Query 041875
Match_columns 195
No_of_seqs 215 out of 1291
Neff 8.5
Searched_HMMs 46136
Date Fri Mar 29 11:37:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041875.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041875hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701 Focal adhesion adaptor 99.9 1.1E-29 2.3E-34 211.4 -1.3 134 8-175 275-411 (468)
2 KOG2272 Focal adhesion protein 99.9 1.8E-25 4E-30 175.0 -1.6 160 7-168 73-264 (332)
3 KOG1701 Focal adhesion adaptor 99.9 1.1E-24 2.3E-29 181.6 0.8 126 3-161 330-466 (468)
4 KOG4577 Transcription factor L 99.9 2.3E-23 5E-28 165.9 -2.3 125 6-163 32-159 (383)
5 KOG2272 Focal adhesion protein 99.8 3.2E-22 6.9E-27 156.9 -0.3 117 6-156 194-311 (332)
6 KOG1700 Regulatory protein MLP 99.8 2.2E-21 4.8E-26 151.7 3.5 176 1-176 1-185 (200)
7 KOG1703 Adaptor protein Enigma 99.8 1.2E-20 2.7E-25 165.5 5.8 130 6-168 302-431 (479)
8 KOG1044 Actin-binding LIM Zn-f 99.8 1.9E-20 4.1E-25 161.2 4.8 161 8-171 17-204 (670)
9 KOG1703 Adaptor protein Enigma 99.7 1.4E-19 3E-24 158.9 0.2 117 5-154 361-478 (479)
10 KOG1044 Actin-binding LIM Zn-f 99.7 4.5E-18 9.8E-23 146.7 2.1 115 6-154 132-247 (670)
11 PF00412 LIM: LIM domain; Int 99.6 1.1E-15 2.4E-20 96.5 5.2 57 10-66 1-58 (58)
12 PF00412 LIM: LIM domain; Int 99.6 2.4E-15 5.3E-20 94.9 5.2 57 102-158 1-58 (58)
13 KOG4577 Transcription factor L 99.2 6.5E-13 1.4E-17 106.5 -2.3 82 98-180 32-114 (383)
14 smart00132 LIM Zinc-binding do 98.8 3E-09 6.6E-14 61.0 2.7 37 9-45 1-38 (39)
15 smart00132 LIM Zinc-binding do 98.7 1.6E-08 3.4E-13 58.0 2.7 37 101-137 1-38 (39)
16 KOG1700 Regulatory protein MLP 98.5 2.4E-08 5.1E-13 78.4 1.2 68 100-167 8-76 (200)
17 KOG1702 Nebulin repeat protein 98.4 2.8E-08 6E-13 76.6 -1.8 81 100-185 5-85 (264)
18 KOG0490 Transcription factor, 97.9 1.6E-06 3.5E-11 69.1 -1.4 111 13-157 2-119 (235)
19 KOG1702 Nebulin repeat protein 97.8 1.8E-06 3.8E-11 66.8 -2.3 59 7-65 4-62 (264)
20 KOG0490 Transcription factor, 92.3 0.047 1E-06 43.3 0.4 58 105-163 2-63 (235)
21 smart00504 Ubox Modified RING 89.3 0.59 1.3E-05 29.0 3.4 32 35-67 2-33 (63)
22 PF14446 Prok-RING_1: Prokaryo 87.9 0.38 8.3E-06 29.5 1.7 37 100-136 6-51 (54)
23 PF08394 Arc_trans_TRASH: Arch 86.7 0.37 8E-06 27.2 1.1 28 10-37 1-29 (37)
24 PF09943 DUF2175: Uncharacteri 86.2 0.31 6.7E-06 33.9 0.7 31 100-130 3-34 (101)
25 PF09943 DUF2175: Uncharacteri 85.0 0.29 6.3E-06 34.0 0.1 31 9-39 4-35 (101)
26 PF14835 zf-RING_6: zf-RING of 84.9 0.84 1.8E-05 29.1 2.2 33 35-67 8-40 (65)
27 KOG0320 Predicted E3 ubiquitin 83.6 0.88 1.9E-05 34.9 2.2 53 31-113 128-181 (187)
28 PF10367 Vps39_2: Vacuolar sor 80.7 1.4 3E-05 30.3 2.3 30 99-128 78-108 (109)
29 PF11781 RRN7: RNA polymerase 80.5 1.1 2.4E-05 25.1 1.3 24 35-62 9-32 (36)
30 PF01258 zf-dskA_traR: Prokary 80.2 0.56 1.2E-05 26.1 0.0 28 129-156 6-33 (36)
31 PF10367 Vps39_2: Vacuolar sor 80.0 1.5 3.3E-05 30.2 2.2 29 7-35 78-107 (109)
32 PF08394 Arc_trans_TRASH: Arch 79.8 1.5 3.3E-05 24.7 1.7 28 102-129 1-29 (37)
33 PF10235 Cript: Microtubule-as 79.2 1.3 2.7E-05 30.3 1.5 43 29-111 39-81 (90)
34 PF14471 DUF4428: Domain of un 79.2 1.6 3.6E-05 26.4 1.9 29 36-65 1-30 (51)
35 PF13920 zf-C3HC4_3: Zinc fing 79.0 4.8 0.0001 23.8 4.0 45 35-110 3-48 (50)
36 PF14471 DUF4428: Domain of un 77.4 2.1 4.5E-05 26.0 1.9 29 128-157 1-30 (51)
37 PRK14890 putative Zn-ribbon RN 77.1 2.3 4.9E-05 26.6 2.1 32 3-43 3-34 (59)
38 PF13240 zinc_ribbon_2: zinc-r 76.4 1.4 3E-05 22.0 0.8 9 10-18 2-10 (23)
39 PF14634 zf-RING_5: zinc-RING 75.5 3.6 7.9E-05 23.7 2.6 30 37-66 2-33 (44)
40 PF13923 zf-C3HC4_2: Zinc fing 74.5 4.3 9.3E-05 22.6 2.7 31 37-67 1-31 (39)
41 COG2191 Formylmethanofuran deh 73.7 1.1 2.4E-05 35.1 0.1 31 35-65 173-203 (206)
42 COG2191 Formylmethanofuran deh 73.1 1.2 2.5E-05 34.9 0.1 30 127-156 173-202 (206)
43 KOG2462 C2H2-type Zn-finger pr 69.9 2.1 4.6E-05 35.1 0.9 27 32-58 128-154 (279)
44 PF14835 zf-RING_6: zf-RING of 68.0 3.7 8.1E-05 26.1 1.5 50 127-176 8-57 (65)
45 PF06906 DUF1272: Protein of u 66.3 8.9 0.00019 23.7 2.9 32 36-67 7-41 (57)
46 PF07191 zinc-ribbons_6: zinc- 66.3 3.6 7.7E-05 26.7 1.2 33 100-139 31-63 (70)
47 cd00162 RING RING-finger (Real 65.9 8.2 0.00018 21.2 2.7 31 37-67 2-32 (45)
48 PF02069 Metallothio_Pro: Prok 65.7 3.4 7.3E-05 25.2 1.0 28 128-155 9-37 (52)
49 PF13248 zf-ribbon_3: zinc-rib 63.7 4 8.8E-05 20.8 0.9 11 100-110 3-13 (26)
50 COG4847 Uncharacterized protei 63.3 2.5 5.4E-05 28.9 0.1 31 9-39 8-39 (103)
51 COG5152 Uncharacterized conser 62.7 3 6.4E-05 32.7 0.4 46 34-110 196-241 (259)
52 PRK00807 50S ribosomal protein 62.6 5 0.00011 24.4 1.4 24 8-31 2-28 (52)
53 COG4847 Uncharacterized protei 62.3 3.5 7.6E-05 28.2 0.7 35 100-134 7-42 (103)
54 KOG0978 E3 ubiquitin ligase in 61.8 2.7 5.9E-05 38.9 0.1 51 34-114 643-693 (698)
55 COG1645 Uncharacterized Zn-fin 61.3 3.3 7.2E-05 30.2 0.5 21 129-154 31-51 (131)
56 PF12773 DZR: Double zinc ribb 61.0 4.8 0.0001 23.8 1.1 23 37-63 15-37 (50)
57 PF10083 DUF2321: Uncharacteri 60.3 7.4 0.00016 29.2 2.1 39 100-139 40-81 (158)
58 PF10886 DUF2685: Protein of u 59.9 5.8 0.00013 24.3 1.3 25 100-124 2-26 (54)
59 KOG1813 Predicted E3 ubiquitin 59.0 4.9 0.00011 33.4 1.1 45 35-110 242-286 (313)
60 PF04810 zf-Sec23_Sec24: Sec23 58.4 8.9 0.00019 21.7 1.9 30 100-134 3-32 (40)
61 PF04570 DUF581: Protein of un 55.3 12 0.00025 23.4 2.1 29 36-64 18-49 (58)
62 PF06677 Auto_anti-p27: Sjogre 55.1 4.9 0.00011 23.2 0.4 22 36-61 19-40 (41)
63 PF00645 zf-PARP: Poly(ADP-rib 55.1 5.7 0.00012 26.1 0.8 15 7-21 7-21 (82)
64 COG2888 Predicted Zn-ribbon RN 53.0 11 0.00025 23.5 1.8 30 6-44 8-37 (61)
65 PLN03208 E3 ubiquitin-protein 52.8 22 0.00047 27.8 3.7 32 34-66 18-49 (193)
66 PF07754 DUF1610: Domain of un 52.8 8.5 0.00018 19.5 1.0 10 10-19 1-10 (24)
67 PF04564 U-box: U-box domain; 49.3 38 0.00082 21.7 4.0 34 33-67 3-36 (73)
68 PRK14559 putative protein seri 46.2 11 0.00025 34.9 1.5 11 100-110 42-52 (645)
69 TIGR02098 MJ0042_CXXC MJ0042 f 45.3 11 0.00023 20.8 0.8 32 100-136 3-35 (38)
70 KOG4443 Putative transcription 44.2 8.5 0.00018 35.4 0.3 22 117-138 106-127 (694)
71 cd02249 ZZ Zinc finger, ZZ typ 43.9 19 0.00041 20.9 1.7 11 146-156 22-32 (46)
72 TIGR00570 cdk7 CDK-activating 43.6 29 0.00062 29.2 3.3 30 54-112 27-56 (309)
73 COG2075 RPL24A Ribosomal prote 43.6 15 0.00032 23.5 1.3 14 8-21 4-17 (66)
74 PRK00420 hypothetical protein; 43.5 9.5 0.0002 27.1 0.4 11 100-110 24-34 (112)
75 TIGR00270 conserved hypothetic 43.4 19 0.00042 27.0 2.1 31 128-160 2-35 (154)
76 PF07649 C1_3: C1-like domain; 43.4 13 0.00029 19.4 0.9 12 35-46 1-12 (30)
77 PRK14891 50S ribosomal protein 42.8 16 0.00035 26.5 1.5 25 7-31 4-31 (131)
78 smart00531 TFIIE Transcription 42.5 6.4 0.00014 29.2 -0.6 34 9-45 101-134 (147)
79 cd00472 Ribosomal_L24e_L24 Rib 42.4 14 0.00031 22.6 1.0 24 8-31 4-30 (54)
80 PF13639 zf-RING_2: Ring finge 42.3 8.2 0.00018 22.0 -0.0 27 101-127 2-30 (44)
81 KOG3002 Zn finger protein [Gen 40.8 24 0.00052 29.6 2.5 34 33-66 47-80 (299)
82 PF00097 zf-C3HC4: Zinc finger 40.2 46 0.00099 18.3 3.0 31 37-67 1-31 (41)
83 KOG3476 Microtubule-associated 39.5 4 8.7E-05 27.5 -1.8 38 35-112 55-92 (100)
84 cd02336 ZZ_RSC8 Zinc finger, Z 39.3 35 0.00075 20.0 2.3 29 36-64 2-32 (45)
85 PRK00398 rpoP DNA-directed RNA 39.1 13 0.00027 21.7 0.4 27 9-44 5-31 (46)
86 smart00291 ZnF_ZZ Zinc-binding 38.4 29 0.00063 20.0 1.9 10 147-156 27-36 (44)
87 COG4357 Zinc finger domain con 38.2 2 4.4E-05 29.5 -3.4 53 101-153 37-89 (105)
88 COG1813 Predicted transcriptio 37.5 37 0.0008 25.8 2.8 33 129-163 6-40 (165)
89 PF12855 Ecl1: Life-span regul 37.5 17 0.00036 21.2 0.8 22 129-154 9-31 (43)
90 PF01286 XPA_N: XPA protein N- 36.5 16 0.00035 20.1 0.6 11 100-110 4-14 (34)
91 PF01246 Ribosomal_L24e: Ribos 35.2 18 0.00039 23.5 0.7 24 8-31 4-30 (71)
92 PF07503 zf-HYPF: HypF finger; 34.2 11 0.00024 20.9 -0.3 31 10-45 2-32 (35)
93 KOG4739 Uncharacterized protei 33.4 33 0.00071 27.6 2.1 28 39-66 8-36 (233)
94 PF06827 zf-FPG_IleRS: Zinc fi 33.0 62 0.0013 16.7 2.5 11 100-110 2-12 (30)
95 COG0068 HypF Hydrogenase matur 32.2 22 0.00047 33.3 1.0 84 7-137 101-184 (750)
96 PF00569 ZZ: Zinc finger, ZZ t 31.2 36 0.00078 19.8 1.5 9 56-64 29-37 (46)
97 PF14569 zf-UDP: Zinc-binding 31.1 57 0.0012 21.6 2.5 13 54-66 35-47 (80)
98 PF02591 DUF164: Putative zinc 30.8 10 0.00022 23.1 -0.9 10 9-18 24-33 (56)
99 PF13834 DUF4193: Domain of un 30.8 15 0.00032 25.5 -0.3 27 127-153 71-98 (99)
100 PF08271 TF_Zn_Ribbon: TFIIB z 30.8 27 0.00058 19.9 0.9 11 35-45 20-30 (43)
101 PF00130 C1_1: Phorbol esters/ 30.7 31 0.00068 20.3 1.3 12 6-17 10-21 (53)
102 PF06750 DiS_P_DiS: Bacterial 30.3 26 0.00056 23.9 0.9 42 3-46 29-70 (92)
103 cd02340 ZZ_NBR1_like Zinc fing 30.0 48 0.001 19.0 1.9 7 57-63 25-31 (43)
104 PF12674 Zn_ribbon_2: Putative 29.8 22 0.00048 23.6 0.5 28 37-64 3-35 (81)
105 KOG2932 E3 ubiquitin ligase in 28.7 18 0.00039 30.4 -0.1 16 100-115 124-139 (389)
106 smart00834 CxxC_CXXC_SSSS Puta 28.6 18 0.00038 20.1 -0.1 10 101-110 7-16 (41)
107 PF10080 DUF2318: Predicted me 28.1 38 0.00082 23.6 1.4 38 24-65 25-62 (102)
108 PF09723 Zn-ribbon_8: Zinc rib 28.0 18 0.0004 20.6 -0.1 10 101-110 7-16 (42)
109 PLN02195 cellulose synthase A 27.9 56 0.0012 31.9 2.9 38 5-63 4-41 (977)
110 PF00096 zf-C2H2: Zinc finger, 27.9 26 0.00057 16.6 0.5 12 127-138 1-12 (23)
111 PF08746 zf-RING-like: RING-li 27.3 16 0.00035 21.1 -0.4 9 10-18 1-9 (43)
112 KOG3579 Predicted E3 ubiquitin 27.3 26 0.00056 29.1 0.6 48 100-152 269-316 (352)
113 COG4357 Zinc finger domain con 27.0 7.2 0.00016 26.8 -2.2 50 10-59 38-87 (105)
114 cd02341 ZZ_ZZZ3 Zinc finger, Z 26.9 60 0.0013 19.2 2.0 11 147-157 26-36 (48)
115 PF04641 Rtf2: Rtf2 RING-finge 26.7 1E+02 0.0022 25.0 4.0 57 30-118 109-169 (260)
116 PF10764 Gin: Inhibitor of sig 26.2 65 0.0014 18.9 2.0 29 37-67 2-30 (46)
117 TIGR02605 CxxC_CxxC_SSSS putat 26.0 22 0.00047 21.0 -0.1 10 101-110 7-16 (52)
118 PRK04023 DNA polymerase II lar 25.9 67 0.0014 31.5 3.0 16 100-115 664-679 (1121)
119 PLN02638 cellulose synthase A 25.9 60 0.0013 32.0 2.8 28 8-43 18-45 (1079)
120 PF00628 PHD: PHD-finger; Int 25.7 66 0.0014 18.6 2.1 27 9-35 1-29 (51)
121 PLN02436 cellulose synthase A 25.3 60 0.0013 32.0 2.7 10 54-63 62-71 (1094)
122 COG3813 Uncharacterized protei 25.3 85 0.0018 20.5 2.6 31 37-67 8-41 (84)
123 TIGR00599 rad18 DNA repair pro 25.2 59 0.0013 28.4 2.4 33 34-67 26-58 (397)
124 cd02335 ZZ_ADA2 Zinc finger, Z 25.2 62 0.0013 19.0 1.8 11 55-65 24-34 (49)
125 PF14255 Cys_rich_CPXG: Cystei 24.1 34 0.00074 20.8 0.5 29 9-37 2-30 (52)
126 PF00320 GATA: GATA zinc finge 23.9 97 0.0021 16.9 2.4 28 37-64 1-29 (36)
127 PLN02189 cellulose synthase 23.5 69 0.0015 31.5 2.7 29 36-64 36-70 (1040)
128 PF13894 zf-C2H2_4: C2H2-type 23.1 39 0.00084 15.6 0.6 12 127-138 1-12 (24)
129 smart00249 PHD PHD zinc finger 22.9 56 0.0012 17.9 1.3 27 9-35 1-29 (47)
130 PRK14714 DNA polymerase II lar 22.6 69 0.0015 32.2 2.5 10 101-110 694-703 (1337)
131 PRK12495 hypothetical protein; 22.6 43 0.00093 26.7 1.0 23 35-62 43-65 (226)
132 KOG3579 Predicted E3 ubiquitin 22.2 43 0.00092 27.9 0.9 33 35-67 269-304 (352)
133 KOG0823 Predicted E3 ubiquitin 21.5 1.5E+02 0.0032 23.9 3.8 40 27-67 40-79 (230)
134 PRK00085 recO DNA repair prote 21.4 47 0.001 26.4 1.1 31 32-62 147-177 (247)
135 PF12874 zf-met: Zinc-finger o 21.3 42 0.0009 16.2 0.5 13 127-139 1-13 (25)
136 PF10122 Mu-like_Com: Mu-like 21.2 23 0.00049 21.4 -0.6 26 35-62 5-31 (51)
137 COG4306 Uncharacterized protei 21.2 82 0.0018 22.9 2.1 38 100-138 40-80 (160)
138 PF03854 zf-P11: P-11 zinc fin 21.1 1.2E+02 0.0026 18.1 2.4 11 100-110 36-46 (50)
139 PF13719 zinc_ribbon_5: zinc-r 20.9 49 0.0011 18.3 0.8 31 100-135 3-34 (37)
140 PRK00085 recO DNA repair prote 20.9 42 0.00091 26.7 0.6 28 127-154 150-177 (247)
141 PF14570 zf-RING_4: RING/Ubox 20.8 80 0.0017 18.8 1.7 14 54-67 21-34 (48)
142 TIGR03826 YvyF flagellar opero 20.5 76 0.0017 23.4 1.9 23 127-157 82-104 (137)
143 KOG2893 Zn finger protein [Gen 20.5 24 0.00052 28.6 -0.8 36 100-139 11-47 (341)
144 TIGR00373 conserved hypothetic 20.4 26 0.00056 26.3 -0.6 29 9-45 111-139 (158)
145 PF03107 C1_2: C1 domain; Int 20.2 79 0.0017 16.4 1.5 13 35-47 1-13 (30)
146 PLN02915 cellulose synthase A 20.1 84 0.0018 30.9 2.5 30 7-44 15-44 (1044)
147 COG1381 RecO Recombinational D 20.1 52 0.0011 26.6 1.0 27 128-154 156-182 (251)
148 KOG3039 Uncharacterized conser 20.0 2.8E+02 0.0061 22.7 5.1 80 6-115 182-275 (303)
No 1
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.95 E-value=1.1e-29 Score=211.36 Aligned_cols=134 Identities=23% Similarity=0.512 Sum_probs=123.0
Q ss_pred CcccccccccccCc-eEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCCC
Q 041875 8 EKCKACDKTVHIID-MVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTR 86 (195)
Q Consensus 8 ~~C~~C~~~I~~~~-~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (195)
.+|.+|+|.|.... .+.||++.||..||+|..|++.|.++.||..|+++||+.||+...
