Query 029695
Match_columns 189
No_of_seqs 219 out of 1308
Neff 8.9
Searched_HMMs 46136
Date Fri Mar 29 17:02:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029695.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029695hhsearch_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 4.3E-29 9.4E-34 202.3 -2.0 137 7-183 274-413 (468)
2 KOG1701 Focal adhesion adaptor 99.9 3.1E-25 6.7E-30 180.0 0.4 125 3-166 330-465 (468)
3 KOG1700 Regulatory protein MLP 99.9 1.3E-22 2.9E-27 154.6 5.1 186 1-186 1-189 (200)
4 KOG4577 Transcription factor L 99.9 2.2E-23 4.8E-28 161.6 -2.3 125 6-169 32-159 (383)
5 KOG2272 Focal adhesion protein 99.8 4.3E-22 9.4E-27 151.9 0.8 117 6-162 194-311 (332)
6 KOG1044 Actin-binding LIM Zn-f 99.8 3.8E-20 8.3E-25 155.3 6.8 161 7-169 16-196 (670)
7 KOG2272 Focal adhesion protein 99.8 5.3E-22 1.1E-26 151.5 -4.3 118 6-162 11-129 (332)
8 KOG1703 Adaptor protein Enigma 99.8 5.7E-20 1.2E-24 157.4 6.1 125 6-169 302-426 (479)
9 KOG1703 Adaptor protein Enigma 99.8 6.2E-20 1.3E-24 157.2 1.9 117 5-160 361-478 (479)
10 KOG1044 Actin-binding LIM Zn-f 99.7 3.1E-19 6.6E-24 149.9 2.0 116 6-161 132-248 (670)
11 PF00412 LIM: LIM domain; Int 99.6 4.5E-16 9.8E-21 96.0 4.6 57 10-66 1-58 (58)
12 PF00412 LIM: LIM domain; Int 99.6 1.7E-15 3.8E-20 93.3 4.1 57 108-164 1-58 (58)
13 KOG4577 Transcription factor L 99.6 3.5E-16 7.6E-21 121.8 -0.9 81 105-186 33-114 (383)
14 smart00132 LIM Zinc-binding do 98.9 1.9E-09 4.1E-14 60.4 2.7 37 9-45 1-38 (39)
15 smart00132 LIM Zinc-binding do 98.7 6.4E-09 1.4E-13 58.2 2.4 37 107-143 1-38 (39)
16 KOG1700 Regulatory protein MLP 98.5 4.5E-08 9.7E-13 74.9 0.9 70 3-72 104-173 (200)
17 KOG1702 Nebulin repeat protein 98.4 4.4E-08 9.4E-13 73.5 -0.9 75 106-185 5-79 (264)
18 KOG1702 Nebulin repeat protein 98.1 2E-07 4.3E-12 70.0 -2.3 61 7-67 4-64 (264)
19 KOG0490 Transcription factor, 97.8 3.4E-06 7.3E-11 65.8 0.0 111 13-163 2-119 (235)
20 KOG0490 Transcription factor, 94.9 0.014 3E-07 45.4 1.7 63 111-174 2-69 (235)
21 PF14835 zf-RING_6: zf-RING of 89.3 0.49 1.1E-05 29.3 2.8 33 35-67 8-40 (65)
22 PF14446 Prok-RING_1: Prokaryo 88.4 0.39 8.4E-06 28.7 1.9 28 106-133 6-36 (54)
23 PF10367 Vps39_2: Vacuolar sor 86.6 0.53 1.2E-05 31.8 2.1 30 105-134 78-108 (109)
24 PRK14890 putative Zn-ribbon RN 85.9 0.8 1.7E-05 27.8 2.3 30 5-44 5-35 (59)
25 PF10367 Vps39_2: Vacuolar sor 85.6 0.65 1.4E-05 31.3 2.1 30 6-35 77-107 (109)
26 PF14471 DUF4428: Domain of un 82.8 0.9 2E-05 26.8 1.6 29 36-65 1-30 (51)
27 PF08394 Arc_trans_TRASH: Arch 82.7 0.8 1.7E-05 25.1 1.2 28 108-135 1-29 (37)
28 PF09943 DUF2175: Uncharacteri 82.5 0.36 7.7E-06 32.7 -0.3 32 106-137 3-35 (101)
29 PF13240 zinc_ribbon_2: zinc-r 82.3 0.72 1.6E-05 22.4 0.9 8 10-17 2-9 (23)
30 PF11781 RRN7: RNA polymerase 80.1 1 2.3E-05 24.5 1.1 24 35-62 9-32 (36)
31 PF09943 DUF2175: Uncharacteri 79.9 0.62 1.3E-05 31.5 0.2 32 8-39 3-35 (101)
32 PF10235 Cript: Microtubule-as 79.2 1.2 2.6E-05 29.5 1.4 29 30-64 40-68 (90)
33 smart00504 Ubox Modified RING 78.6 3.3 7.1E-05 24.9 3.2 32 35-67 2-33 (63)
34 KOG0320 Predicted E3 ubiquitin 78.4 1.7 3.6E-05 32.6 2.1 37 31-67 128-165 (187)
35 COG2888 Predicted Zn-ribbon RN 78.0 2.7 5.9E-05 25.5 2.5 31 6-45 8-38 (61)
36 COG1645 Uncharacterized Zn-fin 75.4 1.5 3.3E-05 31.1 1.2 23 36-63 30-52 (131)
37 PF01258 zf-dskA_traR: Prokary 74.8 0.7 1.5E-05 25.0 -0.6 28 37-64 6-33 (36)
38 PF06677 Auto_anti-p27: Sjogre 74.3 1.7 3.7E-05 24.4 0.9 22 36-61 19-40 (41)
39 PF00645 zf-PARP: Poly(ADP-rib 71.4 2.2 4.8E-05 27.5 1.1 16 6-21 6-21 (82)
40 COG2191 Formylmethanofuran deh 69.7 1.9 4.1E-05 33.0 0.6 31 35-65 173-203 (206)
41 PF10083 DUF2321: Uncharacteri 69.0 4 8.7E-05 29.9 2.1 39 106-145 40-81 (158)
42 PF02069 Metallothio_Pro: Prok 68.7 2.8 6E-05 24.8 1.0 27 135-161 10-37 (52)
43 PF12773 DZR: Double zinc ribb 67.5 3.4 7.4E-05 23.8 1.3 23 37-63 15-37 (50)
44 COG2191 Formylmethanofuran deh 65.2 2.3 4.9E-05 32.6 0.2 31 133-163 173-203 (206)
45 KOG0978 E3 ubiquitin ligase in 63.8 2.9 6.4E-05 37.9 0.7 51 33-119 642-692 (698)
46 PF13920 zf-C3HC4_3: Zinc fing 62.0 7.6 0.00016 22.3 2.0 31 36-67 4-35 (50)
47 COG5152 Uncharacterized conser 60.1 4.1 8.9E-05 31.1 0.8 51 34-121 196-246 (259)
48 PF14634 zf-RING_5: zinc-RING 58.7 10 0.00022 21.2 2.1 30 37-66 2-33 (44)
49 PRK00420 hypothetical protein; 58.0 5.9 0.00013 27.4 1.2 25 35-63 24-48 (112)
50 PF13248 zf-ribbon_3: zinc-rib 56.0 9.9 0.00022 18.8 1.6 12 106-117 3-14 (26)
51 PF10886 DUF2685: Protein of u 55.1 8.4 0.00018 22.9 1.4 24 9-32 3-26 (54)
52 KOG1813 Predicted E3 ubiquitin 54.9 7.9 0.00017 31.4 1.6 32 35-67 242-273 (313)
53 PF07191 zinc-ribbons_6: zinc- 54.1 3.2 6.9E-05 26.2 -0.5 23 36-63 3-25 (70)
54 PF13923 zf-C3HC4_2: Zinc fing 53.8 13 0.00028 20.1 2.0 31 37-67 1-31 (39)
55 cd00162 RING RING-finger (Real 53.2 13 0.00028 19.9 2.0 31 37-67 2-32 (45)
56 PRK00807 50S ribosomal protein 53.0 9.9 0.00021 22.4 1.5 25 8-32 2-29 (52)
57 PF07754 DUF1610: Domain of un 53.0 9 0.00019 18.8 1.1 7 11-17 2-8 (24)
58 COG4847 Uncharacterized protei 51.6 5.7 0.00012 26.5 0.3 35 8-42 7-42 (103)
59 cd02249 ZZ Zinc finger, ZZ typ 51.5 14 0.0003 21.0 1.9 11 153-163 23-33 (46)
60 PRK04023 DNA polymerase II lar 51.3 16 0.00035 34.8 3.2 14 106-119 664-677 (1121)
61 PF05502 Dynactin_p62: Dynacti 50.1 8.2 0.00018 33.7 1.2 38 106-144 27-64 (483)
62 KOG3002 Zn finger protein [Gen 49.0 11 0.00024 30.8 1.7 34 33-66 47-80 (299)
63 COG4357 Zinc finger domain con 48.2 2.1 4.6E-05 28.6 -2.1 51 10-60 38-88 (105)
64 PF06906 DUF1272: Protein of u 48.1 17 0.00037 21.8 1.9 26 153-178 29-54 (57)
65 PF07503 zf-HYPF: HypF finger; 46.7 4.1 8.9E-05 22.0 -0.8 31 10-45 2-32 (35)
66 PF12674 Zn_ribbon_2: Putative 46.1 11 0.00023 24.5 0.9 29 36-64 2-35 (81)
67 cd02336 ZZ_RSC8 Zinc finger, Z 44.2 15 0.00033 21.0 1.3 29 36-64 2-32 (45)
68 smart00531 TFIIE Transcription 42.2 7.9 0.00017 28.0 -0.1 37 7-46 99-135 (147)
69 smart00291 ZnF_ZZ Zinc-binding 41.5 28 0.00061 19.5 2.1 12 106-117 5-16 (44)
70 PRK14714 DNA polymerase II lar 41.3 23 0.0005 34.6 2.7 13 106-118 710-722 (1337)
71 KOG2462 C2H2-type Zn-finger pr 39.7 18 0.0004 29.0 1.5 39 106-145 188-228 (279)
72 KOG4443 Putative transcription 39.2 17 0.00036 32.8 1.3 21 124-144 107-127 (694)
73 TIGR00373 conserved hypothetic 38.9 9.5 0.00021 28.0 -0.2 31 8-46 110-140 (158)
74 PLN03208 E3 ubiquitin-protein 38.7 41 0.00089 25.7 3.2 31 34-65 18-48 (193)
75 KOG2932 E3 ubiquitin ligase in 38.3 12 0.00026 30.7 0.3 28 36-63 92-119 (389)
76 PRK14559 putative protein seri 38.2 26 0.00057 31.9 2.4 13 106-118 42-54 (645)
77 PF06750 DiS_P_DiS: Bacterial 37.9 16 0.00034 24.3 0.8 44 2-47 28-71 (92)
78 COG4357 Zinc finger domain con 37.7 3.5 7.6E-05 27.6 -2.3 51 107-157 37-87 (105)
79 PF13834 DUF4193: Domain of un 37.5 12 0.00025 25.3 0.1 29 33-61 69-98 (99)
80 PRK06266 transcription initiat 37.4 13 0.00028 28.0 0.3 32 7-46 117-148 (178)
81 PF06827 zf-FPG_IleRS: Zinc fi 37.2 16 0.00034 18.6 0.6 12 106-117 2-13 (30)
82 PF00628 PHD: PHD-finger; Int 36.3 35 0.00075 19.4 2.0 27 9-35 1-29 (51)
83 TIGR02098 MJ0042_CXXC MJ0042 f 36.2 18 0.0004 19.3 0.8 31 9-44 4-35 (38)
84 PRK00398 rpoP DNA-directed RNA 35.7 19 0.00041 20.3 0.8 10 35-44 22-31 (46)
85 PF04570 DUF581: Protein of un 35.7 22 0.00047 21.6 1.1 25 135-159 19-46 (58)
86 PF00097 zf-C3HC4: Zinc finger 35.0 39 0.00084 18.1 2.0 31 37-67 1-31 (41)
87 cd00472 Ribosomal_L24e_L24 Rib 34.4 25 0.00054 21.0 1.2 25 7-31 3-30 (54)
88 PF12677 DUF3797: Domain of un 34.3 24 0.00053 20.5 1.1 30 5-34 11-42 (49)
89 PF10764 Gin: Inhibitor of sig 33.7 40 0.00087 19.3 1.9 29 135-165 2-30 (46)
90 COG1813 Predicted transcriptio 33.2 39 0.00084 25.1 2.3 39 135-175 6-46 (165)
91 PLN02638 cellulose synthase A 33.0 34 0.00074 32.9 2.4 30 7-44 17-46 (1079)
92 PF00569 ZZ: Zinc finger, ZZ t 32.8 28 0.0006 19.8 1.2 9 56-64 29-37 (46)
93 TIGR00570 cdk7 CDK-activating 32.8 61 0.0013 26.7 3.5 15 53-67 26-40 (309)
94 PLN02195 cellulose synthase A 31.4 41 0.0009 32.0 2.6 31 5-43 4-34 (977)
95 PRK14891 50S ribosomal protein 31.3 28 0.0006 24.7 1.2 26 7-32 4-32 (131)
96 COG2075 RPL24A Ribosomal prote 31.3 29 0.00064 21.5 1.2 24 8-31 4-30 (66)
97 TIGR02605 CxxC_CxxC_SSSS putat 30.1 18 0.00039 20.9 0.1 11 35-45 6-16 (52)
98 PF04641 Rtf2: Rtf2 RING-finge 30.0 66 0.0014 25.6 3.3 55 30-122 109-167 (260)
99 PF14255 Cys_rich_CPXG: Cystei 29.8 25 0.00055 20.8 0.7 34 9-45 2-35 (52)
100 smart00834 CxxC_CXXC_SSSS Puta 29.8 17 0.00038 19.6 -0.0 9 9-17 7-15 (41)
101 cd02335 ZZ_ADA2 Zinc finger, Z 29.7 54 0.0012 18.8 2.1 10 154-163 25-34 (49)
102 PF13717 zinc_ribbon_4: zinc-r 29.3 28 0.00062 18.7 0.8 30 9-43 4-34 (36)
103 cd02340 ZZ_NBR1_like Zinc fing 29.2 51 0.0011 18.4 1.9 11 107-117 2-12 (43)
104 PF13639 zf-RING_2: Ring finge 29.0 15 0.00033 20.3 -0.3 14 53-66 21-34 (44)
105 PF04981 NMD3: NMD3 family ; 28.9 55 0.0012 25.6 2.7 25 37-67 1-25 (236)
106 PF08271 TF_Zn_Ribbon: TFIIB z 28.9 28 0.0006 19.3 0.7 11 35-45 20-30 (43)
107 PF01286 XPA_N: XPA protein N- 28.8 32 0.0007 18.4 0.9 12 7-18 3-14 (34)
108 PRK12495 hypothetical protein; 28.5 32 0.00069 26.8 1.2 23 35-62 43-65 (226)
109 PLN02436 cellulose synthase A 28.4 49 0.0011 31.9 2.6 29 8-44 37-65 (1094)
110 COG0068 HypF Hydrogenase matur 28.1 24 0.00052 32.3 0.6 34 6-44 100-133 (750)
111 PF00096 zf-C2H2: Zinc finger, 28.0 21 0.00045 16.5 0.1 12 35-46 1-12 (23)
112 PLN02189 cellulose synthase 27.9 48 0.001 31.8 2.4 18 9-30 36-53 (1040)
113 cd02341 ZZ_ZZZ3 Zinc finger, Z 27.6 46 0.00099 19.2 1.5 9 56-64 27-35 (48)
114 PF09723 Zn-ribbon_8: Zinc rib 27.0 20 0.00042 20.0 -0.1 10 35-44 6-15 (42)
115 KOG3579 Predicted E3 ubiquitin 26.9 29 0.00062 28.2 0.7 30 9-38 270-299 (352)
116 smart00659 RPOLCX RNA polymera 26.8 36 0.00077 19.3 0.9 26 35-64 3-28 (44)
117 KOG1829 Uncharacterized conser 26.7 23 0.00051 31.6 0.2 34 32-65 338-376 (580)
118 PF01246 Ribosomal_L24e: Ribos 26.7 33 0.00072 21.7 0.9 25 7-31 3-30 (71)
119 COG4306 Uncharacterized protei 26.6 61 0.0013 22.9 2.2 38 106-144 40-80 (160)
120 PF08746 zf-RING-like: RING-li 26.6 16 0.00034 20.6 -0.6 9 10-18 1-9 (43)
121 PF00130 C1_1: Phorbol esters/ 26.0 42 0.00091 19.2 1.2 12 6-17 10-21 (53)
122 PRK00085 recO DNA repair prote 25.5 31 0.00068 26.9 0.7 31 32-62 147-177 (247)
123 PHA00626 hypothetical protein 25.2 57 0.0012 19.6 1.6 39 9-52 2-41 (59)
124 PLN02915 cellulose synthase A 25.0 57 0.0012 31.4 2.4 31 6-44 14-44 (1044)
125 TIGR00270 conserved hypothetic 24.7 61 0.0013 23.7 2.1 30 135-166 3-35 (154)
126 COG1381 RecO Recombinational D 24.2 36 0.00078 26.9 0.9 33 30-62 150-182 (251)
127 PF13719 zinc_ribbon_5: zinc-r 24.1 43 0.00093 18.0 0.9 30 9-43 4-34 (37)
128 PF04810 zf-Sec23_Sec24: Sec23 24.0 59 0.0013 17.8 1.5 30 106-140 3-32 (40)
129 PF05502 Dynactin_p62: Dynacti 23.6 44 0.00095 29.3 1.3 40 7-47 26-65 (483)
130 PRK14873 primosome assembly pr 23.4 50 0.0011 30.2 1.7 27 35-64 393-419 (665)
131 PF10080 DUF2318: Predicted me 23.2 45 0.00098 22.7 1.1 38 25-66 26-63 (102)
132 PF01927 Mut7-C: Mut7-C RNAse 23.2 63 0.0014 23.2 1.9 38 7-44 91-134 (147)
133 PF13894 zf-C2H2_4: C2H2-type 23.1 33 0.00071 15.5 0.3 12 35-46 1-12 (24)
134 PF11571 Med27: Mediator compl 22.7 34 0.00073 22.5 0.4 10 106-115 55-64 (90)
135 PF08792 A2L_zn_ribbon: A2L zi 22.6 54 0.0012 17.3 1.1 23 36-61 5-27 (33)
136 smart00249 PHD PHD zinc finger 22.6 66 0.0014 17.2 1.6 26 10-35 2-29 (47)
137 KOG3476 Microtubule-associated 22.5 9.6 0.00021 25.0 -2.2 14 106-119 80-93 (100)
138 PF02591 DUF164: Putative zinc 22.3 22 0.00047 21.0 -0.6 26 36-61 24-52 (56)
139 PF01844 HNH: HNH endonuclease 21.6 74 0.0016 17.4 1.6 19 145-163 26-44 (47)
140 TIGR02420 dksA RNA polymerase- 21.2 23 0.00049 24.2 -0.7 19 6-25 79-97 (110)
141 PLN02400 cellulose synthase 21.1 67 0.0015 31.0 2.1 19 8-30 37-55 (1085)
142 cd02338 ZZ_PCMF_like Zinc fing 21.0 74 0.0016 18.3 1.6 9 155-163 26-34 (49)
143 KOG2893 Zn finger protein [Gen 20.6 31 0.00068 27.2 -0.1 37 106-145 11-47 (341)
144 PF07649 C1_3: C1-like domain; 20.1 46 0.001 16.8 0.5 12 35-46 1-12 (30)
145 COG4068 Uncharacterized protei 20.0 67 0.0015 19.5 1.2 9 9-17 10-18 (64)
No 1
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.94 E-value=4.3e-29 Score=202.32 Aligned_cols=137 Identities=23% Similarity=0.526 Sum_probs=120.9
Q ss_pred CCcccccCceecccc-eEEeCCccccccCcccccccccCCCCCccccCCeecchhhHHhhhcCCCCCCCCCCCCCCCcCC
Q 029695 7 QQKCKVCEKTVYPVE-QLSADGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNKNFQSPAKSAEK 85 (189)
Q Consensus 7 ~~~C~~C~~~I~~~~-~~~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 85 (189)
..+|.+|+|.|+... .+.||++.||..||+|..|++.|.+..||.+|+++||+.||.+..
