Query 027093
Match_columns 228
No_of_seqs 222 out of 1795
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 04:52:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027093.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027093hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd04714 BAH_BAHCC1 BAH, or Bro 100.0 2.4E-32 5.2E-37 208.1 10.6 121 20-156 1-121 (121)
2 cd04713 BAH_plant_3 BAH, or Br 100.0 7.9E-31 1.7E-35 205.8 13.6 128 3-133 3-134 (146)
3 cd04716 BAH_plantDCM_I BAH, or 100.0 1E-30 2.2E-35 198.5 11.9 113 20-133 1-118 (122)
4 cd04717 BAH_polybromo BAH, or 100.0 4.4E-30 9.4E-35 195.9 10.9 115 20-134 1-118 (121)
5 cd04370 BAH BAH, or Bromo Adja 100.0 1.8E-28 3.9E-33 186.0 10.5 115 20-134 1-121 (123)
6 PF01426 BAH: BAH domain; Int 100.0 3.3E-28 7.1E-33 184.2 11.1 112 21-134 1-117 (119)
7 smart00439 BAH Bromo adjacent 100.0 4.5E-28 9.8E-33 183.6 11.8 113 22-134 1-118 (120)
8 cd04709 BAH_MTA BAH, or Bromo 100.0 5.2E-28 1.1E-32 192.1 11.8 115 21-136 2-140 (164)
9 cd04710 BAH_fungalPHD BAH, or 99.9 1.6E-27 3.6E-32 184.1 12.3 116 16-133 5-134 (135)
10 cd04721 BAH_plant_1 BAH, or Br 99.9 1.8E-27 3.8E-32 183.1 10.2 108 19-128 4-117 (130)
11 cd04715 BAH_Orc1p_like BAH, or 99.9 2.5E-25 5.3E-30 176.3 12.3 104 4-111 13-125 (159)
12 cd04718 BAH_plant_2 BAH, or Br 99.9 5E-27 1.1E-31 181.4 0.7 96 37-133 50-145 (148)
13 cd04708 BAH_plantDCM_II BAH, o 99.9 3.7E-25 8.1E-30 179.9 11.6 115 19-133 4-143 (202)
14 cd04760 BAH_Dnmt1_I BAH, or Br 99.9 5.2E-25 1.1E-29 166.5 10.2 112 20-133 1-124 (124)
15 cd04712 BAH_DCM_I BAH, or Brom 99.9 4.9E-24 1.1E-28 164.0 12.6 110 20-133 3-126 (130)
16 cd04720 BAH_Orc1p_Yeast BAH, o 99.9 4.1E-24 8.9E-29 172.9 11.4 115 19-134 49-176 (179)
17 KOG1886 BAH domain proteins [T 99.9 4.6E-23 1E-27 184.2 10.6 180 5-190 34-219 (464)
18 cd04719 BAH_Orc1p_animal BAH, 99.9 1.9E-22 4.1E-27 154.0 8.7 109 21-130 2-123 (128)
19 cd04711 BAH_Dnmt1_II BAH, or B 99.9 8.2E-22 1.8E-26 149.8 8.6 109 26-134 13-134 (137)
20 KOG1827 Chromatin remodeling c 99.5 1.5E-14 3.2E-19 134.4 6.1 127 14-142 184-313 (629)
21 KOG3554 Histone deacetylase co 99.1 3.4E-12 7.3E-17 113.8 -2.2 117 22-139 5-167 (693)
22 PF00628 PHD: PHD-finger; Int 99.0 6.2E-11 1.3E-15 76.4 1.1 48 140-188 1-50 (51)
23 COG5034 TNG2 Chromatin remodel 99.0 1.4E-10 3.1E-15 96.5 2.6 48 136-188 219-269 (271)
24 KOG1973 Chromatin remodeling p 99.0 1.5E-10 3.3E-15 99.8 2.2 52 136-192 217-271 (274)
25 smart00249 PHD PHD zinc finger 98.8 4.3E-09 9.3E-14 65.7 3.3 44 142-186 4-47 (47)
26 KOG1632 Uncharacterized PHD Zn 98.5 6E-08 1.3E-12 86.2 2.4 111 80-191 3-115 (345)
27 KOG4323 Polycomb-like PHD Zn-f 98.3 2.7E-07 5.9E-12 83.8 1.4 55 136-191 169-226 (464)
28 KOG2752 Uncharacterized conser 96.9 0.00042 9.1E-09 59.9 1.5 37 134-170 124-166 (345)
29 KOG0825 PHD Zn-finger protein 96.8 0.00066 1.4E-08 65.0 2.3 56 136-193 213-270 (1134)
30 KOG0955 PHD finger protein BR1 96.6 0.0035 7.5E-08 62.8 6.0 54 137-193 219-273 (1051)
31 KOG1244 Predicted transcriptio 96.5 0.0011 2.5E-08 56.2 1.2 51 138-190 281-332 (336)
32 KOG1844 PHD Zn-finger proteins 96.4 0.0016 3.4E-08 61.0 1.8 54 136-191 84-137 (508)
33 PF13831 PHD_2: PHD-finger; PD 96.1 0.00089 1.9E-08 39.8 -0.9 35 151-187 2-36 (36)
34 KOG1512 PHD Zn-finger protein 95.9 0.0025 5.4E-08 54.6 0.5 46 142-191 319-365 (381)
35 KOG1632 Uncharacterized PHD Zn 95.4 0.00099 2.1E-08 59.4 -4.1 55 136-190 237-296 (345)
36 KOG4299 PHD Zn-finger protein 94.8 0.012 2.5E-07 55.5 1.0 51 140-191 255-307 (613)
37 KOG0957 PHD finger protein [Ge 94.3 0.021 4.5E-07 52.6 1.6 51 137-188 543-597 (707)
38 KOG0954 PHD finger protein [Ge 94.0 0.022 4.8E-07 54.6 1.1 52 137-191 270-323 (893)
39 cd04718 BAH_plant_2 BAH, or Br 93.2 0.064 1.4E-06 42.0 2.3 30 163-193 2-31 (148)
40 KOG0383 Predicted helicase [Ge 93.1 0.053 1.1E-06 52.4 2.0 50 137-191 47-96 (696)
41 KOG1245 Chromatin remodeling c 90.8 0.044 9.5E-07 57.0 -1.5 53 137-191 1107-1160(1404)
42 KOG2626 Histone H3 (Lys4) meth 90.2 0.26 5.7E-06 45.8 3.1 56 135-190 17-77 (544)
43 PF09926 DUF2158: Uncharacteri 89.4 0.71 1.5E-05 29.7 3.8 41 23-67 1-41 (53)
44 PF07227 DUF1423: Protein of u 89.3 0.38 8.2E-06 44.1 3.3 52 140-191 131-194 (446)
45 KOG1512 PHD Zn-finger protein 89.0 0.15 3.2E-06 44.0 0.5 37 151-187 277-315 (381)
46 KOG0957 PHD finger protein [Ge 88.7 0.32 6.9E-06 45.1 2.4 56 135-190 117-180 (707)
47 PF07496 zf-CW: CW-type Zinc F 88.2 0.19 4E-06 32.0 0.5 33 152-185 2-34 (50)
48 KOG0956 PHD finger protein AF1 86.7 0.31 6.7E-06 46.8 1.2 53 137-192 5-60 (900)
49 COG5076 Transcription factor i 86.4 0.079 1.7E-06 47.8 -2.8 89 21-109 275-363 (371)
50 PF11302 DUF3104: Protein of u 83.4 3.8 8.2E-05 28.3 5.0 31 22-52 5-40 (75)
51 PF14446 Prok-RING_1: Prokaryo 82.2 0.84 1.8E-05 29.5 1.4 27 142-168 10-36 (54)
52 cd05834 HDGF_related The PWWP 81.6 3 6.6E-05 29.3 4.2 43 22-66 2-44 (83)
53 PF13832 zf-HC5HC2H_2: PHD-zin 81.3 0.69 1.5E-05 34.0 0.9 30 138-170 56-87 (110)
54 PF08940 DUF1918: Domain of un 81.1 2.9 6.2E-05 27.4 3.6 39 24-63 4-42 (58)
55 PF13639 zf-RING_2: Ring finge 79.3 0.16 3.4E-06 31.0 -2.7 40 142-187 5-44 (44)
56 cd06080 MUM1_like Mutated mela 78.8 4 8.6E-05 28.6 4.0 39 23-66 1-39 (80)
57 cd05835 Dnmt3b_related The PWW 78.5 3.1 6.8E-05 29.4 3.5 41 23-65 1-44 (87)
58 PRK13251 transcription attenua 76.3 10 0.00022 25.8 5.1 47 58-104 19-65 (75)
59 PF10497 zf-4CXXC_R1: Zinc-fin 75.8 2.3 4.9E-05 31.4 2.2 46 142-189 12-70 (105)
60 PF02081 TrpBP: Tryptophan RNA 75.7 8.1 0.00018 26.3 4.6 47 58-104 19-65 (75)
61 PF10383 Clr2: Transcription-s 74.9 18 0.00039 28.0 7.2 57 10-69 2-75 (139)
62 PF15446 zf-PHD-like: PHD/FYVE 73.8 4 8.7E-05 32.7 3.2 44 150-193 14-64 (175)
63 PF09871 DUF2098: Uncharacteri 73.7 9.8 0.00021 27.3 5.0 43 22-70 2-47 (91)
64 PF13922 PHD_3: PHD domain of 73.1 0.63 1.4E-05 31.1 -1.2 32 136-172 31-62 (69)
65 PF00467 KOW: KOW motif; Inte 72.8 9.1 0.0002 21.6 3.8 26 25-52 1-26 (32)
66 cd05162 PWWP The PWWP domain, 72.3 6.5 0.00014 27.5 3.8 40 23-64 1-46 (87)
67 PF11717 Tudor-knot: RNA bindi 72.1 12 0.00027 23.9 4.8 36 23-61 1-36 (55)
68 COG4014 Uncharacterized protei 72.1 12 0.00026 26.7 4.9 41 24-69 10-53 (97)
69 PRK10708 hypothetical protein; 71.3 19 0.00041 23.4 5.3 43 24-68 2-51 (62)
70 PF10781 DSRB: Dextransucrase 71.1 22 0.00048 23.1 5.6 44 24-69 2-52 (62)
71 smart00293 PWWP domain with co 69.2 7.2 0.00016 25.7 3.3 40 23-64 1-47 (63)
72 KOG4443 Putative transcription 69.1 1.1 2.4E-05 42.9 -1.0 40 150-189 160-202 (694)
73 PTZ00112 origin recognition co 67.8 9.5 0.00021 38.7 5.0 116 7-125 439-600 (1164)
74 KOG4443 Putative transcription 67.0 1.7 3.7E-05 41.6 -0.2 41 150-190 32-72 (694)
75 PF13341 RAG2_PHD: RAG2 PHD do 66.5 1.8 3.8E-05 29.4 -0.2 35 152-186 29-68 (78)
76 PF07154 DUF1392: Protein of u 66.0 18 0.00038 28.2 5.2 51 7-68 74-124 (150)
77 cd05840 SPBC215_ISWI_like The 65.3 8.2 0.00018 27.7 3.1 40 23-64 1-49 (93)
78 COG5415 Predicted integral mem 63.6 5.8 0.00013 32.9 2.3 33 154-191 193-225 (251)
79 PF00855 PWWP: PWWP domain; I 62.8 6.5 0.00014 27.1 2.2 40 23-64 1-43 (86)
80 smart00739 KOW KOW (Kyprides, 62.6 14 0.00031 19.4 3.2 26 23-50 2-27 (28)
81 PF07649 C1_3: C1-like domain; 61.5 2 4.3E-05 23.9 -0.5 26 142-168 5-30 (30)
82 KOG1473 Nucleosome remodeling 59.9 2.4 5.1E-05 43.2 -0.6 54 135-188 1120-1173(1414)
83 KOG4628 Predicted E3 ubiquitin 59.2 9.9 0.00022 34.0 3.2 49 139-192 231-279 (348)
84 PRK12281 rplX 50S ribosomal pr 59.0 21 0.00046 24.6 4.2 30 21-52 5-34 (76)
85 COG1370 Prefoldin, molecular c 57.3 8.4 0.00018 30.2 2.1 39 5-45 94-132 (155)
86 PF13901 DUF4206: Domain of un 53.8 7.3 0.00016 32.1 1.4 31 152-192 171-201 (202)
87 PF13771 zf-HC5HC2H: PHD-like 52.7 8.9 0.00019 26.8 1.5 29 140-171 39-69 (90)
88 COG5475 Uncharacterized small 52.4 56 0.0012 21.3 4.9 38 21-67 3-40 (60)
89 CHL00141 rpl24 ribosomal prote 52.4 27 0.00059 24.5 3.9 36 21-59 7-42 (83)
90 COG5141 PHD zinc finger-contai 51.5 7.2 0.00016 36.4 1.1 46 142-190 198-244 (669)
91 PF13913 zf-C2HC_2: zinc-finge 51.3 5.8 0.00013 21.2 0.3 13 153-165 2-14 (25)
92 COG1096 Predicted RNA-binding 51.3 89 0.0019 25.5 7.2 26 79-105 107-132 (188)
93 PF04810 zf-Sec23_Sec24: Sec23 51.0 6.1 0.00013 23.6 0.4 34 153-191 2-35 (40)
94 cd03703 aeIF5B_II aeIF5B_II: T 50.6 46 0.00099 24.8 5.0 45 3-52 9-53 (110)
95 PF00130 C1_1: Phorbol esters/ 48.8 19 0.0004 22.4 2.4 35 138-172 11-47 (53)
96 PF05502 Dynactin_p62: Dynacti 46.7 14 0.0003 34.7 2.1 10 181-190 53-62 (483)
97 PRK00004 rplX 50S ribosomal pr 46.5 35 0.00076 25.1 3.9 37 21-60 3-39 (105)
98 PF09378 HAS-barrel: HAS barre 46.4 25 0.00054 24.3 3.0 38 11-51 12-49 (91)
99 KOG2879 Predicted E3 ubiquitin 46.3 13 0.00027 32.2 1.7 48 137-191 238-287 (298)
100 cd00730 rubredoxin Rubredoxin; 46.2 16 0.00036 23.1 1.8 36 155-190 3-44 (50)
101 PRK01191 rpl24p 50S ribosomal 44.6 55 0.0012 24.8 4.7 38 21-61 44-81 (120)
102 PF11793 FANCL_C: FANCL C-term 43.8 11 0.00023 25.6 0.7 52 142-193 7-68 (70)
103 PF11926 DUF3444: Domain of un 43.8 52 0.0011 27.5 4.9 56 10-67 15-70 (217)
104 PF15057 DUF4537: Domain of un 42.9 47 0.001 25.1 4.2 41 21-61 54-95 (124)
105 cd00350 rubredoxin_like Rubred 42.6 23 0.00051 20.1 1.9 24 155-189 3-26 (33)
106 KOG1568 Mitochondrial inner me 41.9 83 0.0018 25.2 5.5 85 10-103 58-147 (174)
107 TIGR01079 rplX_bact ribosomal 41.7 46 0.001 24.4 3.9 34 22-58 3-36 (104)
108 PF00667 FAD_binding_1: FAD bi 41.5 36 0.00078 28.1 3.7 23 13-35 32-54 (219)
109 cd05836 N_Pac_NP60 The PWWP do 41.3 41 0.00088 23.7 3.4 42 23-66 1-46 (86)
110 PF03107 C1_2: C1 domain; Int 41.3 34 0.00075 18.9 2.5 26 142-168 5-30 (30)
111 PF13717 zinc_ribbon_4: zinc-r 40.4 20 0.00044 20.9 1.5 14 150-163 22-35 (36)
112 COG5047 SEC23 Vesicle coat com 40.4 28 0.00061 33.4 3.1 68 154-226 54-135 (755)
113 PF03144 GTP_EFTU_D2: Elongati 39.8 61 0.0013 21.3 4.1 30 22-51 12-41 (74)
114 KOG2133 Transcriptional corepr 39.0 19 0.00042 36.3 1.9 113 20-133 143-281 (1229)
115 smart00064 FYVE Protein presen 38.5 20 0.00043 23.6 1.4 52 138-189 10-65 (68)
116 PF06940 DUF1287: Domain of un 38.5 45 0.00097 26.6 3.5 43 13-58 97-139 (164)
117 KOG2752 Uncharacterized conser 37.7 32 0.00069 30.4 2.8 54 137-193 52-105 (345)
118 cd06530 S26_SPase_I The S26 Ty 37.6 1.3E+02 0.0028 20.3 6.0 26 22-47 31-56 (85)
119 cd05837 MSH6_like The PWWP dom 37.3 44 0.00095 24.6 3.2 44 22-67 2-54 (110)
120 COG3257 GlxB Uncharacterized p 37.3 90 0.0019 26.3 5.2 60 14-89 96-156 (264)
121 PTZ00194 60S ribosomal protein 36.9 75 0.0016 24.8 4.5 40 21-63 45-84 (143)
122 PF00301 Rubredoxin: Rubredoxi 35.5 46 0.00099 20.8 2.6 37 154-190 2-44 (47)
123 PHA02862 5L protein; Provision 34.8 7.7 0.00017 30.3 -1.2 49 142-193 7-55 (156)
124 cd06541 ASCH ASC-1 homology or 34.2 84 0.0018 22.7 4.3 28 21-50 29-56 (105)
125 PF11132 SplA: Transcriptional 33.8 29 0.00064 23.8 1.6 25 22-47 5-29 (75)
126 cd05793 S1_IF1A S1_IF1A: Trans 33.3 79 0.0017 21.8 3.8 28 20-49 36-63 (77)
127 COG0198 RplX Ribosomal protein 32.8 87 0.0019 23.1 4.1 36 21-61 3-38 (104)
128 smart00652 eIF1a eukaryotic tr 32.5 89 0.0019 21.9 4.0 29 20-50 41-69 (83)
129 CHL00174 accD acetyl-CoA carbo 31.6 21 0.00045 31.3 0.8 36 149-192 34-69 (296)
130 PF12503 CMV_1a_C: Cucumber mo 31.4 1.8E+02 0.0038 20.5 5.1 44 45-90 20-73 (85)
131 cd03701 IF2_IF5B_II IF2_IF5B_I 31.3 1.4E+02 0.0031 21.2 5.0 41 3-52 9-49 (95)
132 cd03702 IF2_mtIF2_II This fami 30.8 1.2E+02 0.0027 21.7 4.6 41 4-53 10-50 (95)
133 PRK08359 transcription factor; 30.7 5.8 0.00013 32.1 -2.6 36 154-192 7-42 (176)
134 PF07494 Reg_prop: Two compone 30.3 72 0.0016 16.5 2.5 15 44-58 6-20 (24)
135 COG1188 Ribosome-associated he 30.0 96 0.0021 22.7 3.9 45 6-54 33-77 (100)
136 TIGR00515 accD acetyl-CoA carb 30.0 24 0.00053 30.7 0.9 37 148-192 21-57 (285)
137 TIGR02227 sigpep_I_bact signal 29.5 1.2E+02 0.0026 23.7 4.8 40 22-61 51-94 (163)
138 KOG1246 DNA-binding protein ju 29.2 48 0.001 33.6 3.0 48 142-192 160-207 (904)
139 PRK05654 acetyl-CoA carboxylas 29.1 25 0.00055 30.7 0.9 37 148-192 22-58 (292)
140 TIGR01080 rplX_A_E ribosomal p 28.8 1.3E+02 0.0029 22.4 4.6 39 21-62 40-78 (114)
141 smart00743 Agenet Tudor-like d 28.7 75 0.0016 20.2 3.0 28 22-50 2-29 (61)
142 KOG1986 Vesicle coat complex C 27.8 51 0.0011 32.3 2.7 34 154-192 54-87 (745)
143 PF02318 FYVE_2: FYVE-type zin 27.6 17 0.00037 27.1 -0.4 52 138-193 54-107 (118)
144 cd04456 S1_IF1A_like S1_IF1A_l 27.3 1.3E+02 0.0029 20.7 4.1 30 20-50 36-65 (78)
145 PF09416 UPF1_Zn_bind: RNA hel 27.3 31 0.00067 27.2 1.0 19 150-168 11-29 (152)
146 KOG2932 E3 ubiquitin ligase in 27.0 24 0.00052 31.1 0.3 31 139-172 91-122 (389)