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 48999999998543 589999999999999999999999999999999999999999876
Q ss_pred CCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccCCcccccCCeecc-CCccccHHHHHhhhcCCCc-c
Q 041875 87 TPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAAL-DGILYCKSHFAQLFKEKGC-Y 164 (195)
Q Consensus 87 ~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~-dg~~yC~~c~~~~f~~k~~-~ 164 (195)
.+|..|+++|+ +.++.+.|+.||..||+|..|.+.|++..|++. ++++||-.||+++|++||+ +
T Consensus 335 -------------ekC~~Cg~~I~-d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C 400 (468)
T KOG1701|consen 335 -------------EKCNKCGEPIM-DRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVC 400 (468)
T ss_pred -------------HHHhhhhhHHH-HHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhc
Confidence 79999999998 556799999999999999999999999999887 7999999999999999999 7
Q ss_pred CCCCCcchhhh
Q 041875 165 NHLTKTASQKK 175 (195)
Q Consensus 165 ~~~~~~~~~~~ 175 (195)
+..|+|...++
T Consensus 401 ~~PI~P~~G~~ 411 (468)
T KOG1701|consen 401 GNPILPRDGKD 411 (468)
T ss_pred cCCccCCCCCc
Confidence 78888877665
No 2
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.90 E-value=1.8e-25 Score=174.99 Aligned_cols=160 Identities=21% Similarity=0.431 Sum_probs=125.5
Q ss_pred CCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccC-Ccc-------ccCCCc
Q 041875 7 QEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKET-GSF-------TNKLKP 78 (195)
Q Consensus 7 ~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~-~~~-------~~~~~~ 78 (195)
+|.|+.|++.|. |.+|.+++.+||+.||+|..|++.|.+..|+-..|..+|..|.++..+.. |.| .++-++
T Consensus 73 aPcC~kC~EFii-GrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~ 151 (332)
T KOG2272|consen 73 APCCGKCGEFII-GRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQP 151 (332)
T ss_pred chhhcccccchh-hHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhccccc
Confidence 489999999998 99999999999999999999999999999999999999999998744322 111 122222
Q ss_pred cCCCCCCCCCCCC--------------------ccccC---CCCCcCccCCceeecCceEEECCceecccccccccCCcc
Q 041875 79 AQKNGLTRTPSKF--------------------STMFC---GTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCL 135 (195)
Q Consensus 79 ~~~~~~~~~p~~~--------------------~~~~~---~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~ 135 (195)
.+..+.+.+|-.+ +..+. -+.++|..|.++|. +..|.++|+.||.+.|+|+.|.++
T Consensus 152 l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIe-ervi~amgKhWHveHFvCa~CekP 230 (332)
T KOG2272|consen 152 LTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIE-ERVIFAMGKHWHVEHFVCAKCEKP 230 (332)
T ss_pred ccccCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCchH-HHHHHHhccccchhheeehhcCCc
Confidence 2222222222211 11111 25689999999997 556789999999999999999999
Q ss_pred cccCCeeccCCccccHHHHHhhhcCCCc-cCCCC
Q 041875 136 LTTSSYAALDGILYCKSHFAQLFKEKGC-YNHLT 168 (195)
Q Consensus 136 L~~~~~~~~dg~~yC~~c~~~~f~~k~~-~~~~~ 168 (195)
+-+...+++.|.+||+.+|.++||--|. ++.++
T Consensus 231 FlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i 264 (332)
T KOG2272|consen 231 FLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVI 264 (332)
T ss_pred ccchhhhhhcCchhHHHHHHHHhhhhheecCCcc
Confidence 9999999999999999999999999987 44433
No 3
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.89 E-value=1.1e-24 Score=181.63 Aligned_cols=126 Identities=29% Similarity=0.669 Sum_probs=112.9
Q ss_pred cCCCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceee-cCCeecchhhHHHhhccCCccccCCCccCC
Q 041875 3 FCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSS-MEGVLYCKPHFEQLFKETGSFTNKLKPAQK 81 (195)
Q Consensus 3 ~~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~-~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~ 81 (195)
|..+.++|..|+++|. +.+|.|+|+.||+.||+|-.|.+.|++..|.+ .++++||..||.+.|+
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 5566789999999998 78899999999999999999999999999974 5789999999999998
Q ss_pred CCCCCCCCCCccccCCCCCcCccCCceeecCc------eEEECCceecccccccccCCccccc----CCeeccCCccccH
Q 041875 82 NGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLE------KVTVEGESFHKTCFRCSHGGCLLTT----SSYAALDGILYCK 151 (195)
Q Consensus 82 ~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~------~v~~~~~~~H~~CF~C~~C~~~L~~----~~~~~~dg~~yC~ 151 (195)
++|+.|+++|++.+ +|+++++.||.+|++|+.|+.+|+. ...+-.||.++|+
T Consensus 395 ------------------PrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk 456 (468)
T KOG1701|consen 395 ------------------PRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCK 456 (468)
T ss_pred ------------------cchhhccCCccCCCCCcceEEEEEccccccccceehhhcCccccccCCCCcceeccCceeec
Confidence 99999999999843 4689999999999999999999983 3588999999999
Q ss_pred HHHHhhhcCC
Q 041875 152 SHFAQLFKEK 161 (195)
Q Consensus 152 ~c~~~~f~~k 161 (195)
.|..++....
T Consensus 457 ~Ch~~Rl~~~ 466 (468)
T KOG1701|consen 457 TCHLKRLQAG 466 (468)
T ss_pred hhhhhhhccc
Confidence 9998876554
No 4
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.85 E-value=2.3e-23 Score=165.91 Aligned_cols=125 Identities=26% Similarity=0.543 Sum_probs=111.8
Q ss_pred CCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCC
Q 041875 6 TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLT 85 (195)
Q Consensus 6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 85 (195)
.+++|+.|.+.|.+..++.+++++||..|++|+.|..+|.. ..|.+++.+||+.+|.++|+
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 67899999999997678899999999999999999999986 55669999999999999999
Q ss_pred CCCCCCccccCCCCCcCccCCceeecCceE-EECCceecccccccccCCcccccC-Ceecc-CCccccHHHHHhhhcCCC
Q 041875 86 RTPSKFSTMFCGTQDKCTSCKKTVYPLEKV-TVEGESFHKTCFRCSHGGCLLTTS-SYAAL-DGILYCKSHFAQLFKEKG 162 (195)
Q Consensus 86 ~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v-~~~~~~~H~~CF~C~~C~~~L~~~-~~~~~-dg~~yC~~c~~~~f~~k~ 162 (195)
.+|..|...|.+.+.| .+.+..||..||.|..|+++|..+ .|+.+ |++++|+.+|.+.-+..+
T Consensus 93 --------------TKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~ 158 (383)
T KOG4577|consen 93 --------------TKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHC 158 (383)
T ss_pred --------------CcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccc
Confidence 8999999999998887 689999999999999999999955 46654 899999999998766655
Q ss_pred c
Q 041875 163 C 163 (195)
Q Consensus 163 ~ 163 (195)
.
T Consensus 159 ~ 159 (383)
T KOG4577|consen 159 N 159 (383)
T ss_pred c
Confidence 3
No 5
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.83 E-value=3.2e-22 Score=156.85 Aligned_cols=117 Identities=24% Similarity=0.534 Sum_probs=110.3
Q ss_pred CCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCC
Q 041875 6 TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLT 85 (195)
Q Consensus 6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 85 (195)
+.++|..|.+||. +.+|.++|++||.+.|+|+.|-+++-+...+++.|..||+.+|.++|+
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 5689999999997 788999999999999999999999988899999999999999999999
Q ss_pred CCCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccCCccccc-CCeeccCCccccHHHHHh
Q 041875 86 RTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTT-SSYAALDGILYCKSHFAQ 156 (195)
Q Consensus 86 ~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~-~~~~~~dg~~yC~~c~~~ 156 (195)
..|..|+..|. ++.+.++++.|-.+||+|+.|.+.|.. ..|++.|-.|.|+.||.+
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 89999999998 888999999999999999999999984 469999999999999985
No 6
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.83 E-value=2.2e-21 Score=151.71 Aligned_cols=176 Identities=46% Similarity=0.860 Sum_probs=144.4
Q ss_pred CCcCCCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCC-ccccCCCcc
Q 041875 1 MAFCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETG-SFTNKLKPA 79 (195)
Q Consensus 1 ~~~~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~-~~~~~~~~~ 79 (195)
|++.+....|..|++.|+..+.+...|..||+.||+|..|.+.|....+..+++.+||+.||...+++++ .....|+..
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 7888888999999999998888889999999999999999999999999999999999998888888765 233333321
Q ss_pred CC--------CCCCCCCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccH
Q 041875 80 QK--------NGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCK 151 (195)
Q Consensus 80 ~~--------~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~ 151 (195)
.. +.....+......+.++...|.+|.+.+++.+.++..+..||+.||+|+.|++.|+.+.+....|.+||.
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 1111111123344567889999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhhcCCCccCCCCCcchhhhh
Q 041875 152 SHFAQLFKEKGCYNHLTKTASQKKI 176 (195)
Q Consensus 152 ~c~~~~f~~k~~~~~~~~~~~~~~~ 176 (195)
.++.++|-.++.++........++.
T Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~ 185 (200)
T KOG1700|consen 161 HHFAQLFKGKGNYNEGFGARENKEA 185 (200)
T ss_pred hhhheeecCCCcccccchhhhhhhh
Confidence 9888888888778877766666654
No 7
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.82 E-value=1.2e-20 Score=165.50 Aligned_cols=130 Identities=28% Similarity=0.611 Sum_probs=120.4
Q ss_pred CCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCC
Q 041875 6 TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLT 85 (195)
Q Consensus 6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 85 (195)
..++|..|.+.|....++.++++.||+.+|.|..|...+..+.+...+|++||..|+...+.
T Consensus 302 ~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~------------------ 363 (479)
T KOG1703|consen 302 TRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFR------------------ 363 (479)
T ss_pred ccccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhC------------------
Confidence 45899999999984489999999999999999999999999999999999999999999987
Q ss_pred CCCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCccC
Q 041875 86 RTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYN 165 (195)
Q Consensus 86 ~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~~ 165 (195)
++|.+|+++|. ++.|.+.+..||++||.|..|++.|....|+..||.+||+.||+++|++++.++
T Consensus 364 --------------p~C~~C~~~i~-~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~ 428 (479)
T KOG1703|consen 364 --------------PNCKRCLLPIL-EEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYC 428 (479)
T ss_pred --------------ccccccCCchH-HhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhc
Confidence 99999999998 778888899999999999999999999999999999999999999999998766
Q ss_pred CCC
Q 041875 166 HLT 168 (195)
Q Consensus 166 ~~~ 168 (195)
...