T Consensus 274 ~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl------------------- 334 (468)
T KOG1701|consen 274 FGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL------------------- 334 (468)
T ss_pred hhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH-------------------
Confidence 348999999997554 389999999999999999999999999999999999999998766
Q ss_pred CCccccCCcccccccCCCCCCCCCcCCcccccccceeccCccccccccccccCCCCCCCCCeec-cCCccccHhHHHhhh
Q 029695 86 LTPELTRSPSKAASMFSGTQEKCASCSKTVYPLEKVAVENQAYHKTCFKCSHGGCSISPSNYAA-LEGILYCKHHFSQLF 164 (189)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~-~~g~~~C~~c~~~~~ 164 (189)
.+|..|+++|.+. ++.+.|+.||+.||+|.+|++.|++..|+. .++++||..||.++|
T Consensus 335 --------------------ekC~~Cg~~I~d~-iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kf 393 (468)
T KOG1701|consen 335 --------------------EKCNKCGEPIMDR-ILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKF 393 (468)
T ss_pred --------------------HHHhhhhhHHHHH-HHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhc
Confidence 7999999999886 478999999999999999999999998875 468999999999999
Q ss_pred cCCCC-CCcccCchHHHHHh
Q 029695 165 KEKGS-YNHLIKSASMKRAA 183 (189)
Q Consensus 165 ~~k~~-~~~~~~~~~~~r~~ 183 (189)
++||+ +..-|-+.+-+-++
T Consensus 394 APrCs~C~~PI~P~~G~~et 413 (468)
T KOG1701|consen 394 APRCSVCGNPILPRDGKDET 413 (468)
T ss_pred CcchhhccCCccCCCCCcce
Confidence 99998 66666655544433
No 2
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.90 E-value=3.1e-25 Score=180.03 Aligned_cols=125 Identities=27% Similarity=0.669 Sum_probs=112.0
Q ss_pred CCCCCCcccccCceecccceEEeCCccccccCcccccccccCCCCCccc-cCCeecchhhHHhhhcCCCCCCCCCCCCCC
Q 029695 3 FIGTQQKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLKLSNYSS-MEGVLYCKPHFEQLFKESGNFNKNFQSPAK 81 (189)
Q Consensus 3 ~~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~~~~-~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~ 81 (189)
|..+..+|..|++.|. +.+|.|+|+.||+.||+|-.|++.|++..|.+ .++++||..||++.|+
T Consensus 330 yq~tlekC~~Cg~~I~-d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfA-------------- 394 (468)
T KOG1701|consen 330 YQDTLEKCNKCGEPIM-DRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFA-------------- 394 (468)
T ss_pred HHHHHHHHhhhhhHHH-HHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcC--------------
Confidence 3456679999999994 67899999999999999999999999999985 5999999999999998
Q ss_pred CcCCCCccccCCcccccccCCCCCCCCCcCCccccccc------ceeccCccccccccccccCCCCCCCC----CeeccC
Q 029695 82 SAEKLTPELTRSPSKAASMFSGTQEKCASCSKTVYPLE------KVAVENQAYHKTCFKCSHGGCSISPS----NYAALE 151 (189)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~------~v~~~g~~~H~~Cf~C~~C~~~l~~~----~~~~~~ 151 (189)
++|+.|+++|++.+ +|+++++.||.+|++|+.|+..|+.+ ..|..|
T Consensus 395 ------------------------PrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld 450 (468)
T KOG1701|consen 395 ------------------------PRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLD 450 (468)
T ss_pred ------------------------cchhhccCCccCCCCCcceEEEEEccccccccceehhhcCccccccCCCCcceecc
Confidence 99999999999765 47899999999999999999999842 588999
Q ss_pred CccccHhHHHhhhcC
Q 029695 152 GILYCKHHFSQLFKE 166 (189)
Q Consensus 152 g~~~C~~c~~~~~~~ 166 (189)
|.++|+.|..++...
T Consensus 451 ~HllCk~Ch~~Rl~~ 465 (468)
T KOG1701|consen 451 GHLLCKTCHLKRLQA 465 (468)
T ss_pred Cceeechhhhhhhcc
Confidence 999999999887654
No 3
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.87 E-value=1.3e-22 Score=154.62 Aligned_cols=186 Identities=52% Similarity=0.898 Sum_probs=153.1
Q ss_pred CCCCCCCCcccccCceecccceEEeCCccccccCcccccccccCCCCCccccCCeecchhhHHhhhcCCC-CCCCCCCCC
Q 029695 1 MSFIGTQQKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESG-NFNKNFQSP 79 (189)
Q Consensus 1 ~~~~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~-~~~~~~~~~ 79 (189)
|++++....|..|++.|+..+.+..+|..||+.||+|..|.+.|....+.+.++.+||+.+|..++++.+ ..++.|+..
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 7788899999999999999999999999999999999999999999999999999999998777777553 555554431
Q ss_pred CCC--cCCCCccccCCcccccccCCCCCCCCCcCCcccccccceeccCccccccccccccCCCCCCCCCeeccCCccccH
Q 029695 80 AKS--AEKLTPELTRSPSKAASMFSGTQEKCASCSKTVYPLEKVAVENQAYHKTCFKCSHGGCSISPSNYAALEGILYCK 157 (189)
Q Consensus 80 ~~~--~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~ 157 (189)
... +.................+.++...|..|.+.+++.+.+...+..||..||+|+.|+..|..+.+...+|.+||.
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 111112222333345566778889999999999999989999999999999999999999999999999999999
Q ss_pred hHHHhhhcCCCCCCcccCchHHHHHhhCC
Q 029695 158 HHFSQLFKEKGSYNHLIKSASMKRAAASV 186 (189)
Q Consensus 158 ~c~~~~~~~k~~~~~~~~~~~~~r~~~~~ 186 (189)
.++..+|..+..+.++...+..++.+...
T Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 (200)
T KOG1700|consen 161 HHFAQLFKGKGNYNEGFGARENKEAAAAA 189 (200)
T ss_pred hhhheeecCCCcccccchhhhhhhhhhhh
Confidence 99999999999988888877777765543
No 4
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.85 E-value=2.2e-23 Score=161.56 Aligned_cols=125 Identities=26% Similarity=0.536 Sum_probs=112.4
Q ss_pred CCCcccccCceecccceEEeCCccccccCcccccccccCCCCCccccCCeecchhhHHhhhcCCCCCCCCCCCCCCCcCC
Q 029695 6 TQQKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNKNFQSPAKSAEK 85 (189)
Q Consensus 6 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 85 (189)
..++|+.|.+.|.+.-++.++++.||..|++|+.|..+|... .+.++|.+||+.+|.++|+
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~dr-CFsR~~s~yCkedFfKrfG------------------ 92 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADR-CFSREGSVYCKEDFFKRFG------------------ 92 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHH-HhhcCCceeehHHHHHHhC------------------
Confidence 578999999999877778999999999999999999999885 6689999999999999999
Q ss_pred CCccccCCcccccccCCCCCCCCCcCCcccccccce-eccCccccccccccccCCCCCCCC-Cee-ccCCccccHhHHHh
Q 029695 86 LTPELTRSPSKAASMFSGTQEKCASCSKTVYPLEKV-AVENQAYHKTCFKCSHGGCSISPS-NYA-ALEGILYCKHHFSQ 162 (189)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v-~~~g~~~H~~Cf~C~~C~~~l~~~-~~~-~~~g~~~C~~c~~~ 162 (189)
.+|..|.+.|.+...| .+.+..||..||.|..|+++|..+ .|| +.|+++.|+.+|+.
T Consensus 93 --------------------TKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~ 152 (383)
T KOG4577|consen 93 --------------------TKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYET 152 (383)
T ss_pred --------------------CcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHH
Confidence 9999999999998865 589999999999999999999987 555 56799999999998
Q ss_pred hhcCCCC
Q 029695 163 LFKEKGS 169 (189)
Q Consensus 163 ~~~~k~~ 169 (189)
.-...+.
T Consensus 153 Ak~k~~~ 159 (383)
T KOG4577|consen 153 AKQKHCN 159 (383)
T ss_pred HHhcccc
Confidence 7666654
No 5
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.83 E-value=4.3e-22 Score=151.95 Aligned_cols=117 Identities=22% Similarity=0.528 Sum_probs=109.2
Q ss_pred CCCcccccCceecccceEEeCCccccccCcccccccccCCCCCccccCCeecchhhHHhhhcCCCCCCCCCCCCCCCcCC
Q 029695 6 TQQKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNKNFQSPAKSAEK 85 (189)
Q Consensus 6 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 85 (189)
+.++|..|.++| +...+.++|+.||.+.|+|+.|-+++-+...|++.|.+||+.+|.++|+
T Consensus 194 gipiCgaC~rpI-eervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG------------------ 254 (332)
T KOG2272|consen 194 GIPICGACRRPI-EERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFG------------------ 254 (332)
T ss_pred CCcccccccCch-HHHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhh------------------
Confidence 568999999999 5778999999999999999999999988889999999999999999999
Q ss_pred CCccccCCcccccccCCCCCCCCCcCCcccccccceeccCccccccccccccCCCCCCCC-CeeccCCccccHhHHHh
Q 029695 86 LTPELTRSPSKAASMFSGTQEKCASCSKTVYPLEKVAVENQAYHKTCFKCSHGGCSISPS-NYAALEGILYCKHHFSQ 162 (189)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~-~~~~~~g~~~C~~c~~~ 162 (189)
..|..|+++|.+ +.+.++++.|-++||+|+.|.+.|... +|+..|-.|.|+.||.+
T Consensus 255 --------------------~~CF~C~~~i~G-~vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~r 311 (332)
T KOG2272|consen 255 --------------------NLCFICNRVIGG-DVVSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDR 311 (332)
T ss_pred --------------------hhheecCCccCc-cHHHHhhhhhccccccccccccccccccceeeeccchHHHHHHhh
Confidence 899999999966 568999999999999999999999976 79999999999999974
No 6
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.81 E-value=3.8e-20 Score=155.27 Aligned_cols=161 Identities=21% Similarity=0.455 Sum_probs=121.3
Q ss_pred CCcccccCceecccceEEeCCccccccCcccccccccCCCCCcccc-CCeecchhhHHhhh-cCC-CCCCCCCCCCCCC-
Q 029695 7 QQKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLKLSNYSSM-EGVLYCKPHFEQLF-KES-GNFNKNFQSPAKS- 82 (189)
Q Consensus 7 ~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~~~~~-~g~~yC~~c~~~~~-~~~-~~~~~~~~~~~~~- 82 (189)
...|.+|.+.- .++++.+.++.||..||.|..|+..|..+.|+.+ +..+|+.....+.. +.. .+++++++...++
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 6999999999999999999999999999999876 45677763332221 111 2556666655543
Q ss_pred ----cCCCCcccc------------CCcccccccCCCCCCCCCcCCcccccccceeccCccccccccccccCCCCCCCCC
Q 029695 83 ----AEKLTPELT------------RSPSKAASMFSGTQEKCASCSKTVYPLEKVAVENQAYHKTCFKCSHGGCSISPSN 146 (189)
Q Consensus 83 ----~~~~~~~~~------------~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~ 146 (189)
.|.++.+.. ......++....+...|++|++.|..++.+.++++.||..||+|..|...|.++
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 122222211 011111222233558899999999988888999999999999999999998885
Q ss_pred eeccCCccccHhHHHhhhcCCCC
Q 029695 147 YAALEGILYCKHHFSQLFKEKGS 169 (189)
Q Consensus 147 ~~~~~g~~~C~~c~~~~~~~k~~ 169 (189)
|+..||.|||+.+|.+.||.||.
T Consensus 174 y~skdg~pyce~dy~~~fgvkc~ 196 (670)
T KOG1044|consen 174 YMSKDGVPYCEKDYQAKFGVKCE 196 (670)
T ss_pred eeccCCCcchhhhhhhhcCeehH
Confidence 89999999999999999999997
No 7
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.80 E-value=5.3e-22 Score=151.47 Aligned_cols=118 Identities=22% Similarity=0.607 Sum_probs=108.5
Q ss_pred CCCcccccCceecccce-EEeCCccccccCcccccccccCCCCCccccCCeecchhhHHhhhcCCCCCCCCCCCCCCCcC
Q 029695 6 TQQKCKVCEKTVYPVEQ-LSADGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNKNFQSPAKSAE 84 (189)
Q Consensus 6 ~~~~C~~C~~~I~~~~~-~~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~ 84 (189)
....|.+|.......+. +..+|..||..||.|+.|-.+|.++.|++.+|+.||+.+|..+|+
T Consensus 11 ~~~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~Lfa----------------- 73 (332)
T KOG2272|consen 11 ANMVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFA----------------- 73 (332)
T ss_pred HHHHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhc-----------------
Confidence 45679999998876664 788999999999999999999999999999999999999999998
Q ss_pred CCCccccCCcccccccCCCCCCCCCcCCcccccccceeccCccccccccccccCCCCCCCCCeeccCCccccHhHHHh
Q 029695 85 KLTPELTRSPSKAASMFSGTQEKCASCSKTVYPLEKVAVENQAYHKTCFKCSHGGCSISPSNYAALEGILYCKHHFSQ 162 (189)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~~~ 162 (189)
|-|+.|++-|.+. .|.+++.+||+.||+|..|++.|.+..|+...|+.+|..|..+
T Consensus 74 ---------------------PcC~kC~EFiiGr-VikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k 129 (332)
T KOG2272|consen 74 ---------------------PCCGKCGEFIIGR-VIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQK 129 (332)
T ss_pred ---------------------hhhcccccchhhH-HHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhh
Confidence 9999999999876 4889999999999999999999999889988999999999766
No 8
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.80 E-value=5.7e-20 Score=157.43 Aligned_cols=125 Identities=24% Similarity=0.570 Sum_probs=116.3
Q ss_pred CCCcccccCceecccceEEeCCccccccCcccccccccCCCCCccccCCeecchhhHHhhhcCCCCCCCCCCCCCCCcCC
Q 029695 6 TQQKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNKNFQSPAKSAEK 85 (189)
Q Consensus 6 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 85 (189)
..+.|..|...|.....+.++++.||+.+|.|..|...+....+...+|++||..||.+.+.
