y~C~~Cg~~~~~~----~~~~irC~~CG~rI 29 (44)
T smart00659 3 YICGECGRENEIK----SKDVVRCRECGYRI 29 (44)
T ss_pred EECCCCCCEeecC----CCCceECCCCCceE
Confidence 5688888876543 45667787776553
No 89
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=33.05 E-value=16 Score=25.50 Aligned_cols=33 Identities=36% Similarity=0.581 Sum_probs=23.6
Q ss_pred CCCCCCCcccCCceeccCceEEeCCccccccccccccccccccC
Q 046210 3 FIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKL 46 (186)
Q Consensus 3 ~~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~ 46 (186)
...-+-.|+.|+++. ..+|+. =.|-.|+++|.-
T Consensus 65 tkav~V~CP~C~K~T------KmLGr~-----D~CM~C~~pLTL 97 (114)
T PF11023_consen 65 TKAVQVECPNCGKQT------KMLGRV-----DACMHCKEPLTL 97 (114)
T ss_pred ccceeeECCCCCChH------hhhchh-----hccCcCCCcCcc
Confidence 344556799999887 455666 268889999864
No 90
>PRK08359 transcription factor; Validated
Probab=32.86 E-value=75 Score=24.12 Aligned_cols=32 Identities=22% Similarity=0.497 Sum_probs=24.3
Q ss_pred eccccccccCCCCcee-cCC--ccccHHHHhhhhcC
Q 046210 131 KCSHGGYSISPSNYAA-LEG--IWYCKHHFSKLFKE 163 (186)
Q Consensus 131 ~C~~C~~~L~~~~~~~-~~g--~~yC~~cy~k~~~~ 163 (186)
.|..|++.+.+..+.+ .+| ...|..|+.+ ||+
T Consensus 8 ~CEiCG~~i~g~~~~v~ieGael~VC~~Ca~k-~G~ 42 (176)
T PRK08359 8 YCEICGAEIRGPGHRIRIEGAELLVCDRCYEK-YGR 42 (176)
T ss_pred eeecCCCccCCCCeEEEEcCeEEehHHHHHHH-hCC
Confidence 4999999998876665 576 4459999855 566
No 91
>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=32.66 E-value=40 Score=19.34 Aligned_cols=36 Identities=25% Similarity=0.515 Sum_probs=21.4
Q ss_pred ecccccc-ccCCCCceec--CCccccHHHHhhhhcCCCCC
Q 046210 131 KCSHGGY-SISPSNYAAL--EGIWYCKHHFSKLFKEKDSY 167 (186)
Q Consensus 131 ~C~~C~~-~L~~~~~~~~--~g~~yC~~cy~k~~~~k~~~ 167 (186)
.|..|+. +|.+.+|.-. .+-=+|+.||.+ ++.+..|
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~-~~n~~~y 40 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSR-MGNEGEY 40 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhh-hcChhhe
Confidence 4667774 5666666532 455589999865 3444333
No 92
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=32.55 E-value=14 Score=20.27 Aligned_cols=10 Identities=20% Similarity=0.826 Sum_probs=6.1
Q ss_pred eecccccccc
Q 046210 130 FKCSHGGYSI 139 (186)
Q Consensus 130 F~C~~C~~~L 139 (186)
|+|..|+..+
T Consensus 6 y~C~~Cg~~f 15 (41)
T smart00834 6 YRCEDCGHTF 15 (41)
T ss_pred EEcCCCCCEE
Confidence 4566666655
No 93
>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=32.48 E-value=30 Score=20.23 Aligned_cols=30 Identities=13% Similarity=0.276 Sum_probs=17.8
Q ss_pred eccccc-cccCCCCcee--cCCccccHHHHhhh
Q 046210 131 KCSHGG-YSISPSNYAA--LEGIWYCKHHFSKL 160 (186)
Q Consensus 131 ~C~~C~-~~L~~~~~~~--~~g~~yC~~cy~k~ 160 (186)
+|..|+ .+|.+..|.- =.+--+|.+||...
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~~ 34 (49)
T cd02338 2 SCDGCGKSNFTGRRYKCLICYDYDLCADCYDSG 34 (49)
T ss_pred CCCCCcCCCcEEeeEEeCCCCCCccchhHHhCC
Confidence 466666 4555443331 24556899999864
No 94
>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=32.32 E-value=35 Score=18.97 Aligned_cols=10 Identities=20% Similarity=0.826 Sum_probs=2.9
Q ss_pred CCcccCCcee
Q 046210 8 QKCKVCEKTV 17 (186)
Q Consensus 8 ~~C~~C~~~I 17 (186)
.+|..|+.-|
T Consensus 3 ~rC~~C~ayl 12 (40)
T PF04810_consen 3 VRCRRCRAYL 12 (40)
T ss_dssp -B-TTT--BS
T ss_pred cccCCCCCEE
Confidence 3455555444
No 95
>PRK02935 hypothetical protein; Provisional
Probab=32.23 E-value=22 Score=24.60 Aligned_cols=30 Identities=40% Similarity=0.698 Sum_probs=21.3
Q ss_pred CCCCcccCCceeccCceEEeCCccccccccccccccccccC
Q 046210 6 TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKL 46 (186)
Q Consensus 6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~ 46 (186)
-+-.|+.|+++. ..+|+.- .|-.|++||.-
T Consensus 69 vqV~CP~C~K~T------KmLGrvD-----~CM~C~~PLTL 98 (110)
T PRK02935 69 VQVICPSCEKPT------KMLGRVD-----ACMHCNQPLTL 98 (110)
T ss_pred eeeECCCCCchh------hhcccee-----ecCcCCCcCCc
Confidence 355799999887 3445443 68899999864
No 96
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=32.10 E-value=16 Score=28.35 Aligned_cols=34 Identities=15% Similarity=0.229 Sum_probs=27.0
Q ss_pred ccccccccccccCCCccccCCeeecCcchhhhhcc
Q 046210 34 CFKCSHCKGTLKLSNYSSMEGVLYFKPHFEQLFKE 68 (186)
Q Consensus 34 CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~ 68 (186)
=|.|..|.+.... ..+..-|..+|..|+.+.+..