T Consensus 429 ~~p 431 (479)
T KOG1703|consen 429 KKP 431 (479)
T ss_pred cch
Confidence 543
No 8
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.81 E-value=1.9e-20 Score=161.24 Aligned_cols=161 Identities=20% Similarity=0.439 Sum_probs=119.2
Q ss_pred CcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCC-eecchhhHHHhhccCC---ccccCCCc-----
Q 041875 8 EKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEG-VLYCKPHFEQLFKETG---SFTNKLKP----- 78 (195)
Q Consensus 8 ~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g-~~yC~~c~~~~~~~~~---~~~~~~~~----- 78 (195)
-.|..|.+.-. ++++.+.+++||..||+|..|++.|..+.|+.+++ .+|+...... |..+. +....|++
T Consensus 17 i~c~~c~~kc~-gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~-~~~gevvsa~gktyh~~cf~c 94 (670)
T KOG1044|consen 17 IKCDKCRKKCS-GEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRA-FVEGEVVSTLGKTYHPKCFSC 94 (670)
T ss_pred eehhhhCCccc-cceeEeeccccceeeeeccccCCCcccccceecccceeecccchhh-hccceeEecccceecccccee
Confidence 36999999998 99999999999999999999999999998887654 5777633221 11111 11111211
Q ss_pred ----------cCCC--------CCCCCCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccCCcccccCC
Q 041875 79 ----------AQKN--------GLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSS 140 (195)
Q Consensus 79 ----------~~~~--------~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~ 140 (195)
++.. .....+...+.....+...|++|++.|..++.+.++++.||..||+|..|+..|.++
T Consensus 95 s~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~ge- 173 (670)
T KOG1044|consen 95 STCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNGE- 173 (670)
T ss_pred cccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccce-
Confidence 1100 011122222222223567999999999999999999999999999999999999884
Q ss_pred eeccCCccccHHHHHhhhcCCCccCCCCCcc
Q 041875 141 YAALDGILYCKSHFAQLFKEKGCYNHLTKTA 171 (195)
Q Consensus 141 ~~~~dg~~yC~~c~~~~f~~k~~~~~~~~~~ 171 (195)
|+.+||.|||+.+|.+.||.||..++.++.+
T Consensus 174 y~skdg~pyce~dy~~~fgvkc~~c~~fisg 204 (670)
T KOG1044|consen 174 YMSKDGVPYCEKDYQAKFGVKCEECEKFISG 204 (670)
T ss_pred eeccCCCcchhhhhhhhcCeehHHhhhhhhh
Confidence 9999999999999999999999976655443
No 9
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.75 E-value=1.4e-19 Score=158.88 Aligned_cols=117 Identities=32% Similarity=0.638 Sum_probs=108.0
Q ss_pred CCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCC
Q 041875 5 GTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGL 84 (195)
Q Consensus 5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~ 84 (195)
...+.|.+|+++|. ++.|.+.++.||++||.|..|+++|.+..|+..++.+||+.||..++.
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 45689999999998 888999999999999999999999999999999999999999999987
Q ss_pred CCCCCCCccccCCCCCcCccCCceeecCc-eEEECCceecccccccccCCcccccCCeeccCCccccHHHH
Q 041875 85 TRTPSKFSTMFCGTQDKCTSCKKTVYPLE-KVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHF 154 (195)
Q Consensus 85 ~~~p~~~~~~~~~~~~~C~~C~~~I~~~~-~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~ 154 (195)
.+|..|.++|.... .+.+.+..||..||+|..|.+.|.++.|+...++|+|..|+
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 79999999877544 47899999999999999999999999999999999998875
No 10
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.69 E-value=4.5e-18 Score=146.68 Aligned_cols=115 Identities=25% Similarity=0.547 Sum_probs=104.0
Q ss_pred CCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCC
Q 041875 6 TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLT 85 (195)
Q Consensus 6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~ 85 (195)
+...|++|++.|..+..+.|+++.||..||+|..|+..|. +.|..++|.+||+.||+..|+
T Consensus 132 ~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~-gey~skdg~pyce~dy~~~fg------------------ 192 (670)
T KOG1044|consen 132 GPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLN-GEYMSKDGVPYCEKDYQAKFG------------------ 192 (670)
T ss_pred CCccccchhhhhhccceeeeeccceeeeeeehhhhccccc-ceeeccCCCcchhhhhhhhcC------------------
Confidence 5578999999999999999999999999999999999997 588899999999999999998
Q ss_pred CCCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccCCcccccC-CeeccCCccccHHHH
Q 041875 86 RTPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTS-SYAALDGILYCKSHF 154 (195)
Q Consensus 86 ~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~-~~~~~dg~~yC~~c~ 154 (195)
.+|..|.+.|. +..+.+.|++||+.|-+|+.|+..+..+ ..++....++-..|-
T Consensus 193 --------------vkc~~c~~fis-gkvLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~ 247 (670)
T KOG1044|consen 193 --------------VKCEECEKFIS-GKVLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCK 247 (670)
T ss_pred --------------eehHHhhhhhh-hhhhhccCcccCcchhhhhhhccccccchheeeccccccCCccc
Confidence 89999999998 7778999999999999999999999854 577777788766664
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=99.61 E-value=1.1e-15 Score=96.48 Aligned_cols=57 Identities=37% Similarity=0.786 Sum_probs=52.7
Q ss_pred ccccccccccCceE-eeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhh
Q 041875 10 CKACDKTVHIIDMV-TADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF 66 (195)
Q Consensus 10 C~~C~~~I~~~~~i-~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~ 66 (195)
|.+|+++|.+++.+ .++|+.||++||+|..|+++|.+..|+..+|++||+.||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 78999999977765 7999999999999999999999989999999999999998875
No 12
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.58 E-value=2.4e-15 Score=94.91 Aligned_cols=57 Identities=35% Similarity=0.769 Sum_probs=53.4
Q ss_pred CccCCceeecCceE-EECCceecccccccccCCcccccCCeeccCCccccHHHHHhhh
Q 041875 102 CTSCKKTVYPLEKV-TVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLF 158 (195)
Q Consensus 102 C~~C~~~I~~~~~v-~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f 158 (195)
|.+|+++|.+.+.+ .+.|+.||++||+|..|+++|.++.++..||++||+.||.++|
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 78999999987776 6999999999999999999999888999999999999999987
No 13
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.22 E-value=6.5e-13 Score=106.48 Aligned_cols=82 Identities=18% Similarity=0.348 Sum_probs=72.6
Q ss_pred CCCcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCc-cCCCCCcchhhhh
Q 041875 98 TQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGC-YNHLTKTASQKKI 176 (195)
Q Consensus 98 ~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~-~~~~~~~~~~~~~ 176 (195)
..++|++|.+.|...-.+.++++.||..|++|+.|+.+|.. ..+.++|.+||+.+|.++||+||+ +..+|.|....|+
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 45899999999984434589999999999999999999987 588999999999999999999998 8889999998888
Q ss_pred hhhc
Q 041875 177 VAAS 180 (195)
Q Consensus 177 ~~~~ 180 (195)
.+..
T Consensus 111 Aqd~ 114 (383)
T KOG4577|consen 111 AQDF 114 (383)
T ss_pred hhcc
Confidence 7653
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=98.81 E-value=3e-09 Score=61.04 Aligned_cols=37 Identities=38% Similarity=0.714 Sum_probs=33.6
Q ss_pred cccccccccccC-ceEeeCCcccccCccccccccccCC
Q 041875 9 KCKACDKTVHII-DMVTADGISYHKICFKCSHCNGKLV 45 (195)
Q Consensus 9 ~C~~C~~~I~~~-~~i~~~g~~~H~~CF~C~~C~~~L~ 45 (195)
+|.+|+++|.++ ..+.++++.||+.||+|..|+++|.
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 6788999999999999999999986
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=98.67 E-value=1.6e-08 Score=58.00 Aligned_cols=37 Identities=32% Similarity=0.655 Sum_probs=33.0
Q ss_pred cCccCCceeecC-ceEEECCceecccccccccCCcccc
Q 041875 101 KCTSCKKTVYPL-EKVTVEGESFHKTCFRCSHGGCLLT 137 (195)
Q Consensus 101 ~C~~C~~~I~~~-~~v~~~~~~~H~~CF~C~~C~~~L~ 137 (195)
+|.+|+++|.+. ..+.+.++.||..||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 589999999976 5668899999999999999999985
No 16
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.54 E-value=2.4e-08 Score=78.37 Aligned_cols=68 Identities=43% Similarity=0.810 Sum_probs=63.5
Q ss_pred CcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCc-cCCC
Q 041875 100 DKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGC-YNHL 167 (195)
Q Consensus 100 ~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~-~~~~ 167 (195)
.+|.+|++.++..+.+...|..||+.||+|..|.+.|..+.+..+++.+||+.+|...|++++. ++..
T Consensus 8 ~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~ 76 (200)
T KOG1700|consen 8 DKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKG 76 (200)
T ss_pred chhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCccccccccc
Confidence 6999999999998889999999999999999999999999999999999999999999999986 6664
No 17
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=98.39 E-value=2.8e-08 Score=76.62 Aligned_cols=81 Identities=28% Similarity=0.596 Sum_probs=70.0
Q ss_pred CcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHHHHhhhcCCCccCCCCCcchhhhhhhh
Q 041875 100 DKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKIVAA 179 (195)
Q Consensus 100 ~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~~~~~~~~~~~~~~~~ 179 (195)
..|..|++.+++.+.|..+++.||+.||+|..|+-+|.-..+.-.|.++||..+|.+ -.+.-+..+++.+|+.++
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpk-----q~at~~adTPEm~Rik~n 79 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPK-----QVATVMADTPEMRRIKEN 79 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccc-----ceeeeecCCHHHHHHHhh
Confidence 578899999999999999999999999999999999998888888999999999954 346667888998887777
Q ss_pred ccCCCC
Q 041875 180 SADQNP 185 (195)
Q Consensus 180 ~~~~~~ 185 (195)
...++.
T Consensus 80 ~enqS~ 85 (264)
T KOG1702|consen 80 TENQSN 85 (264)
T ss_pred hccchh
Confidence 666543
No 18
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.87 E-value=1.6e-06 Score=69.14 Aligned_cols=111 Identities=23% Similarity=0.470 Sum_probs=87.4
Q ss_pred cccccccCceEeeCCcccccCccccccccccCC--CCceeecCCeecchhhHHH--hhccCCccccCCCccCCCCCCCCC
Q 041875 13 CDKTVHIIDMVTADGISYHKICFKCSHCNGKLV--MGNFSSMEGVLYCKPHFEQ--LFKETGSFTNKLKPAQKNGLTRTP 88 (195)
Q Consensus 13 C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~--~~~~~~~~g~~yC~~c~~~--~~~~~~~~~~~~~~~~~~~~~~~p 88 (195)
|+..|.+...+.+.+..||..|+.|..|...|. ...|.. +|..||..+|.+ .+.
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~--------------------- 59 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFS--------------------- 59 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcc---------------------
Confidence 677787555677789999999999999999997 445555 999999999987 333
Q ss_pred CCCccccCCCCCcCccCCceeecCceE-EECCceecccccccccCCcccc-cCCeeccCC-ccccHHHHHhh
Q 041875 89 SKFSTMFCGTQDKCTSCKKTVYPLEKV-TVEGESFHKTCFRCSHGGCLLT-TSSYAALDG-ILYCKSHFAQL 157 (195)
Q Consensus 89 ~~~~~~~~~~~~~C~~C~~~I~~~~~v-~~~~~~~H~~CF~C~~C~~~L~-~~~~~~~dg-~~yC~~c~~~~ 157 (195)
.+|.+|...+...+.+ .+..+. |..||.|..|...+. ...+.+.+. +.+|..++.+.
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 7999999998766665 455555 999999999999766 445666554 99999888653
No 19
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=97.79 E-value=1.8e-06 Score=66.80 Aligned_cols=59 Identities=32% Similarity=0.656 Sum_probs=53.3
Q ss_pred CCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHh
Q 041875 7 QEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQL 65 (195)
Q Consensus 7 ~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~ 65 (195)
...|..|++.+++.+.|..+++.||..||+|..|+-+|.-.+|-..+.++||..+|...
T Consensus 4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq 62 (264)
T KOG1702|consen 4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQ 62 (264)
T ss_pred cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccc
Confidence 35678899999999999999999999999999999999888888889999999999653
No 20
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=92.26 E-value=0.047 Score=43.27 Aligned_cols=58 Identities=21% Similarity=0.588 Sum_probs=45.7
Q ss_pred CCceeecCceEEECCceecccccccccCCcccc--cCCeeccCCccccHHHHHh--hhcCCCc
Q 041875 105 CKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLT--TSSYAALDGILYCKSHFAQ--LFKEKGC 163 (195)
Q Consensus 105 C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~--~~~~~~~dg~~yC~~c~~~--~f~~k~~ 163 (195)
|+..|.+...+.+.+..||..|..|..|...|. ...+.. +|..||...|.. .+..++.
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~ 63 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCA 63 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcccccc
Confidence 556666444456669999999999999999997 444555 999999999998 6666665
No 21
>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=89.27 E-value=0.59 Score=28.97 Aligned_cols=32 Identities=16% Similarity=0.161 Sum_probs=26.2
Q ss_pred cccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875 35 FKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK 67 (195)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~ 67 (195)
|.|..|+..+.+ ......|..||+.|..+.+.
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~ 33 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLL 33 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHH
Confidence 678999998876 45567799999999988775
No 22
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=87.91 E-value=0.38 Score=29.52 Aligned_cols=37 Identities=27% Similarity=0.599 Sum_probs=26.1
Q ss_pred CcCccCCceeecCce-EE--ECCceeccccc----cccc--CCccc
Q 041875 100 DKCTSCKKTVYPLEK-VT--VEGESFHKTCF----RCSH--GGCLL 136 (195)
Q Consensus 100 ~~C~~C~~~I~~~~~-v~--~~~~~~H~~CF----~C~~--C~~~L 136 (195)
.+|..|+++|.+.+- |. .=+..||++|. .|.. |+..+
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~ 51 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF 51 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence 799999999975444 43 45788999987 4655 55443
No 23
>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=86.75 E-value=0.37 Score=27.20 Aligned_cols=28 Identities=21% Similarity=0.408 Sum_probs=18.0
Q ss_pred ccccccccccC-ceEeeCCcccccCcccc
Q 041875 10 CKACDKTVHII-DMVTADGISYHKICFKC 37 (195)
Q Consensus 10 C~~C~~~I~~~-~~i~~~g~~~H~~CF~C 37 (195)
|.-|+.+|... .++...++.||.-|-+|
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 56788888732 25677778887655444
No 24
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=86.23 E-value=0.31 Score=33.87 Aligned_cols=31 Identities=32% Similarity=0.557 Sum_probs=23.6
Q ss_pred CcCccCCceeecCceEEE-CCceecccccccc
Q 041875 100 DKCTSCKKTVYPLEKVTV-EGESFHKTCFRCS 130 (195)
Q Consensus 100 ~~C~~C~~~I~~~~~v~~-~~~~~H~~CF~C~ 130 (195)
-+|..|+++|..++.+++ .+..-|..||+=.
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~ 34 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREK 34 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHH
Confidence 478899999988888754 4567888888743
No 25
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=84.98 E-value=0.29 Score=34.01 Aligned_cols=31 Identities=26% Similarity=0.397 Sum_probs=19.7
Q ss_pred cccccccccccCceEeeC-CcccccCcccccc
Q 041875 9 KCKACDKTVHIIDMVTAD-GISYHKICFKCSH 39 (195)
Q Consensus 9 ~C~~C~~~I~~~~~i~~~-g~~~H~~CF~C~~ 39 (195)
+|..|+++|+.|+.+... +..-|-.||+=..