T Consensus 302 ~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~------------------ 363 (479)
T KOG1703|consen 302 TRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFR------------------ 363 (479)
T ss_pred ccccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhC------------------
Confidence 45899999999954488999999999999999999999999989999999999999999998
Q ss_pred CCccccCCcccccccCCCCCCCCCcCCcccccccceeccCccccccccccccCCCCCCCCCeeccCCccccHhHHHhhhc
Q 029695 86 LTPELTRSPSKAASMFSGTQEKCASCSKTVYPLEKVAVENQAYHKTCFKCSHGGCSISPSNYAALEGILYCKHHFSQLFK 165 (189)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~~ 165 (189)
+.|.+|+++|.+. .|.+.++.||++||.|..|++.+....|+..+|.+||+.||.++++
T Consensus 364 --------------------p~C~~C~~~i~~~-~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~ 422 (479)
T KOG1703|consen 364 --------------------PNCKRCLLPILEE-GVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFT 422 (479)
T ss_pred --------------------ccccccCCchHHh-HhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhcc
Confidence 9999999999885 4888899999999999999999999999999999999999999999
Q ss_pred CCCC
Q 029695 166 EKGS 169 (189)
Q Consensus 166 ~k~~ 169 (189)
+++.
T Consensus 423 ~~~~ 426 (479)
T KOG1703|consen 423 TKCD 426 (479)
T ss_pred ccch
Confidence 8875
No 9
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.77 E-value=6.2e-20 Score=157.19 Aligned_cols=117 Identities=27% Similarity=0.640 Sum_probs=107.7
Q ss_pred CCCCcccccCceecccceEEeCCccccccCcccccccccCCCCCccccCCeecchhhHHhhhcCCCCCCCCCCCCCCCcC
Q 029695 5 GTQQKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNKNFQSPAKSAE 84 (189)
Q Consensus 5 ~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~ 84 (189)
...+.|.+|.++| .++.|.+.++.||++||.|..|+++|....|++.++.+||+.||.+++.
T Consensus 361 ~~~p~C~~C~~~i-~~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~----------------- 422 (479)
T KOG1703|consen 361 PFRPNCKRCLLPI-LEEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFT----------------- 422 (479)
T ss_pred hhCccccccCCch-HHhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhcc-----------------
Confidence 3568999999999 5788888899999999999999999999999999999999999999997
Q ss_pred CCCccccCCcccccccCCCCCCCCCcCCcccccccc-eeccCccccccccccccCCCCCCCCCeeccCCccccHhHH
Q 029695 85 KLTPELTRSPSKAASMFSGTQEKCASCSKTVYPLEK-VAVENQAYHKTCFKCSHGGCSISPSNYAALEGILYCKHHF 160 (189)
Q Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~-v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~ 160 (189)
++|..|.++|..... +.+++..||..||+|..|...|..+.|+...++++|..|+
T Consensus 423 ---------------------~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~~~~~~~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 423 ---------------------TKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKKLTKKTFFETLDKPLCQKHF 478 (479)
T ss_pred ---------------------ccchhccchhHhhhhHhhccCccccccceehhhhhccccCCceeecCCccccccCC
Confidence 789999999874443 8899999999999999999999999999999999999875
No 10
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.75 E-value=3.1e-19 Score=149.89 Aligned_cols=116 Identities=25% Similarity=0.513 Sum_probs=107.1
Q ss_pred CCCcccccCceecccceEEeCCccccccCcccccccccCCCCCccccCCeecchhhHHhhhcCCCCCCCCCCCCCCCcCC
Q 029695 6 TQQKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNKNFQSPAKSAEK 85 (189)
Q Consensus 6 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 85 (189)
+...|++|++.|..+..+.|+++.||..||+|..|+..|.+ .|+.+||.+||+.||.+.|+
T Consensus 132 ~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~g-ey~skdg~pyce~dy~~~fg------------------ 192 (670)
T KOG1044|consen 132 GPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNG-EYMSKDGVPYCEKDYQAKFG------------------ 192 (670)
T ss_pred CCccccchhhhhhccceeeeeccceeeeeeehhhhcccccc-eeeccCCCcchhhhhhhhcC------------------
Confidence 56789999999999999999999999999999999999977 59999999999999999998
Q ss_pred CCccccCCcccccccCCCCCCCCCcCCcccccccceeccCccccccccccccCCCCCCCC-CeeccCCccccHhHHH
Q 029695 86 LTPELTRSPSKAASMFSGTQEKCASCSKTVYPLEKVAVENQAYHKTCFKCSHGGCSISPS-NYAALEGILYCKHHFS 161 (189)
Q Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~-~~~~~~g~~~C~~c~~ 161 (189)
.+|..|.+-|.+. .+.+.|++||+.|-+|+.|+..++.+ .++..+..++-..|-.
T Consensus 193 --------------------vkc~~c~~fisgk-vLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~q 248 (670)
T KOG1044|consen 193 --------------------VKCEECEKFISGK-VLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCKQ 248 (670)
T ss_pred --------------------eehHHhhhhhhhh-hhhccCcccCcchhhhhhhccccccchheeeccccccCCcccc
Confidence 9999999999876 47899999999999999999999987 7899899999888853
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=99.62 E-value=4.5e-16 Score=95.97 Aligned_cols=57 Identities=35% Similarity=0.817 Sum_probs=52.9
Q ss_pred ccccCceecccceE-EeCCccccccCcccccccccCCCCCccccCCeecchhhHHhhh
Q 029695 10 CKVCEKTVYPVEQL-SADGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66 (189)
Q Consensus 10 C~~C~~~I~~~~~~-~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~ 66 (189)
|.+|+++|.+.+.+ .++|+.||++||+|+.|+++|.+..|+..+|++||+.||.++|
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 78999999877765 7999999999999999999999988999999999999999875
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=99.58 E-value=1.7e-15 Score=93.32 Aligned_cols=57 Identities=33% Similarity=0.767 Sum_probs=53.1
Q ss_pred CCcCCcccccccce-eccCccccccccccccCCCCCCCCCeeccCCccccHhHHHhhh
Q 029695 108 CASCSKTVYPLEKV-AVENQAYHKTCFKCSHGGCSISPSNYAALEGILYCKHHFSQLF 164 (189)
Q Consensus 108 C~~C~~~I~~~~~v-~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~ 164 (189)
|++|+++|.+.+.+ .++|+.||++||+|..|+++|..+.++..+|++||..||.++|
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 78999999988765 6999999999999999999999988999999999999999886
No 13
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.55 E-value=3.5e-16 Score=121.77 Aligned_cols=81 Identities=26% Similarity=0.459 Sum_probs=75.7
Q ss_pred CCCCCcCCcccccccceeccCccccccccccccCCCCCCCCCeeccCCccccHhHHHhhhcCCCC-CCcccCchHHHHHh
Q 029695 105 QEKCASCSKTVYPLEKVAVENQAYHKTCFKCSHGGCSISPSNYAALEGILYCKHHFSQLFKEKGS-YNHLIKSASMKRAA 183 (189)
Q Consensus 105 ~~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~~~k~~-~~~~~~~~~~~r~~ 183 (189)
.++|++|++.|.+..++.++++.||..|++|+.|+.+|... ++.++|.+||+++|.++||+||. +++||++++++|.+
T Consensus 33 ip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~dr-CFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRkA 111 (383)
T KOG4577|consen 33 IPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADR-CFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRKA 111 (383)
T ss_pred cccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHH-HhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHHh
Confidence 38999999999998777899999999999999999999874 88899999999999999999998 99999999999999
Q ss_pred hCC
Q 029695 184 ASV 186 (189)
Q Consensus 184 ~~~ 186 (189)
++.
T Consensus 112 qd~ 114 (383)
T KOG4577|consen 112 QDF 114 (383)
T ss_pred hcc
Confidence 863
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=98.85 E-value=1.9e-09 Score=60.44 Aligned_cols=37 Identities=43% Similarity=0.771 Sum_probs=33.5
Q ss_pred cccccCceeccc-ceEEeCCccccccCcccccccccCC
Q 029695 9 KCKVCEKTVYPV-EQLSADGVVYHKSCFKCSHCKGTLK 45 (189)
Q Consensus 9 ~C~~C~~~I~~~-~~~~~~g~~~H~~CF~C~~C~~~L~ 45 (189)
+|.+|+++|.+. ..+.++++.||++||+|..|+++|.
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 6689999999999999999999985
No 15
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.74 E-value=6.4e-09 Score=58.23 Aligned_cols=37 Identities=32% Similarity=0.674 Sum_probs=32.8
Q ss_pred CCCcCCcccccc-cceeccCccccccccccccCCCCCC
Q 029695 107 KCASCSKTVYPL-EKVAVENQAYHKTCFKCSHGGCSIS 143 (189)
Q Consensus 107 ~C~~C~~~I~~~-~~v~~~g~~~H~~Cf~C~~C~~~l~ 143 (189)
+|.+|+++|.+. ..+.+.++.||+.||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 489999999987 4477899999999999999999875
No 16
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.46 E-value=4.5e-08 Score=74.92 Aligned_cols=70 Identities=54% Similarity=1.206 Sum_probs=61.6
Q ss_pred CCCCCCcccccCceecccceEEeCCccccccCcccccccccCCCCCccccCCeecchhhHHhhhcCCCCC
Q 029695 3 FIGTQQKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNF 72 (189)
Q Consensus 3 ~~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~ 72 (189)
+.+....|..|.+.+++.+.+...+..||+.||+|+.|+..|+..++...++.+||...+.+++.....+
T Consensus 104 ~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~~~~~~~ 173 (200)
T KOG1700|consen 104 FAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLFKGKGNY 173 (200)
T ss_pred hhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheeecCCCcc
Confidence 3456789999999999999999999999999999999999999999999999999998887776544433
No 17
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=98.38 E-value=4.4e-08 Score=73.54 Aligned_cols=75 Identities=29% Similarity=0.649 Sum_probs=63.1
Q ss_pred CCCCcCCcccccccceeccCccccccccccccCCCCCCCCCeeccCCccccHhHHHhhhcCCCCCCcccCchHHHHHhhC
Q 029695 106 EKCASCSKTVYPLEKVAVENQAYHKTCFKCSHGGCSISPSNYAALEGILYCKHHFSQLFKEKGSYNHLIKSASMKRAAAS 185 (189)
Q Consensus 106 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~~~k~~~~~~~~~~~~~r~~~~ 185 (189)
..|..|++.+++.+.+..+++.||..||+|+.|+.+|....+...|.++||..+|.+.. .......+++.|..++
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~-----at~~adTPEm~Rik~n 79 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQV-----ATVMADTPEMRRIKEN 79 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccce-----eeeecCCHHHHHHHhh
Confidence 56788999999999999999999999999999999999988888999999999998655 3445556666666554
No 18
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=98.12 E-value=2e-07 Score=70.05 Aligned_cols=61 Identities=39% Similarity=0.817 Sum_probs=54.9
Q ss_pred CCcccccCceecccceEEeCCccccccCcccccccccCCCCCccccCCeecchhhHHhhhc
Q 029695 7 QQKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK 67 (189)
Q Consensus 7 ~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~ 67 (189)
...|..|++.+++.+.|.-+++.||+.||+|..|+.+|.-.+|-..+.++||..+|.+..+
T Consensus 4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVA 64 (264)
T ss_pred cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccccee
Confidence 3457899999999999999999999999999999999998888888999999999976543
No 19
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.85 E-value=3.4e-06 Score=65.84 Aligned_cols=111 Identities=22% Similarity=0.486 Sum_probs=86.6
Q ss_pred cCceecccceEEeCCccccccCcccccccccCC--CCCccccCCeecchhhHHh--hhcCCCCCCCCCCCCCCCcCCCCc
Q 029695 13 CEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLK--LSNYSSMEGVLYCKPHFEQ--LFKESGNFNKNFQSPAKSAEKLTP 88 (189)
Q Consensus 13 C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~--~~~~~~~~g~~yC~~c~~~--~~~~~~~~~~~~~~~~~~~~~~~~ 88 (189)
|+..|.+...+.+.+..||..|..|..|...|. ...|.. +|..||..+|.. .+.
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~--------------------- 59 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFS--------------------- 59 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcc---------------------
Confidence 677786666678889999999999999999997 444555 999999999987 333
Q ss_pred cccCCcccccccCCCCCCCCCcCCcccccccce-eccCccccccccccccCCCCCCCC-CeeccC-CccccHhHHHhh
Q 029695 89 ELTRSPSKAASMFSGTQEKCASCSKTVYPLEKV-AVENQAYHKTCFKCSHGGCSISPS-NYAALE-GILYCKHHFSQL 163 (189)
Q Consensus 89 ~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v-~~~g~~~H~~Cf~C~~C~~~l~~~-~~~~~~-g~~~C~~c~~~~ 163 (189)
.+|.+|...|...+.+ .+..+. |.-||.|..|...+... .+.+.+ -+.+|...+.+.