T Consensus 196 PF~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~k 229 (259)
T COG5152 196 PFLCGICKKDYES-PVVTECGHSFCSLCAIRKYQK 229 (259)
T ss_pred ceeehhchhhccc-hhhhhcchhHHHHHHHHHhcc
Confidence 3889999888765 556667889999999988854
No 97
>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=31.87 E-value=11 Score=26.15 Aligned_cols=20 Identities=25% Similarity=0.602 Sum_probs=12.8
Q ss_pred CCCCCcccCCceeccCceEEe
Q 046210 5 GTQQKCKVCEKTVYPVEQLSA 25 (186)
Q Consensus 5 ~~~~~C~~C~~~I~~~~~i~~ 25 (186)
|+-..|..||++| +.+.+.+
T Consensus 78 g~yG~C~~Cge~I-~~~RL~a 97 (110)
T TIGR02420 78 GEYGYCEECGEEI-GLRRLEA 97 (110)
T ss_pred CCCCchhccCCcc-cHHHHhh
Confidence 3445788888888 4455444
No 98
>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=31.53 E-value=35 Score=20.09 Aligned_cols=28 Identities=21% Similarity=0.456 Sum_probs=20.8
Q ss_pred CCCcccCCceec-cCc-eEEeCCccccccc
Q 046210 7 QQKCKVCEKTVY-PVE-QLSADGIVYHKSC 34 (186)
Q Consensus 7 ~~~C~~C~~~I~-~~~-~i~~~g~~~H~~C 34 (186)
-..|+.|+-... .+| .|.+.+.+|++.|
T Consensus 13 Y~~Cp~CGN~~vGngEG~liV~edtfkRtC 42 (49)
T PF12677_consen 13 YCKCPKCGNDKVGNGEGTLIVEEDTFKRTC 42 (49)
T ss_pred hccCcccCCcEeecCcceEEEeccceeeee
Confidence 357999988653 334 3788899999887
No 99
>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=31.41 E-value=12 Score=20.93 Aligned_cols=10 Identities=20% Similarity=0.747 Sum_probs=5.1
Q ss_pred CcccCCceec
Q 046210 9 KCKVCEKTVY 18 (186)
Q Consensus 9 ~C~~C~~~I~ 18 (186)
.|..|.+.+.
T Consensus 2 ~C~IC~~~~~ 11 (44)
T PF13639_consen 2 ECPICLEEFE 11 (44)
T ss_dssp CETTTTCBHH
T ss_pred CCcCCChhhc
Confidence 3555555553
No 100
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=31.38 E-value=46 Score=18.62 Aligned_cols=30 Identities=17% Similarity=0.171 Sum_probs=21.2
Q ss_pred cccccccc-CCCCcee-cCCccccHHHHhhhh
Q 046210 132 CSHGGYSI-SPSNYAA-LEGIWYCKHHFSKLF 161 (186)
Q Consensus 132 C~~C~~~L-~~~~~~~-~~g~~yC~~cy~k~~ 161 (186)
|..|...+ ....+++ .=|..+|..|..++.
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~ 33 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLK 33 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhc
Confidence 66777777 2334444 358999999998876
No 101
>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=31.36 E-value=40 Score=19.56 Aligned_cols=31 Identities=16% Similarity=0.207 Sum_probs=19.3
Q ss_pred eeccccccccCCCCce---ecCCccccHHHHhhh
Q 046210 130 FKCSHGGYSISPSNYA---ALEGIWYCKHHFSKL 160 (186)
Q Consensus 130 F~C~~C~~~L~~~~~~---~~~g~~yC~~cy~k~ 160 (186)
++|..|.+.+..+..+ .=.+--+|..||...
