Query 040947
Match_columns 210
No_of_seqs 240 out of 1490
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 13:24:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040947.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040947hhsearch_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 2.6E-29 5.7E-34 216.2 -0.6 134 8-179 275-411 (468)
2 KOG1701 Focal adhesion adaptor 99.9 1.4E-25 3.1E-30 193.2 0.9 126 3-165 330-466 (468)
3 KOG4577 Transcription factor L 99.9 1.7E-23 3.6E-28 172.4 -2.0 137 6-181 32-171 (383)
4 KOG1700 Regulatory protein MLP 99.8 1.1E-21 2.3E-26 158.5 3.5 180 1-180 1-185 (200)
5 KOG2272 Focal adhesion protein 99.8 3.5E-22 7.6E-27 162.0 -0.3 117 6-160 194-311 (332)
6 KOG2272 Focal adhesion protein 99.8 2.2E-22 4.8E-27 163.2 -2.7 164 6-171 72-263 (332)
7 KOG1044 Actin-binding LIM Zn-f 99.8 2.3E-21 5E-26 172.3 3.0 158 6-201 132-291 (670)
8 KOG1703 Adaptor protein Enigma 99.8 1.6E-20 3.4E-25 170.1 5.0 128 6-170 302-429 (479)
9 KOG1703 Adaptor protein Enigma 99.8 5.4E-20 1.2E-24 166.6 -0.0 117 5-158 361-478 (479)
10 KOG1044 Actin-binding LIM Zn-f 99.7 1.4E-18 3E-23 154.8 5.6 161 8-172 17-201 (670)
11 PF00412 LIM: LIM domain; Int 99.6 2.1E-15 4.5E-20 98.2 5.4 57 106-162 1-58 (58)
12 PF00412 LIM: LIM domain; Int 99.6 2.4E-15 5.2E-20 97.9 4.6 57 10-66 1-58 (58)
13 KOG4577 Transcription factor L 99.0 1.6E-11 3.4E-16 102.0 -3.2 80 102-182 32-112 (383)
14 smart00132 LIM Zinc-binding do 98.7 7.1E-09 1.5E-13 61.3 2.9 37 9-45 1-38 (39)
15 smart00132 LIM Zinc-binding do 98.7 7.6E-09 1.6E-13 61.2 2.4 37 105-141 1-38 (39)
16 KOG1700 Regulatory protein MLP 98.4 5.7E-08 1.2E-12 78.7 0.5 73 3-75 104-176 (200)
17 KOG1702 Nebulin repeat protein 98.0 3.7E-07 8E-12 72.9 -2.7 61 104-164 5-65 (264)
18 KOG1702 Nebulin repeat protein 97.9 9.3E-07 2E-11 70.6 -2.4 59 8-66 5-63 (264)
19 KOG0490 Transcription factor, 97.8 2.7E-06 5.9E-11 69.8 -1.9 111 13-161 2-119 (235)
20 KOG0490 Transcription factor, 91.3 0.052 1.1E-06 44.3 -0.4 58 109-167 2-63 (235)
21 PF14446 Prok-RING_1: Prokaryo 88.2 0.32 6.8E-06 30.9 1.5 36 104-139 6-50 (54)
22 PF09943 DUF2175: Uncharacteri 86.7 0.27 5.9E-06 35.3 0.7 30 105-134 4-34 (101)
23 PF14446 Prok-RING_1: Prokaryo 85.0 0.61 1.3E-05 29.6 1.5 29 7-35 5-36 (54)
24 PF14835 zf-RING_6: zf-RING of 83.6 1 2.2E-05 29.7 2.2 33 35-67 8-40 (65)
25 smart00504 Ubox Modified RING 83.6 1.6 3.5E-05 27.8 3.3 32 35-67 2-33 (63)
26 PF10367 Vps39_2: Vacuolar sor 82.2 1.1 2.4E-05 31.8 2.2 30 7-36 78-108 (109)
27 PF10367 Vps39_2: Vacuolar sor 81.9 0.94 2E-05 32.2 1.8 29 104-132 79-108 (109)
28 PF14471 DUF4428: Domain of un 81.5 1.3 2.8E-05 27.8 2.0 29 132-161 1-30 (51)
29 PF01258 zf-dskA_traR: Prokary 79.7 0.47 1E-05 27.3 -0.4 28 133-160 6-33 (36)
30 PF08394 Arc_trans_TRASH: Arch 78.0 1.2 2.6E-05 26.0 1.0 28 10-37 1-29 (37)
31 PF11781 RRN7: RNA polymerase 75.5 1.8 3.9E-05 25.1 1.3 25 35-63 9-33 (36)
32 PF10235 Cript: Microtubule-as 75.4 1.6 3.4E-05 30.8 1.2 30 30-65 40-69 (90)
33 COG2191 Formylmethanofuran deh 75.0 1.1 2.3E-05 36.3 0.3 31 131-161 173-203 (206)
34 PF08394 Arc_trans_TRASH: Arch 75.0 1.7 3.6E-05 25.4 1.1 28 106-133 1-29 (37)
35 PF13920 zf-C3HC4_3: Zinc fing 74.6 4.9 0.00011 24.5 3.3 32 35-67 3-35 (50)
36 KOG0320 Predicted E3 ubiquitin 74.2 2 4.3E-05 34.1 1.6 37 31-67 128-165 (187)
37 PRK14890 putative Zn-ribbon RN 73.8 2.3 5E-05 27.5 1.6 31 5-44 5-35 (59)
38 PF10083 DUF2321: Uncharacteri 73.5 2.2 4.8E-05 33.1 1.7 37 104-141 40-79 (158)
39 COG4847 Uncharacterized protei 72.6 1.7 3.6E-05 30.8 0.8 32 104-135 7-39 (103)
40 PF13240 zinc_ribbon_2: zinc-r 72.4 1.9 4.2E-05 22.3 0.8 9 10-18 2-10 (23)
41 KOG0978 E3 ubiquitin ligase in 69.6 1.5 3.2E-05 41.9 -0.1 35 33-68 642-676 (698)
42 PF02069 Metallothio_Pro: Prok 66.6 4 8.7E-05 25.7 1.5 27 133-159 10-37 (52)
43 PF07191 zinc-ribbons_6: zinc- 64.3 4 8.8E-05 27.3 1.2 33 104-143 31-63 (70)
44 COG1645 Uncharacterized Zn-fin 62.2 4 8.7E-05 30.8 1.0 22 133-159 31-52 (131)
45 PRK00807 50S ribosomal protein 61.5 5.3 0.00011 25.1 1.4 27 8-34 2-31 (52)
46 COG2191 Formylmethanofuran deh 61.1 3.4 7.3E-05 33.5 0.5 31 35-65 173-203 (206)
47 PF13923 zf-C3HC4_2: Zinc fing 61.1 8.6 0.00019 22.1 2.2 31 37-67 1-31 (39)
48 PF00645 zf-PARP: Poly(ADP-rib 59.3 5.1 0.00011 27.2 1.1 14 104-117 8-21 (82)
49 cd00162 RING RING-finger (Real 58.6 8.8 0.00019 21.8 2.0 31 37-67 2-32 (45)
50 PLN03208 E3 ubiquitin-protein 58.4 16 0.00034 29.5 3.9 33 33-66 17-49 (193)
51 PF10886 DUF2685: Protein of u 58.2 6 0.00013 25.1 1.2 25 104-128 2-26 (54)
52 PF06677 Auto_anti-p27: Sjogre 56.3 6.2 0.00013 23.6 1.0 11 104-114 18-28 (41)
53 PF13248 zf-ribbon_3: zinc-rib 54.9 7.5 0.00016 20.5 1.1 11 104-114 3-13 (26)
54 PF14634 zf-RING_5: zinc-RING 53.0 10 0.00022 22.5 1.6 30 37-66 2-33 (44)
55 COG1645 Uncharacterized Zn-fin 51.5 9.4 0.0002 28.8 1.5 22 37-63 31-52 (131)
56 COG2888 Predicted Zn-ribbon RN 51.0 13 0.00029 24.0 1.9 31 6-45 8-38 (61)
57 cd02249 ZZ Zinc finger, ZZ typ 50.9 13 0.00028 22.4 1.8 11 151-161 23-33 (46)
58 PF07754 DUF1610: Domain of un 50.9 8.7 0.00019 20.2 0.9 9 10-18 1-9 (24)
59 PF06906 DUF1272: Protein of u 48.5 17 0.00038 23.2 2.1 32 36-67 7-41 (57)
60 PF09943 DUF2175: Uncharacteri 47.3 14 0.00031 26.5 1.8 40 131-170 3-43 (101)
61 KOG1813 Predicted E3 ubiquitin 46.0 11 0.00025 32.3 1.3 32 35-67 242-273 (313)
62 smart00291 ZnF_ZZ Zinc-binding 45.2 20 0.00044 21.3 2.1 8 153-160 29-36 (44)
63 PF06689 zf-C4_ClpX: ClpX C4-t 44.9 39 0.00085 19.9 3.2 30 132-161 3-34 (41)
64 PF13639 zf-RING_2: Ring finge 44.5 7.3 0.00016 23.0 -0.0 9 106-114 3-11 (44)
65 PRK00420 hypothetical protein; 44.4 12 0.00025 27.6 1.0 11 104-114 24-34 (112)
66 COG5152 Uncharacterized conser 43.9 8.1 0.00018 31.3 0.2 33 34-67 196-228 (259)
67 PF00097 zf-C3HC4: Zinc finger 40.1 33 0.00072 19.5 2.4 31 37-67 1-31 (41)
68 PF06750 DiS_P_DiS: Bacterial 38.5 14 0.0003 26.0 0.6 42 3-46 29-70 (92)
69 PRK14891 50S ribosomal protein 37.5 19 0.00041 27.1 1.2 24 8-31 5-31 (131)
70 PF07503 zf-HYPF: HypF finger; 37.5 8.2 0.00018 22.2 -0.5 31 10-45 2-32 (35)
71 cd02336 ZZ_RSC8 Zinc finger, Z 37.3 30 0.00064 21.0 1.9 30 132-161 2-33 (45)
72 KOG4443 Putative transcription 37.0 18 0.00039 34.3 1.3 22 121-142 106-127 (694)
73 PF04810 zf-Sec23_Sec24: Sec23 36.5 26 0.00056 20.5 1.5 30 104-138 3-32 (40)
74 KOG3002 Zn finger protein [Gen 36.4 26 0.00056 30.2 2.1 34 33-66 47-80 (299)
75 cd00472 Ribosomal_L24e_L24 Rib 36.1 23 0.0005 22.4 1.3 24 8-31 4-30 (54)
76 PRK00398 rpoP DNA-directed RNA 35.9 16 0.00035 21.9 0.6 28 9-45 5-32 (46)
77 COG1813 Predicted transcriptio 35.9 79 0.0017 24.9 4.5 35 133-169 6-42 (165)
78 PF13834 DUF4193: Domain of un 35.8 13 0.00028 26.6 0.1 30 32-61 68-98 (99)
79 PF04564 U-box: U-box domain; 34.5 57 0.0012 21.5 3.2 34 33-67 3-36 (73)
80 smart00531 TFIIE Transcription 33.6 11 0.00025 28.7 -0.4 34 9-45 101-134 (147)
81 PRK06266 transcription initiat 33.2 15 0.00033 29.1 0.2 30 9-46 119-148 (178)
82 PF06827 zf-FPG_IleRS: Zinc fi 32.5 15 0.00032 19.9 -0.0 11 104-114 2-12 (30)
83 TIGR00570 cdk7 CDK-activating 32.5 41 0.00089 29.2 2.7 15 53-67 26-40 (309)
84 TIGR00270 conserved hypothetic 32.4 1E+02 0.0022 23.8 4.7 31 133-165 3-36 (154)
85 PLN03208 E3 ubiquitin-protein 32.4 75 0.0016 25.6 4.0 27 104-131 19-45 (193)
86 PF00569 ZZ: Zinc finger, ZZ t 32.3 42 0.0009 20.2 2.0 8 153-160 30-37 (46)
87 COG0068 HypF Hydrogenase matur 31.9 19 0.00042 34.6 0.6 83 7-140 101-183 (750)
88 PF04502 DUF572: Family of unk 31.8 24 0.00051 30.7 1.1 38 8-45 41-88 (324)
89 PF01246 Ribosomal_L24e: Ribos 31.0 24 0.00053 23.7 0.8 24 8-31 4-30 (71)
90 KOG2932 E3 ubiquitin ligase in 31.0 13 0.00029 32.1 -0.5 29 35-63 91-119 (389)
91 cd02341 ZZ_ZZZ3 Zinc finger, Z 30.7 47 0.001 20.4 2.0 9 153-161 28-36 (48)
92 COG2075 RPL24A Ribosomal prote 30.7 28 0.0006 23.0 1.1 13 8-20 4-16 (66)
93 PRK14559 putative protein seri 30.7 32 0.00068 33.0 1.9 10 104-113 42-51 (645)
94 KOG4739 Uncharacterized protei 30.7 31 0.00067 28.6 1.6 28 40-67 9-37 (233)
95 TIGR02098 MJ0042_CXXC MJ0042 f 29.8 18 0.00039 20.6 0.1 31 9-44 4-35 (38)
96 PF02591 DUF164: Putative zinc 29.7 10 0.00022 23.9 -1.2 26 36-61 24-52 (56)
97 PRK09710 lar restriction allev 29.2 48 0.001 21.8 1.9 33 5-43 4-36 (64)
98 PF09723 Zn-ribbon_8: Zinc rib 28.8 15 0.00032 21.8 -0.4 9 105-113 7-15 (42)
99 cd02340 ZZ_NBR1_like Zinc fing 28.6 48 0.001 19.7 1.8 9 153-161 25-33 (43)
100 PF08271 TF_Zn_Ribbon: TFIIB z 27.6 34 0.00074 20.2 1.0 12 35-46 20-31 (43)
101 PF00130 C1_1: Phorbol esters/ 27.4 41 0.0009 20.4 1.4 12 6-17 10-21 (53)
102 PRK04023 DNA polymerase II lar 27.1 61 0.0013 32.7 3.1 16 104-119 664-679 (1121)
103 PF00628 PHD: PHD-finger; Int 27.1 39 0.00084 20.3 1.2 28 9-36 1-30 (51)
104 PF12674 Zn_ribbon_2: Putative 26.5 34 0.00073 23.5 1.0 28 133-160 3-35 (81)
105 COG4357 Zinc finger domain con 25.8 7.4 0.00016 27.7 -2.4 50 10-59 38-87 (105)
106 PLN02195 cellulose synthase A 25.4 58 0.0013 32.7 2.7 38 5-63 4-41 (977)
107 smart00659 RPOLCX RNA polymera 24.9 33 0.00071 20.7 0.6 9 105-113 4-12 (44)
108 PF08746 zf-RING-like: RING-li 24.7 19 0.00041 21.5 -0.5 26 106-131 1-28 (43)
109 TIGR02605 CxxC_CxxC_SSSS putat 24.5 22 0.00047 21.8 -0.3 8 105-112 7-14 (52)
110 PRK14714 DNA polymerase II lar 24.1 59 0.0013 33.6 2.5 10 105-114 711-720 (1337)
111 PRK12495 hypothetical protein; 23.9 45 0.00097 27.5 1.4 27 33-64 41-67 (226)
112 COG1381 RecO Recombinational D 23.7 40 0.00088 28.1 1.1 30 129-158 153-182 (251)
113 TIGR00373 conserved hypothetic 23.7 22 0.00047 27.6 -0.5 30 9-46 111-140 (158)
114 smart00834 CxxC_CXXC_SSSS Puta 23.3 22 0.00048 20.3 -0.4 10 105-114 7-16 (41)
115 COG4306 Uncharacterized protei 23.3 59 0.0013 24.4 1.8 37 104-141 40-79 (160)
116 PF03604 DNA_RNApol_7kD: DNA d 23.1 45 0.00097 18.7 0.9 10 9-18 2-11 (32)
117 COG0266 Nei Formamidopyrimidin 23.1 42 0.00091 28.6 1.1 26 104-130 246-271 (273)
118 PF10122 Mu-like_Com: Mu-like 23.1 24 0.00051 22.1 -0.3 26 35-62 5-31 (51)
119 PF01286 XPA_N: XPA protein N- 23.0 38 0.00083 19.3 0.6 11 8-18 4-14 (34)
120 PF13717 zinc_ribbon_4: zinc-r 22.9 35 0.00076 19.5 0.4 30 9-43 4-34 (36)
121 PF14569 zf-UDP: Zinc-binding 22.8 1.3E+02 0.0027 20.7 3.1 38 104-162 10-47 (80)
122 PHA00080 DksA-like zinc finger 22.7 29 0.00063 23.3 0.1 11 104-114 32-42 (72)
123 KOG3579 Predicted E3 ubiquitin 22.6 40 0.00086 29.0 0.8 33 35-67 269-304 (352)
124 COG4068 Uncharacterized protei 22.5 32 0.0007 22.2 0.2 15 104-118 9-23 (64)
125 PF09845 DUF2072: Zn-ribbon co 22.4 80 0.0017 23.8 2.3 28 132-162 3-30 (131)
126 TIGR00599 rad18 DNA repair pro 22.3 60 0.0013 29.2 2.0 33 34-67 26-58 (397)
127 KOG2462 C2H2-type Zn-finger pr 22.3 45 0.00098 28.4 1.1 18 31-48 127-144 (279)
128 PLN02436 cellulose synthase A 22.0 70 0.0015 32.5 2.5 55 4-112 33-87 (1094)
129 PLN02638 cellulose synthase A 21.9 72 0.0016 32.4 2.6 55 4-112 14-68 (1079)
130 PF01844 HNH: HNH endonuclease 21.9 69 0.0015 18.6 1.6 20 142-161 25-44 (47)
131 smart00249 PHD PHD zinc finger 21.9 59 0.0013 18.4 1.3 27 9-35 1-29 (47)
132 PF00096 zf-C2H2: Zinc finger, 21.8 36 0.00077 16.7 0.3 12 131-142 1-12 (23)
133 PLN02189 cellulose synthase 21.7 72 0.0016 32.3 2.5 55 4-112 31-85 (1040)
134 PHA02929 N1R/p28-like protein; 21.7 52 0.0011 27.4 1.4 38 104-141 175-227 (238)
135 cd02338 ZZ_PCMF_like Zinc fing 21.4 75 0.0016 19.4 1.7 11 152-162 25-35 (49)
136 PF14255 Cys_rich_CPXG: Cystei 21.3 46 0.001 20.9 0.8 30 105-134 2-31 (52)
137 COG1381 RecO Recombinational D 21.2 46 0.001 27.7 1.0 33 30-62 150-182 (251)
138 KOG2186 Cell growth-regulating 21.1 21 0.00046 30.0 -1.0 41 9-50 5-45 (276)
139 PF04570 DUF581: Protein of un 20.6 59 0.0013 20.9 1.1 28 36-63 18-48 (58)
140 KOG1829 Uncharacterized conser 20.5 38 0.00082 32.0 0.3 33 32-64 338-375 (580)
141 cd02345 ZZ_dah Zinc finger, ZZ 20.4 1.1E+02 0.0023 18.7 2.3 9 153-161 26-34 (49)
No 1
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.95 E-value=2.6e-29 Score=216.16 Aligned_cols=134 Identities=22% Similarity=0.518 Sum_probs=122.7
Q ss_pred CCcccCCcceecce-eEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCCCCC
