Query 005013
Match_columns 719
No_of_seqs 278 out of 1748
Neff 4.3
Searched_HMMs 46136
Date Thu Mar 28 16:38:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005013.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005013hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4443 Putative transcription 100.0 2.4E-73 5.3E-78 629.0 11.7 593 1-718 17-620 (694)
2 KOG1244 Predicted transcriptio 99.7 2E-17 4.3E-22 170.4 1.1 102 1-102 226-329 (336)
3 KOG1512 PHD Zn-finger protein 99.5 4.4E-15 9.6E-20 154.0 1.4 97 1-99 260-357 (381)
4 KOG0954 PHD finger protein [Ge 99.2 1.4E-12 3E-17 148.3 -0.6 246 1-288 273-536 (893)
5 KOG0825 PHD Zn-finger protein 98.6 6.7E-09 1.5E-13 119.3 -0.2 48 56-103 217-265 (1134)
6 KOG0383 Predicted helicase [Ge 98.5 5E-08 1.1E-12 113.3 4.7 89 24-120 1-108 (696)
7 KOG4299 PHD Zn-finger protein 98.5 5E-08 1.1E-12 110.8 3.9 48 56-103 255-304 (613)
8 KOG0956 PHD finger protein AF1 98.5 5.7E-08 1.2E-12 110.8 1.8 138 57-196 8-180 (900)
9 PF00628 PHD: PHD-finger; Int 98.4 6.8E-08 1.5E-12 76.4 0.0 48 56-103 1-50 (51)
10 PF15446 zf-PHD-like: PHD/FYVE 98.3 6.6E-07 1.4E-11 88.2 5.2 86 1-88 1-143 (175)
11 KOG4299 PHD Zn-finger protein 98.3 3.7E-07 8E-12 103.9 3.7 49 4-55 255-303 (613)
12 PF09465 LBR_tudor: Lamin-B re 98.3 9.3E-07 2E-11 72.8 4.8 47 656-702 5-51 (55)
13 KOG4323 Polycomb-like PHD Zn-f 98.2 1E-06 2.2E-11 98.4 5.1 137 56-200 85-228 (464)
14 smart00249 PHD PHD zinc finger 98.2 1.3E-06 2.8E-11 66.0 3.7 46 56-101 1-47 (47)
15 KOG0955 PHD finger protein BR1 98.1 1.6E-06 3.4E-11 104.6 4.1 126 1-171 221-361 (1051)
16 PF00628 PHD: PHD-finger; Int 98.1 6.7E-07 1.4E-11 70.7 0.3 50 1-56 1-50 (51)
17 KOG4323 Polycomb-like PHD Zn-f 98.1 1.6E-06 3.5E-11 96.8 2.5 90 14-103 95-223 (464)
18 KOG1512 PHD Zn-finger protein 98.0 1.7E-06 3.7E-11 91.1 1.7 89 56-191 260-357 (381)
19 KOG1244 Predicted transcriptio 98.0 1.6E-06 3.4E-11 90.8 0.3 89 62-195 239-330 (336)
20 KOG4443 Putative transcription 97.9 3.5E-06 7.5E-11 96.6 1.1 89 48-149 12-103 (694)
21 KOG0956 PHD finger protein AF1 97.8 7E-06 1.5E-10 94.3 2.6 46 5-55 8-55 (900)
22 smart00249 PHD PHD zinc finger 97.8 1.7E-05 3.7E-10 59.8 3.6 47 1-54 1-47 (47)
23 COG5141 PHD zinc finger-contai 97.7 1.5E-05 3.2E-10 89.0 2.3 133 1-171 192-334 (669)
24 KOG0383 Predicted helicase [Ge 97.6 3E-05 6.5E-10 90.7 3.3 91 74-194 1-92 (696)
25 KOG1973 Chromatin remodeling p 97.5 3.8E-05 8.2E-10 81.2 1.2 39 60-103 226-267 (274)
26 KOG1973 Chromatin remodeling p 97.2 0.00012 2.6E-09 77.5 1.2 38 151-196 228-268 (274)
27 KOG1473 Nucleosome remodeling 97.1 8E-05 1.7E-09 89.5 -1.0 80 18-103 355-478 (1414)
28 COG5034 TNG2 Chromatin remodel 97.1 0.00021 4.6E-09 74.7 1.5 46 137-195 221-269 (271)
29 KOG0825 PHD Zn-finger protein 97.1 0.0002 4.3E-09 83.6 1.3 46 2-55 218-264 (1134)
30 KOG1473 Nucleosome remodeling 97.0 0.0003 6.4E-09 84.8 2.5 125 56-199 346-482 (1414)
31 smart00333 TUDOR Tudor domain. 97.0 0.00098 2.1E-08 53.5 4.5 53 657-713 3-56 (57)
32 KOG0954 PHD finger protein [Ge 96.9 0.00048 1E-08 80.3 2.8 46 56-103 273-320 (893)
33 smart00743 Agenet Tudor-like d 96.9 0.0012 2.6E-08 54.1 4.4 36 658-694 4-39 (61)
34 KOG0957 PHD finger protein [Ge 96.6 0.00029 6.2E-09 79.2 -1.7 52 4-55 121-177 (707)
35 COG5034 TNG2 Chromatin remodel 96.6 0.00095 2.1E-08 70.0 1.9 41 59-102 225-268 (271)
36 cd04718 BAH_plant_2 BAH, or Br 96.6 0.0012 2.5E-08 64.7 2.4 26 78-103 1-26 (148)
37 PF15446 zf-PHD-like: PHD/FYVE 96.6 0.0033 7.1E-08 62.7 5.2 33 56-88 1-36 (175)
38 KOG1701 Focal adhesion adaptor 96.4 0.00052 1.1E-08 76.1 -1.4 129 18-170 287-428 (468)
39 KOG0955 PHD finger protein BR1 96.4 0.0019 4.2E-08 78.8 3.2 53 56-110 221-282 (1051)
40 KOG0957 PHD finger protein [Ge 96.4 0.0012 2.6E-08 74.5 0.9 46 56-101 546-595 (707)
41 cd04508 TUDOR Tudor domains ar 96.2 0.0067 1.4E-07 47.1 4.1 42 660-702 1-43 (48)
42 KOG2752 Uncharacterized conser 96.0 0.0042 9.1E-08 66.9 3.0 90 68-171 67-165 (345)
43 KOG1245 Chromatin remodeling c 96.0 0.0016 3.4E-08 82.0 -0.7 48 56-103 1110-1157(1404)
44 COG5141 PHD zinc finger-contai 95.9 0.0033 7.2E-08 70.9 1.7 67 54-122 193-270 (669)
45 PF07227 DUF1423: Protein of u 93.8 0.064 1.4E-06 60.5 4.5 73 125-207 124-203 (446)
46 PF09038 53-BP1_Tudor: Tumour 93.6 0.084 1.8E-06 50.4 4.1 43 655-698 1-43 (122)
47 KOG1952 Transcription factor N 93.4 0.08 1.7E-06 63.4 4.5 50 17-67 205-264 (950)
48 PF13831 PHD_2: PHD-finger; PD 93.3 0.015 3.2E-07 44.4 -1.1 33 67-101 2-35 (36)
49 cd04718 BAH_plant_2 BAH, or Br 92.7 0.059 1.3E-06 53.0 1.7 24 28-54 1-24 (148)
50 PF13831 PHD_2: PHD-finger; PD 92.2 0.039 8.5E-07 42.0 -0.1 35 17-55 2-36 (36)
51 KOG1245 Chromatin remodeling c 91.9 0.044 9.6E-07 69.5 -0.2 47 4-55 1110-1156(1404)
52 KOG1632 Uncharacterized PHD Zn 91.9 0.043 9.4E-07 60.3 -0.3 173 18-199 74-298 (345)
53 PF13639 zf-RING_2: Ring finge 91.7 0.039 8.4E-07 42.6 -0.6 42 2-55 3-44 (44)
54 PF11793 FANCL_C: FANCL C-term 88.7 0.12 2.6E-06 44.5 -0.3 52 2-55 5-62 (70)
55 KOG0804 Cytoplasmic Zn-finger 88.6 0.22 4.7E-06 56.4 1.6 80 1-112 177-256 (493)
56 PF14446 Prok-RING_1: Prokaryo 87.0 0.43 9.4E-06 39.8 2.1 21 17-37 19-39 (54)
57 KOG4628 Predicted E3 ubiquitin 85.3 0.4 8.7E-06 53.0 1.4 35 1-40 231-265 (348)
58 PF13832 zf-HC5HC2H_2: PHD-zin 84.2 0.76 1.7E-05 41.8 2.5 61 19-85 12-86 (110)
59 PF13832 zf-HC5HC2H_2: PHD-zin 84.0 0.75 1.6E-05 41.9 2.4 29 139-172 57-87 (110)
60 PF12861 zf-Apc11: Anaphase-pr 83.6 0.37 8.1E-06 43.6 0.2 52 50-103 23-79 (85)
61 PF05641 Agenet: Agenet domain 82.8 3.9 8.4E-05 34.8 6.1 56 659-716 3-61 (68)
62 PF06003 SMN: Survival motor n 80.9 2.1 4.7E-05 45.6 4.7 46 658-703 70-116 (264)
63 PF15057 DUF4537: Domain of un 80.8 2.3 5E-05 40.5 4.4 39 660-699 1-39 (124)
64 PF13901 DUF4206: Domain of un 80.7 0.95 2.1E-05 46.3 1.9 45 50-103 144-197 (202)
65 PF13639 zf-RING_2: Ring finge 80.5 0.27 5.8E-06 38.0 -1.6 43 139-194 2-44 (44)
66 smart00744 RINGv The RING-vari 77.7 0.88 1.9E-05 36.8 0.5 45 1-54 1-48 (49)
67 PF02237 BPL_C: Biotin protein 77.6 5.3 0.00012 31.9 4.9 42 659-703 2-43 (48)
68 PHA02929 N1R/p28-like protein; 77.4 1.3 2.9E-05 46.7 1.8 26 23-55 198-223 (238)
69 PF12861 zf-Apc11: Anaphase-pr 76.4 1.7 3.6E-05 39.5 1.9 33 18-55 46-78 (85)
70 KOG1081 Transcription factor N 76.0 3.2 7E-05 47.7 4.5 72 136-222 88-163 (463)
71 KOG1701 Focal adhesion adaptor 75.2 1.8 4E-05 49.0 2.3 6 156-161 453-458 (468)
72 KOG2807 RNA polymerase II tran 74.6 2.2 4.7E-05 47.1 2.6 92 91-195 272-375 (378)
73 PF11717 Tudor-knot: RNA bindi 74.0 11 0.00024 30.9 6.0 49 658-714 2-52 (55)
74 PF07227 DUF1423: Protein of u 73.8 2.5 5.4E-05 48.3 2.9 36 49-85 124-162 (446)
75 PF14446 Prok-RING_1: Prokaryo 72.2 2.3 5E-05 35.6 1.6 31 56-86 7-38 (54)
76 PF00130 C1_1: Phorbol esters/ 72.2 3.5 7.6E-05 32.8 2.7 37 135-172 9-45 (53)
77 KOG1169 Diacylglycerol kinase 70.1 4.6 9.9E-05 48.0 4.0 70 18-89 57-149 (634)
78 cd00162 RING RING-finger (Real 69.5 2.5 5.5E-05 30.9 1.2 32 18-55 11-42 (45)
79 PF12678 zf-rbx1: RING-H2 zinc 69.4 1.1 2.4E-05 38.8 -0.9 26 23-55 48-73 (73)
80 KOG2272 Focal adhesion protein 68.1 2 4.2E-05 46.0 0.5 58 77-134 160-231 (332)
81 PF07076 DUF1344: Protein of u 67.9 4.3 9.4E-05 34.8 2.4 25 674-700 5-29 (61)
82 KOG1246 DNA-binding protein ju 67.5 4.2 9.1E-05 50.1 3.2 47 56-103 157-203 (904)
83 KOG1829 Uncharacterized conser 65.6 1.5 3.3E-05 51.5 -1.0 47 50-103 503-558 (580)
84 PF00567 TUDOR: Tudor domain; 63.3 13 0.00029 32.6 4.7 56 654-712 49-105 (121)
85 PF13771 zf-HC5HC2H: PHD-like 63.3 2.8 6.1E-05 36.6 0.5 28 56-86 38-68 (90)
86 KOG3612 PHD Zn-finger protein 62.2 5 0.00011 46.8 2.3 48 4-58 62-109 (588)
87 KOG1632 Uncharacterized PHD Zn 61.6 4.5 9.7E-05 44.9 1.7 39 154-197 74-114 (345)
88 KOG3970 Predicted E3 ubiquitin 61.0 3 6.5E-05 44.0 0.3 90 140-243 53-146 (299)
89 PF11793 FANCL_C: FANCL C-term 59.6 4.1 8.9E-05 35.1 0.8 55 139-196 4-64 (70)
90 KOG1044 Actin-binding LIM Zn-f 58.6 7.1 0.00015 46.0 2.7 43 117-163 153-200 (670)
91 KOG2041 WD40 repeat protein [G 56.5 7.7 0.00017 46.9 2.5 48 56-105 1119-1166(1189)
92 KOG2752 Uncharacterized conser 56.1 7.6 0.00017 42.8 2.3 63 18-86 67-166 (345)
93 KOG0827 Predicted E3 ubiquitin 55.6 3.6 7.8E-05 46.4 -0.3 25 16-40 17-41 (465)
94 PRK11911 flgD flagellar basal 55.2 27 0.00059 34.5 5.7 40 657-697 90-129 (140)
95 KOG1169 Diacylglycerol kinase 54.8 2.9 6.3E-05 49.6 -1.1 100 56-176 46-150 (634)
96 PF10497 zf-4CXXC_R1: Zinc-fin 54.0 8.1 0.00017 36.1 1.8 47 18-64 20-80 (105)
97 PF02576 DUF150: Uncharacteris 53.4 19 0.00041 34.6 4.3 39 656-696 83-124 (141)
98 COG1107 Archaea-specific RecJ- 53.0 14 0.0003 43.9 3.9 32 47-81 52-92 (715)
99 PF05502 Dynactin_p62: Dynacti 52.4 13 0.00028 43.1 3.5 31 17-55 3-33 (483)
100 PF13771 zf-HC5HC2H: PHD-like 52.3 9.8 0.00021 33.2 2.0 30 4-38 38-70 (90)
101 PRK09618 flgD flagellar basal 51.4 36 0.00078 33.7 5.8 79 616-700 44-131 (142)
102 COG5151 SSL1 RNA polymerase II 51.1 7.9 0.00017 42.7 1.4 11 45-55 305-315 (421)
103 PF07191 zinc-ribbons_6: zinc- 49.7 9.6 0.00021 33.6 1.5 29 117-145 10-38 (70)
104 PRK14637 hypothetical protein; 49.5 19 0.00042 35.6 3.7 42 657-701 95-136 (151)
105 KOG1829 Uncharacterized conser 48.9 6.5 0.00014 46.5 0.4 37 1-37 513-549 (580)
106 PF07649 C1_3: C1-like domain; 46.4 7.3 0.00016 28.2 0.2 29 56-84 2-30 (30)
107 PF04216 FdhE: Protein involve 46.1 5.2 0.00011 42.7 -0.8 59 138-196 173-247 (290)
108 PHA02926 zinc finger-like prot 44.7 11 0.00025 39.8 1.4 33 24-57 196-228 (242)
109 COG5243 HRD1 HRD ubiquitin lig 44.1 5.9 0.00013 44.6 -0.8 17 24-40 317-333 (491)
110 PRK06009 flgD flagellar basal 43.8 44 0.00096 33.1 5.2 43 655-701 92-134 (140)
111 PF12678 zf-rbx1: RING-H2 zinc 43.4 8.6 0.00019 33.3 0.2 29 156-194 45-73 (73)
112 cd00029 C1 Protein kinase C co 43.2 13 0.00028 28.7 1.2 35 137-172 11-45 (50)
113 smart00109 C1 Protein kinase C 43.1 9.8 0.00021 29.0 0.5 34 137-172 11-44 (49)
114 KOG1844 PHD Zn-finger proteins 42.6 14 0.00029 42.2 1.7 41 152-199 98-138 (508)
115 PF13923 zf-C3HC4_2: Zinc fing 40.5 11 0.00024 28.4 0.4 30 18-54 10-39 (39)
116 smart00184 RING Ring finger. E 40.3 13 0.00029 25.9 0.8 26 23-54 14-39 (39)
117 KOG4628 Predicted E3 ubiquitin 38.4 17 0.00036 40.7 1.5 45 56-103 231-275 (348)
118 COG1198 PriA Primosomal protei 38.1 24 0.00051 43.1 2.9 25 224-248 625-649 (730)
119 PF05502 Dynactin_p62: Dynacti 38.1 23 0.0005 41.1 2.7 31 68-103 4-34 (483)
120 PF02736 Myosin_N: Myosin N-te 37.8 42 0.00092 26.2 3.3 29 670-700 10-38 (42)
121 cd00600 Sm_like The eukaryotic 36.3 43 0.00092 27.3 3.3 36 656-695 2-37 (63)
122 COG5151 SSL1 RNA polymerase II 35.9 7.8 0.00017 42.7 -1.4 47 139-195 364-418 (421)
123 PF13901 DUF4206: Domain of un 35.8 22 0.00048 36.5 1.8 43 126-171 144-188 (202)
124 KOG1734 Predicted RING-contain 35.3 10 0.00022 41.1 -0.6 79 136-226 223-305 (328)
125 PF01423 LSM: LSM domain ; In 35.3 46 0.001 27.6 3.4 29 656-685 4-32 (67)
126 PF06524 NOA36: NOA36 protein; 34.8 21 0.00046 38.7 1.6 26 139-165 127-152 (314)
127 PLN03208 E3 ubiquitin-protein 34.6 23 0.0005 36.7 1.7 16 23-38 34-49 (193)
128 PRK03564 formate dehydrogenase 34.3 26 0.00057 38.6 2.2 63 136-198 186-263 (309)
129 PF00130 C1_1: Phorbol esters/ 34.3 27 0.00058 27.7 1.7 31 56-86 13-45 (53)
130 PTZ00275 biotin-acetyl-CoA-car 34.3 47 0.001 35.8 4.1 42 659-703 236-277 (285)
131 TIGR00622 ssl1 transcription f 33.3 73 0.0016 30.5 4.7 48 138-195 56-111 (112)
132 PRK14633 hypothetical protein; 31.9 61 0.0013 32.0 4.1 43 657-701 91-136 (150)
133 PF12773 DZR: Double zinc ribb 31.7 42 0.0009 26.5 2.4 10 69-78 12-21 (50)
134 KOG4198 RNA-binding Ran Zn-fin 31.7 71 0.0015 34.9 4.9 21 45-65 61-89 (280)
135 PF08746 zf-RING-like: RING-li 31.5 12 0.00025 29.7 -0.7 41 57-101 1-43 (43)
136 COG5082 AIR1 Arginine methyltr 31.2 45 0.00098 34.6 3.2 13 19-31 60-72 (190)
137 cd01731 archaeal_Sm1 The archa 31.0 59 0.0013 27.6 3.4 28 657-685 7-34 (68)
138 KOG4577 Transcription factor L 30.9 11 0.00024 41.2 -1.3 19 18-36 32-63 (383)
139 cd01734 YlxS_C YxlS is a Bacil 30.7 71 0.0015 28.2 4.0 36 657-694 22-60 (83)
140 PRK14639 hypothetical protein; 30.6 67 0.0014 31.4 4.1 43 657-702 85-128 (140)
141 smart00547 ZnF_RBZ Zinc finger 30.4 32 0.0007 23.7 1.4 9 47-55 1-9 (26)
142 PHA02862 5L protein; Provision 30.3 19 0.00042 35.9 0.4 22 18-39 17-38 (156)
143 KOG0802 E3 ubiquitin ligase [P 30.2 16 0.00035 42.7 -0.2 26 24-56 313-338 (543)
144 PRK14559 putative protein seri 29.9 36 0.00077 41.0 2.5 7 20-26 2-8 (645)
145 PF00097 zf-C3HC4: Zinc finger 29.9 21 0.00046 26.7 0.5 29 21-54 13-41 (41)
146 KOG3268 Predicted E3 ubiquitin 29.6 20 0.00043 36.9 0.4 21 19-39 182-204 (234)
147 TIGR01562 FdhE formate dehydro 29.6 36 0.00079 37.4 2.3 59 138-196 185-261 (305)
148 PF13717 zinc_ribbon_4: zinc-r 28.8 39 0.00085 25.8 1.7 27 140-166 5-36 (36)
149 KOG0804 Cytoplasmic Zn-finger 28.6 25 0.00053 40.6 0.9 31 56-86 177-208 (493)
150 PRK08330 biotin--protein ligas 27.9 78 0.0017 32.8 4.4 46 658-706 186-232 (236)
151 PRK02001 hypothetical protein; 27.9 78 0.0017 31.5 4.1 35 657-694 87-121 (152)
152 KOG1280 Uncharacterized conser 27.7 32 0.00069 38.6 1.5 35 17-65 6-43 (381)
153 PF13341 RAG2_PHD: RAG2 PHD do 27.4 39 0.00084 30.1 1.7 39 153-192 28-67 (78)
154 cd01726 LSm6 The eukaryotic Sm 27.3 1E+02 0.0022 26.1 4.2 35 657-695 7-41 (67)
155 PRK14634 hypothetical protein; 27.0 79 0.0017 31.4 4.0 42 657-701 97-141 (155)
156 KOG1246 DNA-binding protein ju 26.9 44 0.00095 41.5 2.7 35 18-55 168-202 (904)
157 PF00641 zf-RanBP: Zn-finger i 26.6 34 0.00073 24.7 1.0 11 93-103 2-12 (30)
158 COG5219 Uncharacterized conser 26.4 14 0.00029 46.0 -1.7 50 139-196 1471-1521(1525)
159 KOG3612 PHD Zn-finger protein 26.2 44 0.00096 39.4 2.3 47 56-105 62-109 (588)
160 PF07649 C1_3: C1-like domain; 25.9 45 0.00098 24.1 1.6 17 18-34 14-30 (30)
161 KOG2807 RNA polymerase II tran 25.7 44 0.00095 37.4 2.1 19 91-109 341-361 (378)
162 KOG3576 Ovo and related transc 25.5 20 0.00043 37.8 -0.5 16 16-31 114-129 (267)
163 PF15057 DUF4537: Domain of un 25.4 1.2E+02 0.0025 29.1 4.7 53 658-712 57-114 (124)
164 PF09297 zf-NADH-PPase: NADH p 25.3 52 0.0011 24.2 1.8 28 137-164 3-30 (32)
165 PF13437 HlyD_3: HlyD family s 25.2 1.9E+02 0.004 25.6 5.7 39 658-696 52-97 (105)
166 KOG2462 C2H2-type Zn-finger pr 25.1 57 0.0012 35.6 2.8 11 139-149 163-173 (279)
167 PRK14873 primosome assembly pr 24.7 45 0.00098 40.3 2.2 17 224-240 560-576 (665)
168 PRK06955 biotin--protein ligas 24.5 1E+02 0.0023 33.3 4.7 44 658-704 247-290 (300)
169 COG5194 APC11 Component of SCF 24.3 43 0.00093 30.6 1.4 26 23-55 52-77 (88)
170 PF07593 UnbV_ASPIC: ASPIC and 24.0 80 0.0017 27.0 3.0 16 657-673 1-16 (71)
171 PF13719 zinc_ribbon_5: zinc-r 23.9 46 0.001 25.4 1.3 27 140-166 5-36 (37)
172 KOG4675 Uncharacterized conser 23.6 21 0.00046 38.7 -0.7 54 658-711 160-221 (273)
173 PLN00104 MYST -like histone ac 23.6 1.3E+02 0.0027 35.1 5.3 37 658-694 55-97 (450)
174 PRK14640 hypothetical protein; 23.4 1.2E+02 0.0026 30.0 4.4 35 657-693 94-131 (152)
175 TIGR00595 priA primosomal prot 23.3 57 0.0012 37.9 2.6 25 224-248 403-427 (505)
176 PRK00737 small nuclear ribonuc 23.1 97 0.0021 26.8 3.3 35 657-695 11-45 (72)
177 KOG1081 Transcription factor N 22.8 63 0.0014 37.5 2.8 31 4-39 91-121 (463)
178 PRK14559 putative protein seri 22.5 60 0.0013 39.2 2.6 23 4-29 3-25 (645)
179 KOG3026 Splicing factor SPF30 21.9 85 0.0018 33.8 3.2 36 657-692 91-126 (262)
180 PF10497 zf-4CXXC_R1: Zinc-fin 21.8 68 0.0015 30.0 2.3 35 162-198 37-72 (105)
181 COG2888 Predicted Zn-ribbon RN 21.6 58 0.0013 28.1 1.6 35 19-64 9-48 (61)
182 KOG2177 Predicted E3 ubiquitin 21.4 62 0.0014 32.0 2.1 28 22-56 28-55 (386)
183 KOG1844 PHD Zn-finger proteins 21.4 54 0.0012 37.4 1.9 44 59-103 90-134 (508)
184 KOG3970 Predicted E3 ubiquitin 20.9 54 0.0012 35.0 1.6 32 24-55 69-101 (299)
185 KOG2272 Focal adhesion protein 20.8 43 0.00094 36.3 0.9 39 27-65 160-206 (332)
186 PF13922 PHD_3: PHD domain of 20.5 20 0.00044 31.4 -1.3 21 17-37 41-61 (69)
187 PF07593 UnbV_ASPIC: ASPIC and 20.4 62 0.0013 27.7 1.6 18 653-670 37-54 (71)
188 PRK14714 DNA polymerase II lar 20.4 60 0.0013 41.9 2.0 94 127-241 670-766 (1337)
189 PRK04023 DNA polymerase II lar 20.1 73 0.0016 40.4 2.6 8 21-28 628-635 (1121)
No 1
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=100.00 E-value=2.4e-73 Score=628.96 Aligned_cols=593 Identities=40% Similarity=0.681 Sum_probs=501.9
Q ss_pred CCccCcCCccCCcccCCceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCccccccccCCCCCceeecCCCCCccc
Q 005013 1 MCRLCFVGENEGCERARRMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCRICEICRRTGDPNKFMFCRRCDAAYH 80 (719)
Q Consensus 1 ~C~iC~~Ce~~Gse~~eeLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr~C~VC~~sgd~~kLL~CdrC~raYH 80 (719)
+|.+|.+|+..|.+.++.|+.|..|+..||.+|+..|.....+. ..|+||.|++|..|+..+++.++++|+.|+..||
T Consensus 17 ~~~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~--~gWrC~~crvCe~c~~~gD~~kf~~Ck~cDvsyh 94 (694)
T KOG4443|consen 17 VCLMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLS--GGWRCPSCRVCEACGTTGDPKKFLLCKRCDVSYH 94 (694)
T ss_pred hhhhhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHHhc--CCcccCCceeeeeccccCCccccccccccccccc
Confidence 58899999999999999999999999999999999998866543 5599999999999999999999999999999999
Q ss_pred ccccCCCCcCCCCCCcccCCCCccCCCCCCCCCCCCccccccCccccCCCccccccccccccccccccCCCCCCceeccC
Q 005013 81 CYCQHPPHKNVSSGPYLCPKHTKCHSCGSNVPGNGLSVRWFLGYTCCDACGRLFVKGNYCPVCLKVYRDSESTPMVCCDV 160 (719)
Q Consensus 81 ~~CL~PpL~~Ip~g~W~CP~C~~C~sCg~r~pgki~s~RW~~~~slC~aC~~lfvK~nyC~VC~K~Y~dsdgg~MIqCD~ 160 (719)
.+|+.|++..++.+.|+|+.|..|..|+...++ +..+|..++..|.+|.. ..|||+|.+.|++.+..+|++|+.
T Consensus 95 ~yc~~P~~~~v~sg~~~ckk~~~c~qc~~~lpg--~s~~~~~~~~~~~~c~s----~~~cPvc~~~Y~~~e~~~~~~c~~ 168 (694)
T KOG4443|consen 95 CYCQKPPNDKVPSGPWLCKKCTRCRQCDSTLPG--LSLDLQEGYLQCAPCAS----LSYCPVCLIVYQDSESLPMVCCSI 168 (694)
T ss_pred ccccCCccccccCcccccHHHHhhhhccccccc--cchhhhccCcccccccc----cccCchHHHhhhhccchhhHHHHH
Confidence 999999999999999999999999999998887 67788889999999986 689999999999999999999999
Q ss_pred CCCeeccCCCCCChHHHhhhccCCCCceeCCCCCCCCCCCCchHHHHHHhhcccccccHHHHHHHHHHcCCCCccccccC
Q 005013 161 CQRWVHCQCDGISDEKYLQFQVDGNLQYRCPTCRGECYQVRDLEDAVRELWRRKDMADKDLIASLRAAAGLPTEDEIFSI 240 (719)
Q Consensus 161 C~~wFH~eCL~lsdEkye~~~id~d~~Y~CptCr~~~~qIk~~kda~~r~Wrare~~~r~lI~slR~~~GLp~~eei~s~ 240 (719)
|.+|.|..|+++.++.|.++.++ ..|.|.+||.+.++++++.+++.+.|++.......++..+++..-|..
T Consensus 169 c~rwsh~~c~~~sdd~~~q~~vD--~~~~CS~CR~es~qvKdi~~~vqe~~~~k~~~~~~~~~tls~~a~lq~------- 239 (694)
T KOG4443|consen 169 CQRWSHGGCDGISDDKYMQAQVD--LQYKCSTCRGESYQVKDISDALQETWKAKDKPDKILIATLSAQAALQM------- 239 (694)
T ss_pred hcccccCCCCccchHHHHHHhhh--hhcccceeehhhhhhhhHHHHHHhhcchhhccccceeehhhhhhhhhh-------
Confidence 99999999999999999998875 799999999999999999999999999998888889988887765533
Q ss_pred CCCCCCCCCCcchhhhhhccccccccCCCCCCCCCchhhhhccccCccCCCccCCCCCCCCCCCCCCCCCCcccccccC-
Q 005013 241 SPYSDDEENGPVVLKNEFGRSLKLSLKGVVDKSPKKVKEHGKKWLNKKYPRKKGYQMPLNSKPEPDQSFEGYHDVHSYG- 319 (719)
Q Consensus 241 ~P~sdDe~~~p~~~~~~~~~~~~~s~k~~~~k~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 319 (719)
+.++. .++.+++.++..++++.++....+..+.+.+...+|..+ .+ ..+.|+.+|+
T Consensus 240 --------~~~~~-----~~s~~~k~~~~~~~~~~~s~a~gq~s~~~~~~~~~g~~~-----dp-----~~~~e~~sE~~ 296 (694)
T KOG4443|consen 240 --------HHAVI-----GDSSADKAGSSANSGSATSGASGQLSLTTANTPTLGVSL-----DP-----VKLQEVGSERK 296 (694)
T ss_pred --------ccccc-----cccccccccCcccCCcccccccccCCcccccccccCccc-----ch-----hhhhhccchhh
Confidence 23333 566788889999999999999999999888888888777 22 4566777777
Q ss_pred ---CCCCCCCCCCCCCCCCCCCCcccccccCCCccccCCCCcccccccceeeccCCCccce-eEeecCCCCCCCCCCccc
Q 005013 320 ---NSFGDDTQSPKNEGLDIPSSVAGIVSHTEGVCSISQPGILKHKYVDEVMVSDDDKISR-VKFKTSKPHDLDSGEDDG 395 (719)
Q Consensus 320 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~ 395 (719)
..+..+...+ .++...+.+..|++++-.-+-.+.+..+.+.||+.+|...| ++||++||+++++ ++..