T Consensus 1 ~~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g 34 (49)
T cd02335 1 YHCDYCSKDITGTIRIKCAECPDFDLCLECFSAG 34 (49)
T ss_pred CCCCCcCCCCCCCcEEECCCCCCcchhHHhhhCc
Confidence 3577777777554222 124566899999754
No 102
>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=31.14 E-value=13 Score=21.23 Aligned_cols=26 Identities=27% Similarity=0.661 Sum_probs=9.6
Q ss_pred cccCCceeccCceEE--eCCcccccccc
Q 046210 10 CKVCEKTVYPVEQLS--ADGIVYHKSCF 35 (186)
Q Consensus 10 C~~C~~~I~~~~~i~--~~g~~~H~~CF 35 (186)
|..|++.+..|..-. .-+..||..|+
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~ 28 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCF 28 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHH
T ss_pred CcccchhHeeeccCCCCccCchHHHHHH
Confidence 556666664444322 22334666665
No 103
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=30.28 E-value=37 Score=17.14 Aligned_cols=9 Identities=33% Similarity=0.840 Sum_probs=6.4
Q ss_pred CcccCCcee
Q 046210 9 KCKVCEKTV 17 (186)
Q Consensus 9 ~C~~C~~~I 17 (186)
+|..|++.|
T Consensus 2 ~CP~C~~~V 10 (26)
T PF10571_consen 2 TCPECGAEV 10 (26)
T ss_pred cCCCCcCCc
Confidence 577777777
No 104
>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=30.20 E-value=21 Score=20.82 Aligned_cols=28 Identities=11% Similarity=0.234 Sum_probs=13.7
Q ss_pred cccccccccccCCCccccCCeeecCcch
Q 046210 35 FKCSHCKGTLKLSNYSSMEGVLYFKPHF 62 (186)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~cy 62 (186)
|+|..|+..+........+..+-|..|-
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg 33 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSDDPLATCPECG 33 (52)
T ss_pred EEeCCCCCEeEEEEecCCCCCCCCCCCC
Confidence 5666676655432211223445566664
No 105
>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=30.12 E-value=32 Score=19.28 Aligned_cols=9 Identities=22% Similarity=0.165 Sum_probs=4.3
Q ss_pred CCeeecCcc
Q 046210 53 EGVLYFKPH 61 (186)
Q Consensus 53 ~g~~yC~~c 61 (186)
.|.+.|..|
T Consensus 17 ~g~~vC~~C 25 (43)
T PF08271_consen 17 RGELVCPNC 25 (43)
T ss_dssp TTEEEETTT
T ss_pred CCeEECCCC
Confidence 444455444
No 106
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=29.76 E-value=35 Score=21.46 Aligned_cols=33 Identities=36% Similarity=0.545 Sum_probs=21.4
Q ss_pred eccccccccCCC---CceecCCccc--c-HHHHhhhhcCC
Q 046210 131 KCSHGGYSISPS---NYAALEGIWY--C-KHHFSKLFKEK 164 (186)
Q Consensus 131 ~C~~C~~~L~~~---~~~~~~g~~y--C-~~cy~k~~~~k 164 (186)
+|+.|+..|..+ -|...||.++ | ..|. ++|+-+
T Consensus 5 ~CsFcG~~I~PGtG~m~Vr~Dg~v~~FcssKc~-k~~~~~ 43 (66)
T COG2075 5 VCSFCGKKIEPGTGIMYVRNDGKVLRFCSSKCE-KLFKLG 43 (66)
T ss_pred EecCcCCccCCCceEEEEecCCeEEEEechhHH-HHHHcc
Confidence 699999999443 3445688765 7 4554 366443
No 107
>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=28.50 E-value=28 Score=15.91 Aligned_cols=12 Identities=33% Similarity=0.670 Sum_probs=7.2
Q ss_pred eeccccccccCC
Q 046210 130 FKCSHGGYSISP 141 (186)
Q Consensus 130 F~C~~C~~~L~~ 141 (186)
|.|..|+..+..
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 578888887754
No 108
>PRK12495 hypothetical protein; Provisional
Probab=28.32 E-value=36 Score=26.79 Aligned_cols=23 Identities=13% Similarity=0.352 Sum_probs=12.2
Q ss_pred cccccccccccCCCccccCCeeecCcch
Q 046210 35 FKCSHCKGTLKLSNYSSMEGVLYFKPHF 62 (186)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~cy 62 (186)
+.|..|+.+|- ...|..+|..|.
T Consensus 43 ~hC~~CG~PIp-----a~pG~~~Cp~CQ 65 (226)
T PRK12495 43 AHCDECGDPIF-----RHDGQEFCPTCQ 65 (226)
T ss_pred hhcccccCccc-----CCCCeeECCCCC
Confidence 44555555553 235556666554
No 109
>smart00746 TRASH metallochaperone-like domain.
Probab=28.13 E-value=46 Score=16.46 Aligned_cols=22 Identities=36% Similarity=0.844 Sum_probs=12.6
Q ss_pred cccCCceec-cCc--eEEeCCcccc
Q 046210 10 CKVCEKTVY-PVE--QLSADGIVYH 31 (186)
Q Consensus 10 C~~C~~~I~-~~~--~i~~~g~~~H 31 (186)
|..|+..|. ... .+...|..+|
T Consensus 1 c~~C~~~~~~~~~~~~~~~~g~~~~ 25 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVVNDGKVFY 25 (39)
T ss_pred CCCCCCCccCCCCceEEEECCEEEE
Confidence 667888775 222 2345566665
No 110
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=27.91 E-value=28 Score=17.86 Aligned_cols=12 Identities=33% Similarity=0.742 Sum_probs=4.1
Q ss_pred eeccccccccCC
Q 046210 130 FKCSHGGYSISP 141 (186)
Q Consensus 130 F~C~~C~~~L~~ 141 (186)
|+|..|++++.+
T Consensus 1 ~~C~~C~~~~~~ 12 (30)
T PF07649_consen 1 FRCDACGKPIDG 12 (30)
T ss_dssp ---TTTS----S
T ss_pred CcCCcCCCcCCC
Confidence 578888888866
No 111
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=27.84 E-value=40 Score=29.78 Aligned_cols=39 Identities=23% Similarity=0.553 Sum_probs=28.4
Q ss_pred CCcccCCceeccCceEEeCCccccccccccccccccccCC
Q 046210 8 QKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLS 47 (186)
Q Consensus 8 ~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~ 47 (186)
-.|..|-..+ +...+.+.+..--+.||.|-.|..+|...