T Consensus 60 -----------------~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 60 -----------------KRCARCKFTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred -----------------ccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 7899999998766654 355666 99999999998876654 555555 488998887543
No 20
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=94.93 E-value=0.014 Score=45.37 Aligned_cols=63 Identities=19% Similarity=0.585 Sum_probs=49.8
Q ss_pred CCcccccccceeccCccccccccccccCCCCCC--CCCeeccCCccccHhHHHh--hhcCCCC-CCccc
Q 029695 111 CSKTVYPLEKVAVENQAYHKTCFKCSHGGCSIS--PSNYAALEGILYCKHHFSQ--LFKEKGS-YNHLI 174 (189)
Q Consensus 111 C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~--~~~~~~~~g~~~C~~c~~~--~~~~k~~-~~~~~ 174 (189)
|+..|.+...+.+.+..||..|..|..|...+. ...|.. +|..||...+.. .++.++. ..-.+
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~ 69 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTI 69 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCc
Confidence 677787776667779999999999999999998 334555 999999999998 6777766 44433
No 21
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=89.27 E-value=0.49 Score=29.30 Aligned_cols=33 Identities=18% Similarity=0.348 Sum_probs=16.6
Q ss_pred cccccccccCCCCCccccCCeecchhhHHhhhc
Q 029695 35 FKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK 67 (189)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~ 67 (189)
++|+.|..-|...-....=+..||..|..+.++
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~ 40 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIG 40 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTT
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcC
Confidence 678888888876533445567889999877666
No 22
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=88.42 E-value=0.39 Score=28.68 Aligned_cols=28 Identities=29% Similarity=0.600 Sum_probs=21.7
Q ss_pred CCCCcCCccccccc-cee--ccCcccccccc
Q 029695 106 EKCASCSKTVYPLE-KVA--VENQAYHKTCF 133 (189)
Q Consensus 106 ~~C~~C~~~I~~~~-~v~--~~g~~~H~~Cf 133 (189)
.+|..|+++|.+.+ .|. .=+..||++|+
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 78999999997544 333 45788999988
No 23
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=86.63 E-value=0.53 Score=31.76 Aligned_cols=30 Identities=27% Similarity=0.420 Sum_probs=22.7
Q ss_pred CCCCCcCCcccccccc-eeccCccccccccc
Q 029695 105 QEKCASCSKTVYPLEK-VAVENQAYHKTCFK 134 (189)
Q Consensus 105 ~~~C~~C~~~I~~~~~-v~~~g~~~H~~Cf~ 134 (189)
...|+.|+++|..... +...|..+|..|++
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 4789999999986543 34677888988863
No 24
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=85.95 E-value=0.8 Score=27.81 Aligned_cols=30 Identities=27% Similarity=0.691 Sum_probs=20.3
Q ss_pred CCCCcccccCceecccce-EEeCCccccccCcccccccccC
Q 029695 5 GTQQKCKVCEKTVYPVEQ-LSADGVVYHKSCFKCSHCKGTL 44 (189)
Q Consensus 5 ~~~~~C~~C~~~I~~~~~-~~~~g~~~H~~CF~C~~C~~~L 44 (189)
...++|..|+..|.+.+. +. |.|-.|+..+
T Consensus 5 ~~~~~CtSCg~~i~~~~~~~~----------F~CPnCG~~~ 35 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREKAVK----------FLCPNCGEVI 35 (59)
T ss_pred ccCccccCCCCcccCCCccCE----------eeCCCCCCee
Confidence 345678888888865542 22 7788887763
No 25
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=85.55 E-value=0.65 Score=31.35 Aligned_cols=30 Identities=33% Similarity=0.504 Sum_probs=17.4
Q ss_pred CCCcccccCceecccce-EEeCCccccccCc
Q 029695 6 TQQKCKVCEKTVYPVEQ-LSADGVVYHKSCF 35 (189)
Q Consensus 6 ~~~~C~~C~~~I~~~~~-~~~~g~~~H~~CF 35 (189)
....|..|+++|..... +-..|..+|..|+
T Consensus 77 ~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCCCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 34567777777754333 3444556676665
No 26
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=82.84 E-value=0.9 Score=26.81 Aligned_cols=29 Identities=28% Similarity=0.675 Sum_probs=22.8
Q ss_pred ccccccccCCCCC-ccccCCeecchhhHHhh
Q 029695 36 KCSHCKGTLKLSN-YSSMEGVLYCKPHFEQL 65 (189)
Q Consensus 36 ~C~~C~~~L~~~~-~~~~~g~~yC~~c~~~~ 65 (189)
.|..|+..+.--. +-..|| ..|..|+.++
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 4888999887633 556777 7999999887
No 27
>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=82.75 E-value=0.8 Score=25.11 Aligned_cols=28 Identities=25% Similarity=0.548 Sum_probs=19.4
Q ss_pred CCcCCcccccccc-eeccCcccccccccc
Q 029695 108 CASCSKTVYPLEK-VAVENQAYHKTCFKC 135 (189)
Q Consensus 108 C~~C~~~I~~~~~-v~~~g~~~H~~Cf~C 135 (189)
|.-|+++|.+... +...++.||--|-.|
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC 29 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTC 29 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHH
Confidence 6778888886543 467888888655444
No 28
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=82.48 E-value=0.36 Score=32.69 Aligned_cols=32 Identities=25% Similarity=0.516 Sum_probs=22.9
Q ss_pred CCCCcCCcccccccceec-cCcccccccccccc
Q 029695 106 EKCASCSKTVYPLEKVAV-ENQAYHKTCFKCSH 137 (189)
Q Consensus 106 ~~C~~C~~~I~~~~~v~~-~g~~~H~~Cf~C~~ 137 (189)
-+|..|+++|..++.+++ .+..-|..||+=..
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~ 35 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREKA 35 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHHH
Confidence 468888888888887653 34667888886543
No 29
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=82.33 E-value=0.72 Score=22.42 Aligned_cols=8 Identities=25% Similarity=0.916 Sum_probs=4.6
Q ss_pred ccccCcee
Q 029695 10 CKVCEKTV 17 (189)
Q Consensus 10 C~~C~~~I 17 (189)
|..|+..|
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 55555555
No 30
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=80.13 E-value=1 Score=24.48 Aligned_cols=24 Identities=25% Similarity=0.509 Sum_probs=18.1
Q ss_pred cccccccccCCCCCccccCCeecchhhH
Q 029695 35 FKCSHCKGTLKLSNYSSMEGVLYCKPHF 62 (189)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~ 62 (189)
+.|..|+.. .|...+|..||..|-
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYCDRCG 32 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEhhhCc
Confidence 457888765 377889999998774
No 31
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=79.91 E-value=0.62 Score=31.54 Aligned_cols=32 Identities=25% Similarity=0.518 Sum_probs=22.5
Q ss_pred CcccccCceecccceEEeCC-ccccccCccccc
Q 029695 8 QKCKVCEKTVYPVEQLSADG-VVYHKSCFKCSH 39 (189)
Q Consensus 8 ~~C~~C~~~I~~~~~~~~~g-~~~H~~CF~C~~ 39 (189)
-+|..|+++|+.++.+.... ..-|-.||+=..
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~ 35 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREKA 35 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHHH
Confidence 46888888888887754433 567888886543
No 32
>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=79.17 E-value=1.2 Score=29.54 Aligned_cols=29 Identities=28% Similarity=0.565 Sum_probs=18.6
Q ss_pred ccccCcccccccccCCCCCccccCCeecchhhHHh
Q 029695 30 YHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQ 64 (189)
Q Consensus 30 ~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~ 64 (189)
|=+.=-.|..|...+.. .|.-||..|..+
T Consensus 40 y~~~~~~C~~CK~~v~q------~g~~YCq~CAYk 68 (90)
T PF10235_consen 40 YAPYSSKCKICKTKVHQ------PGAKYCQTCAYK 68 (90)
T ss_pred ccccCcccccccccccc------CCCccChhhhcc
Confidence 44433467888776643 256789999654
No 33
>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=78.61 E-value=3.3 Score=24.88 Aligned_cols=32 Identities=19% Similarity=0.230 Sum_probs=25.4
Q ss_pred cccccccccCCCCCccccCCeecchhhHHhhhc
Q 029695 35 FKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK 67 (189)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~ 67 (189)
|.|..|+..+... .....|..||..+..+.+.
T Consensus 2 ~~Cpi~~~~~~~P-v~~~~G~v~~~~~i~~~~~ 33 (63)
T smart00504 2 FLCPISLEVMKDP-VILPSGQTYERRAIEKWLL 33 (63)
T ss_pred cCCcCCCCcCCCC-EECCCCCEEeHHHHHHHHH
Confidence 5788898888764 4556889999999987764
No 34
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.37 E-value=1.7 Score=32.56 Aligned_cols=37 Identities=19% Similarity=0.493 Sum_probs=29.0
Q ss_pred cccCcccccccccCCCCC-ccccCCeecchhhHHhhhc
Q 029695 31 HKSCFKCSHCKGTLKLSN-YSSMEGVLYCKPHFEQLFK 67 (189)
Q Consensus 31 H~~CF~C~~C~~~L~~~~-~~~~~g~~yC~~c~~~~~~ 67 (189)
-..+|+|-.|-....... +..+=|.+||..|......
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk 165 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALK 165 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHHH
Confidence 456899999977776654 5577899999999987764
No 35
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=78.02 E-value=2.7 Score=25.51 Aligned_cols=31 Identities=23% Similarity=0.562 Sum_probs=20.1
Q ss_pred CCCcccccCceecccceEEeCCccccccCcccccccccCC
Q 029695 6 TQQKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLK 45 (189)
Q Consensus 6 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~ 45 (189)
..++|..|+..|..++.-.. |.|-.|+..+-
T Consensus 8 ~~~~CtSCg~~i~p~e~~v~---------F~CPnCGe~~I 38 (61)
T COG2888 8 DPPVCTSCGREIAPGETAVK---------FPCPNCGEVEI 38 (61)
T ss_pred CCceeccCCCEeccCCceeE---------eeCCCCCceee
Confidence 35788888888855544222 77788875443
No 36
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=75.40 E-value=1.5 Score=31.12 Aligned_cols=23 Identities=22% Similarity=0.641 Sum_probs=18.9
Q ss_pred ccccccccCCCCCccccCCeecchhhHH
Q 029695 36 KCSHCKGTLKLSNYSSMEGVLYCKPHFE 63 (189)
Q Consensus 36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~ 63 (189)
.|..|+.+| |. ++|.+||..|-.
T Consensus 30 hCp~Cg~PL----F~-KdG~v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTPL----FR-KDGEVFCPVCGY 52 (131)
T ss_pred hCcccCCcc----ee-eCCeEECCCCCc
Confidence 378888888 54 999999999974
No 37
>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=74.78 E-value=0.7 Score=24.99 Aligned_cols=28 Identities=18% Similarity=0.463 Sum_probs=15.3
Q ss_pred cccccccCCCCCccccCCeecchhhHHh
Q 029695 37 CSHCKGTLKLSNYSSMEGVLYCKPHFEQ 64 (189)
Q Consensus 37 C~~C~~~L~~~~~~~~~g~~yC~~c~~~ 64 (189)
|..|+.++....-....+..+|..|...
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQER 33 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHhCc
Confidence 5566666555444455666677766654
No 38
>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=74.29 E-value=1.7 Score=24.40 Aligned_cols=22 Identities=27% Similarity=0.771 Sum_probs=14.3
Q ss_pred ccccccccCCCCCccccCCeecchhh
Q 029695 36 KCSHCKGTLKLSNYSSMEGVLYCKPH 61 (189)
Q Consensus 36 ~C~~C~~~L~~~~~~~~~g~~yC~~c 61 (189)
.|..|+.+|- ..++|+.||..|
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 3556777663 346778888765
No 39
>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=71.44 E-value=2.2 Score=27.50 Aligned_cols=16 Identities=38% Similarity=0.655 Sum_probs=11.5
Q ss_pred CCCcccccCceecccc
Q 029695 6 TQQKCKVCEKTVYPVE 21 (189)
Q Consensus 6 ~~~~C~~C~~~I~~~~ 21 (189)
+-..|..|++.|..++
T Consensus 6 ~Ra~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 6 GRAKCKGCKKKIAKGE 21 (82)
T ss_dssp STEBETTTSCBE-TTS
T ss_pred CCccCcccCCcCCCCC
Confidence 3458999999996555
No 40
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=69.68 E-value=1.9 Score=32.97 Aligned_cols=31 Identities=26% Similarity=0.502 Sum_probs=26.5
Q ss_pred cccccccccCCCCCccccCCeecchhhHHhh
Q 029695 35 FKCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 65 (189)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~ 65 (189)
-+|+.|+..+....-...+|++.|..||.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 6899999988887667889999999999753
No 41
>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=68.98 E-value=4 Score=29.86 Aligned_cols=39 Identities=18% Similarity=0.238 Sum_probs=27.9
Q ss_pred CCCCcCCcccccccc---eeccCccccccccccccCCCCCCCC
Q 029695 106 EKCASCSKTVYPLEK---VAVENQAYHKTCFKCSHGGCSISPS 145 (189)
Q Consensus 106 ~~C~~C~~~I~~~~~---v~~~g~~~H~~Cf~C~~C~~~l~~~ 145 (189)
..|+.|+-+|.+... +...|..|+.- --|..|+++....
T Consensus 40 ~~Cp~C~~~IrG~y~v~gv~~~g~~~~~P-sYC~~CGkpyPWt 81 (158)
T PF10083_consen 40 TSCPNCSTPIRGDYHVEGVFGLGGHYEAP-SYCHNCGKPYPWT 81 (158)
T ss_pred HHCcCCCCCCCCceecCCeeeeCCCCCCC-hhHHhCCCCCchH
Confidence 689999999988753 34556777743 3477888887653
No 42
>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=68.68 E-value=2.8 Score=24.85 Aligned_cols=27 Identities=22% Similarity=0.561 Sum_probs=15.4
Q ss_pred cccCCCCCCCCCeeccCCcccc-HhHHH
Q 029695 135 CSHGGCSISPSNYAALEGILYC-KHHFS 161 (189)
Q Consensus 135 C~~C~~~l~~~~~~~~~g~~~C-~~c~~ 161 (189)
|..|...++...-+..||+.|| ..|..
T Consensus 10 C~~C~C~V~~~~Ai~~dGk~YCS~aCA~ 37 (52)
T PF02069_consen 10 CPSCSCVVSEEEAIQKDGKYYCSEACAN 37 (52)
T ss_dssp STT----B-TTTSEESSS-EESSHHHHH
T ss_pred CCCCEeEECchHhHHhCCEeeecHHHhc
Confidence 6677777776667888999998 55644
No 43
>PF12773 DZR: Double zinc ribbon
Probab=67.54 E-value=3.4 Score=23.78 Aligned_cols=23 Identities=22% Similarity=0.430 Sum_probs=10.4
Q ss_pred cccccccCCCCCccccCCeecchhhHH
Q 029695 37 CSHCKGTLKLSNYSSMEGVLYCKPHFE 63 (189)
Q Consensus 37 C~~C~~~L~~~~~~~~~g~~yC~~c~~ 63 (189)
|..|+..|. .......+|..|-.
T Consensus 15 C~~CG~~l~----~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 15 CPHCGTPLP----PPDQSKKICPNCGA 37 (50)
T ss_pred ChhhcCChh----hccCCCCCCcCCcC
Confidence 455555554 11223345555543
No 44
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=65.23 E-value=2.3 Score=32.56 Aligned_cols=31 Identities=23% Similarity=0.324 Sum_probs=24.3
Q ss_pred cccccCCCCCCCCCeeccCCccccHhHHHhh
Q 029695 133 FKCSHGGCSISPSNYAALEGILYCKHHFSQL 163 (189)
Q Consensus 133 f~C~~C~~~l~~~~~~~~~g~~~C~~c~~~~ 163 (189)
-+|+.|+..+-...-...||+++|..|+.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 5788888877666666778999999998753
No 45
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=63.84 E-value=2.9 Score=37.87 Aligned_cols=51 Identities=22% Similarity=0.493 Sum_probs=38.0
Q ss_pred cCcccccccccCCCCCccccCCeecchhhHHhhhcCCCCCCCCCCCCCCCcCCCCccccCCcccccccCCCCCCCCCcCC
Q 029695 33 SCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNKNFQSPAKSAEKLTPELTRSPSKAASMFSGTQEKCASCS 112 (189)
Q Consensus 33 ~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~ 112 (189)
.=++|+.|+....+. -..+=+..||..|...++..+ ..+|+.|+
T Consensus 642 ~~LkCs~Cn~R~Kd~-vI~kC~H~FC~~Cvq~r~etR-----------------------------------qRKCP~Cn 685 (698)
T KOG0978|consen 642 ELLKCSVCNTRWKDA-VITKCGHVFCEECVQTRYETR-----------------------------------QRKCPKCN 685 (698)
T ss_pred hceeCCCccCchhhH-HHHhcchHHHHHHHHHHHHHh-----------------------------------cCCCCCCC
Confidence 347899998665542 345677899999999888622 27999999
Q ss_pred ccccccc
Q 029695 113 KTVYPLE 119 (189)
Q Consensus 113 ~~I~~~~ 119 (189)
.++...+
T Consensus 686 ~aFganD 692 (698)
T KOG0978|consen 686 AAFGAND 692 (698)
T ss_pred CCCCccc
Confidence 9887766
No 46
>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=62.03 E-value=7.6 Score=22.32 Aligned_cols=31 Identities=26% Similarity=0.432 Sum_probs=19.5
Q ss_pred ccccccccCCCCCccccCCee-cchhhHHhhhc
Q 029695 36 KCSHCKGTLKLSNYSSMEGVL-YCKPHFEQLFK 67 (189)
Q Consensus 36 ~C~~C~~~L~~~~~~~~~g~~-yC~~c~~~~~~ 67 (189)
.|..|....... ....=|.. +|..|+.+...
T Consensus 4 ~C~iC~~~~~~~-~~~pCgH~~~C~~C~~~~~~ 35 (50)
T PF13920_consen 4 ECPICFENPRDV-VLLPCGHLCFCEECAERLLK 35 (50)
T ss_dssp B-TTTSSSBSSE-EEETTCEEEEEHHHHHHHHH
T ss_pred CCccCCccCCce-EEeCCCChHHHHHHhHHhcc
Confidence 466666655442 33456667 99999988764
No 47
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=60.06 E-value=4.1 Score=31.08 Aligned_cols=51 Identities=22% Similarity=0.435 Sum_probs=37.6
Q ss_pred CcccccccccCCCCCccccCCeecchhhHHhhhcCCCCCCCCCCCCCCCcCCCCccccCCcccccccCCCCCCCCCcCCc
Q 029695 34 CFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNKNFQSPAKSAEKLTPELTRSPSKAASMFSGTQEKCASCSK 113 (189)
Q Consensus 34 CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~ 113 (189)
=|.|..|.+...+. ....=|..||..|+...+.. .+.|..|++
T Consensus 196 PF~C~iCKkdy~sp-vvt~CGH~FC~~Cai~~y~k------------------------------------g~~C~~Cgk 238 (259)
T COG5152 196 PFLCGICKKDYESP-VVTECGHSFCSLCAIRKYQK------------------------------------GDECGVCGK 238 (259)
T ss_pred ceeehhchhhccch-hhhhcchhHHHHHHHHHhcc------------------------------------CCcceecch
Confidence 37888888877653 34456788999999888751 178999999
Q ss_pred ccccccce
Q 029695 114 TVYPLEKV 121 (189)
Q Consensus 114 ~I~~~~~v 121 (189)
...+..+|
T Consensus 239 ~t~G~f~V 246 (259)
T COG5152 239 ATYGRFWV 246 (259)
T ss_pred hhccceeH
Confidence 88776543
No 48
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=58.73 E-value=10 Score=21.21 Aligned_cols=30 Identities=17% Similarity=0.399 Sum_probs=18.7
Q ss_pred cccccccCCC--CCccccCCeecchhhHHhhh
Q 029695 37 CSHCKGTLKL--SNYSSMEGVLYCKPHFEQLF 66 (189)
Q Consensus 37 C~~C~~~L~~--~~~~~~~g~~yC~~c~~~~~ 66 (189)
|..|...+.. ..+...=|..+|..|..++.