147 cd06555 ASCH_PF0470_like ASC-1 26.8 1.6E+02 0.0034 21.8 4.6 28 22-50 31-58 (109)
148 cd04466 S1_YloQ_GTPase S1_YloQ 26.7 71 0.0015 20.6 2.6 25 22-50 37-61 (68)
149 KOG1740 Predicted mitochondria 26.5 46 0.001 24.3 1.7 28 9-36 36-63 (107)
150 KOG3799 Rab3 effector RIM1 and 26.4 28 0.0006 26.9 0.6 77 138-215 66-148 (169)
151 KOG1829 Uncharacterized conser 26.3 10 0.00022 36.3 -2.2 32 152-191 530-561 (580)
152 PF12961 DUF3850: Domain of Un 25.5 52 0.0011 22.5 1.7 37 13-49 19-58 (72)
153 PF09986 DUF2225: Uncharacteri 25.5 37 0.0008 28.2 1.2 39 153-191 5-59 (214)
154 smart00109 C1 Protein kinase C 25.5 22 0.00048 21.3 -0.1 32 138-170 11-44 (49)
155 PF02559 CarD_CdnL_TRCF: CarD- 25.3 94 0.002 22.0 3.2 24 23-52 2-25 (98)
156 PF01363 FYVE: FYVE zinc finge 25.1 77 0.0017 20.8 2.5 57 133-189 4-66 (69)
157 TIGR00270 conserved hypothetic 25.0 29 0.00064 27.3 0.5 34 155-192 2-35 (154)
158 PF09345 DUF1987: Domain of un 24.7 52 0.0011 23.9 1.7 16 55-70 76-91 (99)
159 COG0250 NusG Transcription ant 24.7 1.7E+02 0.0036 23.7 4.8 45 21-68 122-166 (178)
160 PF01176 eIF-1a: Translation i 24.4 84 0.0018 20.7 2.6 25 21-47 40-64 (65)
161 COG0662 {ManC} Mannose-6-phosp 24.2 71 0.0015 23.9 2.5 22 14-35 70-91 (127)
162 COG0777 AccD Acetyl-CoA carbox 24.0 37 0.0008 29.5 0.9 37 149-193 24-60 (294)
163 PRK04012 translation initiatio 24.0 1.4E+02 0.003 21.8 3.8 27 21-49 58-84 (100)
164 KOG3896 Dynactin, subunit p62 23.6 56 0.0012 29.3 2.0 9 162-170 46-54 (449)
165 cd05838 WHSC1_related The PWWP 23.2 1.1E+02 0.0025 21.8 3.3 23 24-48 2-24 (95)
166 PF14353 CpXC: CpXC protein 23.1 64 0.0014 24.1 2.1 38 154-191 2-49 (128)
167 TIGR01956 NusG_myco NusG famil 23.1 1.7E+02 0.0037 25.2 4.7 46 21-69 204-249 (258)
168 PF08921 DUF1904: Domain of un 22.9 35 0.00075 25.3 0.5 17 54-70 54-70 (108)
169 KOG3342 Signal peptidase I [In 22.9 43 0.00093 26.6 1.0 34 21-55 76-109 (180)
170 PF04322 DUF473: Protein of un 22.3 1.4E+02 0.003 22.6 3.6 29 22-50 38-71 (119)
171 COG4127 Uncharacterized conser 22.3 56 0.0012 28.5 1.7 41 22-63 72-117 (318)
172 KOG1734 Predicted RING-contain 22.2 14 0.00031 31.9 -1.9 55 138-195 225-285 (328)
173 PF07883 Cupin_2: Cupin domain 22.0 76 0.0016 20.3 2.0 21 15-35 33-53 (71)
174 PF07754 DUF1610: Domain of un 22.0 65 0.0014 17.2 1.3 9 179-187 15-23 (24)
175 PF01079 Hint: Hint module; I 22.0 2.3E+02 0.0049 23.6 5.3 28 22-50 105-132 (217)
176 PF14047 DCR: Dppa2/4 conserve 21.6 35 0.00075 22.9 0.2 23 165-190 43-65 (66)
177 COG1917 Uncharacterized conser 21.3 1.1E+02 0.0024 22.7 3.0 22 14-35 77-98 (131)
178 TIGR00922 nusG transcription t 21.0 2.1E+02 0.0045 22.4 4.7 45 22-69 119-163 (172)
179 COG4101 Predicted mannose-6-ph 20.9 1.7E+02 0.0036 22.3 3.7 28 21-48 90-123 (142)
180 PF13453 zf-TFIIB: Transcripti 20.8 51 0.0011 19.5 0.9 9 179-187 18-26 (41)
181 PF12861 zf-Apc11: Anaphase-pr 20.8 20 0.00044 25.4 -1.0 62 116-192 22-83 (85)
182 PF12678 zf-rbx1: RING-H2 zinc 20.6 16 0.00036 24.8 -1.5 26 157-187 48-73 (73)
183 PF08274 PhnA_Zn_Ribbon: PhnA 20.2 55 0.0012 18.4 0.8 10 179-188 18-27 (30)
184 PF13912 zf-C2H2_6: C2H2-type 20.1 50 0.0011 17.2 0.7 10 155-164 3-12 (27)
185 PF10844 DUF2577: Protein of u 20.0 81 0.0017 22.8 1.9 21 22-42 76-96 (100)
186 cd06203 methionine_synthase_re 20.0 1.2E+02 0.0026 27.5 3.5 22 15-36 23-44 (398)
No 1
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. 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=99.98 E-value=2.4e-32 Score=208.13 Aligned_cols=121 Identities=47% Similarity=0.857 Sum_probs=107.7
Q ss_pred CeEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeecccccCCccccCCCCeEEeeCCceeeeccceEee
Q 027093 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGK 99 (228)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~d~~~~~~~~~~~~ELFlS~~~d~i~~~~I~gk 99 (228)
|++|++||+|+|.+++.+.++|||+|++||++.+|.++++|+|||||+||.+++++.++++|||+|++.|.+|+++|.||
T Consensus 1 ~~~~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~~g~~~~~v~WfyrPeEt~~~~~~~~~~~EvF~S~~~d~~~~~~I~gk 80 (121)
T cd04714 1 KEIIRVGDCVLFKSPGRPSLPYVARIESLWEDPEGNMVVRVKWYYRPEETKGGRKPNHGEKELFASDHQDENSVQTIEHK 80 (121)
T ss_pred CCEEEcCCEEEEeCCCCCCCCEEEEEEEEEEcCCCCEEEEEEEEEcHHHccCcccccCCCCceEecCCcccccHHHhCcc
Confidence 46999999999999875688999999999999999999999999999999999888899999999999999999999999
Q ss_pred eEEEeecccccccCCCCcceEEeeccccccccccCCCceeeecCCCCCCCCCceEEC
Q 027093 100 CTVHTFKNYTKLENVGAEDYFCRFEYKAATGGFTPDRVAVYCKCEMPYNPDDLMVQC 156 (228)
Q Consensus 100 c~V~~~~~~~~~~~~~~~~Ffcr~~Yd~~~~~f~p~~~~~~C~C~~~~~~~~~mi~C 156 (228)
|.|++.++|.++..... .+.....+|+|..++||+..||||
T Consensus 81 c~V~~~~ey~~~~~~~~----------------~~~~~~d~~~Ce~~yn~~~~~~~c 121 (121)
T cd04714 81 CYVLTFAEYERLARVKK----------------KPQDGVDFYYCAGTYNPDTGMLKC 121 (121)
T ss_pred cEEEehhHheecccccC----------------CCCcCCCEEEEeccCCCCcCcccC
Confidence 99999999987764321 233467788888889999999988
No 2
>cd04713 BAH_plant_3 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=99.97 E-value=7.9e-31 Score=205.79 Aligned_cols=128 Identities=29% Similarity=0.477 Sum_probs=113.2
Q ss_pred CCCCCceeeeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeecccccCCcc---ccCCC
Q 027093 3 KTKPGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRR---QFHGA 79 (228)
Q Consensus 3 ~~~~~~~~y~s~~v~g~~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~d~~~~~~---~~~~~ 79 (228)
|.+++++||.+|.++| .+|++||+|||.+++ +.++|||+|++||++.++.++|+|+|||||+|+..... ..+++
T Consensus 3 ~~~~~~~~y~s~~~dg--~~y~vgD~Vlv~~~~-~~~pyI~~I~~i~~~~~~~~~v~V~WFyRpeEi~~~~~~~~~~~~~ 79 (146)
T cd04713 3 KGKKKKCHYTSFEKDG--NKYRLEDCVLLVPED-DQKPYIAIIKDIYKQEEGSLKLEVQWLYRPEEIEKKKGGNWKAEDP 79 (146)
T ss_pred CCccceeeeeeEEECC--EEEECCCEEEEeCCC-CCCCEEEEEEEEEEcCCCCEEEEEEeeECHHHhccccccccccCCC
Confidence 5677999999999987 799999999999987 38899999999999988999999999999999975432 23468
Q ss_pred CeEEeeCCceeeeccceEeeeEEEeecccccccCC-CCcceEEeecccccccccc
Q 027093 80 KELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLENV-GAEDYFCRFEYKAATGGFT 133 (228)
Q Consensus 80 ~ELFlS~~~d~i~~~~I~gkc~V~~~~~~~~~~~~-~~~~Ffcr~~Yd~~~~~f~ 133 (228)
+|||+|.+.|.+|+++|+|||.|+..+++.+++.. ..++||||+.||...++|.
T Consensus 80 ~ElF~S~~~d~~~~~~I~gkc~V~~~~~~~~~~~~~~~~~F~cr~~yD~~~~~~~ 134 (146)
T cd04713 80 RELFYSFHRDEVPAESVLHPCKVAFVPKGKQIPLRKGHSGFIVRRVYDNVNKKLW 134 (146)
T ss_pred CeEEEeCCCCcCCHHHCcceeEEEECCccccCCccCCCCeEEEEEEEcCCCCcEe
Confidence 99999999999999999999999998888776654 5678999999999998875
No 3
>cd04716 BAH_plantDCM_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. 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=99.97 E-value=1e-30 Score=198.51 Aligned_cols=113 Identities=17% Similarity=0.342 Sum_probs=103.8
Q ss_pred CeEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeecccccCCc-cccCCCCeEEeeCCceeeeccceEe
Q 027093 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGR-RQFHGAKELFLSDHYDVQSAHTIEG 98 (228)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~d~~~~~-~~~~~~~ELFlS~~~d~i~~~~I~g 98 (228)
|..|++||+|||.+++ +.++|||||++||++.+|..+++|+|||||+||..++ ...++++|||+|++.|.+|+++|+|
T Consensus 1 g~~~~lgD~V~v~~~~-~~~~yi~rI~~i~e~~~g~~~~~v~WyyRpeet~~~r~~~~~~~rEvFlS~~~D~~pl~~I~~ 79 (122)
T cd04716 1 GITYNLGDDAYVQGGE-GEEPFICKITEFFEGTDGKTYFTAQWFYRAEDTVIERQATNHDKKRVFYSEIKNDNPLDCLIS 79 (122)
T ss_pred CcEEEcCCEEEEECCC-CCCCEEEEEEEEEEcCCCceEEEEEEEEcHHHhccccccccCCCceEEEecccCccchhheee
Confidence 4789999999999997 4899999999999999999999999999999999887 4578899999999999999999999
Q ss_pred eeEEEeecccccc----cCCCCcceEEeecccccccccc
Q 027093 99 KCTVHTFKNYTKL----ENVGAEDYFCRFEYKAATGGFT 133 (228)
Q Consensus 99 kc~V~~~~~~~~~----~~~~~~~Ffcr~~Yd~~~~~f~ 133 (228)
||+|++.+++..+ ...+.++|||++.|+....+|.
T Consensus 80 Kc~V~~~~~~~~~~~~~~~~~~~df~c~~~Y~~~~~tF~ 118 (122)
T cd04716 80 KVKILQVPPNVGTKRKKPNSEKCDYYYDMEYCVPYSTFQ 118 (122)
T ss_pred eeEEEEeCCCCCcccccccCCCceEEEeeEeccchhheE
Confidence 9999999888766 4467889999999999988886
No 4
>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. 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=99.97 E-value=4.4e-30 Score=195.91 Aligned_cols=115 Identities=27% Similarity=0.491 Sum_probs=105.4
Q ss_pred CeEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeecccccCCccccCCCCeEEeeCCceeeeccceEee
Q 027093 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGK 99 (228)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~d~~~~~~~~~~~~ELFlS~~~d~i~~~~I~gk 99 (228)
|..|++||+|||.+++.+.+++||+|.+||++.+|..+++|+|||||+||.+++...+.++|||+|++.|.+|+++|+||
T Consensus 1 g~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~Wf~rP~et~~~~~~~~~~~Evfls~~~d~~~~~~I~~k 80 (121)
T cd04717 1 GLQYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGK 80 (121)
T ss_pred CCEEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEEEEEeChHHccCCCccccccCceEEcCccccccHHHhcCe
Confidence 46899999999999886688999999999999999999999999999999988777789999999999999999999999
Q ss_pred eEEEeecccccccCC---CCcceEEeeccccccccccC
Q 027093 100 CTVHTFKNYTKLENV---GAEDYFCRFEYKAATGGFTP 134 (228)
Q Consensus 100 c~V~~~~~~~~~~~~---~~~~Ffcr~~Yd~~~~~f~p 134 (228)
|.|++.++|.+.++. ..++||||+.||...+.|.+
T Consensus 81 c~Vl~~~~y~~~~p~~~~~~dvy~ce~~y~~~~~~~~~ 118 (121)
T cd04717 81 CAVMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKK 118 (121)
T ss_pred eEEEehHHHhcCCCCCCCCCCEEEEeEEECcccccEec
Confidence 999999999877643 45789999999999988864
No 5
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=99.95 E-value=1.8e-28 Score=186.03 Aligned_cols=115 Identities=39% Similarity=0.772 Sum_probs=104.4
Q ss_pred CeEEccCCEEEEccCCC--CCCCeEEEEeEEEEcCCCCEEEEEEEEeecccccCCccccCCCCeEEeeCCceeeeccceE
Q 027093 20 NKVVRPGDCVLMRPADS--DKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIE 97 (228)
Q Consensus 20 ~~~~~vGD~V~v~~~~~--~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~d~~~~~~~~~~~~ELFlS~~~d~i~~~~I~ 97 (228)
|.+|++||+|+|.+++. ++++|||+|.+||++.++.++++|+|||||+||+++....+.+||||+|++.+.+++++|.
T Consensus 1 g~~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~~~~~~~~~~v~wf~rp~e~~~~~~~~~~~~Elf~s~~~~~i~v~~I~ 80 (123)
T cd04370 1 GITYEVGDSVYVEPDDSIKSDPPYIARIEELWEDTNGSKQVKVRWFYRPEETPKGLSPFALRRELFLSDHLDEIPVESII 80 (123)
T ss_pred CCEEecCCEEEEecCCcCCCCCCEEEEEeeeeECCCCCEEEEEEEEEchhHhccccccccccceeEEecCccccCHHHhc
Confidence 47899999999999874 4789999999999999999999999999999999987777899999999999999999999
Q ss_pred eeeEEEeeccccccc----CCCCcceEEeeccccccccccC
Q 027093 98 GKCTVHTFKNYTKLE----NVGAEDYFCRFEYKAATGGFTP 134 (228)
Q Consensus 98 gkc~V~~~~~~~~~~----~~~~~~Ffcr~~Yd~~~~~f~p 134 (228)
|||.|+..+++.+.. ....+.||||+.||+.+++|.+
T Consensus 81 gkc~V~~~~~~~~~~~~~~~~~~~~f~~r~~yd~~~~~fk~ 121 (123)
T cd04370 81 GKCKVLFVSEFEGLKQRPNKIDTDDFFCRLAYDPTTKEFKA 121 (123)
T ss_pred cccEEEechHhhccccccccCCCCeEEEEEEECcCcceEEe
Confidence 999999999997663 2456789999999999888864
No 6
>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation. The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation [].; GO: 0003677 DNA binding; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 3SWR_A 3PTA_A 1M4Z_A 1ZBX_A ....
Probab=99.95 E-value=3.3e-28 Score=184.20 Aligned_cols=112 Identities=38% Similarity=0.779 Sum_probs=100.5
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCC--EEEEEEEEeecccccCCccccCCCCeEEeeCCceeeeccceEe
Q 027093 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNN--VKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEG 98 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~--~~v~v~WfyRp~d~~~~~~~~~~~~ELFlS~~~d~i~~~~I~g 98 (228)
++|++||+|||.+++.+.+++||+|++||++.++. ++++|+|||||+||..+ ....++|||+|++++.+|+++|+|
T Consensus 1 ~~~~vGD~V~v~~~~~~~~~~v~~I~~i~~~~~~~~~~~~~v~Wf~rp~d~~~~--~~~~~~Elf~s~~~~~~~~~~I~g 78 (119)
T PF01426_consen 1 VTYKVGDFVYVKPDDPPEPPYVARIEEIWEDKDGNKEKMVKVRWFYRPEDTSLG--KTFSPRELFLSDHCDDIPVESIRG 78 (119)
T ss_dssp EEEETTSEEEEECTSTTSEEEEEEEEEEEEETTTSEEEEEEEEEEEEGGGSTTG--GHSCTTEEEEEEEEEEEEGGGEEE
T ss_pred CEEeCCCEEEEeCCCCCCCCEEEEEEEEEcCCCCCEEEEEEEEEeECccccccc--ccCCCCEEEEECcEeEEehhhEEe
Confidence 47999999999999877899999999999998888 99999999999999333 335669999999999999999999
Q ss_pred eeEEEeecccccccCC---CCcceEEeeccccccccccC
Q 027093 99 KCTVHTFKNYTKLENV---GAEDYFCRFEYKAATGGFTP 134 (228)
Q Consensus 99 kc~V~~~~~~~~~~~~---~~~~Ffcr~~Yd~~~~~f~p 134 (228)
||.|++.+++.+.... ..++||||+.||+.+++|.+
T Consensus 79 kc~V~~~~~~~~~~~~~~~~~~~F~cr~~yd~~~~~f~~ 117 (119)
T PF01426_consen 79 KCNVLHLEDYEQARPYGKEEPDTFFCRYAYDPQKKRFKK 117 (119)
T ss_dssp EEEEEEHHHHTTGCCHCHHTTTEEEEEEEEETTTTEEEE
T ss_pred eeEEEECCccccccccccCCCCEEEEEEEEeCCcCEEeC
Confidence 9999999999877643 67899999999999999974
No 7
>smart00439 BAH Bromo adjacent homology domain.