Q 040947 8 DKCKACDKTVYVVD-MLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSCS 86 (210)
Q Consensus 8 ~~C~~C~~~I~~~~-~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~ 86 (210)
.+|.+|+|.|+... .+.||++.||..||+|..|++.|.++.||.+++++||+.||+..+
T Consensus 275 ~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl-------------------- 334 (468)
T KOG1701|consen 275 GICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL-------------------- 334 (468)
T ss_pred hhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH--------------------
Confidence 48999999999555 389999999999999999999999999999999999999999876
Q ss_pred CCCCCCCCcccccCCCCCccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeec-CCeeecHhHHHhhhcCC
Q 040947 87 NQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAAL-DGVLYCKHHFAQLFMEK 165 (210)
Q Consensus 87 ~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~-dg~~yC~~c~~~~f~~k 165 (210)
.+|..|+++|+ +.++.++|+.||+.||+|..|++.|++..|++. ++++||..||.++|++|
T Consensus 335 -----------------ekC~~Cg~~I~-d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPr 396 (468)
T KOG1701|consen 335 -----------------EKCNKCGEPIM-DRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPR 396 (468)
T ss_pred -----------------HHHhhhhhHHH-HHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcc
Confidence 59999999997 667899999999999999999999999999876 79999999999999999
Q ss_pred CC-cccccccccccc
Q 040947 166 GN-YSHVLKAANHKR 179 (210)
Q Consensus 166 ~~-~~~~~~~~~~~~ 179 (210)
|. ++..+.+...+.
T Consensus 397 Cs~C~~PI~P~~G~~ 411 (468)
T KOG1701|consen 397 CSVCGNPILPRDGKD 411 (468)
T ss_pred hhhccCCccCCCCCc
Confidence 96 777777776654
No 2
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.90 E-value=1.4e-25 Score=193.18 Aligned_cols=126 Identities=28% Similarity=0.664 Sum_probs=113.1
Q ss_pred CCCCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeec-cCCeeeccchHHHhhhccCCCCCCccCCCC
Q 040947 3 FTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSS-MDGVLYCKPHFEQLFKESGNFSKNFQTGKN 81 (210)
Q Consensus 3 ~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~-~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~ 81 (210)
|..++.+|..|++.|+ +.+|.|+|+.||+.||+|..|++.|++..|.+ .++++||.+||+++|+
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 4556789999999997 66799999999999999999999999999985 4899999999999999
Q ss_pred CCCCCCCCCCCCCcccccCCCCCccccccceeecCc------eeEecCccccccccccCCCCCcCC----CCCeeecCCe
Q 040947 82 PSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLE------KVTMEGDCFHKTCFRCAHGGCPLT----HSSYAALDGV 151 (210)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e------~v~~~g~~~H~~CF~C~~C~~~l~----~~~f~~~dg~ 151 (210)
++|+.|+++|++.+ +|++|++.||.+|++|+.|+.+|. +...+-.||.
T Consensus 395 ----------------------PrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~H 452 (468)
T KOG1701|consen 395 ----------------------PRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGH 452 (468)
T ss_pred ----------------------cchhhccCCccCCCCCcceEEEEEccccccccceehhhcCccccccCCCCcceeccCc
Confidence 89999999999743 378999999999999999999997 3357889999
Q ss_pred eecHhHHHhhhcCC
Q 040947 152 LYCKHHFAQLFMEK 165 (210)
Q Consensus 152 ~yC~~c~~~~f~~k 165 (210)
++|+.|..+++...
T Consensus 453 llCk~Ch~~Rl~~~ 466 (468)
T KOG1701|consen 453 LLCKTCHLKRLQAG 466 (468)
T ss_pred eeechhhhhhhccc
Confidence 99999999887654
No 3
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.86 E-value=1.7e-23 Score=172.38 Aligned_cols=137 Identities=28% Similarity=0.545 Sum_probs=118.0
Q ss_pred CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCCCC
Q 040947 6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSC 85 (210)
Q Consensus 6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~ 85 (210)
..++|+.|.+.|.+..++.++++.||..|++|+.|...|.. ..+.++|.+||+.+|.++|+
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfG------------------ 92 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFG------------------ 92 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhC------------------
Confidence 57899999999986667899999999999999999999998 56679999999999999998
Q ss_pred CCCCCCCCCcccccCCCCCccccccceeecCcee-EecCccccccccccCCCCCcCC-CCCeee-cCCeeecHhHHHhhh
Q 040947 86 SNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKV-TMEGDCFHKTCFRCAHGGCPLT-HSSYAA-LDGVLYCKHHFAQLF 162 (210)
Q Consensus 86 ~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v-~~~g~~~H~~CF~C~~C~~~l~-~~~f~~-~dg~~yC~~c~~~~f 162 (210)
.+|..|...|.+.++| .+.+.+||.+||.|..|+++|. +..|++ .|+++.|+.+|+..-
T Consensus 93 ------------------TKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak 154 (383)
T KOG4577|consen 93 ------------------TKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAK 154 (383)
T ss_pred ------------------CcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHH
Confidence 7999999999988887 5889999999999999999997 556765 489999999999876
Q ss_pred cCCCCcccccccccccccC
Q 040947 163 MEKGNYSHVLKAANHKRTA 181 (210)
Q Consensus 163 ~~k~~~~~~~~~~~~~~~~ 181 (210)
...++ ...+.+..||+.
T Consensus 155 ~k~~~--~l~gd~~nKRPR 171 (383)
T KOG4577|consen 155 QKHCN--ELEGDASNKRPR 171 (383)
T ss_pred hcccc--ccccccccCCCc
Confidence 65554 444555555544
No 4
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.84 E-value=1.1e-21 Score=158.54 Aligned_cols=180 Identities=50% Similarity=0.905 Sum_probs=147.7
Q ss_pred CCCCCCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCC-CCCCccCC
Q 040947 1 MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGN-FSKNFQTG 79 (210)
Q Consensus 1 ~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~-~~~~~~~~ 79 (210)
|++++....|..|++.|+..+.+...|..||+.||+|..|.+.|....+.++++.+||+.||...+++++. +...|+..
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 78899999999999999988888899999999999999999999999999999999999988888887653 44443321
Q ss_pred CC-CCCCC-CC--CCCCCCcccccCCCCCccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecH
Q 040947 80 KN-PSSCS-NQ--NRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCK 155 (210)
Q Consensus 80 ~~-~~~~~-~~--~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~ 155 (210)
.. ..+.- .. ..........+.|+...|.+|.+.+++.+.|...+..||+.||+|+.|+..|....+...+|.+||.
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 11 11111 11 1122245566788889999999999999999999999999999999999999999999999999999
Q ss_pred hHHHhhhcCCCCccccccccccccc
Q 040947 156 HHFAQLFMEKGNYSHVLKAANHKRT 180 (210)
Q Consensus 156 ~c~~~~f~~k~~~~~~~~~~~~~~~ 180 (210)
.++-++|-.+..+.++...+..++.
T Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~ 185 (200)
T KOG1700|consen 161 HHFAQLFKGKGNYNEGFGARENKEA 185 (200)
T ss_pred hhhheeecCCCcccccchhhhhhhh
Confidence 9999988888888877666655553
No 5
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.83 E-value=3.5e-22 Score=161.99 Aligned_cols=117 Identities=22% Similarity=0.540 Sum_probs=109.6
Q ss_pred CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCCCC
Q 040947 6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSC 85 (210)
Q Consensus 6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~ 85 (210)
+.|+|..|.++|. ..+|.++|+.||.+.|+|+.|-+++-+-..|++.|.+||+.+|.++|+
T Consensus 194 gipiCgaC~rpIe-ervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG------------------ 254 (332)
T KOG2272|consen 194 GIPICGACRRPIE-ERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFG------------------ 254 (332)
T ss_pred CCcccccccCchH-HHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhh------------------
Confidence 5789999999996 667899999999999999999999998899999999999999999998
Q ss_pred CCCCCCCCCcccccCCCCCccccccceeecCceeEecCccccccccccCCCCCcCCC-CCeeecCCeeecHhHHHh
Q 040947 86 SNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTH-SSYAALDGVLYCKHHFAQ 160 (210)
Q Consensus 86 ~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~-~~f~~~dg~~yC~~c~~~ 160 (210)
..|..|+.+|- +++|.++++.|.++||.|+.|.+.|.. ..|++.|-.|.|+.||.+
T Consensus 255 ------------------~~CF~C~~~i~-G~vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~r 311 (332)
T KOG2272|consen 255 ------------------NLCFICNRVIG-GDVVSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDR 311 (332)
T ss_pred ------------------hhheecCCccC-ccHHHHhhhhhccccccccccccccccccceeeeccchHHHHHHhh
Confidence 79999999996 889999999999999999999999984 478999999999999984
No 6
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.83 E-value=2.2e-22 Score=163.17 Aligned_cols=164 Identities=19% Similarity=0.414 Sum_probs=123.8
Q ss_pred CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhc-cCCCC----C------
Q 040947 6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE-SGNFS----K------ 74 (210)
Q Consensus 6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~-~~~~~----~------ 74 (210)
.+|.|+.|++.|. +.+|.+++.+||+.||+|..|++.|.+..|+-..|+.+|..|.++.-+. .|-|. .
T Consensus 72 faPcC~kC~EFii-GrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~ 150 (332)
T KOG2272|consen 72 FAPCCGKCGEFII-GRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQ 150 (332)
T ss_pred hchhhcccccchh-hHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccc
Confidence 4689999999998 9999999999999999999999999999999999999999999874332 12121 0
Q ss_pred --CccCCCCCC---CCCCCCCCCCCcc-----ccc------CCCCCccccccceeecCceeEecCccccccccccCCCCC
Q 040947 75 --NFQTGKNPS---SCSNQNRTPSKLS-----SLF------SGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGC 138 (210)
Q Consensus 75 --~~~~~~~~~---~~~~~~~~~~~~~-----~~~------~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~ 138 (210)
.|++....+ .|.++...-...+ .++ .-+.|+|..|.+||. +..|.++|+.||.+.|+|+.|.+
T Consensus 151 ~l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIe-ervi~amgKhWHveHFvCa~Cek 229 (332)
T KOG2272|consen 151 PLTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIE-ERVIFAMGKHWHVEHFVCAKCEK 229 (332)
T ss_pred cccccCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCchH-HHHHHHhccccchhheeehhcCC
Confidence 112221111 2222211111111 111 124589999999996 66689999999999999999999
Q ss_pred cCCCCCeeecCCeeecHhHHHhhhcCCCC-cccc
Q 040947 139 PLTHSSYAALDGVLYCKHHFAQLFMEKGN-YSHV 171 (210)
Q Consensus 139 ~l~~~~f~~~dg~~yC~~c~~~~f~~k~~-~~~~ 171 (210)
++-+-+.+++.|.+||+.+|.++||--+. ++++
T Consensus 230 PFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~ 263 (332)
T KOG2272|consen 230 PFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRV 263 (332)
T ss_pred cccchhhhhhcCchhHHHHHHHHhhhhheecCCc
Confidence 99998999999999999999999999886 4443
No 7
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.82 E-value=2.3e-21 Score=172.35 Aligned_cols=158 Identities=26% Similarity=0.402 Sum_probs=134.1
Q ss_pred CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCCCC
Q 040947 6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSC 85 (210)
Q Consensus 6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~ 85 (210)
+...|++|++.|..+..+.|+++.||..||+|..|...|.+ .|..++|.+||+.||++.|+
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 45789999999998999999999999999999999999987 78899999999999999998
Q ss_pred CCCCCCCCCcccccCCCCCccccccceeecCceeEecCccccccccccCCCCCcCC-CCCeeecCCeeecHhHHHhhhcC
Q 040947 86 SNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLT-HSSYAALDGVLYCKHHFAQLFME 164 (210)
Q Consensus 86 ~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~-~~~f~~~dg~~yC~~c~~~~f~~ 164 (210)
.+|..|.+.|. +.++.+.|++||+.|-+|+.|+..+. ++..++....+|-..|-...-.+
T Consensus 193 ------------------vkc~~c~~fis-gkvLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~qa~~tE 253 (670)
T KOG1044|consen 193 ------------------VKCEECEKFIS-GKVLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCKQATKTE 253 (670)
T ss_pred ------------------eehHHhhhhhh-hhhhhccCcccCcchhhhhhhccccccchheeeccccccCCccccccchh
Confidence 89999999997 88899999999999999999999997 66788888999988887654444
Q ss_pred CCCc-ccccccccccccCCCCCCCCCccCCCCCCCCCc
Q 040947 165 KGNY-SHVLKAANHKRTASSSSTSPAEQIENKPDDESG 201 (210)
Q Consensus 165 k~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 (210)
+-.. ..........++.+++..+|...|-+++|+|-.