T Consensus 27 ~yCp~CL~~~-p~~e~~~~~nrC~r~Cf~CP~C~~~L~~~ 65 (483)
T PF05502_consen 27 YYCPNCLFEV-PSSEARSEKNRCSRNCFDCPICFSPLSVR 65 (483)
T ss_pred eECccccccC-ChhhheeccceeccccccCCCCCCcceeE
Confidence 3577777766 33345556666778999999999999764
No 112
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=27.81 E-value=31 Score=27.53 Aligned_cols=33 Identities=15% Similarity=0.376 Sum_probs=27.2
Q ss_pred ccccceeccccccccCCCCceecCCccccHHHH
Q 046210 125 HHKSCFKCSHGGYSISPSNYAALEGIWYCKHHF 157 (186)
Q Consensus 125 ~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy 157 (186)
|=++=-.|..|+++++...|+...|...|..|+
T Consensus 150 ~~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 150 IGPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred CccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 334444699999999887888999999999997
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=27.51 E-value=46 Score=19.22 Aligned_cols=29 Identities=14% Similarity=0.450 Sum_probs=18.9
Q ss_pred ecccccc-ccCCCCcee--cCCccccHHHHhh
Q 046210 131 KCSHGGY-SISPSNYAA--LEGIWYCKHHFSK 159 (186)
Q Consensus 131 ~C~~C~~-~L~~~~~~~--~~g~~yC~~cy~k 159 (186)
+|..|+. +|.+..|.- =.+--+|+.||..
T Consensus 2 ~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~ 33 (45)
T cd02344 2 TCDGCQMFPINGPRFKCRNCDDFDFCENCFKT 33 (45)
T ss_pred CCCCCCCCCCccCeEECCCCCCccchHHhhCC
Confidence 4677764 566555542 2456689999977
No 114
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=27.51 E-value=27 Score=16.66 Aligned_cols=13 Identities=31% Similarity=0.437 Sum_probs=10.0
Q ss_pred eeccccccccCCC
Q 046210 130 FKCSHGGYSISPS 142 (186)
Q Consensus 130 F~C~~C~~~L~~~ 142 (186)
|.|..|++.+.+.
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 6788998887654
No 115
>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=27.48 E-value=54 Score=17.70 Aligned_cols=32 Identities=13% Similarity=0.202 Sum_probs=21.6
Q ss_pred ccccccccCCCCceecCCccccHHHHhhhhcC
Q 046210 132 CSHGGYSISPSNYAALEGIWYCKHHFSKLFKE 163 (186)
Q Consensus 132 C~~C~~~L~~~~~~~~~g~~yC~~cy~k~~~~ 163 (186)
|..|...+........=|..||..|..+.+..
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~~ 32 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLEN 32 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHHHHHHHHHH
T ss_pred CCcCCccccCCCEEecCCCcchHHHHHHHHHh
Confidence 55677766544434455788999999887653
No 116
>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=27.46 E-value=38 Score=24.63 Aligned_cols=38 Identities=16% Similarity=0.418 Sum_probs=22.7
Q ss_pred CCCcccCCceeccCceEE----eCCc--cccccccccccccccc
Q 046210 7 QQKCKVCEKTVYPVEQLS----ADGI--VYHKSCFKCSHCKGTL 44 (186)
Q Consensus 7 ~~~C~~C~~~I~~~~~i~----~~g~--~~H~~CF~C~~C~~~L 44 (186)
-.+|..|+..+...+.-. +... ..+..-.+|..|++..
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 468999998774433211 1222 2355677888887754
No 117
>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=27.04 E-value=42 Score=20.22 Aligned_cols=24 Identities=33% Similarity=0.826 Sum_probs=17.3
Q ss_pred CCcccCCceeccCce---EEeCCcccc
Q 046210 8 QKCKVCEKTVYPVEQ---LSADGIVYH 31 (186)
Q Consensus 8 ~~C~~C~~~I~~~~~---i~~~g~~~H 31 (186)
..|.-|+..|++|.- |..+|+.++
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~ 30 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFR 30 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEE
Confidence 468888888888753 556677666
No 118
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=26.78 E-value=26 Score=27.49 Aligned_cols=32 Identities=16% Similarity=0.098 Sum_probs=24.1
Q ss_pred cccceeccccccccCCCCceecCCccccHHHH
Q 046210 126 HKSCFKCSHGGYSISPSNYAALEGIWYCKHHF 157 (186)
Q Consensus 126 H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy 157 (186)
=++=..|..|+++++...|...+|..+|..|.