T Consensus 297 a~~~v~~e~vv~d-------~t~~~~~~~~~e~~~~p~~r~~~~~~m~~~~~vt~~e~~~r~~r~~Stk~~~~~~-~~~~ 368 (694)
T KOG4443|consen 297 AKLLVKQEAVVKD-------STETPTVNSRAEEIGTPEKRLNANATMTAINQVTSEEKPTRTARIKSTKPPDSDS-ENNL 368 (694)
T ss_pred hhhccchhhhhhc-------cccCcccccchhhccCccccccccceeeeeeccccccccceeeecCCCCCCCcch-hhhh
Confidence 3455555555 34445556778999999999999999999999985554445 9999999999999 5888
Q ss_pred cccccccccceeeEEEeeccccccccCCCCCCCcchhcccccccCCCCCChhhhhccccccccccCCCCcCCCCCccccc
Q 005013 396 KHVSKSKTIKAKKLVINLGARKINVTNSPRSDASSCQREQDLTTSNGIEDPSLQRMNSKFVLDRHDGSSKLGDGDRVDHS 475 (719)
Q Consensus 396 ~~~~~~~~~k~~~lv~~~g~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 475 (719)
.+++...++++++||||+|+|+||+.++.+.++.+---+-+ + ++..++ |+++|-+
T Consensus 369 r~a~edn~ll~~~l~~n~st~kl~~~~~t~~~v~~~~~~a~-----l----~~~~l~----------------~~~~~s~ 423 (694)
T KOG4443|consen 369 RSAAEDNALLAKKLVINSSSRKLNVISSTSAHVGSASSSAP-----L----SQRKLI----------------GVRAPSM 423 (694)
T ss_pred hhccchhhHHhhhcccccCccccccccccccccccccccCh-----h----hHHHhc----------------cCcCcch
Confidence 88999999999999999999999999999999874322211 1 222222 5888888
Q ss_pred cccccceecccCCceeeeecccccccccCcccCCCCCCCCCCccccccccccchhhhhhhhcccccceeEEecCcccccc
Q 005013 476 SQSRGLKIAGRGGNVIKFGRVRQEVSDSNTKVSRGSSADEHEPEHMHVLSGKRNIDRSRAAVSRVGEVAALRGDRKQLES 555 (719)
Q Consensus 476 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 555 (719)
++.|++..+ |+.+.-. .++.++.++.....
T Consensus 424 ~k~rsle~e---------gs~~~~~-----------------------------------------~v~~~~~a~~ssgs 453 (694)
T KOG4443|consen 424 GKVRSLEDE---------GSRGVIG-----------------------------------------PVTTATAAAGSSGS 453 (694)
T ss_pred hhhhhhhhh---------cccCCCC-----------------------------------------CcCCcCcccccccC
Confidence 888888662 2222211 12222222222222
Q ss_pred CCCccccCCCCcccccCCCCCCCCceeeeecCCCcccCCCCcCchHH--HhhhhhcccccCCCCCccccccccccc-hhh
Q 005013 556 RPNASRESNDDTSVLQSLPKDSKPPLRLKFRKPNLENQNSQVSQPEE--EKSLIKGQRSKRKRPSPFTEKTLFNED-EDA 632 (719)
Q Consensus 556 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~k~k~~~~~~~~~~~~~~~~--~~~~~~gqrskrkr~~~~~~~~~~~~~-~~~ 632 (719)
+.+.. ...+.+.+.+..++.+|+|+++|++|+.+.|++..++..| .+...+|+|+|+||+++..+++.++++ |..
T Consensus 454 s~~~~--~s~t~g~~~s~~~~~~~~l~~a~a~~~s~~~~s~~~v~~~~E~~~d~~~a~~~n~~~n~~~~~~~~~~~~q~l 531 (694)
T KOG4443|consen 454 SGDVK--TSTTPGTVASGQKSQRPLLKSAIAKPNSAVQISEPGVGSEAEQKSDGKGARSKNKRQNQAPPPPPPPEDQQQL 531 (694)
T ss_pred CCCCC--CCCCCCcCCcchhhhhhhhhhhhhcCCcccccccccccccccccCCcccccccccccCCCCCCCCCcchhhhc
Confidence 22221 2233444668899999999999999999999988777665 459999999999999999999999999 999
Q ss_pred hhhhhh-chhhhhhhhHHHHHHhCcccccceEEEEecCCCCeeeeeEEEee--cCceeEEEEecCCchhhhhcCcceeEe
Q 005013 633 AQSNQD-SLMSEIMDANWILKKLGKDAIGKRVEVHQQSDNSWHKGVVTDTV--EGTSTLSITLDDSRVKTLELGKQGVRF 709 (719)
Q Consensus 633 ~~~~~~-~~~~~~~d~~~il~~lg~~~i~krv~v~~~~d~~w~~g~v~~~~--~~~~~~~v~~ddg~~~~~~lgk~~i~~ 709 (719)
..+++| ++.||||||+|||++||++++|||++||-.++|+|-+|+|+.++ ..++.+.|++|+|.++++++|++.|||
T Consensus 532 ~~s~~d~~~~d~~~~a~~~~~~~g~~~~~~~t~vhs~~~ns~~~g~vt~~~s~~~~s~~~~~~~~~~v~~~~~~~~~v~f 611 (694)
T KOG4443|consen 532 QPSPHDVSRLDEMVDAEWILKKLGKDAKTKRTEVHSKSMNSWPKGNVTIVISTGQTSPLEVQLKPGAVKTVELGKQGVRF 611 (694)
T ss_pred CCCHHHHHHHHhhhccccccccCCCCCCcceeccccCCCCCCCCccceeeeccCCcccceeecccccccccccccccccc
Confidence 999999 79999999999999999999999999999999999999999998 899999999999999999999999999
Q ss_pred eeccccccC
Q 005013 710 VPQKQKRSM 718 (719)
Q Consensus 710 ~~~~~k~~~ 718 (719)
+|++|||.+
T Consensus 612 ~pe~~k~~~ 620 (694)
T KOG4443|consen 612 LPEKQKRVR 620 (694)
T ss_pred Chhhhhccc
Confidence 999999876
No 2
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=99.65 E-value=2e-17 Score=170.43 Aligned_cols=102 Identities=28% Similarity=0.770 Sum_probs=90.1
Q ss_pred CCccCcCCc--cCCcccCCceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCccccccccCCCCCceeecCCCCCc
Q 005013 1 MCRLCFVGE--NEGCERARRMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCRICEICRRTGDPNKFMFCRRCDAA 78 (719)
Q Consensus 1 ~C~iC~~Ce--~~Gse~~eeLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr~C~VC~~sgd~~kLL~CdrC~ra 78 (719)
||+||+... +..-+-+++||.|..||++-|++||.-...+...+.++.|+|.+|+.|.+|+.+.+++.+|+|+.|+++
T Consensus 226 YCDFclgdsr~nkkt~~peelvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~csicgtsenddqllfcddcdrg 305 (336)
T KOG1244|consen 226 YCDFCLGDSRENKKTGMPEELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGTSENDDQLLFCDDCDRG 305 (336)
T ss_pred ccceeccccccccccCCchhhcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeecceeccccCcCCCceeEeecccCCc
Confidence 699998663 122235789999999999999999998876666678899999999999999999999999999999999
Q ss_pred ccccccCCCCcCCCCCCcccCCCC
Q 005013 79 YHCYCQHPPHKNVSSGPYLCPKHT 102 (719)
Q Consensus 79 YH~~CL~PpL~~Ip~g~W~CP~C~ 102 (719)
||++||.|++.+.|.+.|.|..|.
T Consensus 306 yhmyclsppm~eppegswsc~KOG 329 (336)
T KOG1244|consen 306 YHMYCLSPPMVEPPEGSWSCHLCL 329 (336)
T ss_pred eeeEecCCCcCCCCCCchhHHHHH
Confidence 999999999999999999998774
No 3
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=99.50 E-value=4.4e-15 Score=154.05 Aligned_cols=97 Identities=24% Similarity=0.565 Sum_probs=86.5
Q ss_pred CCccCcCCc-cCCcccCCceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCccccccccCCCCCceeecCCCCCcc
Q 005013 1 MCRLCFVGE-NEGCERARRMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCRICEICRRTGDPNKFMFCRRCDAAY 79 (719)
Q Consensus 1 ~C~iC~~Ce-~~Gse~~eeLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr~C~VC~~sgd~~kLL~CdrC~raY 79 (719)
.|.+|+... ..-..+.+.||.|..|-.+||++|+...++....+.++.|.|-.|++|.+|+.+..++.+++|+.|+++|
T Consensus 260 ~~~~~~~~~~~~~~~r~~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~lC~IC~~P~~E~E~~FCD~CDRG~ 339 (381)
T KOG1512|consen 260 ERKHFWDIQTNIIQSRRNSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSCELCRICLGPVIESEHLFCDVCDRGP 339 (381)
T ss_pred hhhhhhcchhhhhhhhhccceeecccccCCCCcchhcCHHHHhHHhhcchhhcccHhhhccCCcccchheeccccccCCC
Confidence 367777763 3334467899999999999999999999988877888999999999999999999999999999999999
Q ss_pred cccccCCCCcCCCCCCcccC
Q 005013 80 HCYCQHPPHKNVSSGPYLCP 99 (719)
Q Consensus 80 H~~CL~PpL~~Ip~g~W~CP 99 (719)
|++|++ |..+|.|.|+|.
T Consensus 340 HT~CVG--L~~lP~G~WICD 357 (381)
T KOG1512|consen 340 HTLCVG--LQDLPRGEWICD 357 (381)
T ss_pred Cccccc--cccccCccchhh
Confidence 999999 778999999996
No 4
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=99.22 E-value=1.4e-12 Score=148.30 Aligned_cols=246 Identities=18% Similarity=0.249 Sum_probs=151.5
Q ss_pred CCccCcCCccCCcccCCceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCc-----cccccccCCCCCceeecCCC
Q 005013 1 MCRLCFVGENEGCERARRMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR-----ICEICRRTGDPNKFMFCRRC 75 (719)
Q Consensus 1 ~C~iC~~Ce~~Gse~~eeLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr-----~C~VC~~sgd~~kLL~CdrC 75 (719)
+|++|... ..+..++||+|+.|.---|..|.+.... +.+.|.|..|. -|..|=..|.. |--=..=
T Consensus 273 iCDvCrsp---D~e~~neMVfCd~Cn~cVHqaCyGIle~-----p~gpWlCr~Calg~~ppCvLCPkkGGa--mK~~~sg 342 (893)
T KOG0954|consen 273 ICDVCRSP---DSEEANEMVFCDKCNICVHQACYGILEV-----PEGPWLCRTCALGIEPPCVLCPKKGGA--MKPTKSG 342 (893)
T ss_pred eeceecCC---CccccceeEEeccchhHHHHhhhceeec-----CCCCeeehhccccCCCCeeeccccCCc--ccccCCC
Confidence 47777755 3456789999999999999999998543 34899999997 67777655531 1111111
Q ss_pred CCcccccccCCCCcCCCCCCcccCCCCccCCCCCCCCCCCCccccccCccccCCCccccccccccccccccccCCCCCCc
Q 005013 76 DAAYHCYCQHPPHKNVSSGPYLCPKHTKCHSCGSNVPGNGLSVRWFLGYTCCDACGRLFVKGNYCPVCLKVYRDSESTPM 155 (719)
Q Consensus 76 ~raYH~~CL~PpL~~Ip~g~W~CP~C~~C~sCg~r~pgki~s~RW~~~~slC~aC~~lfvK~nyC~VC~K~Y~dsdgg~M 155 (719)
-.|-|..|.-= ||.-.+-|+. .....++...+...||..-..+ |..- .+--
T Consensus 343 T~wAHvsCALw----IPEVsie~~e----kmePItkfs~IpesRwslvC~L----------------Ck~k-----~GAC 393 (893)
T KOG0954|consen 343 TKWAHVSCALW----IPEVSIECPE----KMEPITKFSHIPESRWSLVCNL----------------CKVK-----SGAC 393 (893)
T ss_pred CeeeEeeeeec----cceeeccCHh----hcCcccccCCCcHHHHHHHHHH----------------hccc-----Ccce
Confidence 26778888651 1222222322 1122233456677788663333 3321 2334
Q ss_pred eecc--CCCCeeccCCCCCChHHHhhhc--cC-CCCceeCCCCCCCCCCCCchHHHHHHhhcccccc-cH-HHHH---HH
Q 005013 156 VCCD--VCQRWVHCQCDGISDEKYLQFQ--VD-GNLQYRCPTCRGECYQVRDLEDAVRELWRRKDMA-DK-DLIA---SL 225 (719)
Q Consensus 156 IqCD--~C~~wFH~eCL~lsdEkye~~~--id-~d~~Y~CptCr~~~~qIk~~kda~~r~Wrare~~-~r-~lI~---sl 225 (719)
|+|. .|...||..|....--...... .+ -...=+|+.|-.... -+.+.. ..--|+..+. +. .+++ +-
T Consensus 394 IqCs~k~C~t~fHv~CA~~aG~~~~~~~~~~D~v~~~s~c~khs~~~~-~~s~g~--~~e~p~p~~~~p~~~~~e~~~~s 470 (893)
T KOG0954|consen 394 IQCSNKTCRTAFHVTCAFEAGLEMKTILKENDEVKFKSYCSKHSDHRE-GKSLGN--EAESPHPRCHLPEQSVGEGHRSS 470 (893)
T ss_pred EEecccchhhhccchhhhhcCCeeeeeeccCCchhheeeccccccccc-cccccc--ccCCCCccccChhhhhhhhhhhh
Confidence 6765 6999999999863211111111 11 123557777765432 111111 1112222222 22 2222 22
Q ss_pred HHHcCCCCccccccCCCCCCCCCCC---cchhhhhhccccccccCCCCCCCCCchhhhhccccCcc
Q 005013 226 RAAAGLPTEDEIFSISPYSDDEENG---PVVLKNEFGRSLKLSLKGVVDKSPKKVKEHGKKWLNKK 288 (719)
Q Consensus 226 R~~~GLp~~eei~s~~P~sdDe~~~---p~~~~~~~~~~~~~s~k~~~~k~~~~~k~~~~~~~~~~ 288 (719)
-+++-|...|+.|+....-+|.+.. |..+++++|+|||+.+|+++++++.++|+++.....|+
T Consensus 471 ~r~q~l~~~e~ef~~~v~~~diae~l~~~e~~vs~iynywklkrks~~n~~lippk~d~~~~i~kk 536 (893)
T KOG0954|consen 471 DRAQKLQELEGEFYDIVRNEDIAELLSMPEFAVSAIYNYWKLKRKSRFNKELIPPKSDEVGLIAKK 536 (893)
T ss_pred HHHHHHhhcchhHhhhhhHHHHHHHhcCchHHHHHHHHHHHHhhhccCCCcCCCCcchhccchhhH
Confidence 2355778889999998888887753 88999999999999999999999999999999877665
No 5
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.61 E-value=6.7e-09 Score=119.28 Aligned_cols=48 Identities=23% Similarity=0.740 Sum_probs=45.4
Q ss_pred cccccccCCCCCceeecCCCCCc-ccccccCCCCcCCCCCCcccCCCCc
Q 005013 56 ICEICRRTGDPNKFMFCRRCDAA-YHCYCQHPPHKNVSSGPYLCPKHTK 103 (719)
Q Consensus 56 ~C~VC~~sgd~~kLL~CdrC~ra-YH~~CL~PpL~~Ip~g~W~CP~C~~ 103 (719)
-|.+|.....++.||+|+.|+.+ ||++||+|++.++|-+.|||++|.-
T Consensus 217 ~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~d 265 (1134)
T KOG0825|consen 217 KCDICTVHDPEDVLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCSL 265 (1134)
T ss_pred cceeeccCChHHhheeecccccceeeccccCcccccccccceecCcchh
Confidence 79999999988899999999998 9999999999999999999999964
No 6
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=98.55 E-value=5e-08 Score=113.28 Aligned_cols=89 Identities=31% Similarity=0.820 Sum_probs=70.4
Q ss_pred cCCCcchhhhcCCCcccccccCCCCCCCCCCc-------------------cccccccCCCCCceeecCCCCCccccccc
Q 005013 24 SCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR-------------------ICEICRRTGDPNKFMFCRRCDAAYHCYCQ 84 (719)
Q Consensus 24 ~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr-------------------~C~VC~~sgd~~kLL~CdrC~raYH~~CL 84 (719)
.|.+.||..|+.+.....+ ...|.||.|- .|.+|+..+ .+++|+.|+.+||.+|+
T Consensus 1 ~~~r~~~~~~~~p~~~~~~---~~~~k~~~~e~~~~~~~~~~~~~~~~~~e~c~ic~~~g---~~l~c~tC~~s~h~~cl 74 (696)
T KOG0383|consen 1 TCPRAYHRVCLDPKLKEEP---EMDPKCPGCESSSAQVEAKDDDWDDAEQEACRICADGG---ELLWCDTCPASFHASCL 74 (696)
T ss_pred CCCcccCcCCCCcccccCC---cCCccCcchhhcccccccccCCcchhhhhhhhhhcCCC---cEEEeccccHHHHHHcc
Confidence 4899999999998765433 5889999887 899999888 89999999999999999
Q ss_pred CCCCcCCCCCCcccCCCCccCCCCCCCCCCCCcccc
Q 005013 85 HPPHKNVSSGPYLCPKHTKCHSCGSNVPGNGLSVRW 120 (719)
Q Consensus 85 ~PpL~~Ip~g~W~CP~C~~C~sCg~r~pgki~s~RW 120 (719)
++++...|.+.|.|+.| .|.. +..+...+..++|
T Consensus 75 ~~pl~~~p~~~~~c~Rc-~~p~-~~~k~~~il~~~~ 108 (696)
T KOG0383|consen 75 GPPLTPQPNGEFICPRC-FCPK-NAGKIEKILGWRW 108 (696)
T ss_pred CCCCCcCCccceeeeee-ccCC-CcccccccceeEe
Confidence 99999999888999987 4432 1112334445555
No 7
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.53 E-value=5e-08 Score=110.82 Aligned_cols=48 Identities=29% Similarity=0.839 Sum_probs=43.0
Q ss_pred cccccccCCCCCceeecCCCCCcccccccCCCC--cCCCCCCcccCCCCc
Q 005013 56 ICEICRRTGDPNKFMFCRRCDAAYHCYCQHPPH--KNVSSGPYLCPKHTK 103 (719)
Q Consensus 56 ~C~VC~~sgd~~kLL~CdrC~raYH~~CL~PpL--~~Ip~g~W~CP~C~~ 103 (719)
+|..|+..+.-..+++|+.|++.||+.||.||+ ..+|.+.|+|+.|..
T Consensus 255 fCsaCn~~~~F~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~ 304 (613)
T KOG4299|consen 255 FCSACNGSGLFNDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKI 304 (613)
T ss_pred HHHHhCCccccccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCee
Confidence 899999988666779999999999999999995 468999999999964
No 8
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=98.45 E-value=5.7e-08 Score=110.80 Aligned_cols=138 Identities=19% Similarity=0.374 Sum_probs=85.6
Q ss_pred ccccccCCC--CCceeecC--CCCCcccccccCCCCcCCCCCCcccCCCC--------ccCCCCCCCC--CCCCcccccc
Q 005013 57 CEICRRTGD--PNKFMFCR--RCDAAYHCYCQHPPHKNVSSGPYLCPKHT--------KCHSCGSNVP--GNGLSVRWFL 122 (719)
Q Consensus 57 C~VC~~sgd--~~kLL~Cd--rC~raYH~~CL~PpL~~Ip~g~W~CP~C~--------~C~sCg~r~p--gki~s~RW~~ 122 (719)
|.||.+... ++.|+.|| .|..+.|..|++ +..+|.++|||..|. +|.-|..+.- .+-.+.-|.+
T Consensus 8 CCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYG--IvqVPtGpWfCrKCesqeraarvrCeLCP~kdGALKkTDn~GWAH 85 (900)
T KOG0956|consen 8 CCVCSDERGWAENPLVYCDGHNCSVAVHQACYG--IVQVPTGPWFCRKCESQERAARVRCELCPHKDGALKKTDNGGWAH 85 (900)
T ss_pred eeeecCcCCCccCceeeecCCCceeeeehhcce--eEecCCCchhhhhhhhhhhhccceeecccCcccceecccCCCceE
Confidence 557776544 35799999 699999999999 789999999999995 4888875431 1112223543
Q ss_pred C-ccccCCCcccc---------------c-cccccccccccccCCC--CCCceecc--CCCCeeccCCCCCChHHHhhhc
Q 005013 123 G-YTCCDACGRLF---------------V-KGNYCPVCLKVYRDSE--STPMVCCD--VCQRWVHCQCDGISDEKYLQFQ 181 (719)
Q Consensus 123 ~-~slC~aC~~lf---------------v-K~nyC~VC~K~Y~dsd--gg~MIqCD--~C~~wFH~eCL~lsdEkye~~~ 181 (719)
. +-+=+...++- . -.+.|+||...-+.++ .+--++|. .|.+.||..|....--..++.+
T Consensus 86 VVCALYIPEVrFgNV~TMEPIiLq~VP~dRfnKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~g 165 (900)
T KOG0956|consen 86 VVCALYIPEVRFGNVHTMEPIILQDVPHDRFNKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEG 165 (900)
T ss_pred EEEEeeccceeecccccccceeeccCchhhhcceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccc
Confidence 1 11101111110 0 1124999987654433 34456784 4999999999863211122222
Q ss_pred cCCCCceeCCCCCCC
Q 005013 182 VDGNLQYRCPTCRGE 196 (719)
Q Consensus 182 id~d~~Y~CptCr~~ 196 (719)
+--+..-+|-+|+.+
T Consensus 166 n~~dNVKYCGYCk~H 180 (900)
T KOG0956|consen 166 NISDNVKYCGYCKYH 180 (900)
T ss_pred cccccceechhHHHH
Confidence 333568899999865
No 9
>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=98.37 E-value=6.8e-08 Score=76.36 Aligned_cols=48 Identities=31% Similarity=0.863 Sum_probs=40.5
Q ss_pred cccccccCCCCCceeecCCCCCcccccccCCCCc--CCCCCCcccCCCCc
Q 005013 56 ICEICRRTGDPNKFMFCRRCDAAYHCYCQHPPHK--NVSSGPYLCPKHTK 103 (719)
Q Consensus 56 ~C~VC~~sgd~~kLL~CdrC~raYH~~CL~PpL~--~Ip~g~W~CP~C~~ 103 (719)
+|.+|+...+.+.||.|+.|+++||..|++++.. .++...|+|+.|..
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 5788898777789999999999999999998776 34455999999864
No 10
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=98.31 E-value=6.6e-07 Score=88.22 Aligned_cols=86 Identities=26% Similarity=0.637 Sum_probs=63.0
Q ss_pred CCccCcCCccCCcccCCceEEeCcCCCcchhhhcCCCccccccc---CC--CCCCCCCCc--------------cccccc
Q 005013 1 MCRLCFVGENEGCERARRMLSCKSCGKKYHRNCLKNWAQNRDLF---HW--SSWKCPSCR--------------ICEICR 61 (719)
Q Consensus 1 ~C~iC~~Ce~~Gse~~eeLL~Cd~CgksYH~~CL~p~~e~~~~~---~~--~~W~Cp~Cr--------------~C~VC~ 61 (719)
+|+.|...+ ++...+.||+|.+|..+||..||++......++ .. .-.+|..|. .|..|.
T Consensus 1 ~C~~C~~~g--~~~~kG~Lv~CQGCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~~~kKD~~aP~~~~C~~C~ 78 (175)
T PF15446_consen 1 TCDTCGYEG--DDRNKGPLVYCQGCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGIAHKKDPRAPHHGMCQQCK 78 (175)
T ss_pred CcccccCCC--CCccCCCeEEcCccChHHHhhhcCCccccceeeEEEcCCceEEechhhcChhhcccCCCCCCCcccccC
Confidence 577775432 233456999999999999999999976533222 12 235888888 899998
Q ss_pred cCCC--------------------------------------CCceeecCCCCCcccccccCCCC
Q 005013 62 RTGD--------------------------------------PNKFMFCRRCDAAYHCYCQHPPH 88 (719)
Q Consensus 62 ~sgd--------------------------------------~~kLL~CdrC~raYH~~CL~PpL 88 (719)
..|. ++.|.+|..|.++||..-|++..
T Consensus 79 ~~G~~c~pfr~r~T~kQEe~~ReeNgG~DPit~Vd~~lvnN~~nVLFRC~~C~RawH~~HLP~~~ 143 (175)
T PF15446_consen 79 KPGPSCKPFRPRKTPKQEEKLREENGGVDPITPVDPELVNNPDNVLFRCTSCHRAWHFEHLPPPS 143 (175)
T ss_pred CCCCCCcccCCCCCcHHHHHHHHHcCCCCCCccCCHHHccChhheEEecCCccceeehhhCCCCc
Confidence 7654 12477899999999999998753
No 11
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.30 E-value=3.7e-07 Score=103.95 Aligned_cols=49 Identities=24% Similarity=0.713 Sum_probs=39.3
Q ss_pred cCcCCccCCcccCCceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCc
Q 005013 4 LCFVGENEGCERARRMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR 55 (719)
Q Consensus 4 iC~~Ce~~Gse~~eeLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr 55 (719)
||..|...|.- .++|+|++|+++||+.||.|+.+.. .++.+.|+|+.|.
T Consensus 255 fCsaCn~~~~F--~~~i~CD~Cp~sFH~~CLePPl~~e-niP~g~W~C~ec~ 303 (613)
T KOG4299|consen 255 FCSACNGSGLF--NDIICCDGCPRSFHQTCLEPPLEPE-NIPPGSWFCPECK 303 (613)
T ss_pred HHHHhCCcccc--ccceeecCCchHHHHhhcCCCCCcc-cCCCCccccCCCe
Confidence 67777666533 5779999999999999999985543 3456899999998
No 12
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=98.29 E-value=9.3e-07 Score=72.82 Aligned_cols=47 Identities=21% Similarity=0.208 Sum_probs=38.0
Q ss_pred cccccceEEEEecCCCCeeeeeEEEeecCceeEEEEecCCchhhhhc
Q 005013 656 KDAIGKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITLDDSRVKTLEL 702 (719)
Q Consensus 656 ~~~i~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~ddg~~~~~~l 702 (719)
+=++|.+|.|-||-++.||+|.|.+|+..+..+.|.|+||.+.+|..
T Consensus 5 k~~~Ge~V~~rWP~s~lYYe~kV~~~d~~~~~y~V~Y~DGtel~lke 51 (55)
T PF09465_consen 5 KFAIGEVVMVRWPGSSLYYEGKVLSYDSKSDRYTVLYEDGTELELKE 51 (55)
T ss_dssp SS-SS-EEEEE-TTTS-EEEEEEEEEETTTTEEEEEETTS-EEEEEC
T ss_pred cccCCCEEEEECCCCCcEEEEEEEEecccCceEEEEEcCCCEEEecc
Confidence 34789999999999999999999999999999999999999955543
No 13
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=98.23 E-value=1e-06 Score=98.36 Aligned_cols=137 Identities=21% Similarity=0.301 Sum_probs=78.9
Q ss_pred cccccccC--CCCCceeecCCCCCcccccccCCCCcCCCCCCcccCCCCccC---CCCCCCCCCCCccccccCccccCCC
Q 005013 56 ICEICRRT--GDPNKFMFCRRCDAAYHCYCQHPPHKNVSSGPYLCPKHTKCH---SCGSNVPGNGLSVRWFLGYTCCDAC 130 (719)
Q Consensus 56 ~C~VC~~s--gd~~kLL~CdrC~raYH~~CL~PpL~~Ip~g~W~CP~C~~C~---sCg~r~pgki~s~RW~~~~slC~aC 130 (719)
.|-+|... ..++.++.|.+|..+||..|.-+... ..+.|.+..|+.-. .-+..+.+. ..+-...|..-..-
T Consensus 85 ~~nv~~s~~~~p~~e~~~~~r~~~~~~q~~~i~~~~--~~~~~~~~~c~~~~~~~~g~a~K~g~--~a~~~l~y~~~~l~ 160 (464)
T KOG4323|consen 85 NPNVLTSETVLPENEKVICGRCKSGYHQGCNIPRFP--SLDIGESTECVFPIFSQEGGALKKGR--LARPSLPYPEASLD 160 (464)
T ss_pred CCcccccccccCchhhhhhhhhccCcccccCccCcC--cCCccccccccccccccccccccccc--cccccccCcccccc
Confidence 44455532 23346889999999999999986543 34567777665422 111111111 11100011100000
Q ss_pred --ccccccccccccccccccCCCCCCceeccCCCCeeccCCCCCChHHHhhhccCCCCceeCCCCCCCCCCC
Q 005013 131 --GRLFVKGNYCPVCLKVYRDSESTPMVCCDVCQRWVHCQCDGISDEKYLQFQVDGNLQYRCPTCRGECYQV 200 (719)
Q Consensus 131 --~~lfvK~nyC~VC~K~Y~dsdgg~MIqCD~C~~wFH~eCL~lsdEkye~~~id~d~~Y~CptCr~~~~qI 200 (719)
....+... |.||++.-..... .||+|+.|..|||..|-.+.... .+..++++.|+|..|.++...+
T Consensus 161 wD~~~~~n~q-c~vC~~g~~~~~N-rmlqC~~C~~~fHq~Chqp~i~~--~l~~D~~~~w~C~~C~~~~~~~ 228 (464)
T KOG4323|consen 161 WDSGHKVNLQ-CSVCYCGGPGAGN-RMLQCDKCRQWYHQACHQPLIKD--ELAGDPFYEWFCDVCNRGPKKV 228 (464)
T ss_pred cCccccccce-eeeeecCCcCccc-eeeeecccccHHHHHhccCCCCH--hhccCccceEeehhhccchhhc
Confidence 01112222 8888876555555 89999999999999999843221 1223478899999999875543
No 14
>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 KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=98.12 E-value=1.6e-06 Score=104.62 Aligned_cols=126 Identities=21% Similarity=0.496 Sum_probs=76.2
Q ss_pred CCccCcCCccCCcccCCceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCccccccccCCCCCceeecCCCCCccc
Q 005013 1 MCRLCFVGENEGCERARRMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCRICEICRRTGDPNKFMFCRRCDAAYH 80 (719)
Q Consensus 1 ~C~iC~~Ce~~Gse~~eeLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr~C~VC~~sgd~~kLL~CdrC~raYH 80 (719)
+|.||...+.. ..+.+|+||.|+.++|+.|.+.++ ++.+.|.|..|- ... ...+.|..|+..=|
T Consensus 221 ~C~iC~~~~~~---n~n~ivfCD~Cnl~VHq~Cygi~~-----ipeg~WlCr~Cl------~s~--~~~v~c~~cp~~~g 284 (1051)
T KOG0955|consen 221 VCCICLDGECQ---NSNVIVFCDGCNLAVHQECYGIPF-----IPEGQWLCRRCL------QSP--QRPVRCLLCPSKGG 284 (1051)
T ss_pred cceeecccccC---CCceEEEcCCCcchhhhhccCCCC-----CCCCcEeehhhc------cCc--CcccceEeccCCCC
Confidence 47777765533 346899999999999999999543 345999999983 211 13467777776665
Q ss_pred ccccCCCCcCCCCCCcccCCCCccC-----C--------CCCCCCCCCCccccccCccccCCCccccccccccccccccc
Q 005013 81 CYCQHPPHKNVSSGPYLCPKHTKCH-----S--------CGSNVPGNGLSVRWFLGYTCCDACGRLFVKGNYCPVCLKVY 147 (719)
Q Consensus 81 ~~CL~PpL~~Ip~g~W~CP~C~~C~-----s--------Cg~r~pgki~s~RW~~~~slC~aC~~lfvK~nyC~VC~K~Y 147 (719)
.++-. ..+.|. ++.|. . -+.....++...||.. .|++|....