Probab=99.95 E-value=4.5e-28 Score=183.57 Aligned_cols=113 Identities=38% Similarity=0.744 Sum_probs=102.9
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCC-EEEEEEEEeecccccCCccccCCCCeEEeeCCceeeeccceEeee
Q 027093 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNN-VKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKC 100 (228)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~-~~v~v~WfyRp~d~~~~~~~~~~~~ELFlS~~~d~i~~~~I~gkc 100 (228)
.|++||+|||.+++...+++||+|.+||++.++. ++++|+|||||+||++++...++++|||+|++.+++++++|.|||
T Consensus 1 ~~~vgd~V~v~~~~~~~~~~i~~I~~i~~~~~~~~~~~~v~Wf~rp~e~~~~~~~~~~~~Elf~s~~~~~i~~~~I~~kc 80 (120)
T smart00439 1 TIRVGDFVLVEPDDADEPYYIGRIEEIFETKKNSEKMVRVRWFYRPEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGKC 80 (120)
T ss_pred CcccCCEEEEeCCCCCCCCEEEEEEEEEECCCCCEEEEEEEEEEChhhccccccccCCCcceEEEccCccCChHHeeeEE
Confidence 3789999999999866789999999999999998 899999999999999988777889999999999999999999999
Q ss_pred EEEeecccccccCC----CCcceEEeeccccccccccC
Q 027093 101 TVHTFKNYTKLENV----GAEDYFCRFEYKAATGGFTP 134 (228)
Q Consensus 101 ~V~~~~~~~~~~~~----~~~~Ffcr~~Yd~~~~~f~p 134 (228)
.|+..+++...... ..+.||||+.||..+++|.+
T Consensus 81 ~V~~~~~~~~~~~~~~~~~~~~f~cr~~yd~~~~~f~~ 118 (120)
T smart00439 81 NVLSKSDYPGLRPEGKIGEPDVFFCESLYDPEKGAFKK 118 (120)
T ss_pred EEEEcchhcccccccCCCCCCeEEEEEEEccccCcccC
Confidence 99999999766543 46889999999999998864
No 8
>cd04709 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. 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=99.95 E-value=5.2e-28 Score=192.12 Aligned_cols=115 Identities=24% Similarity=0.467 Sum_probs=101.5
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeecccccCCc----------------------cccCC
Q 027093 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGR----------------------RQFHG 78 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~d~~~~~----------------------~~~~~ 78 (228)
..|++||+|||.++. +.+++||||++|+++.+|.++++|+|||||+|++... ....+
T Consensus 2 ~~yrvGD~Vy~~~~~-~~Py~I~rI~e~~~~~~~~~~vkV~wfYRp~DI~~~~~~l~~~~r~~~~~~~~~~~~~~~~~~~ 80 (164)
T cd04709 2 NMYRVGDYVYFESSP-NNPYLIRRIEELNKTARGHVEAKVVCYYRRRDIPDSLYQLADQHRRELEEKSDDLTPKQRHQLR 80 (164)
T ss_pred cEEecCCEEEEECCC-CCCCEEEEEEEEEeCCCCCEEEEEEEEEChhHccchhhhhcccccccccccccccchhhhhccC
Confidence 489999999999984 5688999999999999999999999999999986421 12357
Q ss_pred CCeEEeeCCceeeeccceEeeeEEEeecccccccCC--CCcceEEeeccccccccccCCC
Q 027093 79 AKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLENV--GAEDYFCRFEYKAATGGFTPDR 136 (228)
Q Consensus 79 ~~ELFlS~~~d~i~~~~I~gkc~V~~~~~~~~~~~~--~~~~Ffcr~~Yd~~~~~f~p~~ 136 (228)
.+|||+|+|.|.+|+.+|+|||.|+..+++.++... .+++|||+..||+.+++|..+.
T Consensus 81 ~rELF~S~~~d~~p~~~IrGKC~V~~~~d~~~l~~~~~~~d~Ff~~~~YDP~~k~l~~~~ 140 (164)
T cd04709 81 HRELFLSRQVETLPATHIRGKCSVTLLNDTESARSYLAREDTFFYSLVYDPEQKTLLADQ 140 (164)
T ss_pred cceeEEecccccccHHHeeeeEEEEEehhhhhhhhccCCCCEEEEEEEECCCCCeecccc
Confidence 999999999999999999999999999999887653 5789999999999999998743
No 9
>cd04710 BAH_fungalPHD BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains. 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=99.95 E-value=1.6e-27 Score=184.08 Aligned_cols=116 Identities=21% Similarity=0.443 Sum_probs=101.0
Q ss_pred EcCCCeEEccCCEEEEccCCCCCCCeEEEEeEEEEcCC------------CCEEEEEEEEeecccccCCccccCCCCeEE
Q 027093 16 IKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHR------------NNVKVRVRWYYRPEESIGGRRQFHGAKELF 83 (228)
Q Consensus 16 v~g~~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~------------~~~~v~v~WfyRp~d~~~~~~~~~~~~ELF 83 (228)
+..+|.+|++||+|||.++++++|++||||++|+..++ +.++++|+|||||+|+.... .++.+|||
T Consensus 5 ~~~~g~~~~vgD~Vyv~~~~~~ePyyIgrI~e~~~~~~~~~~~~~~~~~~~~~~vrV~wfYRp~Di~~~~--~~d~relf 82 (135)
T cd04710 5 VLKNGELLKVNDHIYMSSEPPGEPYYIGRIMEFVPKHEFPSGIHARVFPASYFQVRLNWYYRPRDISRRV--VADSRLLY 82 (135)
T ss_pred EccCCeEEeCCCEEEEecCCCCCCCEEEEEEEEEecCCCCccccccccCCCcEEEEEEEEeCHHHcCCcc--cCCceEEE
Confidence 34468999999999999998889999999999998642 23789999999999986544 57999999
Q ss_pred eeCCceeeeccceEeeeEEEeecccccccC--CCCcceEEeecccccccccc
Q 027093 84 LSDHYDVQSAHTIEGKCTVHTFKNYTKLEN--VGAEDYFCRFEYKAATGGFT 133 (228)
Q Consensus 84 lS~~~d~i~~~~I~gkc~V~~~~~~~~~~~--~~~~~Ffcr~~Yd~~~~~f~ 133 (228)
+|+|.|.+|+++|+|||+|.+.+++..+.. ..++.|||...||+.+++|.
T Consensus 83 ~S~h~d~~p~~si~gKC~V~~~~di~~l~~~~~~~~~Fyf~~lyD~~~~r~~ 134 (135)
T cd04710 83 ASMHSDICPIGSVRGKCTVRHRDQIPDLEEYKKRPNHFYFDQLFDRYILRYY 134 (135)
T ss_pred EEeeEeeechHHEEeEEEEEEecccchhhhhccCCCEEEEEeeeCcchhhcc
Confidence 999999999999999999999998877654 35788999999999998874
No 10
>cd04721 BAH_plant_1 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=99.95 E-value=1.8e-27 Score=183.10 Aligned_cols=108 Identities=27% Similarity=0.444 Sum_probs=97.8
Q ss_pred CCeEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeecccccCCcccc-CCCCeEEeeCCceeeeccceE
Q 027093 19 TNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQF-HGAKELFLSDHYDVQSAHTIE 97 (228)
Q Consensus 19 ~~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~d~~~~~~~~-~~~~ELFlS~~~d~i~~~~I~ 97 (228)
+|.++++||+|||.+++ +++|||+|++||++.+|.++++|+||+||+|+.+++.+. +.++|||+|++.+.+|+++|.
T Consensus 4 ~~~~i~vGD~V~v~~~~--~~~~va~Ie~i~ed~~g~~~v~v~WF~~p~E~~~~~~~~~~~~~EvFlS~~~d~i~~~~I~ 81 (130)
T cd04721 4 NGVTISVHDFVYVLSEE--EDRYVAYIEDLYEDKKGSKMVKVRWFHTTDEVGAALSPDSVNPREIFLSPNLQVISVECID 81 (130)
T ss_pred CCEEEECCCEEEEeCCC--CCcEEEEEEEEEEcCCCCEEEEEEEecCHHHhccccCCCCCCCCeEEEcCCccccchHHee
Confidence 46899999999999886 678999999999999999999999999999999876655 899999999999999999999
Q ss_pred eeeEEEeecccccccCC-----CCcceEEeeccccc
Q 027093 98 GKCTVHTFKNYTKLENV-----GAEDYFCRFEYKAA 128 (228)
Q Consensus 98 gkc~V~~~~~~~~~~~~-----~~~~Ffcr~~Yd~~ 128 (228)
|||+|++.++|.++... ..++||||+.||..
T Consensus 82 gk~~Vls~~~y~k~~~~~~~~~~~~~f~C~~~~d~~ 117 (130)
T cd04721 82 GLATVLTREHYEKFQSVPKNSSELQAYFCYRQIDNN 117 (130)
T ss_pred eeeEECCHHHHhhhhccccCccccccEEEEEEecCC
Confidence 99999999999877643 25689999999976
No 11
>cd04715 BAH_Orc1p_like BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins. Orc1 is part of the Yeast Sir1-origin recognition complex, the Orc1p BAH doman functions in epigenetic silencing. 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=99.93 E-value=2.5e-25 Score=176.25 Aligned_cols=104 Identities=25% Similarity=0.370 Sum_probs=90.9
Q ss_pred CCCCceeeeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEeEEEEcCC--CCEEEEEEEEeecccccCCcc--ccCCC
Q 027093 4 TKPGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHR--NNVKVRVRWYYRPEESIGGRR--QFHGA 79 (228)
Q Consensus 4 ~~~~~~~y~s~~v~g~~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~--~~~~v~v~WfyRp~d~~~~~~--~~~~~ 79 (228)
+++++++|.++.++| ++|++||+|+|.+++ .++|||+|.+||+..+ |.++++|+|||||+||..... +.+.+
T Consensus 13 ~~~~~~~Y~s~~~~g--~~y~lGD~Vlv~s~~--~~~yIgkI~~iwe~~~~~g~~~~~v~WfyRp~E~~~~~~~~~~~~~ 88 (159)
T cd04715 13 KKKDGQFYRSFTYDG--VEYRLYDDVYVHNGD--SEPYIGKIIKIYETAIDSGKKKVKVIWFFRPSEIRMELKGEPKRHI 88 (159)
T ss_pred ccCCceEEEEEEECC--EEEeCCCEEEEeCCC--CCCEEEEEEEEEEcCCcCCceEEEEEeeeCHHHhccccccCcccCC
Confidence 456778999999987 799999999999866 8999999999999865 889999999999999985432 35789
Q ss_pred CeEEeeCCc-----eeeeccceEeeeEEEeecccccc
Q 027093 80 KELFLSDHY-----DVQSAHTIEGKCTVHTFKNYTKL 111 (228)
Q Consensus 80 ~ELFlS~~~-----d~i~~~~I~gkc~V~~~~~~~~~ 111 (228)
+|||+|.|. +++|+++|.|||.|++.++|.+.
T Consensus 89 nEvFlS~~~d~~~~~~n~l~sI~gKC~Vl~~~ey~~~ 125 (159)
T cd04715 89 NEVFLACGRGEGLANINLLESIIGKCNVVCISEDFRN 125 (159)
T ss_pred CcEEEecCcCccccccCcHHHccceeEEEEehHhhhC
Confidence 999999886 56899999999999999999754
No 12
>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=99.92 E-value=5e-27 Score=181.35 Aligned_cols=96 Identities=26% Similarity=0.516 Sum_probs=92.2
Q ss_pred CCCCeEEEEeEEEEcCCCCEEEEEEEEeecccccCCccccCCCCeEEeeCCceeeeccceEeeeEEEeecccccccCCCC
Q 027093 37 DKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLENVGA 116 (228)
Q Consensus 37 ~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~d~~~~~~~~~~~~ELFlS~~~d~i~~~~I~gkc~V~~~~~~~~~~~~~~ 116 (228)
+.++|||||++||++. |..+++|+|||||+||.++++++++++|||+|++.|.+++++|+|||.|+++++|.+++..+.
T Consensus 50 ~~~~~vArIekiW~~~-G~~~~~grWy~rPEET~~gr~~~~~~kEvFlS~~~d~~~~~~I~gkC~V~~~keY~k~e~~g~ 128 (148)
T cd04718 50 SGDLWLARIEKLWEEN-GTYWYAARWYTLPEETHMGRQPHNLRRELYLTNDFADIEMECILRHCSVKCPKEFRDASNDGD 128 (148)
T ss_pred cCchHHHHHHHHHhcc-CceEEEEEEEeCchhccCccccccccceeeeccccccccHHHHhcccEEcCHHHcccccCCCC
Confidence 4678999999999976 999999999999999999999999999999999999999999999999999999999998999
Q ss_pred cceEEeecccccccccc
Q 027093 117 EDYFCRFEYKAATGGFT 133 (228)
Q Consensus 117 ~~Ffcr~~Yd~~~~~f~ 133 (228)
++|||++.||..+++|.
T Consensus 129 Dvy~Ce~~Yd~~~~~Fk 145 (148)
T cd04718 129 DVFLCEYEYDVHWQSFK 145 (148)
T ss_pred ceEEEEEEEhhhcCcee
Confidence 99999999999999986
No 13
>cd04708 BAH_plantDCM_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. 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=99.92 E-value=3.7e-25 Score=179.93 Aligned_cols=115 Identities=23% Similarity=0.427 Sum_probs=99.3
Q ss_pred CCeEEccCCEEEEccCC-----------------CCCCCeEEEEeEEEEcCCC------CEEEEEEEEeecccccCCccc
Q 027093 19 TNKVVRPGDCVLMRPAD-----------------SDKPPYVARVEKIEADHRN------NVKVRVRWYYRPEESIGGRRQ 75 (228)
Q Consensus 19 ~~~~~~vGD~V~v~~~~-----------------~~~~~~I~rI~~i~~~~~~------~~~v~v~WfyRp~d~~~~~~~ 75 (228)
+|++|++||+|||.++. ...++.||+|.+|+..+++ .+.++|+|||||+||......
T Consensus 4 ~Gv~Y~vgD~VYv~p~~f~~~~~~~~~~~~G~N~~~~p~~I~qI~ei~~~k~~~~~~~~~~~vrVrwFYRPEdt~~~~~y 83 (202)
T cd04708 4 DGVTYSVGDFLYVSPDAFAEEERERATFKAGRNVGLKAFVVCQVLEIVVEKESKQADVASTQVKVRRFYRPEDVSPEKAY 83 (202)
T ss_pred CCEEEecCCeEEECcccccccccccccccccccCCCCCcEEEEEEEEEecccCCCCCCcceEEEEEEEechhhcCcccce
Confidence 35899999999999991 1358999999999986544 589999999999998653334
Q ss_pred cCCCCeEEeeCCceeeeccceEeeeEEEeecccccccC--CCCcceEEeecccccccccc
Q 027093 76 FHGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLEN--VGAEDYFCRFEYKAATGGFT 133 (228)
Q Consensus 76 ~~~~~ELFlS~~~d~i~~~~I~gkc~V~~~~~~~~~~~--~~~~~Ffcr~~Yd~~~~~f~ 133 (228)
..+.+|||+|++.+++|+++|.|||+|....++..+.. ...+.|||+..||+.++.|+
T Consensus 84 ~sd~rely~Sde~~~~~~~~I~GKC~V~~~~d~~~~~~~~~~~~~Ffc~~~Yd~~tg~f~ 143 (202)
T cd04708 84 ASDIREVYYSEDTLTVPVEAVEGKCEVRKKSDLPDSDAPVIFEHVFFCELLYDPAKGSLK 143 (202)
T ss_pred ecCceeEEEeccceeechhHcceEEEEEecCcchhhhccccCCCceEEEEEEcCCCCccC
Confidence 45999999999999999999999999999999876654 45789999999999999997
No 14
>cd04760 BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. 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=99.92 E-value=5.2e-25 Score=166.47 Aligned_cols=112 Identities=26% Similarity=0.449 Sum_probs=97.3
Q ss_pred CeEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeecccccCCccccCCCCeEEeeCCceeeeccceEee
Q 027093 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGK 99 (228)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~d~~~~~~~~~~~~ELFlS~~~d~i~~~~I~gk 99 (228)
|.+|.+||+|+|.++++..+++||+|+.||++.+|..+++|+|||||+||.+++. ++++|||+|++++.+++.+|.+|
T Consensus 1 g~~i~vGD~V~v~~~~~~~p~~I~rV~~mfe~~~g~k~~h~rWf~Rg~dTVlG~~--~~~kEvFlsd~c~d~~l~~I~~K 78 (124)
T cd04760 1 GEELEAGDCVSVKPDDPTKPLYIARVTYMWKDSIGGKMFHAHWFCRGSDTVLGET--SDPLELFLVDECEDMALSSIHGK 78 (124)
T ss_pred CCEEecCCEEEEecCCCCCCcEEEEEhhheecCCCCcEEEEEEEEECCccccccc--CCCcEEEeecccCCcchHHheee
Confidence 4689999999999987788999999999999999999999999999999999986 88999999999999999999999
Q ss_pred eEEEeeccccc---c-----c----CCCCcceEEeecccccccccc
Q 027093 100 CTVHTFKNYTK---L-----E----NVGAEDYFCRFEYKAATGGFT 133 (228)
Q Consensus 100 c~V~~~~~~~~---~-----~----~~~~~~Ffcr~~Yd~~~~~f~ 133 (228)
|.|...+.-.. + + .-+.++|||+.-||+...+|.
T Consensus 79 v~V~~~~p~~~w~~~~g~~~~~~~~~ddg~tffyq~~yd~~~arf~ 124 (124)
T cd04760 79 VNVIYKAPSENWSMEGGMDEEDEIFEDDGKTFFYQKWYDPECARFE 124 (124)
T ss_pred eEEEEeCCCcchhhhcCCCCccccccCCCCeEEEEEeeChhhhccC
Confidence 99997544311 1 1 123478999999999888873
No 15
>cd04712 BAH_DCM_I BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. 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=99.91 E-value=4.9e-24 Score=163.97 Aligned_cols=110 Identities=25% Similarity=0.328 Sum_probs=92.9
Q ss_pred CeEEccCCEEEEccCCCC----------CCCeEEEEeEEEEcCCCCEEEEEEEEeecccccCCccccCCCCeEEeeCCce
Q 027093 20 NKVVRPGDCVLMRPADSD----------KPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYD 89 (228)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~----------~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~d~~~~~~~~~~~~ELFlS~~~d 89 (228)
|..|++||+|+|.+++++ .+++|++|+.||++.+|..+++++|||||+||.+++ +++++|||||++++
T Consensus 3 ~~~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~~~g~~~~h~~W~yrp~eTv~g~--~~~~~ElFLSd~c~ 80 (130)
T cd04712 3 GLTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKGSDGSKMFHGRWLYRGCDTVLGN--YANERELFLTNECT 80 (130)
T ss_pred CCEEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeecCCCceEEEEEEEEcchhccccc--cCCCceEEEecccc
Confidence 468999999999999855 388999999999999999999999999999999998 68999999999999
Q ss_pred eeecc----ceEeeeEEEeecccccccCCCCcceEEeecccccccccc
Q 027093 90 VQSAH----TIEGKCTVHTFKNYTKLENVGAEDYFCRFEYKAATGGFT 133 (228)
Q Consensus 90 ~i~~~----~I~gkc~V~~~~~~~~~~~~~~~~Ffcr~~Yd~~~~~f~ 133 (228)
.+++. .|.+||.|........ ...++.|||+.-|++.++.|.
T Consensus 81 ~~~~~~~~~~I~~k~~V~~~~~~~~--~~~~~~F~r~syy~~e~~~F~ 126 (130)
T cd04712 81 CLELDLLSTEIKGVHKVDWSGTPWG--KGLPEFFVRQSYYWPERGAFT 126 (130)
T ss_pred ccccccccceeEEEEEEEEecCcCC--cCCCCEEEEEEEECccCCceE
Confidence 99999 9999999998765542 113334555555555888886
No 16
>cd04720 BAH_Orc1p_Yeast BAH, or Bromo Adjacent Homology domain, as present in Orc1p, which again is part of the Saccharomyces cerevisiae Sir1-origin recognition complex, and as present in Sir3p. The Orc1p BAH doman functions in epigenetic silencing. 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=99.91 E-value=4.1e-24 Score=172.89 Aligned_cols=115 Identities=23% Similarity=0.357 Sum_probs=101.2
Q ss_pred CCeEEccCCEEEEccCCCCCCCeEEEEeEEEEcCC-CCEEEEEEEEeecccccCCcc--c-------cCCCCeEEeeCCc
Q 027093 19 TNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHR-NNVKVRVRWYYRPEESIGGRR--Q-------FHGAKELFLSDHY 88 (228)
Q Consensus 19 ~~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~-~~~~v~v~WfyRp~d~~~~~~--~-------~~~~~ELFlS~~~ 88 (228)
+|.++++||+|+|.+++ ..++|||.|.+|+.+.. +.+.+.|+|||||.|+..++. + ...++|||+|.+.