T Consensus 146 ~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 146 GLDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred ccchhhHhcCCCCCCceEEecccCCccccccc
Confidence 34445799999988744555689999999995
No 119
>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=26.45 E-value=29 Score=23.82 Aligned_cols=35 Identities=14% Similarity=0.158 Sum_probs=24.8
Q ss_pred ccccccceeccccccccCCCCceecCCccccHHHHhhhh
Q 046210 123 QAHHKSCFKCSHGGYSISPSNYAALEGIWYCKHHFSKLF 161 (186)
Q Consensus 123 ~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~k~~ 161 (186)
..+...==.|..| ....|++.++++.|..|-.+.+
T Consensus 29 g~~~va~daCeiC----~~~GY~q~g~~lvC~~C~~~~~ 63 (102)
T PF10080_consen 29 GSYRVAFDACEIC----GPKGYYQEGDQLVCKNCGVRFN 63 (102)
T ss_pred CCEEEEEEecccc----CCCceEEECCEEEEecCCCEEe
Confidence 3344443358888 4567999999999999976643
No 120
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=26.24 E-value=45 Score=22.07 Aligned_cols=31 Identities=29% Similarity=0.544 Sum_probs=18.8
Q ss_pred CcccCCceeccCce--EEeCCccccccccccccccc
Q 046210 9 KCKVCEKTVYPVEQ--LSADGIVYHKSCFKCSHCKG 42 (186)
Q Consensus 9 ~C~~C~~~I~~~~~--i~~~g~~~H~~CF~C~~C~~ 42 (186)
.|..|+.+|..+.. +.+.|..-+ |-|..|..
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~---FCC~GC~~ 34 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERP---FCCPGCQA 34 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccc---cccHHHHH
Confidence 58888888843433 455565544 66666644
No 121
>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=26.19 E-value=1.2e+02 Score=18.50 Aligned_cols=41 Identities=10% Similarity=0.225 Sum_probs=24.3
Q ss_pred eccccccccCCC---CceecCCccccHHHHhhhhcCCC-CCCccc
Q 046210 131 KCSHGGYSISPS---NYAALEGIWYCKHHFSKLFKEKD-SYNHLI 171 (186)
Q Consensus 131 ~C~~C~~~L~~~---~~~~~~g~~yC~~cy~k~~~~k~-~~~~~~ 171 (186)
.|..|++.|... .+.---.=-||..|...++.-.| +.+..+
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCgGel 51 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCGGEL 51 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCCCcc
Confidence 367777777433 23323445688888888876666 443333
No 122
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=25.84 E-value=31 Score=27.06 Aligned_cols=32 Identities=16% Similarity=0.096 Sum_probs=23.7
Q ss_pred cccccccccccccccCCCccccCCeeecCcch
Q 046210 31 HKSCFKCSHCKGTLKLSNYSSMEGVLYFKPHF 62 (186)
Q Consensus 31 H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy 62 (186)
=++=..|..|++++....|...+|.++|..|.
T Consensus 146 ~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 146 GLDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred ccchhhHhcCCCCCCceEEecccCCccccccc
Confidence 34445788888888754566778899998886
No 123
>PHA00080 DksA-like zinc finger domain containing protein
Probab=25.14 E-value=32 Score=21.99 Aligned_cols=28 Identities=21% Similarity=0.359 Sum_probs=19.0
Q ss_pred eccccccccCCCCceecCCccccHHHHh
Q 046210 131 KCSHGGYSISPSNYAALEGIWYCKHHFS 158 (186)
Q Consensus 131 ~C~~C~~~L~~~~~~~~~g~~yC~~cy~ 158 (186)
.|..|+.+|........-+-.||-.|-.
T Consensus 33 ~C~~Cg~~Ip~~Rl~a~P~~~~Cv~Cq~ 60 (72)
T PHA00080 33 HCEECGDPIPEARREAVPGCRTCVSCQE 60 (72)
T ss_pred EecCCCCcCcHHHHHhCCCccCcHHHHH
Confidence 4777777776665555667777777754
No 124
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.83 E-value=61 Score=26.62 Aligned_cols=34 Identities=18% Similarity=0.387 Sum_probs=21.9
Q ss_pred cccccccccccCCCcc---ccCCeeecCcchhhhhcc
Q 046210 35 FKCSHCKGTLKLSNYS---SMEGVLYFKPHFEQLFKE 68 (186)
Q Consensus 35 F~C~~C~~~L~~~~~~---~~~g~~yC~~cy~~~~~~ 68 (186)
++|+.|+..|.+..|. .....-||-.|-.+.+..
T Consensus 269 LcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~ 305 (352)
T KOG3579|consen 269 LCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQ 305 (352)
T ss_pred eeehhhhhhhccCceeecCCCcccceecccCHHHHHh
Confidence 6777777777777664 335566677776555443
No 125
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.34 E-value=44 Score=27.54 Aligned_cols=33 Identities=15% Similarity=0.290 Sum_probs=25.5
Q ss_pred cccccccccccCCCccccCCeeecCcchhhhhcc
Q 046210 35 FKCSHCKGTLKLSNYSSMEGVLYFKPHFEQLFKE 68 (186)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~ 68 (186)
|.|..|.+.+.. .....-+..+|..|..+.+..