T Consensus 285 AFkqt------~dgrw~---Hv~caiwipev~F~nt~~~E~I~~i~~i~~aRwkL----------------~cy~cK~~~ 339 (1051)
T KOG0955|consen 285 AFKQT------DDGRWA---HVVCAIWIPEVSFANTVFLEPIDSIENIPPARWKL----------------TCYICKQKG 339 (1051)
T ss_pred cceec------cCCcee---eeehhhcccccccccchhhccccchhcCcHhhhhc----------------eeeeeccCC
Confidence 54433 233443 11111 0 0111123344555644 466665431
Q ss_pred cCCCCCCceeccC--CCCeeccCCCC
Q 005013 148 RDSESTPMVCCDV--CQRWVHCQCDG 171 (719)
Q Consensus 148 ~dsdgg~MIqCD~--C~~wFH~eCL~ 171 (719)
-+--|||.. |-.|||..|..
T Consensus 340 ----~gaciqcs~~~c~~a~hvtca~ 361 (1051)
T KOG0955|consen 340 ----LGACIQCSKANCYTAFHVTCAR 361 (1051)
T ss_pred ----CCcceecchhhhhhhhhhhhHh
Confidence 144577754 99999999986
No 16
>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=98.10 E-value=6.7e-07 Score=70.73 Aligned_cols=50 Identities=28% Similarity=0.817 Sum_probs=36.7
Q ss_pred CCccCcCCccCCcccCCceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCcc
Q 005013 1 MCRLCFVGENEGCERARRMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCRI 56 (719)
Q Consensus 1 ~C~iC~~Ce~~Gse~~eeLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr~ 56 (719)
+|.+|... +..++||.|+.|.++||..|+++....... ....|.|+.|..
T Consensus 1 ~C~vC~~~-----~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~-~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQS-----DDDGDMIQCDSCNRWYHQECVGPPEKAEEI-PSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSS-----CTTSSEEEBSTTSCEEETTTSTSSHSHHSH-HSSSBSSHHHHH
T ss_pred eCcCCCCc-----CCCCCeEEcCCCChhhCcccCCCChhhccC-CCCcEECcCCcC
Confidence 46666652 234589999999999999999998654332 224899999853
No 17
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=98.07 E-value=1.6e-06 Score=96.77 Aligned_cols=90 Identities=21% Similarity=0.493 Sum_probs=60.9
Q ss_pred ccCCceEEeCcCCCcchhhhcCCCcccccc-------------------------------cCCCCCCCCCCc--ccccc
Q 005013 14 ERARRMLSCKSCGKKYHRNCLKNWAQNRDL-------------------------------FHWSSWKCPSCR--ICEIC 60 (719)
Q Consensus 14 e~~eeLL~Cd~CgksYH~~CL~p~~e~~~~-------------------------------~~~~~W~Cp~Cr--~C~VC 60 (719)
..+.++..|..|...||..|-.+....... ...-.|-=.++. .|.+|
T Consensus 95 ~p~~e~~~~~r~~~~~~q~~~i~~~~~~~~~~~~~c~~~~~~~~g~a~K~g~~a~~~l~y~~~~l~wD~~~~~n~qc~vC 174 (464)
T KOG4323|consen 95 LPENEKVICGRCKSGYHQGCNIPRFPSLDIGESTECVFPIFSQEGGALKKGRLARPSLPYPEASLDWDSGHKVNLQCSVC 174 (464)
T ss_pred cCchhhhhhhhhccCcccccCccCcCcCCccccccccccccccccccccccccccccccCcccccccCccccccceeeee
Confidence 345689999999999999998775321100 001123222111 45555
Q ss_pred --ccCCCCCceeecCCCCCcccccccCCCCcC----CCCCCcccCCCCc
Q 005013 61 --RRTGDPNKFMFCRRCDAAYHCYCQHPPHKN----VSSGPYLCPKHTK 103 (719)
Q Consensus 61 --~~sgd~~kLL~CdrC~raYH~~CL~PpL~~----Ip~g~W~CP~C~~ 103 (719)
+.++..++||+|+.|..|||..|..|+... -+...|+|..|..
T Consensus 175 ~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~ 223 (464)
T KOG4323|consen 175 YCGGPGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNR 223 (464)
T ss_pred ecCCcCccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhcc
Confidence 456666799999999999999999987653 2567899988854
No 18
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.03 E-value=1.7e-06 Score=91.06 Aligned_cols=89 Identities=21% Similarity=0.421 Sum_probs=65.6
Q ss_pred cccccccC------CCCCceeecCCCCCcccccccCCCCcC---CCCCCcccCCCCccCCCCCCCCCCCCccccccCccc
Q 005013 56 ICEICRRT------GDPNKFMFCRRCDAAYHCYCQHPPHKN---VSSGPYLCPKHTKCHSCGSNVPGNGLSVRWFLGYTC 126 (719)
Q Consensus 56 ~C~VC~~s------gd~~kLL~CdrC~raYH~~CL~PpL~~---Ip~g~W~CP~C~~C~sCg~r~pgki~s~RW~~~~sl 126 (719)
.|.+|-+. +..+.|++|..|-.+||++|+.-+... +-...|.|..|..|.-|+.
T Consensus 260 ~~~~~~~~~~~~~~~r~~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~lC~IC~~----------------- 322 (381)
T KOG1512|consen 260 ERKHFWDIQTNIIQSRRNSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSCELCRICLG----------------- 322 (381)
T ss_pred hhhhhhcchhhhhhhhhccceeecccccCCCCcchhcCHHHHhHHhhcchhhcccHhhhccCC-----------------
Confidence 56666543 233469999999999999999854433 3467899999977665542
Q ss_pred cCCCccccccccccccccccccCCCCCCceeccCCCCeeccCCCCCChHHHhhhccCCCCceeCC
Q 005013 127 CDACGRLFVKGNYCPVCLKVYRDSESTPMVCCDVCQRWVHCQCDGISDEKYLQFQVDGNLQYRCP 191 (719)
Q Consensus 127 C~aC~~lfvK~nyC~VC~K~Y~dsdgg~MIqCD~C~~wFH~eCL~lsdEkye~~~id~d~~Y~Cp 191 (719)
+ ....+|+.||.|++-||.-|+++-. -+.+.|+|-
T Consensus 323 -------------------P---~~E~E~~FCD~CDRG~HT~CVGL~~--------lP~G~WICD 357 (381)
T KOG1512|consen 323 -------------------P---VIESEHLFCDVCDRGPHTLCVGLQD--------LPRGEWICD 357 (381)
T ss_pred -------------------c---ccchheeccccccCCCCcccccccc--------ccCccchhh
Confidence 2 1234688999999999999999632 257899997
No 19
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=97.98 E-value=1.6e-06 Score=90.85 Aligned_cols=89 Identities=22% Similarity=0.479 Sum_probs=67.4
Q ss_pred cCCCCCceeecCCCCCcccccccCCCCcC---CCCCCcccCCCCccCCCCCCCCCCCCccccccCccccCCCcccccccc
Q 005013 62 RTGDPNKFMFCRRCDAAYHCYCQHPPHKN---VSSGPYLCPKHTKCHSCGSNVPGNGLSVRWFLGYTCCDACGRLFVKGN 138 (719)
Q Consensus 62 ~sgd~~kLL~CdrC~raYH~~CL~PpL~~---Ip~g~W~CP~C~~C~sCg~r~pgki~s~RW~~~~slC~aC~~lfvK~n 138 (719)
+.+-++.++-|..|++.=|+.||+-...+ +-..+|.|-.|..|.-||.
T Consensus 239 kt~~peelvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~csicgt----------------------------- 289 (336)
T KOG1244|consen 239 KTGMPEELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGT----------------------------- 289 (336)
T ss_pred ccCCchhhcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeecceeccccC-----------------------------
Confidence 34556789999999999999999943332 4468999988866555553
Q ss_pred ccccccccccCCCCCCceeccCCCCeeccCCCCCChHHHhhhccCCCCceeCCCCCC
Q 005013 139 YCPVCLKVYRDSESTPMVCCDVCQRWVHCQCDGISDEKYLQFQVDGNLQYRCPTCRG 195 (719)
Q Consensus 139 yC~VC~K~Y~dsdgg~MIqCD~C~~wFH~eCL~lsdEkye~~~id~d~~Y~CptCr~ 195 (719)
.-+ +.++|.||.|++-||-.|+.+.+ .-++++.|.|-.|..
T Consensus 290 -------sen---ddqllfcddcdrgyhmyclsppm------~eppegswsc~KOG~ 330 (336)
T KOG1244|consen 290 -------SEN---DDQLLFCDDCDRGYHMYCLSPPM------VEPPEGSWSCHLCLE 330 (336)
T ss_pred -------cCC---CceeEeecccCCceeeEecCCCc------CCCCCCchhHHHHHH
Confidence 222 34689999999999999998643 245789999999964
No 20
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=97.89 E-value=3.5e-06 Score=96.56 Aligned_cols=89 Identities=26% Similarity=0.645 Sum_probs=62.1
Q ss_pred CCCCCCCccccccccCCC--CCceeecCCCCCcccccccCCCCcCC-CCCCcccCCCCccCCCCCCCCCCCCccccccCc
Q 005013 48 SWKCPSCRICEICRRTGD--PNKFMFCRRCDAAYHCYCQHPPHKNV-SSGPYLCPKHTKCHSCGSNVPGNGLSVRWFLGY 124 (719)
Q Consensus 48 ~W~Cp~Cr~C~VC~~sgd--~~kLL~CdrC~raYH~~CL~PpL~~I-p~g~W~CP~C~~C~sCg~r~pgki~s~RW~~~~ 124 (719)
.=.|..|..|.+|...|. +..|+.|..|...||.+|+..-+... -.+.|.||.|++|..|+.... | ..+
T Consensus 12 ~~~~~~~~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~~~gD-------~-~kf 83 (694)
T KOG4443|consen 12 DKAIIVCLMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACGTTGD-------P-KKF 83 (694)
T ss_pred chhhhhhhhhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeeeeccccCC-------c-ccc
Confidence 335777889999987664 34699999999999999998533322 234499999999999995421 1 135
Q ss_pred cccCCCccccccccccccccccccC
Q 005013 125 TCCDACGRLFVKGNYCPVCLKVYRD 149 (719)
Q Consensus 125 slC~aC~~lfvK~nyC~VC~K~Y~d 149 (719)
.+|..|- ..|...|.++.++
T Consensus 84 ~~Ck~cD-----vsyh~yc~~P~~~ 103 (694)
T KOG4443|consen 84 LLCKRCD-----VSYHCYCQKPPND 103 (694)
T ss_pred ccccccc-----ccccccccCCccc
Confidence 6677665 3455666665544
No 21
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=97.85 E-value=7e-06 Score=94.26 Aligned_cols=46 Identities=22% Similarity=0.549 Sum_probs=34.0
Q ss_pred CcCCccCCcccCCceEEeC--cCCCcchhhhcCCCcccccccCCCCCCCCCCc
Q 005013 5 CFVGENEGCERARRMLSCK--SCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR 55 (719)
Q Consensus 5 C~~Ce~~Gse~~eeLL~Cd--~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr 55 (719)
|-+|-++..=..+.||+|| .|--+.|+.|.++-. ++.+.|+|..|.
T Consensus 8 CCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvq-----VPtGpWfCrKCe 55 (900)
T KOG0956|consen 8 CCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQ-----VPTGPWFCRKCE 55 (900)
T ss_pred eeeecCcCCCccCceeeecCCCceeeeehhcceeEe-----cCCCchhhhhhh
Confidence 4555322223446899999 999999999999743 446999999985
No 22
>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 COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=97.71 E-value=1.5e-05 Score=89.00 Aligned_cols=133 Identities=21% Similarity=0.399 Sum_probs=78.7
Q ss_pred CCccCcCCccCCcccCCceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCc-------cccccccCCCCCceeecC
Q 005013 1 MCRLCFVGENEGCERARRMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR-------ICEICRRTGDPNKFMFCR 73 (719)
Q Consensus 1 ~C~iC~~Ce~~Gse~~eeLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr-------~C~VC~~sgd~~kLL~Cd 73 (719)
+|++|..|-....++.+-+++|++|.-.-|..|.+.... +.+.|.|..|. .|..|-... -.+|.
T Consensus 192 ~d~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~f~-----peG~WlCrkCi~~~~~i~~C~fCps~d----GaFkq 262 (669)
T COG5141 192 FDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFL-----PEGFWLCRKCIYGEYQIRCCSFCPSSD----GAFKQ 262 (669)
T ss_pred hhhhhHhccccccCCcceEEEecCcchhhhhhcccceec-----CcchhhhhhhcccccceeEEEeccCCC----Cceee
Confidence 477888886555667788999999999999999998654 34889999995 244443222 12232
Q ss_pred C-CCCcccccccCCCCcCCCCCCcccCCCCccCCCCCCCCCCCCccccccCccccCCCccccccccccccccccccCCCC
Q 005013 74 R-CDAAYHCYCQHPPHKNVSSGPYLCPKHTKCHSCGSNVPGNGLSVRWFLGYTCCDACGRLFVKGNYCPVCLKVYRDSES 152 (719)
Q Consensus 74 r-C~raYH~~CL~PpL~~Ip~g~W~CP~C~~C~sCg~r~pgki~s~RW~~~~slC~aC~~lfvK~nyC~VC~K~Y~dsdg 152 (719)
. =++|-|..|..-. +++.-+.-. ..-........+..||.. -|.+|.+. +
T Consensus 263 T~dgrW~H~iCA~~~-pelsF~~l~-------~~dpI~~i~sVs~srwkl----------------~C~iCk~~-----~ 313 (669)
T COG5141 263 TSDGRWGHVICAMFN-PELSFGHLL-------SKDPIDNIASVSSSRWKL----------------GCLICKEF-----G 313 (669)
T ss_pred ccCCchHhHhHHHhc-chhcccccc-------ccchhhhhcccchhhHhh----------------eeeEEccc-----C
Confidence 2 2345555554310 111000000 000011122344556644 35566543 5
Q ss_pred CCceeccC--CCCeeccCCCC
Q 005013 153 TPMVCCDV--CQRWVHCQCDG 171 (719)
Q Consensus 153 g~MIqCD~--C~~wFH~eCL~ 171 (719)
|.-|||.. |-++||..|..
T Consensus 314 GtcIqCs~~nC~~aYHVtCAr 334 (669)
T COG5141 314 GTCIQCSYFNCTRAYHVTCAR 334 (669)
T ss_pred cceeeecccchhhhhhhhhhh
Confidence 66788865 99999999976
No 24
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.63 E-value=3e-05 Score=90.73 Aligned_cols=91 Identities=24% Similarity=0.502 Sum_probs=64.2
Q ss_pred CCCCcccccccCCCCcCCCCCCcccCCCCccCCCCCCCCCCCCccccccCccccCCCccccccccccccccccccCCCCC
Q 005013 74 RCDAAYHCYCQHPPHKNVSSGPYLCPKHTKCHSCGSNVPGNGLSVRWFLGYTCCDACGRLFVKGNYCPVCLKVYRDSEST 153 (719)
Q Consensus 74 rC~raYH~~CL~PpL~~Ip~g~W~CP~C~~C~sCg~r~pgki~s~RW~~~~slC~aC~~lfvK~nyC~VC~K~Y~dsdgg 153 (719)
.|+++||..|++|.+...+...|.||.|.. -+.....+... ......++|.+|. +++
T Consensus 1 ~~~r~~~~~~~~p~~~~~~~~~~k~~~~e~---~~~~~~~~~~~--------------~~~~~~e~c~ic~------~~g 57 (696)
T KOG0383|consen 1 TCPRAYHRVCLDPKLKEEPEMDPKCPGCES---SSAQVEAKDDD--------------WDDAEQEACRICA------DGG 57 (696)
T ss_pred CCCcccCcCCCCcccccCCcCCccCcchhh---cccccccccCC--------------cchhhhhhhhhhc------CCC
Confidence 489999999999998888889999999743 11111111111 2234556888997 478
Q ss_pred CceeccCCCCeeccCCCCC-ChHHHhhhccCCCCceeCCCCC
Q 005013 154 PMVCCDVCQRWVHCQCDGI-SDEKYLQFQVDGNLQYRCPTCR 194 (719)
Q Consensus 154 ~MIqCD~C~~wFH~eCL~l-sdEkye~~~id~d~~Y~CptCr 194 (719)
.+|+|+.|+.|||..|++. +.+ . +...|.|+-|.
T Consensus 58 ~~l~c~tC~~s~h~~cl~~pl~~------~-p~~~~~c~Rc~ 92 (696)
T KOG0383|consen 58 ELLWCDTCPASFHASCLGPPLTP------Q-PNGEFICPRCF 92 (696)
T ss_pred cEEEeccccHHHHHHccCCCCCc------C-Cccceeeeeec
Confidence 9999999999999999973 211 1 23449999993
No 25
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.47 E-value=3.8e-05 Score=81.16 Aligned_cols=39 Identities=26% Similarity=0.589 Sum_probs=33.7
Q ss_pred cccCCCCCceeecCC--CC-CcccccccCCCCcCCCCCCcccCCCCc
Q 005013 60 CRRTGDPNKFMFCRR--CD-AAYHCYCQHPPHKNVSSGPYLCPKHTK 103 (719)
Q Consensus 60 C~~sgd~~kLL~Cdr--C~-raYH~~CL~PpL~~Ip~g~W~CP~C~~ 103 (719)
|...+ .|+-|+. |+ .|||..|++ +...|.+.||||.|..
T Consensus 226 qvsyg---~Mi~CDn~~C~~eWFH~~CVG--L~~~PkgkWyC~~C~~ 267 (274)
T KOG1973|consen 226 QVSYG---KMIGCDNPGCPIEWFHFTCVG--LKTKPKGKWYCPRCKA 267 (274)
T ss_pred ccccc---cccccCCCCCCcceEEEeccc--cccCCCCcccchhhhh
Confidence 45555 8999997 99 999999999 6788999999999865
No 26
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.20 E-value=0.00012 Score=77.50 Aligned_cols=38 Identities=32% Similarity=0.897 Sum_probs=31.8
Q ss_pred CCCCceeccC--CC-CeeccCCCCCChHHHhhhccCCCCceeCCCCCCC
Q 005013 151 ESTPMVCCDV--CQ-RWVHCQCDGISDEKYLQFQVDGNLQYRCPTCRGE 196 (719)
Q Consensus 151 dgg~MIqCD~--C~-~wFH~eCL~lsdEkye~~~id~d~~Y~CptCr~~ 196 (719)
..+.||.||- |+ .|||..|+++..+ +.+.|+|+.|+..
T Consensus 228 syg~Mi~CDn~~C~~eWFH~~CVGL~~~--------PkgkWyC~~C~~~ 268 (274)
T KOG1973|consen 228 SYGKMIGCDNPGCPIEWFHFTCVGLKTK--------PKGKWYCPRCKAE 268 (274)
T ss_pred ccccccccCCCCCCcceEEEeccccccC--------CCCcccchhhhhh
Confidence 3688999998 99 9999999998632 4567999999864
No 27
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=97.13 E-value=8e-05 Score=89.47 Aligned_cols=80 Identities=18% Similarity=0.406 Sum_probs=62.6
Q ss_pred ceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCc----------------------------------------cc
Q 005013 18 RMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR----------------------------------------IC 57 (719)
Q Consensus 18 eLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr----------------------------------------~C 57 (719)
.+++|..|++.||..|+.++....+ ...|.|--|. .|
T Consensus 355 ~~lc~Et~prvvhlEcv~hP~~~~~---s~~~e~evc~~hkvngvvd~vl~~~K~~~~iR~~~iG~dr~gr~ywfi~rrl 431 (1414)
T KOG1473|consen 355 DLLCCETCPRVVHLECVFHPRFAVP---SAFWECEVCNIHKVNGVVDCVLPPSKNVDSIRHTPIGRDRYGRKYWFISRRL 431 (1414)
T ss_pred ceeecccCCceEEeeecCCccccCC---CccchhhhhhhhccCcccccccChhhcccceeccCCCcCccccchhceeeee
Confidence 8999999999999999998765433 4779998887 34
Q ss_pred cccccCCCCCceeecCC-CCCcccc-cccCCCC--cCCCCCCcccCCCCc
Q 005013 58 EICRRTGDPNKFMFCRR-CDAAYHC-YCQHPPH--KNVSSGPYLCPKHTK 103 (719)
Q Consensus 58 ~VC~~sgd~~kLL~Cdr-C~raYH~-~CL~PpL--~~Ip~g~W~CP~C~~ 103 (719)
.+|+.. +.+++|.. |+.+||. .|++... ..++.+.|.|+.|+.
T Consensus 432 ~Ie~~d---et~l~yysT~pqly~ll~cLd~~~~e~~L~d~i~~~~ee~~ 478 (1414)
T KOG1473|consen 432 RIEGMD---ETLLWYYSTCPQLYHLLRCLDRTYVEMYLCDGIWERREEII 478 (1414)
T ss_pred EEecCC---CcEEEEecCcHHHHHHHHHhchHHHHHhhccchhhhHHHHH
Confidence 444422 36888887 9999999 9999543 347889999999865
No 28
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.07 E-value=0.00021 Score=74.74 Aligned_cols=46 Identities=35% Similarity=0.944 Sum_probs=35.9
Q ss_pred ccccccccccccCCCCCCceeccC--CC-CeeccCCCCCChHHHhhhccCCCCceeCCCCCC
Q 005013 137 GNYCPVCLKVYRDSESTPMVCCDV--CQ-RWVHCQCDGISDEKYLQFQVDGNLQYRCPTCRG 195 (719)
Q Consensus 137 ~nyC~VC~K~Y~dsdgg~MIqCD~--C~-~wFH~eCL~lsdEkye~~~id~d~~Y~CptCr~ 195 (719)
.-||+ |+++ -.++||-||. |. -|||..|+++.. ++.+.|+|+.|+.
T Consensus 221 ~lYCf-Cqqv----SyGqMVaCDn~nCkrEWFH~~CVGLk~--------pPKG~WYC~eCk~ 269 (271)
T COG5034 221 ELYCF-CQQV----SYGQMVACDNANCKREWFHLECVGLKE--------PPKGKWYCPECKK 269 (271)
T ss_pred eeEEE-eccc----ccccceecCCCCCchhheeccccccCC--------CCCCcEeCHHhHh
Confidence 34775 7765 3689999987 76 599999999743 4678999999974
No 29
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.06 E-value=0.0002 Score=83.64 Aligned_cols=46 Identities=33% Similarity=0.834 Sum_probs=36.3
Q ss_pred CccCcCCccCCcccCCceEEeCcCCCc-chhhhcCCCcccccccCCCCCCCCCCc
Q 005013 2 CRLCFVGENEGCERARRMLSCKSCGKK-YHRNCLKNWAQNRDLFHWSSWKCPSCR 55 (719)
Q Consensus 2 C~iC~~Ce~~Gse~~eeLL~Cd~Cgks-YH~~CL~p~~e~~~~~~~~~W~Cp~Cr 55 (719)
|.||..-+ ..+-||+|+.|... ||.+||++..-..++ ..|+|++|.
T Consensus 218 C~IC~~~D-----pEdVLLLCDsCN~~~YH~YCLDPdl~eiP~---~eWYC~NC~ 264 (1134)
T KOG0825|consen 218 CDICTVHD-----PEDVLLLCDSCNKVYYHVYCLDPDLSESPV---NEWYCTNCS 264 (1134)
T ss_pred ceeeccCC-----hHHhheeecccccceeeccccCcccccccc---cceecCcch
Confidence 77776643 34579999999998 999999997644443 789999995
No 30
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=97.04 E-value=0.0003 Score=84.82 Aligned_cols=125 Identities=14% Similarity=0.271 Sum_probs=81.5
Q ss_pred cccccccCCCCCceeecCCCCCcccccccCCCCcCCCCCCcccCCCCccCCCCCCC----CCCCCccccccCccccCCCc
Q 005013 56 ICEICRRTGDPNKFMFCRRCDAAYHCYCQHPPHKNVSSGPYLCPKHTKCHSCGSNV----PGNGLSVRWFLGYTCCDACG 131 (719)
Q Consensus 56 ~C~VC~~sgd~~kLL~CdrC~raYH~~CL~PpL~~Ip~g~W~CP~C~~C~sCg~r~----pgki~s~RW~~~~slC~aC~ 131 (719)
.|.+|.+.+ .+++|..|++.||..|+.++...++...|-|--|..|..-+... +.+.... ..+..=+
T Consensus 346 hcrf~~d~~---~~lc~Et~prvvhlEcv~hP~~~~~s~~~e~evc~~hkvngvvd~vl~~~K~~~~------iR~~~iG 416 (1414)
T KOG1473|consen 346 HCRFCHDLG---DLLCCETCPRVVHLECVFHPRFAVPSAFWECEVCNIHKVNGVVDCVLPPSKNVDS------IRHTPIG 416 (1414)
T ss_pred cccccCccc---ceeecccCCceEEeeecCCccccCCCccchhhhhhhhccCcccccccChhhcccc------eeccCCC
Confidence 666677766 79999999999999999999999999999999988766443221 1111111 1111101
Q ss_pred ------cccccccccccccccccCCCCCCceeccC-CCCeecc-CCCCCChHHHhhhccCCCCceeCCCCCCCCCC
Q 005013 132 ------RLFVKGNYCPVCLKVYRDSESTPMVCCDV-CQRWVHC-QCDGISDEKYLQFQVDGNLQYRCPTCRGECYQ 199 (719)
Q Consensus 132 ------~lfvK~nyC~VC~K~Y~dsdgg~MIqCD~-C~~wFH~-eCL~lsdEkye~~~id~d~~Y~CptCr~~~~q 199 (719)
...-...-|.+|. .+..+++|.. |+..||. .|++-+ |....+ .++.|.|+.|....+.
T Consensus 417 ~dr~gr~ywfi~rrl~Ie~------~det~l~yysT~pqly~ll~cLd~~---~~e~~L-~d~i~~~~ee~~rqM~ 482 (1414)
T KOG1473|consen 417 RDRYGRKYWFISRRLRIEG------MDETLLWYYSTCPQLYHLLRCLDRT---YVEMYL-CDGIWERREEIIRQMG 482 (1414)
T ss_pred cCccccchhceeeeeEEec------CCCcEEEEecCcHHHHHHHHHhchH---HHHHhh-ccchhhhHHHHHHhcc
Confidence 1111122377776 2456788877 9999999 998742 222222 3568999999765543
No 31
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=97.01 E-value=0.00098 Score=53.46 Aligned_cols=53 Identities=13% Similarity=0.288 Sum_probs=43.7
Q ss_pred ccccceEEEEecCCCCeeeeeEEEeecCceeEEEEecC-CchhhhhcCcceeEeeecc
Q 005013 657 DAIGKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITLDD-SRVKTLELGKQGVRFVPQK 713 (719)
Q Consensus 657 ~~i~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~dd-g~~~~~~lgk~~i~~~~~~ 713 (719)
-++|..|.+.| .|+.||.|+|.++... ....|.|.| |..+++. .+.|+.+|+.
T Consensus 3 ~~~G~~~~a~~-~d~~wyra~I~~~~~~-~~~~V~f~D~G~~~~v~--~~~l~~l~~~ 56 (57)
T smart00333 3 FKVGDKVAARW-EDGEWYRARIIKVDGE-QLYEVFFIDYGNEEVVP--PSDLRPLPEE 56 (57)
T ss_pred CCCCCEEEEEe-CCCCEEEEEEEEECCC-CEEEEEEECCCccEEEe--HHHeecCCCC
Confidence 36899999999 9999999999999985 569999999 9988665 5556666653
No 32
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=96.93 E-value=0.00048 Score=80.31 Aligned_cols=46 Identities=33% Similarity=0.865 Sum_probs=39.9
Q ss_pred cccccccCCCC--CceeecCCCCCcccccccCCCCcCCCCCCcccCCCCc
Q 005013 56 ICEICRRTGDP--NKFMFCRRCDAAYHCYCQHPPHKNVSSGPYLCPKHTK 103 (719)
Q Consensus 56 ~C~VC~~sgd~--~kLL~CdrC~raYH~~CL~PpL~~Ip~g~W~CP~C~~ 103 (719)
+|.+|+.+..+ +.|++|+.|+...|..|++ +..+|.+.|.|..|..
T Consensus 273 iCDvCrspD~e~~neMVfCd~Cn~cVHqaCyG--Ile~p~gpWlCr~Cal 320 (893)
T KOG0954|consen 273 ICDVCRSPDSEEANEMVFCDKCNICVHQACYG--ILEVPEGPWLCRTCAL 320 (893)
T ss_pred eeceecCCCccccceeEEeccchhHHHHhhhc--eeecCCCCeeehhccc
Confidence 88899877433 4799999999999999999 7789999999999854
No 33
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=96.91 E-value=0.0012 Score=54.13 Aligned_cols=36 Identities=28% Similarity=0.481 Sum_probs=33.2
Q ss_pred cccceEEEEecCCCCeeeeeEEEeecCceeEEEEecC
Q 005013 658 AIGKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITLDD 694 (719)
Q Consensus 658 ~i~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~dd 694 (719)
.+|.+|+|+|+-+++||.|+|+.+.. ..++.|.|++
T Consensus 4 ~~G~~Ve~~~~~~~~W~~a~V~~~~~-~~~~~V~~~~ 39 (61)
T smart00743 4 KKGDRVEVFSKEEDSWWEAVVTKVLG-DGKYLVRYLT 39 (61)
T ss_pred CCCCEEEEEECCCCEEEEEEEEEECC-CCEEEEEECC
Confidence 48999999999999999999999988 5579999998
No 34
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=96.64 E-value=0.00029 Score=79.18 Aligned_cols=52 Identities=23% Similarity=0.556 Sum_probs=37.7
Q ss_pred cCcCCccCCcccCCceEEeCcCCCcchhhhcCCCc-----ccccccCCCCCCCCCCc
Q 005013 4 LCFVGENEGCERARRMLSCKSCGKKYHRNCLKNWA-----QNRDLFHWSSWKCPSCR 55 (719)
Q Consensus 4 iC~~Ce~~Gse~~eeLL~Cd~CgksYH~~CL~p~~-----e~~~~~~~~~W~Cp~Cr 55 (719)
||.+|-...++..+++|.|+.||-..|..|.+... .....-....|+|.-|.
T Consensus 121 iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~ 177 (707)
T KOG0957|consen 121 ICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACL 177 (707)
T ss_pred EEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHh
Confidence 56666445578889999999999999999998751 11111234789998884
No 35
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=96.60 E-value=0.00095 Score=70.00 Aligned_cols=41 Identities=22% Similarity=0.655 Sum_probs=33.3
Q ss_pred ccccCCCCCceeecC--CCCC-cccccccCCCCcCCCCCCcccCCCC
Q 005013 59 ICRRTGDPNKFMFCR--RCDA-AYHCYCQHPPHKNVSSGPYLCPKHT 102 (719)
Q Consensus 59 VC~~sgd~~kLL~Cd--rC~r-aYH~~CL~PpL~~Ip~g~W~CP~C~ 102 (719)
.|.+.. -..|+-|| .|.+ |||..|++ +...|.+.|||+.|.