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~ 33 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLK 33 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhc
Confidence 5566666622 22334567788999987765
No 49
>PRK00420 hypothetical protein; Validated
Probab=58.00 E-value=5.9 Score=27.44 Aligned_cols=25 Identities=24% Similarity=0.511 Sum_probs=17.8
Q ss_pred cccccccccCCCCCccccCCeecchhhHH
Q 029695 35 FKCSHCKGTLKLSNYSSMEGVLYCKPHFE 63 (189)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~~ 63 (189)
-.|..|+.+| |..++|+.||..|-.
T Consensus 24 ~~CP~Cg~pL----f~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPL----FELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcc----eecCCCceECCCCCC
Confidence 4567787776 334788889988865
No 50
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=56.00 E-value=9.9 Score=18.79 Aligned_cols=12 Identities=25% Similarity=0.742 Sum_probs=7.4
Q ss_pred CCCCcCCccccc
Q 029695 106 EKCASCSKTVYP 117 (189)
Q Consensus 106 ~~C~~C~~~I~~ 117 (189)
..|..|+..|.+
T Consensus 3 ~~Cp~Cg~~~~~ 14 (26)
T PF13248_consen 3 MFCPNCGAEIDP 14 (26)
T ss_pred CCCcccCCcCCc
Confidence 567777765543
No 51
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=55.12 E-value=8.4 Score=22.94 Aligned_cols=24 Identities=17% Similarity=0.358 Sum_probs=11.5
Q ss_pred cccccCceecccceEEeCCccccc
Q 029695 9 KCKVCEKTVYPVEQLSADGVVYHK 32 (189)
Q Consensus 9 ~C~~C~~~I~~~~~~~~~g~~~H~ 32 (189)
+|..|+.+|.+...+...+..-|+
T Consensus 3 ~CvVCKqpi~~a~~v~T~~G~VH~ 26 (54)
T PF10886_consen 3 ICVVCKQPIDDALVVETESGPVHP 26 (54)
T ss_pred eeeeeCCccCcceEEEcCCCccCc
Confidence 455555555444444444444443
No 52
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.88 E-value=7.9 Score=31.41 Aligned_cols=32 Identities=19% Similarity=0.428 Sum_probs=22.5
Q ss_pred cccccccccCCCCCccccCCeecchhhHHhhhc
Q 029695 35 FKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK 67 (189)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~ 67 (189)
|.|..|++.+... -...-+..+|+.|..+.+.
T Consensus 242 f~c~icr~~f~~p-Vvt~c~h~fc~~ca~~~~q 273 (313)
T KOG1813|consen 242 FKCFICRKYFYRP-VVTKCGHYFCEVCALKPYQ 273 (313)
T ss_pred ccccccccccccc-hhhcCCceeehhhhccccc
Confidence 6677777766542 3445778899999877664
No 53
>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=54.06 E-value=3.2 Score=26.18 Aligned_cols=23 Identities=22% Similarity=0.596 Sum_probs=10.4
Q ss_pred ccccccccCCCCCccccCCeecchhhHH
Q 029695 36 KCSHCKGTLKLSNYSSMEGVLYCKPHFE 63 (189)
Q Consensus 36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~ 63 (189)
.|..|..+|... ++.++|..|..
T Consensus 3 ~CP~C~~~L~~~-----~~~~~C~~C~~ 25 (70)
T PF07191_consen 3 TCPKCQQELEWQ-----GGHYHCEACQK 25 (70)
T ss_dssp B-SSS-SBEEEE-----TTEEEETTT--
T ss_pred cCCCCCCccEEe-----CCEEECccccc
Confidence 355566665442 25666666654
No 54
>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=53.82 E-value=13 Score=20.07 Aligned_cols=31 Identities=23% Similarity=0.472 Sum_probs=20.6
Q ss_pred cccccccCCCCCccccCCeecchhhHHhhhc
Q 029695 37 CSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK 67 (189)
Q Consensus 37 C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~ 67 (189)
|..|...+........=|..||..|..+...
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~ 31 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLE 31 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHH
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHH
Confidence 4556666655324566788999999887765
No 55
>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=53.24 E-value=13 Score=19.88 Aligned_cols=31 Identities=16% Similarity=0.454 Sum_probs=16.3
Q ss_pred cccccccCCCCCccccCCeecchhhHHhhhc
Q 029695 37 CSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK 67 (189)
Q Consensus 37 C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~ 67 (189)
|..|...+........=|..||..|....+.
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~ 32 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLK 32 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHH
Confidence 4555555522212222556677777766553
No 56
>PRK00807 50S ribosomal protein L24e; Validated
Probab=53.03 E-value=9.9 Score=22.44 Aligned_cols=25 Identities=24% Similarity=0.549 Sum_probs=16.6
Q ss_pred CcccccCceecccce---EEeCCccccc
Q 029695 8 QKCKVCEKTVYPVEQ---LSADGVVYHK 32 (189)
Q Consensus 8 ~~C~~C~~~I~~~~~---~~~~g~~~H~ 32 (189)
..|..|+..|+++.. +..+|+.|.-
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~F 29 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILYF 29 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEEE
Confidence 468888888875542 5566776653
No 57
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=52.99 E-value=9 Score=18.84 Aligned_cols=7 Identities=14% Similarity=0.748 Sum_probs=3.0
Q ss_pred cccCcee
Q 029695 11 KVCEKTV 17 (189)
Q Consensus 11 ~~C~~~I 17 (189)
..|+..|
T Consensus 2 ~sC~~~i 8 (24)
T PF07754_consen 2 TSCGRPI 8 (24)
T ss_pred ccCCCcc
Confidence 3444444
No 58
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=51.59 E-value=5.7 Score=26.53 Aligned_cols=35 Identities=26% Similarity=0.371 Sum_probs=20.9
Q ss_pred CcccccCceecccceEEeCC-ccccccCcccccccc
Q 029695 8 QKCKVCEKTVYPVEQLSADG-VVYHKSCFKCSHCKG 42 (189)
Q Consensus 8 ~~C~~C~~~I~~~~~~~~~g-~~~H~~CF~C~~C~~ 42 (189)
-+|..|+.+|..++.+..-. ..-|-+||.=+.-++
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~k 42 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECLAESKRKK 42 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHHHHHHhcC
Confidence 46777777777676643333 456777766554433
No 59
>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=51.52 E-value=14 Score=20.97 Aligned_cols=11 Identities=9% Similarity=0.316 Sum_probs=7.7
Q ss_pred ccccHhHHHhh
Q 029695 153 ILYCKHHFSQL 163 (189)
Q Consensus 153 ~~~C~~c~~~~ 163 (189)
--+|..||...
T Consensus 23 ~dLC~~Cf~~~ 33 (46)
T cd02249 23 FDLCSSCYAKG 33 (46)
T ss_pred CcCHHHHHCcC
Confidence 34688888754
No 60
>PRK04023 DNA polymerase II large subunit; Validated
Probab=51.33 E-value=16 Score=34.75 Aligned_cols=14 Identities=21% Similarity=0.812 Sum_probs=9.7
Q ss_pred CCCCcCCccccccc
Q 029695 106 EKCASCSKTVYPLE 119 (189)
Q Consensus 106 ~~C~~C~~~I~~~~ 119 (189)
..|..|+..+.+..
T Consensus 664 y~CPKCG~El~~~s 677 (1121)
T PRK04023 664 DECEKCGREPTPYS 677 (1121)
T ss_pred CcCCCCCCCCCccc
Confidence 56888877776554
No 61
>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=50.14 E-value=8.2 Score=33.74 Aligned_cols=38 Identities=24% Similarity=0.412 Sum_probs=17.1
Q ss_pred CCCCcCCcccccccceeccCccccccccccccCCCCCCC
Q 029695 106 EKCASCSKTVYPLEKVAVENQAYHKTCFKCSHGGCSISP 144 (189)
Q Consensus 106 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~ 144 (189)
..|+.|-..+...+ +...+..=-++||.|-.|..+|..
T Consensus 27 ~yCp~CL~~~p~~e-~~~~~nrC~r~Cf~CP~C~~~L~~ 64 (483)
T PF05502_consen 27 YYCPNCLFEVPSSE-ARSEKNRCSRNCFDCPICFSPLSV 64 (483)
T ss_pred eECccccccCChhh-heeccceeccccccCCCCCCccee
Confidence 34555544443332 222222223356666666655554
No 62
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=48.96 E-value=11 Score=30.80 Aligned_cols=34 Identities=18% Similarity=0.365 Sum_probs=27.0
Q ss_pred cCcccccccccCCCCCccccCCeecchhhHHhhh
Q 029695 33 SCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66 (189)
Q Consensus 33 ~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~ 66 (189)
+=+-|..|...|....|+=.+|.+.|..|-.++.
T Consensus 47 ~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~ 80 (299)
T KOG3002|consen 47 DLLDCPVCFNPLSPPIFQCDNGHLACSSCRTKVS 80 (299)
T ss_pred hhccCchhhccCcccceecCCCcEehhhhhhhhc
Confidence 3467888888888887888899999999986544
No 63
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=48.22 E-value=2.1 Score=28.61 Aligned_cols=51 Identities=16% Similarity=0.357 Sum_probs=34.6
Q ss_pred ccccCceecccceEEeCCccccccCcccccccccCCCCCccccCCeecchh
Q 029695 10 CKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKP 60 (189)
Q Consensus 10 C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~ 60 (189)
|..|...+..-......-..+++.+..|-.|.+.|.-..|.+...-|||..
T Consensus 38 Cy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~s 88 (105)
T COG4357 38 CYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYCQS 88 (105)
T ss_pred HHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCcCC
Confidence 556666665444555566778888999999998887666665555555543
No 64
>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=48.09 E-value=17 Score=21.82 Aligned_cols=26 Identities=4% Similarity=-0.040 Sum_probs=15.6
Q ss_pred ccccHhHHHhhhcCCCCCCcccCchH
Q 029695 153 ILYCKHHFSQLFKEKGSYNHLIKSAS 178 (189)
Q Consensus 153 ~~~C~~c~~~~~~~k~~~~~~~~~~~ 178 (189)
=.||..|...++.-.|.+-.|.-.+.
T Consensus 29 CTFC~~C~e~~l~~~CPNCgGelv~R 54 (57)
T PF06906_consen 29 CTFCADCAETMLNGVCPNCGGELVRR 54 (57)
T ss_pred CcccHHHHHHHhcCcCcCCCCccccC
Confidence 34677777777666666555544333
No 65
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=46.70 E-value=4.1 Score=21.99 Aligned_cols=31 Identities=19% Similarity=0.559 Sum_probs=19.1
Q ss_pred ccccCceecccceEEeCCccccccCcccccccccCC
Q 029695 10 CKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLK 45 (189)
Q Consensus 10 C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~ 45 (189)
|..|.+.+ ....++.||..=..|..|+-.+.
T Consensus 2 C~~C~~Ey-----~~p~~RR~~~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 2 CDDCLKEY-----FDPSNRRFHYQFISCTNCGPRYS 32 (35)
T ss_dssp -HHHHHHH-----CSTTSTTTT-TT--BTTCC-SCC
T ss_pred CHHHHHHH-----cCCCCCcccCcCccCCCCCCCEE
Confidence 55665544 34568999999999999988764
No 66
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=46.12 E-value=11 Score=24.55 Aligned_cols=29 Identities=17% Similarity=0.354 Sum_probs=19.0
Q ss_pred ccccccccCCCCCcc--cc---CCeecchhhHHh
Q 029695 36 KCSHCKGTLKLSNYS--SM---EGVLYCKPHFEQ 64 (189)
Q Consensus 36 ~C~~C~~~L~~~~~~--~~---~g~~yC~~c~~~ 64 (189)
.|..|+-||.....+ .. .+.-||.-||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 377888888775522 22 334599999963
No 67
>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=44.17 E-value=15 Score=20.96 Aligned_cols=29 Identities=14% Similarity=0.415 Sum_probs=18.0
Q ss_pred ccccccccCCCCCcc--ccCCeecchhhHHh
Q 029695 36 KCSHCKGTLKLSNYS--SMEGVLYCKPHFEQ 64 (189)
Q Consensus 36 ~C~~C~~~L~~~~~~--~~~g~~yC~~c~~~ 64 (189)
.|..|+..+....|. ...+..+|.+||.+
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhC
Confidence 466677776643333 12346789999975
No 68
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=42.23 E-value=7.9 Score=28.01 Aligned_cols=37 Identities=22% Similarity=0.415 Sum_probs=24.2
Q ss_pred CCcccccCceecccceEEeCCccccccCcccccccccCCC
Q 029695 7 QQKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLKL 46 (189)
Q Consensus 7 ~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~ 46 (189)
.-.|+.|+..+...+.+...+. ..=|.|..|+..|..
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~~d~---~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQLLDM---DGTFTCPRCGEELEE 135 (147)
T ss_pred EEECcCCCCEeeHHHHHHhcCC---CCcEECCCCCCEEEE
Confidence 3478999888765454443331 233999999988854
No 69
>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=41.47 E-value=28 Score=19.49 Aligned_cols=12 Identities=25% Similarity=0.714 Sum_probs=8.1
Q ss_pred CCCCcCCccccc
Q 029695 106 EKCASCSKTVYP 117 (189)
Q Consensus 106 ~~C~~C~~~I~~ 117 (189)
..|..|+.+|.+
T Consensus 5 ~~C~~C~~~i~g 16 (44)
T smart00291 5 YSCDTCGKPIVG 16 (44)
T ss_pred cCCCCCCCCCcC
Confidence 668888776543
No 70
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=41.30 E-value=23 Score=34.56 Aligned_cols=13 Identities=23% Similarity=0.733 Sum_probs=7.3
Q ss_pred CCCCcCCcccccc
Q 029695 106 EKCASCSKTVYPL 118 (189)
Q Consensus 106 ~~C~~C~~~I~~~ 118 (189)
..|+.|+.++...
T Consensus 710 ~~CP~CGtplv~~ 722 (1337)
T PRK14714 710 VECPRCDVELTPY 722 (1337)
T ss_pred ccCCCCCCccccc
Confidence 4566666655543
No 71
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=39.67 E-value=18 Score=29.05 Aligned_cols=39 Identities=21% Similarity=0.377 Sum_probs=22.5
Q ss_pred CCCCcCCcccccccceeccCcccc--ccccccccCCCCCCCC
Q 029695 106 EKCASCSKTVYPLEKVAVENQAYH--KTCFKCSHGGCSISPS 145 (189)
Q Consensus 106 ~~C~~C~~~I~~~~~v~~~g~~~H--~~Cf~C~~C~~~l~~~ 145 (189)
-.|..|++.+.-. ++.-.-..-| ..=|.|..|++.+.+.
T Consensus 188 c~C~iCGKaFSRP-WLLQGHiRTHTGEKPF~C~hC~kAFADR 228 (279)
T KOG2462|consen 188 CECGICGKAFSRP-WLLQGHIRTHTGEKPFSCPHCGKAFADR 228 (279)
T ss_pred cccccccccccch-HHhhcccccccCCCCccCCcccchhcch
Confidence 5688888776422 2322222233 2457888888877653
No 72
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=39.23 E-value=17 Score=32.84 Aligned_cols=21 Identities=14% Similarity=0.392 Sum_probs=13.9
Q ss_pred cCccccccccccccCCCCCCC
Q 029695 124 ENQAYHKTCFKCSHGGCSISP 144 (189)
Q Consensus 124 ~g~~~H~~Cf~C~~C~~~l~~ 144 (189)
.|..+-++|++|..|+..+.+
T Consensus 107 sg~~~ckk~~~c~qc~~~lpg 127 (694)
T KOG4443|consen 107 SGPWLCKKCTRCRQCDSTLPG 127 (694)
T ss_pred CcccccHHHHhhhhccccccc
Confidence 345556677777777776666
No 73
>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=38.88 E-value=9.5 Score=28.05 Aligned_cols=31 Identities=19% Similarity=0.305 Sum_probs=23.0
Q ss_pred CcccccCceecccceEEeCCccccccCcccccccccCCC
Q 029695 8 QKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLKL 46 (189)
Q Consensus 8 ~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~ 46 (189)
-.|+.|+..+...+.+.. =|.|..|+..|..