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~ 35 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKA 35 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHHH
Confidence 577777777777765543 3466777776543
No 26
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=84.94 E-value=0.84 Score=29.06 Aligned_cols=33 Identities=15% Similarity=0.270 Sum_probs=16.8
Q ss_pred cccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875 35 FKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK 67 (195)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~ 67 (195)
++|+.|...|...-....=...||..|..+.++
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 688999888875433344467899999987776
No 27
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.62 E-value=0.88 Score=34.89 Aligned_cols=53 Identities=23% Similarity=0.543 Sum_probs=40.7
Q ss_pred ccCccccccccccCCCCc-eeecCCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCcee
Q 041875 31 HKICFKCSHCNGKLVMGN-FSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTV 109 (195)
Q Consensus 31 H~~CF~C~~C~~~L~~~~-~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I 109 (195)
-..++.|-.|-....... +...=|.+||+.|..+..... .+|+.|++.|
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~------------------------------~~CP~C~kkI 177 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNT------------------------------NKCPTCRKKI 177 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHHHhC------------------------------CCCCCccccc
Confidence 357899999977776553 556779999999999877522 7999999988
Q ss_pred ecCc
Q 041875 110 YPLE 113 (195)
Q Consensus 110 ~~~~ 113 (195)
...+
T Consensus 178 t~k~ 181 (187)
T KOG0320|consen 178 THKQ 181 (187)
T ss_pred chhh
Confidence 7443
No 28
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=80.74 E-value=1.4 Score=30.33 Aligned_cols=30 Identities=27% Similarity=0.490 Sum_probs=21.9
Q ss_pred CCcCccCCceeecCceEE-ECCceecccccc
Q 041875 99 QDKCTSCKKTVYPLEKVT-VEGESFHKTCFR 128 (195)
Q Consensus 99 ~~~C~~C~~~I~~~~~v~-~~~~~~H~~CF~ 128 (195)
...|..|+++|.....+. ..|..+|..|++
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 378999999998544333 457779988864
No 29
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=80.54 E-value=1.1 Score=25.09 Aligned_cols=24 Identities=29% Similarity=0.596 Sum_probs=17.8
Q ss_pred cccccccccCCCCceeecCCeecchhhH
Q 041875 35 FKCSHCNGKLVMGNFSSMEGVLYCKPHF 62 (195)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~ 62 (195)
+.|..|+.. .|...+|..||..|-
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYCDRCG 32 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEhhhCc
Confidence 347777664 567789999998774
No 30
>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=80.19 E-value=0.56 Score=26.10 Aligned_cols=28 Identities=18% Similarity=0.357 Sum_probs=17.1
Q ss_pred cccCCcccccCCeeccCCccccHHHHHh
Q 041875 129 CSHGGCLLTTSSYAALDGILYCKSHFAQ 156 (195)
Q Consensus 129 C~~C~~~L~~~~~~~~dg~~yC~~c~~~ 156 (195)
|..|+..+.........+..+|..|..+
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 6666666666566666677777777654
No 31
>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=79.98 E-value=1.5 Score=30.17 Aligned_cols=29 Identities=28% Similarity=0.456 Sum_probs=16.5
Q ss_pred CCcccccccccccCce-EeeCCcccccCcc
Q 041875 7 QEKCKACDKTVHIIDM-VTADGISYHKICF 35 (195)
Q Consensus 7 ~~~C~~C~~~I~~~~~-i~~~g~~~H~~CF 35 (195)
...|..|+++|..... +.-+|..+|..|+
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 4567777777764333 2334556666665
No 32
>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=79.79 E-value=1.5 Score=24.72 Aligned_cols=28 Identities=18% Similarity=0.447 Sum_probs=17.8
Q ss_pred CccCCceeecCceE-EECCceeccccccc
Q 041875 102 CTSCKKTVYPLEKV-TVEGESFHKTCFRC 129 (195)
Q Consensus 102 C~~C~~~I~~~~~v-~~~~~~~H~~CF~C 129 (195)
|.-|+++|.....+ ...++.||.-|-.|
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 56788888743333 57788887555444
No 33
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=79.19 E-value=1.3 Score=30.25 Aligned_cols=43 Identities=26% Similarity=0.559 Sum_probs=30.3
Q ss_pred ccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCce
Q 041875 29 SYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKT 108 (195)
Q Consensus 29 ~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~ 108 (195)
.|-+.=-.|..|...+.. .|..||..|..+. .+|+.|++.
T Consensus 39 Py~~~~~~C~~CK~~v~q------~g~~YCq~CAYkk----------------------------------GiCamCGKk 78 (90)
T PF10235_consen 39 PYAPYSSKCKICKTKVHQ------PGAKYCQTCAYKK----------------------------------GICAMCGKK 78 (90)
T ss_pred cccccCcccccccccccc------CCCccChhhhccc----------------------------------CcccccCCe
Confidence 344443467888776652 3667999996543 699999999
Q ss_pred eec
Q 041875 109 VYP 111 (195)
Q Consensus 109 I~~ 111 (195)
|.+
T Consensus 79 i~d 81 (90)
T PF10235_consen 79 ILD 81 (90)
T ss_pred ecc
Confidence 974
No 34
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=79.17 E-value=1.6 Score=26.39 Aligned_cols=29 Identities=31% Similarity=0.683 Sum_probs=22.6
Q ss_pred ccccccccCCCCc-eeecCCeecchhhHHHh
Q 041875 36 KCSHCNGKLVMGN-FSSMEGVLYCKPHFEQL 65 (195)
Q Consensus 36 ~C~~C~~~L~~~~-~~~~~g~~yC~~c~~~~ 65 (195)
.|..|++.+.-.. +-..|| ..|..|+.++
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 4889999887543 556777 7999999876
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=78.98 E-value=4.8 Score=23.79 Aligned_cols=45 Identities=24% Similarity=0.469 Sum_probs=30.5
Q ss_pred cccccccccCCCCceeecCCee-cchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceee
Q 041875 35 FKCSHCNGKLVMGNFSSMEGVL-YCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVY 110 (195)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~-yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~ 110 (195)
+.|..|...... ..+..=|.. +|..|..+..... ..|+.|.++|.
T Consensus 3 ~~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~~~------------------------------~~CP~Cr~~i~ 48 (50)
T PF13920_consen 3 EECPICFENPRD-VVLLPCGHLCFCEECAERLLKRK------------------------------KKCPICRQPIE 48 (50)
T ss_dssp SB-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHHTT------------------------------SBBTTTTBB-S
T ss_pred CCCccCCccCCc-eEEeCCCChHHHHHHhHHhcccC------------------------------CCCCcCChhhc
Confidence 356777776554 333445777 9999999886522 79999999885
No 36
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=77.37 E-value=2.1 Score=25.96 Aligned_cols=29 Identities=24% Similarity=0.502 Sum_probs=22.3
Q ss_pred ccccCCcccccC-CeeccCCccccHHHHHhh
Q 041875 128 RCSHGGCLLTTS-SYAALDGILYCKSHFAQL 157 (195)
Q Consensus 128 ~C~~C~~~L~~~-~~~~~dg~~yC~~c~~~~ 157 (195)
.|..|+..+.-- .+-..|| ..|..|+.++
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 478888888742 3667788 6899999886
No 37
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=77.12 E-value=2.3 Score=26.56 Aligned_cols=32 Identities=19% Similarity=0.413 Sum_probs=21.9
Q ss_pred cCCCCCcccccccccccCceEeeCCcccccCcccccccccc
Q 041875 3 FCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGK 43 (195)
Q Consensus 3 ~~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~ 43 (195)
-....+.|..|+..|.+.+.-. =|.|-.|++.
T Consensus 3 ~~~~~~~CtSCg~~i~~~~~~~---------~F~CPnCG~~ 34 (59)
T PRK14890 3 EMMEPPKCTSCGIEIAPREKAV---------KFLCPNCGEV 34 (59)
T ss_pred ccccCccccCCCCcccCCCccC---------EeeCCCCCCe
Confidence 3445678999999987554211 2888888876
No 38
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=76.41 E-value=1.4 Score=22.04 Aligned_cols=9 Identities=22% Similarity=0.933 Sum_probs=5.2
Q ss_pred ccccccccc
Q 041875 10 CKACDKTVH 18 (195)
Q Consensus 10 C~~C~~~I~ 18 (195)
|..|+..|.
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 555666554
No 39
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=75.52 E-value=3.6 Score=23.71 Aligned_cols=30 Identities=20% Similarity=0.396 Sum_probs=20.4
Q ss_pred cccccccCC-CCceee-cCCeecchhhHHHhh
Q 041875 37 CSHCNGKLV-MGNFSS-MEGVLYCKPHFEQLF 66 (195)
Q Consensus 37 C~~C~~~L~-~~~~~~-~~g~~yC~~c~~~~~ 66 (195)
|..|.+.+. ...+++ .=|..+|..|..+..
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~ 33 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLK 33 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhc
Confidence 667777772 224443 348899999998775
No 40
>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=74.54 E-value=4.3 Score=22.64 Aligned_cols=31 Identities=23% Similarity=0.428 Sum_probs=21.5
Q ss_pred cccccccCCCCceeecCCeecchhhHHHhhc
Q 041875 37 CSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK 67 (195)
Q Consensus 37 C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~ 67 (195)
|..|...+.+......=|..||..|..+.+.
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 4567676665334556699999999988775
No 41
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=73.67 E-value=1.1 Score=35.06 Aligned_cols=31 Identities=26% Similarity=0.528 Sum_probs=27.2
Q ss_pred cccccccccCCCCceeecCCeecchhhHHHh
Q 041875 35 FKCSHCNGKLVMGNFSSMEGVLYCKPHFEQL 65 (195)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~ 65 (195)
-+|+.|+.......-...+|++.|..||.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 6899999999887778889999999999753
No 42
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=73.14 E-value=1.2 Score=34.94 Aligned_cols=30 Identities=30% Similarity=0.495 Sum_probs=25.2
Q ss_pred cccccCCcccccCCeeccCCccccHHHHHh
Q 041875 127 FRCSHGGCLLTTSSYAALDGILYCKSHFAQ 156 (195)
Q Consensus 127 F~C~~C~~~L~~~~~~~~dg~~yC~~c~~~ 156 (195)
-+|+.|+-.+-...-...+|+++|..||.+
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~ 202 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEK 202 (206)
T ss_pred eeccccCcccccchhhhcCCceeccccccc
Confidence 578889988877777788999999999874
No 43
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=69.90 E-value=2.1 Score=35.07 Aligned_cols=27 Identities=15% Similarity=0.180 Sum_probs=16.9
Q ss_pred cCccccccccccCCCCceeecCCeecc
Q 041875 32 KICFKCSHCNGKLVMGNFSSMEGVLYC 58 (195)
Q Consensus 32 ~~CF~C~~C~~~L~~~~~~~~~g~~yC 58 (195)
...++|..|++.+....-..+..+.-|
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~ 154 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHKQTHR 154 (279)
T ss_pred CCceeccccccccccccccchhhcccc
Confidence 456889999998875543334444444
No 44
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=68.01 E-value=3.7 Score=26.14 Aligned_cols=50 Identities=16% Similarity=0.137 Sum_probs=18.4
Q ss_pred cccccCCcccccCCeeccCCccccHHHHHhhhcCCCccCCCCCcchhhhh
Q 041875 127 FRCSHGGCLLTTSSYAALDGILYCKSHFAQLFKEKGCYNHLTKTASQKKI 176 (195)
Q Consensus 127 F~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~f~~k~~~~~~~~~~~~~~~ 176 (195)
++|+.|...|...-....=+.+||..|....+|..|--++.....+..++
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD~~~ 57 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQDIQI 57 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-SS---
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHHHHHh
Confidence 45666666665421222235677777777777766655554444333333
No 45
>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=66.34 E-value=8.9 Score=23.66 Aligned_cols=32 Identities=16% Similarity=0.441 Sum_probs=21.2
Q ss_pred ccccccccCCCCc---eeecCCeecchhhHHHhhc
Q 041875 36 KCSHCNGKLVMGN---FSSMEGVLYCKPHFEQLFK 67 (195)
Q Consensus 36 ~C~~C~~~L~~~~---~~~~~g~~yC~~c~~~~~~ 67 (195)
.|..|++.|.... +.-.-.-.||..|....+.
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 4677888885442 3323345789999988876
No 46
>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=66.29 E-value=3.6 Score=26.67 Aligned_cols=33 Identities=18% Similarity=0.419 Sum_probs=14.4
Q ss_pred CcCccCCceeecCceEEECCceecccccccccCCcccccC
Q 041875 100 DKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTS 139 (195)
Q Consensus 100 ~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~ 139 (195)
..|+.|++++. .+.+-|..= |-|..|+-.++..
T Consensus 31 a~CPdC~~~Le---~LkACGAvd----YFC~~c~gLiSKk 63 (70)
T PF07191_consen 31 AFCPDCGQPLE---VLKACGAVD----YFCNHCHGLISKK 63 (70)
T ss_dssp EE-TTT-SB-E---EEEETTEEE----EE-TTTT-EE-TT
T ss_pred ccCCCcccHHH---HHHHhcccc----eeeccCCceeecc
Confidence 46777777764 445544211 3466666666544
No 47
>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=65.91 E-value=8.2 Score=21.22 Aligned_cols=31 Identities=16% Similarity=0.408 Sum_probs=18.2
Q ss_pred cccccccCCCCceeecCCeecchhhHHHhhc
Q 041875 37 CSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK 67 (195)
Q Consensus 37 C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~ 67 (195)
|..|...+........=+..||..|....+.
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~ 32 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLK 32 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHH
Confidence 5666666632222222567788888876654
No 48
>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=65.69 E-value=3.4 Score=25.16 Aligned_cols=28 Identities=21% Similarity=0.572 Sum_probs=16.5
Q ss_pred ccccCCcccccCCeeccCCcccc-HHHHH
Q 041875 128 RCSHGGCLLTTSSYAALDGILYC-KSHFA 155 (195)
Q Consensus 128 ~C~~C~~~L~~~~~~~~dg~~yC-~~c~~ 155 (195)
.|..|...++...-+.+||+.|| +.|..
T Consensus 9 aC~~C~C~V~~~~Ai~~dGk~YCS~aCA~ 37 (52)
T PF02069_consen 9 ACPSCSCVVSEEEAIQKDGKYYCSEACAN 37 (52)
T ss_dssp SSTT----B-TTTSEESSS-EESSHHHHH
T ss_pred cCCCCEeEECchHhHHhCCEeeecHHHhc
Confidence 36778888887778888999998 56654
No 49
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=63.74 E-value=4 Score=20.84 Aligned_cols=11 Identities=18% Similarity=0.498 Sum_probs=6.9
Q ss_pred CcCccCCceee
Q 041875 100 DKCTSCKKTVY 110 (195)
Q Consensus 100 ~~C~~C~~~I~ 110 (195)
..|+.|+..|.
T Consensus 3 ~~Cp~Cg~~~~ 13 (26)
T PF13248_consen 3 MFCPNCGAEID 13 (26)
T ss_pred CCCcccCCcCC
Confidence 46777776554
No 50
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=63.34 E-value=2.5 Score=28.94 Aligned_cols=31 Identities=29% Similarity=0.311 Sum_probs=15.5
Q ss_pred cccccccccccCceEeeC-CcccccCcccccc
Q 041875 9 KCKACDKTVHIIDMVTAD-GISYHKICFKCSH 39 (195)
Q Consensus 9 ~C~~C~~~I~~~~~i~~~-g~~~H~~CF~C~~ 39 (195)
.|..|+.+|..|+.+..- ...-|-+||.=+.
T Consensus 8 kC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~ 39 (103)
T COG4847 8 KCYVCGGTIIEGQKFTFTKKGSVHYECLAESK 39 (103)
T ss_pred eEeeeCCEeeeccEEEEeeCCcchHHHHHHHH
Confidence 455666665555544332 2245555554443
No 51
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=62.68 E-value=3 Score=32.66 Aligned_cols=46 Identities=22% Similarity=0.498 Sum_probs=35.6
Q ss_pred ccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceee
Q 041875 34 CFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVY 110 (195)
Q Consensus 34 CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~ 110 (195)
=|.|..|.+...+ ..+..=|..+|..|+.+.+..+ +.|..|++..+
T Consensus 196 PF~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~kg------------------------------~~C~~Cgk~t~ 241 (259)
T COG5152 196 PFLCGICKKDYES-PVVTECGHSFCSLCAIRKYQKG------------------------------DECGVCGKATY 241 (259)
T ss_pred ceeehhchhhccc-hhhhhcchhHHHHHHHHHhccC------------------------------Ccceecchhhc
Confidence 3788889887764 3444567889999999888633 79999998776
No 52
>PRK00807 50S ribosomal protein L24e; Validated
Probab=62.62 E-value=5 Score=24.37 Aligned_cols=24 Identities=25% Similarity=0.425 Sum_probs=13.9
Q ss_pred CcccccccccccCc---eEeeCCcccc
Q 041875 8 EKCKACDKTVHIID---MVTADGISYH 31 (195)
Q Consensus 8 ~~C~~C~~~I~~~~---~i~~~g~~~H 31 (195)
..|..|+..|+++. .+..+|+.|.