T Consensus 225 fCqqvS-yGqMVaCDn~nCkrEWFH~~CVG--Lk~pPKG~WYC~eCk 268 (271)
T COG5034 225 FCQQVS-YGQMVACDNANCKREWFHLECVG--LKEPPKGKWYCPECK 268 (271)
T ss_pred Eecccc-cccceecCCCCCchhheeccccc--cCCCCCCcEeCHHhH
Confidence 455432 23899999 5886 99999999 788899999999985
No 36
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=96.60 E-value=0.0012 Score=64.68 Aligned_cols=26 Identities=35% Similarity=0.859 Sum_probs=24.6
Q ss_pred cccccccCCCCcCCCCCCcccCCCCc
Q 005013 78 AYHCYCQHPPHKNVSSGPYLCPKHTK 103 (719)
Q Consensus 78 aYH~~CL~PpL~~Ip~g~W~CP~C~~ 103 (719)
+||+.||.||+..+|.+.|+||.|..
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~ 26 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCEV 26 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCcC
Confidence 59999999999999999999999975
No 37
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=96.56 E-value=0.0033 Score=62.69 Aligned_cols=33 Identities=24% Similarity=0.815 Sum_probs=25.3
Q ss_pred cccccccC---CCCCceeecCCCCCcccccccCCCC
Q 005013 56 ICEICRRT---GDPNKFMFCRRCDAAYHCYCQHPPH 88 (719)
Q Consensus 56 ~C~VC~~s---gd~~kLL~CdrC~raYH~~CL~PpL 88 (719)
+|.+|... ..-..|++|..|..+||..||++-.
T Consensus 1 ~C~~C~~~g~~~~kG~Lv~CQGCs~sYHk~CLG~Rs 36 (175)
T PF15446_consen 1 TCDTCGYEGDDRNKGPLVYCQGCSSSYHKACLGPRS 36 (175)
T ss_pred CcccccCCCCCccCCCeEEcCccChHHHhhhcCCcc
Confidence 36666543 3335799999999999999999754
No 38
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=96.42 E-value=0.00052 Score=76.14 Aligned_cols=129 Identities=19% Similarity=0.267 Sum_probs=64.3
Q ss_pred ceEEeCcCCCcchhhhcCCCcccccc------cCCCCCCCCCCc-----cccccccCCCCCceeecCCCCCcccccccCC
Q 005013 18 RMLSCKSCGKKYHRNCLKNWAQNRDL------FHWSSWKCPSCR-----ICEICRRTGDPNKFMFCRRCDAAYHCYCQHP 86 (719)
Q Consensus 18 eLL~Cd~CgksYH~~CL~p~~e~~~~------~~~~~W~Cp~Cr-----~C~VC~~sgd~~kLL~CdrC~raYH~~CL~P 86 (719)
+-.-|..=++-||..|..-..-.+.+ ...+.-+|-.|- .|.+|+....+ .+=..|+++||..|..
T Consensus 287 ~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tlekC~~Cg~~I~d---~iLrA~GkayHp~CF~- 362 (468)
T KOG1701|consen 287 QGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLEKCNKCGEPIMD---RILRALGKAYHPGCFT- 362 (468)
T ss_pred cchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHHHHHhhhhhHHHH---HHHHhcccccCCCceE-
Confidence 44556666778888776432110000 011334566665 67777765521 2234688999976643
Q ss_pred CCcCCCCCCcccCCCCccCCCCCCCCCCCCccc-cccCccccCCCccccccccccccccccccCCCCCC-ceeccCCCCe
Q 005013 87 PHKNVSSGPYLCPKHTKCHSCGSNVPGNGLSVR-WFLGYTCCDACGRLFVKGNYCPVCLKVYRDSESTP-MVCCDVCQRW 164 (719)
Q Consensus 87 pL~~Ip~g~W~CP~C~~C~sCg~r~pgki~s~R-W~~~~slC~aC~~lfvK~nyC~VC~K~Y~dsdgg~-MIqCD~C~~w 164 (719)
|+.|..|- .+ .+.. -..+...|..|... +----|.+|.+.....++.+ .|.=..=++-
T Consensus 363 --------------Cv~C~r~l---dg--ipFtvd~~n~v~Cv~dfh~-kfAPrCs~C~~PI~P~~G~~etvRvvamdr~ 422 (468)
T KOG1701|consen 363 --------------CVVCARCL---DG--IPFTVDSQNNVYCVPDFHK-KFAPRCSVCGNPILPRDGKDETVRVVAMDRD 422 (468)
T ss_pred --------------EEEecccc---CC--ccccccCCCceeeehhhhh-hcCcchhhccCCccCCCCCcceEEEEEcccc
Confidence 33333332 11 1111 01244566655421 00112899988776555533 3332233567
Q ss_pred eccCCC
Q 005013 165 VHCQCD 170 (719)
Q Consensus 165 FH~eCL 170 (719)
||.+|-
T Consensus 423 fHv~CY 428 (468)
T KOG1701|consen 423 FHVNCY 428 (468)
T ss_pred ccccce
Confidence 787773
No 39
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=96.41 E-value=0.0019 Score=78.80 Aligned_cols=53 Identities=30% Similarity=0.687 Sum_probs=43.5
Q ss_pred cccccccCCCC--CceeecCCCCCcccccccCCCCcCCCCCCcccCCCCc-------cCCCCCC
Q 005013 56 ICEICRRTGDP--NKFMFCRRCDAAYHCYCQHPPHKNVSSGPYLCPKHTK-------CHSCGSN 110 (719)
Q Consensus 56 ~C~VC~~sgd~--~kLL~CdrC~raYH~~CL~PpL~~Ip~g~W~CP~C~~-------C~sCg~r 110 (719)
+|.||.+..-. +..|+|+.|+.++|..|++ ...+|.+.|+|..|.. |..|...
T Consensus 221 ~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cyg--i~~ipeg~WlCr~Cl~s~~~~v~c~~cp~~ 282 (1051)
T KOG0955|consen 221 VCCICLDGECQNSNVIVFCDGCNLAVHQECYG--IPFIPEGQWLCRRCLQSPQRPVRCLLCPSK 282 (1051)
T ss_pred cceeecccccCCCceEEEcCCCcchhhhhccC--CCCCCCCcEeehhhccCcCcccceEeccCC
Confidence 78888876554 5799999999999999999 5568999999999964 6666543
No 40
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=96.36 E-value=0.0012 Score=74.46 Aligned_cols=46 Identities=26% Similarity=0.689 Sum_probs=41.7
Q ss_pred cccccccCCCCCceeecCCCCCcccccccCCCCcCCCC----CCcccCCC
Q 005013 56 ICEICRRTGDPNKFMFCRRCDAAYHCYCQHPPHKNVSS----GPYLCPKH 101 (719)
Q Consensus 56 ~C~VC~~sgd~~kLL~CdrC~raYH~~CL~PpL~~Ip~----g~W~CP~C 101 (719)
.|.+|++..+.-.++.|+.|...||..||.|||..+|. ..|.|..|
T Consensus 546 sCgiCkks~dQHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsEC 595 (707)
T KOG0957|consen 546 SCGICKKSTDQHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSEC 595 (707)
T ss_pred eeeeeccchhhHHHhhcchhhceeeccccCCccccCcccccCcceeeccc
Confidence 79999999888789999999999999999999998885 36999997
No 41
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=96.19 E-value=0.0067 Score=47.09 Aligned_cols=42 Identities=14% Similarity=0.338 Sum_probs=35.8
Q ss_pred cceEEEEecCCCCeeeeeEEEeecCceeEEEEecC-Cchhhhhc
Q 005013 660 GKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITLDD-SRVKTLEL 702 (719)
Q Consensus 660 ~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~dd-g~~~~~~l 702 (719)
|..+-+.|+.|+.||.|+|..+.. .....|.|.| |..+++.+
T Consensus 1 G~~c~a~~~~d~~wyra~V~~~~~-~~~~~V~f~DyG~~~~v~~ 43 (48)
T cd04508 1 GDLCLAKYSDDGKWYRAKITSILS-DGKVEVFFVDYGNTEVVPL 43 (48)
T ss_pred CCEEEEEECCCCeEEEEEEEEECC-CCcEEEEEEcCCCcEEEeH
Confidence 567889999999999999999986 5559999999 98887654
No 42
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=96.04 E-value=0.0042 Score=66.95 Aligned_cols=90 Identities=20% Similarity=0.418 Sum_probs=58.7
Q ss_pred ceeecCCCCCcccccccCCCCcCCCCCCcccCCCCccC---CCCCCC--CCCCCccccccCccccCCCcccccccccccc
Q 005013 68 KFMFCRRCDAAYHCYCQHPPHKNVSSGPYLCPKHTKCH---SCGSNV--PGNGLSVRWFLGYTCCDACGRLFVKGNYCPV 142 (719)
Q Consensus 68 kLL~CdrC~raYH~~CL~PpL~~Ip~g~W~CP~C~~C~---sCg~r~--pgki~s~RW~~~~slC~aC~~lfvK~nyC~V 142 (719)
.+.+|..|.-++|..=... ....++.|+|.-|..|. +|.... .......-|.+++ ++.|| .
T Consensus 67 ~agvC~~C~~~CH~~H~lv--eL~tKR~FrCDCg~sk~g~~sc~l~~~~~~~n~~N~YNhNf-----------qG~~C-~ 132 (345)
T KOG2752|consen 67 MAGVCYACSLSCHDGHELV--ELYTKRNFRCDCGNSKFGRCSCNLLEDKDAENSENLYNHNF-----------QGLFC-K 132 (345)
T ss_pred hceeEEEeeeeecCCceee--eccccCCcccccccccccccccccccccccccchhhhhhhh-----------cceeE-E
Confidence 6789999999999755442 22346788887666554 332111 1112222344433 44566 4
Q ss_pred ccccccC---CCCCCceeccCCCCeec-cCCCC
Q 005013 143 CLKVYRD---SESTPMVCCDVCQRWVH-CQCDG 171 (719)
Q Consensus 143 C~K~Y~d---sdgg~MIqCD~C~~wFH-~eCL~ 171 (719)
|.+.|++ ..++.|+||..|.-||| -.|.+
T Consensus 133 Cd~~Ypdp~~~~e~~m~QC~iCEDWFHce~c~~ 165 (345)
T KOG2752|consen 133 CDTPYPDPVRTEEGEMLQCVICEDWFHCEGCMQ 165 (345)
T ss_pred ecCCCCCccccccceeeeEEeccchhcccccCc
Confidence 9999977 34688999999999999 77776
No 43
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=95.95 E-value=0.0016 Score=81.96 Aligned_cols=48 Identities=31% Similarity=0.971 Sum_probs=45.0
Q ss_pred cccccccCCCCCceeecCCCCCcccccccCCCCcCCCCCCcccCCCCc
Q 005013 56 ICEICRRTGDPNKFMFCRRCDAAYHCYCQHPPHKNVSSGPYLCPKHTK 103 (719)
Q Consensus 56 ~C~VC~~sgd~~kLL~CdrC~raYH~~CL~PpL~~Ip~g~W~CP~C~~ 103 (719)
.|.+|+..++...|+.|+.|..+||.+|+.|.+..++.+.|+||.|..
T Consensus 1110 ~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~ 1157 (1404)
T KOG1245|consen 1110 LCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRK 1157 (1404)
T ss_pred hhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccch
Confidence 788889988888999999999999999999999999999999999865
No 44
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=95.92 E-value=0.0033 Score=70.89 Aligned_cols=67 Identities=28% Similarity=0.555 Sum_probs=48.2
Q ss_pred CccccccccCCCC--CceeecCCCCCcccccccCCCCcCCCCCCcccCCCCc-------cCCCCCCCC--CCCCcccccc
Q 005013 54 CRICEICRRTGDP--NKFMFCRRCDAAYHCYCQHPPHKNVSSGPYLCPKHTK-------CHSCGSNVP--GNGLSVRWFL 122 (719)
Q Consensus 54 Cr~C~VC~~sgd~--~kLL~CdrC~raYH~~CL~PpL~~Ip~g~W~CP~C~~-------C~sCg~r~p--gki~s~RW~~ 122 (719)
|..|.+|.....+ +.+++|+.|+.+.|..|++ +.-+|.|.|+|..|.. |..|....- ......||.+
T Consensus 193 d~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYG--I~f~peG~WlCrkCi~~~~~i~~C~fCps~dGaFkqT~dgrW~H 270 (669)
T COG5141 193 DDICTKCTSTHNENSNAIVFCDGCEICVHQSCYG--IQFLPEGFWLCRKCIYGEYQIRCCSFCPSSDGAFKQTSDGRWGH 270 (669)
T ss_pred hhhhHhccccccCCcceEEEecCcchhhhhhccc--ceecCcchhhhhhhcccccceeEEEeccCCCCceeeccCCchHh
Confidence 3455666665543 4689999999999999999 5668999999999974 777876532 1223456654
No 45
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=93.84 E-value=0.064 Score=60.53 Aligned_cols=73 Identities=21% Similarity=0.568 Sum_probs=49.4
Q ss_pred cccCCCccccccccccccccccccCCCCCCceeccCCCCeeccCCCCCChHHHhhhcc-------CCCCceeCCCCCCCC
Q 005013 125 TCCDACGRLFVKGNYCPVCLKVYRDSESTPMVCCDVCQRWVHCQCDGISDEKYLQFQV-------DGNLQYRCPTCRGEC 197 (719)
Q Consensus 125 slC~aC~~lfvK~nyC~VC~K~Y~dsdgg~MIqCD~C~~wFH~eCL~lsdEkye~~~i-------d~d~~Y~CptCr~~~ 197 (719)
.+|..| .|.+|.+.-...++-.||.||.|.+|-|.+|--. ..++..+. .-+..|.|..|-...
T Consensus 124 gFC~~C--------~C~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr--~~~i~~G~s~~g~~g~~d~~f~C~~C~~~s 193 (446)
T PF07227_consen 124 GFCRRC--------MCCICSKFDDNKNTCSWIGCDVCGHWCHLDCALR--HELIGTGPSVKGSIGTLDMQFHCRACGKTS 193 (446)
T ss_pred CccccC--------CccccCCcccCCCCeeEEeccCCCceehhhhhcc--cccccCCccCCCCCccCceEEEccCCCChh
Confidence 466666 5999988434445667999999999999999642 11222221 125699999998766
Q ss_pred CCCCchHHHH
Q 005013 198 YQVRDLEDAV 207 (719)
Q Consensus 198 ~qIk~~kda~ 207 (719)
.-+.|+++..
T Consensus 194 eLlG~vk~vf 203 (446)
T PF07227_consen 194 ELLGFVKKVF 203 (446)
T ss_pred hHHHHHHHHH
Confidence 5555555554
No 46
>PF09038 53-BP1_Tudor: Tumour suppressor p53-binding protein-1 Tudor; InterPro: IPR015125 This domain consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. The domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3 []. ; PDB: 3LGL_A 1XNI_B 3LGF_A 2G3R_A 2IG0_A 3LH0_A 1SSF_A.
Probab=93.59 E-value=0.084 Score=50.40 Aligned_cols=43 Identities=23% Similarity=0.331 Sum_probs=32.1
Q ss_pred CcccccceEEEEecCCCCeeeeeEEEeecCceeEEEEecCCchh
Q 005013 655 GKDAIGKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITLDDSRVK 698 (719)
Q Consensus 655 g~~~i~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~ddg~~~ 698 (719)
|.+.||+||---|.+++-.|-|+|+. +.+..+..|.||||.+.
T Consensus 1 ~~~~iG~rV~AkWS~n~yyY~G~I~~-~~~~~kykv~FdDG~~~ 43 (122)
T PF09038_consen 1 GSSFIGLRVFAKWSDNGYYYPGKITS-DKGKNKYKVLFDDGYEC 43 (122)
T ss_dssp ---STT-EEEEESSTTSEEEEEEEEE-EETTTEEEEEETTS-EE
T ss_pred CCcccccEEEEEEccCCcccCceEee-cCCCCeEEEEecCCccc
Confidence 67899999999996444558999999 57777999999999764
No 47
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=93.41 E-value=0.08 Score=63.44 Aligned_cols=50 Identities=36% Similarity=1.053 Sum_probs=39.1
Q ss_pred CceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCc----------cccccccCCCCC
Q 005013 17 RRMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR----------ICEICRRTGDPN 67 (719)
Q Consensus 17 eeLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr----------~C~VC~~sgd~~ 67 (719)
..+-.|..|...||+.|+..|...+.......|.||.|. +| .|++..+++
T Consensus 205 ~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~~~~~~y~C-~CGk~~nP~ 264 (950)
T KOG1952|consen 205 APVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSKTVPKTYLC-FCGKVKNPE 264 (950)
T ss_pred CCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhccCCcccce-ecCcccCCC
Confidence 479999999999999999999765433334789999998 55 577665553
No 48
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=93.33 E-value=0.015 Score=44.37 Aligned_cols=33 Identities=33% Similarity=0.822 Sum_probs=18.5
Q ss_pred CceeecCCCCCcccccccCCCCcCCCCC-CcccCCC
Q 005013 67 NKFMFCRRCDAAYHCYCQHPPHKNVSSG-PYLCPKH 101 (719)
Q Consensus 67 ~kLL~CdrC~raYH~~CL~PpL~~Ip~g-~W~CP~C 101 (719)
+.|++|+.|....|..|++. ..++.+ .|+|..|
T Consensus 2 n~ll~C~~C~v~VH~~CYGv--~~~~~~~~W~C~~C 35 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGV--SEVPDGDDWLCDRC 35 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT---SS--SS-----HHH
T ss_pred CceEEeCCCCCcCChhhCCc--ccCCCCCcEECCcC
Confidence 47999999999999999994 344444 6999765
No 49
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=92.65 E-value=0.059 Score=53.02 Aligned_cols=24 Identities=29% Similarity=0.740 Sum_probs=20.5
Q ss_pred cchhhhcCCCcccccccCCCCCCCCCC
Q 005013 28 KYHRNCLKNWAQNRDLFHWSSWKCPSC 54 (719)
Q Consensus 28 sYH~~CL~p~~e~~~~~~~~~W~Cp~C 54 (719)
.||..||.|+....| .+.|.||.|
T Consensus 1 g~H~~CL~Ppl~~~P---~g~W~Cp~C 24 (148)
T cd04718 1 GFHLCCLRPPLKEVP---EGDWICPFC 24 (148)
T ss_pred CcccccCCCCCCCCC---CCCcCCCCC
Confidence 599999999886544 599999999
No 50
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=92.23 E-value=0.039 Score=42.05 Aligned_cols=35 Identities=23% Similarity=0.640 Sum_probs=19.2
Q ss_pred CceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCc
Q 005013 17 RRMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR 55 (719)
Q Consensus 17 eeLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr 55 (719)
++||.|+.|.-..|..|.+....+. ...|.|..|+
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~~~~~----~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVSEVPD----GDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-SS--S----S-----HHH-
T ss_pred CceEEeCCCCCcCChhhCCcccCCC----CCcEECCcCC
Confidence 4799999999999999999875532 2359998773
No 51
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=91.90 E-value=0.044 Score=69.48 Aligned_cols=47 Identities=34% Similarity=0.752 Sum_probs=35.9
Q ss_pred cCcCCccCCcccCCceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCc
Q 005013 4 LCFVGENEGCERARRMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR 55 (719)
Q Consensus 4 iC~~Ce~~Gse~~eeLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr 55 (719)
+|..|-..+ ..+.|+.|+.|...||..|+.+.....+ .+.|.||.|+
T Consensus 1110 ~c~~cr~k~--~~~~m~lc~~c~~~~h~~C~rp~~~~~~---~~dW~C~~c~ 1156 (1404)
T KOG1245|consen 1110 LCKVCRRKK--QDEKMLLCDECLSGFHLFCLRPALSSVP---PGDWMCPSCR 1156 (1404)
T ss_pred hhhhhhhcc--cchhhhhhHhhhhhHHHHhhhhhhccCC---cCCccCCccc
Confidence 355553322 2358999999999999999999876544 4889999997
No 52
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=91.89 E-value=0.043 Score=60.30 Aligned_cols=173 Identities=16% Similarity=0.317 Sum_probs=91.9
Q ss_pred ceEEeCcCCCcchhhh--cCCCcccccccCCCCCCCCCCc------------cccccccCCCC----CceeecCCCCCcc
Q 005013 18 RMLSCKSCGKKYHRNC--LKNWAQNRDLFHWSSWKCPSCR------------ICEICRRTGDP----NKFMFCRRCDAAY 79 (719)
Q Consensus 18 eLL~Cd~CgksYH~~C--L~p~~e~~~~~~~~~W~Cp~Cr------------~C~VC~~sgd~----~kLL~CdrC~raY 79 (719)
.++.|+.|-.+||..| ++......+ +...|.|..|. .| +|.....+ ...+-+..|..++
T Consensus 74 ~~~~cd~C~~~~~~ec~~v~~~~~e~p--~~~~~~c~~c~~~~~~~~~~~~l~~-~~~~~~~~~~s~s~~~~~~~~~~~~ 150 (345)
T KOG1632|consen 74 LMEQCDLCEDWYHGECWEVGTAEKEAP--KEDPKVCDECKEAQDGMSESDGLSC-VCRQDDSELLSPSFYFGKRGCQFWV 150 (345)
T ss_pred hhhccccccccccccccccCchhhcCC--ccccccccccchhhhhhhhhcccee-ecccccccccccccccCCccccccc
Confidence 6899999999999999 777654333 34679999997 22 33332211 1235677788888
Q ss_pred cccccCCCCcC-CCCCCcccCCCCccCC-------------------CCCCCCC--CCCcccccc--C----c----ccc
Q 005013 80 HCYCQHPPHKN-VSSGPYLCPKHTKCHS-------------------CGSNVPG--NGLSVRWFL--G----Y----TCC 127 (719)
Q Consensus 80 H~~CL~PpL~~-Ip~g~W~CP~C~~C~s-------------------Cg~r~pg--ki~s~RW~~--~----~----slC 127 (719)
|..|+..-... .-...-.|+.|..=.. ++..... ......|.+ + - ..|
T Consensus 151 ~~~~~~~~r~~~~~~~~~t~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 230 (345)
T KOG1632|consen 151 KLQKLGRVRLEAEKNDDPTVFEVVSGTATGELPSKDKSSNDRGSKSKTRKKRNRESELEEKKRKHFSNEELTEPAREPVD 230 (345)
T ss_pred cchhhhhhhhhhhhcccchhhhcccccccccccccccccccccceecccCcccccchhhhhhhhhccCcccccccccCCC
Confidence 88887742211 1112223333221000 0000000 000000110 0 0 022
Q ss_pred CCCccccccccccccccccccCCCCCCceeccCCCCeeccCCCCCChH--HHhhhccCCCCceeCCCCCCCCCC
Q 005013 128 DACGRLFVKGNYCPVCLKVYRDSESTPMVCCDVCQRWVHCQCDGISDE--KYLQFQVDGNLQYRCPTCRGECYQ 199 (719)
Q Consensus 128 ~aC~~lfvK~nyC~VC~K~Y~dsdgg~MIqCD~C~~wFH~eCL~lsdE--kye~~~id~d~~Y~CptCr~~~~q 199 (719)
..+.. ...+..|-.|+-.+... .-+++|+.|..|||..|+.+... .|.... +..|+|+.|..-.+.
T Consensus 231 ~~~~~-~~~~~~~~~cg~~~~~~--~~~~~~~~~e~w~~~~~v~~~~a~~~~~~~~---~~~~~c~~~~~~~~~ 298 (345)
T KOG1632|consen 231 ESEAP-DYSKLICDPCGLSDANK--KFEICCDLCESWFHGDCVQIFEARKRLNEIR---NEVYKCPHCTVLKFE 298 (345)
T ss_pred ccccc-ccccccccccCcchHHH--HHHHHHHHHHHHhcccccccccchhhhhhhh---ccceecCceeecccc
Confidence 22211 12334577777544222 45788999999999999996543 232221 256999999864443
No 53
>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=91.75 E-value=0.039 Score=42.63 Aligned_cols=42 Identities=33% Similarity=1.054 Sum_probs=28.8
Q ss_pred CccCcCCccCCcccCCceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCc
Q 005013 2 CRLCFVGENEGCERARRMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR 55 (719)
Q Consensus 2 C~iC~~Ce~~Gse~~eeLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr 55 (719)
|.||+..-..+ +.++... |+..||..|+..|.... ..||.|+
T Consensus 3 C~IC~~~~~~~----~~~~~l~-C~H~fh~~Ci~~~~~~~-------~~CP~CR 44 (44)
T PF13639_consen 3 CPICLEEFEDG----EKVVKLP-CGHVFHRSCIKEWLKRN-------NSCPVCR 44 (44)
T ss_dssp ETTTTCBHHTT----SCEEEET-TSEEEEHHHHHHHHHHS-------SB-TTTH
T ss_pred CcCCChhhcCC----CeEEEcc-CCCeeCHHHHHHHHHhC-------CcCCccC
Confidence 77777653332 3555555 99999999999987542 2788874
No 54
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=88.68 E-value=0.12 Score=44.54 Aligned_cols=52 Identities=31% Similarity=0.699 Sum_probs=20.3
Q ss_pred CccCcCCccCCcccCCceEEeC--cCCCcchhhhcCCCcccccc----cCCCCCCCCCCc
Q 005013 2 CRLCFVGENEGCERARRMLSCK--SCGKKYHRNCLKNWAQNRDL----FHWSSWKCPSCR 55 (719)
Q Consensus 2 C~iC~~Ce~~Gse~~eeLL~Cd--~CgksYH~~CL~p~~e~~~~----~~~~~W~Cp~Cr 55 (719)
|.||+.-.... .....+.|. .|+..||..||..|....+. +..-.+.||.|.
T Consensus 5 C~IC~~~~~~~--~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~ 62 (70)
T PF11793_consen 5 CGICYSYRLDD--GEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCS 62 (70)
T ss_dssp -SSS--SS-TT-------B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-
T ss_pred CCcCCcEecCC--CCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCC
Confidence 77777543211 122468998 99999999999998643221 112234688884
No 55
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=88.64 E-value=0.22 Score=56.42 Aligned_cols=80 Identities=21% Similarity=0.622 Sum_probs=49.0
Q ss_pred CCccCcCCccCCcccCCceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCccccccccCCCCCceeecCCCCCccc
Q 005013 1 MCRLCFVGENEGCERARRMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCRICEICRRTGDPNKFMFCRRCDAAYH 80 (719)
Q Consensus 1 ~C~iC~~Ce~~Gse~~eeLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr~C~VC~~sgd~~kLL~CdrC~raYH 80 (719)
.|.+|..-.+.. -.+|.=..|.++||..|+..|... .||-|++|+. -... ....|..|+..
T Consensus 177 TCpVCLERMD~s----~~gi~t~~c~Hsfh~~cl~~w~~~---------scpvcR~~q~-p~~v---e~~~c~~c~~~-- 237 (493)
T KOG0804|consen 177 TCPVCLERMDSS----TTGILTILCNHSFHCSCLMKWWDS---------SCPVCRYCQS-PSVV---ESSLCLACGCT-- 237 (493)
T ss_pred CcchhHhhcCcc----ccceeeeecccccchHHHhhcccC---------cChhhhhhcC-cchh---hhhhhhhhccc--
Confidence 477777554322 134555689999999999987542 6999888865 2222 23344444332
Q ss_pred ccccCCCCcCCCCCCcccCCCCccCCCCCCCC
Q 005013 81 CYCQHPPHKNVSSGPYLCPKHTKCHSCGSNVP 112 (719)
Q Consensus 81 ~~CL~PpL~~Ip~g~W~CP~C~~C~sCg~r~p 112 (719)
..-|.|--|.. ..||....
T Consensus 238 ------------~~LwicliCg~-vgcgrY~e 256 (493)
T KOG0804|consen 238 ------------EDLWICLICGN-VGCGRYKE 256 (493)
T ss_pred ------------ccEEEEEEccc-eecccccc
Confidence 23588777654 46776543
No 56
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=86.97 E-value=0.43 Score=39.83 Aligned_cols=21 Identities=33% Similarity=0.964 Sum_probs=19.0
Q ss_pred CceEEeCcCCCcchhhhcCCC
Q 005013 17 RRMLSCKSCGKKYHRNCLKNW 37 (719)
Q Consensus 17 eeLL~Cd~CgksYH~~CL~p~ 37 (719)
++++.|..|+..||+.|....
T Consensus 19 dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 19 DDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred CCEEECCCCCCcccHHHHhhC
Confidence 589999999999999999754
No 57
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.28 E-value=0.4 Score=53.03 Aligned_cols=35 Identities=29% Similarity=0.822 Sum_probs=25.8
Q ss_pred CCccCcCCccCCcccCCceEEeCcCCCcchhhhcCCCccc
Q 005013 1 MCRLCFVGENEGCERARRMLSCKSCGKKYHRNCLKNWAQN 40 (719)
Q Consensus 1 ~C~iC~~Ce~~Gse~~eeLL~Cd~CgksYH~~CL~p~~e~ 40 (719)
.|.||+.--..| +.|.==-|.+.||..|+++|...
T Consensus 231 ~CaIClEdY~~G-----dklRiLPC~H~FH~~CIDpWL~~ 265 (348)
T KOG4628|consen 231 TCAICLEDYEKG-----DKLRILPCSHKFHVNCIDPWLTQ 265 (348)
T ss_pred eEEEeecccccC-----CeeeEecCCCchhhccchhhHhh
Confidence 377777655555 44444679999999999999753
No 58
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=84.24 E-value=0.76 Score=41.83 Aligned_cols=61 Identities=28% Similarity=0.473 Sum_probs=39.9
Q ss_pred eEEeCcCCCcchhhhcCCCcccc----------c--ccCCCCCCCCCCccccccccCCCCCceeecCC--CCCccccccc
Q 005013 19 MLSCKSCGKKYHRNCLKNWAQNR----------D--LFHWSSWKCPSCRICEICRRTGDPNKFMFCRR--CDAAYHCYCQ 84 (719)
Q Consensus 19 LL~Cd~CgksYH~~CL~p~~e~~----------~--~~~~~~W~Cp~Cr~C~VC~~sgd~~kLL~Cdr--C~raYH~~CL 84 (719)
.+.-..-+++.|..|....++.. . .+....|. ..|.+|+... +..+.|.. |.++||+.|.
T Consensus 12 alk~t~~~~WvHv~Cal~~~~~~~~~~~~~~~v~~~~i~~~~~~----~~C~iC~~~~--G~~i~C~~~~C~~~fH~~CA 85 (110)
T PF13832_consen 12 ALKRTSDGQWVHVLCALWIPEVIFNNGESMEPVDISNIPPSRFK----LKCSICGKSG--GACIKCSHPGCSTAFHPTCA 85 (110)
T ss_pred cccCccCCcEEEeEccceeCccEEeechhcCcccceeecchhcC----CcCcCCCCCC--ceeEEcCCCCCCcCCCHHHH
Confidence 34444579999999997644310 0 01111121 2777888763 26899998 9999999997
Q ss_pred C
Q 005013 85 H 85 (719)
Q Consensus 85 ~ 85 (719)
.
T Consensus 86 ~ 86 (110)
T PF13832_consen 86 R 86 (110)
T ss_pred H
Confidence 6
No 59
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=84.02 E-value=0.75 Score=41.89 Aligned_cols=29 Identities=24% Similarity=0.577 Sum_probs=24.0
Q ss_pred ccccccccccCCCCCCceeccC--CCCeeccCCCCC
Q 005013 139 YCPVCLKVYRDSESTPMVCCDV--CQRWVHCQCDGI 172 (719)
Q Consensus 139 yC~VC~K~Y~dsdgg~MIqCD~--C~~wFH~eCL~l 172 (719)
.|.+|++. .+-.|+|.. |..+||+.|...