T Consensus 49 d~~~~~vGD~Vlik~~~-~~~~~V~iI~ei~~~~~~~~v~i~v~Wy~r~~Ei~~~~~~~~~~~~~~~~~~~nElflT~~~ 127 (179)
T cd04720 49 DGLELSVGDTILVKDDV-ANSPSVYLIHEIRLNTLNNEVELWVMWFLRWFEINPARYYKQFDPEFRSESNKNELYLTAEL 127 (179)
T ss_pred CCeEEeCCCEEEEeCCC-CCCCEEEEEEEEEeCCCCCEEEEEEEEcCCHHHcccccccccccchhcccCCCceEEEeccc
Confidence 57999999999999987 48899999999998876 558999999999999977553 2 2237999999999
Q ss_pred eeeeccceEeeeEEEeecccccccCC---CCcceEEeeccccccccccC
Q 027093 89 DVQSAHTIEGKCTVHTFKNYTKLENV---GAEDYFCRFEYKAATGGFTP 134 (228)
Q Consensus 89 d~i~~~~I~gkc~V~~~~~~~~~~~~---~~~~Ffcr~~Yd~~~~~f~p 134 (228)
|.+++.+|++||.|++.++|.++... ...+||||++||+.++.|.+
T Consensus 128 d~i~l~~Ii~k~~Vls~~ef~~~~~~~~~~~~~F~cR~~~d~~~~~F~~ 176 (179)
T cd04720 128 SEIKLKDIIDKANVLSESEFNDLSTDDKNGERTFFCRYACEPDGEEFVW 176 (179)
T ss_pred ceEEhhheeeeEEEecHHHhhhhcccccCCCceEEEEEEEeCCCCeEcc
Confidence 99999999999999999999877643 57899999999999999986
No 17
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=99.89 E-value=4.6e-23 Score=184.23 Aligned_cols=180 Identities=32% Similarity=0.419 Sum_probs=157.3
Q ss_pred CCCceeeeeEEEcCCCeEEcc-CCEEEEccCCCCCCCeEEEEeEEEEcCC-CCEEEEEEEEeecccccCCccc---cCCC
Q 027093 5 KPGKKDLDSYNIKGTNKVVRP-GDCVLMRPADSDKPPYVARVEKIEADHR-NNVKVRVRWYYRPEESIGGRRQ---FHGA 79 (228)
Q Consensus 5 ~~~~~~y~s~~v~g~~~~~~v-GD~V~v~~~~~~~~~~I~rI~~i~~~~~-~~~~v~v~WfyRp~d~~~~~~~---~~~~ 79 (228)
..++.||+.+..+++ .|.. ||.|++.+++++.++|||+|..|+.+.. +.+.+.|+|||||+|+.++... ...+
T Consensus 34 ~~k~~h~~t~~~~~g--~~~~~~d~vllvped~~~pPyvaii~~i~a~~~g~~~k~ev~W~YrPee~~~~~~~~~~a~~~ 111 (464)
T KOG1886|consen 34 GVKSLHFETFIYRGG--RYINYGDSVLLVPEDPGKPPYVAIIEDIYAQERGGNVKVEVQWFYRPEESEGGGSGKWGAKQP 111 (464)
T ss_pred ccccccccceeeccC--cccccCcceeecCCCCCCCCeeEEEeeeeccccCCCcceecccccCCCccCCCCCCCcccCCC
Confidence 346789999999874 5555 9999999999899999999999999887 5899999999999999876443 3456
Q ss_pred CeEEeeCCceeeeccceEeeeEEEeecccccccC-CCCcceEEeeccccccccccCCCceeeecCCCCCCCCCceEECCC
Q 027093 80 KELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLEN-VGAEDYFCRFEYKAATGGFTPDRVAVYCKCEMPYNPDDLMVQCEG 158 (228)
Q Consensus 80 ~ELFlS~~~d~i~~~~I~gkc~V~~~~~~~~~~~-~~~~~Ffcr~~Yd~~~~~f~p~~~~~~C~C~~~~~~~~~mi~C~~ 158 (228)
+|||+|.|.|.+++++|.++|.|.++..+.++.. .+.+.|+||..||..++.|.......||.|++..++...|.+|..
T Consensus 112 relF~SfH~De~~A~ti~~rC~V~fvp~~kqlp~~~~~~~f~~r~vYd~~~~~~~~~~~~~~~~~~k~e~d~~~~kt~~~ 191 (464)
T KOG1886|consen 112 RELFLSFHEDEAFAETILHRCKVHFVPAYKQLPNRVGHESFICRRVYDAVTSKLRKLRDGDFGDGQKLEIDMLVPKTGPR 191 (464)
T ss_pred ccccccccccchhhhhhcccceeeeccccccccccCCCCCcccccccccccccccCccccchhcccccCCccchhhhccc
Confidence 7999999999999999999999999999998876 678899999999999999998888999999999998889999999
Q ss_pred CCceecCCCCCCChhhhCCCCeEEcccccccc
Q 027093 159 CKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDV 190 (228)
Q Consensus 159 C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~ 190 (228)
|..|+|..|+...... ....|..|..-.
T Consensus 192 ~~~~~~p~~~~t~~~~----~~~~~~~~s~~~ 219 (464)
T KOG1886|consen 192 RGTLPDPKKVQTLNAA----ASKRSQQKSEIS 219 (464)
T ss_pred CCCCCCcccccccccc----ccceeccccccc
Confidence 9999999999987632 467777775443
No 18
>cd04719 BAH_Orc1p_animal BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces cerevisiae Orc1p. Orc1 is part of the Yeast Sir1-origin recognition complex. The Orc1p BAH doman functions in epigenetic silencing. In vertebrates, a similar ORC protein complex exists, which has been shown essential for DNA replication in Xenopus laevis. 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=99.88 E-value=1.9e-22 Score=154.04 Aligned_cols=109 Identities=25% Similarity=0.347 Sum_probs=91.8
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCC---CEEEEEEEEeecccccCCc----cccCCCCeEEeeCCce---e
Q 027093 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRN---NVKVRVRWYYRPEESIGGR----RQFHGAKELFLSDHYD---V 90 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~---~~~v~v~WfyRp~d~~~~~----~~~~~~~ELFlS~~~d---~ 90 (228)
.+|++||+|+|.+++. +++|||+|++|+++.++ ...++|+|||||+|++... ....+++|||+|++.+ .
T Consensus 2 ~~i~vGd~VlI~~~d~-~~~yVAkI~~i~e~~~~~~~~~~~~VqWy~R~~Ev~~~~~~~~~~~~~~~EvF~~~~~~~~~~ 80 (128)
T cd04719 2 LTIEVGDFVLIEGEDA-DGPDVARILHLYEDGNEDDDPKRAIVQWFSRPSEVPKNKRKLLGREPHSQEVFFYSRSSCDND 80 (128)
T ss_pred eEEecCCEEEEECCCC-CCCcEeeehhhhccccCCcccceEEEEcccChHHccccchhhccCCCCCcEEEEecCccccCc
Confidence 5799999999999985 78899999999998766 5799999999999997421 1235899999999874 8
Q ss_pred eeccceEeeeEEEeecccccccCC---CCcceEEeeccccccc
Q 027093 91 QSAHTIEGKCTVHTFKNYTKLENV---GAEDYFCRFEYKAATG 130 (228)
Q Consensus 91 i~~~~I~gkc~V~~~~~~~~~~~~---~~~~Ffcr~~Yd~~~~ 130 (228)
+++++|.|+|.|++.++|.++... ....||.|..++.+..
T Consensus 81 i~~etI~gkc~V~~~~~y~~l~~~~~~~~~~~F~r~~~~~k~~ 123 (128)
T cd04719 81 IDAETIIGKVRVEPVEPKTDLPETKKKTGGPLFVKRYWDTKTF 123 (128)
T ss_pred EeHHHcccEEEEEEcCCccchhhhccccCceEEEEEEeccccc
Confidence 999999999999999999887732 3567899988887654
No 19
>cd04711 BAH_Dnmt1_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. 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=99.86 E-value=8.2e-22 Score=149.78 Aligned_cols=109 Identities=24% Similarity=0.478 Sum_probs=87.3
Q ss_pred CCEEEEccCCCCCCCeEEEEeEEEEcCCC-------CEEEEEEEEeecccccCCccc-cC-CCCeEEeeCCceeeeccce
Q 027093 26 GDCVLMRPADSDKPPYVARVEKIEADHRN-------NVKVRVRWYYRPEESIGGRRQ-FH-GAKELFLSDHYDVQSAHTI 96 (228)
Q Consensus 26 GD~V~v~~~~~~~~~~I~rI~~i~~~~~~-------~~~v~v~WfyRp~d~~~~~~~-~~-~~~ELFlS~~~d~i~~~~I 96 (228)
+|.|-=.+-+.+.+++||||++|...+++ .++|+|+|||||+|+..++.. ++ +-+|||+|+|.+++|+.+|
T Consensus 13 ~~~~~~~~~d~~ePy~VgrI~eI~~~k~~~~k~~~~~ikvrV~~fYRPEdi~~g~~~ayhsDirevy~Sd~~~~~~~~~I 92 (137)
T cd04711 13 SDYIKGSNLDAPEPFRIGRIKEIFCAKRSNGKPNESDIKLRINKFYRPENTHKGFKATYHADINMLYWSDEEATVDFSAV 92 (137)
T ss_pred ccccccccCCCCCCcEEEEEEEEecCCCCCCCCCccceEEEEEEEecccccccccccccccceeeEEeecceeecChhhc
Confidence 33333334456789999999999986543 378999999999999987543 44 4599999999999999999
Q ss_pred EeeeEEEeeccccc-c---cCCCCcceEEeeccccccccccC
Q 027093 97 EGKCTVHTFKNYTK-L---ENVGAEDYFCRFEYKAATGGFTP 134 (228)
Q Consensus 97 ~gkc~V~~~~~~~~-~---~~~~~~~Ffcr~~Yd~~~~~f~p 134 (228)
.|||+|...++... + ...+.+.|||+.+||..++.|..
T Consensus 93 ~GKC~V~~~~di~~s~~~y~~~gpd~Fyf~~~Y~a~t~~F~d 134 (137)
T cd04711 93 QGRCTVEYGEDLPESVQEYSGGGPDRFYFLEAYNAKTKSFED 134 (137)
T ss_pred cceEEEEeccccchhHHHHhcCCCcceEEhhhhccccCcccC
Confidence 99999997665542 2 33568999999999999999974
No 20
>KOG1827 consensus Chromatin remodeling complex RSC, subunit RSC1/Polybromo and related proteins [Chromatin structure and dynamics; Transcription]
Probab=99.51 E-value=1.5e-14 Score=134.45 Aligned_cols=127 Identities=21% Similarity=0.305 Sum_probs=111.9
Q ss_pred EEEcCCCeEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeecccccCCccccCCCCeEEeeCCceeeec
Q 027093 14 YNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSA 93 (228)
Q Consensus 14 ~~v~g~~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~d~~~~~~~~~~~~ELFlS~~~d~i~~ 93 (228)
+.++ |..|.+||.|||.+......+.|++|.++|++.+|..++.+.|||||++|.+...+.+.++|+|.+......++
T Consensus 184 ~~i~--~~~~~~gd~vlv~~~~d~~~p~v~~Ier~w~~~dg~k~~~~~w~~rP~~T~H~a~r~F~k~Evfkt~~~~~~~~ 261 (629)
T KOG1827|consen 184 VEID--GTKYIVGDYVLVQNPADNLKPIVAQIERLWKLPDGEKWPQGCWIYRPEETVHRADRKFYKQEVFKTSLYRDDLV 261 (629)
T ss_pred cccc--CcccccCceeeecCcccccCCceeeecccccCcccccccceeEeeCCccCccccccchhcccceecccccccHH
Confidence 4555 47999999999999985689999999999999999999999999999999998777789999999999999999
Q ss_pred cceEeeeEEEeecccccccCC---CCcceEEeeccccccccccCCCceeeec
Q 027093 94 HTIEGKCTVHTFKNYTKLENV---GAEDYFCRFEYKAATGGFTPDRVAVYCK 142 (228)
Q Consensus 94 ~~I~gkc~V~~~~~~~~~~~~---~~~~Ffcr~~Yd~~~~~f~p~~~~~~C~ 142 (228)
..|+|+|.|+.+.+|...++. ..+.|.|.+.|+...+.|..-.....|.
T Consensus 262 q~l~g~c~v~~~~~yi~~~p~~ls~~dv~lcesRyn~~~K~f~kirsw~~~~ 313 (629)
T KOG1827|consen 262 QRLLGKCYVMKPTEYISGDPENLSEEDVFLCESRYNEQLKKFNKIRSWKAFL 313 (629)
T ss_pred HHhhcceEEeehhHhhhcCcccccccceeeEEeeeccchhhhccccCchhcC
Confidence 999999999999999877653 5688999999999999998644444443
No 21
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=99.13 E-value=3.4e-12 Score=113.77 Aligned_cols=117 Identities=24% Similarity=0.428 Sum_probs=96.6
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeecccccCC---------c-------------------
Q 027093 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGG---------R------------------- 73 (228)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~d~~~~---------~------------------- 73 (228)
.|++||+||+.... ..++.|-||+++.++.+|++.++|--|||..|++.. +
T Consensus 5 ~y~vgd~vYf~~ss-s~PYliRrIEELnKTa~GnVeAkvVc~~RRRDIs~~L~~lAD~~ar~~~~y~a~~~a~~~~e~e~ 83 (693)
T KOG3554|consen 5 MYRVGDYVYFENSS-SNPYLIRRIEELNKTANGNVEAKVVCYLRRRDISSHLLKLADKHARRFDNYAAPEAAPEATEAEI 83 (693)
T ss_pred cceecceEEEecCC-CChHHHHHHHHHhccccCCcceEEEEEEEccchHHHHHHHHHHHhhhcccccCcccCcccchhhh
Confidence 79999999999997 468999999999999999999999999999987410 0
Q ss_pred -----cc-----------cCCCCeEEeeCCceeeeccceEeeeEEEeecccccccC--CCCcceEEeeccccccccccCC
Q 027093 74 -----RQ-----------FHGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLEN--VGAEDYFCRFEYKAATGGFTPD 135 (228)
Q Consensus 74 -----~~-----------~~~~~ELFlS~~~d~i~~~~I~gkc~V~~~~~~~~~~~--~~~~~Ffcr~~Yd~~~~~f~p~ 135 (228)
.+ .--.+|||+|......|+..|+|||.|.-+.+-+.+.+ ..+++||+...||+..+++..+
T Consensus 84 EEe~e~p~~vdlt~~qrhqLrhrElFlsRQ~EsLPAthIRGKCsV~LLnete~~~~YL~~eDtFfySLVyDP~~kTLLAD 163 (693)
T KOG3554|consen 84 EEESECPAPVDLTEKQRHQLRHRELFLSRQSESLPATHIRGKCSVTLLNETESLQSYLEKEDTFFYSLVYDPNQKTLLAD 163 (693)
T ss_pred hhhccCCCcCCCCHHHHHHHHHHHHHHhhhhccCchhhhccceeEEEecChHHHHhhccccceeEEEeeeccchhhhhcc
Confidence 00 01236999999999999999999999999887765544 4678999999999999988765
Q ss_pred Ccee
Q 027093 136 RVAV 139 (228)
Q Consensus 136 ~~~~ 139 (228)
+...
T Consensus 164 kGeI 167 (693)
T KOG3554|consen 164 KGEI 167 (693)
T ss_pred Ccce
Confidence 4433
No 22
>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=99.03 E-value=6.2e-11 Score=76.37 Aligned_cols=48 Identities=29% Similarity=0.918 Sum_probs=39.1
Q ss_pred ee-cCCCCCCCCCceEECCCCCceecCCCCCCChhhhCCC-CeEEcccccc
Q 027093 140 YC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKL-DHFLCSDCSS 188 (228)
Q Consensus 140 ~C-~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~-~~~~C~~C~~ 188 (228)
+| +|++ .++++.||+|+.|+.|||..|++++....... ..|+|+.|..
T Consensus 1 ~C~vC~~-~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQ-SDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTS-SCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCC-cCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 47 8998 44688999999999999999999986643222 3899999975
No 23
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=99.01 E-value=1.4e-10 Score=96.47 Aligned_cols=48 Identities=29% Similarity=0.934 Sum_probs=42.0
Q ss_pred CceeeecCCCCCCCCCceEECC--CC-CceecCCCCCCChhhhCCCCeEEcccccc
Q 027093 136 RVAVYCKCEMPYNPDDLMVQCE--GC-KDWFHPSCMGMTIEEAKKLDHFLCSDCSS 188 (228)
Q Consensus 136 ~~~~~C~C~~~~~~~~~mi~C~--~C-~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~ 188 (228)
...+||.|+++ ..+.||.|| .| .+|||+.|||+..++- .+|+|+.|..
T Consensus 219 ~e~lYCfCqqv--SyGqMVaCDn~nCkrEWFH~~CVGLk~pPK---G~WYC~eCk~ 269 (271)
T COG5034 219 GEELYCFCQQV--SYGQMVACDNANCKREWFHLECVGLKEPPK---GKWYCPECKK 269 (271)
T ss_pred CceeEEEeccc--ccccceecCCCCCchhheeccccccCCCCC---CcEeCHHhHh
Confidence 47999999998 689999999 79 7999999999976553 6899999975
No 24
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=98.99 E-value=1.5e-10 Score=99.85 Aligned_cols=52 Identities=25% Similarity=0.843 Sum_probs=44.5
Q ss_pred CceeeecCCCCCCCCCceEECCC--CC-ceecCCCCCCChhhhCCCCeEEcccccccccc
Q 027093 136 RVAVYCKCEMPYNPDDLMVQCEG--CK-DWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (228)
Q Consensus 136 ~~~~~C~C~~~~~~~~~mi~C~~--C~-~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (228)
..+.||+|.+. ..+.||.||. |. +|||..|||+...+. ++|+|+.|......
T Consensus 217 ~e~~yC~Cnqv--syg~Mi~CDn~~C~~eWFH~~CVGL~~~Pk---gkWyC~~C~~~~~~ 271 (274)
T KOG1973|consen 217 DEPTYCICNQV--SYGKMIGCDNPGCPIEWFHFTCVGLKTKPK---GKWYCPRCKAENKK 271 (274)
T ss_pred CCCEEEEeccc--ccccccccCCCCCCcceEEEeccccccCCC---Ccccchhhhhhhhc
Confidence 57999999954 6899999995 98 999999999986654 57999999987654
No 25
>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 KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=98.48 E-value=6e-08 Score=86.19 Aligned_cols=111 Identities=28% Similarity=0.465 Sum_probs=90.4
Q ss_pred CeEEeeCCceeeeccceEeeeEEEeecccccccCCCCcceEEeeccccccccccCCCceeeecCCCCCCCCCceEECCCC
Q 027093 80 KELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLENVGAEDYFCRFEYKAATGGFTPDRVAVYCKCEMPYNPDDLMVQCEGC 159 (228)
Q Consensus 80 ~ELFlS~~~d~i~~~~I~gkc~V~~~~~~~~~~~~~~~~Ffcr~~Yd~~~~~f~p~~~~~~C~C~~~~~~~~~mi~C~~C 159 (228)
.+.+++.+........+.+++.......+... .....+.+.+..+....+.+.+.....+|.|..+.+++.+|++|+.|
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~k~~~~~~~~a~~~~~~~~~~~~~p~~~~~~cd~C 81 (345)
T KOG1632|consen 3 KIPKTSKTFSKTESDRRAPIAQKTTKPPKEPV-PIERPVPDVFRGRKGRRGGLLKALTQRYCKCYKPCDPDDLMEQCDLC 81 (345)
T ss_pred CcccccceecccccccccccccccccCCcCCC-CCCCCCcccccccccccccccHhhhhchhhcccccCchhhhhccccc
Confidence 45556666666677777777777776666544 44556667777888888888887778899999999999999999999
Q ss_pred CceecCCC--CCCChhhhCCCCeEEccccccccc
Q 027093 160 KDWFHPSC--MGMTIEEAKKLDHFLCSDCSSDVD 191 (228)
Q Consensus 160 ~~w~H~~C--v~~~~~~~~~~~~~~C~~C~~~~~ 191 (228)
..|||+.| ||++..+...++.|+|..|.....