T Consensus 242 f~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~qk 274 (313)
T KOG1813|consen 242 FKCFICRKYFYR-PVVTKCGHYFCEVCALKPYQK 274 (313)
T ss_pred cccccccccccc-chhhcCCceeehhhhcccccc
Confidence 778888888765 556667889999999887743
No 126
>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=24.19 E-value=34 Score=16.67 Aligned_cols=13 Identities=31% Similarity=0.670 Sum_probs=9.9
Q ss_pred eeccccccccCCC
Q 046210 130 FKCSHGGYSISPS 142 (186)
Q Consensus 130 F~C~~C~~~L~~~ 142 (186)
|.|..|++.+...
T Consensus 2 ~~C~~C~~~F~~~ 14 (27)
T PF13912_consen 2 FECDECGKTFSSL 14 (27)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCccCCccCCh
Confidence 6789999887543
No 127
>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=23.90 E-value=37 Score=16.77 Aligned_cols=13 Identities=23% Similarity=0.360 Sum_probs=10.3
Q ss_pred eeccccccccCCC
Q 046210 130 FKCSHGGYSISPS 142 (186)
Q Consensus 130 F~C~~C~~~L~~~ 142 (186)
|.|..|++.+.++
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 6789999888655
No 128
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=23.90 E-value=27 Score=25.06 Aligned_cols=32 Identities=28% Similarity=0.560 Sum_probs=21.6
Q ss_pred CCcccCCceeccCce---EEeCCccccccccccccccc
Q 046210 8 QKCKVCEKTVYPVEQ---LSADGIVYHKSCFKCSHCKG 42 (186)
Q Consensus 8 ~~C~~C~~~I~~~~~---i~~~g~~~H~~CF~C~~C~~ 42 (186)
..|.-|+..|++|.- |...|++|+ |.=+.|.+
T Consensus 5 e~CsFcG~kIyPG~G~~fVR~DGkvf~---FcssKC~k 39 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMFVRKDGTVLH---FVDSKCEK 39 (131)
T ss_pred eeecCcCCcccCCCCcEEEecCCCEEE---EecHHHHH
Confidence 468888888888753 556677777 44445543
No 129
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=23.87 E-value=51 Score=19.23 Aligned_cols=30 Identities=20% Similarity=0.274 Sum_probs=16.5
Q ss_pred ecccccc-ccCCCCcee--cCCccccHHHHhhh
Q 046210 131 KCSHGGY-SISPSNYAA--LEGIWYCKHHFSKL 160 (186)
Q Consensus 131 ~C~~C~~-~L~~~~~~~--~~g~~yC~~cy~k~ 160 (186)
.|..|.+ +|.+-.|.- =.+--+|..||...
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~dydLC~~Cf~~~ 34 (49)
T cd02345 2 SCSACRKQDISGIRFPCQVCRDYSLCLGCYTKG 34 (49)
T ss_pred cCCCCCCCCceEeeEECCCCCCcCchHHHHhCC
Confidence 3555555 554333321 13455899999864
No 130
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=23.48 E-value=54 Score=17.29 Aligned_cols=9 Identities=22% Similarity=0.663 Sum_probs=5.9
Q ss_pred CcccCCcee
Q 046210 9 KCKVCEKTV 17 (186)
Q Consensus 9 ~C~~C~~~I 17 (186)
.|..|+..+
T Consensus 3 ~C~~C~t~L 11 (31)
T TIGR01053 3 VCGGCRTLL 11 (31)
T ss_pred CcCCCCcEe
Confidence 567776665
No 131
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=23.45 E-value=35 Score=20.96 Aligned_cols=16 Identities=44% Similarity=0.874 Sum_probs=11.4
Q ss_pred CCCcccCCceeccCce
Q 046210 7 QQKCKVCEKTVYPVEQ 22 (186)
Q Consensus 7 ~~~C~~C~~~I~~~~~ 22 (186)
-..|..|+++|..+|.
T Consensus 8 H~HC~VCg~aIp~de~ 23 (64)
T COG4068 8 HRHCVVCGKAIPPDEQ 23 (64)
T ss_pred CccccccCCcCCCccc
Confidence 3468888888865554
No 132
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=23.20 E-value=61 Score=23.53 Aligned_cols=24 Identities=25% Similarity=0.504 Sum_probs=19.3
Q ss_pred eeccccccccCCCCceecCCccccHHHHhhhh
Q 046210 130 FKCSHGGYSISPSNYAALEGIWYCKHHFSKLF 161 (186)
Q Consensus 130 F~C~~C~~~L~~~~~~~~~g~~yC~~cy~k~~ 161 (186)
..|..|+.+|..+. ||..|...+-
T Consensus 82 ~~CE~CG~~I~~Gr--------~C~~C~~~l~ 105 (137)
T TIGR03826 82 YPCERCGTSIREGR--------LCDSCAGELK 105 (137)
T ss_pred CcccccCCcCCCCC--------ccHHHHHHHH
Confidence 67999999997663 8999987763
No 133
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=22.98 E-value=35 Score=21.90 Aligned_cols=28 Identities=18% Similarity=0.356 Sum_probs=19.2
Q ss_pred eccccccccCCCCceecCCccccHHHHh
Q 046210 131 KCSHGGYSISPSNYAALEGIWYCKHHFS 158 (186)
Q Consensus 131 ~C~~C~~~L~~~~~~~~~g~~yC~~cy~ 158 (186)
-|..|+.+|........-|-.+|..|-.