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~ 28 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILY 28 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEE
Confidence 35677777776543 2445566555
No 53
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=62.30 E-value=3.5 Score=28.24 Aligned_cols=35 Identities=29% Similarity=0.351 Sum_probs=24.8
Q ss_pred CcCccCCceeecCceEEE-CCceecccccccccCCc
Q 041875 100 DKCTSCKKTVYPLEKVTV-EGESFHKTCFRCSHGGC 134 (195)
Q Consensus 100 ~~C~~C~~~I~~~~~v~~-~~~~~H~~CF~C~~C~~ 134 (195)
-+|++|+.+|..++.+++ ....-|.+||.=+.-++
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~k 42 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECLAESKRKK 42 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHHHHHHhcC
Confidence 479999999988888754 35567888886544333
No 54
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=61.80 E-value=2.7 Score=38.94 Aligned_cols=51 Identities=20% Similarity=0.462 Sum_probs=35.8
Q ss_pred ccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceeecCc
Q 041875 34 CFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLE 113 (195)
Q Consensus 34 CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~ 113 (195)
=++|+.|+..--+ .....=+.+||..|...++..+. .+|+.|+.++.+.+
T Consensus 643 ~LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~etRq-----------------------------RKCP~Cn~aFganD 692 (698)
T KOG0978|consen 643 LLKCSVCNTRWKD-AVITKCGHVFCEECVQTRYETRQ-----------------------------RKCPKCNAAFGAND 692 (698)
T ss_pred ceeCCCccCchhh-HHHHhcchHHHHHHHHHHHHHhc-----------------------------CCCCCCCCCCCccc
Confidence 3788999854322 11223467899999999887443 79999999987655
Q ss_pred e
Q 041875 114 K 114 (195)
Q Consensus 114 ~ 114 (195)
.
T Consensus 693 v 693 (698)
T KOG0978|consen 693 V 693 (698)
T ss_pred c
Confidence 4
No 55
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=61.25 E-value=3.3 Score=30.20 Aligned_cols=21 Identities=29% Similarity=0.629 Sum_probs=12.9
Q ss_pred cccCCcccccCCeeccCCccccHHHH
Q 041875 129 CSHGGCLLTTSSYAALDGILYCKSHF 154 (195)
Q Consensus 129 C~~C~~~L~~~~~~~~dg~~yC~~c~ 154 (195)
|..|+.+| |- +||.+||..|=
T Consensus 31 Cp~Cg~PL----F~-KdG~v~CPvC~ 51 (131)
T COG1645 31 CPKCGTPL----FR-KDGEVFCPVCG 51 (131)
T ss_pred CcccCCcc----ee-eCCeEECCCCC
Confidence 55566655 22 67777776663
No 56
>PF12773 DZR: Double zinc ribbon
Probab=60.99 E-value=4.8 Score=23.77 Aligned_cols=23 Identities=22% Similarity=0.424 Sum_probs=10.7
Q ss_pred cccccccCCCCceeecCCeecchhhHH
Q 041875 37 CSHCNGKLVMGNFSSMEGVLYCKPHFE 63 (195)
Q Consensus 37 C~~C~~~L~~~~~~~~~g~~yC~~c~~ 63 (195)
|..|+..|. .......+|..|-.
T Consensus 15 C~~CG~~l~----~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 15 CPHCGTPLP----PPDQSKKICPNCGA 37 (50)
T ss_pred ChhhcCChh----hccCCCCCCcCCcC
Confidence 455555555 11223345555544
No 57
>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=60.27 E-value=7.4 Score=29.24 Aligned_cols=39 Identities=15% Similarity=0.238 Sum_probs=26.8
Q ss_pred CcCccCCceeecCc---eEEECCceecccccccccCCcccccC
Q 041875 100 DKCTSCKKTVYPLE---KVTVEGESFHKTCFRCSHGGCLLTTS 139 (195)
Q Consensus 100 ~~C~~C~~~I~~~~---~v~~~~~~~H~~CF~C~~C~~~L~~~ 139 (195)
..|+.|+.+|.... .|...+..|+.- --|..||++....
T Consensus 40 ~~Cp~C~~~IrG~y~v~gv~~~g~~~~~P-sYC~~CGkpyPWt 81 (158)
T PF10083_consen 40 TSCPNCSTPIRGDYHVEGVFGLGGHYEAP-SYCHNCGKPYPWT 81 (158)
T ss_pred HHCcCCCCCCCCceecCCeeeeCCCCCCC-hhHHhCCCCCchH
Confidence 69999999998432 234456666632 2488899988753
No 58
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=59.86 E-value=5.8 Score=24.27 Aligned_cols=25 Identities=24% Similarity=0.450 Sum_probs=16.0
Q ss_pred CcCccCCceeecCceEEECCceecc
Q 041875 100 DKCTSCKKTVYPLEKVTVEGESFHK 124 (195)
Q Consensus 100 ~~C~~C~~~I~~~~~v~~~~~~~H~ 124 (195)
.+|..|+++|.+...+...+..-|+
T Consensus 2 ~~CvVCKqpi~~a~~v~T~~G~VH~ 26 (54)
T PF10886_consen 2 EICVVCKQPIDDALVVETESGPVHP 26 (54)
T ss_pred CeeeeeCCccCcceEEEcCCCccCc
Confidence 4677777777765555555555555
No 59
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=58.98 E-value=4.9 Score=33.36 Aligned_cols=45 Identities=20% Similarity=0.484 Sum_probs=33.3
Q ss_pred cccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceee
Q 041875 35 FKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVY 110 (195)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~ 110 (195)
|.|..|++.... ..+..-+..+|+.|..+.+..+ +.|..|++.+.
T Consensus 242 f~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~qk~------------------------------~~c~vC~~~t~ 286 (313)
T KOG1813|consen 242 FKCFICRKYFYR-PVVTKCGHYFCEVCALKPYQKG------------------------------EKCYVCSQQTH 286 (313)
T ss_pred cccccccccccc-chhhcCCceeehhhhccccccC------------------------------Ccceecccccc
Confidence 667777777653 3444567889999998777522 78999999887
No 60
>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=58.39 E-value=8.9 Score=21.74 Aligned_cols=30 Identities=20% Similarity=0.607 Sum_probs=16.6
Q ss_pred CcCccCCceeecCceEEECCceecccccccccCCc
Q 041875 100 DKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGC 134 (195)
Q Consensus 100 ~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~ 134 (195)
.+|..|+..|-+--.+...++.| +|..|+.
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 68999988887655566666776 6777766
No 61
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=55.33 E-value=12 Score=23.38 Aligned_cols=29 Identities=24% Similarity=0.374 Sum_probs=21.2
Q ss_pred ccccccccCCCC--ceeecCCeecch-hhHHH
Q 041875 36 KCSHCNGKLVMG--NFSSMEGVLYCK-PHFEQ 64 (195)
Q Consensus 36 ~C~~C~~~L~~~--~~~~~~g~~yC~-~c~~~ 64 (195)
.|..|++.|..+ .|..++.+.+|. .|-.+
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS~ECR~~ 49 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCSEECRSQ 49 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccccHHHHHH
Confidence 477889999843 566788999994 56544
No 62
>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=55.09 E-value=4.9 Score=23.18 Aligned_cols=22 Identities=27% Similarity=0.806 Sum_probs=13.5
Q ss_pred ccccccccCCCCceeecCCeecchhh
Q 041875 36 KCSHCNGKLVMGNFSSMEGVLYCKPH 61 (195)
Q Consensus 36 ~C~~C~~~L~~~~~~~~~g~~yC~~c 61 (195)
.|..|+.+|-. .++|+.||..|
T Consensus 19 ~Cp~C~~PL~~----~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPLMR----DKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCeeEE----ecCCCEECCCC
Confidence 35566666542 46777777655
No 63
>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=55.08 E-value=5.7 Score=26.12 Aligned_cols=15 Identities=33% Similarity=0.747 Sum_probs=11.2
Q ss_pred CCcccccccccccCc
Q 041875 7 QEKCKACDKTVHIID 21 (195)
Q Consensus 7 ~~~C~~C~~~I~~~~ 21 (195)
-..|..|++.|..++
T Consensus 7 Ra~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 7 RAKCKGCKKKIAKGE 21 (82)
T ss_dssp TEBETTTSCBE-TTS
T ss_pred CccCcccCCcCCCCC
Confidence 458999999998655
No 64
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=52.96 E-value=11 Score=23.48 Aligned_cols=30 Identities=17% Similarity=0.530 Sum_probs=19.7
Q ss_pred CCCcccccccccccCceEeeCCcccccCccccccccccC
Q 041875 6 TQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKL 44 (195)
Q Consensus 6 ~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L 44 (195)
..++|..|+..|..++.-.. |.|-.|++.+
T Consensus 8 ~~~~CtSCg~~i~p~e~~v~---------F~CPnCGe~~ 37 (61)
T COG2888 8 DPPVCTSCGREIAPGETAVK---------FPCPNCGEVE 37 (61)
T ss_pred CCceeccCCCEeccCCceeE---------eeCCCCCcee
Confidence 36788888888855553222 7778887543
No 65
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=52.80 E-value=22 Score=27.79 Aligned_cols=32 Identities=22% Similarity=0.510 Sum_probs=23.8
Q ss_pred ccccccccccCCCCceeecCCeecchhhHHHhh
Q 041875 34 CFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF 66 (195)
Q Consensus 34 CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~ 66 (195)
-|.|..|...+.. .....=|..||..|..+..
T Consensus 18 ~~~CpICld~~~d-PVvT~CGH~FC~~CI~~wl 49 (193)
T PLN03208 18 DFDCNICLDQVRD-PVVTLCGHLFCWPCIHKWT 49 (193)
T ss_pred ccCCccCCCcCCC-cEEcCCCchhHHHHHHHHH
Confidence 4889999887754 4445568899999987643
No 66
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=52.77 E-value=8.5 Score=19.50 Aligned_cols=10 Identities=20% Similarity=0.893 Sum_probs=5.1
Q ss_pred cccccccccc
Q 041875 10 CKACDKTVHI 19 (195)
Q Consensus 10 C~~C~~~I~~ 19 (195)
|..|+..|.+
T Consensus 1 C~sC~~~i~~ 10 (24)
T PF07754_consen 1 CTSCGRPIAP 10 (24)
T ss_pred CccCCCcccC
Confidence 4455555543
No 67
>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=49.26 E-value=38 Score=21.70 Aligned_cols=34 Identities=15% Similarity=0.146 Sum_probs=25.5
Q ss_pred CccccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875 33 ICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK 67 (195)
Q Consensus 33 ~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~ 67 (195)
+=|.|..++..+.+ ....-+|..|++.+..+-+.
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 44889998887774 56667889999999988776
No 68
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=46.24 E-value=11 Score=34.86 Aligned_cols=11 Identities=18% Similarity=0.567 Sum_probs=6.3
Q ss_pred CcCccCCceee
Q 041875 100 DKCTSCKKTVY 110 (195)
Q Consensus 100 ~~C~~C~~~I~ 110 (195)
..|..|+..+.
T Consensus 42 ~fC~~CG~~~~ 52 (645)
T PRK14559 42 AHCPNCGAETG 52 (645)
T ss_pred ccccccCCccc
Confidence 45666666544
No 69
>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=45.28 E-value=11 Score=20.84 Aligned_cols=32 Identities=22% Similarity=0.563 Sum_probs=17.8
Q ss_pred CcCccCCceeecCce-EEECCceecccccccccCCccc
Q 041875 100 DKCTSCKKTVYPLEK-VTVEGESFHKTCFRCSHGGCLL 136 (195)
Q Consensus 100 ~~C~~C~~~I~~~~~-v~~~~~~~H~~CF~C~~C~~~L 136 (195)
..|+.|+..+...+. +...+. -++|..|+..|
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~-----~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGG-----KVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCC-----EEECCCCCCEE
Confidence 368888876653322 222221 25677777765
No 70
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=44.18 E-value=8.5 Score=35.40 Aligned_cols=22 Identities=27% Similarity=0.480 Sum_probs=14.8
Q ss_pred ECCceecccccccccCCccccc
Q 041875 117 VEGESFHKTCFRCSHGGCLLTT 138 (195)
Q Consensus 117 ~~~~~~H~~CF~C~~C~~~L~~ 138 (195)
..+..+-++|++|..|+..|.+
T Consensus 106 ~sg~~~ckk~~~c~qc~~~lpg 127 (694)
T KOG4443|consen 106 PSGPWLCKKCTRCRQCDSTLPG 127 (694)
T ss_pred cCcccccHHHHhhhhccccccc
Confidence 4455556677777777777765
No 71
>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=43.91 E-value=19 Score=20.92 Aligned_cols=11 Identities=27% Similarity=0.564 Sum_probs=7.7
Q ss_pred CccccHHHHHh
Q 041875 146 GILYCKSHFAQ 156 (195)
Q Consensus 146 g~~yC~~c~~~ 156 (195)
+--+|..||..
T Consensus 22 d~dLC~~Cf~~ 32 (46)
T cd02249 22 DFDLCSSCYAK 32 (46)
T ss_pred CCcCHHHHHCc
Confidence 34568888874
No 72
>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=43.62 E-value=29 Score=29.19 Aligned_cols=30 Identities=20% Similarity=0.509 Sum_probs=22.8
Q ss_pred CeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceeecC
Q 041875 54 GVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPL 112 (195)
Q Consensus 54 g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~ 112 (195)
|..+|..|..+.+.. +...|+.|++++...
T Consensus 27 GH~~C~sCv~~l~~~-----------------------------~~~~CP~C~~~lrk~ 56 (309)
T TIGR00570 27 GHTLCESCVDLLFVR-----------------------------GSGSCPECDTPLRKN 56 (309)
T ss_pred CCcccHHHHHHHhcC-----------------------------CCCCCCCCCCccchh
Confidence 778999999988752 125899999888743
No 73
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=43.59 E-value=15 Score=23.46 Aligned_cols=14 Identities=21% Similarity=0.460 Sum_probs=7.7
Q ss_pred CcccccccccccCc
Q 041875 8 EKCKACDKTVHIID 21 (195)
Q Consensus 8 ~~C~~C~~~I~~~~ 21 (195)
.+|.-|+..|++|.
T Consensus 4 ~~CsFcG~~I~PGt 17 (66)
T COG2075 4 RVCSFCGKKIEPGT 17 (66)
T ss_pred eEecCcCCccCCCc
Confidence 35555666665543
No 74
>PRK00420 hypothetical protein; Validated
Probab=43.50 E-value=9.5 Score=27.12 Aligned_cols=11 Identities=18% Similarity=0.818 Sum_probs=6.4
Q ss_pred CcCccCCceee
Q 041875 100 DKCTSCKKTVY 110 (195)
Q Consensus 100 ~~C~~C~~~I~ 110 (195)
..|+.|+.+++
T Consensus 24 ~~CP~Cg~pLf 34 (112)
T PRK00420 24 KHCPVCGLPLF 34 (112)
T ss_pred CCCCCCCCcce
Confidence 45666665554
No 75
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=43.42 E-value=19 Score=27.01 Aligned_cols=31 Identities=16% Similarity=0.427 Sum_probs=22.5
Q ss_pred ccccCCcccccCCeec-cCC--ccccHHHHHhhhcC
Q 041875 128 RCSHGGCLLTTSSYAA-LDG--ILYCKSHFAQLFKE 160 (195)
Q Consensus 128 ~C~~C~~~L~~~~~~~-~dg--~~yC~~c~~~~f~~ 160 (195)
.|..||+.+.+..+.. .+| ..+|..|+ +||.
T Consensus 2 ~CEiCG~~i~~~~~~v~iega~l~vC~~C~--k~G~ 35 (154)
T TIGR00270 2 NCEICGRKIKGKGFKIVIEGSEMTVCGECR--KFGK 35 (154)
T ss_pred ccccCCCccCCCCeEEEEcCeEEehhhhHH--hcCC
Confidence 3889999998764444 365 44599998 7777
No 76
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=43.36 E-value=13 Score=19.44 Aligned_cols=12 Identities=25% Similarity=0.764 Sum_probs=2.9
Q ss_pred cccccccccCCC
Q 041875 35 FKCSHCNGKLVM 46 (195)
Q Consensus 35 F~C~~C~~~L~~ 46 (195)
|+|..|++++.+
T Consensus 1 ~~C~~C~~~~~~ 12 (30)
T PF07649_consen 1 FRCDACGKPIDG 12 (30)
T ss_dssp ---TTTS----S
T ss_pred CcCCcCCCcCCC
Confidence 455666665554
No 77
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=42.84 E-value=16 Score=26.49 Aligned_cols=25 Identities=20% Similarity=0.368 Sum_probs=14.5
Q ss_pred CCcccccccccccCc---eEeeCCcccc
Q 041875 7 QEKCKACDKTVHIID---MVTADGISYH 31 (195)
Q Consensus 7 ~~~C~~C~~~I~~~~---~i~~~g~~~H 31 (195)
..+|..|+..|++|. +|..+|+.|+
T Consensus 4 ~e~CsFcG~kIyPG~G~~fVR~DGkvf~ 31 (131)
T PRK14891 4 TRTCDYTGEEIEPGTGTMFVRKDGTVLH 31 (131)
T ss_pred eeeecCcCCcccCCCCcEEEecCCCEEE
Confidence 356777777777654 3444454444
No 78
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=42.45 E-value=6.4 Score=29.19 Aligned_cols=34 Identities=21% Similarity=0.545 Sum_probs=23.5
Q ss_pred cccccccccccCceEeeCCcccccCccccccccccCC
Q 041875 9 KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLV 45 (195)
Q Consensus 9 ~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~ 45 (195)
.|..|+..+...+.+..++. ..=|+|..|+..|.