T Consensus 82 ~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~~ 115 (345)
T KOG1632|consen 82 EDWYHGECWEVGTAEKEAPKEDPKVCDECKEAQD 115 (345)
T ss_pred cccccccccccCchhhcCCccccccccccchhhh
Confidence 99999999 999999888889999999998764
No 27
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=98.27 E-value=2.7e-07 Score=83.77 Aligned_cols=55 Identities=25% Similarity=0.642 Sum_probs=43.9
Q ss_pred CceeeecCCCCCCCCCceEECCCCCceecCCCCCCC--hhhhCC-CCeEEccccccccc
Q 027093 136 RVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMT--IEEAKK-LDHFLCSDCSSDVD 191 (228)
Q Consensus 136 ~~~~~C~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~--~~~~~~-~~~~~C~~C~~~~~ 191 (228)
.+-.||.|+.+...+ .|+||+.|+.|||..|.... .....+ ..+|+|.-|.....
T Consensus 169 ~qc~vC~~g~~~~~N-rmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~ 226 (464)
T KOG4323|consen 169 LQCSVCYCGGPGAGN-RMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPK 226 (464)
T ss_pred ceeeeeecCCcCccc-eeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccchh
Confidence 457889999988655 99999999999999999774 233333 35999999998765
No 28
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=96.89 E-value=0.00042 Score=59.90 Aligned_cols=37 Identities=41% Similarity=1.066 Sum_probs=31.4
Q ss_pred CCCceeeecCCCCCCC-----CCceEECCCCCceec-CCCCCC
Q 027093 134 PDRVAVYCKCEMPYNP-----DDLMVQCEGCKDWFH-PSCMGM 170 (228)
Q Consensus 134 p~~~~~~C~C~~~~~~-----~~~mi~C~~C~~w~H-~~Cv~~ 170 (228)
.+.+..||.|..||++ ++.|+||..|..||| ..|+..
T Consensus 124 hNfqG~~C~Cd~~Ypdp~~~~e~~m~QC~iCEDWFHce~c~~~ 166 (345)
T KOG2752|consen 124 HNFQGLFCKCDTPYPDPVRTEEGEMLQCVICEDWFHCEGCMQA 166 (345)
T ss_pred hhhcceeEEecCCCCCccccccceeeeEEeccchhcccccCcc
Confidence 3567999999999976 469999999999999 778744
No 29
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.82 E-value=0.00066 Score=65.03 Aligned_cols=56 Identities=23% Similarity=0.699 Sum_probs=42.9
Q ss_pred Cceeee-cCCCCCCCCCceEECCCCCce-ecCCCCCCChhhhCCCCeEEccccccccccc
Q 027093 136 RVAVYC-KCEMPYNPDDLMVQCEGCKDW-FHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 193 (228)
Q Consensus 136 ~~~~~C-~C~~~~~~~~~mi~C~~C~~w-~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~k 193 (228)
....-| +|..+. +.+.|+.|+.|..- ||+.|+..+..+. -+..|+|+.|....-+.
T Consensus 213 ~E~~~C~IC~~~D-pEdVLLLCDsCN~~~YH~YCLDPdl~ei-P~~eWYC~NC~dL~~~e 270 (1134)
T KOG0825|consen 213 QEEVKCDICTVHD-PEDVLLLCDSCNKVYYHVYCLDPDLSES-PVNEWYCTNCSLLEITE 270 (1134)
T ss_pred cccccceeeccCC-hHHhheeecccccceeeccccCcccccc-cccceecCcchhhhhhh
Confidence 345556 788765 57899999999766 9999999976554 22689999999876544
No 30
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=96.65 E-value=0.0035 Score=62.79 Aligned_cols=54 Identities=26% Similarity=0.598 Sum_probs=42.7
Q ss_pred ceeeecCCCCCCC-CCceEECCCCCceecCCCCCCChhhhCCCCeEEccccccccccc
Q 027093 137 VAVYCKCEMPYNP-DDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 193 (228)
Q Consensus 137 ~~~~C~C~~~~~~-~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~k 193 (228)
...+|+|...... ....++||.|+.-+|..|.|++..+. ..|.|..|..+....
T Consensus 219 D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~ipe---g~WlCr~Cl~s~~~~ 273 (1051)
T KOG0955|consen 219 DAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPFIPE---GQWLCRRCLQSPQRP 273 (1051)
T ss_pred CccceeecccccCCCceEEEcCCCcchhhhhccCCCCCCC---CcEeehhhccCcCcc
Confidence 4677899875432 26889999999999999999765443 579999999987654
No 31
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=96.46 E-value=0.0011 Score=56.22 Aligned_cols=51 Identities=25% Similarity=0.696 Sum_probs=42.0
Q ss_pred eeee-cCCCCCCCCCceEECCCCCceecCCCCCCChhhhCCCCeEEcccccccc
Q 027093 138 AVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDV 190 (228)
Q Consensus 138 ~~~C-~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~ 190 (228)
-+|| +|+...| |.....||.|..=||+-|+..+..++.. ..|.|..|....
T Consensus 281 ck~csicgtsen-ddqllfcddcdrgyhmyclsppm~eppe-gswsc~KOG~~~ 332 (336)
T KOG1244|consen 281 CKYCSICGTSEN-DDQLLFCDDCDRGYHMYCLSPPMVEPPE-GSWSCHLCLEEL 332 (336)
T ss_pred cceeccccCcCC-CceeEeecccCCceeeEecCCCcCCCCC-CchhHHHHHHHH
Confidence 4566 8888776 6788999999999999999998776644 689999998653
No 32
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=96.39 E-value=0.0016 Score=60.98 Aligned_cols=54 Identities=28% Similarity=0.704 Sum_probs=45.8
Q ss_pred CceeeecCCCCCCCCCceEECCCCCceecCCCCCCChhhhCCCCeEEccccccccc
Q 027093 136 RVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 191 (228)
Q Consensus 136 ~~~~~C~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 191 (228)
.....|+|+.....++.||+|+.|..|-|..|+|...... ++.|.|..|....-
T Consensus 84 ~~~~~c~c~~~~~~~g~~i~c~~c~~Wqh~~C~g~~~~~~--p~~y~c~~c~~~~~ 137 (508)
T KOG1844|consen 84 REISRCDCGLEDDMEGLMIQCDWCGRWQHKICCGSFKSTK--PDKYVCEICTPRNK 137 (508)
T ss_pred CcccccccccccCCCceeeCCcccCcccCceeeeecCCCC--chhceeeeeccccc
Confidence 4677899998776589999999999999999999976543 57999999997753
No 33
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=96.12 E-value=0.00089 Score=39.77 Aligned_cols=35 Identities=29% Similarity=0.771 Sum_probs=19.8
Q ss_pred CceEECCCCCceecCCCCCCChhhhCCCCeEEccccc
Q 027093 151 DLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCS 187 (228)
Q Consensus 151 ~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~ 187 (228)
+.|++|+.|....|..|=|+...+.. +.|+|..|.
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~~~~~~--~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVSEVPDG--DDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-SS--SS-------HHH-
T ss_pred CceEEeCCCCCcCChhhCCcccCCCC--CcEECCcCC
Confidence 47999999999999999999876542 359999884
No 34
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.90 E-value=0.0025 Score=54.58 Aligned_cols=46 Identities=20% Similarity=0.468 Sum_probs=37.4
Q ss_pred cCCCCCCCCCceEECCCCCceecCCCCCCChhhhCCCCeEEcc-ccccccc
Q 027093 142 KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCS-DCSSDVD 191 (228)
Q Consensus 142 ~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~-~C~~~~~ 191 (228)
+|.+|.. .+.|+.||.|..=||.-|||+...+. ..|+|. .|.....
T Consensus 319 IC~~P~~-E~E~~FCD~CDRG~HT~CVGL~~lP~---G~WICD~~C~~~~~ 365 (381)
T KOG1512|consen 319 ICLGPVI-ESEHLFCDVCDRGPHTLCVGLQDLPR---GEWICDMRCREATL 365 (381)
T ss_pred ccCCccc-chheeccccccCCCCccccccccccC---ccchhhhHHHHhcC
Confidence 7888875 67899999999999999999987664 689999 4555443
No 35
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=95.36 E-value=0.00099 Score=59.42 Aligned_cols=55 Identities=18% Similarity=0.600 Sum_probs=41.9
Q ss_pred Cceeee-cCCCCCCCCCceEECCCCCceecCCCCCCChhhhCCCCe----EEcccccccc
Q 027093 136 RVAVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDH----FLCSDCSSDV 190 (228)
Q Consensus 136 ~~~~~C-~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~----~~C~~C~~~~ 190 (228)
.....| .|+..+....+||.|+.|..|||+.||.+.+.....+.. |.|+.|....
T Consensus 237 ~~~~~~~~cg~~~~~~~~~~~~~~~e~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~~~ 296 (345)
T KOG1632|consen 237 YSKLICDPCGLSDANKKFEICCDLCESWFHGDCVQIFEARKRLNEIRNEVYKCPHCTVLK 296 (345)
T ss_pred cccccccccCcchHHHHHHHHHHHHHHHhcccccccccchhhhhhhhccceecCceeecc
Confidence 345566 445444445789999999999999999998776655555 9999999843
No 36
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=94.75 E-value=0.012 Score=55.49 Aligned_cols=51 Identities=22% Similarity=0.644 Sum_probs=37.9
Q ss_pred ee-cCCCCCCCCCceEECCCCCceecCCCCCCChhhhCC-CCeEEccccccccc
Q 027093 140 YC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKK-LDHFLCSDCSSDVD 191 (228)
Q Consensus 140 ~C-~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~-~~~~~C~~C~~~~~ 191 (228)
|| .|.+...- ...|+||+|-.-||..|+..+...-.. .+.|+|+.|....-
T Consensus 255 fCsaCn~~~~F-~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k~~ 307 (613)
T KOG4299|consen 255 FCSACNGSGLF-NDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKIKSV 307 (613)
T ss_pred HHHHhCCcccc-ccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCeeeee
Confidence 77 78776432 345999999999999999997322211 25899999998764
No 37
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=94.32 E-value=0.021 Score=52.57 Aligned_cols=51 Identities=24% Similarity=0.645 Sum_probs=37.0
Q ss_pred ceeee-cCCCCCCCCCceEECCCCCceecCCCCCCChhhhCC---CCeEEcccccc
Q 027093 137 VAVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKK---LDHFLCSDCSS 188 (228)
Q Consensus 137 ~~~~C-~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~---~~~~~C~~C~~ 188 (228)
....| +|++..+ .-..++||.|..-||..|+..+.-.... -.-|.|..|-+
T Consensus 543 ~~ysCgiCkks~d-QHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECdk 597 (707)
T KOG0957|consen 543 MNYSCGICKKSTD-QHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECDK 597 (707)
T ss_pred cceeeeeeccchh-hHHHhhcchhhceeeccccCCccccCcccccCcceeeccccc
Confidence 34456 8887643 4477999999999999999987433211 14799999943
No 38
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=94.04 E-value=0.022 Score=54.63 Aligned_cols=52 Identities=27% Similarity=0.680 Sum_probs=42.3
Q ss_pred ceeee-cCCCCCCC-CCceEECCCCCceecCCCCCCChhhhCCCCeEEccccccccc
Q 027093 137 VAVYC-KCEMPYNP-DDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 191 (228)
Q Consensus 137 ~~~~C-~C~~~~~~-~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 191 (228)
+.+.| +|+.|+.. ...||.||.|+.--|..|-|+.+.+. ..|.|..|.....
T Consensus 270 edviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIle~p~---gpWlCr~Calg~~ 323 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGILEVPE---GPWLCRTCALGIE 323 (893)
T ss_pred ccceeceecCCCccccceeEEeccchhHHHHhhhceeecCC---CCeeehhccccCC
Confidence 45667 88887643 35999999999999999999987654 5799999988754
No 39
>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=93.23 E-value=0.064 Score=42.01 Aligned_cols=30 Identities=20% Similarity=0.651 Sum_probs=24.2
Q ss_pred ecCCCCCCChhhhCCCCeEEccccccccccc
Q 027093 163 FHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 193 (228)
Q Consensus 163 ~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~k 193 (228)
||+.|+..+...+.. ..|+|+.|..+...+
T Consensus 2 ~H~~CL~Ppl~~~P~-g~W~Cp~C~~~~~~~ 31 (148)
T cd04718 2 FHLCCLRPPLKEVPE-GDWICPFCEVEKSGQ 31 (148)
T ss_pred cccccCCCCCCCCCC-CCcCCCCCcCCCCCC
Confidence 899999998766544 579999999876544
No 40
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=93.08 E-value=0.053 Score=52.45 Aligned_cols=50 Identities=22% Similarity=0.578 Sum_probs=38.3
Q ss_pred ceeeecCCCCCCCCCceEECCCCCceecCCCCCCChhhhCCCCeEEccccccccc
Q 027093 137 VAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 191 (228)
Q Consensus 137 ~~~~C~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 191 (228)
....|+|.. ++..+.|+.|..|||..|.+.+..+....+ |+|+.|.....
T Consensus 47 ~e~c~ic~~----~g~~l~c~tC~~s~h~~cl~~pl~~~p~~~-~~c~Rc~~p~~ 96 (696)
T KOG0383|consen 47 QEACRICAD----GGELLWCDTCPASFHASCLGPPLTPQPNGE-FICPRCFCPKN 96 (696)
T ss_pred hhhhhhhcC----CCcEEEeccccHHHHHHccCCCCCcCCccc-eeeeeeccCCC
Confidence 344568884 567788999999999999999876665545 99999954443
No 41
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=90.76 E-value=0.044 Score=57.04 Aligned_cols=53 Identities=23% Similarity=0.631 Sum_probs=41.3
Q ss_pred ceeee-cCCCCCCCCCceEECCCCCceecCCCCCCChhhhCCCCeEEccccccccc
Q 027093 137 VAVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 191 (228)
Q Consensus 137 ~~~~C-~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 191 (228)
....| +|+... .+..|+.|+.|..|||.-|+.+..... .+..|.|+.|....+
T Consensus 1107 ~~~~c~~cr~k~-~~~~m~lc~~c~~~~h~~C~rp~~~~~-~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1107 VNALCKVCRRKK-QDEKMLLCDECLSGFHLFCLRPALSSV-PPGDWMCPSCRKEHR 1160 (1404)
T ss_pred chhhhhhhhhcc-cchhhhhhHhhhhhHHHHhhhhhhccC-CcCCccCCccchhhh
Confidence 34455 676654 357999999999999999999875554 335799999999885
No 42
>KOG2626 consensus Histone H3 (Lys4) methyltransferase complex, subunit CPS60/ASH2/BRE2 [Chromatin structure and dynamics; Transcription]
Probab=90.20 E-value=0.26 Score=45.84 Aligned_cols=56 Identities=25% Similarity=0.513 Sum_probs=43.1
Q ss_pred CCceeeecCCCCCCCCCceEECCCCCceecCCCCCCChhhhCC-----CCeEEcccccccc
Q 027093 135 DRVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKK-----LDHFLCSDCSSDV 190 (228)
Q Consensus 135 ~~~~~~C~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~-----~~~~~C~~C~~~~ 190 (228)
.....+|.|+...+....-+||..|.+|||..|+-....-... -+.|+|..|....
T Consensus 17 ~~~~~~~y~e~~r~l~~~elqcs~clk~~~~~~~~~~~~~~s~~pf~t~y~fvc~~c~~~~ 77 (544)
T KOG2626|consen 17 MKQATVCYCEGERNLGIVELQCSTCLKWFHLPTLEAFHLIKSSLPFMTSYEFVCKECTPSG 77 (544)
T ss_pred ccCccccccccccccCceeeEeeecccccccccccccccccccCCcccceeEEeccccCcc
Confidence 3568899999988888888999999999998776554322111 1589999999874
No 43
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=89.36 E-value=0.71 Score=29.75 Aligned_cols=41 Identities=17% Similarity=0.235 Sum_probs=27.6
Q ss_pred EccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeecc
Q 027093 23 VRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPE 67 (228)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~ 67 (228)
+++||.|.++++. ...-|..|..- .....-++.++||---.
T Consensus 1 f~~GDvV~LKSGG--p~MTV~~v~~~--~~~~~~~v~C~WFd~~~ 41 (53)
T PF09926_consen 1 FKIGDVVQLKSGG--PRMTVTEVGPN--AGASGGWVECQWFDGHG 41 (53)
T ss_pred CCCCCEEEEccCC--CCeEEEEcccc--ccCCCCeEEEEeCCCCC
Confidence 5789999999997 34455544433 12334689999997443
No 44
>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=89.27 E-value=0.38 Score=44.07 Aligned_cols=52 Identities=19% Similarity=0.517 Sum_probs=34.9
Q ss_pred eecCCCCCCC--CCceEECCCCCceecCCCCCC--------Chhhh-C-CCCeEEccccccccc
Q 027093 140 YCKCEMPYNP--DDLMVQCEGCKDWFHPSCMGM--------TIEEA-K-KLDHFLCSDCSSDVD 191 (228)
Q Consensus 140 ~C~C~~~~~~--~~~mi~C~~C~~w~H~~Cv~~--------~~~~~-~-~~~~~~C~~C~~~~~ 191 (228)
.|+|.+-++. +-.||.||.|+.|-|.+|.=- +.... . ....|.|..|.....
T Consensus 131 C~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~se 194 (446)
T PF07227_consen 131 CCICSKFDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTSE 194 (446)
T ss_pred ccccCCcccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChhh
Confidence 4578774322 247899999999999999722 11111 1 113899999998775
No 45
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=89.02 E-value=0.15 Score=44.01 Aligned_cols=37 Identities=27% Similarity=0.628 Sum_probs=29.9
Q ss_pred CceEECCCCCceecCCCCCCChhhhCCC--CeEEccccc
Q 027093 151 DLMVQCEGCKDWFHPSCMGMTIEEAKKL--DHFLCSDCS 187 (228)
Q Consensus 151 ~~mi~C~~C~~w~H~~Cv~~~~~~~~~~--~~~~C~~C~ 187 (228)
+.||.|..|..-+|+.|+..++..+..+ ..|.|..|.
T Consensus 277 ~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~ 315 (381)
T KOG1512|consen 277 NSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSCE 315 (381)
T ss_pred ccceeecccccCCCCcchhcCHHHHhHHhhcchhhcccH
Confidence 5899999999999999999988766443 467666664
No 46
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=88.67 E-value=0.32 Score=45.08 Aligned_cols=56 Identities=20% Similarity=0.522 Sum_probs=40.3
Q ss_pred CCceeeecCCCCCCC-CCceEECCCCCceecCCCCCCChhh-----hCC--CCeEEcccccccc
Q 027093 135 DRVAVYCKCEMPYNP-DDLMVQCEGCKDWFHPSCMGMTIEE-----AKK--LDHFLCSDCSSDV 190 (228)
Q Consensus 135 ~~~~~~C~C~~~~~~-~~~mi~C~~C~~w~H~~Cv~~~~~~-----~~~--~~~~~C~~C~~~~ 190 (228)
.++...|+|-..... -+..+||+.|+--.|..|-|+.... ..+ ...|+|..|.-..
T Consensus 117 kk~~iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~Gv 180 (707)
T KOG0957|consen 117 KKAVICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYGV 180 (707)
T ss_pred ccceEEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHhcCC
Confidence 456688999654433 3688999999999999999986221 111 2579999998754
No 47
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=88.16 E-value=0.19 Score=31.96 Aligned_cols=33 Identities=24% Similarity=0.485 Sum_probs=16.3
Q ss_pred ceEECCCCCceecCCCCCCChhhhCCCCeEEccc
Q 027093 152 LMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSD 185 (228)
Q Consensus 152 ~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~ 185 (228)
..|||+.|.+|=... .++.......++.|+|..