T Consensus 110 Y~Cp~c~~r~tf~eA~~~--------~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 110 FICPNMCVRFTFNEAMEL--------NFTCPRCGAMLDY 140 (158)
T ss_pred EECCCCCcEeeHHHHHHc--------CCcCCCCCCEeee
Confidence 469999988765555542 3999999999864
No 74
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=38.67 E-value=41 Score=25.67 Aligned_cols=31 Identities=23% Similarity=0.584 Sum_probs=22.0
Q ss_pred CcccccccccCCCCCccccCCeecchhhHHhh
Q 029695 34 CFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 65 (189)
Q Consensus 34 CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~ 65 (189)
-|.|..|...+... ....=|..||..|..+.
T Consensus 18 ~~~CpICld~~~dP-VvT~CGH~FC~~CI~~w 48 (193)
T PLN03208 18 DFDCNICLDQVRDP-VVTLCGHLFCWPCIHKW 48 (193)
T ss_pred ccCCccCCCcCCCc-EEcCCCchhHHHHHHHH
Confidence 47888887766543 33457888999998754
No 75
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=38.29 E-value=12 Score=30.67 Aligned_cols=28 Identities=11% Similarity=0.228 Sum_probs=17.1
Q ss_pred ccccccccCCCCCccccCCeecchhhHH
Q 029695 36 KCSHCKGTLKLSNYSSMEGVLYCKPHFE 63 (189)
Q Consensus 36 ~C~~C~~~L~~~~~~~~~g~~yC~~c~~ 63 (189)
.|..|+.++.--.-.+.=+.+||.+|..
T Consensus 92 fCd~Cd~PI~IYGRmIPCkHvFCl~CAr 119 (389)
T KOG2932|consen 92 FCDRCDFPIAIYGRMIPCKHVFCLECAR 119 (389)
T ss_pred eecccCCcceeeecccccchhhhhhhhh
Confidence 4788888776422234455667777763
No 76
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=38.15 E-value=26 Score=31.87 Aligned_cols=13 Identities=15% Similarity=0.606 Sum_probs=8.4
Q ss_pred CCCCcCCcccccc
Q 029695 106 EKCASCSKTVYPL 118 (189)
Q Consensus 106 ~~C~~C~~~I~~~ 118 (189)
..|..|+.++...
T Consensus 42 ~fC~~CG~~~~~~ 54 (645)
T PRK14559 42 AHCPNCGAETGTI 54 (645)
T ss_pred ccccccCCcccch
Confidence 5677777766443
No 77
>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=37.93 E-value=16 Score=24.29 Aligned_cols=44 Identities=14% Similarity=0.235 Sum_probs=28.3
Q ss_pred CCCCCCCcccccCceecccceEEeCCccccccCcccccccccCCCC
Q 029695 2 SFIGTQQKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLKLS 47 (189)
Q Consensus 2 ~~~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~ 47 (189)
++......|..|++++.--+.+.+.+-.+. =-+|..|+++++..
T Consensus 28 ~i~~~rS~C~~C~~~L~~~~lIPi~S~l~l--rGrCr~C~~~I~~~ 71 (92)
T PF06750_consen 28 SIIFPRSHCPHCGHPLSWWDLIPILSYLLL--RGRCRYCGAPIPPR 71 (92)
T ss_pred CccCCCCcCcCCCCcCcccccchHHHHHHh--CCCCcccCCCCChH
Confidence 344556789999988865555555443333 34678888888653
No 78
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=37.74 E-value=3.5 Score=27.59 Aligned_cols=51 Identities=14% Similarity=0.286 Sum_probs=34.5
Q ss_pred CCCcCCcccccccceeccCccccccccccccCCCCCCCCCeeccCCccccH
Q 029695 107 KCASCSKTVYPLEKVAVENQAYHKTCFKCSHGGCSISPSNYAALEGILYCK 157 (189)
Q Consensus 107 ~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~~C~ 157 (189)
.|..|...+..-...-+.-..+++.+.-|.+|...|....|...+.=|||.
T Consensus 37 aCy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~ 87 (105)
T COG4357 37 ACYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYCQ 87 (105)
T ss_pred hHHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCcC
Confidence 467777776654433444567888888899998888877666665555553
No 79
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=37.53 E-value=12 Score=25.30 Aligned_cols=29 Identities=24% Similarity=0.400 Sum_probs=18.3
Q ss_pred cCcccccccccCCCCC-ccccCCeecchhh
Q 029695 33 SCFKCSHCKGTLKLSN-YSSMEGVLYCKPH 61 (189)
Q Consensus 33 ~CF~C~~C~~~L~~~~-~~~~~g~~yC~~c 61 (189)
.=|+|+.|-..-..+. -...+|.+||..|
T Consensus 69 DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 69 DEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CceeeeeeeeEechhhhccccCCCEecccc
Confidence 3488888854332221 1256899999887
No 80
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=37.44 E-value=13 Score=27.98 Aligned_cols=32 Identities=22% Similarity=0.397 Sum_probs=23.1
Q ss_pred CCcccccCceecccceEEeCCccccccCcccccccccCCC
Q 029695 7 QQKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLKL 46 (189)
Q Consensus 7 ~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~ 46 (189)
.-.|+.|+......+.+. .=|.|..|+..|..
T Consensus 117 ~Y~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAME--------YGFRCPQCGEMLEE 148 (178)
T ss_pred EEECCCCCcEEeHHHHhh--------cCCcCCCCCCCCee
Confidence 346899988875555443 13999999999965
No 81
>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=37.15 E-value=16 Score=18.57 Aligned_cols=12 Identities=33% Similarity=0.700 Sum_probs=6.8
Q ss_pred CCCCcCCccccc
Q 029695 106 EKCASCSKTVYP 117 (189)
Q Consensus 106 ~~C~~C~~~I~~ 117 (189)
.+|.+|...|..
T Consensus 2 ~~C~rC~~~~~~ 13 (30)
T PF06827_consen 2 EKCPRCWNYIED 13 (30)
T ss_dssp SB-TTT--BBEE
T ss_pred CcCccCCCcceE
Confidence 579999988754
No 82
>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=36.25 E-value=35 Score=19.37 Aligned_cols=27 Identities=26% Similarity=0.605 Sum_probs=15.6
Q ss_pred cccccCceecccceEEeCC--ccccccCc
Q 029695 9 KCKVCEKTVYPVEQLSADG--VVYHKSCF 35 (189)
Q Consensus 9 ~C~~C~~~I~~~~~~~~~g--~~~H~~CF 35 (189)
+|..|++.-..++.|.-++ +.||..|.
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~ 29 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECV 29 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTS
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccC
Confidence 3677777443444454433 56788774
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=36.25 E-value=18 Score=19.35 Aligned_cols=31 Identities=29% Similarity=0.677 Sum_probs=17.1
Q ss_pred cccccCceecccc-eEEeCCccccccCcccccccccC
Q 029695 9 KCKVCEKTVYPVE-QLSADGVVYHKSCFKCSHCKGTL 44 (189)
Q Consensus 9 ~C~~C~~~I~~~~-~~~~~g~~~H~~CF~C~~C~~~L 44 (189)
.|+.|+..+.-.+ .+...+. -++|..|+..|
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~-----~v~C~~C~~~~ 35 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGG-----KVRCGKCGHVW 35 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCC-----EEECCCCCCEE
Confidence 5778877664222 2332222 36677777665
No 84
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=35.70 E-value=19 Score=20.34 Aligned_cols=10 Identities=20% Similarity=0.717 Sum_probs=6.0
Q ss_pred cccccccccC
Q 029695 35 FKCSHCKGTL 44 (189)
Q Consensus 35 F~C~~C~~~L 44 (189)
++|..|+.++
T Consensus 22 ~~Cp~CG~~~ 31 (46)
T PRK00398 22 VRCPYCGYRI 31 (46)
T ss_pred eECCCCCCeE
Confidence 5666666544
No 85
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=35.69 E-value=22 Score=21.58 Aligned_cols=25 Identities=16% Similarity=0.333 Sum_probs=17.1
Q ss_pred cccCCCCCCCC--CeeccCCccccH-hH
Q 029695 135 CSHGGCSISPS--NYAALEGILYCK-HH 159 (189)
Q Consensus 135 C~~C~~~l~~~--~~~~~~g~~~C~-~c 159 (189)
|..|++.|..+ .|..++.+.+|. .|
T Consensus 19 C~~C~k~L~~~~DiymYrGd~aFCS~EC 46 (58)
T PF04570_consen 19 CYLCKKKLDPGKDIYMYRGDKAFCSEEC 46 (58)
T ss_pred HHccCCCCCCCCCeeeeccccccccHHH
Confidence 56667888854 466667788884 45
No 86
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=35.00 E-value=39 Score=18.10 Aligned_cols=31 Identities=13% Similarity=0.342 Sum_probs=20.6
Q ss_pred cccccccCCCCCccccCCeecchhhHHhhhc
Q 029695 37 CSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK 67 (189)
Q Consensus 37 C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~ 67 (189)
|..|...+........=|..||..|..+...
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~ 31 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLE 31 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHHHHHHHHH
T ss_pred CCcCCccccCCCEEecCCCcchHHHHHHHHH
Confidence 4556666655444455677889999887764
No 87
>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=34.43 E-value=25 Score=20.95 Aligned_cols=25 Identities=32% Similarity=0.789 Sum_probs=16.7
Q ss_pred CCcccccCceecccc---eEEeCCcccc
Q 029695 7 QQKCKVCEKTVYPVE---QLSADGVVYH 31 (189)
Q Consensus 7 ~~~C~~C~~~I~~~~---~~~~~g~~~H 31 (189)
...|..|+..|+++. +|..+|+.++
T Consensus 3 ~~~C~f~g~~I~PG~G~~~Vr~Dgkv~~ 30 (54)
T cd00472 3 TEKCSFCGYKIYPGHGKMYVRNDGKVFR 30 (54)
T ss_pred EEEecCcCCeecCCCccEEEecCCCEEE
Confidence 356888888888774 3556666554
No 88
>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=34.30 E-value=24 Score=20.48 Aligned_cols=30 Identities=20% Similarity=0.445 Sum_probs=21.9
Q ss_pred CCCCcccccCceeccc-c-eEEeCCccccccC
Q 029695 5 GTQQKCKVCEKTVYPV-E-QLSADGVVYHKSC 34 (189)
Q Consensus 5 ~~~~~C~~C~~~I~~~-~-~~~~~g~~~H~~C 34 (189)
..-..|+.|+-..... + .|.+.+..|++.|
T Consensus 11 ~kY~~Cp~CGN~~vGngEG~liV~edtfkRtC 42 (49)
T PF12677_consen 11 NKYCKCPKCGNDKVGNGEGTLIVEEDTFKRTC 42 (49)
T ss_pred hhhccCcccCCcEeecCcceEEEeccceeeee
Confidence 3446799998776422 3 4889999999988
No 89
>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=33.74 E-value=40 Score=19.31 Aligned_cols=29 Identities=14% Similarity=0.279 Sum_probs=15.9
Q ss_pred cccCCCCCCCCCeeccCCccccHhHHHhhhc
Q 029695 135 CSHGGCSISPSNYAALEGILYCKHHFSQLFK 165 (189)
Q Consensus 135 C~~C~~~l~~~~~~~~~g~~~C~~c~~~~~~ 165 (189)
|..|++....| ....|...|..|-.++..
T Consensus 2 CiiC~~~~~~G--I~I~~~fIC~~CE~~iv~ 30 (46)
T PF10764_consen 2 CIICGKEKEEG--IHIYGKFICSDCEKEIVN 30 (46)
T ss_pred eEeCCCcCCCC--EEEECeEehHHHHHHhcc
Confidence 44555555443 334566677777655543
No 90
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=33.16 E-value=39 Score=25.12 Aligned_cols=39 Identities=18% Similarity=0.219 Sum_probs=24.8
Q ss_pred cccCCCCCCCCCeeccCC--ccccHhHHHhhhcCCCCCCcccC
Q 029695 135 CSHGGCSISPSNYAALEG--ILYCKHHFSQLFKEKGSYNHLIK 175 (189)
Q Consensus 135 C~~C~~~l~~~~~~~~~g--~~~C~~c~~~~~~~k~~~~~~~~ 175 (189)
|..|++.+....-+..+| .-.|..|+ .||++-....+.+
T Consensus 6 CEiCG~~i~~~~~v~vegsel~VC~~Ca--k~G~~~~~~~~~~ 46 (165)
T COG1813 6 CELCGREIDKPIKVKVEGAELTVCDDCA--KFGTAAKTASGDP 46 (165)
T ss_pred eeccccccCCCeeEEeecceeehhHHHH--HhccCccccCCCc
Confidence 788888877444444454 44589998 7886665444433
No 91
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=33.03 E-value=34 Score=32.90 Aligned_cols=30 Identities=27% Similarity=0.633 Sum_probs=20.1
Q ss_pred CCcccccCceecccceEEeCCccccccCcccccccccC
Q 029695 7 QQKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTL 44 (189)
Q Consensus 7 ~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L 44 (189)
..+|..|+..|- +.++|..| -.|..|+-++
T Consensus 17 ~qiCqICGD~vg----~~~~Ge~F----VAC~eC~FPV 46 (1079)
T PLN02638 17 GQVCQICGDNVG----KTVDGEPF----VACDVCAFPV 46 (1079)
T ss_pred CceeeecccccC----cCCCCCEE----EEeccCCCcc
Confidence 348999988873 55777777 4456665544
No 92
>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=32.82 E-value=28 Score=19.75 Aligned_cols=9 Identities=22% Similarity=0.571 Sum_probs=7.2
Q ss_pred ecchhhHHh
Q 029695 56 LYCKPHFEQ 64 (189)
Q Consensus 56 ~yC~~c~~~ 64 (189)
-+|..||.+
T Consensus 29 dLC~~C~~~ 37 (46)
T PF00569_consen 29 DLCEDCFSK 37 (46)
T ss_dssp EEEHHHHHH
T ss_pred chhhHHHhC
Confidence 479999976
No 93
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=32.77 E-value=61 Score=26.68 Aligned_cols=15 Identities=27% Similarity=0.503 Sum_probs=11.7
Q ss_pred CCeecchhhHHhhhc
Q 029695 53 EGVLYCKPHFEQLFK 67 (189)
Q Consensus 53 ~g~~yC~~c~~~~~~ 67 (189)
=|..+|..|...++.
T Consensus 26 CGH~~C~sCv~~l~~ 40 (309)
T TIGR00570 26 CGHTLCESCVDLLFV 40 (309)
T ss_pred CCCcccHHHHHHHhc
Confidence 466789999988774
No 94
>PLN02195 cellulose synthase A
Probab=31.39 E-value=41 Score=32.01 Aligned_cols=31 Identities=19% Similarity=0.578 Sum_probs=20.1
Q ss_pred CCCCcccccCceecccceEEeCCccccccCccccccccc
Q 029695 5 GTQQKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGT 43 (189)
Q Consensus 5 ~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~ 43 (189)
.+.+.|..|+..|- +..+|..| -.|..|+-+
T Consensus 4 ~~~~~c~~cgd~~~----~~~~g~~f----vaC~eC~~p 34 (977)
T PLN02195 4 SGAPICATCGEEVG----VDSNGEAF----VACHECSYP 34 (977)
T ss_pred CCCccceecccccC----cCCCCCeE----EEeccCCCc
Confidence 35568999988873 45677766 445666443
No 95
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=31.32 E-value=28 Score=24.68 Aligned_cols=26 Identities=23% Similarity=0.423 Sum_probs=18.6
Q ss_pred CCcccccCceecccc---eEEeCCccccc
Q 029695 7 QQKCKVCEKTVYPVE---QLSADGVVYHK 32 (189)
Q Consensus 7 ~~~C~~C~~~I~~~~---~~~~~g~~~H~ 32 (189)
..+|..|+..|+++. +|..+|++|+.