T Consensus 254 ~i~~~~rtst~Si~~~~~~Ss~Gsp~~ti~akvdneiL 291 (670)
T KOG1044|consen 254 EILKPGRTSTESIYSRPGSSTPGSPGHTIYAKVDNEIL 291 (670)
T ss_pred hcccCCCCCcccccCCCCCCCCCCCCcEehhhhcchhh
Confidence 4332 223333344556777788999999999888754
No 8
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.81 E-value=1.6e-20 Score=170.11 Aligned_cols=128 Identities=30% Similarity=0.649 Sum_probs=119.3
Q ss_pred CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCCCC
Q 040947 6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSC 85 (210)
Q Consensus 6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~ 85 (210)
..+.|..|++.|....++.++++.||+.+|.|..|...|....|...+|.+||..||.+.+.
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 45899999999984488999999999999999999999999899999999999999999987
Q ss_pred CCCCCCCCCcccccCCCCCccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCC
Q 040947 86 SNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEK 165 (210)
Q Consensus 86 ~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k 165 (210)
+.|.+|+++|. ++.|.++++.||++||+|..|++.|....|++.+|.+||+.||.++|+++
T Consensus 364 ------------------p~C~~C~~~i~-~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~ 424 (479)
T KOG1703|consen 364 ------------------PNCKRCLLPIL-EEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTK 424 (479)
T ss_pred ------------------ccccccCCchH-HhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhcccc
Confidence 89999999998 88899999999999999999999999999999999999999999999988
Q ss_pred CCccc
Q 040947 166 GNYSH 170 (210)
Q Consensus 166 ~~~~~ 170 (210)
+.++.
T Consensus 425 ~~~~~ 429 (479)
T KOG1703|consen 425 CDYCK 429 (479)
T ss_pred chhcc
Confidence 86553
No 9
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.76 E-value=5.4e-20 Score=166.64 Aligned_cols=117 Identities=31% Similarity=0.631 Sum_probs=108.2
Q ss_pred CCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCCC
Q 040947 5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSS 84 (210)
Q Consensus 5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~ 84 (210)
-..+.|.+|+++|. ++.|.++++.||++||.|..|++.|.+..|+.+++.+||+.||.+++.
T Consensus 361 ~~~p~C~~C~~~i~-~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~----------------- 422 (479)
T KOG1703|consen 361 PFRPNCKRCLLPIL-EEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFT----------------- 422 (479)
T ss_pred hhCccccccCCchH-HhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhcc-----------------
Confidence 35789999999998 888989999999999999999999999999999999999999999987
Q ss_pred CCCCCCCCCCcccccCCCCCccccccceeecCc-eeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHH
Q 040947 85 CSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLE-KVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHF 158 (210)
Q Consensus 85 ~~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e-~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~ 158 (210)
.+|..|.++|.... .|.+++..||..||+|+.|...|.++.|+...++|+|..|+
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 68999999986544 48999999999999999999999999999999999999876
No 10
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.74 E-value=1.4e-18 Score=154.82 Aligned_cols=161 Identities=21% Similarity=0.439 Sum_probs=114.2
Q ss_pred CCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCC-eeeccchHHHhh------------hccCCC--
Q 040947 8 DKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDG-VLYCKPHFEQLF------------KESGNF-- 72 (210)
Q Consensus 8 ~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g-~~yC~~cy~~~~------------~~~~~~-- 72 (210)
-.|.+|.+.-. ++++.+.+++||..||.|..|+..|..+.|+.+++ ++|+.....+.. .+++.+
T Consensus 17 i~c~~c~~kc~-gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~~~~gevvsa~gktyh~~cf~cs 95 (670)
T KOG1044|consen 17 IKCDKCRKKCS-GEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRAFVEGEVVSTLGKTYHPKCFSCS 95 (670)
T ss_pred eehhhhCCccc-cceeEeeccccceeeeeccccCCCcccccceecccceeecccchhhhccceeEecccceeccccceec
Confidence 57999999998 99999999999999999999999999998887744 677763222111 011100
Q ss_pred --CCCccCCCC------CCCCCCC-CCCCCCcccccCCCCCccccccceeecCceeEecCccccccccccCCCCCcCCCC
Q 040947 73 --SKNFQTGKN------PSSCSNQ-NRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHS 143 (210)
Q Consensus 73 --~~~~~~~~~------~~~~~~~-~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~ 143 (210)
..-|..+.. ...|..+ ..++.. ....-+...|++|++.|..++.+.++++.||..||+|..|...|.++
T Consensus 96 ~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~--p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~ge 173 (670)
T KOG1044|consen 96 TCKSPFKSGDKVTFSGKECLCQTCSQPMPVS--PAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNGE 173 (670)
T ss_pred ccCCCCCCCCeeeecchhhhhhhhcCcccCC--cccccCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccce
Confidence 000111000 0011111 011111 11111336899999999989999999999999999999999999874
Q ss_pred CeeecCCeeecHhHHHhhhcCCCCccccc
Q 040947 144 SYAALDGVLYCKHHFAQLFMEKGNYSHVL 172 (210)
Q Consensus 144 ~f~~~dg~~yC~~c~~~~f~~k~~~~~~~ 172 (210)
|+..||.|||+.||.+.|+.||..++-+
T Consensus 174 -y~skdg~pyce~dy~~~fgvkc~~c~~f 201 (670)
T KOG1044|consen 174 -YMSKDGVPYCEKDYQAKFGVKCEECEKF 201 (670)
T ss_pred -eeccCCCcchhhhhhhhcCeehHHhhhh
Confidence 8999999999999999999999755433
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=99.59 E-value=2.1e-15 Score=98.16 Aligned_cols=57 Identities=37% Similarity=0.838 Sum_probs=53.0
Q ss_pred cccccceeecCcee-EecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhh
Q 040947 106 CAACEKTVYPLEKV-TMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLF 162 (210)
Q Consensus 106 C~~C~~~I~~~e~v-~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f 162 (210)
|.+|+++|.+.+.+ .++|+.||++||+|..|+++|..+.|+..+|++||+.||.++|
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 78999999977775 6999999999999999999999888999999999999999986
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=99.57 E-value=2.4e-15 Score=97.87 Aligned_cols=57 Identities=33% Similarity=0.805 Sum_probs=53.1
Q ss_pred cccCCcceecceeE-eeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhh
Q 040947 10 CKACDKTVYVVDML-SLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66 (210)
Q Consensus 10 C~~C~~~I~~~~~v-~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~ 66 (210)
|.+|+++|.+.+.+ .++|+.||++||+|..|+++|.+..|+..+|++||+.||.++|
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 88999999977765 7999999999999999999999988999999999999999876
No 13
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.00 E-value=1.6e-11 Score=101.96 Aligned_cols=80 Identities=20% Similarity=0.418 Sum_probs=69.5
Q ss_pred CCCccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCC-ccccccccccccc
Q 040947 102 TQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGN-YSHVLKAANHKRT 180 (210)
Q Consensus 102 ~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~-~~~~~~~~~~~~~ 180 (210)
..++|+.|.+.|...-++.++++.||..|++|+.|+-+|.. +.+.++|.+||+++|-++||+||. +..++.+...-|.
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRk 110 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRK 110 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHH
Confidence 45899999999985545689999999999999999999976 477899999999999999999995 7788888777665
Q ss_pred CC
Q 040947 181 AS 182 (210)
Q Consensus 181 ~~ 182 (210)
+.
T Consensus 111 Aq 112 (383)
T KOG4577|consen 111 AQ 112 (383)
T ss_pred hh
Confidence 54
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=98.75 E-value=7.1e-09 Score=61.29 Aligned_cols=37 Identities=38% Similarity=0.730 Sum_probs=33.6
Q ss_pred CcccCCcceecc-eeEeeCCccccCCCcccccccCCCC
Q 040947 9 KCKACDKTVYVV-DMLSLEGMPYHKSCFKCSHCKGTLV 45 (210)
Q Consensus 9 ~C~~C~~~I~~~-~~v~~~g~~~H~~CF~C~~C~~~L~ 45 (210)
+|..|+++|.+. ..+.++++.||+.||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 589999999866 6689999999999999999999986
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=98.72 E-value=7.6e-09 Score=61.18 Aligned_cols=37 Identities=35% Similarity=0.750 Sum_probs=33.0
Q ss_pred ccccccceeecC-ceeEecCccccccccccCCCCCcCC
Q 040947 105 KCAACEKTVYPL-EKVTMEGDCFHKTCFRCAHGGCPLT 141 (210)
Q Consensus 105 ~C~~C~~~I~~~-e~v~~~g~~~H~~CF~C~~C~~~l~ 141 (210)
+|..|+++|.+. ..+.+.++.||+.||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 589999999866 5578999999999999999999885
No 16
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.42 E-value=5.7e-08 Score=78.70 Aligned_cols=73 Identities=48% Similarity=1.078 Sum_probs=63.5
Q ss_pred CCCCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCC
Q 040947 3 FTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKN 75 (210)
Q Consensus 3 ~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~ 75 (210)
+.+....|.+|++.+++.+.+...+..||..||+|+.|+..|+...+....+.+||...+.++|-..+.++..
T Consensus 104 ~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~~~~~~~~~~ 176 (200)
T KOG1700|consen 104 FAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLFKGKGNYNEG 176 (200)
T ss_pred hhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheeecCCCccccc
Confidence 3466789999999999999999999999999999999999999999999999999988887776655555443
No 17
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=98.02 E-value=3.7e-07 Score=72.87 Aligned_cols=61 Identities=33% Similarity=0.688 Sum_probs=55.4
Q ss_pred CccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcC
Q 040947 104 DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFME 164 (210)
Q Consensus 104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~ 164 (210)
..|..|++.++|.|.|..+++.||+.||+|..|+-+|.-.++.-.|.++||..+|.+..+.
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~at 65 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVAT 65 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccceee
Confidence 5788999999999999999999999999999999999888888889999999999776543
No 18
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=97.89 E-value=9.3e-07 Score=70.63 Aligned_cols=59 Identities=39% Similarity=0.745 Sum_probs=54.2
Q ss_pred CCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhh
Q 040947 8 DKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66 (210)
Q Consensus 8 ~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~ 66 (210)
..|..|++.+++.|.|..+++.||..||+|..|+-+|.-.+|-..+.++||..+|....
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~ 63 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQV 63 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccce
Confidence 56889999999999999999999999999999999999888888899999999996554
No 19
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.76 E-value=2.7e-06 Score=69.81 Aligned_cols=111 Identities=23% Similarity=0.488 Sum_probs=87.6
Q ss_pred CCcceecceeEeeCCccccCCCcccccccCCCC--CCCeeccCCeeeccchHHH--hhhccCCCCCCccCCCCCCCCCCC
Q 040947 13 CDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLV--MSNYSSMDGVLYCKPHFEQ--LFKESGNFSKNFQTGKNPSSCSNQ 88 (210)
Q Consensus 13 C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~--~~~f~~~~g~~yC~~cy~~--~~~~~~~~~~~~~~~~~~~~~~~~ 88 (210)
|+..|.+...+.+.+..||..|+.|..|...|. ...|.. +|..||..+|.+ .+.
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~--------------------- 59 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFS--------------------- 59 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcc---------------------
Confidence 677787555577789999999999999999998 555555 999999999987 333
Q ss_pred CCCCCCcccccCCCCCccccccceeecCcee-EecCccccccccccCCCCCcCC-CCCeeecCC-eeecHhHHHhh
Q 040947 89 NRTPSKLSSLFSGTQDKCAACEKTVYPLEKV-TMEGDCFHKTCFRCAHGGCPLT-HSSYAALDG-VLYCKHHFAQL 161 (210)
Q Consensus 89 ~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v-~~~g~~~H~~CF~C~~C~~~l~-~~~f~~~dg-~~yC~~c~~~~ 161 (210)
.+|.+|...|...+.| .+..+. |.-||.|..|...+. +..+.+.+. +.+|..++.+.
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 6899999998665554 566666 999999999988665 556666654 99999888654
No 20
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=91.28 E-value=0.052 Score=44.28 Aligned_cols=58 Identities=22% Similarity=0.646 Sum_probs=45.3
Q ss_pred ccceeecCceeEecCccccccccccCCCCCcCC--CCCeeecCCeeecHhHHHh--hhcCCCC
Q 040947 109 CEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLT--HSSYAALDGVLYCKHHFAQ--LFMEKGN 167 (210)
Q Consensus 109 C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~--~~~f~~~dg~~yC~~c~~~--~f~~k~~ 167 (210)
|+..|.+...+.+.+..||..|..|..|...|. ...|.. +|..||...|.. .+..++.
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~ 63 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCA 63 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcccccc
Confidence 566676444466779999999999999999997 555566 999999999998 5555543
No 21
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=88.18 E-value=0.32 Score=30.93 Aligned_cols=36 Identities=28% Similarity=0.611 Sum_probs=25.5
Q ss_pred CccccccceeecCce-eE--ecCcccccccc----ccCC--CCCc
Q 040947 104 DKCAACEKTVYPLEK-VT--MEGDCFHKTCF----RCAH--GGCP 139 (210)
Q Consensus 104 ~~C~~C~~~I~~~e~-v~--~~g~~~H~~CF----~C~~--C~~~ 139 (210)
.+|..|+++|.+++- |. .-+..||++|+ .|.. |+..
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~ 50 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTG 50 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCC
Confidence 689999999975444 43 34788999988 4655 5443
No 22
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=86.72 E-value=0.27 Score=35.28 Aligned_cols=30 Identities=33% Similarity=0.626 Sum_probs=21.6
Q ss_pred ccccccceeecCceeEe-cCccccccccccC
Q 040947 105 KCAACEKTVYPLEKVTM-EGDCFHKTCFRCA 134 (210)
Q Consensus 105 ~C~~C~~~I~~~e~v~~-~g~~~H~~CF~C~ 134 (210)
+|..|+++|+.++.+++ .+..-|..||+=.