T Consensus 2 ~WVQCd~C~KWR~lp-~~~~~~~~~~~d~W~C~~ 34 (50)
T PF07496_consen 2 YWVQCDSCLKWRRLP-EEVDPIREELPDPWYCSM 34 (50)
T ss_dssp EEEE-TTT--EEEE--CCHHCTSCCSSTT--GGG
T ss_pred eEEECCCCCceeeCC-hhhCcccccCCCeEEcCC
Confidence 579999999998866 222221122335899986
No 48
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=86.72 E-value=0.31 Score=46.76 Aligned_cols=53 Identities=25% Similarity=0.589 Sum_probs=41.4
Q ss_pred ceeeecCCCCCCC-CCceEECC--CCCceecCCCCCCChhhhCCCCeEEcccccccccc
Q 027093 137 VAVYCKCEMPYNP-DDLMVQCE--GCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (228)
Q Consensus 137 ~~~~C~C~~~~~~-~~~mi~C~--~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (228)
..-+|+|.+...+ +...|-|| .|..-.|..|-||-..+. ..|+|..|....++
T Consensus 5 VGGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVPt---GpWfCrKCesqera 60 (900)
T KOG0956|consen 5 VGGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVPT---GPWFCRKCESQERA 60 (900)
T ss_pred ccceeeecCcCCCccCceeeecCCCceeeeehhcceeEecCC---Cchhhhhhhhhhhh
Confidence 3568999654333 56889999 799999999999976554 57999999887663
No 49
>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]
Probab=86.37 E-value=0.079 Score=47.77 Aligned_cols=89 Identities=13% Similarity=0.075 Sum_probs=75.9
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeecccccCCccccCCCCeEEeeCCceeeeccceEeee
Q 027093 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKC 100 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~d~~~~~~~~~~~~ELFlS~~~d~i~~~~I~gkc 100 (228)
....+|+.+.+.+......+.++.+..+|.+.++..+.-+.|||+|.++.......+..+++......+........+.|
T Consensus 275 ~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 (371)
T COG5076 275 SQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTDYYKNANVLED 354 (371)
T ss_pred cccccccccccccCCcccccchhhhhhcccccccchhhhhcccCCCccccccccchhhhcccccchhhhhhhhhccchhh
Confidence 48899999999998877889999999999999888888999999999877776667788999998888888888888888
Q ss_pred EEEeecccc
Q 027093 101 TVHTFKNYT 109 (228)
Q Consensus 101 ~V~~~~~~~ 109 (228)
.|....++.
T Consensus 355 ~~~~~~~~~ 363 (371)
T COG5076 355 FVIKKTRLI 363 (371)
T ss_pred hHhhhhhhh
Confidence 877655443
No 50
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=83.37 E-value=3.8 Score=28.32 Aligned_cols=31 Identities=29% Similarity=0.503 Sum_probs=25.3
Q ss_pred EEccCCEEEEccCC-----CCCCCeEEEEeEEEEcC
Q 027093 22 VVRPGDCVLMRPAD-----SDKPPYVARVEKIEADH 52 (228)
Q Consensus 22 ~~~vGD~V~v~~~~-----~~~~~~I~rI~~i~~~~ 52 (228)
-++.||+|.|..+. .+...|+|.|+......
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~gga 40 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGA 40 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEeccc
Confidence 36899999999976 24678999999998754
No 51
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=82.21 E-value=0.84 Score=29.50 Aligned_cols=27 Identities=26% Similarity=0.666 Sum_probs=24.4
Q ss_pred cCCCCCCCCCceEECCCCCceecCCCC
Q 027093 142 KCEMPYNPDDLMVQCEGCKDWFHPSCM 168 (228)
Q Consensus 142 ~C~~~~~~~~~mi~C~~C~~w~H~~Cv 168 (228)
.|+.+..+.+..+.|..|+.=||..|-
T Consensus 10 ~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 10 VCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred hhCCcccCCCCEEECCCCCCcccHHHH
Confidence 788888778899999999999999997
No 52
>cd05834 HDGF_related The PWWP domain is an essential part of the Hepatoma Derived Growth Factor (HDGF) family of proteins, and is necessary for DNA binding by HDGF. This family of endogenous nuclear-targeted mitogens includes HRP (HDGF-related proteins 1, 2, 3, 4, or HPR1, HPR2, HPR3, HPR4, respectively) and lens epithelium-derived growth factor, LEDGF. Members of the HDGF family have been linked to human diseases, and HDGF is a prognostic factor in several types of cancer. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=81.55 E-value=3 Score=29.30 Aligned_cols=43 Identities=23% Similarity=0.299 Sum_probs=34.5
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeec
Q 027093 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRP 66 (228)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp 66 (228)
.+++||.|.-.-.. -++|-|+|.+.-........+.|+||-..
T Consensus 2 ~f~~GdlVwaK~kG--yp~WPa~I~~~~~~~~~~~~~~V~FfGt~ 44 (83)
T cd05834 2 QFKAGDLVFAKVKG--YPAWPARVDEPEDWKPPGKKYPVYFFGTH 44 (83)
T ss_pred CCCCCCEEEEecCC--CCCCCEEEecccccCCCCCEEEEEEeCCC
Confidence 47899999999875 79999999998765444567889888854
No 53
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=81.26 E-value=0.69 Score=34.01 Aligned_cols=30 Identities=23% Similarity=0.620 Sum_probs=24.2
Q ss_pred eeeecCCCCCCCCCceEECCC--CCceecCCCCCC
Q 027093 138 AVYCKCEMPYNPDDLMVQCEG--CKDWFHPSCMGM 170 (228)
Q Consensus 138 ~~~C~C~~~~~~~~~mi~C~~--C~~w~H~~Cv~~ 170 (228)
....+|++. .+..|+|.. |..+||..|...
T Consensus 56 ~~C~iC~~~---~G~~i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 56 LKCSICGKS---GGACIKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred CcCcCCCCC---CceeEEcCCCCCCcCCCHHHHHH
Confidence 345589875 678999996 999999999844
No 54
>PF08940 DUF1918: Domain of unknown function (DUF1918); InterPro: IPR015035 This domain is found in various hypothetical bacterial proteins, and has no known function. ; PDB: 2A7Y_A.
Probab=81.10 E-value=2.9 Score=27.41 Aligned_cols=39 Identities=15% Similarity=0.304 Sum_probs=26.7
Q ss_pred ccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEE
Q 027093 24 RPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWY 63 (228)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~Wf 63 (228)
++||.+.|.....+.+...|.|.++.. .+|..-..|+|-
T Consensus 4 ~vGD~lvv~g~~vg~~~r~GeIveV~g-~dG~PPY~VRw~ 42 (58)
T PF08940_consen 4 SVGDRLVVHGRTVGQPDRHGEIVEVRG-PDGSPPYLVRWD 42 (58)
T ss_dssp -TTEEEEES-TTTS--EEEEEEEE-S--SSS-S-EEEEET
T ss_pred CCCCEEEEcCCcCCCCCcEeEEEEEEC-CCCCCCEEEEec
Confidence 689999999987778899999999988 566677788885
No 55
>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=79.25 E-value=0.16 Score=31.04 Aligned_cols=40 Identities=23% Similarity=0.544 Sum_probs=27.6
Q ss_pred cCCCCCCCCCceEECCCCCceecCCCCCCChhhhCCCCeEEccccc
Q 027093 142 KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCS 187 (228)
Q Consensus 142 ~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~ 187 (228)
+|.....++..++... |+..||.+|+..-... ...||.|+
T Consensus 5 IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~-----~~~CP~CR 44 (44)
T PF13639_consen 5 ICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKR-----NNSCPVCR 44 (44)
T ss_dssp TTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHH-----SSB-TTTH
T ss_pred CCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHh-----CCcCCccC
Confidence 7777776566677666 9999999998654333 13688874
No 56
>cd06080 MUM1_like Mutated melanoma-associated antigen 1 (MUM-1) is a melanoma-associated antigen (MAA). MUM-1 belongs to the mutated or aberrantly expressed type of MAAs, along with antigens such as CDK4, beta-catenin, gp100-in4, p15, and N-acetylglucosaminyltransferase V. It is highly expressed in several types of human cancers. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=78.76 E-value=4 Score=28.63 Aligned_cols=39 Identities=21% Similarity=0.226 Sum_probs=31.6
Q ss_pred EccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeec
Q 027093 23 VRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRP 66 (228)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp 66 (228)
+.+||.|.-.-.. -+.|.|+|.++.. +...+.|.||--.
T Consensus 1 f~~gdlVWaK~~g--~P~WPa~I~~~~~---~~~k~~V~FfG~~ 39 (80)
T cd06080 1 FEKNDLVWAKIQG--YPWWPAVIKSISR---KKQKARVNFIGDN 39 (80)
T ss_pred CCCCCEEEEeCCC--CCCCCEEEeeecC---CCCEEEEEEeCCC
Confidence 4689999988876 7899999999854 3567889888766
No 57
>cd05835 Dnmt3b_related The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of Dnmt3b has been identified in patients with ICF syndrome (immunodeficiency, centromeric instability, and facial anomalies), a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=78.49 E-value=3.1 Score=29.44 Aligned_cols=41 Identities=22% Similarity=0.229 Sum_probs=31.7
Q ss_pred EccCCEEEEccCCCCCCCeEEEEeEEEEcCC---CCEEEEEEEEee
Q 027093 23 VRPGDCVLMRPADSDKPPYVARVEKIEADHR---NNVKVRVRWYYR 65 (228)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~---~~~~v~v~WfyR 65 (228)
+.+||.|..+-.. -+.|-|+|.+...... ..-.+.|.||-.
T Consensus 1 f~vGDlVWaK~kg--~pwWP~~V~~~~~~~~~~~~~~~~~V~fFGs 44 (87)
T cd05835 1 FNVGDLVWGKIKG--FPWWPGRVVSITVTSKRPPVVGMRWVTWFGS 44 (87)
T ss_pred CCCCCEEEEecCC--CCCCCeEEechhhcccccCCCCeEEEEEeCC
Confidence 4689999999976 7899999999866431 235688888863
No 58
>PRK13251 transcription attenuation protein MtrB; Provisional
Probab=76.29 E-value=10 Score=25.80 Aligned_cols=47 Identities=21% Similarity=0.204 Sum_probs=37.4
Q ss_pred EEEEEEeecccccCCccccCCCCeEEeeCCceeeeccceEeeeEEEe
Q 027093 58 VRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHT 104 (228)
Q Consensus 58 v~v~WfyRp~d~~~~~~~~~~~~ELFlS~~~d~i~~~~I~gkc~V~~ 104 (228)
|.|.=+-|..|+.-.....-++.||.+...++-.++-.|+||+.|..
T Consensus 19 V~vIgltrg~dtkfhhtEkLDkGEVmiaqftehtsaiKirGkA~I~t 65 (75)
T PRK13251 19 VNVIGLTRGKDTKFHHTEKLDKGEVMIAQFTEHTSAIKIRGKAEIQT 65 (75)
T ss_pred eEEEEEecCCCccchhhhhcCCCcEEEEEeecceeEEEEeceEEEEe
Confidence 66666788888753322335889999999999999999999999986
No 59
>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=75.81 E-value=2.3 Score=31.40 Aligned_cols=46 Identities=22% Similarity=0.559 Sum_probs=28.7
Q ss_pred cCCCCCCCCCceEEC------CCC---CceecCCCCCC----ChhhhCCCCeEEccccccc
Q 027093 142 KCEMPYNPDDLMVQC------EGC---KDWFHPSCMGM----TIEEAKKLDHFLCSDCSSD 189 (228)
Q Consensus 142 ~C~~~~~~~~~mi~C------~~C---~~w~H~~Cv~~----~~~~~~~~~~~~C~~C~~~ 189 (228)
.|++... +..+.| ..| ..-|...|+.. ...++.....|.||.|+.-
T Consensus 12 qCrqKt~--~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crgi 70 (105)
T PF10497_consen 12 QCRQKTL--DFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGI 70 (105)
T ss_pred hhcCCCC--CCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCCe
Confidence 6666432 233455 556 88899999844 2333333368999999863
No 60
>PF02081 TrpBP: Tryptophan RNA-binding attenuator protein; InterPro: IPR023558 The tryptophan RNA-binding attenuation protein (TRAP) regulates expression of the tryptophan biosynthetic genes in Bacillus sp. by binding to the leader region of the nascent trp operon mRNA []. The crystal structure of the Trp RNA-binding attenuation protein of Bacillus subtilis has been solved []. TRAP forms an oligomeric ring consisting of 11 single-domain subunits, where each subunit adopts a double-stranded beta-helix structure with the appearance of a beta-sandwich of distinct architecture and jelly-roll fold. The 11 subunits are stabilised by 11 inter-subunit strands, forming a beta-wheel with a large central hole. TRAP is activated by binding to tryptophan in clefts between adjacent beta-strands, which induces conformational changes in the protein. Activated TRAP binds an mRNA target sequence consisting of 11 (G/U)AG repeats, separated by 2-3 spacer nucleotides. The spacer nucleotides do not make direct contact with the TRAP protein, but they do influence the conformation of the RNA, which might influence the specificity of TRAP []. This entry represents the structural domain in the TRAP family of proteins.; PDB: 3ZTE_U 1GTN_H 1UTD_D 1GTF_D 1UTF_F 2ZP9_K 1C9S_Q 2EXT_A 3AQD_T 1QAW_C ....
Probab=75.74 E-value=8.1 Score=26.29 Aligned_cols=47 Identities=21% Similarity=0.169 Sum_probs=34.8
Q ss_pred EEEEEEeecccccCCccccCCCCeEEeeCCceeeeccceEeeeEEEe
Q 027093 58 VRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHT 104 (228)
Q Consensus 58 v~v~WfyRp~d~~~~~~~~~~~~ELFlS~~~d~i~~~~I~gkc~V~~ 104 (228)
|.|.=+-|..||.-.....-++.||.+...++-.++-.|+|++.|++
T Consensus 19 V~ViGlTRG~dtkfhHtEkLDkGEVmIaQFTehtsaiKiRGkA~I~t 65 (75)
T PF02081_consen 19 VTVIGLTRGTDTKFHHTEKLDKGEVMIAQFTEHTSAIKIRGKAEILT 65 (75)
T ss_dssp EEEEEEESSSSSSEEEEEEE-TT-EEEEE-BSSEEEEEEESSEEEEE
T ss_pred eEEEEEecCCcccchhhhccCCCcEEEEEeecceEEEEEeeeEEEEe
Confidence 66667788888753322235789999999999999999999999987
No 61
>PF10383 Clr2: Transcription-silencing protein Clr2 ; InterPro: IPR018839 Clr2 (cryptic loci regulator) is a chromatin silencing protein, one of a quartet of proteins forming the core of SHREC, a multienzyme effector complex that mediates hetero-chromatic transcriptional gene silencing in fission yeast []. Clr2 does not have any obvious well-conserved domains but, along with the other core proteins, binds to the histone deacetylase Clr3, and on its own might also have a role in chromatin organisation at the cnt domain, the site of kinetochore assembly.
Probab=74.89 E-value=18 Score=27.96 Aligned_cols=57 Identities=18% Similarity=0.269 Sum_probs=39.8
Q ss_pred eeeeEEEcCCCeEEccCCEEEEccCC----------CCCCCeEEEEeEEEEcCCC-------CEEEEEEEEeecccc
Q 027093 10 DLDSYNIKGTNKVVRPGDCVLMRPAD----------SDKPPYVARVEKIEADHRN-------NVKVRVRWYYRPEES 69 (228)
Q Consensus 10 ~y~s~~v~g~~~~~~vGD~V~v~~~~----------~~~~~~I~rI~~i~~~~~~-------~~~v~v~WfyRp~d~ 69 (228)
||+++-+.. +.+.+||.|-|.+.. .++..-|-.|.+|...... .+.|++. .|++...
T Consensus 2 ~y~GiflGA--E~I~vGD~VRl~~~~~~~~~~~~~~~~~~tdvMvI~~I~~~~~~~~~~~~~~v~~~G~-lY~~~~~ 75 (139)
T PF10383_consen 2 YYRGIFLGA--EMIWVGDAVRLKPLNASPSPNQSDGNPDVTDVMVIDEIQLRLINCDPDSPSTVRFRGD-LYTLAPQ 75 (139)
T ss_pred eECeEEEee--EEEEeCCEEEECccCCCcccccccCCCCceeEEEEeEEEEecccCCCCCCceEEEEeE-eceeccc
Confidence 677887743 899999999995432 2355678888899876433 4778876 5555543
No 62
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=73.84 E-value=4 Score=32.67 Aligned_cols=44 Identities=23% Similarity=0.558 Sum_probs=31.5
Q ss_pred CCceEECCCCCceecCCCCCCChhh-------hCCCCeEEccccccccccc
Q 027093 150 DDLMVQCEGCKDWFHPSCMGMTIEE-------AKKLDHFLCSDCSSDVDAK 193 (228)
Q Consensus 150 ~~~mi~C~~C~~w~H~~Cv~~~~~~-------~~~~~~~~C~~C~~~~~~k 193 (228)
-+.||.|.+|..-||..|+|..... .++...--|..|......|
T Consensus 14 kG~Lv~CQGCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~~~kK 64 (175)
T PF15446_consen 14 KGPLVYCQGCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGIAHKK 64 (175)
T ss_pred CCCeEEcCccChHHHhhhcCCccccceeeEEEcCCceEEechhhcChhhcc
Confidence 4699999999999999999985432 1122344677777666655
No 63
>PF09871 DUF2098: Uncharacterized protein conserved in archaea (DUF2098); InterPro: IPR019209 This family of proteins have no known function.
Probab=73.67 E-value=9.8 Score=27.35 Aligned_cols=43 Identities=23% Similarity=0.328 Sum_probs=32.8
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEE---EEEeeccccc
Q 027093 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRV---RWYYRPEESI 70 (228)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v---~WfyRp~d~~ 70 (228)
.|.+|++|--.+.. -+|+|.+|.. .++..|+.+ .-||||+-+.
T Consensus 2 ~I~vGs~VRY~~TG-----T~G~V~diK~-ed~~~wv~LD~t~L~Yr~~~Le 47 (91)
T PF09871_consen 2 PIKVGSYVRYINTG-----TVGKVVDIKE-EDGETWVLLDSTDLYYRPDYLE 47 (91)
T ss_pred cceeCCEEEECCCC-----eEEEEEEEEE-eCCCeEEEEccCCceeecceeE
Confidence 57889999766655 4999999944 677788887 5788888654
No 64
>PF13922 PHD_3: PHD domain of transcriptional enhancer, Asx
Probab=73.10 E-value=0.63 Score=31.14 Aligned_cols=32 Identities=28% Similarity=0.863 Sum_probs=26.8
Q ss_pred CceeeecCCCCCCCCCceEECCCCCceecCCCCCCCh
Q 027093 136 RVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTI 172 (228)
Q Consensus 136 ~~~~~C~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~ 172 (228)
....-|.|... -||.|..|+.+-|.+|+|.++
T Consensus 31 ~~~~~C~C~Lk-----AMi~Cq~CGAFCHDDCIgpsk 62 (69)
T PF13922_consen 31 STSNKCACSLK-----AMIMCQGCGAFCHDDCIGPSK 62 (69)
T ss_pred ccccccccchH-----HHHHHhhccchhccccccHHH
Confidence 45667888843 799999999999999999865
No 65
>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=72.82 E-value=9.1 Score=21.57 Aligned_cols=26 Identities=15% Similarity=0.233 Sum_probs=22.1
Q ss_pred cCCEEEEccCCCCCCCeEEEEeEEEEcC
Q 027093 25 PGDCVLMRPADSDKPPYVARVEKIEADH 52 (228)
Q Consensus 25 vGD~V~v~~~~~~~~~~I~rI~~i~~~~ 52 (228)
+||.|.|..+. ..-.+|+|.+|....