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 69999888775555444332 33399999999884
No 79
>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=42.38 E-value=14 Score=22.59 Aligned_cols=24 Identities=29% Similarity=0.508 Sum_probs=14.2
Q ss_pred CcccccccccccCc---eEeeCCcccc
Q 041875 8 EKCKACDKTVHIID---MVTADGISYH 31 (195)
Q Consensus 8 ~~C~~C~~~I~~~~---~i~~~g~~~H 31 (195)
..|.-|+..|+++. .|..+|+.++
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~ 30 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFR 30 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEE
Confidence 46777777777654 3444555443
No 80
>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=42.28 E-value=8.2 Score=22.01 Aligned_cols=27 Identities=33% Similarity=0.678 Sum_probs=12.8
Q ss_pred cCccCCceeecCceEE--ECCceeccccc
Q 041875 101 KCTSCKKTVYPLEKVT--VEGESFHKTCF 127 (195)
Q Consensus 101 ~C~~C~~~I~~~~~v~--~~~~~~H~~CF 127 (195)
.|+.|...+...+.+. .=+..||..|+
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci 30 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCI 30 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHH
Confidence 3556666665433332 12445555554
No 81
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=40.81 E-value=24 Score=29.55 Aligned_cols=34 Identities=21% Similarity=0.305 Sum_probs=27.7
Q ss_pred CccccccccccCCCCceeecCCeecchhhHHHhh
Q 041875 33 ICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLF 66 (195)
Q Consensus 33 ~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~ 66 (195)
+=|-|..|...|....|.=.+|.+.|..|-.++.
T Consensus 47 ~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~ 80 (299)
T KOG3002|consen 47 DLLDCPVCFNPLSPPIFQCDNGHLACSSCRTKVS 80 (299)
T ss_pred hhccCchhhccCcccceecCCCcEehhhhhhhhc
Confidence 3367889999998878887889999999986553
No 82
>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=40.20 E-value=46 Score=18.28 Aligned_cols=31 Identities=13% Similarity=0.299 Sum_probs=21.3
Q ss_pred cccccccCCCCceeecCCeecchhhHHHhhc
Q 041875 37 CSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK 67 (195)
Q Consensus 37 C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~ 67 (195)
|..|...+........=|..||..|..+.+.
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 4566666665443444478899999988775
No 83
>KOG3476 consensus Microtubule-associated protein CRIPT [Cytoskeleton]
Probab=39.51 E-value=4 Score=27.48 Aligned_cols=38 Identities=24% Similarity=0.514 Sum_probs=27.1
Q ss_pred cccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceeecC
Q 041875 35 FKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPL 112 (195)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~ 112 (195)
-+|..|...+. ..|.-||..|..+. .+|+-|++.|...
T Consensus 55 ~kC~iCk~~vH------Q~GshYC~tCAY~K----------------------------------giCAMCGKki~nT 92 (100)
T KOG3476|consen 55 AKCRICKQLVH------QPGSHYCQTCAYKK----------------------------------GICAMCGKKILNT 92 (100)
T ss_pred chhHHHHHHhc------CCcchhHhHhhhhh----------------------------------hHHHHhhhHhhcc
Confidence 35777765443 36777899887644 6899999999753
No 84
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=39.33 E-value=35 Score=20.00 Aligned_cols=29 Identities=10% Similarity=0.386 Sum_probs=18.5
Q ss_pred ccccccccCCCCceee-c-CCeecchhhHHH
Q 041875 36 KCSHCNGKLVMGNFSS-M-EGVLYCKPHFEQ 64 (195)
Q Consensus 36 ~C~~C~~~L~~~~~~~-~-~g~~yC~~c~~~ 64 (195)
.|..|+..+....|.- + .+-.+|..||.+
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhC
Confidence 4677777776444431 1 245789999975
No 85
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=39.07 E-value=13 Score=21.66 Aligned_cols=27 Identities=26% Similarity=0.695 Sum_probs=15.1
Q ss_pred cccccccccccCceEeeCCcccccCccccccccccC
Q 041875 9 KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKL 44 (195)
Q Consensus 9 ~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L 44 (195)
+|..|+..+...+... =++|..|+..+
T Consensus 5 ~C~~CG~~~~~~~~~~---------~~~Cp~CG~~~ 31 (46)
T PRK00398 5 KCARCGREVELDEYGT---------GVRCPYCGYRI 31 (46)
T ss_pred ECCCCCCEEEECCCCC---------ceECCCCCCeE
Confidence 5777776664322111 36777776654
No 86
>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=38.39 E-value=29 Score=19.95 Aligned_cols=10 Identities=40% Similarity=0.670 Sum_probs=7.0
Q ss_pred ccccHHHHHh
Q 041875 147 ILYCKSHFAQ 156 (195)
Q Consensus 147 ~~yC~~c~~~ 156 (195)
.-+|..||.+
T Consensus 27 ~dlC~~Cf~~ 36 (44)
T smart00291 27 YDLCQSCFAK 36 (44)
T ss_pred ccchHHHHhC
Confidence 3368888864
No 87
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=38.21 E-value=2 Score=29.49 Aligned_cols=53 Identities=21% Similarity=0.342 Sum_probs=37.4
Q ss_pred cCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHHH
Q 041875 101 KCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKSH 153 (195)
Q Consensus 101 ~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~c 153 (195)
.|..|...+..-....+.-..++..+.-|-+|.+.|....|.+...-|||.+-
T Consensus 37 aCy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~sp 89 (105)
T COG4357 37 ACYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYCQSP 89 (105)
T ss_pred hHHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCcCCC
Confidence 47777777763333345556788888899999999887777777777777543
No 88
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=37.50 E-value=37 Score=25.84 Aligned_cols=33 Identities=15% Similarity=0.304 Sum_probs=23.4
Q ss_pred cccCCcccccCCeeccCC--ccccHHHHHhhhcCCCc
Q 041875 129 CSHGGCLLTTSSYAALDG--ILYCKSHFAQLFKEKGC 163 (195)
Q Consensus 129 C~~C~~~L~~~~~~~~dg--~~yC~~c~~~~f~~k~~ 163 (195)
|..|++.+.....+..+| .-.|..|+ .||....
T Consensus 6 CEiCG~~i~~~~~v~vegsel~VC~~Ca--k~G~~~~ 40 (165)
T COG1813 6 CELCGREIDKPIKVKVEGAELTVCDDCA--KFGTAAK 40 (165)
T ss_pred eeccccccCCCeeEEeecceeehhHHHH--HhccCcc
Confidence 889999988433444454 44599999 8986655
No 89
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=37.46 E-value=17 Score=21.18 Aligned_cols=22 Identities=27% Similarity=0.460 Sum_probs=13.4
Q ss_pred cccCCcccccCCeeccCCcccc-HHHH
Q 041875 129 CSHGGCLLTTSSYAALDGILYC-KSHF 154 (195)
Q Consensus 129 C~~C~~~L~~~~~~~~dg~~yC-~~c~ 154 (195)
|..|.+.+.. ..++.+|| +.|-
T Consensus 9 C~~Cdk~~~~----~~~~~lYCSe~Cr 31 (43)
T PF12855_consen 9 CIVCDKQIDP----PDDGSLYCSEECR 31 (43)
T ss_pred HHHhhccccC----CCCCccccCHHHH
Confidence 4455666543 45788999 4563
No 90
>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=36.49 E-value=16 Score=20.12 Aligned_cols=11 Identities=36% Similarity=0.842 Sum_probs=4.2
Q ss_pred CcCccCCceee
Q 041875 100 DKCTSCKKTVY 110 (195)
Q Consensus 100 ~~C~~C~~~I~ 110 (195)
+.|..|++++.
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 45555555554
No 91
>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=35.20 E-value=18 Score=23.48 Aligned_cols=24 Identities=25% Similarity=0.311 Sum_probs=10.6
Q ss_pred CcccccccccccCc---eEeeCCcccc
Q 041875 8 EKCKACDKTVHIID---MVTADGISYH 31 (195)
Q Consensus 8 ~~C~~C~~~I~~~~---~i~~~g~~~H 31 (195)
.+|.-|+..|++|. +|..+|+.++
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 46777777777654 2344444443
No 92
>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=34.18 E-value=11 Score=20.87 Aligned_cols=31 Identities=19% Similarity=0.576 Sum_probs=18.7
Q ss_pred ccccccccccCceEeeCCcccccCccccccccccCC
Q 041875 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLV 45 (195)
Q Consensus 10 C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~ 45 (195)
|..|.+.+ ....++.||..=..|..|+-.+.
T Consensus 2 C~~C~~Ey-----~~p~~RR~~~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 2 CDDCLKEY-----FDPSNRRFHYQFISCTNCGPRYS 32 (35)
T ss_dssp -HHHHHHH-----CSTTSTTTT-TT--BTTCC-SCC
T ss_pred CHHHHHHH-----cCCCCCcccCcCccCCCCCCCEE
Confidence 55665544 34568999999999999987664
No 93
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=33.44 E-value=33 Score=27.65 Aligned_cols=28 Identities=14% Similarity=0.265 Sum_probs=16.8
Q ss_pred cccccCCCCceeecC-CeecchhhHHHhh
Q 041875 39 HCNGKLVMGNFSSME-GVLYCKPHFEQLF 66 (195)
Q Consensus 39 ~C~~~L~~~~~~~~~-g~~yC~~c~~~~~ 66 (195)
.|...-....|+... ..++|..|.....
T Consensus 8 ~C~~~~~~~~f~LTaC~HvfC~~C~k~~~ 36 (233)
T KOG4739|consen 8 KCFRFPSQDPFFLTACRHVFCEPCLKASS 36 (233)
T ss_pred cccccCCCCceeeeechhhhhhhhcccCC
Confidence 344433345666544 6788998876444
No 94
>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=33.03 E-value=62 Score=16.73 Aligned_cols=11 Identities=27% Similarity=0.746 Sum_probs=6.2
Q ss_pred CcCccCCceee
Q 041875 100 DKCTSCKKTVY 110 (195)
Q Consensus 100 ~~C~~C~~~I~ 110 (195)
.+|.+|...|.
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 57899998876
No 95
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=32.16 E-value=22 Score=33.31 Aligned_cols=84 Identities=20% Similarity=0.433 Sum_probs=52.7
Q ss_pred CCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHHHhhccCCccccCCCccCCCCCCC
Q 041875 7 QEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFKETGSFTNKLKPAQKNGLTR 86 (195)
Q Consensus 7 ~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (195)
..+|..|-+.|. .-.++.||--=-.|+.|+-. |.+....||=. .. +.+.+|
T Consensus 101 ~a~C~~Cl~Ei~-----dp~~rrY~YPF~~CT~CGPR-----fTIi~alPYDR-----~n----TsM~~F---------- 151 (750)
T COG0068 101 AATCEDCLEEIF-----DPNSRRYLYPFINCTNCGPR-----FTIIEALPYDR-----EN----TSMADF---------- 151 (750)
T ss_pred hhhhHHHHHHhc-----CCCCcceeccccccCCCCcc-----eeeeccCCCCc-----cc----CccccC----------
Confidence 457888876665 34577888777788888654 44444444311 00 111111
Q ss_pred CCCCCccccCCCCCcCccCCceeecCceEEECCceecccccccccCCcccc
Q 041875 87 TPSKFSTMFCGTQDKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLT 137 (195)
Q Consensus 87 ~p~~~~~~~~~~~~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~ 137 (195)
+.|..|.+ +.-...++.||..=..|..|+-.+.
T Consensus 152 -------------~lC~~C~~-----EY~dP~nRRfHAQp~aCp~CGP~~~ 184 (750)
T COG0068 152 -------------PLCPFCDK-----EYKDPLNRRFHAQPIACPKCGPHLF 184 (750)
T ss_pred -------------cCCHHHHH-----HhcCccccccccccccCcccCCCeE
Confidence 67877765 3345778889988888888888663
No 96
>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=31.23 E-value=36 Score=19.78 Aligned_cols=9 Identities=22% Similarity=0.571 Sum_probs=7.3
Q ss_pred ecchhhHHH
Q 041875 56 LYCKPHFEQ 64 (195)
Q Consensus 56 ~yC~~c~~~ 64 (195)
-+|..||.+
T Consensus 29 dLC~~C~~~ 37 (46)
T PF00569_consen 29 DLCEDCFSK 37 (46)
T ss_dssp EEEHHHHHH
T ss_pred chhhHHHhC
Confidence 479999976
No 97
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=31.06 E-value=57 Score=21.60 Aligned_cols=13 Identities=23% Similarity=0.480 Sum_probs=5.8
Q ss_pred CeecchhhHHHhh
Q 041875 54 GVLYCKPHFEQLF 66 (195)
Q Consensus 54 g~~yC~~c~~~~~ 66 (195)
+-+.|+.||+-..
T Consensus 35 ~fPvCr~CyEYEr 47 (80)
T PF14569_consen 35 AFPVCRPCYEYER 47 (80)
T ss_dssp -----HHHHHHHH
T ss_pred CCccchhHHHHHh
Confidence 3467899987544
No 98
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=30.80 E-value=10 Score=23.08 Aligned_cols=10 Identities=20% Similarity=0.777 Sum_probs=4.8
Q ss_pred cccccccccc
Q 041875 9 KCKACDKTVH 18 (195)
Q Consensus 9 ~C~~C~~~I~ 18 (195)
+|.+|+-.|.
T Consensus 24 ~C~gC~~~l~ 33 (56)
T PF02591_consen 24 TCSGCHMELP 33 (56)
T ss_pred ccCCCCEEcC
Confidence 4444544444
No 99
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=30.78 E-value=15 Score=25.49 Aligned_cols=27 Identities=30% Similarity=0.415 Sum_probs=18.0
Q ss_pred cccccCCcccccCCee-ccCCccccHHH
Q 041875 127 FRCSHGGCLLTTSSYA-ALDGILYCKSH 153 (195)
Q Consensus 127 F~C~~C~~~L~~~~~~-~~dg~~yC~~c 153 (195)
|+|+.|-..-..+... ..+|++||..|
T Consensus 71 FTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 71 FTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred eeeeeeeeEechhhhccccCCCEecccc
Confidence 7777776655433322 45899999877
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=30.75 E-value=27 Score=19.93 Aligned_cols=11 Identities=27% Similarity=0.646 Sum_probs=5.0
Q ss_pred cccccccccCC
Q 041875 35 FKCSHCNGKLV 45 (195)
Q Consensus 35 F~C~~C~~~L~ 45 (195)
+.|..|+..|.
T Consensus 20 ~vC~~CG~Vl~ 30 (43)
T PF08271_consen 20 LVCPNCGLVLE 30 (43)
T ss_dssp EEETTT-BBEE
T ss_pred EECCCCCCEee
Confidence 45555555443
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=30.75 E-value=31 Score=20.30 Aligned_cols=12 Identities=25% Similarity=0.708 Sum_probs=8.5
Q ss_pred CCCccccccccc
Q 041875 6 TQEKCKACDKTV 17 (195)
Q Consensus 6 ~~~~C~~C~~~I 17 (195)
....|..|++.|
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
>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=30.25 E-value=26 Score=23.86 Aligned_cols=42 Identities=12% Similarity=0.309 Sum_probs=27.5
Q ss_pred cCCCCCcccccccccccCceEeeCCcccccCccccccccccCCC
Q 041875 3 FCGTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVM 46 (195)
Q Consensus 3 ~~~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~ 46 (195)
+......|..|++++..-+.|.+.+-.+.+ -+|..|+.++..