T Consensus 57 ~C~iC~~~-----~G~~i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 57 KCSICGKS-----GGACIKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred cCcCCCCC-----CceeEEcCCCCCCcCCCHHHHHH
Confidence 58888764 677899999 999999999753
No 60
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=83.63 E-value=0.37 Score=43.56 Aligned_cols=52 Identities=25% Similarity=0.566 Sum_probs=36.3
Q ss_pred CCCCCc-----cccccccCCCCCceeecCCCCCcccccccCCCCcCCCCCCcccCCCCc
Q 005013 50 KCPSCR-----ICEICRRTGDPNKFMFCRRCDAAYHCYCQHPPHKNVSSGPYLCPKHTK 103 (719)
Q Consensus 50 ~Cp~Cr-----~C~VC~~sgd~~kLL~CdrC~raYH~~CL~PpL~~Ip~g~W~CP~C~~ 103 (719)
.|.-|+ .|..|..+|++-.++.+. |...||..|+..-+..- ...=.||.|+.
T Consensus 23 ~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~-C~H~FH~hCI~kWl~~~-~~~~~CPmCR~ 79 (85)
T PF12861_consen 23 VCGICRMPFDGCCPDCKFPGDDCPLVWGK-CSHNFHMHCILKWLSTQ-SSKGQCPMCRQ 79 (85)
T ss_pred ceeeEecccccCCCCccCCCCCCceeecc-CccHHHHHHHHHHHccc-cCCCCCCCcCC
Confidence 466666 577778888876777666 99999999988544332 22337887754
No 61
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=82.82 E-value=3.9 Score=34.79 Aligned_cols=56 Identities=20% Similarity=0.260 Sum_probs=32.9
Q ss_pred ccceEEEEecC---CCCeeeeeEEEeecCceeEEEEecCCchhhhhcCcceeEeeeccccc
Q 005013 659 IGKRVEVHQQS---DNSWHKGVVTDTVEGTSTLSITLDDSRVKTLELGKQGVRFVPQKQKR 716 (719)
Q Consensus 659 i~krv~v~~~~---d~~w~~g~v~~~~~~~~~~~v~~ddg~~~~~~lgk~~i~~~~~~~k~ 716 (719)
.|-+|||.--- .++|+.|+|....... ++.|+|+|-..+.-. ++.-.+||+.++-|
T Consensus 3 ~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~-~~~V~Y~~~~~~~~~-~~~l~e~V~~~~iR 61 (68)
T PF05641_consen 3 KGDEVEVSSDEDGFRGAWFPATVLKENGDD-KYLVEYDDLPDEDGE-SPPLKEWVDARRIR 61 (68)
T ss_dssp TT-EEEEEE-SBTT--EEEEEEEEEEETT--EEEEEETT-SS---------EEEEEGGGEE
T ss_pred CCCEEEEEEcCCCCCcEEEEEEEEEeCCCc-EEEEEECCccccccc-ccccEEEechheEE
Confidence 68899998533 5799999999999885 699999764432111 00034666665543
No 62
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=80.88 E-value=2.1 Score=45.60 Aligned_cols=46 Identities=11% Similarity=0.218 Sum_probs=35.6
Q ss_pred cccceEEEEecCCCCeeeeeEEEeecCceeEEEEecC-CchhhhhcC
Q 005013 658 AIGKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITLDD-SRVKTLELG 703 (719)
Q Consensus 658 ~i~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~dd-g~~~~~~lg 703 (719)
.||-+....|.-|+.||+++|.+|+....+..|.|+. |..|.+.|.
T Consensus 70 kvGd~C~A~~s~Dg~~Y~A~I~~i~~~~~~~~V~f~gYgn~e~v~l~ 116 (264)
T PF06003_consen 70 KVGDKCMAVYSEDGQYYPATIESIDEEDGTCVVVFTGYGNEEEVNLS 116 (264)
T ss_dssp -TT-EEEEE-TTTSSEEEEEEEEEETTTTEEEEEETTTTEEEEEEGG
T ss_pred CCCCEEEEEECCCCCEEEEEEEEEcCCCCEEEEEEcccCCeEeeehh
Confidence 6999999999889999999999999877779999976 444544444
No 63
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=80.76 E-value=2.3 Score=40.48 Aligned_cols=39 Identities=21% Similarity=0.434 Sum_probs=34.5
Q ss_pred cceEEEEecCCCCeeeeeEEEeecCceeEEEEecCCchhh
Q 005013 660 GKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITLDDSRVKT 699 (719)
Q Consensus 660 ~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~ddg~~~~ 699 (719)
|.+|-.-|..|+-+|-|+|+... ....+.|+|++++...
T Consensus 1 g~~VlAR~~~DG~YY~GtV~~~~-~~~~~lV~f~~~~~~~ 39 (124)
T PF15057_consen 1 GQKVLARREEDGFYYPGTVKKCV-SSGQFLVEFDDGDTQE 39 (124)
T ss_pred CCeEEEeeCCCCcEEeEEEEEcc-CCCEEEEEECCCCEEE
Confidence 67899999999999999999998 6678999998887763
No 64
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=80.67 E-value=0.95 Score=46.26 Aligned_cols=45 Identities=31% Similarity=0.820 Sum_probs=34.4
Q ss_pred CCCCCc----cccccccCCC-----CCceeecCCCCCcccccccCCCCcCCCCCCcccCCCCc
Q 005013 50 KCPSCR----ICEICRRTGD-----PNKFMFCRRCDAAYHCYCQHPPHKNVSSGPYLCPKHTK 103 (719)
Q Consensus 50 ~Cp~Cr----~C~VC~~sgd-----~~kLL~CdrC~raYH~~CL~PpL~~Ip~g~W~CP~C~~ 103 (719)
.|+.|. +|.+|....- .+....|..|...||..|... -.||.|.+
T Consensus 144 ~C~lC~~kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~---------~~CpkC~R 197 (202)
T PF13901_consen 144 SCELCQQKGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK---------KSCPKCAR 197 (202)
T ss_pred HhHHHHhCCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC---------CCCCCcHh
Confidence 688887 8999986532 236789999999999999983 12888754
No 65
>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=80.47 E-value=0.27 Score=37.95 Aligned_cols=43 Identities=33% Similarity=0.787 Sum_probs=28.3
Q ss_pred ccccccccccCCCCCCceeccCCCCeeccCCCCCChHHHhhhccCCCCceeCCCCC
Q 005013 139 YCPVCLKVYRDSESTPMVCCDVCQRWVHCQCDGISDEKYLQFQVDGNLQYRCPTCR 194 (719)
Q Consensus 139 yC~VC~K~Y~dsdgg~MIqCD~C~~wFH~eCL~lsdEkye~~~id~d~~Y~CptCr 194 (719)
.|+||...+.+. ..++... |.+.||.+|+.. |.+. ...||.||
T Consensus 2 ~C~IC~~~~~~~--~~~~~l~-C~H~fh~~Ci~~----~~~~------~~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDG--EKVVKLP-CGHVFHRSCIKE----WLKR------NNSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTT--SCEEEET-TSEEEEHHHHHH----HHHH------SSB-TTTH
T ss_pred CCcCCChhhcCC--CeEEEcc-CCCeeCHHHHHH----HHHh------CCcCCccC
Confidence 488898877552 3345555 999999999652 2222 35999996
No 66
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=77.66 E-value=0.88 Score=36.78 Aligned_cols=45 Identities=29% Similarity=0.842 Sum_probs=26.9
Q ss_pred CCccCcCCccCCcccCCceE-EeC--cCCCcchhhhcCCCcccccccCCCCCCCCCC
Q 005013 1 MCRLCFVGENEGCERARRML-SCK--SCGKKYHRNCLKNWAQNRDLFHWSSWKCPSC 54 (719)
Q Consensus 1 ~C~iC~~Ce~~Gse~~eeLL-~Cd--~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~C 54 (719)
+|.||+..+..+ +.|+ .|. +--+.+|..||..|.... ..-.|+.|
T Consensus 1 ~CrIC~~~~~~~----~~l~~PC~C~G~~~~vH~~Cl~~W~~~~-----~~~~C~iC 48 (49)
T smart00744 1 ICRICHDEGDEG----DPLVSPCRCKGSLKYVHQECLERWINES-----GNKTCEIC 48 (49)
T ss_pred CccCCCCCCCCC----CeeEeccccCCchhHHHHHHHHHHHHHc-----CCCcCCCC
Confidence 589998722222 2333 333 223789999999997643 22366665
No 67
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=77.61 E-value=5.3 Score=31.86 Aligned_cols=42 Identities=19% Similarity=0.424 Sum_probs=33.1
Q ss_pred ccceEEEEecCCCCeeeeeEEEeecCceeEEEEecCCchhhhhcC
Q 005013 659 IGKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITLDDSRVKTLELG 703 (719)
Q Consensus 659 i~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~ddg~~~~~~lg 703 (719)
+||+|+|.. .+..++|++..++.. ..|.|+.+||..+++--|
T Consensus 2 lG~~V~v~~--~~~~~~G~~~gId~~-G~L~v~~~~g~~~~i~sG 43 (48)
T PF02237_consen 2 LGQEVRVET--GDGEIEGIAEGIDDD-GALLVRTEDGSIRTISSG 43 (48)
T ss_dssp TTSEEEEEE--TSCEEEEEEEEEETT-SEEEEEETTEEEEEESSS
T ss_pred CCCEEEEEE--CCeEEEEEEEEECCC-CEEEEEECCCCEEEEEEE
Confidence 799999998 556669999999653 459999999976665433
No 68
>PHA02929 N1R/p28-like protein; Provisional
Probab=77.35 E-value=1.3 Score=46.73 Aligned_cols=26 Identities=27% Similarity=0.971 Sum_probs=20.4
Q ss_pred CcCCCcchhhhcCCCcccccccCCCCCCCCCCc
Q 005013 23 KSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR 55 (719)
Q Consensus 23 d~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr 55 (719)
..|++.||..|+..|.... -.||.|+
T Consensus 198 ~~C~H~FC~~CI~~Wl~~~-------~tCPlCR 223 (238)
T PHA02929 198 SNCNHVFCIECIDIWKKEK-------NTCPVCR 223 (238)
T ss_pred CCCCCcccHHHHHHHHhcC-------CCCCCCC
Confidence 4799999999999886532 2688886
No 69
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=76.44 E-value=1.7 Score=39.50 Aligned_cols=33 Identities=30% Similarity=0.887 Sum_probs=23.8
Q ss_pred ceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCc
Q 005013 18 RMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR 55 (719)
Q Consensus 18 eLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr 55 (719)
.|+.+. |+..||.-||..|..... ..=.||-|+
T Consensus 46 plv~g~-C~H~FH~hCI~kWl~~~~----~~~~CPmCR 78 (85)
T PF12861_consen 46 PLVWGK-CSHNFHMHCILKWLSTQS----SKGQCPMCR 78 (85)
T ss_pred ceeecc-CccHHHHHHHHHHHcccc----CCCCCCCcC
Confidence 466555 999999999999876421 233788885
No 70
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=76.03 E-value=3.2 Score=47.68 Aligned_cols=72 Identities=22% Similarity=0.290 Sum_probs=52.1
Q ss_pred cccccccccccccCCCCCCceeccCCCCeeccCCCCCChHHHhhhccCCCCceeCCCCCCCC----CCCCchHHHHHHhh
Q 005013 136 KGNYCPVCLKVYRDSESTPMVCCDVCQRWVHCQCDGISDEKYLQFQVDGNLQYRCPTCRGEC----YQVRDLEDAVRELW 211 (719)
Q Consensus 136 K~nyC~VC~K~Y~dsdgg~MIqCD~C~~wFH~eCL~lsdEkye~~~id~d~~Y~CptCr~~~----~qIk~~kda~~r~W 211 (719)
...+|++|.+ ++.++.|+.|...+|..|.+...+ .-.|.|.+|+... ..+.|..-+.+.||
T Consensus 88 ~~~~c~vc~~------ggs~v~~~s~~~~~~r~c~~~~~~---------~c~~~~~d~~~~~~~~~~~~vw~~vg~~~~~ 152 (463)
T KOG1081|consen 88 EPSECFVCFK------GGSLVTCKSRIQAPHRKCKPAQLE---------KCSKRCTDCRAFKKREVGDLVWSKVGEYPWW 152 (463)
T ss_pred CcchhccccC------CCccceeccccccccccCcCccCc---------ccccCCcceeeeccccceeEEeEEcCccccc
Confidence 4457888874 788999999999999999885333 3467777776543 23567777778999
Q ss_pred cccccccHHHH
Q 005013 212 RRKDMADKDLI 222 (719)
Q Consensus 212 rare~~~r~lI 222 (719)
+...+.+..+.
T Consensus 153 ~c~vc~~~~~~ 163 (463)
T KOG1081|consen 153 PCMVCHDPLLP 163 (463)
T ss_pred ccceecCcccc
Confidence 97777765444
No 71
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=75.21 E-value=1.8 Score=49.02 Aligned_cols=6 Identities=33% Similarity=1.320 Sum_probs=3.2
Q ss_pred eeccCC
Q 005013 156 VCCDVC 161 (719)
Q Consensus 156 IqCD~C 161 (719)
|.|..|
T Consensus 453 llCk~C 458 (468)
T KOG1701|consen 453 LLCKTC 458 (468)
T ss_pred eeechh
Confidence 445555
No 72
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=74.60 E-value=2.2 Score=47.05 Aligned_cols=92 Identities=21% Similarity=0.430 Sum_probs=50.8
Q ss_pred CCCCCcccCCCCc--------cCCCCCCCCCCCCccc-cccCcccc-CCCcc--ccccccccccccccccCCCCCCceec
Q 005013 91 VSSGPYLCPKHTK--------CHSCGSNVPGNGLSVR-WFLGYTCC-DACGR--LFVKGNYCPVCLKVYRDSESTPMVCC 158 (719)
Q Consensus 91 Ip~g~W~CP~C~~--------C~sCg~r~pgki~s~R-W~~~~slC-~aC~~--lfvK~nyC~VC~K~Y~dsdgg~MIqC 158 (719)
+..+.++||.|.. |..|+........-.| +++=+++= ..... ...+.++|+.|+.- ..+..-.+|
T Consensus 272 ~~~~Gy~CP~CkakvCsLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~---~~~~~~y~C 348 (378)
T KOG2807|consen 272 LSGGGYFCPQCKAKVCSLPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGE---LLSSGRYRC 348 (378)
T ss_pred cccCceeCCcccCeeecCCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccc---cCCCCcEEc
Confidence 4467899999964 5566644322111111 11111110 11111 12244568899422 224556889
Q ss_pred cCCCCeeccCCCCCChHHHhhhccCCCCceeCCCCCC
Q 005013 159 DVCQRWVHCQCDGISDEKYLQFQVDGNLQYRCPTCRG 195 (719)
Q Consensus 159 D~C~~wFH~eCL~lsdEkye~~~id~d~~Y~CptCr~ 195 (719)
..|...|-.+|+-...+. --.||.|..
T Consensus 349 ~~Ck~~FCldCDv~iHes----------Lh~CpgCeh 375 (378)
T KOG2807|consen 349 ESCKNVFCLDCDVFIHES----------LHNCPGCEH 375 (378)
T ss_pred hhccceeeccchHHHHhh----------hhcCCCcCC
Confidence 999999999998743332 367999973
No 73
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=73.96 E-value=11 Score=30.88 Aligned_cols=49 Identities=20% Similarity=0.433 Sum_probs=37.4
Q ss_pred cccceEEEEecCCCCeeeeeEEEeecC--ceeEEEEecCCchhhhhcCcceeEeeeccc
Q 005013 658 AIGKRVEVHQQSDNSWHKGVVTDTVEG--TSTLSITLDDSRVKTLELGKQGVRFVPQKQ 714 (719)
Q Consensus 658 ~i~krv~v~~~~d~~w~~g~v~~~~~~--~~~~~v~~ddg~~~~~~lgk~~i~~~~~~~ 714 (719)
.||-+|-|.+ .++.||++.|.++... .-...|-|. |=-+.+| |||+..+
T Consensus 2 ~vG~~v~~~~-~~~~~y~A~I~~~r~~~~~~~YyVHY~-g~nkR~D------eWV~~~~ 52 (55)
T PF11717_consen 2 EVGEKVLCKY-KDGQWYEAKILDIREKNGEPEYYVHYQ-GWNKRLD------EWVPESR 52 (55)
T ss_dssp -TTEEEEEEE-TTTEEEEEEEEEEEECTTCEEEEEEET-TSTGCC-------EEEETTT
T ss_pred CcCCEEEEEE-CCCcEEEEEEEEEEecCCCEEEEEEcC-CCCCCce------eeecHHH
Confidence 4899999999 9999999999999654 367889998 4444444 7887654
No 74
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=73.78 E-value=2.5 Score=48.26 Aligned_cols=36 Identities=28% Similarity=0.662 Sum_probs=29.6
Q ss_pred CCCCCCccccccccCCCC---CceeecCCCCCcccccccC
Q 005013 49 WKCPSCRICEICRRTGDP---NKFMFCRRCDAAYHCYCQH 85 (719)
Q Consensus 49 W~Cp~Cr~C~VC~~sgd~---~kLL~CdrC~raYH~~CL~ 85 (719)
=+|..| .|.+|.+.... ...+.|+.|+.|-|..|.-
T Consensus 124 gFC~~C-~C~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCAL 162 (446)
T PF07227_consen 124 GFCRRC-MCCICSKFDDNKNTCSWIGCDVCGHWCHLDCAL 162 (446)
T ss_pred CccccC-CccccCCcccCCCCeeEEeccCCCceehhhhhc
Confidence 469999 99999875432 3589999999999999965
No 75
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=72.22 E-value=2.3 Score=35.64 Aligned_cols=31 Identities=26% Similarity=0.721 Sum_probs=25.4
Q ss_pred cccccccCCC-CCceeecCCCCCcccccccCC
Q 005013 56 ICEICRRTGD-PNKFMFCRRCDAAYHCYCQHP 86 (719)
Q Consensus 56 ~C~VC~~sgd-~~kLL~CdrC~raYH~~CL~P 86 (719)
.|.+|++.-. .+..++|..|+.-||..|...
T Consensus 7 ~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred cChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 5777787664 457999999999999999863
No 76
>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=72.18 E-value=3.5 Score=32.78 Aligned_cols=37 Identities=27% Similarity=0.430 Sum_probs=27.0
Q ss_pred ccccccccccccccCCCCCCceeccCCCCeeccCCCCC
Q 005013 135 VKGNYCPVCLKVYRDSESTPMVCCDVCQRWVHCQCDGI 172 (719)
Q Consensus 135 vK~nyC~VC~K~Y~dsdgg~MIqCD~C~~wFH~eCL~l 172 (719)
.+..+|.+|.+..-. .....+.|..|...+|..|...
T Consensus 9 ~~~~~C~~C~~~i~g-~~~~g~~C~~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWG-LGKQGYRCSWCGLVCHKKCLSK 45 (53)
T ss_dssp SSTEB-TTSSSBECS-SSSCEEEETTTT-EEETTGGCT
T ss_pred CCCCCCcccCcccCC-CCCCeEEECCCCChHhhhhhhh
Confidence 355678888877533 4567789999999999999874
No 77
>KOG1169 consensus Diacylglycerol kinase [Lipid transport and metabolism; Signal transduction mechanisms]
Probab=70.09 E-value=4.6 Score=48.02 Aligned_cols=70 Identities=20% Similarity=0.403 Sum_probs=45.3
Q ss_pred ceEEeCcCCCcchhhhcCCCcccccc------------------cCC----CCCCCCCCc-cccccccCCCCCceeecCC
Q 005013 18 RMLSCKSCGKKYHRNCLKNWAQNRDL------------------FHW----SSWKCPSCR-ICEICRRTGDPNKFMFCRR 74 (719)
Q Consensus 18 eLL~Cd~CgksYH~~CL~p~~e~~~~------------------~~~----~~W~Cp~Cr-~C~VC~~sgd~~kLL~Cdr 74 (719)
.-+.|+.|+-.+|..|........+. ... ..-.|..|. +|.+|+.... ..++|+.
T Consensus 57 ~~~~~~~~g~~~~~~~~~~~~s~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~c~~c~~~c~~~~~~~~--~g~~C~~ 134 (634)
T KOG1169|consen 57 PSVDCDVDGGVSHEECVSGAASDCPLLVLLGFENQRHKTDGDHVWRPKHLWKPAYCFVCPKSCGSCGVGIK--QGLCCDW 134 (634)
T ss_pred cccceeccccchhhhhhcccccchHHHHHHHhhhhhhhccCceeccCCCCCCCceEEeccccccchhhccc--Cceeecc
Confidence 57899999999999999775321000 001 122344443 5555554432 5799999
Q ss_pred CCCcccccccCCCCc
Q 005013 75 CDAAYHCYCQHPPHK 89 (719)
Q Consensus 75 C~raYH~~CL~PpL~ 89 (719)
|+.-.|..|+....+
T Consensus 135 C~~~vh~~C~~~~~~ 149 (634)
T KOG1169|consen 135 CGRTVHERCVRRADP 149 (634)
T ss_pred ccchHHHHHHhhcCc
Confidence 999999999985443
No 78
>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=69.49 E-value=2.5 Score=30.87 Aligned_cols=32 Identities=28% Similarity=0.866 Sum_probs=23.0
Q ss_pred ceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCc
Q 005013 18 RMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR 55 (719)
Q Consensus 18 eLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr 55 (719)
..+.-..|+..||..|+..+... ....||.|+
T Consensus 11 ~~~~~~~C~H~~c~~C~~~~~~~------~~~~Cp~C~ 42 (45)
T cd00162 11 EPVVLLPCGHVFCRSCIDKWLKS------GKNTCPLCR 42 (45)
T ss_pred CceEecCCCChhcHHHHHHHHHh------CcCCCCCCC
Confidence 34455579999999999876542 345788874
No 79
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 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 domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=69.43 E-value=1.1 Score=38.78 Aligned_cols=26 Identities=35% Similarity=1.092 Sum_probs=19.9
Q ss_pred CcCCCcchhhhcCCCcccccccCCCCCCCCCCc
Q 005013 23 KSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR 55 (719)
Q Consensus 23 d~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr 55 (719)
..|+..||..||..|.... ..||-|+
T Consensus 48 ~~C~H~FH~~Ci~~Wl~~~-------~~CP~CR 73 (73)
T PF12678_consen 48 GPCGHIFHFHCISQWLKQN-------NTCPLCR 73 (73)
T ss_dssp ETTSEEEEHHHHHHHHTTS-------SB-TTSS
T ss_pred cccCCCEEHHHHHHHHhcC-------CcCCCCC
Confidence 4799999999999887532 3798885
No 80
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=68.07 E-value=2 Score=46.00 Aligned_cols=58 Identities=21% Similarity=0.505 Sum_probs=31.2
Q ss_pred CcccccccCCC--CcC---CCCCCcccCCCCc---cCCCCCC-CCCC-----CCccccccCccccCCCcccc
Q 005013 77 AAYHCYCQHPP--HKN---VSSGPYLCPKHTK---CHSCGSN-VPGN-----GLSVRWFLGYTCCDACGRLF 134 (719)
Q Consensus 77 raYH~~CL~Pp--L~~---Ip~g~W~CP~C~~---C~sCg~r-~pgk-----i~s~RW~~~~slC~aC~~lf 134 (719)
..||..|..-. +.. .-.+..+|+.|.- |..|+.- .|.. ...-.|+..-..|..|.+-|
T Consensus 160 H~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~CekPF 231 (332)
T KOG2272|consen 160 HPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKPF 231 (332)
T ss_pred CccceecccccccccchhhhhccceeccccccccCCcccccccCchHHHHHHHhccccchhheeehhcCCcc
Confidence 46777776532 111 1256789988864 2233321 1211 12345888778887776543
No 81
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=67.93 E-value=4.3 Score=34.82 Aligned_cols=25 Identities=32% Similarity=0.474 Sum_probs=21.8
Q ss_pred eeeeEEEeecCceeEEEEecCCchhhh
Q 005013 674 HKGVVTDTVEGTSTLSITLDDSRVKTL 700 (719)
Q Consensus 674 ~~g~v~~~~~~~~~~~v~~ddg~~~~~ 700 (719)
-+|+|++|+..+ +.|+||||+.-.|
T Consensus 5 veG~I~~id~~~--~titLdDGksy~l 29 (61)
T PF07076_consen 5 VEGTIKSIDPET--MTITLDDGKSYKL 29 (61)
T ss_pred ceEEEEEEcCCc--eEEEecCCCEEEC
Confidence 389999999999 9999999987644
No 82
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=67.54 E-value=4.2 Score=50.12 Aligned_cols=47 Identities=36% Similarity=0.986 Sum_probs=41.1
Q ss_pred cccccccCCCCCceeecCCCCCcccccccCCCCcCCCCCCcccCCCCc
Q 005013 56 ICEICRRTGDPNKFMFCRRCDAAYHCYCQHPPHKNVSSGPYLCPKHTK 103 (719)
Q Consensus 56 ~C~VC~~sgd~~kLL~CdrC~raYH~~CL~PpL~~Ip~g~W~CP~C~~ 103 (719)
.|..|.+...+ .++.|+.|...||..|..+++..++.+.|.|+.|..
T Consensus 157 ~~~~~~k~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 203 (904)
T KOG1246|consen 157 QCNTCSKGKEE-KLLLCDSCDDSYHTYCLRPPLTRVPDGDWRCPKCIP 203 (904)
T ss_pred hhhccccCCCc-cceecccccCcccccccCCCCCcCCcCcccCCcccc
Confidence 67778877766 555999999999999999999999999999999865
No 83
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=65.61 E-value=1.5 Score=51.50 Aligned_cols=47 Identities=28% Similarity=0.723 Sum_probs=33.4
Q ss_pred CCCCCc----cccccccCCCC-----CceeecCCCCCcccccccCCCCcCCCCCCcccCCCCc
Q 005013 50 KCPSCR----ICEICRRTGDP-----NKFMFCRRCDAAYHCYCQHPPHKNVSSGPYLCPKHTK 103 (719)
Q Consensus 50 ~Cp~Cr----~C~VC~~sgd~-----~kLL~CdrC~raYH~~CL~PpL~~Ip~g~W~CP~C~~ 103 (719)
.|..|. +|.+|....-. .....|..|..+||..|+.-... .||.|.+
T Consensus 503 ~C~lC~~~gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r~s~-------~CPrC~R 558 (580)
T KOG1829|consen 503 ECDLCTGKGFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRRKSP-------CCPRCER 558 (580)
T ss_pred hchhhccCeeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhccCC-------CCCchHH
Confidence 588887 78888443322 24578999999999999984321 2888865
No 84
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []. Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
Probab=63.33 E-value=13 Score=32.57 Aligned_cols=56 Identities=14% Similarity=0.243 Sum_probs=37.3
Q ss_pred hCcccccceEEEEecCCCCeeeeeEEEeecCceeEEEEe-cCCchhhhhcCcceeEeeec
Q 005013 654 LGKDAIGKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITL-DDSRVKTLELGKQGVRFVPQ 712 (719)
Q Consensus 654 lg~~~i~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~-ddg~~~~~~lgk~~i~~~~~ 712 (719)
+-...+|.-+-+.-+.|+.||-|+| ..........|.| |-|..+++. ...|+.+|.
T Consensus 49 ~~~~~~~~~~~~~~~~~~~w~Ra~I-~~~~~~~~~~V~~iD~G~~~~v~--~~~l~~l~~ 105 (121)
T PF00567_consen 49 SPESNPGEGCLCVVSEDGRWYRAVI-TVDIDENQYKVFLIDYGNTEKVS--ASDLRPLPP 105 (121)
T ss_dssp CST--TTEEEEEEETTTSEEEEEEE-EEEECTTEEEEEETTTTEEEEEE--GGGEEE--H
T ss_pred ccccccCCEEEEEEecCCceeeEEE-EEecccceeEEEEEecCceEEEc--HHHhhhhCH
Confidence 3455688888888899999999999 4444444477765 778887744 446777663
No 85
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=63.31 E-value=2.8 Score=36.65 Aligned_cols=28 Identities=29% Similarity=0.916 Sum_probs=23.8
Q ss_pred cccccccC-CCCCceeecCC--CCCcccccccCC
Q 005013 56 ICEICRRT-GDPNKFMFCRR--CDAAYHCYCQHP 86 (719)
Q Consensus 56 ~C~VC~~s-gd~~kLL~Cdr--C~raYH~~CL~P 86 (719)
.|.+|++. | -.+.|.. |.+.||..|...
T Consensus 38 ~C~~C~~~~G---a~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 38 KCSICKKKGG---ACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred CCcCCCCCCC---eEEEEeCCCCCcEEChHHHcc
Confidence 78888988 6 6888885 999999999874
No 86
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=62.19 E-value=5 Score=46.81 Aligned_cols=48 Identities=25% Similarity=0.476 Sum_probs=39.2
Q ss_pred cCcCCccCCcccCCceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCcccc
Q 005013 4 LCFVGENEGCERARRMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCRICE 58 (719)
Q Consensus 4 iC~~Ce~~Gse~~eeLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr~C~ 58 (719)
+|+.|.-+| ..+.|..|.+.||..|+.+.++.+.. ...|.|+.|..|.
T Consensus 62 ~cfechlpg-----~vl~c~vc~Rs~h~~c~sp~~q~r~~--s~p~~~p~p~s~k 109 (588)
T KOG3612|consen 62 FCFECHLPG-----AVLKCIVCHRSFHENCQSPDPQKRNY--SVPSDKPQPYSFK 109 (588)
T ss_pred ccccccCCc-----ceeeeehhhccccccccCcchhhccc--cccccCCcccccC
Confidence 688888777 79999999999999999998775542 4679998886663
No 87
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=61.64 E-value=4.5 Score=44.90 Aligned_cols=39 Identities=26% Similarity=0.695 Sum_probs=31.4
Q ss_pred CceeccCCCCeeccCC--CCCChHHHhhhccCCCCceeCCCCCCCC
Q 005013 154 PMVCCDVCQRWVHCQC--DGISDEKYLQFQVDGNLQYRCPTCRGEC 197 (719)
Q Consensus 154 ~MIqCD~C~~wFH~eC--L~lsdEkye~~~id~d~~Y~CptCr~~~ 197 (719)
-|++|+.|..|||.+| +++... ..+....|+|..|....
T Consensus 74 ~~~~cd~C~~~~~~ec~~v~~~~~-----e~p~~~~~~c~~c~~~~ 114 (345)
T KOG1632|consen 74 LMEQCDLCEDWYHGECWEVGTAEK-----EAPKEDPKVCDECKEAQ 114 (345)
T ss_pred hhhccccccccccccccccCchhh-----cCCccccccccccchhh
Confidence 6899999999999999 886533 34556789999997654
No 88
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=61.02 E-value=3 Score=44.02 Aligned_cols=90 Identities=26% Similarity=0.473 Sum_probs=47.2
Q ss_pred cccccccccCCCCCCceeccCCCCeeccCCCCCChHHHhhhccC-CCCceeCCCCCCCCCCCCchHHHHHHhhccccccc
Q 005013 140 CPVCLKVYRDSESTPMVCCDVCQRWVHCQCDGISDEKYLQFQVD-GNLQYRCPTCRGECYQVRDLEDAVRELWRRKDMAD 218 (719)
Q Consensus 140 C~VC~K~Y~dsdgg~MIqCD~C~~wFH~eCL~lsdEkye~~~id-~d~~Y~CptCr~~~~qIk~~kda~~r~Wrare~~~ 218 (719)
|.+|.-.....+...++ |-..||=.|++. ....+..+ -...|.||.|..+-....++-.-+. ...