T Consensus 1 ~Gd~V~V~~G~--~~G~~G~I~~i~~~~ 26 (32)
T PF00467_consen 1 VGDTVKVISGP--FKGKIGKIVEIDRSK 26 (32)
T ss_dssp TTSEEEESSST--TTTEEEEEEEEETTT
T ss_pred CCCEEEEeEcC--CCCceEEEEEEECCC
Confidence 59999999997 567899999998754
No 66
>cd05162 PWWP The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors.
Probab=72.31 E-value=6.5 Score=27.50 Aligned_cols=40 Identities=30% Similarity=0.348 Sum_probs=30.9
Q ss_pred EccCCEEEEccCCCCCCCeEEEEeEEEEcCC------CCEEEEEEEEe
Q 027093 23 VRPGDCVLMRPADSDKPPYVARVEKIEADHR------NNVKVRVRWYY 64 (228)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~------~~~~v~v~Wfy 64 (228)
|++||.|...-.. -+.|-|+|.+...... ....+.|++|-
T Consensus 1 f~~GdlVwaK~~g--~pwWPa~V~~~~~~~~~~~~~~~~~~~~V~Ffg 46 (87)
T cd05162 1 FRPGDLVWAKMKG--YPWWPALVVDPPKDSKKAKKKAKEGKVLVLFFG 46 (87)
T ss_pred CCCCCEEEEeCCC--CCCCCEEEccccccchhhhccCCCCEEEEEEeC
Confidence 5789999999986 7899999999887532 23467777775
No 67
>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=72.12 E-value=12 Score=23.88 Aligned_cols=36 Identities=22% Similarity=0.263 Sum_probs=25.6
Q ss_pred EccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEE
Q 027093 23 VRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVR 61 (228)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~ 61 (228)
+.+|+.|++.-.+ ...+-|+|+++.. ..+.....|.
T Consensus 1 ~~vG~~v~~~~~~--~~~y~A~I~~~r~-~~~~~~YyVH 36 (55)
T PF11717_consen 1 FEVGEKVLCKYKD--GQWYEAKILDIRE-KNGEPEYYVH 36 (55)
T ss_dssp --TTEEEEEEETT--TEEEEEEEEEEEE-CTTCEEEEEE
T ss_pred CCcCCEEEEEECC--CcEEEEEEEEEEe-cCCCEEEEEE
Confidence 4689999999943 6889999999999 4444444443
No 68
>COG4014 Uncharacterized protein conserved in archaea [Function unknown]
Probab=72.12 E-value=12 Score=26.71 Aligned_cols=41 Identities=27% Similarity=0.375 Sum_probs=30.1
Q ss_pred ccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEE---EEeecccc
Q 027093 24 RPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVR---WYYRPEES 69 (228)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~---WfyRp~d~ 69 (228)
.+||.|---+.+ .+|+|..|.++.+|.+|+.+- -+||+.=+
T Consensus 10 ~VG~avrYvnTg-----TvgrV~dIkkdEdG~~WV~LdstdLwYre~~l 53 (97)
T COG4014 10 KVGDAVRYVNTG-----TVGRVVDIKKDEDGDIWVVLDSTDLWYREHYL 53 (97)
T ss_pred hhcceEEEeecC-----ceeeEEEEEeecCCceEEEEecCCceecccce
Confidence 478866444333 399999999999999998874 46777643
No 69
>PRK10708 hypothetical protein; Provisional
Probab=71.35 E-value=19 Score=23.43 Aligned_cols=43 Identities=14% Similarity=0.241 Sum_probs=31.9
Q ss_pred ccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEE-------EEEEEeeccc
Q 027093 24 RPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKV-------RVRWYYRPEE 68 (228)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v-------~v~WfyRp~d 68 (228)
+++|.|.|+.+. .+...|.|..+..-..|.+++ .+.||+.-.+
T Consensus 2 kvnD~VtVKTDG--~~rR~G~iLavE~F~EG~MyLvaL~dYP~GiWFFNE~~ 51 (62)
T PRK10708 2 KVNDRVTVKTDG--GPRRPGVVLAVEEFSEGTMYLVSLEDYPLGIWFFNEAG 51 (62)
T ss_pred ccccEEEEecCC--CccccceEEEEeeccCcEEEEEEcCcCCCceEEEeccC
Confidence 578999999987 677788888887766776543 3567776444
No 70
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=71.07 E-value=22 Score=23.13 Aligned_cols=44 Identities=14% Similarity=0.310 Sum_probs=31.8
Q ss_pred ccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEE-------EEEEEeecccc
Q 027093 24 RPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKV-------RVRWYYRPEES 69 (228)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v-------~v~WfyRp~d~ 69 (228)
+++|.|.|+.+. .+..-|.|..+..-..|.+++ .+.||+.-.+-
T Consensus 2 kvnD~VtVKTDG--~~rR~G~ilavE~F~EG~MYLvaL~dYP~GiWFFNE~~~ 52 (62)
T PF10781_consen 2 KVNDRVTVKTDG--GPRREGVILAVEPFNEGTMYLVALEDYPAGIWFFNEKDS 52 (62)
T ss_pred ccccEEEEecCC--cccccceEEEEeeccCcEEEEEEcCcCCcceEEEecCCC
Confidence 578999999987 567788888887766675543 35677765443
No 71
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=69.20 E-value=7.2 Score=25.68 Aligned_cols=40 Identities=23% Similarity=0.212 Sum_probs=29.9
Q ss_pred EccCCEEEEccCCCCCCCeEEEEeEEEEcC-------CCCEEEEEEEEe
Q 027093 23 VRPGDCVLMRPADSDKPPYVARVEKIEADH-------RNNVKVRVRWYY 64 (228)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~-------~~~~~v~v~Wfy 64 (228)
|++||.|..+-.. -+.|-|+|..-.... .....+.|++|-
T Consensus 1 f~~GdlVwaK~~G--~p~WPa~V~~~~~~~~~~~~~~~~~~~~~V~Ffg 47 (63)
T smart00293 1 FKPGDLVWAKMKG--FPWWPALVVSPKETPDNIRKRKRFENLYPVLFFG 47 (63)
T ss_pred CCCCCEEEEECCC--CCCCCeEEcCcccCChhHhhccCCCCEEEEEEeC
Confidence 5789999999986 789999999887543 223466676664
No 72
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=69.05 E-value=1.1 Score=42.90 Aligned_cols=40 Identities=30% Similarity=0.762 Sum_probs=30.8
Q ss_pred CCceEECCCCCceecCCCCCCChhhhC--CCC-eEEccccccc
Q 027093 150 DDLMVQCEGCKDWFHPSCMGMTIEEAK--KLD-HFLCSDCSSD 189 (228)
Q Consensus 150 ~~~mi~C~~C~~w~H~~Cv~~~~~~~~--~~~-~~~C~~C~~~ 189 (228)
...|++|+.|+.|.|..|.++...... ..| .|.|..|+-.
T Consensus 160 ~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~CR~e 202 (694)
T KOG4443|consen 160 SLPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTCRGE 202 (694)
T ss_pred chhhHHHHHhcccccCCCCccchHHHHHHhhhhhcccceeehh
Confidence 347799999999999999999754321 124 7999999843
No 73
>PTZ00112 origin recognition complex 1 protein; Provisional
Probab=67.83 E-value=9.5 Score=38.72 Aligned_cols=116 Identities=21% Similarity=0.275 Sum_probs=71.5
Q ss_pred CceeeeeEEEcCCCeEEccCCEEEEccCCCC--------------------CCC--eEEEEeEEEEcCC-CCEEEEEEEE
Q 027093 7 GKKDLDSYNIKGTNKVVRPGDCVLMRPADSD--------------------KPP--YVARVEKIEADHR-NNVKVRVRWY 63 (228)
Q Consensus 7 ~~~~y~s~~v~g~~~~~~vGD~V~v~~~~~~--------------------~~~--~I~rI~~i~~~~~-~~~~v~v~Wf 63 (228)
.+.-|.|+.+++ +.|.+||.|+|.....+ ..+ -=|+|.+|+.... ..+.+.|..|
T Consensus 439 ~g~iye~~~in~--~~ys~g~dv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~kg~is~fy~~~~~~~~~~e~c~y 516 (1164)
T PTZ00112 439 DGVIYESIQIND--VEYSIGDDVLIFCTGNGNTYNGKSGTKKNQNNKNIKENIYQLRKGKISSFYKNTNSNQVEAEVCIY 516 (1164)
T ss_pred CceEEEEEEEcc--eeeccCCcEEEEEcCCCCccccccCccccccccchhhhhheecccccchhhhcCCCceeeEEEEEE
Confidence 456788999986 79999999999876421 112 2389999998754 4589999999
Q ss_pred eeccccc---------CCccccCCCCeEEeeCC-----------ceeeeccceEeeeEEEeeccccc---ccCCCCcceE
Q 027093 64 YRPEESI---------GGRRQFHGAKELFLSDH-----------YDVQSAHTIEGKCTVHTFKNYTK---LENVGAEDYF 120 (228)
Q Consensus 64 yRp~d~~---------~~~~~~~~~~ELFlS~~-----------~d~i~~~~I~gkc~V~~~~~~~~---~~~~~~~~Ff 120 (228)
|-..|.. ..|. .-..-|+|+-+. +-...+.-|..|..|....+-.. ....+.+-|+
T Consensus 517 ~d~~d~~~i~~~~~~~~~rr-~~~~f~~~~d~~~~~~~llgni~f~~~~~~~i~kki~~~ne~~~~~~d~~~~~g~~kfl 595 (1164)
T PTZ00112 517 YDQHDAQYIKELEEKQKSRR-CKADFEVFLDDDTKNFYLLGNIHFKILDAKMILKKIYVYNEKELYDEDKTAKQGKDKFL 595 (1164)
T ss_pred EccccHHHHHHHHHHHHhhh-hhhhhhHhcccccceeEEecceeEEEechHhhhhhheeecchhhcccchhhhcccchhh
Confidence 9988843 0111 112334444433 23455566777777765433211 1123566677
Q ss_pred Eeecc
Q 027093 121 CRFEY 125 (228)
Q Consensus 121 cr~~Y 125 (228)
|-+..
T Consensus 596 c~~~~ 600 (1164)
T PTZ00112 596 CTHYL 600 (1164)
T ss_pred hhHhh
Confidence 76543
No 74
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=66.95 E-value=1.7 Score=41.64 Aligned_cols=41 Identities=20% Similarity=0.497 Sum_probs=31.6
Q ss_pred CCceEECCCCCceecCCCCCCChhhhCCCCeEEcccccccc
Q 027093 150 DDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDV 190 (228)
Q Consensus 150 ~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~ 190 (228)
.+.|.-|..|+..||+.||.+-...+....-|-|+.|+.-.
T Consensus 32 ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe 72 (694)
T KOG4443|consen 32 AGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCE 72 (694)
T ss_pred cCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeee
Confidence 46799999999999999999765555444558888887543
No 75
>PF13341 RAG2_PHD: RAG2 PHD domain; PDB: 2JWO_A 2V86_B 2V85_B 2V87_A 2V83_C 2V89_A 2V88_A.
Probab=66.52 E-value=1.8 Score=29.42 Aligned_cols=35 Identities=23% Similarity=0.665 Sum_probs=19.3
Q ss_pred ceEECCC-CCceecCCCCCCChhhh----CCCCeEEcccc
Q 027093 152 LMVQCEG-CKDWFHPSCMGMTIEEA----KKLDHFLCSDC 186 (228)
Q Consensus 152 ~mi~C~~-C~~w~H~~Cv~~~~~~~----~~~~~~~C~~C 186 (228)
-||.|.. =+.|-|..|+.+++... +.-.+|+|..=
T Consensus 29 AMI~cs~~~GHWvhaqCm~LsE~~L~~LSq~n~KYfC~dH 68 (78)
T PF13341_consen 29 AMIFCSRGGGHWVHAQCMDLSETMLIQLSQENTKYFCNDH 68 (78)
T ss_dssp -EEEE-STT-EEEETGGGT--HHHHHHHHHSSS-B--TTT
T ss_pred eEEEEeCCCceEeEeecccchHHHHHHHccCCceEEEhhh
Confidence 7899984 58999999999986542 22257888653
No 76
>PF07154 DUF1392: Protein of unknown function (DUF1392); InterPro: IPR009824 This family consists of several hypothetical cyanobacterial proteins of around 150 residues in length, which seem to be specific to Anabaena species. The function of this family is unknown.
Probab=66.01 E-value=18 Score=28.20 Aligned_cols=51 Identities=25% Similarity=0.346 Sum_probs=35.7
Q ss_pred CceeeeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeeccc
Q 027093 7 GKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEE 68 (228)
Q Consensus 7 ~~~~y~s~~v~g~~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~d 68 (228)
+....++.++.. -.+++||-|.+...+ +.+-.-.|..|.- ++-.|||-=+-
T Consensus 74 ~tg~~q~~tv~k--p~F~LGd~V~~~f~~--~~pkqRlIlGv~l-------v~~~W~Y~VE~ 124 (150)
T PF07154_consen 74 GTGQLQSLTVQK--PAFRLGDRVEFRFYS--DGPKQRLILGVFL-------VNNSWFYAVEW 124 (150)
T ss_pred ecCccceeeccC--CceecCCEEEEEecC--CCCceEEEEEEEE-------ecCceEEEEEE
Confidence 455566666765 478899999988864 4556677777755 66679997664
No 77
>cd05840 SPBC215_ISWI_like The PWWP domain is a component of the S. pombe hypothetical protein SPBC215, as well as ISWI complex protein 4. The ISWI (imitation switch) proteins are ATPases responsible for chromatin remodeling in eukaryotes, and SPBC215 is proposed to also bind chromatin. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=65.26 E-value=8.2 Score=27.72 Aligned_cols=40 Identities=28% Similarity=0.382 Sum_probs=29.4
Q ss_pred EccCCEEEEccCCCCCCCeEEEEeEEE---------EcCCCCEEEEEEEEe
Q 027093 23 VRPGDCVLMRPADSDKPPYVARVEKIE---------ADHRNNVKVRVRWYY 64 (228)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~rI~~i~---------~~~~~~~~v~v~Wfy 64 (228)
|++||.|...-.. -+.|-|+|..=. ..+.....+.|++|-
T Consensus 1 f~~GDlVwaK~~G--yPwWPA~V~~~~~~p~~~l~~~~~~~~~~~~V~FFg 49 (93)
T cd05840 1 FQPGDRVLAKVKG--FPAWPAIVVPEEMLPDSVLKGKKKKNKRTYPVMFFP 49 (93)
T ss_pred CCCCCEEEEeCCC--CCCCCEEECChHHCCHHHHhcccCCCCCeEEEEEeC
Confidence 5789999999986 799999998632 112334668888774
No 78
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=63.62 E-value=5.8 Score=32.88 Aligned_cols=33 Identities=21% Similarity=0.598 Sum_probs=25.5
Q ss_pred EECCCCCceecCCCCCCChhhhCCCCeEEccccccccc
Q 027093 154 VQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 191 (228)
Q Consensus 154 i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 191 (228)
+.|..|. .|..|+.+.+.+. +.|+|+.|...++
T Consensus 193 lIC~~C~--hhngl~~~~ek~~---~efiC~~Cn~~n~ 225 (251)
T COG5415 193 LICPQCH--HHNGLYRLAEKPI---IEFICPHCNHKND 225 (251)
T ss_pred hcccccc--ccccccccccccc---hheecccchhhcC
Confidence 6677775 3788888876654 5899999999884
No 79
>PF00855 PWWP: PWWP domain; InterPro: IPR000313 Upon characterisation of WHSC1, a gene mapping to the Wolf-Hirschhornsyndrome critical region and at its C terminus similar to the Drosophila melanogaster ASH1/trithorax group proteins, a novel protein domain designated PWWP domain was identified []. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. It is present in proteins of nuclear origin and plays a role in cell growth and differentiation. Due to its position, the composition of amino acids close to the PWWP motif and the pattern of other domains present it has been suggested that the domain is involved in protein-protein interactions [].; PDB: 3LYI_B 2L89_A 2NLU_A 1RI0_A 1KHC_A 3QKJ_C 2DAQ_A 1N27_A 3PFS_B 3QJ6_A ....
Probab=62.84 E-value=6.5 Score=27.11 Aligned_cols=40 Identities=33% Similarity=0.455 Sum_probs=28.5
Q ss_pred EccCCEEEEccCCCCCCCeEEEEeEEEEcC---CCCEEEEEEEEe
Q 027093 23 VRPGDCVLMRPADSDKPPYVARVEKIEADH---RNNVKVRVRWYY 64 (228)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~---~~~~~v~v~Wfy 64 (228)
|++||.|...-.. -+.|-|+|....... ...-.+.|.||-
T Consensus 1 f~~GdlVWaK~~g--~pwWPa~V~~~~~~~~~~~~~~~~~V~Ffg 43 (86)
T PF00855_consen 1 FRPGDLVWAKLKG--YPWWPARVCDPDEKSKKKRKDGHVLVRFFG 43 (86)
T ss_dssp -STTEEEEEEETT--SEEEEEEEEECCHCTSCSSSSTEEEEEETT
T ss_pred CCCCCEEEEEeCC--CCCCceEEeecccccccCCCCCEEEEEecC
Confidence 5789999999976 689999999987532 223456666554
No 80
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=62.63 E-value=14 Score=19.44 Aligned_cols=26 Identities=19% Similarity=0.221 Sum_probs=20.7
Q ss_pred EccCCEEEEccCCCCCCCeEEEEeEEEE
Q 027093 23 VRPGDCVLMRPADSDKPPYVARVEKIEA 50 (228)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~rI~~i~~ 50 (228)
+.+||.|.|..+. ..-.+|.|.++..
T Consensus 2 ~~~G~~V~I~~G~--~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGP--FKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECC--CCCcEEEEEEEcC
Confidence 5689999999986 5567899988753
No 81
>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=61.46 E-value=2 Score=23.95 Aligned_cols=26 Identities=23% Similarity=0.635 Sum_probs=10.3
Q ss_pred cCCCCCCCCCceEECCCCCceecCCCC
Q 027093 142 KCEMPYNPDDLMVQCEGCKDWFHPSCM 168 (228)
Q Consensus 142 ~C~~~~~~~~~mi~C~~C~~w~H~~Cv 168 (228)
.|+.+... .....|..|+-..|..|+
T Consensus 5 ~C~~~~~~-~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 5 ACGKPIDG-GWFYRCSECDFDLHEECA 30 (30)
T ss_dssp TTS----S---EEE-TTT-----HHHH
T ss_pred cCCCcCCC-CceEECccCCCccChhcC
Confidence 56766542 467889999999998874
No 82
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=59.95 E-value=2.4 Score=43.18 Aligned_cols=54 Identities=24% Similarity=0.604 Sum_probs=40.6
Q ss_pred CCceeeecCCCCCCCCCceEECCCCCceecCCCCCCChhhhCCCCeEEcccccc
Q 027093 135 DRVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSS 188 (228)
Q Consensus 135 ~~~~~~C~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~ 188 (228)
...+++=+|..|++|+...|.|..|..|+|..-|.+........-.+.|-.|..
T Consensus 1120 ~~~p~~~i~~~p~~pg~~~i~~~~~~~~~~~~~v~ln~s~~p~~~~~k~~~~~r 1173 (1414)
T KOG1473|consen 1120 TLSPVCFICTLPYNPGLTYIHCTVCMTWGHKEAVKLNSSPIPEVVGFKCCQCRR 1173 (1414)
T ss_pred CCCccccceeeccCCCCCcceEEEeeccCcceeEecCCCcchHHhhhhHHhhhc
Confidence 334555599999999999999999999999999988643321223567777764
No 83
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=59.16 E-value=9.9 Score=34.04 Aligned_cols=49 Identities=20% Similarity=0.490 Sum_probs=36.5
Q ss_pred eeecCCCCCCCCCceEECCCCCceecCCCCCCChhhhCCCCeEEcccccccccc
Q 027093 139 VYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (228)
Q Consensus 139 ~~C~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (228)
.+|||-..|.+++.... =-|+.-||..||..=..+. .-+||-|..+.+.