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 334456889998888766666654443333 467788888764
No 103
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=30.01 E-value=48 Score=19.05 Aligned_cols=7 Identities=14% Similarity=0.377 Sum_probs=5.0
Q ss_pred cchhhHH
Q 041875 57 YCKPHFE 63 (195)
Q Consensus 57 yC~~c~~ 63 (195)
+|..||.
T Consensus 25 LC~~C~~ 31 (43)
T cd02340 25 LCESCEA 31 (43)
T ss_pred chHHhhC
Confidence 6777775
No 104
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=29.82 E-value=22 Score=23.62 Aligned_cols=28 Identities=18% Similarity=0.403 Sum_probs=17.5
Q ss_pred cccccccCCCCcee--ecC---CeecchhhHHH
Q 041875 37 CSHCNGKLVMGNFS--SME---GVLYCKPHFEQ 64 (195)
Q Consensus 37 C~~C~~~L~~~~~~--~~~---g~~yC~~c~~~ 64 (195)
|..|+-+|.....+ ..| +.-||.-||..
T Consensus 3 CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 3 CQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred CCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 67778887655422 112 34699999863
No 105
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=28.70 E-value=18 Score=30.42 Aligned_cols=16 Identities=25% Similarity=0.667 Sum_probs=11.4
Q ss_pred CcCccCCceeecCceE
Q 041875 100 DKCTSCKKTVYPLEKV 115 (195)
Q Consensus 100 ~~C~~C~~~I~~~~~v 115 (195)
..|..|...|.-.|.+
T Consensus 124 K~Cp~C~d~VqrIeq~ 139 (389)
T KOG2932|consen 124 KICPLCDDRVQRIEQI 139 (389)
T ss_pred ccCcCcccHHHHHHHh
Confidence 6899999888644433
No 106
>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=28.63 E-value=18 Score=20.11 Aligned_cols=10 Identities=30% Similarity=0.850 Sum_probs=6.3
Q ss_pred cCccCCceee
Q 041875 101 KCTSCKKTVY 110 (195)
Q Consensus 101 ~C~~C~~~I~ 110 (195)
+|..|+..+.
T Consensus 7 ~C~~Cg~~fe 16 (41)
T smart00834 7 RCEDCGHTFE 16 (41)
T ss_pred EcCCCCCEEE
Confidence 5677766554
No 107
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=28.12 E-value=38 Score=23.61 Aligned_cols=38 Identities=18% Similarity=0.200 Sum_probs=28.2
Q ss_pred eeCCcccccCccccccccccCCCCceeecCCeecchhhHHHh
Q 041875 24 TADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQL 65 (195)
Q Consensus 24 ~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~ 65 (195)
...+..+...==.|..| .+..|+..++.+.|..|-.+.
T Consensus 25 ~~~dg~~~va~daCeiC----~~~GY~q~g~~lvC~~C~~~~ 62 (102)
T PF10080_consen 25 KKPDGSYRVAFDACEIC----GPKGYYQEGDQLVCKNCGVRF 62 (102)
T ss_pred ECCCCCEEEEEEecccc----CCCceEEECCEEEEecCCCEE
Confidence 33445566655568888 557899999999999997653
No 108
>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=27.97 E-value=18 Score=20.64 Aligned_cols=10 Identities=20% Similarity=0.753 Sum_probs=5.6
Q ss_pred cCccCCceee
Q 041875 101 KCTSCKKTVY 110 (195)
Q Consensus 101 ~C~~C~~~I~ 110 (195)
+|..|+..+.
T Consensus 7 ~C~~Cg~~fe 16 (42)
T PF09723_consen 7 RCEECGHEFE 16 (42)
T ss_pred EeCCCCCEEE
Confidence 5666665443
No 109
>PLN02195 cellulose synthase A
Probab=27.95 E-value=56 Score=31.85 Aligned_cols=38 Identities=26% Similarity=0.652 Sum_probs=23.9
Q ss_pred CCCCcccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecchhhHH
Q 041875 5 GTQEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFE 63 (195)
Q Consensus 5 ~~~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~ 63 (195)
++..+|..|+..|. +..+|..| .. |..|+- +.|+.||+
T Consensus 4 ~~~~~c~~cgd~~~----~~~~g~~f-va---C~eC~~-------------pvCrpCye 41 (977)
T PLN02195 4 SGAPICATCGEEVG----VDSNGEAF-VA---CHECSY-------------PLCKACLE 41 (977)
T ss_pred CCCccceecccccC----cCCCCCeE-EE---eccCCC-------------ccccchhh
Confidence 45568999988775 44566655 33 455533 45777775
No 110
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=27.87 E-value=26 Score=16.57 Aligned_cols=12 Identities=17% Similarity=0.617 Sum_probs=8.6
Q ss_pred cccccCCccccc
Q 041875 127 FRCSHGGCLLTT 138 (195)
Q Consensus 127 F~C~~C~~~L~~ 138 (195)
|+|..|++.+..
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 567888887654
No 111
>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=27.29 E-value=16 Score=21.08 Aligned_cols=9 Identities=44% Similarity=1.139 Sum_probs=2.7
Q ss_pred ccccccccc
Q 041875 10 CKACDKTVH 18 (195)
Q Consensus 10 C~~C~~~I~ 18 (195)
|..|.+.+.
T Consensus 1 C~~C~~iv~ 9 (43)
T PF08746_consen 1 CEACKEIVT 9 (43)
T ss_dssp -TTT-SB-S
T ss_pred CcccchhHe
Confidence 344444444
No 112
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.28 E-value=26 Score=29.10 Aligned_cols=48 Identities=29% Similarity=0.517 Sum_probs=34.9
Q ss_pred CcCccCCceeecCceEEECCceecccccccccCCcccccCCeeccCCccccHH
Q 041875 100 DKCTSCKKTVYPLEKVTVEGESFHKTCFRCSHGGCLLTTSSYAALDGILYCKS 152 (195)
Q Consensus 100 ~~C~~C~~~I~~~~~v~~~~~~~H~~CF~C~~C~~~L~~~~~~~~dg~~yC~~ 152 (195)
..|.-|.+.+.+...|.--...-|+-||-|++ ..|.. .-.-|.+||..
T Consensus 269 LcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSR--esIK~---Qg~sgevYCPS 316 (352)
T KOG3579|consen 269 LCCTLCHERLEDTHFVQCPSVPSHKFCFPCSR--ESIKQ---QGASGEVYCPS 316 (352)
T ss_pred eeehhhhhhhccCceeecCCCcccceecccCH--HHHHh---hcCCCceeCCC
Confidence 57999999998877888888889999999976 22211 12236888854
No 113
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=27.01 E-value=7.2 Score=26.85 Aligned_cols=50 Identities=14% Similarity=0.355 Sum_probs=30.3
Q ss_pred ccccccccccCceEeeCCcccccCccccccccccCCCCceeecCCeecch
Q 041875 10 CKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLVMGNFSSMEGVLYCK 59 (195)
Q Consensus 10 C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~ 59 (195)
|..|...+..--.....-..+++.+..|-.|++.|.-..|...+.-+||.
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 45555555432334444567788888888888887765665555555554
No 114
>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=26.85 E-value=60 Score=19.22 Aligned_cols=11 Identities=9% Similarity=0.199 Sum_probs=7.6
Q ss_pred ccccHHHHHhh
Q 041875 147 ILYCKSHFAQL 157 (195)
Q Consensus 147 ~~yC~~c~~~~ 157 (195)
-=+|..||...
T Consensus 26 ~DlC~~C~~~~ 36 (48)
T cd02341 26 FDLCQDCVVKG 36 (48)
T ss_pred CccCHHHHhCc
Confidence 33699998753
No 115
>PF04641 Rtf2: Rtf2 RING-finger
Probab=26.75 E-value=1e+02 Score=25.04 Aligned_cols=57 Identities=16% Similarity=0.309 Sum_probs=42.2
Q ss_pred cccCccccccccccCCCC-cee--ecCCeecchhhHHHhh-ccCCccccCCCccCCCCCCCCCCCCccccCCCCCcCccC
Q 041875 30 YHKICFKCSHCNGKLVMG-NFS--SMEGVLYCKPHFEQLF-KETGSFTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSC 105 (195)
Q Consensus 30 ~H~~CF~C~~C~~~L~~~-~~~--~~~g~~yC~~c~~~~~-~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C 105 (195)
....-|.|...+..|.+. .|+ ..-|.+|+.......- . ..|..|
T Consensus 109 ~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k~~--------------------------------~~Cp~c 156 (260)
T PF04641_consen 109 NSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELKKS--------------------------------KKCPVC 156 (260)
T ss_pred cCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhccc--------------------------------cccccc
Confidence 457789999999999654 443 3458899988887663 2 579999
Q ss_pred CceeecCceEEEC
Q 041875 106 KKTVYPLEKVTVE 118 (195)
Q Consensus 106 ~~~I~~~~~v~~~ 118 (195)
++++...+.|.++
T Consensus 157 ~~~f~~~DiI~Ln 169 (260)
T PF04641_consen 157 GKPFTEEDIIPLN 169 (260)
T ss_pred CCccccCCEEEec
Confidence 9999866666544
No 116
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=26.18 E-value=65 Score=18.93 Aligned_cols=29 Identities=17% Similarity=0.408 Sum_probs=15.1
Q ss_pred cccccccCCCCceeecCCeecchhhHHHhhc
Q 041875 37 CSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK 67 (195)
Q Consensus 37 C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~ 67 (195)
|-.|++....+- ...|++.|..|-.+++.
T Consensus 2 CiiC~~~~~~GI--~I~~~fIC~~CE~~iv~ 30 (46)
T PF10764_consen 2 CIICGKEKEEGI--HIYGKFICSDCEKEIVN 30 (46)
T ss_pred eEeCCCcCCCCE--EEECeEehHHHHHHhcc
Confidence 445555555421 12456666666665543
No 117
>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=25.96 E-value=22 Score=21.05 Aligned_cols=10 Identities=30% Similarity=0.866 Sum_probs=5.8
Q ss_pred cCccCCceee
Q 041875 101 KCTSCKKTVY 110 (195)
Q Consensus 101 ~C~~C~~~I~ 110 (195)
+|..|+....
T Consensus 7 ~C~~Cg~~fe 16 (52)
T TIGR02605 7 RCTACGHRFE 16 (52)
T ss_pred EeCCCCCEeE
Confidence 5666665443
No 118
>PRK04023 DNA polymerase II large subunit; Validated
Probab=25.95 E-value=67 Score=31.53 Aligned_cols=16 Identities=31% Similarity=0.744 Sum_probs=10.1
Q ss_pred CcCccCCceeecCceE
Q 041875 100 DKCTSCKKTVYPLEKV 115 (195)
Q Consensus 100 ~~C~~C~~~I~~~~~v 115 (195)
..|+.|+..+.+...+
T Consensus 664 y~CPKCG~El~~~s~~ 679 (1121)
T PRK04023 664 DECEKCGREPTPYSKR 679 (1121)
T ss_pred CcCCCCCCCCCccceE
Confidence 4677777777654443
No 119
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=25.87 E-value=60 Score=31.98 Aligned_cols=28 Identities=29% Similarity=0.678 Sum_probs=16.3
Q ss_pred CcccccccccccCceEeeCCcccccCcccccccccc
Q 041875 8 EKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGK 43 (195)
Q Consensus 8 ~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~ 43 (195)
.+|..|+..|. +.++|..| .-|..|+-+
T Consensus 18 qiCqICGD~vg----~~~~Ge~F----VAC~eC~FP 45 (1079)
T PLN02638 18 QVCQICGDNVG----KTVDGEPF----VACDVCAFP 45 (1079)
T ss_pred ceeeecccccC----cCCCCCEE----EEeccCCCc
Confidence 47888877764 34566655 334555443
No 120
>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=25.73 E-value=66 Score=18.62 Aligned_cols=27 Identities=26% Similarity=0.507 Sum_probs=14.8
Q ss_pred cccccccccccCceEee--CCcccccCcc
Q 041875 9 KCKACDKTVHIIDMVTA--DGISYHKICF 35 (195)
Q Consensus 9 ~C~~C~~~I~~~~~i~~--~g~~~H~~CF 35 (195)
+|..|++.-..++.|.- =++.||..|.
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~ 29 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECV 29 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTS
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccC
Confidence 36677774333444433 2356777774
No 121
>PLN02436 cellulose synthase A
Probab=25.35 E-value=60 Score=31.99 Aligned_cols=10 Identities=30% Similarity=0.879 Sum_probs=6.1
Q ss_pred CeecchhhHH
Q 041875 54 GVLYCKPHFE 63 (195)
Q Consensus 54 g~~yC~~c~~ 63 (195)
+-+.|..||+
T Consensus 62 ~fpvCr~Cye 71 (1094)
T PLN02436 62 AFPVCRPCYE 71 (1094)
T ss_pred CCccccchhh
Confidence 3456777775
No 122
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.33 E-value=85 Score=20.47 Aligned_cols=31 Identities=16% Similarity=0.329 Sum_probs=19.1
Q ss_pred cccccccCCCCce---eecCCeecchhhHHHhhc
Q 041875 37 CSHCNGKLVMGNF---SSMEGVLYCKPHFEQLFK 67 (195)
Q Consensus 37 C~~C~~~L~~~~~---~~~~g~~yC~~c~~~~~~ 67 (195)
|.-|++.|....- .-.-.-.||.+|....+.
T Consensus 8 CECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~ 41 (84)
T COG3813 8 CECCDRDLPPDSTDARICTFECTFCADCAENRLH 41 (84)
T ss_pred CcccCCCCCCCCCceeEEEEeeehhHhHHHHhhc
Confidence 5667787754321 111234688899988876
No 123
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.20 E-value=59 Score=28.41 Aligned_cols=33 Identities=9% Similarity=0.313 Sum_probs=21.9
Q ss_pred ccccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875 34 CFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK 67 (195)
Q Consensus 34 CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~ 67 (195)
-|+|..|...+... ....=|..||..|....+.
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 47788887777532 2333477888888877654
No 124
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=25.19 E-value=62 Score=19.04 Aligned_cols=11 Identities=18% Similarity=0.193 Sum_probs=7.3
Q ss_pred eecchhhHHHh
Q 041875 55 VLYCKPHFEQL 65 (195)
Q Consensus 55 ~~yC~~c~~~~ 65 (195)
--+|..||...
T Consensus 24 ~dLC~~Cf~~g 34 (49)
T cd02335 24 FDLCLECFSAG 34 (49)
T ss_pred cchhHHhhhCc
Confidence 34788888643
No 125
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=24.14 E-value=34 Score=20.76 Aligned_cols=29 Identities=24% Similarity=0.563 Sum_probs=19.6
Q ss_pred cccccccccccCceEeeCCcccccCcccc
Q 041875 9 KCKACDKTVHIIDMVTADGISYHKICFKC 37 (195)
Q Consensus 9 ~C~~C~~~I~~~~~i~~~g~~~H~~CF~C 37 (195)
.|..|+.+|...--.+..++.|=.+|-.|
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vC 30 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVC 30 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhc
Confidence 58889998863222455567888888555
No 126
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=23.86 E-value=97 Score=16.92 Aligned_cols=28 Identities=18% Similarity=0.184 Sum_probs=15.7
Q ss_pred cccccccCCCCceeecCCee-cchhhHHH
Q 041875 37 CSHCNGKLVMGNFSSMEGVL-YCKPHFEQ 64 (195)
Q Consensus 37 C~~C~~~L~~~~~~~~~g~~-yC~~c~~~ 64 (195)
|..|+..-...--...+|.. +|..|...