T Consensus 53 C~LC~t~La~gdt~RLv----CyhlfHW~Clne---raA~lPanTAPaGyqCP~Cs~eiFPp~NlvsPva-------~aL 118 (299)
T KOG3970|consen 53 CRLCNTPLASGDTTRLV----CYHLFHWKCLNE---RAANLPANTAPAGYQCPCCSQEIFPPINLVSPVA-------EAL 118 (299)
T ss_pred CceeCCccccCcceeeh----hhhhHHHHHhhH---HHhhCCCcCCCCcccCCCCCCccCCCccccchhH-------HHH
Confidence 33454433333433343 778999999873 22222111 1347999999987543222110000 011
Q ss_pred H---HHHHHHHHHcCCCCccccccCCCC
Q 005013 219 K---DLIASLRAAAGLPTEDEIFSISPY 243 (719)
Q Consensus 219 r---~lI~slR~~~GLp~~eei~s~~P~ 243 (719)
+ ....=-|+..|||-+.|+.+..|.
T Consensus 119 re~L~qvNWaRagLGLpll~E~~sp~p~ 146 (299)
T KOG3970|consen 119 REQLKQVNWARAGLGLPLLPELNSPVPS 146 (299)
T ss_pred HHHHHhhhHHhhccCCccchhhcCCCCC
Confidence 1 222234777899988888665554
No 89
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=59.64 E-value=4.1 Score=35.15 Aligned_cols=55 Identities=24% Similarity=0.533 Sum_probs=19.8
Q ss_pred ccccccccccCCCCCCceecc--CCCCeeccCCCCCChHHHhhhccCC----CCceeCCCCCCC
Q 005013 139 YCPVCLKVYRDSESTPMVCCD--VCQRWVHCQCDGISDEKYLQFQVDG----NLQYRCPTCRGE 196 (719)
Q Consensus 139 yC~VC~K~Y~dsdgg~MIqCD--~C~~wFH~eCL~lsdEkye~~~id~----d~~Y~CptCr~~ 196 (719)
.|+||.....+.+..+.+.|+ .|..-||..||.. -+......+ ...-.||.|+..
T Consensus 4 ~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~---wf~~~~~~~~~~~~~~G~CP~C~~~ 64 (70)
T PF11793_consen 4 ECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSE---WFLSLEKSRQSFIPIFGECPYCSSP 64 (70)
T ss_dssp S-SSS--SS-TT-----B--S-TT----B-SGGGHH---HHHHHHSSS-TTT--EEE-TTT-SE
T ss_pred CCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHH---HHHHcccCCeeecccccCCcCCCCe
Confidence 588887654434445567787 8999999999751 111111111 124579999863
No 90
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=58.64 E-value=7.1 Score=45.97 Aligned_cols=43 Identities=28% Similarity=0.816 Sum_probs=23.0
Q ss_pred ccccccCccccCCCccccccccc-----cccccccccCCCCCCceeccCCCC
Q 005013 117 SVRWFLGYTCCDACGRLFVKGNY-----CPVCLKVYRDSESTPMVCCDVCQR 163 (719)
Q Consensus 117 s~RW~~~~slC~aC~~lfvK~ny-----C~VC~K~Y~dsdgg~MIqCD~C~~ 163 (719)
..+|+.....|..|.... .+.| =+.|.+.|+...+ |.|..|.+
T Consensus 153 d~qwhv~cfkc~~c~~vL-~gey~skdg~pyce~dy~~~fg---vkc~~c~~ 200 (670)
T KOG1044|consen 153 DKQWHVSCFKCKSCSAVL-NGEYMSKDGVPYCEKDYQAKFG---VKCEECEK 200 (670)
T ss_pred ccceeeeeeehhhhcccc-cceeeccCCCcchhhhhhhhcC---eehHHhhh
Confidence 456777777777776432 2222 3444454544333 55666654
No 91
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=56.52 E-value=7.7 Score=46.85 Aligned_cols=48 Identities=21% Similarity=0.499 Sum_probs=32.1
Q ss_pred cccccccCCCCCceeecCCCCCcccccccCCCCcCCCCCCcccCCCCccC
Q 005013 56 ICEICRRTGDPNKFMFCRRCDAAYHCYCQHPPHKNVSSGPYLCPKHTKCH 105 (719)
Q Consensus 56 ~C~VC~~sgd~~kLL~CdrC~raYH~~CL~PpL~~Ip~g~W~CP~C~~C~ 105 (719)
-|.+|+-+-++ --+.|..|..-| +.|+..+.+-...--|.||.|..|.
T Consensus 1119 dc~~cg~~i~~-~~~~c~ec~~kf-P~CiasG~pIt~~~fWlC~~CkH~a 1166 (1189)
T KOG2041|consen 1119 DCSVCGAKIDP-YDLQCSECQTKF-PVCIASGRPITDNIFWLCPRCKHRA 1166 (1189)
T ss_pred eeeecCCcCCc-cCCCChhhcCcC-ceeeccCCccccceEEEcccccccc
Confidence 67777776655 357888888766 5677754433334479999986644
No 92
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=56.09 E-value=7.6 Score=42.77 Aligned_cols=63 Identities=17% Similarity=0.461 Sum_probs=40.0
Q ss_pred ceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCc------------------------------cccccccCCCC-
Q 005013 18 RMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR------------------------------ICEICRRTGDP- 66 (719)
Q Consensus 18 eLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr------------------------------~C~VC~~sgd~- 66 (719)
.+..|..|.-++|.-=+.. .+.....|+|.-|. +| .|..+.++
T Consensus 67 ~agvC~~C~~~CH~~H~lv-----eL~tKR~FrCDCg~sk~g~~sc~l~~~~~~~n~~N~YNhNfqG~~C-~Cd~~Ypdp 140 (345)
T KOG2752|consen 67 MAGVCYACSLSCHDGHELV-----ELYTKRNFRCDCGNSKFGRCSCNLLEDKDAENSENLYNHNFQGLFC-KCDTPYPDP 140 (345)
T ss_pred hceeEEEeeeeecCCceee-----eccccCCcccccccccccccccccccccccccchhhhhhhhcceeE-EecCCCCCc
Confidence 6778888887777632221 12234567776554 33 34444332
Q ss_pred -----CceeecCCCCCccc-ccccCC
Q 005013 67 -----NKFMFCRRCDAAYH-CYCQHP 86 (719)
Q Consensus 67 -----~kLL~CdrC~raYH-~~CL~P 86 (719)
..|++|.-|.-||| ..|++.
T Consensus 141 ~~~~e~~m~QC~iCEDWFHce~c~~~ 166 (345)
T KOG2752|consen 141 VRTEEGEMLQCVICEDWFHCEGCMQA 166 (345)
T ss_pred cccccceeeeEEeccchhcccccCcc
Confidence 26999999999999 788874
No 93
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=55.58 E-value=3.6 Score=46.36 Aligned_cols=25 Identities=24% Similarity=0.761 Sum_probs=20.7
Q ss_pred CCceEEeCcCCCcchhhhcCCCccc
Q 005013 16 ARRMLSCKSCGKKYHRNCLKNWAQN 40 (719)
Q Consensus 16 ~eeLL~Cd~CgksYH~~CL~p~~e~ 40 (719)
..+|-.-..||..||..||..|.+.
T Consensus 17 ~~~l~~i~~cGhifh~~cl~qwfe~ 41 (465)
T KOG0827|consen 17 DHELGPIGTCGHIFHTTCLTQWFEG 41 (465)
T ss_pred ccccccccchhhHHHHHHHHHHHcc
Confidence 3466666789999999999999874
No 94
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=55.23 E-value=27 Score=34.47 Aligned_cols=40 Identities=20% Similarity=0.258 Sum_probs=30.5
Q ss_pred ccccceEEEEecCCCCeeeeeEEEeecCceeEEEEecCCch
Q 005013 657 DAIGKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITLDDSRV 697 (719)
Q Consensus 657 ~~i~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~ddg~~ 697 (719)
-.|||.|.... .|+.=..|+|.+|....+...+.++||..
T Consensus 90 ~lIGk~V~~~~-~~g~~~tG~V~sV~~~~~~~~~~v~d~~~ 129 (140)
T PRK11911 90 NFIGKDIKGVS-LNGEVISGKVESVQQTTNGVMLKLKDNDS 129 (140)
T ss_pred HhhCceeEEEe-cCCCEEEEEEEEEEEcCCceEEEEEcCCE
Confidence 56999998544 55666899999998777778887777654
No 95
>KOG1169 consensus Diacylglycerol kinase [Lipid transport and metabolism; Signal transduction mechanisms]
Probab=54.83 E-value=2.9 Score=49.59 Aligned_cols=100 Identities=19% Similarity=0.322 Sum_probs=56.2
Q ss_pred cccccccCCCCCceeecCCCCCcccccccCCCCcCCCCCCcccCCCCccC-CCCCCCCCCCCccccccC----ccccCCC
Q 005013 56 ICEICRRTGDPNKFMFCRRCDAAYHCYCQHPPHKNVSSGPYLCPKHTKCH-SCGSNVPGNGLSVRWFLG----YTCCDAC 130 (719)
Q Consensus 56 ~C~VC~~sgd~~kLL~CdrC~raYH~~CL~PpL~~Ip~g~W~CP~C~~C~-sCg~r~pgki~s~RW~~~----~slC~aC 130 (719)
+|.+|.. ......+.|+.|+..+|..|..+.....+ +..|. .+... -...-.+-|... ..+|..|
T Consensus 46 ~~~~~~~-~~~~~~~~~~~~g~~~~~~~~~~~~s~~~--------~~~~~~~~~~~-~k~~~~~~~~~~~~~~~~~c~~c 115 (634)
T KOG1169|consen 46 VCCVCLW-SEMAPSVDCDVDGGVSHEECVSGAASDCP--------LLVLLGFENQR-HKTDGDHVWRPKHLWKPAYCFVC 115 (634)
T ss_pred hhhhhhh-cccccccceeccccchhhhhhcccccchH--------HHHHHHhhhhh-hhccCceeccCCCCCCCceEEec
Confidence 5666666 22335688999999999999986543221 11111 11110 000111123221 2234444
Q ss_pred ccccccccccccccccccCCCCCCceeccCCCCeeccCCCCCChHH
Q 005013 131 GRLFVKGNYCPVCLKVYRDSESTPMVCCDVCQRWVHCQCDGISDEK 176 (719)
Q Consensus 131 ~~lfvK~nyC~VC~K~Y~dsdgg~MIqCD~C~~wFH~eCL~lsdEk 176 (719)
. ++|.+|.- ...+.++|+-|..-+|..|.....++
T Consensus 116 ~------~~c~~~~~-----~~~~g~~C~~C~~~vh~~C~~~~~~~ 150 (634)
T KOG1169|consen 116 P------KSCGSCGV-----GIKQGLCCDWCGRTVHERCVRRADPE 150 (634)
T ss_pred c------ccccchhh-----cccCceeeccccchHHHHHHhhcCcc
Confidence 3 35555542 23678999999999999999855544
No 96
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=53.97 E-value=8.1 Score=36.06 Aligned_cols=47 Identities=36% Similarity=0.894 Sum_probs=33.5
Q ss_pred ceEEe------CcC---CCcchhhhcCCCccc--ccccCCCCCCCCCCc---cccccccCC
Q 005013 18 RMLSC------KSC---GKKYHRNCLKNWAQN--RDLFHWSSWKCPSCR---ICEICRRTG 64 (719)
Q Consensus 18 eLL~C------d~C---gksYH~~CL~p~~e~--~~~~~~~~W~Cp~Cr---~C~VC~~sg 64 (719)
..+.| ..| ...|-..||...... ...+....|.||.|+ .|..|.+..
T Consensus 20 ~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~CrgiCnCs~Crrk~ 80 (105)
T PF10497_consen 20 FKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGICNCSFCRRKR 80 (105)
T ss_pred CceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCCeeCCHhhhccC
Confidence 45677 677 899999999765432 122345789999999 777787654
No 97
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=53.41 E-value=19 Score=34.62 Aligned_cols=39 Identities=15% Similarity=0.320 Sum_probs=28.8
Q ss_pred cccccceEEEEe--cC-CCCeeeeeEEEeecCceeEEEEecCCc
Q 005013 656 KDAIGKRVEVHQ--QS-DNSWHKGVVTDTVEGTSTLSITLDDSR 696 (719)
Q Consensus 656 ~~~i~krv~v~~--~~-d~~w~~g~v~~~~~~~~~~~v~~ddg~ 696 (719)
.-+||+.|+|.. |. ...|+.|.+.++++.+ +.++++++.
T Consensus 83 ~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~~~--i~l~~~~~~ 124 (141)
T PF02576_consen 83 ERFIGRKVKVKLKQPVNGRKEFEGKLLEVDEDE--ITLEVEGKG 124 (141)
T ss_dssp HHH-SEEEEEE-SS-SSS-SEEEEEEEEEETTE--EEEEEE-SS
T ss_pred HHhcCCeEEEEEeccCCCcEEEEEEEEEEeCCE--EEEEECCcc
Confidence 468999999997 33 4479999999999988 888888774
No 98
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=52.99 E-value=14 Score=43.87 Aligned_cols=32 Identities=34% Similarity=0.772 Sum_probs=26.9
Q ss_pred CCCCCCCCc---------cccccccCCCCCceeecCCCCCcccc
Q 005013 47 SSWKCPSCR---------ICEICRRTGDPNKFMFCRRCDAAYHC 81 (719)
Q Consensus 47 ~~W~Cp~Cr---------~C~VC~~sgd~~kLL~CdrC~raYH~ 81 (719)
..--|+.|+ .|..|+..+ +.+.|+.|+..++.
T Consensus 52 ~~~pc~~c~gkG~V~v~~~c~~c~G~g---kv~~c~~cG~~~~~ 92 (715)
T COG1107 52 FEIPCPKCRGKGTVTVYDTCPECGGTG---KVLTCDICGDIIVP 92 (715)
T ss_pred CCCCCCeeccceeEEEEeecccCCCce---eEEeeccccceecC
Confidence 345799999 899999888 89999999998863
No 99
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=52.40 E-value=13 Score=43.09 Aligned_cols=31 Identities=26% Similarity=0.688 Sum_probs=22.0
Q ss_pred CceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCc
Q 005013 17 RRMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR 55 (719)
Q Consensus 17 eeLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr 55 (719)
..|++|..|.+-=...|+.... ..|+||.|-
T Consensus 3 ~~L~fC~~C~~irc~~c~~~Ei--------~~~yCp~CL 33 (483)
T PF05502_consen 3 EELYFCEHCHKIRCPRCVSEEI--------DSYYCPNCL 33 (483)
T ss_pred ccceecccccccCChhhccccc--------ceeECcccc
Confidence 4688898888777777776532 347777773
No 100
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=52.34 E-value=9.8 Score=33.24 Aligned_cols=30 Identities=20% Similarity=0.720 Sum_probs=23.0
Q ss_pred cCcCCccC-CcccCCceEEeC--cCCCcchhhhcCCCc
Q 005013 4 LCFVGENE-GCERARRMLSCK--SCGKKYHRNCLKNWA 38 (719)
Q Consensus 4 iC~~Ce~~-Gse~~eeLL~Cd--~CgksYH~~CL~p~~ 38 (719)
.|..|+.. | -.|.|. .|.+.||..|.....
T Consensus 38 ~C~~C~~~~G-----a~i~C~~~~C~~~fH~~CA~~~~ 70 (90)
T PF13771_consen 38 KCSICKKKGG-----ACIGCSHPGCSRSFHVPCARKAG 70 (90)
T ss_pred CCcCCCCCCC-----eEEEEeCCCCCcEEChHHHccCC
Confidence 45555554 5 699997 799999999998753
No 101
>PRK09618 flgD flagellar basal body rod modification protein; Provisional
Probab=51.36 E-value=36 Score=33.74 Aligned_cols=79 Identities=27% Similarity=0.281 Sum_probs=49.8
Q ss_pred CCCccccccccccchhhhhhhhhchhhhhhhhHHHHHHh---------CcccccceEEEEecCCCCeeeeeEEEeecCce
Q 005013 616 RPSPFTEKTLFNEDEDAAQSNQDSLMSEIMDANWILKKL---------GKDAIGKRVEVHQQSDNSWHKGVVTDTVEGTS 686 (719)
Q Consensus 616 r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~il~~l---------g~~~i~krv~v~~~~d~~w~~g~v~~~~~~~~ 686 (719)
-|..|+| ..+=++|--|=|..+.|..-|=-|..| ..-.|||.|.+- -.|..=..|+|+.|.-..+
T Consensus 44 DPl~P~D-----~tefiaQlAQfs~lEq~~~~n~~l~~l~~~~~~~~~a~slVGk~V~~~-~~~g~~~tG~V~~V~~~~g 117 (142)
T PRK09618 44 DPTNPME-----DKEFIAQMAQFSSLEQMTNMNKSMEKLVSSSDGLTKYSELIGKEVEWE-GEDGEIVSGTVTSVKQKDG 117 (142)
T ss_pred CCCCCCC-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhCCEEEEE-eCCCCEEEEEEEEEEEcCC
Confidence 3666666 334455555544444444444444444 345799999876 3567788999999975555
Q ss_pred eEEEEecCCchhhh
Q 005013 687 TLSITLDDSRVKTL 700 (719)
Q Consensus 687 ~~~v~~ddg~~~~~ 700 (719)
...+-++||.+-.|
T Consensus 118 ~~~~~~v~G~~~~l 131 (142)
T PRK09618 118 DYPLVLDNGTWIVA 131 (142)
T ss_pred cEEEEEECCEEEec
Confidence 56667788865443
No 102
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=51.06 E-value=7.9 Score=42.66 Aligned_cols=11 Identities=27% Similarity=1.059 Sum_probs=9.2
Q ss_pred CCCCCCCCCCc
Q 005013 45 HWSSWKCPSCR 55 (719)
Q Consensus 45 ~~~~W~Cp~Cr 55 (719)
..+++.||.|+
T Consensus 305 ~~gGy~CP~Ck 315 (421)
T COG5151 305 KGGGYECPVCK 315 (421)
T ss_pred ccCceeCCccc
Confidence 45889999996
No 103
>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=49.74 E-value=9.6 Score=33.59 Aligned_cols=29 Identities=31% Similarity=0.827 Sum_probs=21.2
Q ss_pred ccccccCccccCCCccccccccccccccc
Q 005013 117 SVRWFLGYTCCDACGRLFVKGNYCPVCLK 145 (719)
Q Consensus 117 s~RW~~~~slC~aC~~lfvK~nyC~VC~K 145 (719)
.++|..+...|..|...|....+||-|..
T Consensus 10 ~L~~~~~~~~C~~C~~~~~~~a~CPdC~~ 38 (70)
T PF07191_consen 10 ELEWQGGHYHCEACQKDYKKEAFCPDCGQ 38 (70)
T ss_dssp BEEEETTEEEETTT--EEEEEEE-TTT-S
T ss_pred ccEEeCCEEECccccccceecccCCCccc
Confidence 36788888889999999999999999975
No 104
>PRK14637 hypothetical protein; Provisional
Probab=49.54 E-value=19 Score=35.61 Aligned_cols=42 Identities=24% Similarity=0.387 Sum_probs=31.6
Q ss_pred ccccceEEEEecCCCCeeeeeEEEeecCceeEEEEecCCchhhhh
Q 005013 657 DAIGKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITLDDSRVKTLE 701 (719)
Q Consensus 657 ~~i~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~ddg~~~~~~ 701 (719)
-++|+.|+|-+...+.|.+|++.++++++ +.+.. +|+...+.
T Consensus 95 r~~G~~V~V~l~~~~~~~~G~L~~~~d~~--v~l~~-~~~~~~i~ 136 (151)
T PRK14637 95 IFVGETVKVWFECTGQWQVGTIAEADETC--LVLTS-DGVPVTIP 136 (151)
T ss_pred HhCCCEEEEEECCCCcEEEEEEEEEeCCE--EEEEE-CCEEEEEE
Confidence 47999999987567899999999999987 55554 45443333
No 105
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=48.89 E-value=6.5 Score=46.47 Aligned_cols=37 Identities=24% Similarity=0.565 Sum_probs=24.3
Q ss_pred CCccCcCCccCCcccCCceEEeCcCCCcchhhhcCCC
Q 005013 1 MCRLCFVGENEGCERARRMLSCKSCGKKYHRNCLKNW 37 (719)
Q Consensus 1 ~C~iC~~Ce~~Gse~~eeLL~Cd~CgksYH~~CL~p~ 37 (719)
+|.+|...+.--....+....|..|+..||..|+.-.
T Consensus 513 iCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r~ 549 (580)
T KOG1829|consen 513 ICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRRK 549 (580)
T ss_pred eeeeccCCCcccccccccceeHHHHHHHHHHHHHhcc
Confidence 3566644333222223456889999999999999753
No 106
>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=46.35 E-value=7.3 Score=28.19 Aligned_cols=29 Identities=31% Similarity=0.693 Sum_probs=12.2
Q ss_pred cccccccCCCCCceeecCCCCCccccccc
Q 005013 56 ICEICRRTGDPNKFMFCRRCDAAYHCYCQ 84 (719)
Q Consensus 56 ~C~VC~~sgd~~kLL~CdrC~raYH~~CL 84 (719)
.|.+|+.+......-.|..|+-..|..|.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhcC
Confidence 57888988765467789999999998874
No 107
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=46.12 E-value=5.2 Score=42.75 Aligned_cols=59 Identities=27% Similarity=0.512 Sum_probs=26.2
Q ss_pred cccccccccc-----cCCC--CCCceeccCCCCeec------cCCCCCChHHHhhhcc---CCCCceeCCCCCCC
Q 005013 138 NYCPVCLKVY-----RDSE--STPMVCCDVCQRWVH------CQCDGISDEKYLQFQV---DGNLQYRCPTCRGE 196 (719)
Q Consensus 138 nyC~VC~K~Y-----~dsd--gg~MIqCD~C~~wFH------~eCL~lsdEkye~~~i---d~d~~Y~CptCr~~ 196 (719)
.+||||+... ...+ |...+.|..|...+| +.|.+.....|..|.. +....+.|..|.+-
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~Y 247 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSY 247 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---SS-EEE--------SEEEEEETTTTEE
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccch
Confidence 5788887653 2222 557888999988877 3454433333333311 12236889999754
No 108
>PHA02926 zinc finger-like protein; Provisional
Probab=44.71 E-value=11 Score=39.81 Aligned_cols=33 Identities=30% Similarity=0.687 Sum_probs=23.8
Q ss_pred cCCCcchhhhcCCCcccccccCCCCCCCCCCccc
Q 005013 24 SCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCRIC 57 (719)
Q Consensus 24 ~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr~C 57 (719)
.|++.|+..|+..|..... .......||.|+..
T Consensus 196 ~CnHsFCl~CIr~Wr~~r~-~~~~~rsCPiCR~~ 228 (242)
T PHA02926 196 SCNHIFCITCINIWHRTRR-ETGASDNCPICRTR 228 (242)
T ss_pred CCCchHHHHHHHHHHHhcc-ccCcCCcCCCCcce
Confidence 7999999999999876432 12235678888644
No 109
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=44.07 E-value=5.9 Score=44.56 Aligned_cols=17 Identities=47% Similarity=1.165 Sum_probs=14.9
Q ss_pred cCCCcchhhhcCCCccc
Q 005013 24 SCGKKYHRNCLKNWAQN 40 (719)
Q Consensus 24 ~CgksYH~~CL~p~~e~ 40 (719)
.||+-+|..||+.|.+.
T Consensus 317 pCGHilHl~CLknW~ER 333 (491)
T COG5243 317 PCGHILHLHCLKNWLER 333 (491)
T ss_pred cccceeeHHHHHHHHHh
Confidence 59999999999998764
No 110
>PRK06009 flgD flagellar basal body rod modification protein; Reviewed
Probab=43.80 E-value=44 Score=33.06 Aligned_cols=43 Identities=28% Similarity=0.358 Sum_probs=31.8
Q ss_pred CcccccceEEEEecCCCCeeeeeEEEeecCceeEEEEecCCchhhhh
Q 005013 655 GKDAIGKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITLDDSRVKTLE 701 (719)
Q Consensus 655 g~~~i~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~ddg~~~~~~ 701 (719)
+.-.|||.|.+ .|+. ..|+|++|.-........++||.+-.|+
T Consensus 92 a~slIGk~V~~---~~~~-~~G~V~sV~~~~~~~~~~~~dg~~v~l~ 134 (140)
T PRK06009 92 AEGLIGRTVTS---ADGS-ITGVVKSVTVYSDGVIATLEDGKKVLLG 134 (140)
T ss_pred HHHhcCCEEEe---cCCc-EEEEEEEEEEeCCceEEEEECCEEEEeC
Confidence 34579999986 3444 7999999975555588889999876554
No 111
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 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 domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=43.44 E-value=8.6 Score=33.30 Aligned_cols=29 Identities=28% Similarity=0.769 Sum_probs=18.5
Q ss_pred eeccCCCCeeccCCCCCChHHHhhhccCCCCceeCCCCC
Q 005013 156 VCCDVCQRWVHCQCDGISDEKYLQFQVDGNLQYRCPTCR 194 (719)
Q Consensus 156 IqCD~C~~wFH~eCL~lsdEkye~~~id~d~~Y~CptCr 194 (719)
+.=..|.+.||..|+. .+.. ..-.||.||
T Consensus 45 i~~~~C~H~FH~~Ci~----~Wl~------~~~~CP~CR 73 (73)
T PF12678_consen 45 IVWGPCGHIFHFHCIS----QWLK------QNNTCPLCR 73 (73)
T ss_dssp EEEETTSEEEEHHHHH----HHHT------TSSB-TTSS
T ss_pred eEecccCCCEEHHHHH----HHHh------cCCcCCCCC
Confidence 3335699999999974 1211 123999996
No 112
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=43.22 E-value=13 Score=28.67 Aligned_cols=35 Identities=23% Similarity=0.471 Sum_probs=25.6
Q ss_pred ccccccccccccCCCCCCceeccCCCCeeccCCCCC
Q 005013 137 GNYCPVCLKVYRDSESTPMVCCDVCQRWVHCQCDGI 172 (719)
Q Consensus 137 ~nyC~VC~K~Y~dsdgg~MIqCD~C~~wFH~eCL~l 172 (719)
..+|.+|.+..... ...-+.|..|...+|..|...
T Consensus 11 ~~~C~~C~~~i~~~-~~~~~~C~~C~~~~H~~C~~~ 45 (50)
T cd00029 11 PTFCDVCRKSIWGL-FKQGLRCSWCKVKCHKKCADK 45 (50)
T ss_pred CCChhhcchhhhcc-ccceeEcCCCCCchhhhhhcc
Confidence 45677887764332 245678999999999999863
No 113
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=43.11 E-value=9.8 Score=28.99 Aligned_cols=34 Identities=26% Similarity=0.413 Sum_probs=24.8
Q ss_pred ccccccccccccCCCCCCceeccCCCCeeccCCCCC
Q 005013 137 GNYCPVCLKVYRDSESTPMVCCDVCQRWVHCQCDGI 172 (719)
Q Consensus 137 ~nyC~VC~K~Y~dsdgg~MIqCD~C~~wFH~eCL~l 172 (719)
..+|.+|.+...... +.+.|..|...+|..|...
T Consensus 11 ~~~C~~C~~~i~~~~--~~~~C~~C~~~~H~~C~~~ 44 (49)
T smart00109 11 PTKCCVCRKSIWGSF--QGLRCSWCKVKCHKKCAEK 44 (49)
T ss_pred CCCccccccccCcCC--CCcCCCCCCchHHHHHHhh
Confidence 456888877543221 4688999999999999763
No 114
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=42.64 E-value=14 Score=42.22 Aligned_cols=41 Identities=29% Similarity=0.612 Sum_probs=31.8
Q ss_pred CCCceeccCCCCeeccCCCCCChHHHhhhccCCCCceeCCCCCCCCCC
Q 005013 152 STPMVCCDVCQRWVHCQCDGISDEKYLQFQVDGNLQYRCPTCRGECYQ 199 (719)
Q Consensus 152 gg~MIqCD~C~~wFH~eCL~lsdEkye~~~id~d~~Y~CptCr~~~~q 199 (719)
++-|++|+.|..|-|.-|.+.... .....|.|..|+.....
T Consensus 98 ~g~~i~c~~c~~Wqh~~C~g~~~~-------~~p~~y~c~~c~~~~~~ 138 (508)
T KOG1844|consen 98 EGLMIQCDWCGRWQHKICCGSFKS-------TKPDKYVCEICTPRNKE 138 (508)
T ss_pred CceeeCCcccCcccCceeeeecCC-------CCchhceeeeecccccc
Confidence 778999999999999999985322 11247999999976543
No 115
>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=40.47 E-value=11 Score=28.40 Aligned_cols=30 Identities=23% Similarity=0.835 Sum_probs=21.8
Q ss_pred ceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCC
Q 005013 18 RMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSC 54 (719)
Q Consensus 18 eLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~C 54 (719)
+-+....||+.|+..|+..+... ...||.|
T Consensus 10 ~~~~~~~CGH~fC~~C~~~~~~~-------~~~CP~C 39 (39)
T PF13923_consen 10 DPVVVTPCGHSFCKECIEKYLEK-------NPKCPVC 39 (39)
T ss_dssp SEEEECTTSEEEEHHHHHHHHHC-------TSB-TTT
T ss_pred CcCEECCCCCchhHHHHHHHHHC-------cCCCcCC
Confidence 45567899999999999876543 2468766
No 116
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=40.34 E-value=13 Score=25.89 Aligned_cols=26 Identities=31% Similarity=1.051 Sum_probs=18.9
Q ss_pred CcCCCcchhhhcCCCcccccccCCCCCCCCCC
Q 005013 23 KSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSC 54 (719)
Q Consensus 23 d~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~C 54 (719)
..|+..||..|+..+.. .....||.|
T Consensus 14 ~~C~H~~c~~C~~~~~~------~~~~~CP~C 39 (39)
T smart00184 14 LPCGHTFCRSCIRKWLK------SGNNTCPIC 39 (39)
T ss_pred ecCCChHHHHHHHHHHH------hCcCCCCCC
Confidence 46999999999987654 133457765
No 117
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.40 E-value=17 Score=40.72 Aligned_cols=45 Identities=20% Similarity=0.480 Sum_probs=33.5
Q ss_pred cccccccCCCCCceeecCCCCCcccccccCCCCcCCCCCCcccCCCCc
Q 005013 56 ICEICRRTGDPNKFMFCRRCDAAYHCYCQHPPHKNVSSGPYLCPKHTK 103 (719)
Q Consensus 56 ~C~VC~~sgd~~kLL~CdrC~raYH~~CL~PpL~~Ip~g~W~CP~C~~ 103 (719)
.|.+|-+....+..++=--|...||..|++|=+.. .+-+||-|..
T Consensus 231 ~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~---~r~~CPvCK~ 275 (348)
T KOG4628|consen 231 TCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQ---TRTFCPVCKR 275 (348)
T ss_pred eEEEeecccccCCeeeEecCCCchhhccchhhHhh---cCccCCCCCC
Confidence 78899887766666666889999999999975432 2446887754
No 118
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=38.12 E-value=24 Score=43.08 Aligned_cols=25 Identities=24% Similarity=0.388 Sum_probs=15.9
Q ss_pred HHHHHcCCCCccccccCCCCCCCCC
Q 005013 224 SLRAAAGLPTEDEIFSISPYSDDEE 248 (719)
Q Consensus 224 slR~~~GLp~~eei~s~~P~sdDe~ 248 (719)
..|+..+|||..-+.-+.-.+.+++
T Consensus 625 ~~Rk~~~~PPf~~l~~v~~~~~~~~ 649 (730)
T COG1198 625 AERKELGLPPFSRLAAVIASAKNEE 649 (730)
T ss_pred HHHHhcCCCChhhheeeEecCCCHH
Confidence 5677888887777655444444444
No 119
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=38.10 E-value=23 Score=41.10 Aligned_cols=31 Identities=23% Similarity=0.582 Sum_probs=20.8
Q ss_pred ceeecCCCCCcccccccCCCCcCCCCCCcccCCCCc
Q 005013 68 KFMFCRRCDAAYHCYCQHPPHKNVSSGPYLCPKHTK 103 (719)
Q Consensus 68 kLL~CdrC~raYH~~CL~PpL~~Ip~g~W~CP~C~~ 103 (719)
.|.+|..|...-...|+...+ ..||||+|..