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~ 34 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREK 34 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHH
Confidence 68888888887777654 3456788887644
No 23
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=84.97 E-value=0.61 Score=29.65 Aligned_cols=29 Identities=34% Similarity=0.718 Sum_probs=21.4
Q ss_pred CCCcccCCcceecc-eeE--eeCCccccCCCc
Q 040947 7 LDKCKACDKTVYVV-DML--SLEGMPYHKSCF 35 (210)
Q Consensus 7 ~~~C~~C~~~I~~~-~~v--~~~g~~~H~~CF 35 (210)
..+|..|+++|.++ +.| ..-+..||++|.
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 45699999999644 343 556778999886
No 24
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=83.63 E-value=1 Score=29.69 Aligned_cols=33 Identities=15% Similarity=0.304 Sum_probs=17.1
Q ss_pred cccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947 35 FKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK 67 (210)
Q Consensus 35 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~ 67 (210)
++|+.|...|...-....=..+||..|....++
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 688999888876544445667899999987766
No 25
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=83.58 E-value=1.6 Score=27.79 Aligned_cols=32 Identities=16% Similarity=0.179 Sum_probs=26.2
Q ss_pred cccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947 35 FKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK 67 (210)
Q Consensus 35 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~ 67 (210)
|.|..|+..+.. ......|..||+.|..+.+.
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~ 33 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLL 33 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHH
Confidence 678899998887 45557899999999988775
No 26
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=82.24 E-value=1.1 Score=31.83 Aligned_cols=30 Identities=30% Similarity=0.433 Sum_probs=17.2
Q ss_pred CCCcccCCcceeccee-EeeCCccccCCCcc
Q 040947 7 LDKCKACDKTVYVVDM-LSLEGMPYHKSCFK 36 (210)
Q Consensus 7 ~~~C~~C~~~I~~~~~-v~~~g~~~H~~CF~ 36 (210)
...|..|+++|..... +.-.|..+|..|++
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 4557777777764433 33345556766653
No 27
>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=81.89 E-value=0.94 Score=32.16 Aligned_cols=29 Identities=28% Similarity=0.495 Sum_probs=20.6
Q ss_pred CccccccceeecCcee-EecCccccccccc
Q 040947 104 DKCAACEKTVYPLEKV-TMEGDCFHKTCFR 132 (210)
Q Consensus 104 ~~C~~C~~~I~~~e~v-~~~g~~~H~~CF~ 132 (210)
..|+.|+++|.....+ -..|..+|..|++
T Consensus 79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 6799999999754333 3456778888863
No 28
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=81.49 E-value=1.3 Score=27.77 Aligned_cols=29 Identities=28% Similarity=0.559 Sum_probs=22.8
Q ss_pred ccCCCCCcCCC-CCeeecCCeeecHhHHHhh
Q 040947 132 RCAHGGCPLTH-SSYAALDGVLYCKHHFAQL 161 (210)
Q Consensus 132 ~C~~C~~~l~~-~~f~~~dg~~yC~~c~~~~ 161 (210)
.|..|+..+.- ..+.+.|| ..|..|+.++
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 47888888873 33667788 6899999987
No 29
>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=79.65 E-value=0.47 Score=27.31 Aligned_cols=28 Identities=21% Similarity=0.491 Sum_probs=14.8
Q ss_pred cCCCCCcCCCCCeeecCCeeecHhHHHh
Q 040947 133 CAHGGCPLTHSSYAALDGVLYCKHHFAQ 160 (210)
Q Consensus 133 C~~C~~~l~~~~f~~~dg~~yC~~c~~~ 160 (210)
|..|+.++...+....++..+|..|+..
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 5555555554445555666667666654
No 30
>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=77.97 E-value=1.2 Score=26.05 Aligned_cols=28 Identities=18% Similarity=0.476 Sum_probs=18.8
Q ss_pred cccCCcceecce-eEeeCCccccCCCccc
Q 040947 10 CKACDKTVYVVD-MLSLEGMPYHKSCFKC 37 (210)
Q Consensus 10 C~~C~~~I~~~~-~v~~~g~~~H~~CF~C 37 (210)
|..|+.+|.... .+...++.||.-|-.|
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 667888887443 3677888888655444
No 31
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=75.49 E-value=1.8 Score=25.07 Aligned_cols=25 Identities=28% Similarity=0.521 Sum_probs=18.1
Q ss_pred cccccccCCCCCCCeeccCCeeeccchHH
Q 040947 35 FKCSHCKGTLVMSNYSSMDGVLYCKPHFE 63 (210)
Q Consensus 35 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~ 63 (210)
+.|..|+.. .|...+|..||..|-.
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEhhhCce
Confidence 457777765 4667899999977653
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=75.36 E-value=1.6 Score=30.80 Aligned_cols=30 Identities=27% Similarity=0.498 Sum_probs=18.9
Q ss_pred ccCCCcccccccCCCCCCCeeccCCeeeccchHHHh
Q 040947 30 YHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQL 65 (210)
Q Consensus 30 ~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~ 65 (210)
|-..=-.|..|...+.. .|.-||..|..+.
T Consensus 40 y~~~~~~C~~CK~~v~q------~g~~YCq~CAYkk 69 (90)
T PF10235_consen 40 YAPYSSKCKICKTKVHQ------PGAKYCQTCAYKK 69 (90)
T ss_pred ccccCcccccccccccc------CCCccChhhhccc
Confidence 44433467777666542 3667899997654
No 33
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=75.04 E-value=1.1 Score=36.34 Aligned_cols=31 Identities=23% Similarity=0.371 Sum_probs=26.6
Q ss_pred cccCCCCCcCCCCCeeecCCeeecHhHHHhh
Q 040947 131 FRCAHGGCPLTHSSYAALDGVLYCKHHFAQL 161 (210)
Q Consensus 131 F~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~ 161 (210)
-+|+.||..+....-...+|+++|..||.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 6899999988877778889999999999854
No 34
>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=75.02 E-value=1.7 Score=25.42 Aligned_cols=28 Identities=18% Similarity=0.440 Sum_probs=17.6
Q ss_pred cccccceeecCce-eEecCcccccccccc
Q 040947 106 CAACEKTVYPLEK-VTMEGDCFHKTCFRC 133 (210)
Q Consensus 106 C~~C~~~I~~~e~-v~~~g~~~H~~CF~C 133 (210)
|.-|+.+|...-. +...++.||.-|-.|
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 5678888873322 467778887655444
No 35
>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=74.62 E-value=4.9 Score=24.53 Aligned_cols=32 Identities=25% Similarity=0.325 Sum_probs=21.2
Q ss_pred cccccccCCCCCCCeeccCCee-eccchHHHhhh
Q 040947 35 FKCSHCKGTLVMSNYSSMDGVL-YCKPHFEQLFK 67 (210)
Q Consensus 35 F~C~~C~~~L~~~~f~~~~g~~-yC~~cy~~~~~ 67 (210)
+.|..|...... ..+..=|.. +|..|+.+.+.
T Consensus 3 ~~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~ 35 (50)
T PF13920_consen 3 EECPICFENPRD-VVLLPCGHLCFCEECAERLLK 35 (50)
T ss_dssp SB-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHH
T ss_pred CCCccCCccCCc-eEEeCCCChHHHHHHhHHhcc
Confidence 356667666554 334456777 99999998865
No 36
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.16 E-value=2 Score=34.09 Aligned_cols=37 Identities=19% Similarity=0.488 Sum_probs=28.8
Q ss_pred cCCCcccccccCCCCCCC-eeccCCeeeccchHHHhhh
Q 040947 31 HKSCFKCSHCKGTLVMSN-YSSMDGVLYCKPHFEQLFK 67 (210)
Q Consensus 31 H~~CF~C~~C~~~L~~~~-f~~~~g~~yC~~cy~~~~~ 67 (210)
-..+|+|-.|=....... +..+=|.+||..|......
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk 165 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALK 165 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHHH
Confidence 456899999866666543 5578899999999998765
No 37
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=73.85 E-value=2.3 Score=27.46 Aligned_cols=31 Identities=19% Similarity=0.458 Sum_probs=21.0
Q ss_pred CCCCCcccCCcceecceeEeeCCccccCCCcccccccCCC
Q 040947 5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTL 44 (210)
Q Consensus 5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L 44 (210)
-..+.|..|+..|.+.+.- -=|.|-.|+..+
T Consensus 5 ~~~~~CtSCg~~i~~~~~~---------~~F~CPnCG~~~ 35 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREKA---------VKFLCPNCGEVI 35 (59)
T ss_pred ccCccccCCCCcccCCCcc---------CEeeCCCCCCee
Confidence 3456799999888755421 127888888763
No 38
>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=73.47 E-value=2.2 Score=33.06 Aligned_cols=37 Identities=19% Similarity=0.341 Sum_probs=26.2
Q ss_pred CccccccceeecCc---eeEecCccccccccccCCCCCcCC
Q 040947 104 DKCAACEKTVYPLE---KVTMEGDCFHKTCFRCAHGGCPLT 141 (210)
Q Consensus 104 ~~C~~C~~~I~~~e---~v~~~g~~~H~~CF~C~~C~~~l~ 141 (210)
..|..|+.+|...- .|...+..|+.- --|..||+++.
T Consensus 40 ~~Cp~C~~~IrG~y~v~gv~~~g~~~~~P-sYC~~CGkpyP 79 (158)
T PF10083_consen 40 TSCPNCSTPIRGDYHVEGVFGLGGHYEAP-SYCHNCGKPYP 79 (158)
T ss_pred HHCcCCCCCCCCceecCCeeeeCCCCCCC-hhHHhCCCCCc
Confidence 58999999998432 244567777754 34888999875
No 39
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=72.62 E-value=1.7 Score=30.84 Aligned_cols=32 Identities=25% Similarity=0.424 Sum_probs=24.5
Q ss_pred CccccccceeecCceeEec-CccccccccccCC
Q 040947 104 DKCAACEKTVYPLEKVTME-GDCFHKTCFRCAH 135 (210)
Q Consensus 104 ~~C~~C~~~I~~~e~v~~~-g~~~H~~CF~C~~ 135 (210)
-+|+.|+.+|..++..++- ...-|.+||.=+.
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~ 39 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECLAESK 39 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHHHHHH
Confidence 4899999999988887643 4467888886554
No 40
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=72.40 E-value=1.9 Score=22.30 Aligned_cols=9 Identities=22% Similarity=0.818 Sum_probs=5.1
Q ss_pred cccCCccee
Q 040947 10 CKACDKTVY 18 (210)
Q Consensus 10 C~~C~~~I~ 18 (210)
|..|+..|.
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 555666554
No 41
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=69.55 E-value=1.5 Score=41.92 Aligned_cols=35 Identities=17% Similarity=0.412 Sum_probs=26.4
Q ss_pred CCcccccccCCCCCCCeeccCCeeeccchHHHhhhc
Q 040947 33 SCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE 68 (210)
Q Consensus 33 ~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~ 68 (210)
.=++|..|+....+ .....=+.+||..|...++..
T Consensus 642 ~~LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~et 676 (698)
T KOG0978|consen 642 ELLKCSVCNTRWKD-AVITKCGHVFCEECVQTRYET 676 (698)
T ss_pred hceeCCCccCchhh-HHHHhcchHHHHHHHHHHHHH
Confidence 34789999976655 334567789999999998873
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=66.63 E-value=4 Score=25.70 Aligned_cols=27 Identities=22% Similarity=0.543 Sum_probs=16.0
Q ss_pred cCCCCCcCCCCCeeecCCeeec-HhHHH
Q 040947 133 CAHGGCPLTHSSYAALDGVLYC-KHHFA 159 (210)
Q Consensus 133 C~~C~~~l~~~~f~~~dg~~yC-~~c~~ 159 (210)
|..|...++...-+.+||+.|| ..|..
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 6778888887777888999998 55654
No 43
>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=64.26 E-value=4 Score=27.33 Aligned_cols=33 Identities=15% Similarity=0.358 Sum_probs=13.7
Q ss_pred CccccccceeecCceeEecCccccccccccCCCCCcCCCC
Q 040947 104 DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHS 143 (210)
Q Consensus 104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~ 143 (210)
..|+.|++++. .+.+-|.. =|-|..|+..++..
T Consensus 31 a~CPdC~~~Le---~LkACGAv----dYFC~~c~gLiSKk 63 (70)
T PF07191_consen 31 AFCPDCGQPLE---VLKACGAV----DYFCNHCHGLISKK 63 (70)
T ss_dssp EE-TTT-SB-E---EEEETTEE----EEE-TTTT-EE-TT
T ss_pred ccCCCcccHHH---HHHHhccc----ceeeccCCceeecc
Confidence 46777777663 44554421 02366666655533
No 44
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=62.16 E-value=4 Score=30.77 Aligned_cols=22 Identities=32% Similarity=0.712 Sum_probs=16.2
Q ss_pred cCCCCCcCCCCCeeecCCeeecHhHHH
Q 040947 133 CAHGGCPLTHSSYAALDGVLYCKHHFA 159 (210)
Q Consensus 133 C~~C~~~l~~~~f~~~dg~~yC~~c~~ 159 (210)
|..||.+| |. +||.+||..|=.
T Consensus 31 Cp~Cg~PL----F~-KdG~v~CPvC~~ 52 (131)
T COG1645 31 CPKCGTPL----FR-KDGEVFCPVCGY 52 (131)
T ss_pred CcccCCcc----ee-eCCeEECCCCCc
Confidence 67777776 44 788888888854
No 45
>PRK00807 50S ribosomal protein L24e; Validated
Probab=61.54 E-value=5.3 Score=25.10 Aligned_cols=27 Identities=15% Similarity=0.242 Sum_probs=16.8
Q ss_pred CCcccCCcceecce---eEeeCCccccCCC
Q 040947 8 DKCKACDKTVYVVD---MLSLEGMPYHKSC 34 (210)
Q Consensus 8 ~~C~~C~~~I~~~~---~v~~~g~~~H~~C 34 (210)
..|..|+..|+++. ++..+|+.|.--+
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~Fcs 31 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILYFCS 31 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEEEeC
Confidence 46777888887553 2556666665433
No 46
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=61.10 E-value=3.4 Score=33.49 Aligned_cols=31 Identities=26% Similarity=0.557 Sum_probs=27.0
Q ss_pred cccccccCCCCCCCeeccCCeeeccchHHHh
Q 040947 35 FKCSHCKGTLVMSNYSSMDGVLYCKPHFEQL 65 (210)
Q Consensus 35 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~ 65 (210)
-+|..|+..+....-...+|++.|..||...
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 7899999999887777889999999999753
No 47
>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=61.08 E-value=8.6 Score=22.12 Aligned_cols=31 Identities=23% Similarity=0.430 Sum_probs=22.1
Q ss_pred cccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947 37 CSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK 67 (210)
Q Consensus 37 C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~ 67 (210)
|..|...+........=|..||..|..+.+.
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 4566666666334567889999999988776
No 48
>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=59.26 E-value=5.1 Score=27.21 Aligned_cols=14 Identities=36% Similarity=0.714 Sum_probs=10.9
Q ss_pred CccccccceeecCc
Q 040947 104 DKCAACEKTVYPLE 117 (210)
Q Consensus 104 ~~C~~C~~~I~~~e 117 (210)
..|..|++.|.-++
T Consensus 8 a~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 8 AKCKGCKKKIAKGE 21 (82)
T ss_dssp EBETTTSCBE-TTS
T ss_pred ccCcccCCcCCCCC
Confidence 68999999997555
No 49
>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=58.65 E-value=8.8 Score=21.78 Aligned_cols=31 Identities=16% Similarity=0.410 Sum_probs=17.6
Q ss_pred cccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947 37 CSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK 67 (210)
Q Consensus 37 C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~ 67 (210)
|..|...+........=|..||..|..+.+.