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~ 29 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLY 29 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHH
Confidence 56676666554444456666 99999754
No 127
>PLN02189 cellulose synthase
Probab=23.55 E-value=69 Score=31.49 Aligned_cols=29 Identities=24% Similarity=0.598 Sum_probs=15.0
Q ss_pred ccccccccCC----CCceeecC--CeecchhhHHH
Q 041875 36 KCSHCNGKLV----MGNFSSME--GVLYCKPHFEQ 64 (195)
Q Consensus 36 ~C~~C~~~L~----~~~~~~~~--g~~yC~~c~~~ 64 (195)
.|..|+..++ +..|+.-+ +-+.|..||+-
T Consensus 36 ~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyey 70 (1040)
T PLN02189 36 VCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEY 70 (1040)
T ss_pred cccccccccCcCCCCCEEEeeccCCCccccchhhh
Confidence 5566665543 22333222 44677777753
No 128
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=23.08 E-value=39 Score=15.64 Aligned_cols=12 Identities=25% Similarity=0.589 Sum_probs=6.4
Q ss_pred cccccCCccccc
Q 041875 127 FRCSHGGCLLTT 138 (195)
Q Consensus 127 F~C~~C~~~L~~ 138 (195)
|.|..|+..+..
T Consensus 1 ~~C~~C~~~~~~ 12 (24)
T PF13894_consen 1 FQCPICGKSFRS 12 (24)
T ss_dssp EE-SSTS-EESS
T ss_pred CCCcCCCCcCCc
Confidence 467777776654
No 129
>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 PRK14714 DNA polymerase II large subunit; Provisional
Probab=22.61 E-value=69 Score=32.19 Aligned_cols=10 Identities=30% Similarity=0.687 Sum_probs=4.8
Q ss_pred cCccCCceee
Q 041875 101 KCTSCKKTVY 110 (195)
Q Consensus 101 ~C~~C~~~I~ 110 (195)
.|..|+..+.
T Consensus 694 ~CPsCGaev~ 703 (1337)
T PRK14714 694 VCPDCGAEVP 703 (1337)
T ss_pred eCccCCCccC
Confidence 4555555443
No 131
>PRK12495 hypothetical protein; Provisional
Probab=22.58 E-value=43 Score=26.73 Aligned_cols=23 Identities=17% Similarity=0.590 Sum_probs=12.3
Q ss_pred cccccccccCCCCceeecCCeecchhhH
Q 041875 35 FKCSHCNGKLVMGNFSSMEGVLYCKPHF 62 (195)
Q Consensus 35 F~C~~C~~~L~~~~~~~~~g~~yC~~c~ 62 (195)
+.|..|+.+|. .+.|..+|..|-
T Consensus 43 ~hC~~CG~PIp-----a~pG~~~Cp~CQ 65 (226)
T PRK12495 43 AHCDECGDPIF-----RHDGQEFCPTCQ 65 (226)
T ss_pred hhcccccCccc-----CCCCeeECCCCC
Confidence 44555555554 235555565554
No 132
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.15 E-value=43 Score=27.88 Aligned_cols=33 Identities=24% Similarity=0.513 Sum_probs=22.8
Q ss_pred cccccccccCCCCcee---ecCCeecchhhHHHhhc
Q 041875 35 FKCSHCNGKLVMGNFS---SMEGVLYCKPHFEQLFK 67 (195)
Q Consensus 35 F~C~~C~~~L~~~~~~---~~~g~~yC~~c~~~~~~ 67 (195)
++|+.|+..|.++-|+ .....-||-.|....+.
T Consensus 269 LcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK 304 (352)
T KOG3579|consen 269 LCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIK 304 (352)
T ss_pred eeehhhhhhhccCceeecCCCcccceecccCHHHHH
Confidence 6778888888777665 34566677777766554
No 133
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.54 E-value=1.5e+02 Score=23.86 Aligned_cols=40 Identities=23% Similarity=0.426 Sum_probs=27.6
Q ss_pred CcccccCccccccccccCCCCceeecCCeecchhhHHHhhc
Q 041875 27 GISYHKICFKCSHCNGKLVMGNFSSMEGVLYCKPHFEQLFK 67 (195)
Q Consensus 27 g~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~~~~~~ 67 (195)
+..---..|.|..|-..-. ...+..=|.+||=.|..+-..
T Consensus 40 ~~~~~~~~FdCNICLd~ak-dPVvTlCGHLFCWpClyqWl~ 79 (230)
T KOG0823|consen 40 GRNRDGGFFDCNICLDLAK-DPVVTLCGHLFCWPCLYQWLQ 79 (230)
T ss_pred CccCCCCceeeeeeccccC-CCEEeecccceehHHHHHHHh
Confidence 3334456799999955433 466667799999999876543
No 134
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=21.42 E-value=47 Score=26.38 Aligned_cols=31 Identities=23% Similarity=0.190 Sum_probs=22.3
Q ss_pred cCccccccccccCCCCceeecCCeecchhhH
Q 041875 32 KICFKCSHCNGKLVMGNFSSMEGVLYCKPHF 62 (195)
Q Consensus 32 ~~CF~C~~C~~~L~~~~~~~~~g~~yC~~c~ 62 (195)
++=..|..|++.++...|...+|.++|..|.
T Consensus 147 p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 147 LDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred cchhhHhcCCCCCCceEEecccCCccccccc
Confidence 3335778888887744556778888888886
No 135
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=21.28 E-value=42 Score=16.21 Aligned_cols=13 Identities=15% Similarity=0.353 Sum_probs=9.4
Q ss_pred cccccCCcccccC
Q 041875 127 FRCSHGGCLLTTS 139 (195)
Q Consensus 127 F~C~~C~~~L~~~ 139 (195)
|.|..|++.+.+.
T Consensus 1 ~~C~~C~~~f~s~ 13 (25)
T PF12874_consen 1 FYCDICNKSFSSE 13 (25)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCCCCCCcCCH
Confidence 5688888877653
No 136
>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=21.21 E-value=23 Score=21.45 Aligned_cols=26 Identities=31% Similarity=0.585 Sum_probs=15.5
Q ss_pred cccccccccCCC-CceeecCCeecchhhH
Q 041875 35 FKCSHCNGKLVM-GNFSSMEGVLYCKPHF 62 (195)
Q Consensus 35 F~C~~C~~~L~~-~~~~~~~g~~yC~~c~ 62 (195)
++|..|++.|.. +.+. ..++-|.+|-
T Consensus 5 iRC~~CnklLa~~g~~~--~leIKCpRC~ 31 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVI--ELEIKCPRCK 31 (51)
T ss_pred eeccchhHHHhhhcCcc--EEEEECCCCC
Confidence 577777777765 2332 3456666664
No 137
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.21 E-value=82 Score=22.91 Aligned_cols=38 Identities=18% Similarity=0.378 Sum_probs=25.3
Q ss_pred CcCccCCceeecCce---EEECCceecccccccccCCccccc
Q 041875 100 DKCTSCKKTVYPLEK---VTVEGESFHKTCFRCSHGGCLLTT 138 (195)
Q Consensus 100 ~~C~~C~~~I~~~~~---v~~~~~~~H~~CF~C~~C~~~L~~ 138 (195)
..|+.|+.+|..... |.-.|..|-+--| |..|++.+..
T Consensus 40 ~qcp~csasirgd~~vegvlglg~dye~psf-chncgs~fpw 80 (160)
T COG4306 40 TQCPICSASIRGDYYVEGVLGLGGDYEPPSF-CHNCGSRFPW 80 (160)
T ss_pred hcCCccCCcccccceeeeeeccCCCCCCcch-hhcCCCCCCc
Confidence 589999999985433 3445666655433 7778887763
No 138
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 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 RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=21.08 E-value=1.2e+02 Score=18.12 Aligned_cols=11 Identities=36% Similarity=0.896 Sum_probs=8.2
Q ss_pred CcCccCCceee
Q 041875 100 DKCTSCKKTVY 110 (195)
Q Consensus 100 ~~C~~C~~~I~ 110 (195)
..|..|++++.
T Consensus 36 ~~C~iC~~~LP 46 (50)
T PF03854_consen 36 DRCPICGKPLP 46 (50)
T ss_dssp SEETTTTEE--
T ss_pred cCCCcccCcCc
Confidence 79999999875
No 139
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=20.95 E-value=49 Score=18.26 Aligned_cols=31 Identities=23% Similarity=0.565 Sum_probs=15.5
Q ss_pred CcCccCCceeecCc-eEEECCceecccccccccCCcc
Q 041875 100 DKCTSCKKTVYPLE-KVTVEGESFHKTCFRCSHGGCL 135 (195)
Q Consensus 100 ~~C~~C~~~I~~~~-~v~~~~~~~H~~CF~C~~C~~~ 135 (195)
..|+.|+......+ .|...+.. .+|..|+..
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~-----vrC~~C~~~ 34 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRK-----VRCPKCGHV 34 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcE-----EECCCCCcE
Confidence 35777776554322 23333332 456666554
No 140
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=20.91 E-value=42 Score=26.69 Aligned_cols=28 Identities=14% Similarity=0.179 Sum_probs=19.2
Q ss_pred cccccCCcccccCCeeccCCccccHHHH
Q 041875 127 FRCSHGGCLLTTSSYAALDGILYCKSHF 154 (195)
Q Consensus 127 F~C~~C~~~L~~~~~~~~dg~~yC~~c~ 154 (195)
..|..|++.+....|...+|..+|..|.
T Consensus 150 ~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 150 DHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred hhHhcCCCCCCceEEecccCCccccccc
Confidence 3577777776644455667888887774
No 141
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=20.77 E-value=80 Score=18.83 Aligned_cols=14 Identities=14% Similarity=0.617 Sum_probs=7.6
Q ss_pred CeecchhhHHHhhc
Q 041875 54 GVLYCKPHFEQLFK 67 (195)
Q Consensus 54 g~~yC~~c~~~~~~ 67 (195)
|--+|..||.+...
T Consensus 21 gf~IC~~C~~~i~~ 34 (48)
T PF14570_consen 21 GFQICRFCYHDILE 34 (48)
T ss_dssp S----HHHHHHHTT
T ss_pred CCcHHHHHHHHHHh
Confidence 34478999988764
No 142
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=20.51 E-value=76 Score=23.36 Aligned_cols=23 Identities=22% Similarity=0.551 Sum_probs=17.4
Q ss_pred cccccCCcccccCCeeccCCccccHHHHHhh
Q 041875 127 FRCSHGGCLLTTSSYAALDGILYCKSHFAQL 157 (195)
Q Consensus 127 F~C~~C~~~L~~~~~~~~dg~~yC~~c~~~~ 157 (195)
..|..||+++..+. ||..|...+
T Consensus 82 ~~CE~CG~~I~~Gr--------~C~~C~~~l 104 (137)
T TIGR03826 82 YPCERCGTSIREGR--------LCDSCAGEL 104 (137)
T ss_pred CcccccCCcCCCCC--------ccHHHHHHH
Confidence 57888999888763 788887654
No 143
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=20.49 E-value=24 Score=28.58 Aligned_cols=36 Identities=19% Similarity=0.339 Sum_probs=24.2
Q ss_pred CcCccCCceeecCceEEE-CCceecccccccccCCcccccC
Q 041875 100 DKCTSCKKTVYPLEKVTV-EGESFHKTCFRCSHGGCLLTTS 139 (195)
Q Consensus 100 ~~C~~C~~~I~~~~~v~~-~~~~~H~~CF~C~~C~~~L~~~ 139 (195)
+-|.-|+..+- .|.|.+ ..+. ..|+|..|.+.|-++
T Consensus 11 pwcwycnrefd-dekiliqhqka---khfkchichkkl~sg 47 (341)
T KOG2893|consen 11 PWCWYCNREFD-DEKILIQHQKA---KHFKCHICHKKLFSG 47 (341)
T ss_pred ceeeecccccc-hhhhhhhhhhh---ccceeeeehhhhccC
Confidence 67999998887 444432 2232 458999999987544
No 144
>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=20.38 E-value=26 Score=26.35 Aligned_cols=29 Identities=17% Similarity=0.423 Sum_probs=21.8
Q ss_pred cccccccccccCceEeeCCcccccCccccccccccCC
Q 041875 9 KCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKLV 45 (195)
Q Consensus 9 ~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L~ 45 (195)
.|..|+..+...+.+. .=|+|..|+..|.
T Consensus 111 ~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 111 ICPNMCVRFTFNEAME--------LNFTCPRCGAMLD 139 (158)
T ss_pred ECCCCCcEeeHHHHHH--------cCCcCCCCCCEee
Confidence 6888887776555553 2499999999885
No 145
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=20.24 E-value=79 Score=16.45 Aligned_cols=13 Identities=31% Similarity=0.480 Sum_probs=8.9
Q ss_pred cccccccccCCCC
Q 041875 35 FKCSHCNGKLVMG 47 (195)
Q Consensus 35 F~C~~C~~~L~~~ 47 (195)
|.|..|++.+++.
T Consensus 1 ~~C~~C~~~~~~~ 13 (30)
T PF03107_consen 1 FWCDVCRRKIDGF 13 (30)
T ss_pred CCCCCCCCCcCCC
Confidence 4677777777654
No 146
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=20.13 E-value=84 Score=30.95 Aligned_cols=30 Identities=27% Similarity=0.719 Sum_probs=16.9
Q ss_pred CCcccccccccccCceEeeCCcccccCccccccccccC
Q 041875 7 QEKCKACDKTVHIIDMVTADGISYHKICFKCSHCNGKL 44 (195)
Q Consensus 7 ~~~C~~C~~~I~~~~~i~~~g~~~H~~CF~C~~C~~~L 44 (195)
..+|..|+..|. +.++|..| .-|..|+-++
T Consensus 15 ~~~c~iCGd~vg----~~~~Ge~F----VAC~eC~fpv 44 (1044)
T PLN02915 15 AKTCRVCGDEVG----VKEDGQPF----VACHVCGFPV 44 (1044)
T ss_pred cchhhccccccC----cCCCCCEE----EEeccCCCcc
Confidence 457888877764 34566655 3344554433
No 147
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=20.08 E-value=52 Score=26.63 Aligned_cols=27 Identities=15% Similarity=0.383 Sum_probs=0.0
Q ss_pred ccccCCcccccCCeeccCCccccHHHH
Q 041875 128 RCSHGGCLLTTSSYAALDGILYCKSHF 154 (195)
Q Consensus 128 ~C~~C~~~L~~~~~~~~dg~~yC~~c~ 154 (195)
.|..|+.+.....++...|...|..|+
T Consensus 156 ~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 156 SCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred HHhCcCCcCCCcceeeccCcccchhcc
No 148
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.05 E-value=2.8e+02 Score=22.75 Aligned_cols=80 Identities=15% Similarity=0.166 Sum_probs=57.1
Q ss_pred CCCcccccccccccCceE----eeCCc-------ccccCccccccccccCCCC-cee--ecCCeecchhhHHHhhccCCc
Q 041875 6 TQEKCKACDKTVHIIDMV----TADGI-------SYHKICFKCSHCNGKLVMG-NFS--SMEGVLYCKPHFEQLFKETGS 71 (195)
Q Consensus 6 ~~~~C~~C~~~I~~~~~i----~~~g~-------~~H~~CF~C~~C~~~L~~~-~~~--~~~g~~yC~~c~~~~~~~~~~ 71 (195)
...+|..=+++|...+.+ .-++. .-|..=|.|..|+-.|.+. ... -..|.++|..|.++++.-
T Consensus 182 ~~v~CP~s~kplklkdL~~VkFT~l~s~~~et~l~a~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~--- 258 (303)
T KOG3039|consen 182 TTVVCPVSGKPLKLKDLFAVKFTPLNSEETETKLIAASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRK--- 258 (303)
T ss_pred ceeeccCCCCccchhhcceeeeeecCCchhhhhhhhhccceecccchhhhcCccceEEeccCCcEeeHHHHHHhccc---
Confidence 345788888988754432 22222 4566889999999999876 333 346899999999988741
Q ss_pred cccCCCccCCCCCCCCCCCCccccCCCCCcCccCCceeecCceE
Q 041875 72 FTNKLKPAQKNGLTRTPSKFSTMFCGTQDKCTSCKKTVYPLEKV 115 (195)
Q Consensus 72 ~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~C~~C~~~I~~~~~v 115 (195)
-..|+.|++++...+.|
T Consensus 259 ---------------------------D~v~pv~d~plkdrdiI 275 (303)
T KOG3039|consen 259 ---------------------------DMVDPVTDKPLKDRDII 275 (303)
T ss_pred ---------------------------cccccCCCCcCcccceE
Confidence 15899999999866665
Done!