T Consensus 4 ~e~CsFcG~kIyPG~G~~fVR~DGkvf~F 32 (131)
T PRK14891 4 TRTCDYTGEEIEPGTGTMFVRKDGTVLHF 32 (131)
T ss_pred eeeecCcCCcccCCCCcEEEecCCCEEEE
Confidence 357999999998875 35666666653
No 96
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=31.25 E-value=29 Score=21.53 Aligned_cols=24 Identities=29% Similarity=0.612 Sum_probs=13.8
Q ss_pred CcccccCceecccce---EEeCCcccc
Q 029695 8 QKCKVCEKTVYPVEQ---LSADGVVYH 31 (189)
Q Consensus 8 ~~C~~C~~~I~~~~~---~~~~g~~~H 31 (189)
.+|..|+..|+++.. |.-+|+.++
T Consensus 4 ~~CsFcG~~I~PGtG~m~Vr~Dg~v~~ 30 (66)
T COG2075 4 RVCSFCGKKIEPGTGIMYVRNDGKVLR 30 (66)
T ss_pred eEecCcCCccCCCceEEEEecCCeEEE
Confidence 457777777766642 444445443
No 97
>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=30.07 E-value=18 Score=20.90 Aligned_cols=11 Identities=18% Similarity=0.969 Sum_probs=5.7
Q ss_pred cccccccccCC
Q 029695 35 FKCSHCKGTLK 45 (189)
Q Consensus 35 F~C~~C~~~L~ 45 (189)
|+|..|+..+.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 45555655443
No 98
>PF04641 Rtf2: Rtf2 RING-finger
Probab=29.98 E-value=66 Score=25.57 Aligned_cols=55 Identities=15% Similarity=0.334 Sum_probs=40.3
Q ss_pred ccccCcccccccccCCCC-Cc--cccCCeecchhhHHhhh-cCCCCCCCCCCCCCCCcCCCCccccCCcccccccCCCCC
Q 029695 30 YHKSCFKCSHCKGTLKLS-NY--SSMEGVLYCKPHFEQLF-KESGNFNKNFQSPAKSAEKLTPELTRSPSKAASMFSGTQ 105 (189)
Q Consensus 30 ~H~~CF~C~~C~~~L~~~-~~--~~~~g~~yC~~c~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 105 (189)
....-|.|...+..|.+. .| ...-|.+|++....++. .
T Consensus 109 ~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k~~-------------------------------------- 150 (260)
T PF04641_consen 109 NSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELKKS-------------------------------------- 150 (260)
T ss_pred cCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhccc--------------------------------------
Confidence 356678999999999663 23 34688888888887664 2
Q ss_pred CCCCcCCccccccccee
Q 029695 106 EKCASCSKTVYPLEKVA 122 (189)
Q Consensus 106 ~~C~~C~~~I~~~~~v~ 122 (189)
..|..|+++....+.|.
T Consensus 151 ~~Cp~c~~~f~~~DiI~ 167 (260)
T PF04641_consen 151 KKCPVCGKPFTEEDIIP 167 (260)
T ss_pred ccccccCCccccCCEEE
Confidence 67999999988766543
No 99
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=29.85 E-value=25 Score=20.75 Aligned_cols=34 Identities=21% Similarity=0.457 Sum_probs=22.0
Q ss_pred cccccCceecccceEEeCCccccccCcccccccccCC
Q 029695 9 KCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLK 45 (189)
Q Consensus 9 ~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~ 45 (189)
.|+.|+..|...--.+..++.|=..|-.| -+++.
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vC---C~PI~ 35 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVC---CRPIE 35 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhc---CCccE
Confidence 58999999843222455667788887554 45553
No 100
>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=29.79 E-value=17 Score=19.60 Aligned_cols=9 Identities=33% Similarity=0.977 Sum_probs=4.1
Q ss_pred cccccCcee
Q 029695 9 KCKVCEKTV 17 (189)
Q Consensus 9 ~C~~C~~~I 17 (189)
+|..|+..+
T Consensus 7 ~C~~Cg~~f 15 (41)
T smart00834 7 RCEDCGHTF 15 (41)
T ss_pred EcCCCCCEE
Confidence 344554443
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=29.70 E-value=54 Score=18.81 Aligned_cols=10 Identities=30% Similarity=0.305 Sum_probs=7.0
Q ss_pred cccHhHHHhh
Q 029695 154 LYCKHHFSQL 163 (189)
Q Consensus 154 ~~C~~c~~~~ 163 (189)
-+|..||...
T Consensus 25 dLC~~Cf~~g 34 (49)
T cd02335 25 DLCLECFSAG 34 (49)
T ss_pred chhHHhhhCc
Confidence 3688888754
No 102
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=29.29 E-value=28 Score=18.67 Aligned_cols=30 Identities=23% Similarity=0.562 Sum_probs=16.3
Q ss_pred cccccCceeccc-ceEEeCCccccccCccccccccc
Q 029695 9 KCKVCEKTVYPV-EQLSADGVVYHKSCFKCSHCKGT 43 (189)
Q Consensus 9 ~C~~C~~~I~~~-~~~~~~g~~~H~~CF~C~~C~~~ 43 (189)
.|..|+....-. +.|...|.. ++|..|+..
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~-----v~C~~C~~~ 34 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRK-----VRCSKCGHV 34 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcE-----EECCCCCCE
Confidence 477777664322 335544443 566666653
No 103
>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=29.21 E-value=51 Score=18.44 Aligned_cols=11 Identities=18% Similarity=0.625 Sum_probs=7.2
Q ss_pred CCCcCCccccc
Q 029695 107 KCASCSKTVYP 117 (189)
Q Consensus 107 ~C~~C~~~I~~ 117 (189)
.|.+|+++|.+
T Consensus 2 ~Cd~C~~~i~G 12 (43)
T cd02340 2 ICDGCQGPIVG 12 (43)
T ss_pred CCCCCCCcCcC
Confidence 47777776644
No 104
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=29.03 E-value=15 Score=20.28 Aligned_cols=14 Identities=7% Similarity=0.340 Sum_probs=7.3
Q ss_pred CCeecchhhHHhhh
Q 029695 53 EGVLYCKPHFEQLF 66 (189)
Q Consensus 53 ~g~~yC~~c~~~~~ 66 (189)
=|..||..|..+.+
T Consensus 21 C~H~fh~~Ci~~~~ 34 (44)
T PF13639_consen 21 CGHVFHRSCIKEWL 34 (44)
T ss_dssp TSEEEEHHHHHHHH
T ss_pred CCCeeCHHHHHHHH
Confidence 34555556655443
No 105
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=28.94 E-value=55 Score=25.62 Aligned_cols=25 Identities=16% Similarity=0.537 Sum_probs=15.7
Q ss_pred cccccccCCCCCccccCCeecchhhHHhhhc
Q 029695 37 CSHCKGTLKLSNYSSMEGVLYCKPHFEQLFK 67 (189)
Q Consensus 37 C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~ 67 (189)
|..||++.... .+ -+|..||.+.+.
T Consensus 1 C~~CG~~~~~~----~~--~lC~~C~~~~~~ 25 (236)
T PF04981_consen 1 CPRCGREIEPL----ID--GLCPDCYLKRFD 25 (236)
T ss_pred CCCCCCCCCCc----cc--ccChHHhcccCC
Confidence 56777755431 12 279999977664
No 106
>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=28.89 E-value=28 Score=19.34 Aligned_cols=11 Identities=27% Similarity=0.745 Sum_probs=4.7
Q ss_pred cccccccccCC
Q 029695 35 FKCSHCKGTLK 45 (189)
Q Consensus 35 F~C~~C~~~L~ 45 (189)
+.|..|+..|.
T Consensus 20 ~vC~~CG~Vl~ 30 (43)
T PF08271_consen 20 LVCPNCGLVLE 30 (43)
T ss_dssp EEETTT-BBEE
T ss_pred EECCCCCCEee
Confidence 34555544443
No 107
>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=28.85 E-value=32 Score=18.41 Aligned_cols=12 Identities=33% Similarity=0.703 Sum_probs=4.9
Q ss_pred CCcccccCceec
Q 029695 7 QQKCKVCEKTVY 18 (189)
Q Consensus 7 ~~~C~~C~~~I~ 18 (189)
.+.|..|++++.
T Consensus 3 ~~~C~eC~~~f~ 14 (34)
T PF01286_consen 3 YPKCDECGKPFM 14 (34)
T ss_dssp -EE-TTT--EES
T ss_pred CchHhHhCCHHH
Confidence 345666766664
No 108
>PRK12495 hypothetical protein; Provisional
Probab=28.55 E-value=32 Score=26.80 Aligned_cols=23 Identities=17% Similarity=0.530 Sum_probs=12.5
Q ss_pred cccccccccCCCCCccccCCeecchhhH
Q 029695 35 FKCSHCKGTLKLSNYSSMEGVLYCKPHF 62 (189)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~ 62 (189)
+.|..|+.+|. ...|..+|..|-
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 44555665553 235566666554
No 109
>PLN02436 cellulose synthase A
Probab=28.37 E-value=49 Score=31.88 Aligned_cols=29 Identities=28% Similarity=0.793 Sum_probs=15.6
Q ss_pred CcccccCceecccceEEeCCccccccCcccccccccC
Q 029695 8 QKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTL 44 (189)
Q Consensus 8 ~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L 44 (189)
.+|..|+..|- +.++|..| -.|..|+-++
T Consensus 37 ~iCqICGD~Vg----~t~dGe~F----VACn~C~fpv 65 (1094)
T PLN02436 37 QTCQICGDEIE----LTVDGEPF----VACNECAFPV 65 (1094)
T ss_pred ccccccccccC----cCCCCCEE----EeeccCCCcc
Confidence 36777776662 34566655 3344554433
No 110
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=28.13 E-value=24 Score=32.26 Aligned_cols=34 Identities=15% Similarity=0.558 Sum_probs=22.2
Q ss_pred CCCcccccCceecccceEEeCCccccccCcccccccccC
Q 029695 6 TQQKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTL 44 (189)
Q Consensus 6 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L 44 (189)
-..+|..|.+.|. .-.++.||--=-.|+.|+-.+
T Consensus 100 D~a~C~~Cl~Ei~-----dp~~rrY~YPF~~CT~CGPRf 133 (750)
T COG0068 100 DAATCEDCLEEIF-----DPNSRRYLYPFINCTNCGPRF 133 (750)
T ss_pred chhhhHHHHHHhc-----CCCCcceeccccccCCCCcce
Confidence 3457777766664 345677777667788886543
No 111
>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=27.97 E-value=21 Score=16.48 Aligned_cols=12 Identities=25% Similarity=0.800 Sum_probs=8.0
Q ss_pred cccccccccCCC
Q 029695 35 FKCSHCKGTLKL 46 (189)
Q Consensus 35 F~C~~C~~~L~~ 46 (189)
|+|..|++.+..
T Consensus 1 y~C~~C~~~f~~ 12 (23)
T PF00096_consen 1 YKCPICGKSFSS 12 (23)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCccCC
Confidence 567777776654
No 112
>PLN02189 cellulose synthase
Probab=27.95 E-value=48 Score=31.83 Aligned_cols=18 Identities=28% Similarity=0.837 Sum_probs=9.4
Q ss_pred cccccCceecccceEEeCCccc
Q 029695 9 KCKVCEKTVYPVEQLSADGVVY 30 (189)
Q Consensus 9 ~C~~C~~~I~~~~~~~~~g~~~ 30 (189)
+|..|+..|- +.++|..|
T Consensus 36 ~C~iCgd~vg----~~~~g~~f 53 (1040)
T PLN02189 36 VCEICGDEIG----LTVDGDLF 53 (1040)
T ss_pred cccccccccC----cCCCCCEE
Confidence 5666665552 23455554
No 113
>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=27.55 E-value=46 Score=19.22 Aligned_cols=9 Identities=11% Similarity=0.250 Sum_probs=6.5
Q ss_pred ecchhhHHh
Q 029695 56 LYCKPHFEQ 64 (189)
Q Consensus 56 ~yC~~c~~~ 64 (189)
-+|..||..
T Consensus 27 DlC~~C~~~ 35 (48)
T cd02341 27 DLCQDCVVK 35 (48)
T ss_pred ccCHHHHhC
Confidence 368888864
No 114
>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=26.96 E-value=20 Score=19.98 Aligned_cols=10 Identities=20% Similarity=1.026 Sum_probs=4.7
Q ss_pred cccccccccC
Q 029695 35 FKCSHCKGTL 44 (189)
Q Consensus 35 F~C~~C~~~L 44 (189)
|+|..|+..+
T Consensus 6 y~C~~Cg~~f 15 (42)
T PF09723_consen 6 YRCEECGHEF 15 (42)
T ss_pred EEeCCCCCEE
Confidence 4455555443
No 115
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.86 E-value=29 Score=28.18 Aligned_cols=30 Identities=30% Similarity=0.662 Sum_probs=14.0
Q ss_pred cccccCceecccceEEeCCccccccCcccc
Q 029695 9 KCKVCEKTVYPVEQLSADGVVYHKSCFKCS 38 (189)
Q Consensus 9 ~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~ 38 (189)
.|--|++.+.+..+|.--.-.-|+-||-|+
T Consensus 270 cCTLC~ERLEDTHFVQCPSVp~HKFCFPCS 299 (352)
T KOG3579|consen 270 CCTLCHERLEDTHFVQCPSVPSHKFCFPCS 299 (352)
T ss_pred eehhhhhhhccCceeecCCCcccceecccC
Confidence 344455555444444444444455555443
No 116
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=26.76 E-value=36 Score=19.28 Aligned_cols=26 Identities=15% Similarity=0.450 Sum_probs=13.2
Q ss_pred cccccccccCCCCCccccCCeecchhhHHh
Q 029695 35 FKCSHCKGTLKLSNYSSMEGVLYCKPHFEQ 64 (189)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~~~ 64 (189)
+.|..|+..+... ..+.+.|..|-.+
T Consensus 3 Y~C~~Cg~~~~~~----~~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIK----SKDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecC----CCCceECCCCCce
Confidence 4566666654432 3345556655443
No 117
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=26.73 E-value=23 Score=31.64 Aligned_cols=34 Identities=18% Similarity=0.368 Sum_probs=26.0
Q ss_pred ccCcccccccccCCCCCc-----cccCCeecchhhHHhh
Q 029695 32 KSCFKCSHCKGTLKLSNY-----SSMEGVLYCKPHFEQL 65 (189)
Q Consensus 32 ~~CF~C~~C~~~L~~~~~-----~~~~g~~yC~~c~~~~ 65 (189)
..=|+|+.|+..|....+ -...|++||..|...-
T Consensus 338 aQ~~~CAgC~~~i~~~~~~~~R~C~y~G~y~C~~Ch~~~ 376 (580)
T KOG1829|consen 338 AQNFRCAGCGHTIGPDLEQRPRLCRYLGKYFCDCCHQND 376 (580)
T ss_pred ccCceecccCCCcccccccchhHhhhhhhhhCchhcccC
Confidence 356899999999985332 3568999999998643
No 118
>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=26.72 E-value=33 Score=21.68 Aligned_cols=25 Identities=28% Similarity=0.610 Sum_probs=13.2
Q ss_pred CCcccccCceecccce---EEeCCcccc
Q 029695 7 QQKCKVCEKTVYPVEQ---LSADGVVYH 31 (189)
Q Consensus 7 ~~~C~~C~~~I~~~~~---~~~~g~~~H 31 (189)
...|..|+..|+++.. |..+|+.++
T Consensus 3 ~~~C~Fsg~~I~PG~G~~~Vr~DG~v~~ 30 (71)
T PF01246_consen 3 TEKCSFSGYKIYPGHGKMYVRNDGKVFY 30 (71)
T ss_dssp SEE-TTT-SEE-SSSSEEEE-TTS-EEE
T ss_pred eEEecccCCccCCCCCeEEEecCCCeEE
Confidence 3578889999987753 455555554
No 119
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.63 E-value=61 Score=22.95 Aligned_cols=38 Identities=21% Similarity=0.357 Sum_probs=27.0
Q ss_pred CCCCcCCcccccccc---eeccCccccccccccccCCCCCCC
Q 029695 106 EKCASCSKTVYPLEK---VAVENQAYHKTCFKCSHGGCSISP 144 (189)
Q Consensus 106 ~~C~~C~~~I~~~~~---v~~~g~~~H~~Cf~C~~C~~~l~~ 144 (189)
..|+.|+-+|.+... +..+|..|-+--| |..|++++..
T Consensus 40 ~qcp~csasirgd~~vegvlglg~dye~psf-chncgs~fpw 80 (160)
T COG4306 40 TQCPICSASIRGDYYVEGVLGLGGDYEPPSF-CHNCGSRFPW 80 (160)
T ss_pred hcCCccCCcccccceeeeeeccCCCCCCcch-hhcCCCCCCc
Confidence 579999999987754 3466777776433 6777877664
No 120
>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=26.56 E-value=16 Score=20.58 Aligned_cols=9 Identities=33% Similarity=1.021 Sum_probs=2.9
Q ss_pred ccccCceec
Q 029695 10 CKVCEKTVY 18 (189)
Q Consensus 10 C~~C~~~I~ 18 (189)
|..|++.+.