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~ 32 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLK 32 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHH
Confidence 5556555532222223567788888876654
No 50
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=58.36 E-value=16 Score=29.48 Aligned_cols=33 Identities=21% Similarity=0.479 Sum_probs=24.8
Q ss_pred CCcccccccCCCCCCCeeccCCeeeccchHHHhh
Q 040947 33 SCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66 (210)
Q Consensus 33 ~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~ 66 (210)
+-|.|..|...+.. .....=|..||..|..+.+
T Consensus 17 ~~~~CpICld~~~d-PVvT~CGH~FC~~CI~~wl 49 (193)
T PLN03208 17 GDFDCNICLDQVRD-PVVTLCGHLFCWPCIHKWT 49 (193)
T ss_pred CccCCccCCCcCCC-cEEcCCCchhHHHHHHHHH
Confidence 35889999887765 3445688999999997654
No 51
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=58.20 E-value=6 Score=25.06 Aligned_cols=25 Identities=20% Similarity=0.397 Sum_probs=17.3
Q ss_pred CccccccceeecCceeEecCccccc
Q 040947 104 DKCAACEKTVYPLEKVTMEGDCFHK 128 (210)
Q Consensus 104 ~~C~~C~~~I~~~e~v~~~g~~~H~ 128 (210)
.+|..|++||.++..|...+..-|+
T Consensus 2 ~~CvVCKqpi~~a~~v~T~~G~VH~ 26 (54)
T PF10886_consen 2 EICVVCKQPIDDALVVETESGPVHP 26 (54)
T ss_pred CeeeeeCCccCcceEEEcCCCccCc
Confidence 4788888888766556555556665
No 52
>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=56.26 E-value=6.2 Score=23.56 Aligned_cols=11 Identities=18% Similarity=0.827 Sum_probs=6.2
Q ss_pred Cccccccceee
Q 040947 104 DKCAACEKTVY 114 (210)
Q Consensus 104 ~~C~~C~~~I~ 114 (210)
..|+.|+.|+.
T Consensus 18 ~~Cp~C~~PL~ 28 (41)
T PF06677_consen 18 EHCPDCGTPLM 28 (41)
T ss_pred CccCCCCCeeE
Confidence 45666655554
No 53
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=54.91 E-value=7.5 Score=20.55 Aligned_cols=11 Identities=18% Similarity=0.477 Sum_probs=7.1
Q ss_pred Cccccccceee
Q 040947 104 DKCAACEKTVY 114 (210)
Q Consensus 104 ~~C~~C~~~I~ 114 (210)
..|..|+..|.
T Consensus 3 ~~Cp~Cg~~~~ 13 (26)
T PF13248_consen 3 MFCPNCGAEID 13 (26)
T ss_pred CCCcccCCcCC
Confidence 46777777554
No 54
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=53.03 E-value=10 Score=22.50 Aligned_cols=30 Identities=17% Similarity=0.397 Sum_probs=19.7
Q ss_pred cccccCCCC--CCCeeccCCeeeccchHHHhh
Q 040947 37 CSHCKGTLV--MSNYSSMDGVLYCKPHFEQLF 66 (210)
Q Consensus 37 C~~C~~~L~--~~~f~~~~g~~yC~~cy~~~~ 66 (210)
|..|...+. ...+...=|.++|..|..++.
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~ 33 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLK 33 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhc
Confidence 556666662 223334567889999998775
No 55
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=51.48 E-value=9.4 Score=28.79 Aligned_cols=22 Identities=27% Similarity=0.691 Sum_probs=17.1
Q ss_pred cccccCCCCCCCeeccCCeeeccchHH
Q 040947 37 CSHCKGTLVMSNYSSMDGVLYCKPHFE 63 (210)
Q Consensus 37 C~~C~~~L~~~~f~~~~g~~yC~~cy~ 63 (210)
|..|+.+| | .++|.+||.-|-.
T Consensus 31 Cp~Cg~PL----F-~KdG~v~CPvC~~ 52 (131)
T COG1645 31 CPKCGTPL----F-RKDGEVFCPVCGY 52 (131)
T ss_pred CcccCCcc----e-eeCCeEECCCCCc
Confidence 67777776 3 3999999998874
No 56
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=50.99 E-value=13 Score=24.02 Aligned_cols=31 Identities=16% Similarity=0.487 Sum_probs=21.4
Q ss_pred CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCC
Q 040947 6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLV 45 (210)
Q Consensus 6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~ 45 (210)
..+.|..|+..|..++.-.. |.|-.|+..+-
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 36899999999965653222 77888885443
No 57
>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=50.93 E-value=13 Score=22.40 Aligned_cols=11 Identities=18% Similarity=0.329 Sum_probs=8.0
Q ss_pred eeecHhHHHhh
Q 040947 151 VLYCKHHFAQL 161 (210)
Q Consensus 151 ~~yC~~c~~~~ 161 (210)
--+|..||...
T Consensus 23 ~dLC~~Cf~~~ 33 (46)
T cd02249 23 FDLCSSCYAKG 33 (46)
T ss_pred CcCHHHHHCcC
Confidence 34699999854
No 58
>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=50.86 E-value=8.7 Score=20.17 Aligned_cols=9 Identities=22% Similarity=1.036 Sum_probs=4.5
Q ss_pred cccCCccee
Q 040947 10 CKACDKTVY 18 (210)
Q Consensus 10 C~~C~~~I~ 18 (210)
|..|+..|.
T Consensus 1 C~sC~~~i~ 9 (24)
T PF07754_consen 1 CTSCGRPIA 9 (24)
T ss_pred CccCCCccc
Confidence 444555554
No 59
>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=48.51 E-value=17 Score=23.19 Aligned_cols=32 Identities=19% Similarity=0.444 Sum_probs=20.8
Q ss_pred ccccccCCCCCCC---eeccCCeeeccchHHHhhh
Q 040947 36 KCSHCKGTLVMSN---YSSMDGVLYCKPHFEQLFK 67 (210)
Q Consensus 36 ~C~~C~~~L~~~~---f~~~~g~~yC~~cy~~~~~ 67 (210)
.|..|++.|.... ++-.-.=-||.+|...++.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~ 41 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLN 41 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc
Confidence 4677778776432 3333445678889888875
No 60
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=47.33 E-value=14 Score=26.53 Aligned_cols=40 Identities=13% Similarity=0.055 Sum_probs=32.5
Q ss_pred cccCCCCCcCC-CCCeeecCCeeecHhHHHhhhcCCCCccc
Q 040947 131 FRCAHGGCPLT-HSSYAALDGVLYCKHHFAQLFMEKGNYSH 170 (210)
Q Consensus 131 F~C~~C~~~l~-~~~f~~~dg~~yC~~c~~~~f~~k~~~~~ 170 (210)
++|..|+..+- +..|+...+.+..-.||.....++...+.
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~~~k~~~~~ 43 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREKASKKLYGDV 43 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHHHhhhcccCh
Confidence 47899999986 66788887799999999998887776544
No 61
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.97 E-value=11 Score=32.25 Aligned_cols=32 Identities=19% Similarity=0.428 Sum_probs=22.4
Q ss_pred cccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947 35 FKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK 67 (210)
Q Consensus 35 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~ 67 (210)
|.|..|++.... .....-+..+|+.|....|.
T Consensus 242 f~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~q 273 (313)
T KOG1813|consen 242 FKCFICRKYFYR-PVVTKCGHYFCEVCALKPYQ 273 (313)
T ss_pred cccccccccccc-chhhcCCceeehhhhccccc
Confidence 566677776654 33445778899999987765
No 62
>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=45.22 E-value=20 Score=21.32 Aligned_cols=8 Identities=38% Similarity=0.932 Sum_probs=6.5
Q ss_pred ecHhHHHh
Q 040947 153 YCKHHFAQ 160 (210)
Q Consensus 153 yC~~c~~~ 160 (210)
+|..||.+
T Consensus 29 lC~~Cf~~ 36 (44)
T smart00291 29 LCQSCFAK 36 (44)
T ss_pred chHHHHhC
Confidence 69999875
No 63
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=44.88 E-value=39 Score=19.89 Aligned_cols=30 Identities=23% Similarity=0.441 Sum_probs=17.7
Q ss_pred ccCCCCCcCCCCC-eeecC-CeeecHhHHHhh
Q 040947 132 RCAHGGCPLTHSS-YAALD-GVLYCKHHFAQL 161 (210)
Q Consensus 132 ~C~~C~~~l~~~~-f~~~d-g~~yC~~c~~~~ 161 (210)
+|+.|+++..... ...-. +...|..|....
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~~ 34 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQA 34 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHHH
Confidence 5899999887443 33333 677799887654
No 64
>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=44.50 E-value=7.3 Score=22.99 Aligned_cols=9 Identities=22% Similarity=0.674 Sum_probs=4.7
Q ss_pred cccccceee
Q 040947 106 CAACEKTVY 114 (210)
Q Consensus 106 C~~C~~~I~ 114 (210)
|+.|...+.
T Consensus 3 C~IC~~~~~ 11 (44)
T PF13639_consen 3 CPICLEEFE 11 (44)
T ss_dssp ETTTTCBHH
T ss_pred CcCCChhhc
Confidence 555555554
No 65
>PRK00420 hypothetical protein; Validated
Probab=44.43 E-value=12 Score=27.57 Aligned_cols=11 Identities=18% Similarity=0.866 Sum_probs=7.0
Q ss_pred Cccccccceee
Q 040947 104 DKCAACEKTVY 114 (210)
Q Consensus 104 ~~C~~C~~~I~ 114 (210)
..|+.|+.|++
T Consensus 24 ~~CP~Cg~pLf 34 (112)
T PRK00420 24 KHCPVCGLPLF 34 (112)
T ss_pred CCCCCCCCcce
Confidence 46777766654
No 66
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=43.95 E-value=8.1 Score=31.28 Aligned_cols=33 Identities=18% Similarity=0.322 Sum_probs=25.2
Q ss_pred CcccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947 34 CFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK 67 (210)
Q Consensus 34 CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~ 67 (210)
=|.|..|.+...+ .....-|..||..|+.+.+.
T Consensus 196 PF~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~ 228 (259)
T COG5152 196 PFLCGICKKDYES-PVVTECGHSFCSLCAIRKYQ 228 (259)
T ss_pred ceeehhchhhccc-hhhhhcchhHHHHHHHHHhc
Confidence 4788888887765 34445788899999988875
No 67
>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=40.14 E-value=33 Score=19.53 Aligned_cols=31 Identities=13% Similarity=0.317 Sum_probs=22.1
Q ss_pred cccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947 37 CSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK 67 (210)
Q Consensus 37 C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~ 67 (210)
|..|...+........=|..||..|..+.+.
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 4556666665444556778899999988876
No 68
>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=38.46 E-value=14 Score=26.04 Aligned_cols=42 Identities=12% Similarity=0.294 Sum_probs=29.1
Q ss_pred CCCCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCC
Q 040947 3 FTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVM 46 (210)
Q Consensus 3 ~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~ 46 (210)
+......|..|++++..-+.+.+.+-.+.+ -+|..|+++++.
T Consensus 29 i~~~rS~C~~C~~~L~~~~lIPi~S~l~lr--GrCr~C~~~I~~ 70 (92)
T PF06750_consen 29 IIFPRSHCPHCGHPLSWWDLIPILSYLLLR--GRCRYCGAPIPP 70 (92)
T ss_pred ccCCCCcCcCCCCcCcccccchHHHHHHhC--CCCcccCCCCCh
Confidence 334457899999999766766555444433 467888888875
No 69
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=37.54 E-value=19 Score=27.06 Aligned_cols=24 Identities=13% Similarity=0.274 Sum_probs=15.2
Q ss_pred CCcccCCcceecce---eEeeCCcccc
Q 040947 8 DKCKACDKTVYVVD---MLSLEGMPYH 31 (210)
Q Consensus 8 ~~C~~C~~~I~~~~---~v~~~g~~~H 31 (210)
..|..|+..|+++. +|...|+.|+
T Consensus 5 e~CsFcG~kIyPG~G~~fVR~DGkvf~ 31 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMFVRKDGTVLH 31 (131)
T ss_pred eeecCcCCcccCCCCcEEEecCCCEEE
Confidence 46788888887764 3455555554
No 70
>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=37.49 E-value=8.2 Score=22.17 Aligned_cols=31 Identities=19% Similarity=0.546 Sum_probs=18.9
Q ss_pred cccCCcceecceeEeeCCccccCCCcccccccCCCC
Q 040947 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLV 45 (210)
Q Consensus 10 C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~ 45 (210)
|..|.+.+ ....++.||-.=..|..||-.+.
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 55554443 35568999999999999998764
No 71
>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=37.29 E-value=30 Score=21.01 Aligned_cols=30 Identities=20% Similarity=0.319 Sum_probs=17.6
Q ss_pred ccCCCCCcCCCCCeeec--CCeeecHhHHHhh
Q 040947 132 RCAHGGCPLTHSSYAAL--DGVLYCKHHFAQL 161 (210)
Q Consensus 132 ~C~~C~~~l~~~~f~~~--dg~~yC~~c~~~~ 161 (210)
.|..|+..+....|... .+.-+|..||.+-
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~G 33 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQEG 33 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhCc
Confidence 45566666654333322 2466899999863
No 72
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=37.03 E-value=18 Score=34.34 Aligned_cols=22 Identities=27% Similarity=0.513 Sum_probs=16.7
Q ss_pred ecCccccccccccCCCCCcCCC
Q 040947 121 MEGDCFHKTCFRCAHGGCPLTH 142 (210)
Q Consensus 121 ~~g~~~H~~CF~C~~C~~~l~~ 142 (210)
..+..+.++||+|..|+..|.+
T Consensus 106 ~sg~~~ckk~~~c~qc~~~lpg 127 (694)
T KOG4443|consen 106 PSGPWLCKKCTRCRQCDSTLPG 127 (694)
T ss_pred cCcccccHHHHhhhhccccccc
Confidence 3466777888888888887776
No 73
>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=36.54 E-value=26 Score=20.49 Aligned_cols=30 Identities=20% Similarity=0.528 Sum_probs=15.2
Q ss_pred CccccccceeecCceeEecCccccccccccCCCCC
Q 040947 104 DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGC 138 (210)
Q Consensus 104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~ 138 (210)
.+|.+|+--|.+--.+...++.| +|..|+.
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 68999988887544455555554 6777765
No 74
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=36.43 E-value=26 Score=30.23 Aligned_cols=34 Identities=18% Similarity=0.366 Sum_probs=28.2
Q ss_pred CCcccccccCCCCCCCeeccCCeeeccchHHHhh
Q 040947 33 SCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66 (210)
Q Consensus 33 ~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~ 66 (210)
.=|-|-.|...|....|.=.+|.+.|..|-.++.