T Consensus 4 ~L~fC~~C~~irc~~c~~~Ei-----~~~yCp~CL~ 34 (483)
T PF05502_consen 4 ELYFCEHCHKIRCPRCVSEEI-----DSYYCPNCLF 34 (483)
T ss_pred cceecccccccCChhhccccc-----ceeECccccc
Confidence 466777777776677776322 3588888864
No 120
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=37.84 E-value=42 Score=26.23 Aligned_cols=29 Identities=14% Similarity=0.350 Sum_probs=25.0
Q ss_pred CCCeeeeeEEEeecCceeEEEEecCCchhhh
Q 005013 670 DNSWHKGVVTDTVEGTSTLSITLDDSRVKTL 700 (719)
Q Consensus 670 d~~w~~g~v~~~~~~~~~~~v~~ddg~~~~~ 700 (719)
...|-.|.|.+..++. +.|++.||++.++
T Consensus 10 ~egfv~g~I~~~~g~~--vtV~~~~G~~~tv 38 (42)
T PF02736_consen 10 KEGFVKGEIIEEEGDK--VTVKTEDGKEVTV 38 (42)
T ss_dssp SSSEEEEEEEEEESSE--EEEEETTTEEEEE
T ss_pred cccEEEEEEEEEcCCE--EEEEECCCCEEEe
Confidence 4589999999888887 9999999987765
No 121
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=36.28 E-value=43 Score=27.27 Aligned_cols=36 Identities=33% Similarity=0.429 Sum_probs=28.9
Q ss_pred cccccceEEEEecCCCCeeeeeEEEeecCceeEEEEecCC
Q 005013 656 KDAIGKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITLDDS 695 (719)
Q Consensus 656 ~~~i~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~ddg 695 (719)
++++|++|.|.. .|+.=|.|++.+||.-. -+.+.|-
T Consensus 2 ~~~~g~~V~V~l-~~g~~~~G~L~~~D~~~---Ni~L~~~ 37 (63)
T cd00600 2 KDLVGKTVRVEL-KDGRVLEGVLVAFDKYM---NLVLDDV 37 (63)
T ss_pred hHHCCCEEEEEE-CCCcEEEEEEEEECCCC---CEEECCE
Confidence 357999999999 78899999999999765 3445554
No 122
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=35.90 E-value=7.8 Score=42.70 Aligned_cols=47 Identities=26% Similarity=0.492 Sum_probs=31.3
Q ss_pred ccccccccccC--------CCCCCceeccCCCCeeccCCCCCChHHHhhhccCCCCceeCCCCCC
Q 005013 139 YCPVCLKVYRD--------SESTPMVCCDVCQRWVHCQCDGISDEKYLQFQVDGNLQYRCPTCRG 195 (719)
Q Consensus 139 yC~VC~K~Y~d--------sdgg~MIqCD~C~~wFH~eCL~lsdEkye~~~id~d~~Y~CptCr~ 195 (719)
.|++|+..+.. .......+|+.|..-|-.+|+-...+. --+|+.|+-
T Consensus 364 ~Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~----------Lh~C~gCe~ 418 (421)
T COG5151 364 HCFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHET----------LHFCIGCEL 418 (421)
T ss_pred cceeccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHHH----------HhhCCCCcC
Confidence 49999876521 112345689999999999998643331 256888863
No 123
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=35.75 E-value=22 Score=36.49 Aligned_cols=43 Identities=26% Similarity=0.542 Sum_probs=29.1
Q ss_pred ccCCCcccccccccccccccc--ccCCCCCCceeccCCCCeeccCCCC
Q 005013 126 CCDACGRLFVKGNYCPVCLKV--YRDSESTPMVCCDVCQRWVHCQCDG 171 (719)
Q Consensus 126 lC~aC~~lfvK~nyC~VC~K~--Y~dsdgg~MIqCD~C~~wFH~eCL~ 171 (719)
.|..|. .++-.|-+|... .-+=+....+.|..|...||..|..
T Consensus 144 ~C~lC~---~kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~ 188 (202)
T PF13901_consen 144 SCELCQ---QKGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFR 188 (202)
T ss_pred HhHHHH---hCCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcC
Confidence 555564 367778888642 1111123567899999999999975
No 124
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.33 E-value=10 Score=41.13 Aligned_cols=79 Identities=20% Similarity=0.372 Sum_probs=46.7
Q ss_pred cccccccccccccCCCCCC-ce---eccCCCCeeccCCCCCChHHHhhhccCCCCceeCCCCCCCCCCCCchHHHHHHhh
Q 005013 136 KGNYCPVCLKVYRDSESTP-MV---CCDVCQRWVHCQCDGISDEKYLQFQVDGNLQYRCPTCRGECYQVRDLEDAVRELW 211 (719)
Q Consensus 136 K~nyC~VC~K~Y~dsdgg~-MI---qCD~C~~wFH~eCL~lsdEkye~~~id~d~~Y~CptCr~~~~qIk~~kda~~r~W 211 (719)
..+.|.||++....+.+.+ .| -=-.|.+.||..|..- +-.. ...=.||.|+.. .+++......|
T Consensus 223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrG----Wciv----GKkqtCPYCKek----Vdl~rmfsnpW 290 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRG----WCIV----GKKQTCPYCKEK----VDLKRMFSNPW 290 (328)
T ss_pred CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhh----heee----cCCCCCchHHHH----hhHhhhccCcc
Confidence 4456888887654332111 11 1235999999999861 0001 124579999864 23455555667
Q ss_pred cccccccHHHHHHHH
Q 005013 212 RRKDMADKDLIASLR 226 (719)
Q Consensus 212 rare~~~r~lI~slR 226 (719)
...+.....++.-||
T Consensus 291 ekph~~yg~LldwlR 305 (328)
T KOG1734|consen 291 EKPHVWYGQLLDWLR 305 (328)
T ss_pred ccchhHHHHHHHHHH
Confidence 777777776666665
No 125
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=35.32 E-value=46 Score=27.60 Aligned_cols=29 Identities=24% Similarity=0.283 Sum_probs=25.1
Q ss_pred cccccceEEEEecCCCCeeeeeEEEeecCc
Q 005013 656 KDAIGKRVEVHQQSDNSWHKGVVTDTVEGT 685 (719)
Q Consensus 656 ~~~i~krv~v~~~~d~~w~~g~v~~~~~~~ 685 (719)
++++|++|.|.. -|+.=+.|++.+||.-.
T Consensus 4 ~~~~g~~V~V~l-~~g~~~~G~L~~~D~~~ 32 (67)
T PF01423_consen 4 QKLIGKRVRVEL-KNGRTYRGTLVSFDQFM 32 (67)
T ss_dssp HHTTTSEEEEEE-TTSEEEEEEEEEEETTE
T ss_pred HHhCCcEEEEEE-eCCEEEEEEEEEeechh
Confidence 357899999999 77888999999999754
No 126
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=34.78 E-value=21 Score=38.65 Aligned_cols=26 Identities=15% Similarity=0.475 Sum_probs=15.2
Q ss_pred ccccccccccCCCCCCceeccCCCCee
Q 005013 139 YCPVCLKVYRDSESTPMVCCDVCQRWV 165 (719)
Q Consensus 139 yC~VC~K~Y~dsdgg~MIqCD~C~~wF 165 (719)
.|.-|.+.. ...++.|+.|..|..|.
T Consensus 127 ~C~EC~R~v-w~hGGrif~CsfC~~fl 152 (314)
T PF06524_consen 127 VCIECERGV-WDHGGRIFKCSFCDNFL 152 (314)
T ss_pred Eeeeeeccc-ccCCCeEEEeecCCCee
Confidence 345555431 23367777788877764
No 127
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=34.57 E-value=23 Score=36.68 Aligned_cols=16 Identities=25% Similarity=0.966 Sum_probs=13.9
Q ss_pred CcCCCcchhhhcCCCc
Q 005013 23 KSCGKKYHRNCLKNWA 38 (719)
Q Consensus 23 d~CgksYH~~CL~p~~ 38 (719)
..|++.|+..|+..|.
T Consensus 34 T~CGH~FC~~CI~~wl 49 (193)
T PLN03208 34 TLCGHLFCWPCIHKWT 49 (193)
T ss_pred cCCCchhHHHHHHHHH
Confidence 5799999999998764
No 128
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=34.33 E-value=26 Score=38.58 Aligned_cols=63 Identities=17% Similarity=0.486 Sum_probs=36.0
Q ss_pred cccccccccccc-------cCCCCCCceeccCCCCeec------cCCCCCChHHHhhhccC--CCCceeCCCCCCCCC
Q 005013 136 KGNYCPVCLKVY-------RDSESTPMVCCDVCQRWVH------CQCDGISDEKYLQFQVD--GNLQYRCPTCRGECY 198 (719)
Q Consensus 136 K~nyC~VC~K~Y-------~dsdgg~MIqCD~C~~wFH------~eCL~lsdEkye~~~id--~d~~Y~CptCr~~~~ 198 (719)
...+||||+..- ...+|...+.|..|...+| +.|.......|..+... ......|..|.+--+
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK 263 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYLK 263 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCCCCceeeeeecCCCcceEeeecccccccce
Confidence 346788887652 1234667788888888877 34444222234322211 123578999986433
No 129
>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=34.31 E-value=27 Score=27.75 Aligned_cols=31 Identities=19% Similarity=0.443 Sum_probs=21.6
Q ss_pred cccccccCC--CCCceeecCCCCCcccccccCC
Q 005013 56 ICEICRRTG--DPNKFMFCRRCDAAYHCYCQHP 86 (719)
Q Consensus 56 ~C~VC~~sg--d~~kLL~CdrC~raYH~~CL~P 86 (719)
.|.+|++.- ....-+.|..|...+|..|+..
T Consensus 13 ~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 13 YCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSK 45 (53)
T ss_dssp B-TTSSSBECSSSSCEEEETTTT-EEETTGGCT
T ss_pred CCcccCcccCCCCCCeEEECCCCChHhhhhhhh
Confidence 455556543 3336799999999999999983
No 130
>PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional
Probab=34.27 E-value=47 Score=35.80 Aligned_cols=42 Identities=19% Similarity=0.327 Sum_probs=33.8
Q ss_pred ccceEEEEecCCCCeeeeeEEEeecCceeEEEEecCCchhhhhcC
Q 005013 659 IGKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITLDDSRVKTLELG 703 (719)
Q Consensus 659 i~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~ddg~~~~~~lg 703 (719)
+|++|+|.. ++..+.|++..++.. +.|.|+.+||..+++.-|
T Consensus 236 ~g~~V~v~~--~~~~~~G~~~gId~~-G~L~i~~~~G~~~~~~sG 277 (285)
T PTZ00275 236 KDKKVLIDQ--DNELIVGYLQGLLHD-GSLLLLREKNKLVRVNTG 277 (285)
T ss_pred CCCEEEEEe--CCCEEEEEEEEECCC-CeEEEEeCCCCEEEEEEE
Confidence 799999975 677899999999753 359999999987766544
No 131
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=33.30 E-value=73 Score=30.54 Aligned_cols=48 Identities=23% Similarity=0.561 Sum_probs=30.8
Q ss_pred cccccccccccCC--------CCCCceeccCCCCeeccCCCCCChHHHhhhccCCCCceeCCCCCC
Q 005013 138 NYCPVCLKVYRDS--------ESTPMVCCDVCQRWVHCQCDGISDEKYLQFQVDGNLQYRCPTCRG 195 (719)
Q Consensus 138 nyC~VC~K~Y~ds--------dgg~MIqCD~C~~wFH~eCL~lsdEkye~~~id~d~~Y~CptCr~ 195 (719)
..|+.|+..+... ......+|..|..-|=.+||-...+ .-..||.|..
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe----------~Lh~CPGC~~ 111 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHE----------SLHCCPGCIH 111 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhh----------hccCCcCCCC
Confidence 4588887765321 1123467999999999999863322 1356888863
No 132
>PRK14633 hypothetical protein; Provisional
Probab=31.91 E-value=61 Score=31.99 Aligned_cols=43 Identities=16% Similarity=0.299 Sum_probs=31.2
Q ss_pred ccccceEEEE--ecC-CCCeeeeeEEEeecCceeEEEEecCCchhhhh
Q 005013 657 DAIGKRVEVH--QQS-DNSWHKGVVTDTVEGTSTLSITLDDSRVKTLE 701 (719)
Q Consensus 657 ~~i~krv~v~--~~~-d~~w~~g~v~~~~~~~~~~~v~~ddg~~~~~~ 701 (719)
-+||++|+|- .|. +...+.|++.+|++++ +.+.+++|+...+.
T Consensus 91 r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~~--i~l~~~~~~~~~i~ 136 (150)
T PRK14633 91 ALVGFNVKAVTLAPVGSQTKFKGVLERVEGNN--VILNLEDGKEISFD 136 (150)
T ss_pred HhCCCeEEEEEecccCCcEEEEEEEEEEeCCE--EEEEEcCCcEEEEE
Confidence 4789998874 453 5689999999999887 66677666443333
No 133
>PF12773 DZR: Double zinc ribbon
Probab=31.68 E-value=42 Score=26.49 Aligned_cols=10 Identities=30% Similarity=0.899 Sum_probs=5.0
Q ss_pred eeecCCCCCc
Q 005013 69 FMFCRRCDAA 78 (719)
Q Consensus 69 LL~CdrC~ra 78 (719)
..+|..|+..
T Consensus 12 ~~fC~~CG~~ 21 (50)
T PF12773_consen 12 AKFCPHCGTP 21 (50)
T ss_pred ccCChhhcCC
Confidence 4555555543
No 134
>KOG4198 consensus RNA-binding Ran Zn-finger protein and related proteins [General function prediction only]
Probab=31.66 E-value=71 Score=34.94 Aligned_cols=21 Identities=29% Similarity=0.822 Sum_probs=15.9
Q ss_pred CCCCCCCCCCc--------cccccccCCC
Q 005013 45 HWSSWKCPSCR--------ICEICRRTGD 65 (719)
Q Consensus 45 ~~~~W~Cp~Cr--------~C~VC~~sgd 65 (719)
.-+.|.|+.|- .|+.|+.+..
T Consensus 61 ~pgdw~c~~c~~~n~arr~~c~~c~~s~~ 89 (280)
T KOG4198|consen 61 RPGDWNCPLCGFHNSARRLLCFRCGFSKV 89 (280)
T ss_pred CCcccccCccchhhHHHhhhcceecccCC
Confidence 34889999987 7888876543
No 135
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=31.49 E-value=12 Score=29.69 Aligned_cols=41 Identities=24% Similarity=0.544 Sum_probs=19.6
Q ss_pred ccccccCCCCCceeecC--CCCCcccccccCCCCcCCCCCCcccCCC
Q 005013 57 CEICRRTGDPNKFMFCR--RCDAAYHCYCQHPPHKNVSSGPYLCPKH 101 (719)
Q Consensus 57 C~VC~~sgd~~kLL~Cd--rC~raYH~~CL~PpL~~Ip~g~W~CP~C 101 (719)
|.+|++-.- .-+.|. .|+..+|..|+.......... .||.|
T Consensus 1 C~~C~~iv~--~G~~C~~~~C~~r~H~~C~~~y~r~~~~~--~CP~C 43 (43)
T PF08746_consen 1 CEACKEIVT--QGQRCSNRDCNVRLHDDCFKKYFRHRSNP--KCPNC 43 (43)
T ss_dssp -TTT-SB-S--SSEE-SS--S--EE-HHHHHHHTTT-SS---B-TTT
T ss_pred CcccchhHe--eeccCCCCccCchHHHHHHHHHHhcCCCC--CCcCC
Confidence 456665432 346788 699999999998654443322 77775
No 136
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=31.20 E-value=45 Score=34.56 Aligned_cols=13 Identities=31% Similarity=0.611 Sum_probs=7.6
Q ss_pred eEEeCcCCCcchh
Q 005013 19 MLSCKSCGKKYHR 31 (719)
Q Consensus 19 LL~Cd~CgksYH~ 31 (719)
-..|..|++.-|.
T Consensus 60 ~~~C~nCg~~GH~ 72 (190)
T COG5082 60 NPVCFNCGQNGHL 72 (190)
T ss_pred ccccchhcccCcc
Confidence 3456666666665
No 137
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=30.96 E-value=59 Score=27.57 Aligned_cols=28 Identities=18% Similarity=0.161 Sum_probs=24.3
Q ss_pred ccccceEEEEecCCCCeeeeeEEEeecCc
Q 005013 657 DAIGKRVEVHQQSDNSWHKGVVTDTVEGT 685 (719)
Q Consensus 657 ~~i~krv~v~~~~d~~w~~g~v~~~~~~~ 685 (719)
+++||+|.|.. .++.=|.|++.+||.-.
T Consensus 7 ~~~~~~V~V~l-~~g~~~~G~L~~~D~~m 34 (68)
T cd01731 7 DSLNKPVLVKL-KGGKEVRGRLKSYDQHM 34 (68)
T ss_pred HhcCCEEEEEE-CCCCEEEEEEEEECCcc
Confidence 45999999999 57788999999999865
No 138
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=30.93 E-value=11 Score=41.21 Aligned_cols=19 Identities=32% Similarity=0.927 Sum_probs=13.5
Q ss_pred ceEEeCcC-------------CCcchhhhcCC
Q 005013 18 RMLSCKSC-------------GKKYHRNCLKN 36 (719)
Q Consensus 18 eLL~Cd~C-------------gksYH~~CL~p 36 (719)
++-.|.+| .+.||..||.-
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkC 63 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKC 63 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcch
Confidence 45578888 46788888864
No 139
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=30.70 E-value=71 Score=28.19 Aligned_cols=36 Identities=25% Similarity=0.351 Sum_probs=26.9
Q ss_pred ccccceEEEEe--cCCC-CeeeeeEEEeecCceeEEEEecC
Q 005013 657 DAIGKRVEVHQ--QSDN-SWHKGVVTDTVEGTSTLSITLDD 694 (719)
Q Consensus 657 ~~i~krv~v~~--~~d~-~w~~g~v~~~~~~~~~~~v~~dd 694 (719)
-++|+.|+|-. |.++ ..+.|.+.++++++ +.+.++.
T Consensus 22 r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~~--v~l~~~~ 60 (83)
T cd01734 22 RAVGKYVHVKLYQPIDGQKEFEGTLLGVDDDT--VTLEVDI 60 (83)
T ss_pred HhCCCEEEEEEEcccCCeEEEEEEEEeEeCCE--EEEEEec
Confidence 46899888853 4444 58899999999987 6666653
No 140
>PRK14639 hypothetical protein; Provisional
Probab=30.58 E-value=67 Score=31.43 Aligned_cols=43 Identities=12% Similarity=0.347 Sum_probs=31.6
Q ss_pred ccccceEEEEecCCCCeeeeeEEEeecCceeEEEEe-cCCchhhhhc
Q 005013 657 DAIGKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITL-DDSRVKTLEL 702 (719)
Q Consensus 657 ~~i~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~-ddg~~~~~~l 702 (719)
-++|+.|+|-.. +...+.|.+.++++.+ +.+++ .+++..++.+
T Consensus 85 r~~G~~v~v~l~-~~~~~~G~L~~~~~~~--i~l~~~~~~~~~~i~~ 128 (140)
T PRK14639 85 KSIGELVKITTN-EKEKFEGKIVSVDDEN--ITLENLENKEKTTINF 128 (140)
T ss_pred HhCCCEEEEEEC-CCcEEEEEEEEEeCCE--EEEEEccCCcEEEEEh
Confidence 579999999763 7899999999999987 66644 4554334433
No 141
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=30.45 E-value=32 Score=23.75 Aligned_cols=9 Identities=44% Similarity=1.767 Sum_probs=6.8
Q ss_pred CCCCCCCCc
Q 005013 47 SSWKCPSCR 55 (719)
Q Consensus 47 ~~W~Cp~Cr 55 (719)
+.|.|+.|.
T Consensus 1 g~W~C~~C~ 9 (26)
T smart00547 1 GDWECPACT 9 (26)
T ss_pred CcccCCCCC
Confidence 369999884
No 142
>PHA02862 5L protein; Provisional
Probab=30.30 E-value=19 Score=35.90 Aligned_cols=22 Identities=23% Similarity=0.576 Sum_probs=16.7
Q ss_pred ceEEeCcCCCcchhhhcCCCcc
Q 005013 18 RMLSCKSCGKKYHRNCLKNWAQ 39 (719)
Q Consensus 18 eLL~Cd~CgksYH~~CL~p~~e 39 (719)
.--.|.+-.+.-|..||..|..
T Consensus 17 ~PC~C~GS~K~VHq~CL~~WIn 38 (156)
T PHA02862 17 NFCGCNEEYKVVHIKCMQLWIN 38 (156)
T ss_pred ccccccCcchhHHHHHHHHHHh
Confidence 3444557789999999998764
No 143
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.19 E-value=16 Score=42.65 Aligned_cols=26 Identities=38% Similarity=1.239 Sum_probs=21.5
Q ss_pred cCCCcchhhhcCCCcccccccCCCCCCCCCCcc
Q 005013 24 SCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCRI 56 (719)
Q Consensus 24 ~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr~ 56 (719)
.|++.||..|+..|.+.. =.||-|+.
T Consensus 313 ~C~Hifh~~CL~~W~er~-------qtCP~CR~ 338 (543)
T KOG0802|consen 313 PCGHIFHDSCLRSWFERQ-------QTCPTCRT 338 (543)
T ss_pred ecccchHHHHHHHHHHHh-------CcCCcchh
Confidence 699999999999998753 26999963
No 144
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=29.95 E-value=36 Score=41.04 Aligned_cols=7 Identities=43% Similarity=1.132 Sum_probs=3.3
Q ss_pred EEeCcCC
Q 005013 20 LSCKSCG 26 (719)
Q Consensus 20 L~Cd~Cg 26 (719)
+.|..|+
T Consensus 2 ~~Cp~Cg 8 (645)
T PRK14559 2 LICPQCQ 8 (645)
T ss_pred CcCCCCC
Confidence 4444444
No 145
>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=29.94 E-value=21 Score=26.71 Aligned_cols=29 Identities=41% Similarity=1.038 Sum_probs=22.0
Q ss_pred EeCcCCCcchhhhcCCCcccccccCCCCCCCCCC
Q 005013 21 SCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSC 54 (719)
Q Consensus 21 ~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~C 54 (719)
.=..|++.|+..|+..+... .....||.|
T Consensus 13 ~~~~C~H~fC~~C~~~~~~~-----~~~~~CP~C 41 (41)
T PF00097_consen 13 ILLPCGHSFCRDCLRKWLEN-----SGSVKCPLC 41 (41)
T ss_dssp EETTTSEEEEHHHHHHHHHH-----TSSSBTTTT
T ss_pred EEecCCCcchHHHHHHHHHh-----cCCccCCcC
Confidence 45589999999999987653 245678876
No 146
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.60 E-value=20 Score=36.94 Aligned_cols=21 Identities=38% Similarity=1.140 Sum_probs=17.5
Q ss_pred eEEeC--cCCCcchhhhcCCCcc
Q 005013 19 MLSCK--SCGKKYHRNCLKNWAQ 39 (719)
Q Consensus 19 LL~Cd--~CgksYH~~CL~p~~e 39 (719)
--.|+ +|++.||.-||..|..
T Consensus 182 DqtCdN~qCgkpFHqiCL~dWLR 204 (234)
T KOG3268|consen 182 DQTCDNIQCGKPFHQICLTDWLR 204 (234)
T ss_pred cccccccccCCcHHHHHHHHHHH
Confidence 44677 9999999999998854
No 147
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=29.57 E-value=36 Score=37.43 Aligned_cols=59 Identities=24% Similarity=0.550 Sum_probs=33.2
Q ss_pred cccccccccc-----cC---CCCCCceeccCCCCeecc------CCCCCChHHHhhhccC----CCCceeCCCCCCC
Q 005013 138 NYCPVCLKVY-----RD---SESTPMVCCDVCQRWVHC------QCDGISDEKYLQFQVD----GNLQYRCPTCRGE 196 (719)
Q Consensus 138 nyC~VC~K~Y-----~d---sdgg~MIqCD~C~~wFH~------eCL~lsdEkye~~~id----~d~~Y~CptCr~~ 196 (719)
.+||||+..- .. .++...+.|..|...+|. .|.+.....|..+..+ .-....|..|.+-
T Consensus 185 ~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~Y 261 (305)
T TIGR01562 185 TLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGY 261 (305)
T ss_pred CcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCCCceeeEeecCCCCCcceEEeeccccccc
Confidence 3788887652 11 345677888888887773 3443222223333211 1235688888764
No 148
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=28.78 E-value=39 Score=25.80 Aligned_cols=27 Identities=26% Similarity=0.566 Sum_probs=14.6
Q ss_pred cccccccccCC-----CCCCceeccCCCCeec
Q 005013 140 CPVCLKVYRDS-----ESTPMVCCDVCQRWVH 166 (719)
Q Consensus 140 C~VC~K~Y~ds-----dgg~MIqCD~C~~wFH 166 (719)
|+-|...|.-. ..+..++|..|.+.|+
T Consensus 5 Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 5 CPNCQAKYEIDDEKIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred CCCCCCEEeCCHHHCCCCCcEEECCCCCCEeC
Confidence 55555555322 2345667777766553
No 149
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=28.61 E-value=25 Score=40.63 Aligned_cols=31 Identities=23% Similarity=0.668 Sum_probs=22.1
Q ss_pred cccccccCCCC-CceeecCCCCCcccccccCC
Q 005013 56 ICEICRRTGDP-NKFMFCRRCDAAYHCYCQHP 86 (719)
Q Consensus 56 ~C~VC~~sgd~-~kLL~CdrC~raYH~~CL~P 86 (719)
+|.||-..=++ ..+++=-.|...||..|+..
T Consensus 177 TCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~ 208 (493)
T KOG0804|consen 177 TCPVCLERMDSSTTGILTILCNHSFHCSCLMK 208 (493)
T ss_pred CcchhHhhcCccccceeeeecccccchHHHhh
Confidence 45555554333 35778888999999999983
No 150
>PRK08330 biotin--protein ligase; Provisional
Probab=27.92 E-value=78 Score=32.82 Aligned_cols=46 Identities=33% Similarity=0.466 Sum_probs=34.0
Q ss_pred cccceEEEEecCCCCe-eeeeEEEeecCceeEEEEecCCchhhhhcCcce
Q 005013 658 AIGKRVEVHQQSDNSW-HKGVVTDTVEGTSTLSITLDDSRVKTLELGKQG 706 (719)
Q Consensus 658 ~i~krv~v~~~~d~~w-~~g~v~~~~~~~~~~~v~~ddg~~~~~~lgk~~ 706 (719)
.+||+|.|.. ++.- ++|++.+++.. +.|.|+.+||..+++.-|.=.
T Consensus 186 ~~g~~v~~~~--~~~~~~~G~~~gI~~~-G~L~v~~~~g~~~~~~~gev~ 232 (236)
T PRK08330 186 ILGKRVKIIG--DGEILVEGIAEDIDEF-GALILRLDDGTVKKVLYGDVS 232 (236)
T ss_pred hcCCeEEEEE--CCcEEEEEEEEEECCC-CEEEEEECCCCEEEEEEEEEE
Confidence 4799999985 3444 47999999753 349999999988776665433
No 151
>PRK02001 hypothetical protein; Validated
Probab=27.90 E-value=78 Score=31.53 Aligned_cols=35 Identities=17% Similarity=0.366 Sum_probs=29.1
Q ss_pred ccccceEEEEecCCCCeeeeeEEEeecCceeEEEEecC
Q 005013 657 DAIGKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITLDD 694 (719)
Q Consensus 657 ~~i~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~dd 694 (719)
-++|+.|+|... +..++.|++.+|++.+ +.+.+++
T Consensus 87 r~~G~~v~V~l~-~~~~~~G~L~~~~~~~--i~l~~~~ 121 (152)
T PRK02001 87 KNIGRELEVLTK-NGKKIEGELKSADEND--ITLEVKA 121 (152)
T ss_pred HhCCCEEEEEEC-CCCEEEEEEEEEeCCE--EEEEEcc
Confidence 579999999874 7899999999999887 6666653
No 152
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=27.69 E-value=32 Score=38.60 Aligned_cols=35 Identities=34% Similarity=0.915 Sum_probs=23.8
Q ss_pred CceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCc---cccccccCCC
Q 005013 17 RRMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR---ICEICRRTGD 65 (719)
Q Consensus 17 eeLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr---~C~VC~~sgd 65 (719)
.+-|.|++|++.- +....+.|..|. +|..|...+.
T Consensus 6 He~v~CdgC~k~~--------------~t~rrYkCL~C~DyDlC~sCyen~~ 43 (381)
T KOG1280|consen 6 HEGVSCDGCGKTA--------------FTFRRYKCLRCSDYDLCFSCYENGA 43 (381)
T ss_pred cCCceeccccccc--------------eeeeeeEeeeecchhHHHHHhhcCC
Confidence 3678999998421 223445677777 8888887664
No 153
>PF13341 RAG2_PHD: RAG2 PHD domain; PDB: 2JWO_A 2V86_B 2V85_B 2V87_A 2V83_C 2V89_A 2V88_A.
Probab=27.40 E-value=39 Score=30.08 Aligned_cols=39 Identities=31% Similarity=0.691 Sum_probs=21.6
Q ss_pred CCceeccC-CCCeeccCCCCCChHHHhhhccCCCCceeCCC
Q 005013 153 TPMVCCDV-CQRWVHCQCDGISDEKYLQFQVDGNLQYRCPT 192 (719)
Q Consensus 153 g~MIqCD~-C~~wFH~eCL~lsdEkye~~~id~d~~Y~Cpt 192 (719)
+-||-|.. =.+|+|..|..+++..+..+.- .+..|+|..
T Consensus 28 PAMI~cs~~~GHWvhaqCm~LsE~~L~~LSq-~n~KYfC~d 67 (78)
T PF13341_consen 28 PAMIFCSRGGGHWVHAQCMDLSETMLIQLSQ-ENTKYFCND 67 (78)
T ss_dssp --EEEE-STT-EEEETGGGT--HHHHHHHHH-SSS-B--TT
T ss_pred ceEEEEeCCCceEeEeecccchHHHHHHHcc-CCceEEEhh
Confidence 34666754 6799999999987766665532 356899976
No 154
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=27.25 E-value=1e+02 Score=26.12 Aligned_cols=35 Identities=20% Similarity=0.274 Sum_probs=27.6
Q ss_pred ccccceEEEEecCCCCeeeeeEEEeecCceeEEEEecCC
Q 005013 657 DAIGKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITLDDS 695 (719)
Q Consensus 657 ~~i~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~ddg 695 (719)
.++|++|.|.. .++.=|.|++.+||.- +-+.++|-
T Consensus 7 ~~~~~~V~V~L-k~g~~~~G~L~~~D~~---mNlvL~~~ 41 (67)
T cd01726 7 AIIGRPVVVKL-NSGVDYRGILACLDGY---MNIALEQT 41 (67)
T ss_pred hhCCCeEEEEE-CCCCEEEEEEEEEccc---eeeEEeeE
Confidence 35999999999 5778899999999964 35555554
No 155
>PRK14634 hypothetical protein; Provisional
Probab=26.97 E-value=79 Score=31.43 Aligned_cols=42 Identities=24% Similarity=0.376 Sum_probs=29.1
Q ss_pred ccccceEEE--EecCC-CCeeeeeEEEeecCceeEEEEecCCchhhhh
Q 005013 657 DAIGKRVEV--HQQSD-NSWHKGVVTDTVEGTSTLSITLDDSRVKTLE 701 (719)
Q Consensus 657 ~~i~krv~v--~~~~d-~~w~~g~v~~~~~~~~~~~v~~ddg~~~~~~ 701 (719)
-++|+.|+| +.|.+ ...++|.+.+|+++. +.+.++ |+..+|.