T Consensus 36 ~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~ 63 (73)
T PRK13715 36 LCEACGNPIPEARRKIFPGVTLCVECQA 63 (73)
T ss_pred cHhhcCCcCCHHHHhcCCCcCCCHHHHH
Confidence 4777777776665556667777777744
No 134
>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=22.81 E-value=27 Score=17.89 Aligned_cols=10 Identities=30% Similarity=0.767 Sum_probs=4.6
Q ss_pred CCcccCCcee
Q 046210 8 QKCKVCEKTV 17 (186)
Q Consensus 8 ~~C~~C~~~I 17 (186)
..|.+|+..|
T Consensus 2 ~~C~rC~~~~ 11 (30)
T PF06827_consen 2 EKCPRCWNYI 11 (30)
T ss_dssp SB-TTT--BB
T ss_pred CcCccCCCcc
Confidence 4577777776
No 135
>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=22.68 E-value=67 Score=21.56 Aligned_cols=10 Identities=50% Similarity=1.248 Sum_probs=4.9
Q ss_pred CCcccCCcee
Q 046210 8 QKCKVCEKTV 17 (186)
Q Consensus 8 ~~C~~C~~~I 17 (186)
..|..|...|
T Consensus 45 ~~C~~CK~~v 54 (90)
T PF10235_consen 45 SKCKICKTKV 54 (90)
T ss_pred cccccccccc
Confidence 3455555544
No 136
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=22.64 E-value=26 Score=32.30 Aligned_cols=36 Identities=17% Similarity=0.323 Sum_probs=26.8
Q ss_pred cccccccccccccCCCccccCCeeecCcchhhhhccc
Q 046210 33 SCFKCSHCKGTLKLSNYSSMEGVLYFKPHFEQLFKES 69 (186)
Q Consensus 33 ~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~ 69 (186)
.=++|+.|+....+ .....=+.+||..|-..++.++
T Consensus 642 ~~LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~etR 677 (698)
T KOG0978|consen 642 ELLKCSVCNTRWKD-AVITKCGHVFCEECVQTRYETR 677 (698)
T ss_pred hceeCCCccCchhh-HHHHhcchHHHHHHHHHHHHHh
Confidence 34689999865544 4456678899999999998763
No 137
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=22.39 E-value=62 Score=19.55 Aligned_cols=28 Identities=14% Similarity=0.266 Sum_probs=20.3
Q ss_pred eeccccccccCCCCceecCCccccHHHHhhh
Q 046210 130 FKCSHGGYSISPSNYAALEGIWYCKHHFSKL 160 (186)
Q Consensus 130 F~C~~C~~~L~~~~~~~~~g~~yC~~cy~k~ 160 (186)
-+|..|+.+ ..++-+-|.-.|..||.++
T Consensus 17 r~C~vCg~~---~gliRkygL~~CRqCFRe~ 44 (54)
T PTZ00218 17 RQCRVCSNR---HGLIRKYGLNVCRQCFREN 44 (54)
T ss_pred CeeecCCCc---chhhhhcCcchhhHHHHHh
Confidence 357778774 2455567888999999875
No 138
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=22.10 E-value=20 Score=28.79 Aligned_cols=42 Identities=24% Similarity=0.524 Sum_probs=28.4
Q ss_pred CcccCCceeccCceEEeCCccccccccccccccccccCCCccc
Q 046210 9 KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSS 51 (186)
Q Consensus 9 ~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~ 51 (186)
.|-.||+.|- .-.+.-.-..-|..+|.|-.|++.+....|..
T Consensus 5 tCnvCgEsvK-Kp~vekH~srCrn~~fSCIDC~k~F~~~sYkn 46 (276)
T KOG2186|consen 5 TCNVCGESVK-KPQVEKHMSRCRNAYFSCIDCGKTFERVSYKN 46 (276)
T ss_pred ehhhhhhhcc-ccchHHHHHhccCCeeEEeecccccccchhhh
Confidence 5888998883 32222222234668999999999998866643
No 139
>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=21.94 E-value=73 Score=18.66 Aligned_cols=30 Identities=20% Similarity=0.197 Sum_probs=18.0
Q ss_pred ecccccc-ccCCCCcee--cCCccccHHHHhhh
Q 046210 131 KCSHGGY-SISPSNYAA--LEGIWYCKHHFSKL 160 (186)
Q Consensus 131 ~C~~C~~-~L~~~~~~~--~~g~~yC~~cy~k~ 160 (186)
.|..|++ +|.+..|.- =.+--+|..||..-
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g 34 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSG 34 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCC
Confidence 4666664 455544432 14556899999764
No 140
>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=21.71 E-value=31 Score=21.39 Aligned_cols=26 Identities=27% Similarity=0.484 Sum_probs=13.2
Q ss_pred eccccccccCCCCceecCCccccHHH
Q 046210 131 KCSHGGYSISPSNYAALEGIWYCKHH 156 (186)
Q Consensus 131 ~C~~C~~~L~~~~~~~~~g~~yC~~c 156 (186)
.|..|+.+|........-+-.+|-.|
T Consensus 33 ~C~~Cg~~Ip~~Rl~a~p~~~~Cv~C 58 (63)
T TIGR02419 33 ECEDCGEPIPEARREALPGVTRCVSC 58 (63)
T ss_pred eeccCCCcChHHHHhhcCCcCCcHHH
Confidence 35555555544444444455555555