T Consensus 47 ~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~ 80 (299)
T KOG3002|consen 47 DLLDCPVCFNPLSPPIFQCDNGHLACSSCRTKVS 80 (299)
T ss_pred hhccCchhhccCcccceecCCCcEehhhhhhhhc
Confidence 3477888989999888888899999999986654
No 75
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=36.13 E-value=23 Score=22.43 Aligned_cols=24 Identities=21% Similarity=0.573 Sum_probs=15.8
Q ss_pred CCcccCCcceecce---eEeeCCcccc
Q 040947 8 DKCKACDKTVYVVD---MLSLEGMPYH 31 (210)
Q Consensus 8 ~~C~~C~~~I~~~~---~v~~~g~~~H 31 (210)
..|..|+..|+++. +|..+|+.++
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~ 30 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFR 30 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEE
Confidence 46888888888764 3555565554
No 76
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=35.90 E-value=16 Score=21.91 Aligned_cols=28 Identities=21% Similarity=0.577 Sum_probs=15.1
Q ss_pred CcccCCcceecceeEeeCCccccCCCcccccccCCCC
Q 040947 9 KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLV 45 (210)
Q Consensus 9 ~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~ 45 (210)
+|..|+..+...+... =++|..|+.++.
T Consensus 5 ~C~~CG~~~~~~~~~~---------~~~Cp~CG~~~~ 32 (46)
T PRK00398 5 KCARCGREVELDEYGT---------GVRCPYCGYRIL 32 (46)
T ss_pred ECCCCCCEEEECCCCC---------ceECCCCCCeEE
Confidence 4777777664221111 367777776553
No 77
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=35.89 E-value=79 Score=24.86 Aligned_cols=35 Identities=14% Similarity=0.304 Sum_probs=23.8
Q ss_pred cCCCCCcCCCCCeeecCC--eeecHhHHHhhhcCCCCcc
Q 040947 133 CAHGGCPLTHSSYAALDG--VLYCKHHFAQLFMEKGNYS 169 (210)
Q Consensus 133 C~~C~~~l~~~~f~~~dg--~~yC~~c~~~~f~~k~~~~ 169 (210)
|..||+.+....-+..+| .-.|..|+ .|+.+....
T Consensus 6 CEiCG~~i~~~~~v~vegsel~VC~~Ca--k~G~~~~~~ 42 (165)
T COG1813 6 CELCGREIDKPIKVKVEGAELTVCDDCA--KFGTAAKTA 42 (165)
T ss_pred eeccccccCCCeeEEeecceeehhHHHH--HhccCcccc
Confidence 888999888333344454 34699999 888666543
No 78
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=35.79 E-value=13 Score=26.65 Aligned_cols=30 Identities=27% Similarity=0.340 Sum_probs=19.0
Q ss_pred CCCcccccccCCCCCC-CeeccCCeeeccch
Q 040947 32 KSCFKCSHCKGTLVMS-NYSSMDGVLYCKPH 61 (210)
Q Consensus 32 ~~CF~C~~C~~~L~~~-~f~~~~g~~yC~~c 61 (210)
..=|+|..|--.--.. --...+|.+||.+|
T Consensus 68 ~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 68 ADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred CCceeeeeeeeEechhhhccccCCCEecccc
Confidence 4458999885433211 12256899999987
No 79
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=34.52 E-value=57 Score=21.53 Aligned_cols=34 Identities=15% Similarity=0.172 Sum_probs=24.9
Q ss_pred CCcccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947 33 SCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK 67 (210)
Q Consensus 33 ~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~ 67 (210)
.=|.|..++..+.+ ....-+|..|+..+..+-+.
T Consensus 3 ~~f~CpIt~~lM~d-PVi~~~G~tyer~~I~~~l~ 36 (73)
T PF04564_consen 3 DEFLCPITGELMRD-PVILPSGHTYERSAIERWLE 36 (73)
T ss_dssp GGGB-TTTSSB-SS-EEEETTSEEEEHHHHHHHHC
T ss_pred cccCCcCcCcHhhC-ceeCCcCCEEcHHHHHHHHH
Confidence 34788888887776 45567889999999988776
No 80
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=33.64 E-value=11 Score=28.68 Aligned_cols=34 Identities=26% Similarity=0.605 Sum_probs=23.6
Q ss_pred CcccCCcceecceeEeeCCccccCCCcccccccCCCC
Q 040947 9 KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLV 45 (210)
Q Consensus 9 ~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~ 45 (210)
.|+.|+..+...+.+...+. ..=|.|..|+..|.
T Consensus 101 ~Cp~C~~~y~~~ea~~~~d~---~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 101 KCPNCQSKYTFLEANQLLDM---DGTFTCPRCGEELE 134 (147)
T ss_pred ECcCCCCEeeHHHHHHhcCC---CCcEECCCCCCEEE
Confidence 69999988875554443331 33499999999885
No 81
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=33.19 E-value=15 Score=29.11 Aligned_cols=30 Identities=20% Similarity=0.504 Sum_probs=22.7
Q ss_pred CcccCCcceecceeEeeCCccccCCCcccccccCCCCC
Q 040947 9 KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVM 46 (210)
Q Consensus 9 ~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~ 46 (210)
.|..|+......+.+. .=|.|..||..|..
T Consensus 119 ~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 119 FCPNCHIRFTFDEAME--------YGFRCPQCGEMLEE 148 (178)
T ss_pred ECCCCCcEEeHHHHhh--------cCCcCCCCCCCCee
Confidence 6999998887555442 24999999999974
No 82
>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=32.52 E-value=15 Score=19.91 Aligned_cols=11 Identities=27% Similarity=0.715 Sum_probs=6.2
Q ss_pred Cccccccceee
Q 040947 104 DKCAACEKTVY 114 (210)
Q Consensus 104 ~~C~~C~~~I~ 114 (210)
.+|.+|...|.
T Consensus 2 ~~C~rC~~~~~ 12 (30)
T PF06827_consen 2 EKCPRCWNYIE 12 (30)
T ss_dssp SB-TTT--BBE
T ss_pred CcCccCCCcce
Confidence 47999998875
No 83
>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=32.48 E-value=41 Score=29.17 Aligned_cols=15 Identities=27% Similarity=0.499 Sum_probs=12.0
Q ss_pred CCeeeccchHHHhhh
Q 040947 53 DGVLYCKPHFEQLFK 67 (210)
Q Consensus 53 ~g~~yC~~cy~~~~~ 67 (210)
=|..+|..|..++|.
T Consensus 26 CGH~~C~sCv~~l~~ 40 (309)
T TIGR00570 26 CGHTLCESCVDLLFV 40 (309)
T ss_pred CCCcccHHHHHHHhc
Confidence 467889999988875
No 84
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=32.39 E-value=1e+02 Score=23.82 Aligned_cols=31 Identities=16% Similarity=0.424 Sum_probs=22.6
Q ss_pred cCCCCCcCCCCCee-ecCC--eeecHhHHHhhhcCC
Q 040947 133 CAHGGCPLTHSSYA-ALDG--VLYCKHHFAQLFMEK 165 (210)
Q Consensus 133 C~~C~~~l~~~~f~-~~dg--~~yC~~c~~~~f~~k 165 (210)
|..||+.+.+..+. ..+| ...|..|+ +||..
T Consensus 3 CEiCG~~i~~~~~~v~iega~l~vC~~C~--k~G~~ 36 (154)
T TIGR00270 3 CEICGRKIKGKGFKIVIEGSEMTVCGECR--KFGKE 36 (154)
T ss_pred cccCCCccCCCCeEEEEcCeEEehhhhHH--hcCCc
Confidence 88999999876453 4465 34699999 77763
No 85
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=32.39 E-value=75 Score=25.64 Aligned_cols=27 Identities=30% Similarity=0.458 Sum_probs=17.4
Q ss_pred CccccccceeecCceeEecCcccccccc
Q 040947 104 DKCAACEKTVYPLEKVTMEGDCFHKTCF 131 (210)
Q Consensus 104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF 131 (210)
..|..|...+. .-.+..-|..|+..|+
T Consensus 19 ~~CpICld~~~-dPVvT~CGH~FC~~CI 45 (193)
T PLN03208 19 FDCNICLDQVR-DPVVTLCGHLFCWPCI 45 (193)
T ss_pred cCCccCCCcCC-CcEEcCCCchhHHHHH
Confidence 57888888764 3345555666666655
No 86
>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=32.26 E-value=42 Score=20.18 Aligned_cols=8 Identities=25% Similarity=0.891 Sum_probs=7.0
Q ss_pred ecHhHHHh
Q 040947 153 YCKHHFAQ 160 (210)
Q Consensus 153 yC~~c~~~ 160 (210)
+|..||.+
T Consensus 30 LC~~C~~~ 37 (46)
T PF00569_consen 30 LCEDCFSK 37 (46)
T ss_dssp EEHHHHHH
T ss_pred hhhHHHhC
Confidence 69999987
No 87
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=31.86 E-value=19 Score=34.62 Aligned_cols=83 Identities=19% Similarity=0.423 Sum_probs=55.1
Q ss_pred CCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCCCCC
Q 040947 7 LDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSCS 86 (210)
Q Consensus 7 ~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~ 86 (210)
..+|..|-+.|. .-.++.||--=-.|++||-++ .+....||=. .+.
T Consensus 101 ~a~C~~Cl~Ei~-----dp~~rrY~YPF~~CT~CGPRf-----TIi~alPYDR-----~nT------------------- 146 (750)
T COG0068 101 AATCEDCLEEIF-----DPNSRRYLYPFINCTNCGPRF-----TIIEALPYDR-----ENT------------------- 146 (750)
T ss_pred hhhhHHHHHHhc-----CCCCcceeccccccCCCCcce-----eeeccCCCCc-----ccC-------------------
Confidence 467888877775 345778888888899997754 4445555411 000
Q ss_pred CCCCCCCCcccccCCCCCccccccceeecCceeEecCccccccccccCCCCCcC
Q 040947 87 NQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPL 140 (210)
Q Consensus 87 ~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l 140 (210)
.-..| +.|..|.+ |.-...++.||..=..|..||-.+
T Consensus 147 --------sM~~F----~lC~~C~~-----EY~dP~nRRfHAQp~aCp~CGP~~ 183 (750)
T COG0068 147 --------SMADF----PLCPFCDK-----EYKDPLNRRFHAQPIACPKCGPHL 183 (750)
T ss_pred --------ccccC----cCCHHHHH-----HhcCccccccccccccCcccCCCe
Confidence 00011 68988865 334677899999989999998866
No 88
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=31.76 E-value=24 Score=30.75 Aligned_cols=38 Identities=18% Similarity=0.484 Sum_probs=26.8
Q ss_pred CCcccCCcceecceeEe-----eCC-----ccccCCCcccccccCCCC
Q 040947 8 DKCKACDKTVYVVDMLS-----LEG-----MPYHKSCFKCSHCKGTLV 45 (210)
Q Consensus 8 ~~C~~C~~~I~~~~~v~-----~~g-----~~~H~~CF~C~~C~~~L~ 45 (210)
..|..|+..|+-+..+. +.+ -....--|+|..|...|.
T Consensus 41 i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF~~kC~~C~~~i~ 88 (324)
T PF04502_consen 41 IWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRFYIKCPRCSNEIE 88 (324)
T ss_pred CcCCCCccccccceeeeeeeEecCCCccccceEEEEEEEcCCCCCEEe
Confidence 78999999998765332 233 233556788999988775
No 89
>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=30.99 E-value=24 Score=23.66 Aligned_cols=24 Identities=17% Similarity=0.376 Sum_probs=12.2
Q ss_pred CCcccCCcceecce---eEeeCCcccc
Q 040947 8 DKCKACDKTVYVVD---MLSLEGMPYH 31 (210)
Q Consensus 8 ~~C~~C~~~I~~~~---~v~~~g~~~H 31 (210)
..|..|+..|+++. +|..+|+.++
T Consensus 4 ~~C~Fsg~~I~PG~G~~~Vr~DG~v~~ 30 (71)
T PF01246_consen 4 EKCSFSGYKIYPGHGKMYVRNDGKVFY 30 (71)
T ss_dssp EE-TTT-SEE-SSSSEEEE-TTS-EEE
T ss_pred EEecccCCccCCCCCeEEEecCCCeEE
Confidence 46888888888764 3455555554
No 90
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=30.95 E-value=13 Score=32.12 Aligned_cols=29 Identities=10% Similarity=0.219 Sum_probs=17.1
Q ss_pred cccccccCCCCCCCeeccCCeeeccchHH
Q 040947 35 FKCSHCKGTLVMSNYSSMDGVLYCKPHFE 63 (210)
Q Consensus 35 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~ 63 (210)
-.|..|+.+|..=.--+-=+.+||.+|..
T Consensus 91 HfCd~Cd~PI~IYGRmIPCkHvFCl~CAr 119 (389)
T KOG2932|consen 91 HFCDRCDFPIAIYGRMIPCKHVFCLECAR 119 (389)
T ss_pred EeecccCCcceeeecccccchhhhhhhhh
Confidence 34778888776322223355677777764
No 91
>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=30.75 E-value=47 Score=20.41 Aligned_cols=9 Identities=11% Similarity=0.349 Sum_probs=7.2
Q ss_pred ecHhHHHhh
Q 040947 153 YCKHHFAQL 161 (210)
Q Consensus 153 yC~~c~~~~ 161 (210)
+|..||...
T Consensus 28 lC~~C~~~~ 36 (48)
T cd02341 28 LCQDCVVKG 36 (48)
T ss_pred cCHHHHhCc
Confidence 699999864
No 92
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=30.72 E-value=28 Score=23.00 Aligned_cols=13 Identities=23% Similarity=0.450 Sum_probs=7.2
Q ss_pred CCcccCCcceecc
Q 040947 8 DKCKACDKTVYVV 20 (210)
Q Consensus 8 ~~C~~C~~~I~~~ 20 (210)
.+|..|+..|+++
T Consensus 4 ~~CsFcG~~I~PG 16 (66)
T COG2075 4 RVCSFCGKKIEPG 16 (66)
T ss_pred eEecCcCCccCCC
Confidence 3455566666554
No 93
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=30.70 E-value=32 Score=33.00 Aligned_cols=10 Identities=20% Similarity=0.733 Sum_probs=5.8
Q ss_pred Ccccccccee
Q 040947 104 DKCAACEKTV 113 (210)
Q Consensus 104 ~~C~~C~~~I 113 (210)
..|..|+..+
T Consensus 42 ~fC~~CG~~~ 51 (645)
T PRK14559 42 AHCPNCGAET 51 (645)
T ss_pred ccccccCCcc
Confidence 3566666654
No 94
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=30.67 E-value=31 Score=28.65 Aligned_cols=28 Identities=11% Similarity=0.205 Sum_probs=16.6
Q ss_pred ccCCCCCCCeecc-CCeeeccchHHHhhh
Q 040947 40 CKGTLVMSNYSSM-DGVLYCKPHFEQLFK 67 (210)
Q Consensus 40 C~~~L~~~~f~~~-~g~~yC~~cy~~~~~ 67 (210)
|+..-....|+.. =..++|..|...-.+
T Consensus 9 C~~~~~~~~f~LTaC~HvfC~~C~k~~~~ 37 (233)
T KOG4739|consen 9 CFRFPSQDPFFLTACRHVFCEPCLKASSP 37 (233)
T ss_pred ccccCCCCceeeeechhhhhhhhcccCCc
Confidence 3333334456643 567889988865543
No 95
>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=29.83 E-value=18 Score=20.58 Aligned_cols=31 Identities=29% Similarity=0.672 Sum_probs=17.4
Q ss_pred CcccCCcceecce-eEeeCCccccCCCcccccccCCC
Q 040947 9 KCKACDKTVYVVD-MLSLEGMPYHKSCFKCSHCKGTL 44 (210)
Q Consensus 9 ~C~~C~~~I~~~~-~v~~~g~~~H~~CF~C~~C~~~L 44 (210)
.|..|+..+...+ .+...+. -++|..|+..|
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~-----~v~C~~C~~~~ 35 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGG-----KVRCGKCGHVW 35 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCC-----EEECCCCCCEE
Confidence 4888887765332 2222221 36777777665
No 96
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=29.66 E-value=10 Score=23.91 Aligned_cols=26 Identities=23% Similarity=0.616 Sum_probs=14.3
Q ss_pred ccccccCCCCCCCeecc---CCeeeccch
Q 040947 36 KCSHCKGTLVMSNYSSM---DGVLYCKPH 61 (210)
Q Consensus 36 ~C~~C~~~L~~~~f~~~---~g~~yC~~c 61 (210)
+|..|+-.|..+.+... ++.++|..|
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~C 52 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNC 52 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCC
Confidence 56666666665544422 345666655
No 97
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=29.20 E-value=48 Score=21.80 Aligned_cols=33 Identities=18% Similarity=0.426 Sum_probs=22.2
Q ss_pred CCCCCcccCCcceecceeEeeCCccccCCCcccccccCC
Q 040947 5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGT 43 (210)
Q Consensus 5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~ 43 (210)
++...|+.|+..+. .+.+.+..|- |.|..|+..