T Consensus 97 r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~~--v~l~~~-~~~~~i~ 141 (155)
T PRK14634 97 TFRGFPVEVSHRDDDGSEQRLEGLLLERNEDH--LQINIR-GRIKRIP 141 (155)
T ss_pred HhCCCeEEEEEecCCCCeEEEEEEEEEEeCCE--EEEEEC-CEEEEEE
Confidence 478998887 45554 378999999999988 555553 4443343
No 156
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=26.95 E-value=44 Score=41.51 Aligned_cols=35 Identities=34% Similarity=0.906 Sum_probs=28.7
Q ss_pred ceEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCc
Q 005013 18 RMLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR 55 (719)
Q Consensus 18 eLL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr 55 (719)
.++.|+.|...||..|+.+..... ..+.|.|+.|.
T Consensus 168 ~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~ 202 (904)
T KOG1246|consen 168 KLLLCDSCDDSYHTYCLRPPLTRV---PDGDWRCPKCI 202 (904)
T ss_pred cceecccccCcccccccCCCCCcC---CcCcccCCccc
Confidence 344999999999999999987543 45889999983
No 157
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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 zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=26.55 E-value=34 Score=24.70 Aligned_cols=11 Identities=36% Similarity=0.764 Sum_probs=8.4
Q ss_pred CCCcccCCCCc
Q 005013 93 SGPYLCPKHTK 103 (719)
Q Consensus 93 ~g~W~CP~C~~ 103 (719)
.+.|.|+.|..
T Consensus 2 ~g~W~C~~C~~ 12 (30)
T PF00641_consen 2 EGDWKCPSCTF 12 (30)
T ss_dssp SSSEEETTTTE
T ss_pred CcCccCCCCcC
Confidence 46899999864
No 158
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=26.45 E-value=14 Score=46.05 Aligned_cols=50 Identities=30% Similarity=0.656 Sum_probs=34.3
Q ss_pred cccccccccc-CCCCCCceeccCCCCeeccCCCCCChHHHhhhccCCCCceeCCCCCCC
Q 005013 139 YCPVCLKVYR-DSESTPMVCCDVCQRWVHCQCDGISDEKYLQFQVDGNLQYRCPTCRGE 196 (719)
Q Consensus 139 yC~VC~K~Y~-dsdgg~MIqCD~C~~wFH~eCL~lsdEkye~~~id~d~~Y~CptCr~~ 196 (719)
-|++|.-+.. -+...|--.|.+|.+-||..|+- ..|.. .+.-.||.||.+
T Consensus 1471 ECaICYsvL~~vdr~lPskrC~TCknKFH~~CLy------KWf~S--s~~s~CPlCRse 1521 (1525)
T COG5219 1471 ECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLY------KWFAS--SARSNCPLCRSE 1521 (1525)
T ss_pred hhhHHHHHHHHHhccCCccccchhhhhhhHHHHH------HHHHh--cCCCCCCccccc
Confidence 4888876543 12234556799999999999963 33322 346789999964
No 159
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=26.15 E-value=44 Score=39.44 Aligned_cols=47 Identities=26% Similarity=0.496 Sum_probs=35.0
Q ss_pred cccccccCCCCCceeecCCCCCcccccccCCCCcCC-CCCCcccCCCCccC
Q 005013 56 ICEICRRTGDPNKFMFCRRCDAAYHCYCQHPPHKNV-SSGPYLCPKHTKCH 105 (719)
Q Consensus 56 ~C~VC~~sgd~~kLL~CdrC~raYH~~CL~PpL~~I-p~g~W~CP~C~~C~ 105 (719)
+|+-|.-++ ..+.|..|-+.||..|+.|.-... ....|.||.|..|.
T Consensus 62 ~cfechlpg---~vl~c~vc~Rs~h~~c~sp~~q~r~~s~p~~~p~p~s~k 109 (588)
T KOG3612|consen 62 FCFECHLPG---AVLKCIVCHRSFHENCQSPDPQKRNYSVPSDKPQPYSFK 109 (588)
T ss_pred ccccccCCc---ceeeeehhhccccccccCcchhhccccccccCCcccccC
Confidence 445556666 889999999999999999754322 34579999876644
No 160
>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=25.93 E-value=45 Score=24.09 Aligned_cols=17 Identities=24% Similarity=0.745 Sum_probs=9.0
Q ss_pred ceEEeCcCCCcchhhhc
Q 005013 18 RMLSCKSCGKKYHRNCL 34 (719)
Q Consensus 18 eLL~Cd~CgksYH~~CL 34 (719)
....|..|.-..|..|+
T Consensus 14 ~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 14 WFYRCSECDFDLHEECA 30 (30)
T ss_dssp -EEE-TTT-----HHHH
T ss_pred ceEECccCCCccChhcC
Confidence 68999999999999985
No 161
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=25.72 E-value=44 Score=37.36 Aligned_cols=19 Identities=37% Similarity=0.857 Sum_probs=13.5
Q ss_pred CCCCCcccCCCCc--cCCCCC
Q 005013 91 VSSGPYLCPKHTK--CHSCGS 109 (719)
Q Consensus 91 Ip~g~W~CP~C~~--C~sCg~ 109 (719)
.+...+.|+.|.. |..|..
T Consensus 341 ~~~~~y~C~~Ck~~FCldCDv 361 (378)
T KOG2807|consen 341 LSSGRYRCESCKNVFCLDCDV 361 (378)
T ss_pred CCCCcEEchhccceeeccchH
Confidence 4556788888864 778863
No 162
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=25.51 E-value=20 Score=37.78 Aligned_cols=16 Identities=31% Similarity=0.879 Sum_probs=13.3
Q ss_pred CCceEEeCcCCCcchh
Q 005013 16 ARRMLSCKSCGKKYHR 31 (719)
Q Consensus 16 ~eeLL~Cd~CgksYH~ 31 (719)
..+...|..|++.|-+
T Consensus 114 d~d~ftCrvCgK~F~l 129 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGL 129 (267)
T ss_pred CCCeeeeehhhhhhhH
Confidence 3588999999999855
No 163
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=25.41 E-value=1.2e+02 Score=29.10 Aligned_cols=53 Identities=11% Similarity=0.263 Sum_probs=39.1
Q ss_pred cccceEEEEecC-CCCeeeeeEEEe----ecCceeEEEEecCCchhhhhcCcceeEeeec
Q 005013 658 AIGKRVEVHQQS-DNSWHKGVVTDT----VEGTSTLSITLDDSRVKTLELGKQGVRFVPQ 712 (719)
Q Consensus 658 ~i~krv~v~~~~-d~~w~~g~v~~~----~~~~~~~~v~~ddg~~~~~~lgk~~i~~~~~ 712 (719)
.+|-.|-+=|+. +..|.-|+|... ......+.|.|=||+... +-.+.+.|||+
T Consensus 57 ~~GD~VLA~~~~~~~~Y~Pg~V~~~~~~~~~~~~~~~V~f~ng~~~~--vp~~~~~~I~~ 114 (124)
T PF15057_consen 57 QVGDKVLAPWEPDDCRYGPGTVIAGPERRASEDKEYTVRFYNGKTAK--VPRGEVIWISP 114 (124)
T ss_pred CCCCEEEEecCcCCCEEeCEEEEECccccccCCceEEEEEECCCCCc--cchhhEEECCH
Confidence 456666666764 456889999975 444556999999999554 56677899986
No 164
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=25.26 E-value=52 Score=24.15 Aligned_cols=28 Identities=14% Similarity=0.281 Sum_probs=15.3
Q ss_pred ccccccccccccCCCCCCceeccCCCCe
Q 005013 137 GNYCPVCLKVYRDSESTPMVCCDVCQRW 164 (719)
Q Consensus 137 ~nyC~VC~K~Y~dsdgg~MIqCD~C~~w 164 (719)
..||+.|+..-....++-..+|..|...
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred CcccCcCCccccCCCCcCEeECCCCcCE
Confidence 3588888876655566667778888653
No 165
>PF13437 HlyD_3: HlyD family secretion protein
Probab=25.20 E-value=1.9e+02 Score=25.58 Aligned_cols=39 Identities=23% Similarity=0.396 Sum_probs=28.6
Q ss_pred cccceEEEEec-CCCCeeeeeEEEeec------CceeEEEEecCCc
Q 005013 658 AIGKRVEVHQQ-SDNSWHKGVVTDTVE------GTSTLSITLDDSR 696 (719)
Q Consensus 658 ~i~krv~v~~~-~d~~w~~g~v~~~~~------~~~~~~v~~ddg~ 696 (719)
.+|.+|+|+++ ....++.|+|+++.. ++-.+.+.+++..
T Consensus 52 ~~g~~v~v~~~~~~~~~~~g~V~~I~~~~~~~~~~~~v~~~i~~~~ 97 (105)
T PF13437_consen 52 DPGQKVTVRLDPGPEKTIEGKVSSISPSPDPQGGTYRVEISIDNPK 97 (105)
T ss_pred eCCCEEEEEECCCCCcEEEEEEEEEeCcccCCCcEEEEEEEECCCC
Confidence 48999999998 445699999999965 3444555666654
No 166
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=25.15 E-value=57 Score=35.62 Aligned_cols=11 Identities=45% Similarity=0.845 Sum_probs=5.9
Q ss_pred ccccccccccC
Q 005013 139 YCPVCLKVYRD 149 (719)
Q Consensus 139 yC~VC~K~Y~d 149 (719)
.|.+|+|.|..
T Consensus 163 ~C~~C~K~YvS 173 (279)
T KOG2462|consen 163 SCKYCGKVYVS 173 (279)
T ss_pred cCCCCCceeee
Confidence 45555555533
No 167
>PRK14873 primosome assembly protein PriA; Provisional
Probab=24.70 E-value=45 Score=40.27 Aligned_cols=17 Identities=24% Similarity=0.466 Sum_probs=12.4
Q ss_pred HHHHHcCCCCccccccC
Q 005013 224 SLRAAAGLPTEDEIFSI 240 (719)
Q Consensus 224 slR~~~GLp~~eei~s~ 240 (719)
..|+..++|+.--++.+
T Consensus 560 ~~R~~~~~PPf~~la~i 576 (665)
T PRK14873 560 AERAEVGFPPAVRMAAV 576 (665)
T ss_pred HHHHHcCccCceeeEEE
Confidence 46778888887777555
No 168
>PRK06955 biotin--protein ligase; Provisional
Probab=24.47 E-value=1e+02 Score=33.32 Aligned_cols=44 Identities=16% Similarity=0.250 Sum_probs=33.5
Q ss_pred cccceEEEEecCCCCeeeeeEEEeecCceeEEEEecCCchhhhhcCc
Q 005013 658 AIGKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITLDDSRVKTLELGK 704 (719)
Q Consensus 658 ~i~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~ddg~~~~~~lgk 704 (719)
.+|++|+|..+ ++.-+.|++..++.. +.|.|+.+|| .+.+.-|.
T Consensus 247 ~~g~~V~v~~~-~~~~~~G~~~gId~~-G~L~v~~~~g-~~~~~sGe 290 (300)
T PRK06955 247 YAGREVVLLED-GAELARGVAHGIDET-GQLLLDTPAG-RQAIAAGD 290 (300)
T ss_pred cCCCeEEEEEC-CCcEEEEEEeeECCC-ceEEEEeCCC-eEEEEEEE
Confidence 47999999875 567789999999753 4599999999 45555543
No 169
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=24.26 E-value=43 Score=30.56 Aligned_cols=26 Identities=27% Similarity=0.878 Sum_probs=20.0
Q ss_pred CcCCCcchhhhcCCCcccccccCCCCCCCCCCc
Q 005013 23 KSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR 55 (719)
Q Consensus 23 d~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr 55 (719)
..|...||.-|+.-|...+. .||.++
T Consensus 52 G~CnHaFH~HCI~rWL~Tk~-------~CPld~ 77 (88)
T COG5194 52 GVCNHAFHDHCIYRWLDTKG-------VCPLDR 77 (88)
T ss_pred EecchHHHHHHHHHHHhhCC-------CCCCCC
Confidence 48999999999998876433 577664
No 170
>PF07593 UnbV_ASPIC: ASPIC and UnbV; InterPro: IPR011519 This conserved sequence is found associated with IPR001440 from INTERPRO in several paralogous proteins in Rhodopirellula baltica. It is also found associated with IPR000413 from INTERPRO in several eukaryotic integrin-like proteins (e.g. human ASPIC Q9NQ78 from SWISSPROT) and in several other bacterial proteins (e.g. Q84HN1 from SWISSPROT) [].
Probab=24.04 E-value=80 Score=26.99 Aligned_cols=16 Identities=44% Similarity=0.582 Sum_probs=11.4
Q ss_pred ccccceEEEEecCCCCe
Q 005013 657 DAIGKRVEVHQQSDNSW 673 (719)
Q Consensus 657 ~~i~krv~v~~~~d~~w 673 (719)
||||-||+|+ +-+..+
T Consensus 1 dAiGA~V~v~-~~~~~q 16 (71)
T PF07593_consen 1 DAIGARVTVT-ADGRTQ 16 (71)
T ss_pred CCCCeEEEEE-ECCeEE
Confidence 6899999999 444433
No 171
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=23.94 E-value=46 Score=25.44 Aligned_cols=27 Identities=26% Similarity=0.602 Sum_probs=16.3
Q ss_pred cccccccccCC-----CCCCceeccCCCCeec
Q 005013 140 CPVCLKVYRDS-----ESTPMVCCDVCQRWVH 166 (719)
Q Consensus 140 C~VC~K~Y~ds-----dgg~MIqCD~C~~wFH 166 (719)
||-|...|+-. ..+..+.|..|...|+
T Consensus 5 CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 5 CPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred CCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 56666665322 2455777777777664
No 172
>KOG4675 consensus Uncharacterized conserved protein, contains ENT domain [General function prediction only]
Probab=23.63 E-value=21 Score=38.67 Aligned_cols=54 Identities=11% Similarity=0.220 Sum_probs=38.9
Q ss_pred cccceEEEEecCCCCeeeeeEEEeecC-ceeEEEEecCCchh-------hhhcCcceeEeee
Q 005013 658 AIGKRVEVHQQSDNSWHKGVVTDTVEG-TSTLSITLDDSRVK-------TLELGKQGVRFVP 711 (719)
Q Consensus 658 ~i~krv~v~~~~d~~w~~g~v~~~~~~-~~~~~v~~ddg~~~-------~~~lgk~~i~~~~ 711 (719)
.||+||..-||.++..|++.++.|+-. ...|.+-||.-... .-+..-+.|||..
T Consensus 160 lvgr~v~~k~pdk~~~te~iit~~~~~~E~~~~l~~~~~~~~~p~~wvdl~~I~p~DIrw~g 221 (273)
T KOG4675|consen 160 LVGRKVWIKWPDKRKFTEAIITQYDAEKEGHHLLVPDINDCNDPWEWVDLREISPEDIRWEG 221 (273)
T ss_pred hccccccccCcccccccccccccchhhhhhhhhcccccccccCCccccccccCCHHhccccC
Confidence 799999999999999999999996443 34455556544322 3455667788843
No 173
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=23.59 E-value=1.3e+02 Score=35.13 Aligned_cols=37 Identities=19% Similarity=0.309 Sum_probs=31.5
Q ss_pred cccceEEEEecCCCCeeeeeEEEeecC------ceeEEEEecC
Q 005013 658 AIGKRVEVHQQSDNSWHKGVVTDTVEG------TSTLSITLDD 694 (719)
Q Consensus 658 ~i~krv~v~~~~d~~w~~g~v~~~~~~------~~~~~v~~dd 694 (719)
.||-||-|+|..|+.||.+.|..+... .-...|-|..
T Consensus 55 ~VGekVla~~~~Dg~~~~A~VI~~R~~~~~~~~~~~YYVHY~g 97 (450)
T PLN00104 55 EVGTRVMCRWRFDGKYHPVKVIERRRGGSGGPNDYEYYVHYTE 97 (450)
T ss_pred ccCCEEEEEECCCCCEEEEEEEEEeccCCCCCCCceEEEEEec
Confidence 599999999999999999999999762 2468888875
No 174
>PRK14640 hypothetical protein; Provisional
Probab=23.38 E-value=1.2e+02 Score=30.05 Aligned_cols=35 Identities=20% Similarity=0.391 Sum_probs=27.0
Q ss_pred ccccceEEEE--ec-CCCCeeeeeEEEeecCceeEEEEec
Q 005013 657 DAIGKRVEVH--QQ-SDNSWHKGVVTDTVEGTSTLSITLD 693 (719)
Q Consensus 657 ~~i~krv~v~--~~-~d~~w~~g~v~~~~~~~~~~~v~~d 693 (719)
-++|++|+|- .| .+...+.|++.+|++.+ +.+.++
T Consensus 94 r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~~--v~l~~~ 131 (152)
T PRK14640 94 KYVGQEAAVTLRMATNNRRKFKGVIKAVQGDM--ITLTVD 131 (152)
T ss_pred HhCCCeEEEEEecccCCceEEEEEEEEEeCCE--EEEEEC
Confidence 5789988884 45 35689999999999877 666654
No 175
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.29 E-value=57 Score=37.94 Aligned_cols=25 Identities=20% Similarity=0.251 Sum_probs=16.6
Q ss_pred HHHHHcCCCCccccccCCCCCCCCC
Q 005013 224 SLRAAAGLPTEDEIFSISPYSDDEE 248 (719)
Q Consensus 224 slR~~~GLp~~eei~s~~P~sdDe~ 248 (719)
..|+..++||..-+..+.-...+++
T Consensus 403 ~~R~~~~~PPf~~l~~i~~~~~~~~ 427 (505)
T TIGR00595 403 AQRRALNYPPFTRLIRLIFRGKNEE 427 (505)
T ss_pred HHHHHcCCCchhcEEEEEEecCCHH
Confidence 4677788888877766555555444
No 176
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=23.05 E-value=97 Score=26.76 Aligned_cols=35 Identities=17% Similarity=0.207 Sum_probs=27.8
Q ss_pred ccccceEEEEecCCCCeeeeeEEEeecCceeEEEEecCC
Q 005013 657 DAIGKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITLDDS 695 (719)
Q Consensus 657 ~~i~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~ddg 695 (719)
.++||+|.|.. .|+.=|.|++.+||.-. -+.++|-
T Consensus 11 ~~~~k~V~V~l-k~g~~~~G~L~~~D~~m---NlvL~d~ 45 (72)
T PRK00737 11 NALNSPVLVRL-KGGREFRGELQGYDIHM---NLVLDNA 45 (72)
T ss_pred HhCCCEEEEEE-CCCCEEEEEEEEEcccc---eeEEeeE
Confidence 45999999998 57888999999999854 4555554
No 177
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=22.83 E-value=63 Score=37.46 Aligned_cols=31 Identities=32% Similarity=0.556 Sum_probs=24.9
Q ss_pred cCcCCccCCcccCCceEEeCcCCCcchhhhcCCCcc
Q 005013 4 LCFVGENEGCERARRMLSCKSCGKKYHRNCLKNWAQ 39 (719)
Q Consensus 4 iC~~Ce~~Gse~~eeLL~Cd~CgksYH~~CL~p~~e 39 (719)
.|++|..+| .++.|+.|..++|..|.....+
T Consensus 91 ~c~vc~~gg-----s~v~~~s~~~~~~r~c~~~~~~ 121 (463)
T KOG1081|consen 91 ECFVCFKGG-----SLVTCKSRIQAPHRKCKPAQLE 121 (463)
T ss_pred hhccccCCC-----ccceeccccccccccCcCccCc
Confidence 577777777 7999999998889999887543
No 178
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=22.46 E-value=60 Score=39.20 Aligned_cols=23 Identities=22% Similarity=0.536 Sum_probs=14.6
Q ss_pred cCcCCccCCcccCCceEEeCcCCCcc
Q 005013 4 LCFVGENEGCERARRMLSCKSCGKKY 29 (719)
Q Consensus 4 iC~~Ce~~Gse~~eeLL~Cd~CgksY 29 (719)
+|-.|+ .+.+..-.+|..||...
T Consensus 3 ~Cp~Cg---~~n~~~akFC~~CG~~l 25 (645)
T PRK14559 3 ICPQCQ---FENPNNNRFCQKCGTSL 25 (645)
T ss_pred cCCCCC---CcCCCCCccccccCCCC
Confidence 455553 23345678999998765
No 179
>KOG3026 consensus Splicing factor SPF30 [RNA processing and modification]
Probab=21.87 E-value=85 Score=33.75 Aligned_cols=36 Identities=14% Similarity=0.199 Sum_probs=28.5
Q ss_pred ccccceEEEEecCCCCeeeeeEEEeecCceeEEEEe
Q 005013 657 DAIGKRVEVHQQSDNSWHKGVVTDTVEGTSTLSITL 692 (719)
Q Consensus 657 ~~i~krv~v~~~~d~~w~~g~v~~~~~~~~~~~v~~ 692 (719)
=-||.+|.+-|+-|..||.-+|.++..-+...-|.+
T Consensus 91 w~vg~K~~A~~~ddg~~y~AtIe~ita~~~~~ai~f 126 (262)
T KOG3026|consen 91 WKVGDKVQAVFSDDGQIYDATIEHITAMEGTVAIIF 126 (262)
T ss_pred cccCCEEEEeecCCCceEEeehhhccCCCCceeEEE
Confidence 358999999999999999999999987333344444
No 180
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=21.75 E-value=68 Score=29.99 Aligned_cols=35 Identities=26% Similarity=0.515 Sum_probs=20.6
Q ss_pred CCeeccCCCCCC-hHHHhhhccCCCCceeCCCCCCCCC
Q 005013 162 QRWVHCQCDGIS-DEKYLQFQVDGNLQYRCPTCRGECY 198 (719)
Q Consensus 162 ~~wFH~eCL~ls-dEkye~~~id~d~~Y~CptCr~~~~ 198 (719)
..-|=..||... .++... +..+..|.||.|++-+.
T Consensus 37 ~~~fC~~CL~~ryge~~~e--v~~~~~W~CP~CrgiCn 72 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEE--VLEDPNWKCPKCRGICN 72 (105)
T ss_pred cceehHhHHHHHHhhhHHH--HhcCCceECCCCCCeeC
Confidence 777777776531 111111 12356899999997543
No 181
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=21.55 E-value=58 Score=28.13 Aligned_cols=35 Identities=31% Similarity=0.755 Sum_probs=21.1
Q ss_pred eEEeCcCCCcchhhhcCCCcccccccCCCCCCCCCCc-----cccccccCC
Q 005013 19 MLSCKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCR-----ICEICRRTG 64 (719)
Q Consensus 19 LL~Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr-----~C~VC~~sg 64 (719)
.-.|.+|+...|. ......|.||+|- .|..|++.+
T Consensus 9 ~~~CtSCg~~i~p-----------~e~~v~F~CPnCGe~~I~Rc~~CRk~g 48 (61)
T COG2888 9 PPVCTSCGREIAP-----------GETAVKFPCPNCGEVEIYRCAKCRKLG 48 (61)
T ss_pred CceeccCCCEecc-----------CCceeEeeCCCCCceeeehhhhHHHcC
Confidence 3478888765443 1123468899995 455555555
No 182
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.44 E-value=62 Score=31.97 Aligned_cols=28 Identities=32% Similarity=0.799 Sum_probs=20.5
Q ss_pred eCcCCCcchhhhcCCCcccccccCCCCCCCCCCcc
Q 005013 22 CKSCGKKYHRNCLKNWAQNRDLFHWSSWKCPSCRI 56 (719)
Q Consensus 22 Cd~CgksYH~~CL~p~~e~~~~~~~~~W~Cp~Cr~ 56 (719)
...|++.|-..|+..... ..+.||.|+.
T Consensus 28 ~l~C~H~~c~~C~~~~~~-------~~~~Cp~cr~ 55 (386)
T KOG2177|consen 28 LLPCGHNFCRACLTRSWE-------GPLSCPVCRP 55 (386)
T ss_pred cccccchHhHHHHHHhcC-------CCcCCcccCC
Confidence 346999999999986544 3368998873
No 183
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=21.36 E-value=54 Score=37.44 Aligned_cols=44 Identities=20% Similarity=0.373 Sum_probs=33.1
Q ss_pred ccccCCC-CCceeecCCCCCcccccccCCCCcCCCCCCcccCCCCc
Q 005013 59 ICRRTGD-PNKFMFCRRCDAAYHCYCQHPPHKNVSSGPYLCPKHTK 103 (719)
Q Consensus 59 VC~~sgd-~~kLL~CdrC~raYH~~CL~PpL~~Ip~g~W~CP~C~~ 103 (719)
.|+...+ ...++.|+.|++|-|..|++...... ...+.|..|..
T Consensus 90 ~c~~~~~~~g~~i~c~~c~~Wqh~~C~g~~~~~~-p~~y~c~~c~~ 134 (508)
T KOG1844|consen 90 DCGLEDDMEGLMIQCDWCGRWQHKICCGSFKSTK-PDKYVCEICTP 134 (508)
T ss_pred ccccccCCCceeeCCcccCcccCceeeeecCCCC-chhceeeeecc
Confidence 6777776 66789999999999999999643333 45677777653
No 184
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.88 E-value=54 Score=35.02 Aligned_cols=32 Identities=28% Similarity=0.650 Sum_probs=22.8
Q ss_pred cCCCcchhhhcCCCcccccc-cCCCCCCCCCCc
Q 005013 24 SCGKKYHRNCLKNWAQNRDL-FHWSSWKCPSCR 55 (719)
Q Consensus 24 ~CgksYH~~CL~p~~e~~~~-~~~~~W~Cp~Cr 55 (719)
.|..-||..|++.+....+. ..-.+.+||-|.
T Consensus 69 vCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs 101 (299)
T KOG3970|consen 69 VCYHLFHWKCLNERAANLPANTAPAGYQCPCCS 101 (299)
T ss_pred hhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCC
Confidence 69999999999987543322 123678999883
No 185
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=20.78 E-value=43 Score=36.27 Aligned_cols=39 Identities=26% Similarity=0.455 Sum_probs=22.1
Q ss_pred CcchhhhcCCCcccccc--cCCCCCCCCCCc------cccccccCCC
Q 005013 27 KKYHRNCLKNWAQNRDL--FHWSSWKCPSCR------ICEICRRTGD 65 (719)
Q Consensus 27 ksYH~~CL~p~~e~~~~--~~~~~W~Cp~Cr------~C~VC~~sgd 65 (719)
.+||..|..-..+.... .-.+...|++|. +|..|+++.+
T Consensus 160 H~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIe 206 (332)
T KOG2272|consen 160 HPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIE 206 (332)
T ss_pred CccceecccccccccchhhhhccceeccccccccCCcccccccCchH
Confidence 46777777654322111 113567888887 5666666654
No 186
>PF13922 PHD_3: PHD domain of transcriptional enhancer, Asx
Probab=20.50 E-value=20 Score=31.39 Aligned_cols=21 Identities=29% Similarity=0.825 Sum_probs=18.9
Q ss_pred CceEEeCcCCCcchhhhcCCC
Q 005013 17 RRMLSCKSCGKKYHRNCLKNW 37 (719)
Q Consensus 17 eeLL~Cd~CgksYH~~CL~p~ 37 (719)
.-||.|..||..-|-.|++|.
T Consensus 41 kAMi~Cq~CGAFCHDDCIgps 61 (69)
T PF13922_consen 41 KAMIMCQGCGAFCHDDCIGPS 61 (69)
T ss_pred HHHHHHhhccchhccccccHH
Confidence 369999999999999999974
No 187
>PF07593 UnbV_ASPIC: ASPIC and UnbV; InterPro: IPR011519 This conserved sequence is found associated with IPR001440 from INTERPRO in several paralogous proteins in Rhodopirellula baltica. It is also found associated with IPR000413 from INTERPRO in several eukaryotic integrin-like proteins (e.g. human ASPIC Q9NQ78 from SWISSPROT) and in several other bacterial proteins (e.g. Q84HN1 from SWISSPROT) [].
Probab=20.38 E-value=62 Score=27.69 Aligned_cols=18 Identities=28% Similarity=0.265 Sum_probs=14.6
Q ss_pred HhCcccccceEEEEecCC
Q 005013 653 KLGKDAIGKRVEVHQQSD 670 (719)
Q Consensus 653 ~lg~~~i~krv~v~~~~d 670 (719)
=||+...-.+|+|+||+.
T Consensus 37 GLG~~~~v~~v~V~WP~G 54 (71)
T PF07593_consen 37 GLGDATSVDSVEVRWPDG 54 (71)
T ss_pred ECCCCCCEEEEEEECCCC
Confidence 378888888999999953
No 188
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=20.37 E-value=60 Score=41.93 Aligned_cols=94 Identities=22% Similarity=0.415 Sum_probs=0.0
Q ss_pred cCCCccccccccccccccccccCCCCCCceeccCCCCeeccCCCCCChHHHhhhccCCCCceeCCCCCCCCCCCCchHHH
Q 005013 127 CDACGRLFVKGNYCPVCLKVYRDSESTPMVCCDVCQRWVHCQCDGISDEKYLQFQVDGNLQYRCPTCRGECYQVRDLEDA 206 (719)
Q Consensus 127 C~aC~~lfvK~nyC~VC~K~Y~dsdgg~MIqCD~C~~wFH~eCL~lsdEkye~~~id~d~~Y~CptCr~~~~qIk~~kda 206 (719)
|+.|+...... ||+.|+.. ..+...|..|.. .+..++.....||.|-..-....+.+.-
T Consensus 670 CPkCG~~t~~~-fCP~CGs~-----te~vy~CPsCGa---------------ev~~des~a~~CP~CGtplv~~~~~~i~ 728 (1337)
T PRK14714 670 CPSCGTETYEN-RCPDCGTH-----TEPVYVCPDCGA---------------EVPPDESGRVECPRCDVELTPYQRRTIN 728 (1337)
T ss_pred CCCCCCccccc-cCcccCCc-----CCCceeCccCCC---------------ccCCCccccccCCCCCCcccccceEEec
Q ss_pred HHHhhcccccccHHH---HHHHHHHcCCCCccccccCC
Q 005013 207 VRELWRRKDMADKDL---IASLRAAAGLPTEDEIFSIS 241 (719)
Q Consensus 207 ~~r~Wrare~~~r~l---I~slR~~~GLp~~eei~s~~ 241 (719)
...+|.+.....+.. +..++--+||.+.+-+..+.
T Consensus 729 ~~~~~~~A~~~~g~~~~~~~~~KgVkgl~S~~k~~Epl 766 (1337)
T PRK14714 729 VKEEYRSALENVGERENAFDLLKGVKGLTSREKIPEPL 766 (1337)
T ss_pred HHHHHHHHHHHhCcccccccccccceecccCCCCCcch
No 189
>PRK04023 DNA polymerase II large subunit; Validated
Probab=20.07 E-value=73 Score=40.37 Aligned_cols=8 Identities=63% Similarity=1.485 Sum_probs=4.2
Q ss_pred EeCcCCCc
Q 005013 21 SCKSCGKK 28 (719)
Q Consensus 21 ~Cd~Cgks 28 (719)
+|..|+..
T Consensus 628 fCpsCG~~ 635 (1121)
T PRK04023 628 KCPSCGKE 635 (1121)
T ss_pred cCCCCCCc
Confidence 55555543
Done!