No 141
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=21.22 E-value=49 Score=21.14 Aligned_cols=24 Identities=29% Similarity=0.629 Sum_probs=13.5
Q ss_pred CCcccCCceeccCce---EEeCCcccc
Q 046210 8 QKCKVCEKTVYPVEQ---LSADGIVYH 31 (186)
Q Consensus 8 ~~C~~C~~~I~~~~~---i~~~g~~~H 31 (186)
..|.-|+..|++|.- |..+|++++
T Consensus 4 ~~C~Fsg~~I~PG~G~~~Vr~DG~v~~ 30 (71)
T PF01246_consen 4 EKCSFSGYKIYPGHGKMYVRNDGKVFY 30 (71)
T ss_dssp EE-TTT-SEE-SSSSEEEE-TTS-EEE
T ss_pred EEecccCCccCCCCCeEEEecCCCeEE
Confidence 468888899988763 455667666
No 142
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=21.13 E-value=43 Score=26.75 Aligned_cols=31 Identities=13% Similarity=0.257 Sum_probs=25.6
Q ss_pred ccccccccccccccCCCccccCCeeecCcch
Q 046210 32 KSCFKCSHCKGTLKLSNYSSMEGVLYFKPHF 62 (186)
Q Consensus 32 ~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy 62 (186)
++=-.|+.|+.+.....|....|...|..|+
T Consensus 152 ~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 152 PNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred cchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 3445789999999888888889999999887
No 143
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=21.03 E-value=41 Score=23.62 Aligned_cols=24 Identities=25% Similarity=0.652 Sum_probs=17.8
Q ss_pred cccCCceeccCceEEeCCccccccccccccccccccC
Q 046210 10 CKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKL 46 (186)
Q Consensus 10 C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~ 46 (186)
|+.|+..+ +..-++|..|+..+.+
T Consensus 1 CPvCg~~l-------------~vt~l~C~~C~t~i~G 24 (113)
T PF09862_consen 1 CPVCGGEL-------------VVTRLKCPSCGTEIEG 24 (113)
T ss_pred CCCCCCce-------------EEEEEEcCCCCCEEEe
Confidence 67777766 4455788999988876
No 144
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=20.97 E-value=63 Score=20.08 Aligned_cols=14 Identities=21% Similarity=0.052 Sum_probs=11.0
Q ss_pred ccccCCeeecCcch
Q 046210 49 YSSMEGVLYFKPHF 62 (186)
Q Consensus 49 ~~~~~g~~yC~~cy 62 (186)
+...+|.++|..|-
T Consensus 47 ~~i~eg~L~Cp~c~ 60 (68)
T PF03966_consen 47 VEIVEGELICPECG 60 (68)
T ss_dssp EETTTTEEEETTTT
T ss_pred ccccCCEEEcCCCC
Confidence 45678999999883
No 145
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=20.16 E-value=1.5e+02 Score=16.81 Aligned_cols=8 Identities=25% Similarity=0.642 Sum_probs=4.5
Q ss_pred CCcccCCc
Q 046210 8 QKCKVCEK 15 (186)
Q Consensus 8 ~~C~~C~~ 15 (186)
..|..|+.
T Consensus 19 ~~CP~Cg~ 26 (46)
T PF12760_consen 19 FVCPHCGS 26 (46)
T ss_pred CCCCCCCC
Confidence 45666654
No 146
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.10 E-value=46 Score=27.30 Aligned_cols=47 Identities=23% Similarity=0.542 Sum_probs=35.8
Q ss_pred CCcccCCceeccCceEEeCCccccccccccccccccccCCCccccCCeeecC
Q 046210 8 QKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYFK 59 (186)
Q Consensus 8 ~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~ 59 (186)
-.|.-|++.+.+...|.-..-.-|+-||-|+. ..|.. ....|++||.
T Consensus 269 LcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSR--esIK~---Qg~sgevYCP 315 (352)
T KOG3579|consen 269 LCCTLCHERLEDTHFVQCPSVPSHKFCFPCSR--ESIKQ---QGASGEVYCP 315 (352)
T ss_pred eeehhhhhhhccCceeecCCCcccceecccCH--HHHHh---hcCCCceeCC
Confidence 46999999998888888888889999999984 22222 2346789995
No 147
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=20.05 E-value=1.5e+02 Score=16.43 Aligned_cols=33 Identities=18% Similarity=0.312 Sum_probs=21.6
Q ss_pred ccccccccCCCCceecCCccccHHHHhhhhcCCC
Q 046210 132 CSHGGYSISPSNYAALEGIWYCKHHFSKLFKEKD 165 (186)
Q Consensus 132 C~~C~~~L~~~~~~~~~g~~yC~~cy~k~~~~k~ 165 (186)
|..|...|. ......=|..||..|..+......
T Consensus 1 CpiC~~~~~-~Pv~l~CGH~FC~~Cl~~~~~~~~ 33 (42)
T PF15227_consen 1 CPICLDLFK-DPVSLPCGHSFCRSCLERLWKEPS 33 (42)
T ss_dssp ETTTTSB-S-SEEE-SSSSEEEHHHHHHHHCCSS
T ss_pred CCccchhhC-CccccCCcCHHHHHHHHHHHHccC
Confidence 556666664 335556689999999888775544
Done!