T Consensus 4 d~lKPCPFCG~~~~---~v~~~~g~~~---v~C~~CgA~ 36 (64)
T PRK09710 4 DNVKPCPFCGCPSV---TVKAISGYYR---AKCNGCESR 36 (64)
T ss_pred ccccCCCCCCCcee---EEEecCceEE---EEcCCCCcC
Confidence 45678999999875 4556676665 555566553
No 98
>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=28.82 E-value=15 Score=21.76 Aligned_cols=9 Identities=22% Similarity=0.944 Sum_probs=4.8
Q ss_pred cccccccee
Q 040947 105 KCAACEKTV 113 (210)
Q Consensus 105 ~C~~C~~~I 113 (210)
+|..|+...
T Consensus 7 ~C~~Cg~~f 15 (42)
T PF09723_consen 7 RCEECGHEF 15 (42)
T ss_pred EeCCCCCEE
Confidence 455665443
No 99
>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=28.65 E-value=48 Score=19.74 Aligned_cols=9 Identities=22% Similarity=0.253 Sum_probs=6.5
Q ss_pred ecHhHHHhh
Q 040947 153 YCKHHFAQL 161 (210)
Q Consensus 153 yC~~c~~~~ 161 (210)
+|..||...
T Consensus 25 LC~~C~~~~ 33 (43)
T cd02340 25 LCESCEAKG 33 (43)
T ss_pred chHHhhCcC
Confidence 688888753
No 100
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=27.55 E-value=34 Score=20.16 Aligned_cols=12 Identities=25% Similarity=0.542 Sum_probs=5.7
Q ss_pred cccccccCCCCC
Q 040947 35 FKCSHCKGTLVM 46 (210)
Q Consensus 35 F~C~~C~~~L~~ 46 (210)
+.|..||..|..
T Consensus 20 ~vC~~CG~Vl~e 31 (43)
T PF08271_consen 20 LVCPNCGLVLEE 31 (43)
T ss_dssp EEETTT-BBEE-
T ss_pred EECCCCCCEeec
Confidence 556666555543
No 101
>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=27.36 E-value=41 Score=20.41 Aligned_cols=12 Identities=25% Similarity=0.653 Sum_probs=8.5
Q ss_pred CCCCcccCCcce
Q 040947 6 TLDKCKACDKTV 17 (210)
Q Consensus 6 ~~~~C~~C~~~I 17 (210)
....|..|++.|
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 102
>PRK04023 DNA polymerase II large subunit; Validated
Probab=27.13 E-value=61 Score=32.71 Aligned_cols=16 Identities=31% Similarity=0.742 Sum_probs=9.6
Q ss_pred CccccccceeecCcee
Q 040947 104 DKCAACEKTVYPLEKV 119 (210)
Q Consensus 104 ~~C~~C~~~I~~~e~v 119 (210)
..|..|+..+.+...+
T Consensus 664 y~CPKCG~El~~~s~~ 679 (1121)
T PRK04023 664 DECEKCGREPTPYSKR 679 (1121)
T ss_pred CcCCCCCCCCCccceE
Confidence 4577777776654433
No 103
>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=27.05 E-value=39 Score=20.30 Aligned_cols=28 Identities=25% Similarity=0.459 Sum_probs=15.4
Q ss_pred CcccCCcceecceeE--eeCCccccCCCcc
Q 040947 9 KCKACDKTVYVVDML--SLEGMPYHKSCFK 36 (210)
Q Consensus 9 ~C~~C~~~I~~~~~v--~~~g~~~H~~CF~ 36 (210)
+|..|++.-..+++| ..=++.||..|..
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~ 30 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVG 30 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTST
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCC
Confidence 367777743333344 2334677887753
No 104
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=26.52 E-value=34 Score=23.52 Aligned_cols=28 Identities=25% Similarity=0.648 Sum_probs=15.6
Q ss_pred cCCCCCcCCCCC-e-eecC---CeeecHhHHHh
Q 040947 133 CAHGGCPLTHSS-Y-AALD---GVLYCKHHFAQ 160 (210)
Q Consensus 133 C~~C~~~l~~~~-f-~~~d---g~~yC~~c~~~ 160 (210)
|..||-+|.... + ...| ..-||.-||..
T Consensus 3 CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 3 CQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred CCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 666666665443 2 1223 34588888864
No 105
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=25.83 E-value=7.4 Score=27.70 Aligned_cols=50 Identities=16% Similarity=0.416 Sum_probs=32.6
Q ss_pred cccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeecc
Q 040947 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK 59 (210)
Q Consensus 10 C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~ 59 (210)
|..|+..+..-..+...-..+|+.+..|..|.+.|.-..|.....-+||.
T Consensus 38 Cy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~ 87 (105)
T COG4357 38 CYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYCQ 87 (105)
T ss_pred HHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCcC
Confidence 55565555544445555567888888888888888765666555555554
No 106
>PLN02195 cellulose synthase A
Probab=25.38 E-value=58 Score=32.65 Aligned_cols=38 Identities=24% Similarity=0.581 Sum_probs=25.7
Q ss_pred CCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHH
Q 040947 5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFE 63 (210)
Q Consensus 5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~ 63 (210)
++..+|..|+..|- +..+|..| .-|..|+- +.|..||+
T Consensus 4 ~~~~~c~~cgd~~~----~~~~g~~f----vaC~eC~~-------------pvCrpCye 41 (977)
T PLN02195 4 SGAPICATCGEEVG----VDSNGEAF----VACHECSY-------------PLCKACLE 41 (977)
T ss_pred CCCccceecccccC----cCCCCCeE----EEeccCCC-------------ccccchhh
Confidence 45678999998885 55677766 34455533 45888884
No 107
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=24.90 E-value=33 Score=20.69 Aligned_cols=9 Identities=22% Similarity=0.778 Sum_probs=4.3
Q ss_pred cccccccee
Q 040947 105 KCAACEKTV 113 (210)
Q Consensus 105 ~C~~C~~~I 113 (210)
+|..|+..+
T Consensus 4 ~C~~Cg~~~ 12 (44)
T smart00659 4 ICGECGREN 12 (44)
T ss_pred ECCCCCCEe
Confidence 455555444
No 108
>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=24.74 E-value=19 Score=21.53 Aligned_cols=26 Identities=27% Similarity=0.594 Sum_probs=8.7
Q ss_pred cccccceeecCceeE--ecCcccccccc
Q 040947 106 CAACEKTVYPLEKVT--MEGDCFHKTCF 131 (210)
Q Consensus 106 C~~C~~~I~~~e~v~--~~g~~~H~~CF 131 (210)
|..|.+.|+-+.+=. .-+..||..|+
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~ 28 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCF 28 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHH
T ss_pred CcccchhHeeeccCCCCccCchHHHHHH
Confidence 445666555333211 12334666665
No 109
>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=24.53 E-value=22 Score=21.76 Aligned_cols=8 Identities=38% Similarity=1.178 Sum_probs=4.0
Q ss_pred ccccccce
Q 040947 105 KCAACEKT 112 (210)
Q Consensus 105 ~C~~C~~~ 112 (210)
+|..|+..
T Consensus 7 ~C~~Cg~~ 14 (52)
T TIGR02605 7 RCTACGHR 14 (52)
T ss_pred EeCCCCCE
Confidence 45555543
No 110
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=24.15 E-value=59 Score=33.58 Aligned_cols=10 Identities=20% Similarity=0.823 Sum_probs=5.1
Q ss_pred ccccccceee
Q 040947 105 KCAACEKTVY 114 (210)
Q Consensus 105 ~C~~C~~~I~ 114 (210)
.|+.|+.++.
T Consensus 711 ~CP~CGtplv 720 (1337)
T PRK14714 711 ECPRCDVELT 720 (1337)
T ss_pred cCCCCCCccc
Confidence 4555555444
No 111
>PRK12495 hypothetical protein; Provisional
Probab=23.95 E-value=45 Score=27.46 Aligned_cols=27 Identities=19% Similarity=0.533 Sum_probs=17.6
Q ss_pred CCcccccccCCCCCCCeeccCCeeeccchHHH
Q 040947 33 SCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQ 64 (210)
Q Consensus 33 ~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~ 64 (210)
.-|.|..|+.+|. .+.|..||..|-..
T Consensus 41 sa~hC~~CG~PIp-----a~pG~~~Cp~CQ~~ 67 (226)
T PRK12495 41 TNAHCDECGDPIF-----RHDGQEFCPTCQQP 67 (226)
T ss_pred chhhcccccCccc-----CCCCeeECCCCCCc
Confidence 3456777777775 34777777777643
No 112
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=23.75 E-value=40 Score=28.10 Aligned_cols=30 Identities=20% Similarity=0.439 Sum_probs=24.0
Q ss_pred cccccCCCCCcCCCCCeeecCCeeecHhHH
Q 040947 129 TCFRCAHGGCPLTHSSYAALDGVLYCKHHF 158 (210)
Q Consensus 129 ~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~ 158 (210)
+=-.|+.|+.+++...|+...|...|..|+
T Consensus 153 ~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 153 NLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred chHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 334688888888877788888888898887
No 113
>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=23.68 E-value=22 Score=27.61 Aligned_cols=30 Identities=17% Similarity=0.340 Sum_probs=22.7
Q ss_pred CcccCCcceecceeEeeCCccccCCCcccccccCCCCC
Q 040947 9 KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVM 46 (210)
Q Consensus 9 ~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~ 46 (210)
.|..|+......+.+. .=|+|..||..|..
T Consensus 111 ~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 111 ICPNMCVRFTFNEAME--------LNFTCPRCGAMLDY 140 (158)
T ss_pred ECCCCCcEeeHHHHHH--------cCCcCCCCCCEeee
Confidence 6999998887555553 24999999999863
No 114
>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=23.30 E-value=22 Score=20.34 Aligned_cols=10 Identities=30% Similarity=0.836 Sum_probs=6.2
Q ss_pred ccccccceee
Q 040947 105 KCAACEKTVY 114 (210)
Q Consensus 105 ~C~~C~~~I~ 114 (210)
+|..|+..+.
T Consensus 7 ~C~~Cg~~fe 16 (41)
T smart00834 7 RCEDCGHTFE 16 (41)
T ss_pred EcCCCCCEEE
Confidence 5777766553
No 115
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.26 E-value=59 Score=24.42 Aligned_cols=37 Identities=19% Similarity=0.410 Sum_probs=26.5
Q ss_pred CccccccceeecCce---eEecCccccccccccCCCCCcCC
Q 040947 104 DKCAACEKTVYPLEK---VTMEGDCFHKTCFRCAHGGCPLT 141 (210)
Q Consensus 104 ~~C~~C~~~I~~~e~---v~~~g~~~H~~CF~C~~C~~~l~ 141 (210)
..|+.|+.+|..... |..+|.-|-+--| |..|+.++.
T Consensus 40 ~qcp~csasirgd~~vegvlglg~dye~psf-chncgs~fp 79 (160)
T COG4306 40 TQCPICSASIRGDYYVEGVLGLGGDYEPPSF-CHNCGSRFP 79 (160)
T ss_pred hcCCccCCcccccceeeeeeccCCCCCCcch-hhcCCCCCC
Confidence 579999999985433 4456777777554 788888774
No 116
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=23.13 E-value=45 Score=18.69 Aligned_cols=10 Identities=30% Similarity=0.670 Sum_probs=5.5
Q ss_pred CcccCCccee
Q 040947 9 KCKACDKTVY 18 (210)
Q Consensus 9 ~C~~C~~~I~ 18 (210)
+|+.|+..+.
T Consensus 2 ~C~~Cg~~~~ 11 (32)
T PF03604_consen 2 ICGECGAEVE 11 (32)
T ss_dssp BESSSSSSE-
T ss_pred CCCcCCCeeE
Confidence 3666666654
No 117
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=23.12 E-value=42 Score=28.59 Aligned_cols=26 Identities=15% Similarity=0.437 Sum_probs=16.5
Q ss_pred CccccccceeecCceeEecCccccccc
Q 040947 104 DKCAACEKTVYPLEKVTMEGDCFHKTC 130 (210)
Q Consensus 104 ~~C~~C~~~I~~~e~v~~~g~~~H~~C 130 (210)
.-|.+|+.+|. ...+.-.+..|.+.|
T Consensus 246 epC~~CGt~I~-k~~~~gR~t~~CP~C 271 (273)
T COG0266 246 EPCRRCGTPIE-KIKLGGRSTFYCPVC 271 (273)
T ss_pred CCCCccCCEeE-EEEEcCCcCEeCCCC
Confidence 67999999996 333344445555444
No 118
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=23.08 E-value=24 Score=22.13 Aligned_cols=26 Identities=19% Similarity=0.451 Sum_probs=16.5
Q ss_pred cccccccCCCCC-CCeeccCCeeeccchH
Q 040947 35 FKCSHCKGTLVM-SNYSSMDGVLYCKPHF 62 (210)
Q Consensus 35 F~C~~C~~~L~~-~~f~~~~g~~yC~~cy 62 (210)
++|..|++.|.. +.+. ...+-|.+|-
T Consensus 5 iRC~~CnklLa~~g~~~--~leIKCpRC~ 31 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVI--ELEIKCPRCK 31 (51)
T ss_pred eeccchhHHHhhhcCcc--EEEEECCCCC
Confidence 678888888775 2333 4456676664
No 119
>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=22.97 E-value=38 Score=19.31 Aligned_cols=11 Identities=36% Similarity=0.887 Sum_probs=4.8
Q ss_pred CCcccCCccee
Q 040947 8 DKCKACDKTVY 18 (210)
Q Consensus 8 ~~C~~C~~~I~ 18 (210)
+.|..|+++..
T Consensus 4 ~~C~eC~~~f~ 14 (34)
T PF01286_consen 4 PKCDECGKPFM 14 (34)
T ss_dssp EE-TTT--EES
T ss_pred chHhHhCCHHH
Confidence 45666666654
No 120
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=22.92 E-value=35 Score=19.50 Aligned_cols=30 Identities=23% Similarity=0.612 Sum_probs=15.7
Q ss_pred CcccCCcceecce-eEeeCCccccCCCcccccccCC
Q 040947 9 KCKACDKTVYVVD-MLSLEGMPYHKSCFKCSHCKGT 43 (210)
Q Consensus 9 ~C~~C~~~I~~~~-~v~~~g~~~H~~CF~C~~C~~~ 43 (210)
.|..|+......+ .|...|.. ++|..|+..