T Consensus 1 C~~C~~iv~ 9 (43)
T PF08746_consen 1 CEACKEIVT 9 (43)
T ss_dssp -TTT-SB-S
T ss_pred CcccchhHe
Confidence 344555553
No 121
>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=25.96 E-value=42 Score=19.22 Aligned_cols=12 Identities=33% Similarity=0.778 Sum_probs=8.2
Q ss_pred CCCcccccCcee
Q 029695 6 TQQKCKVCEKTV 17 (189)
Q Consensus 6 ~~~~C~~C~~~I 17 (189)
....|..|++.|
T Consensus 10 ~~~~C~~C~~~i 21 (53)
T PF00130_consen 10 KPTYCDVCGKFI 21 (53)
T ss_dssp STEB-TTSSSBE
T ss_pred CCCCCcccCccc
Confidence 456788888888
No 122
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=25.52 E-value=31 Score=26.86 Aligned_cols=31 Identities=19% Similarity=0.246 Sum_probs=23.7
Q ss_pred ccCcccccccccCCCCCccccCCeecchhhH
Q 029695 32 KSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 62 (189)
Q Consensus 32 ~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~ 62 (189)
++=..|..|++++....|...+|..+|..|.
T Consensus 147 p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 147 LDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred cchhhHhcCCCCCCceEEecccCCccccccc
Confidence 4445788899888755566789999999886
No 123
>PHA00626 hypothetical protein
Probab=25.24 E-value=57 Score=19.61 Aligned_cols=39 Identities=10% Similarity=0.308 Sum_probs=23.1
Q ss_pred cccccCc-eecccceEEeCCccccccCcccccccccCCCCCcccc
Q 029695 9 KCKVCEK-TVYPVEQLSADGVVYHKSCFKCSHCKGTLKLSNYSSM 52 (189)
Q Consensus 9 ~C~~C~~-~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~~~~~ 52 (189)
.|+.|+. .|.....+. -|.+=++|..|+-.+....|-++
T Consensus 2 ~CP~CGS~~Ivrcg~cr-----~~snrYkCkdCGY~ft~~~~~~~ 41 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMR-----GWSDDYVCCDCGYNDSKDAFGER 41 (59)
T ss_pred CCCCCCCceeeeeceec-----ccCcceEcCCCCCeechhhhhhc
Confidence 5888887 353222222 24455788888877765555444
No 124
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=25.04 E-value=57 Score=31.37 Aligned_cols=31 Identities=26% Similarity=0.652 Sum_probs=20.2
Q ss_pred CCCcccccCceecccceEEeCCccccccCcccccccccC
Q 029695 6 TQQKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTL 44 (189)
Q Consensus 6 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L 44 (189)
...+|..|+..|- +.++|..| -.|..|+-++
T Consensus 14 ~~~~c~iCGd~vg----~~~~Ge~F----VAC~eC~fpv 44 (1044)
T PLN02915 14 DAKTCRVCGDEVG----VKEDGQPF----VACHVCGFPV 44 (1044)
T ss_pred CcchhhccccccC----cCCCCCEE----EEeccCCCcc
Confidence 3467899988873 45777777 4456665444
No 125
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=24.74 E-value=61 Score=23.74 Aligned_cols=30 Identities=23% Similarity=0.408 Sum_probs=18.3
Q ss_pred cccCCCCCCCCC-eeccCC--ccccHhHHHhhhcC
Q 029695 135 CSHGGCSISPSN-YAALEG--ILYCKHHFSQLFKE 166 (189)
Q Consensus 135 C~~C~~~l~~~~-~~~~~g--~~~C~~c~~~~~~~ 166 (189)
|+.|++.+.+.. -+..+| ...|..|+ .||.
T Consensus 3 CEiCG~~i~~~~~~v~iega~l~vC~~C~--k~G~ 35 (154)
T TIGR00270 3 CEICGRKIKGKGFKIVIEGSEMTVCGECR--KFGK 35 (154)
T ss_pred cccCCCccCCCCeEEEEcCeEEehhhhHH--hcCC
Confidence 777777776652 233444 34578886 5666
No 126
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=24.15 E-value=36 Score=26.94 Aligned_cols=33 Identities=15% Similarity=0.345 Sum_probs=27.2
Q ss_pred ccccCcccccccccCCCCCccccCCeecchhhH
Q 029695 30 YHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHF 62 (189)
Q Consensus 30 ~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~ 62 (189)
|=++=-.|+.|+.+.....|+...|...|..|+
T Consensus 150 ~~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 150 IGPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred CccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 334456799999999888888999999999987
No 127
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=24.12 E-value=43 Score=18.01 Aligned_cols=30 Identities=23% Similarity=0.610 Sum_probs=15.4
Q ss_pred cccccCceeccc-ceEEeCCccccccCccccccccc
Q 029695 9 KCKVCEKTVYPV-EQLSADGVVYHKSCFKCSHCKGT 43 (189)
Q Consensus 9 ~C~~C~~~I~~~-~~~~~~g~~~H~~CF~C~~C~~~ 43 (189)
.|+.|+....-. +.|...+.. ++|..|+..
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~-----vrC~~C~~~ 34 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRK-----VRCPKCGHV 34 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcE-----EECCCCCcE
Confidence 477776664322 234444443 556666543
No 128
>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=23.99 E-value=59 Score=17.77 Aligned_cols=30 Identities=17% Similarity=0.512 Sum_probs=15.1
Q ss_pred CCCCcCCcccccccceeccCccccccccccccCCC
Q 029695 106 EKCASCSKTVYPLEKVAVENQAYHKTCFKCSHGGC 140 (189)
Q Consensus 106 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~ 140 (189)
.+|..|+--|.+--.+...++.| +|..|+.
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w-----~C~~C~~ 32 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTW-----ICNFCGT 32 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEE-----EETTT--
T ss_pred cccCCCCCEECCcceEcCCCCEE-----ECcCCCC
Confidence 67888888877654455555665 6666664
No 129
>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=23.64 E-value=44 Score=29.32 Aligned_cols=40 Identities=20% Similarity=0.457 Sum_probs=28.2
Q ss_pred CCcccccCceecccceEEeCCccccccCcccccccccCCCC
Q 029695 7 QQKCKVCEKTVYPVEQLSADGVVYHKSCFKCSHCKGTLKLS 47 (189)
Q Consensus 7 ~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~ 47 (189)
...|+.|-..+. ..-+...+..=-++||.|-.|...|...
T Consensus 26 ~~yCp~CL~~~p-~~e~~~~~nrC~r~Cf~CP~C~~~L~~~ 65 (483)
T PF05502_consen 26 SYYCPNCLFEVP-SSEARSEKNRCSRNCFDCPICFSPLSVR 65 (483)
T ss_pred eeECccccccCC-hhhheeccceeccccccCCCCCCcceeE
Confidence 346777877773 3334455555667999999999999754
No 130
>PRK14873 primosome assembly protein PriA; Provisional
Probab=23.36 E-value=50 Score=30.23 Aligned_cols=27 Identities=30% Similarity=0.561 Sum_probs=16.2
Q ss_pred cccccccccCCCCCccccCCeecchhhHHh
Q 029695 35 FKCSHCKGTLKLSNYSSMEGVLYCKPHFEQ 64 (189)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~~~ 64 (189)
++|..|+.+|. |...++.+.|..|-..
T Consensus 393 ~~C~~C~~~L~---~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 393 ARCRHCTGPLG---LPSAGGTPRCRWCGRA 419 (665)
T ss_pred eECCCCCCcee---EecCCCeeECCCCcCC
Confidence 34566666654 3344667888888643
No 131
>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=23.20 E-value=45 Score=22.67 Aligned_cols=38 Identities=18% Similarity=0.225 Sum_probs=27.7
Q ss_pred eCCccccccCcccccccccCCCCCccccCCeecchhhHHhhh
Q 029695 25 ADGVVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66 (189)
Q Consensus 25 ~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~ 66 (189)
..+..+...==.|..| .+..|+..++.+.|..|-.+.+
T Consensus 26 ~~dg~~~va~daCeiC----~~~GY~q~g~~lvC~~C~~~~~ 63 (102)
T PF10080_consen 26 KPDGSYRVAFDACEIC----GPKGYYQEGDQLVCKNCGVRFN 63 (102)
T ss_pred CCCCCEEEEEEecccc----CCCceEEECCEEEEecCCCEEe
Confidence 3444555555568888 5677999999999999975543
No 132
>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=23.19 E-value=63 Score=23.25 Aligned_cols=38 Identities=16% Similarity=0.381 Sum_probs=23.0
Q ss_pred CCcccccCceecccceEEe------CCccccccCcccccccccC
Q 029695 7 QQKCKVCEKTVYPVEQLSA------DGVVYHKSCFKCSHCKGTL 44 (189)
Q Consensus 7 ~~~C~~C~~~I~~~~~~~~------~g~~~H~~CF~C~~C~~~L 44 (189)
..+|..|+..+.....-.+ .-...+.....|..|++-.
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 4689999988743322111 1123456677888888743
No 133
>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=23.14 E-value=33 Score=15.46 Aligned_cols=12 Identities=25% Similarity=0.877 Sum_probs=6.1
Q ss_pred cccccccccCCC
Q 029695 35 FKCSHCKGTLKL 46 (189)
Q Consensus 35 F~C~~C~~~L~~ 46 (189)
|.|..|+..+..
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 467777766544
No 134
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=22.74 E-value=34 Score=22.54 Aligned_cols=10 Identities=30% Similarity=0.870 Sum_probs=8.9
Q ss_pred CCCCcCCccc
Q 029695 106 EKCASCSKTV 115 (189)
Q Consensus 106 ~~C~~C~~~I 115 (189)
..|..|++.+
T Consensus 55 ~pC~~C~klL 64 (90)
T PF11571_consen 55 TPCKKCGKLL 64 (90)
T ss_pred chhhHHHhHh
Confidence 7899999888
No 135
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=22.64 E-value=54 Score=17.29 Aligned_cols=23 Identities=26% Similarity=0.414 Sum_probs=12.8
Q ss_pred ccccccccCCCCCccccCCeecchhh
Q 029695 36 KCSHCKGTLKLSNYSSMEGVLYCKPH 61 (189)
Q Consensus 36 ~C~~C~~~L~~~~~~~~~g~~yC~~c 61 (189)
+|..|+..+- +...++..+|..|
T Consensus 5 ~C~~C~~~~i---~~~~~~~~~C~~C 27 (33)
T PF08792_consen 5 KCSKCGGNGI---VNKEDDYEVCIFC 27 (33)
T ss_pred EcCCCCCCeE---EEecCCeEEcccC
Confidence 3556665442 3355666666665
No 136
>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 KOG3476 consensus Microtubule-associated protein CRIPT [Cytoskeleton]
Probab=22.52 E-value=9.6 Score=24.99 Aligned_cols=14 Identities=29% Similarity=0.641 Sum_probs=11.2
Q ss_pred CCCCcCCccccccc
Q 029695 106 EKCASCSKTVYPLE 119 (189)
Q Consensus 106 ~~C~~C~~~I~~~~ 119 (189)
-+|+-|++.|....
T Consensus 80 giCAMCGKki~nTK 93 (100)
T KOG3476|consen 80 GICAMCGKKILNTK 93 (100)
T ss_pred hHHHHhhhHhhccc
Confidence 67999999987653
No 138
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=22.35 E-value=22 Score=21.03 Aligned_cols=26 Identities=19% Similarity=0.530 Sum_probs=14.7
Q ss_pred ccccccccCCCCCccc---cCCeecchhh
Q 029695 36 KCSHCKGTLKLSNYSS---MEGVLYCKPH 61 (189)
Q Consensus 36 ~C~~C~~~L~~~~~~~---~~g~~yC~~c 61 (189)
+|..|+..|..+.+.. .++.++|+.|
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~C 52 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNC 52 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCC
Confidence 5666666666654432 1345666665
No 139
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=21.61 E-value=74 Score=17.41 Aligned_cols=19 Identities=16% Similarity=0.151 Sum_probs=12.5
Q ss_pred CCeeccCCccccHhHHHhh
Q 029695 145 SNYAALEGILYCKHHFSQL 163 (189)
Q Consensus 145 ~~~~~~~g~~~C~~c~~~~ 163 (189)
+.....+-.+.|..|...+
T Consensus 26 g~~~~~Nl~~lC~~Ch~~k 44 (47)
T PF01844_consen 26 GKNDLENLILLCPSCHRKK 44 (47)
T ss_dssp ---STTTEEEEEHHHHHHH
T ss_pred CCCCHHHHHHHhHHHHHHh
Confidence 3456677889999997654
No 140
>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=21.17 E-value=23 Score=24.25 Aligned_cols=19 Identities=21% Similarity=0.518 Sum_probs=11.6
Q ss_pred CCCcccccCceecccceEEe
Q 029695 6 TQQKCKVCEKTVYPVEQLSA 25 (189)
Q Consensus 6 ~~~~C~~C~~~I~~~~~~~~ 25 (189)
+-..|..|+++| +.+.+.+
T Consensus 79 ~yG~C~~Cge~I-~~~RL~a 97 (110)
T TIGR02420 79 EYGYCEECGEEI-GLRRLEA 97 (110)
T ss_pred CCCchhccCCcc-cHHHHhh
Confidence 445777777777 4444443
No 141
>PLN02400 cellulose synthase
Probab=21.15 E-value=67 Score=31.05 Aligned_cols=19 Identities=32% Similarity=0.751 Sum_probs=11.7
Q ss_pred CcccccCceecccceEEeCCccc
Q 029695 8 QKCKVCEKTVYPVEQLSADGVVY 30 (189)
Q Consensus 8 ~~C~~C~~~I~~~~~~~~~g~~~ 30 (189)
.+|..|+..|- +.++|..|
T Consensus 37 qiCqICGD~VG----~t~dGe~F 55 (1085)
T PLN02400 37 QICQICGDDVG----VTETGDVF 55 (1085)
T ss_pred ceeeecccccC----cCCCCCEE
Confidence 37777777662 34566665
No 142
>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=21.04 E-value=74 Score=18.27 Aligned_cols=9 Identities=11% Similarity=0.431 Sum_probs=6.7
Q ss_pred ccHhHHHhh
Q 029695 155 YCKHHFSQL 163 (189)
Q Consensus 155 ~C~~c~~~~ 163 (189)
+|..||...
T Consensus 26 lC~~Cf~~~ 34 (49)
T cd02338 26 LCADCYDSG 34 (49)
T ss_pred cchhHHhCC
Confidence 688888754
No 143
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=20.60 E-value=31 Score=27.24 Aligned_cols=37 Identities=14% Similarity=0.265 Sum_probs=25.0
Q ss_pred CCCCcCCcccccccceeccCccccccccccccCCCCCCCC
Q 029695 106 EKCASCSKTVYPLEKVAVENQAYHKTCFKCSHGGCSISPS 145 (189)
Q Consensus 106 ~~C~~C~~~I~~~~~v~~~g~~~H~~Cf~C~~C~~~l~~~ 145 (189)
+-|.-|++.+.+.. |.+. +--..+|+|..|.+.|-.+
T Consensus 11 pwcwycnrefddek-iliq--hqkakhfkchichkkl~sg 47 (341)
T KOG2893|consen 11 PWCWYCNREFDDEK-ILIQ--HQKAKHFKCHICHKKLFSG 47 (341)
T ss_pred ceeeecccccchhh-hhhh--hhhhccceeeeehhhhccC
Confidence 67999998886643 4332 1223568999999887655
No 144
>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=20.12 E-value=46 Score=16.78 Aligned_cols=12 Identities=25% Similarity=0.811 Sum_probs=3.5
Q ss_pred cccccccccCCC
Q 029695 35 FKCSHCKGTLKL 46 (189)
Q Consensus 35 F~C~~C~~~L~~ 46 (189)
|.|..|++++.+
T Consensus 1 ~~C~~C~~~~~~ 12 (30)
T PF07649_consen 1 FRCDACGKPIDG 12 (30)
T ss_dssp ---TTTS----S
T ss_pred CcCCcCCCcCCC
Confidence 467777776655
No 145
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=20.02 E-value=67 Score=19.50 Aligned_cols=9 Identities=44% Similarity=1.161 Sum_probs=3.7
Q ss_pred cccccCcee
Q 029695 9 KCKVCEKTV 17 (189)
Q Consensus 9 ~C~~C~~~I 17 (189)
.|..|+++|
T Consensus 10 HC~VCg~aI 18 (64)
T COG4068 10 HCVVCGKAI 18 (64)
T ss_pred cccccCCcC
Confidence 344444444
Done!