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 4777776654332 34444433 566666543
No 121
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=22.81 E-value=1.3e+02 Score=20.68 Aligned_cols=38 Identities=21% Similarity=0.470 Sum_probs=13.4
Q ss_pred CccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhh
Q 040947 104 DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLF 162 (210)
Q Consensus 104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f 162 (210)
..|..|+..|- +.+.|..|- . |..| +.|.|+.||+-..
T Consensus 10 qiCqiCGD~VG----l~~~Ge~FV-A---C~eC-------------~fPvCr~CyEYEr 47 (80)
T PF14569_consen 10 QICQICGDDVG----LTENGEVFV-A---CHEC-------------AFPVCRPCYEYER 47 (80)
T ss_dssp -B-SSS--B------B-SSSSB---S----SSS------------------HHHHHHHH
T ss_pred cccccccCccc----cCCCCCEEE-E---Eccc-------------CCccchhHHHHHh
Confidence 67888877763 344444431 1 2222 3467999987543
No 122
>PHA00080 DksA-like zinc finger domain containing protein
Probab=22.71 E-value=29 Score=23.26 Aligned_cols=11 Identities=18% Similarity=0.709 Sum_probs=5.7
Q ss_pred Cccccccceee
Q 040947 104 DKCAACEKTVY 114 (210)
Q Consensus 104 ~~C~~C~~~I~ 114 (210)
..|..|+.+|.
T Consensus 32 ~~C~~Cg~~Ip 42 (72)
T PHA00080 32 THCEECGDPIP 42 (72)
T ss_pred CEecCCCCcCc
Confidence 34555555553
No 123
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.64 E-value=40 Score=28.95 Aligned_cols=33 Identities=21% Similarity=0.483 Sum_probs=20.0
Q ss_pred cccccccCCCCCCCee---ccCCeeeccchHHHhhh
Q 040947 35 FKCSHCKGTLVMSNYS---SMDGVLYCKPHFEQLFK 67 (210)
Q Consensus 35 F~C~~C~~~L~~~~f~---~~~g~~yC~~cy~~~~~ 67 (210)
++|+.|+.+|.+..|. .+...-||-.|-.+...
T Consensus 269 LcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK 304 (352)
T KOG3579|consen 269 LCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIK 304 (352)
T ss_pred eeehhhhhhhccCceeecCCCcccceecccCHHHHH
Confidence 6666666666666655 34555666666655544
No 124
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=22.47 E-value=32 Score=22.18 Aligned_cols=15 Identities=33% Similarity=0.782 Sum_probs=12.4
Q ss_pred CccccccceeecCce
Q 040947 104 DKCAACEKTVYPLEK 118 (210)
Q Consensus 104 ~~C~~C~~~I~~~e~ 118 (210)
..|..|+++|.++|.
T Consensus 9 ~HC~VCg~aIp~de~ 23 (64)
T COG4068 9 RHCVVCGKAIPPDEQ 23 (64)
T ss_pred ccccccCCcCCCccc
Confidence 479999999987764
No 125
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=22.37 E-value=80 Score=23.84 Aligned_cols=28 Identities=25% Similarity=0.463 Sum_probs=15.8
Q ss_pred ccCCCCCcCCCCCeeecCCeeecHhHHHhhh
Q 040947 132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQLF 162 (210)
Q Consensus 132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f 162 (210)
+|..|++.+..+.-.+..| |..|=.++|
T Consensus 3 ~Ct~Cg~~f~dgs~eil~G---CP~CGg~kF 30 (131)
T PF09845_consen 3 QCTKCGRVFEDGSKEILSG---CPECGGNKF 30 (131)
T ss_pred ccCcCCCCcCCCcHHHHcc---CcccCCcce
Confidence 4777777776554444454 444444444
No 126
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.33 E-value=60 Score=29.20 Aligned_cols=33 Identities=12% Similarity=0.355 Sum_probs=23.9
Q ss_pred CcccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947 34 CFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK 67 (210)
Q Consensus 34 CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~ 67 (210)
-|.|..|...+... ....=|..||..|....+.
T Consensus 26 ~l~C~IC~d~~~~P-vitpCgH~FCs~CI~~~l~ 58 (397)
T TIGR00599 26 SLRCHICKDFFDVP-VLTSCSHTFCSLCIRRCLS 58 (397)
T ss_pred ccCCCcCchhhhCc-cCCCCCCchhHHHHHHHHh
Confidence 47888888877653 3445678899999887664
No 127
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=22.25 E-value=45 Score=28.38 Aligned_cols=18 Identities=22% Similarity=0.599 Sum_probs=12.9
Q ss_pred cCCCcccccccCCCCCCC
Q 040947 31 HKSCFKCSHCKGTLVMSN 48 (210)
Q Consensus 31 H~~CF~C~~C~~~L~~~~ 48 (210)
-...++|..|++.+....
T Consensus 127 ~~~r~~c~eCgk~ysT~s 144 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSS 144 (279)
T ss_pred cCCceecccccccccccc
Confidence 345688888988887543
No 128
>PLN02436 cellulose synthase A
Probab=21.98 E-value=70 Score=32.47 Aligned_cols=55 Identities=24% Similarity=0.722 Sum_probs=0.0
Q ss_pred CCCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCC
Q 040947 4 TGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPS 83 (210)
Q Consensus 4 ~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~ 83 (210)
.....+|..|+..|- +.++|..| .-|..|+-++ |..||+-.-....
T Consensus 33 ~~~~~iCqICGD~Vg----~t~dGe~F----VACn~C~fpv-------------Cr~Cyeyer~eg~------------- 78 (1094)
T PLN02436 33 ELSGQTCQICGDEIE----LTVDGEPF----VACNECAFPV-------------CRPCYEYERREGN------------- 78 (1094)
T ss_pred ccCCccccccccccC----cCCCCCEE----EeeccCCCcc-------------ccchhhhhhhcCC-------------
Q ss_pred CCCCCCCCCCCcccccCCCCCccccccce
Q 040947 84 SCSNQNRTPSKLSSLFSGTQDKCAACEKT 112 (210)
Q Consensus 84 ~~~~~~~~~~~~~~~~~g~~~~C~~C~~~ 112 (210)
..|+.|+..
T Consensus 79 --------------------~~Cpqckt~ 87 (1094)
T PLN02436 79 --------------------QACPQCKTR 87 (1094)
T ss_pred --------------------ccCcccCCc
No 129
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=21.88 E-value=72 Score=32.40 Aligned_cols=55 Identities=25% Similarity=0.707 Sum_probs=0.0
Q ss_pred CCCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCC
Q 040947 4 TGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPS 83 (210)
Q Consensus 4 ~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~ 83 (210)
..+..+|..|+..|- +.++|..| .-|..|+-++ |..||+-.-.-..
T Consensus 14 ~~~~qiCqICGD~vg----~~~~Ge~F----VAC~eC~FPV-------------CrpCYEYEr~eG~------------- 59 (1079)
T PLN02638 14 HGGGQVCQICGDNVG----KTVDGEPF----VACDVCAFPV-------------CRPCYEYERKDGN------------- 59 (1079)
T ss_pred ccCCceeeecccccC----cCCCCCEE----EEeccCCCcc-------------ccchhhhhhhcCC-------------
Q ss_pred CCCCCCCCCCCcccccCCCCCccccccce
Q 040947 84 SCSNQNRTPSKLSSLFSGTQDKCAACEKT 112 (210)
Q Consensus 84 ~~~~~~~~~~~~~~~~~g~~~~C~~C~~~ 112 (210)
..|+.|+..
T Consensus 60 --------------------q~CPqCktr 68 (1079)
T PLN02638 60 --------------------QSCPQCKTK 68 (1079)
T ss_pred --------------------ccCCccCCc
No 130
>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=21.87 E-value=69 Score=18.60 Aligned_cols=20 Identities=10% Similarity=0.109 Sum_probs=12.9
Q ss_pred CCCeeecCCeeecHhHHHhh
Q 040947 142 HSSYAALDGVLYCKHHFAQL 161 (210)
Q Consensus 142 ~~~f~~~dg~~yC~~c~~~~ 161 (210)
++.....+-.+.|..|...+
T Consensus 25 gg~~~~~Nl~~lC~~Ch~~k 44 (47)
T PF01844_consen 25 GGKNDLENLILLCPSCHRKK 44 (47)
T ss_dssp T---STTTEEEEEHHHHHHH
T ss_pred CCCCCHHHHHHHhHHHHHHh
Confidence 44455667788999998764
No 131
>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 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=21.77 E-value=36 Score=16.67 Aligned_cols=12 Identities=17% Similarity=0.637 Sum_probs=8.3
Q ss_pred cccCCCCCcCCC
Q 040947 131 FRCAHGGCPLTH 142 (210)
Q Consensus 131 F~C~~C~~~l~~ 142 (210)
|+|..|++.+..
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 567888876653
No 133
>PLN02189 cellulose synthase
Probab=21.73 E-value=72 Score=32.27 Aligned_cols=55 Identities=22% Similarity=0.624 Sum_probs=0.0
Q ss_pred CCCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCC
Q 040947 4 TGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPS 83 (210)
Q Consensus 4 ~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~ 83 (210)
.....+|..|+..|- +..+|..| .-|..|+-++ |..||+-.-....
T Consensus 31 ~~~~~~C~iCgd~vg----~~~~g~~f----vaC~~C~fpv-------------Cr~Cyeyer~eg~------------- 76 (1040)
T PLN02189 31 NLDGQVCEICGDEIG----LTVDGDLF----VACNECGFPV-------------CRPCYEYERREGT------------- 76 (1040)
T ss_pred cccCccccccccccC----cCCCCCEE----EeeccCCCcc-------------ccchhhhhhhcCC-------------
Q ss_pred CCCCCCCCCCCcccccCCCCCccccccce
Q 040947 84 SCSNQNRTPSKLSSLFSGTQDKCAACEKT 112 (210)
Q Consensus 84 ~~~~~~~~~~~~~~~~~g~~~~C~~C~~~ 112 (210)
..|+.|+..
T Consensus 77 --------------------q~CpqCkt~ 85 (1040)
T PLN02189 77 --------------------QNCPQCKTR 85 (1040)
T ss_pred --------------------ccCcccCCc
No 134
>PHA02929 N1R/p28-like protein; Provisional
Probab=21.66 E-value=52 Score=27.44 Aligned_cols=38 Identities=26% Similarity=0.575 Sum_probs=24.0
Q ss_pred CccccccceeecCc-------eeEecCcccccccc--------ccCCCCCcCC
Q 040947 104 DKCAACEKTVYPLE-------KVTMEGDCFHKTCF--------RCAHGGCPLT 141 (210)
Q Consensus 104 ~~C~~C~~~I~~~e-------~v~~~g~~~H~~CF--------~C~~C~~~l~ 141 (210)
..|+.|...+...+ .+..-++.||..|+ .|-.|...+.
T Consensus 175 ~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 175 KECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred CCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 57999988776432 12234677777777 4666666553
No 135
>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=21.44 E-value=75 Score=19.40 Aligned_cols=11 Identities=9% Similarity=0.211 Sum_probs=7.9
Q ss_pred eecHhHHHhhh
Q 040947 152 LYCKHHFAQLF 162 (210)
Q Consensus 152 ~yC~~c~~~~f 162 (210)
-+|..||....
T Consensus 25 dlC~~Cf~~~~ 35 (49)
T cd02338 25 DLCADCYDSGV 35 (49)
T ss_pred ccchhHHhCCC
Confidence 36999998543
No 136
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=21.29 E-value=46 Score=20.87 Aligned_cols=30 Identities=17% Similarity=0.467 Sum_probs=19.0
Q ss_pred ccccccceeecCceeEecCccccccccccC
Q 040947 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCA 134 (210)
Q Consensus 105 ~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~ 134 (210)
.|+-|+.+|...--....++.|-.+|-+|.
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC 31 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCC 31 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcC
Confidence 488888888621113445677888876664
No 137
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=21.24 E-value=46 Score=27.74 Aligned_cols=33 Identities=15% Similarity=0.312 Sum_probs=26.8
Q ss_pred ccCCCcccccccCCCCCCCeeccCCeeeccchH
Q 040947 30 YHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHF 62 (210)
Q Consensus 30 ~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy 62 (210)
|=++=..|..|+.+.+...|+...+...|..|+
T Consensus 150 ~~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 150 IGPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred CccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 445556788999999888888889999998887
No 138
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=21.06 E-value=21 Score=29.96 Aligned_cols=41 Identities=20% Similarity=0.455 Sum_probs=28.6
Q ss_pred CcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCee
Q 040947 9 KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYS 50 (210)
Q Consensus 9 ~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~ 50 (210)
.|..|+..|. ...|.---..-|-.+|.|-.|++.+....|.
T Consensus 5 tCnvCgEsvK-Kp~vekH~srCrn~~fSCIDC~k~F~~~sYk 45 (276)
T KOG2186|consen 5 TCNVCGESVK-KPQVEKHMSRCRNAYFSCIDCGKTFERVSYK 45 (276)
T ss_pred ehhhhhhhcc-ccchHHHHHhccCCeeEEeecccccccchhh
Confidence 5889999886 3323221223477899999999999876654
No 139
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=20.59 E-value=59 Score=20.92 Aligned_cols=28 Identities=21% Similarity=0.312 Sum_probs=19.1
Q ss_pred ccccccCCCCC-C-CeeccCCeeecc-chHH
Q 040947 36 KCSHCKGTLVM-S-NYSSMDGVLYCK-PHFE 63 (210)
Q Consensus 36 ~C~~C~~~L~~-~-~f~~~~g~~yC~-~cy~ 63 (210)
.|..|++.|.. . .|..++.+.+|. .|-.
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS~ECR~ 48 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCSEECRS 48 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccccHHHHH
Confidence 46778899983 3 455667889995 4543
No 140
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=20.46 E-value=38 Score=31.96 Aligned_cols=33 Identities=18% Similarity=0.411 Sum_probs=24.4
Q ss_pred CCCcccccccCCCCCCC-----eeccCCeeeccchHHH
Q 040947 32 KSCFKCSHCKGTLVMSN-----YSSMDGVLYCKPHFEQ 64 (210)
Q Consensus 32 ~~CF~C~~C~~~L~~~~-----f~~~~g~~yC~~cy~~ 64 (210)
..-|+|+.|+.+|.... +-...|+.||..|...
T Consensus 338 aQ~~~CAgC~~~i~~~~~~~~R~C~y~G~y~C~~Ch~~ 375 (580)
T KOG1829|consen 338 AQNFRCAGCGHTIGPDLEQRPRLCRYLGKYFCDCCHQN 375 (580)
T ss_pred ccCceecccCCCcccccccchhHhhhhhhhhCchhccc
Confidence 35689999999998432 2356889999988853
No 141
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=20.38 E-value=1.1e+02 Score=18.74 Aligned_cols=9 Identities=11% Similarity=0.353 Sum_probs=7.2
Q ss_pred ecHhHHHhh
Q 040947 153 YCKHHFAQL 161 (210)
Q Consensus 153 yC~~c~~~~ 161 (210)
+|..||...
T Consensus 26 LC~~Cf~~~ 34 (49)
T cd02345 26 LCLGCYTKG 34 (49)
T ss_pred chHHHHhCC
Confidence 699999854
Done!