T Consensus 231 ~CaIClEdY~~GdklRi-LPC~H~FH~~CIDpWL~~~----r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 231 TCAICLEDYEKGDKLRI-LPCSHKFHVNCIDPWLTQT----RTFCPVCKRDIRT 279 (348)
T ss_pred eEEEeecccccCCeeeE-ecCCCchhhccchhhHhhc----CccCCCCCCcCCC
Confidence 67799988876655433 6799999999997744332 2469999997764
No 84
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=59.05 E-value=21 Score=24.63 Aligned_cols=30 Identities=20% Similarity=0.217 Sum_probs=25.3
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEeEEEEcC
Q 027093 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADH 52 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~ 52 (228)
..++.||-|.|.++. +.--+|+|.++....
T Consensus 5 ~~I~kGD~V~Vi~G~--dKGK~G~V~~V~~~~ 34 (76)
T PRK12281 5 LKVKKGDMVKVIAGD--DKGKTGKVLAVLPKK 34 (76)
T ss_pred ccccCCCEEEEeEcC--CCCcEEEEEEEEcCC
Confidence 358899999999987 677789999998754
No 85
>COG1370 Prefoldin, molecular chaperone implicated in de novo protein folding, alpha subunit [Posttranslational modification, protein turnover, chaperones]
Probab=57.26 E-value=8.4 Score=30.23 Aligned_cols=39 Identities=31% Similarity=0.422 Sum_probs=32.2
Q ss_pred CCCceeeeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEE
Q 027093 5 KPGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARV 45 (228)
Q Consensus 5 ~~~~~~y~s~~v~g~~~~~~vGD~V~v~~~~~~~~~~I~rI 45 (228)
++|+..|..+.+..+ ..+++||-|+|-+++ +...-+|+.
T Consensus 94 r~Gk~VFaKfVi~~D-~~iR~~dEvlVVne~-d~LlAvGra 132 (155)
T COG1370 94 RKGKSVFAKFVIDVD-EEIRAGDEVLVVNED-DELLAVGRA 132 (155)
T ss_pred HhccchhhhheeccC-cccCCCCeEEEECCC-CcEEEeeeE
Confidence 578889999999886 899999999999987 455566664
No 86
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=53.81 E-value=7.3 Score=32.09 Aligned_cols=31 Identities=32% Similarity=0.806 Sum_probs=25.2
Q ss_pred ceEECCCCCceecCCCCCCChhhhCCCCeEEcccccccccc
Q 027093 152 LMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (228)
Q Consensus 152 ~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (228)
.-++|+.|+.-||..|... . . ||.|.+....
T Consensus 171 ~~~~C~~C~~v~H~~C~~~---~--~-----CpkC~R~~~r 201 (202)
T PF13901_consen 171 TTVRCPKCKSVFHKSCFRK---K--S-----CPKCARRQKR 201 (202)
T ss_pred CeeeCCcCccccchhhcCC---C--C-----CCCcHhHhcc
Confidence 5689999999999999983 1 1 9999886554
No 87
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=52.67 E-value=8.9 Score=26.79 Aligned_cols=29 Identities=24% Similarity=0.636 Sum_probs=23.2
Q ss_pred eecCCCCCCCCCceEECC--CCCceecCCCCCCC
Q 027093 140 YCKCEMPYNPDDLMVQCE--GCKDWFHPSCMGMT 171 (228)
Q Consensus 140 ~C~C~~~~~~~~~mi~C~--~C~~w~H~~Cv~~~ 171 (228)
..+|+++ .+-.|+|. .|...||..|....
T Consensus 39 C~~C~~~---~Ga~i~C~~~~C~~~fH~~CA~~~ 69 (90)
T PF13771_consen 39 CSICKKK---GGACIGCSHPGCSRSFHVPCARKA 69 (90)
T ss_pred CcCCCCC---CCeEEEEeCCCCCcEEChHHHccC
Confidence 3478865 46889998 69999999998664
No 88
>COG5475 Uncharacterized small protein [Function unknown]
Probab=52.37 E-value=56 Score=21.25 Aligned_cols=38 Identities=13% Similarity=0.190 Sum_probs=25.3
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeecc
Q 027093 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPE 67 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~ 67 (228)
..+.+||.|.|+++.+ . -|++=.. ..-++.++||-+..
T Consensus 3 ~~FstgdvV~lKsGGP--~----Mtvs~~s---s~Gmy~C~Wf~g~g 40 (60)
T COG5475 3 MSFSTGDVVTLKSGGP--R----MTVSGYS---SDGMYECRWFDGYG 40 (60)
T ss_pred ceeecCcEEEeecCCc--e----EEEeccc---cCCeEEEEEecCCC
Confidence 4688999999999973 1 1221111 12578999998765
No 89
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=52.36 E-value=27 Score=24.55 Aligned_cols=36 Identities=28% Similarity=0.288 Sum_probs=27.5
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEE
Q 027093 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVR 59 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~ 59 (228)
..++.||.|.|..+. +.--+|+|.++.... +.+.+.
T Consensus 7 ~~I~~GD~V~Vi~G~--dKGK~G~V~~V~~~~-~~V~Ve 42 (83)
T CHL00141 7 MHVKIGDTVKIISGS--DKGKIGEVLKIIKKS-NKVIVK 42 (83)
T ss_pred CcccCCCEEEEeEcC--CCCcEEEEEEEEcCC-CEEEEc
Confidence 368899999999986 667799999998754 334443
No 90
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=51.47 E-value=7.2 Score=36.38 Aligned_cols=46 Identities=30% Similarity=0.721 Sum_probs=34.5
Q ss_pred cCCCCCCC-CCceEECCCCCceecCCCCCCChhhhCCCCeEEcccccccc
Q 027093 142 KCEMPYNP-DDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDV 190 (228)
Q Consensus 142 ~C~~~~~~-~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~ 190 (228)
+|....+. .+-.|.||+|+---|..|-|+.-.+. ..|+|..|.-..
T Consensus 198 ~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~f~pe---G~WlCrkCi~~~ 244 (669)
T COG5141 198 KCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPE---GFWLCRKCIYGE 244 (669)
T ss_pred hccccccCCcceEEEecCcchhhhhhcccceecCc---chhhhhhhcccc
Confidence 66655443 25679999999999999999975442 468888888654
No 91
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=51.35 E-value=5.8 Score=21.19 Aligned_cols=13 Identities=38% Similarity=0.894 Sum_probs=9.8
Q ss_pred eEECCCCCceecC
Q 027093 153 MVQCEGCKDWFHP 165 (228)
Q Consensus 153 mi~C~~C~~w~H~ 165 (228)
|++|..|++.|..
T Consensus 2 l~~C~~CgR~F~~ 14 (25)
T PF13913_consen 2 LVPCPICGRKFNP 14 (25)
T ss_pred CCcCCCCCCEECH
Confidence 6788888888754
No 92
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=51.33 E-value=89 Score=25.51 Aligned_cols=26 Identities=12% Similarity=0.087 Sum_probs=14.0
Q ss_pred CCeEEeeCCceeeeccceEeeeEEEee
Q 027093 79 AKELFLSDHYDVQSAHTIEGKCTVHTF 105 (228)
Q Consensus 79 ~~ELFlS~~~d~i~~~~I~gkc~V~~~ 105 (228)
.+..+..+..|.+-+..|+. +.|++.
T Consensus 107 ~~~~~~~~~~d~f~~GDivr-A~Vis~ 132 (188)
T COG1096 107 VRDGYVEKLSDAFRIGDIVR-ARVIST 132 (188)
T ss_pred cccccccccccccccccEEE-EEEEec
Confidence 34445555556666666654 455554
No 93
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=50.97 E-value=6.1 Score=23.65 Aligned_cols=34 Identities=21% Similarity=0.605 Sum_probs=17.3
Q ss_pred eEECCCCCceecCCCCCCChhhhCCCCeEEccccccccc
Q 027093 153 MVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 191 (228)
Q Consensus 153 mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 191 (228)
.+.|..|+...-+-|.-.. ....|+|+.|...+.
T Consensus 2 p~rC~~C~aylNp~~~~~~-----~~~~w~C~~C~~~N~ 35 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDD-----GGKTWICNFCGTKNP 35 (40)
T ss_dssp S-B-TTT--BS-TTSEEET-----TTTEEEETTT--EEE
T ss_pred ccccCCCCCEECCcceEcC-----CCCEEECcCCCCcCC
Confidence 3567777766655554332 225899999998765
No 94
>cd03703 aeIF5B_II aeIF5B_II: This family represents the domain II of archeal and eukaryotic aeIF5B. aeIF5B is a homologue of prokaryotic Initiation Factor 2 (IF2). Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of joining of 60S subunits. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains of EF1A, eEF1A and aeIF2gamma.
Probab=50.57 E-value=46 Score=24.78 Aligned_cols=45 Identities=18% Similarity=0.257 Sum_probs=33.0
Q ss_pred CCCCCceeeeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEeEEEEcC
Q 027093 3 KTKPGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADH 52 (228)
Q Consensus 3 ~~~~~~~~y~s~~v~g~~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~ 52 (228)
|.-+|.-..-.+++.. -++++||.|.+-... .|.+++|..|....
T Consensus 9 k~~~G~G~t~dvIl~~--GtL~~GD~Iv~g~~~---Gpi~tkVRaLl~~~ 53 (110)
T cd03703 9 KEEEGLGTTIDVILYD--GTLREGDTIVVCGLN---GPIVTKVRALLKPQ 53 (110)
T ss_pred EEcCCCceEEEEEEEC--CeEecCCEEEEccCC---CCceEEEeEecCCC
Confidence 3345556666666642 289999999998875 57799999998753
No 95
>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=48.82 E-value=19 Score=22.43 Aligned_cols=35 Identities=20% Similarity=0.416 Sum_probs=24.2
Q ss_pred eeee-cCCCCC-CCCCceEECCCCCceecCCCCCCCh
Q 027093 138 AVYC-KCEMPY-NPDDLMVQCEGCKDWFHPSCMGMTI 172 (228)
Q Consensus 138 ~~~C-~C~~~~-~~~~~mi~C~~C~~w~H~~Cv~~~~ 172 (228)
+.+| .|++.. ........|..|+...|.+|+..-+
T Consensus 11 ~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~~~ 47 (53)
T PF00130_consen 11 PTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSKVP 47 (53)
T ss_dssp TEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCTSS
T ss_pred CCCCcccCcccCCCCCCeEEECCCCChHhhhhhhhcC
Confidence 4555 788765 1234568999999999999997643
No 96
>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=46.70 E-value=14 Score=34.73 Aligned_cols=10 Identities=40% Similarity=0.770 Sum_probs=5.4
Q ss_pred EEcccccccc
Q 027093 181 FLCSDCSSDV 190 (228)
Q Consensus 181 ~~C~~C~~~~ 190 (228)
|-||.|...-
T Consensus 53 f~CP~C~~~L 62 (483)
T PF05502_consen 53 FDCPICFSPL 62 (483)
T ss_pred ccCCCCCCcc
Confidence 5566665443
No 97
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=46.46 E-value=35 Score=25.06 Aligned_cols=37 Identities=19% Similarity=0.231 Sum_probs=28.1
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEE
Q 027093 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRV 60 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v 60 (228)
..++.||.|.|.++. +.--+|.|.++....+ .+.|..
T Consensus 3 ~~i~kGD~V~Vi~G~--dKGk~G~V~~V~~~~~-~V~Veg 39 (105)
T PRK00004 3 MKIKKGDTVIVIAGK--DKGKRGKVLKVLPKKN-KVIVEG 39 (105)
T ss_pred CcccCCCEEEEeEcC--CCCcEEEEEEEEcCCC-EEEEcC
Confidence 358899999999997 6777999999987543 344433
No 98
>PF09378 HAS-barrel: HAS barrel domain; InterPro: IPR018538 The HAS barrel is named after HerA-ATP Synthase. In ATP synthases, this domain is implicated in the assembly of the catalytic toroid and docking of accessory subunits, such as the subunit of the ATP synthase complex. Similar roles in docking of the functional partner, the NurA nuclease, and assembly of the HerA toroid complex appear likely for the HAS-barrel of the HerA family []. ; PDB: 3OAA_I.
Probab=46.40 E-value=25 Score=24.35 Aligned_cols=38 Identities=21% Similarity=0.253 Sum_probs=25.3
Q ss_pred eeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEeEEEEc
Q 027093 11 LDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEAD 51 (228)
Q Consensus 11 y~s~~v~g~~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~ 51 (228)
...|.++.. ...++||+|.+...+ ...-+|+|.+|...
T Consensus 12 ~~~f~~~~~-~~v~~GeyV~i~~~~--~~~vlG~V~~i~~~ 49 (91)
T PF09378_consen 12 EFEFIVEPS-KDVRVGEYVVIEYDD--GEKVLGMVTSISRG 49 (91)
T ss_dssp TTEEEEEE--TT-BTTEEEEES------TTEEEEEEEEES-
T ss_pred eEEEEEeCC-CCCCcCeEEEEEEec--hhhhhhhhheeEEc
Confidence 346667653 479999999999984 56788999999874
No 99
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.33 E-value=13 Score=32.23 Aligned_cols=48 Identities=21% Similarity=0.488 Sum_probs=33.8
Q ss_pred ceeee-cCCCCCCCCCce-EECCCCCceecCCCCCCChhhhCCCCeEEccccccccc
Q 027093 137 VAVYC-KCEMPYNPDDLM-VQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 191 (228)
Q Consensus 137 ~~~~C-~C~~~~~~~~~m-i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 191 (228)
..+.| +|+.+ |..+| ++ -|+.-|..-|+.....-. ..|.|+.|.+..+
T Consensus 238 ~~~~C~~Cg~~--PtiP~~~~--~C~HiyCY~Ci~ts~~~~---asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 238 SDTECPVCGEP--PTIPHVIG--KCGHIYCYYCIATSRLWD---ASFTCPLCGENVE 287 (298)
T ss_pred CCceeeccCCC--CCCCeeec--cccceeehhhhhhhhcch---hhcccCccCCCCc
Confidence 34556 88876 44444 33 278899999998865543 4699999998765
No 100
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=46.23 E-value=16 Score=23.09 Aligned_cols=36 Identities=19% Similarity=0.494 Sum_probs=20.4
Q ss_pred ECCCCCceecCCC----CCCCh--hhhCCCCeEEcccccccc
Q 027093 155 QCEGCKDWFHPSC----MGMTI--EEAKKLDHFLCSDCSSDV 190 (228)
Q Consensus 155 ~C~~C~~w~H~~C----v~~~~--~~~~~~~~~~C~~C~~~~ 190 (228)
+|..|+--|...= -++++ ...+.++.|.|+.|....
T Consensus 3 ~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a~K 44 (50)
T cd00730 3 ECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAGK 44 (50)
T ss_pred CCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCCcH
Confidence 5777776565431 12211 222345789999998643
No 101
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=44.56 E-value=55 Score=24.76 Aligned_cols=38 Identities=24% Similarity=0.227 Sum_probs=28.6
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEE
Q 027093 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVR 61 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~ 61 (228)
..++.||-|.|.++. +.--.|+|.++... ++.+.|.+.
T Consensus 44 ~~IkkGD~V~VisG~--~KGk~GkV~~V~~~-~~~V~VeGv 81 (120)
T PRK01191 44 LPVRKGDTVKVMRGD--FKGEEGKVVEVDLK-RGRIYVEGV 81 (120)
T ss_pred ceEeCCCEEEEeecC--CCCceEEEEEEEcC-CCEEEEeCc
Confidence 578999999999997 55667999999774 334554443
No 102
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=43.85 E-value=11 Score=25.56 Aligned_cols=52 Identities=23% Similarity=0.242 Sum_probs=20.0
Q ss_pred cCCCCCC--CCCceEECC--CCCceecCCCCCCChh--hhC----CCCeEEccccccccccc
Q 027093 142 KCEMPYN--PDDLMVQCE--GCKDWFHPSCMGMTIE--EAK----KLDHFLCSDCSSDVDAK 193 (228)
Q Consensus 142 ~C~~~~~--~~~~mi~C~--~C~~w~H~~Cv~~~~~--~~~----~~~~~~C~~C~~~~~~k 193 (228)
||-.... ....-+.|+ .|+.-||..|+-.--. +.. .+-...||.|......+
T Consensus 7 IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~ 68 (70)
T PF11793_consen 7 ICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS 68 (70)
T ss_dssp SS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred cCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence 5654432 123457787 8999999999944211 110 12357899999876653
No 103
>PF11926 DUF3444: Domain of unknown function (DUF3444); InterPro: IPR024593 This entry represents an uncharacterised domain. This domain is found in DnaJ, cytosine-specific methyltransferases, and members from the zinc finger, C3HC4 type family.
Probab=43.82 E-value=52 Score=27.53 Aligned_cols=56 Identities=20% Similarity=0.425 Sum_probs=41.9
Q ss_pred eeeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeecc
Q 027093 10 DLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPE 67 (228)
Q Consensus 10 ~y~s~~v~g~~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~ 67 (228)
.|+-|.-+.....+++|+.=.+..+....|-+.|+|.++... +...|++.|+---.
T Consensus 15 dF~dF~~~R~~~~F~~gQIWAlYd~~D~mPR~Ya~I~kV~~~--~~Fkl~i~wLe~~~ 70 (217)
T PF11926_consen 15 DFYDFDKDRSEEKFQVGQIWALYDDDDGMPRYYARIKKVDSS--NPFKLHITWLEPCP 70 (217)
T ss_pred ccccccCCchHHhCCCCCEEEEeeCCCCCeeeEEEEEEEecC--CCeEEEEEEccccC
Confidence 344454333346789999999998765789999999999773 45789999987644
No 104
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=42.92 E-value=47 Score=25.09 Aligned_cols=41 Identities=20% Similarity=0.063 Sum_probs=27.3
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEeEEEEcC-CCCEEEEEE
Q 027093 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADH-RNNVKVRVR 61 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~-~~~~~v~v~ 61 (228)
-.+++||.|+...+.....+.-|.|+...+.. .....+.|.
T Consensus 54 ~~L~~GD~VLA~~~~~~~~Y~Pg~V~~~~~~~~~~~~~~~V~ 95 (124)
T PF15057_consen 54 HSLQVGDKVLAPWEPDDCRYGPGTVIAGPERRASEDKEYTVR 95 (124)
T ss_pred CcCCCCCEEEEecCcCCCEEeCEEEEECccccccCCceEEEE
Confidence 37899999999976543444449999876543 223455555
No 105
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=42.56 E-value=23 Score=20.07 Aligned_cols=24 Identities=17% Similarity=0.534 Sum_probs=15.9
Q ss_pred ECCCCCceecCCCCCCChhhhCCCCeEEccccccc
Q 027093 155 QCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSD 189 (228)
Q Consensus 155 ~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~ 189 (228)
+|..|+.-|.+.- +.|.||.|...
T Consensus 3 ~C~~CGy~y~~~~-----------~~~~CP~Cg~~ 26 (33)
T cd00350 3 VCPVCGYIYDGEE-----------APWVCPVCGAP 26 (33)
T ss_pred ECCCCCCEECCCc-----------CCCcCcCCCCc
Confidence 5677766554432 46899999764
No 106
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=41.95 E-value=83 Score=25.23 Aligned_cols=85 Identities=22% Similarity=0.323 Sum_probs=50.1
Q ss_pred eeeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeecccccCCcccc-----CCCCeEEe
Q 027093 10 DLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQF-----HGAKELFL 84 (228)
Q Consensus 10 ~y~s~~v~g~~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~d~~~~~~~~-----~~~~ELFl 84 (228)
....+.++. ..+..||.|.+.++..++..+|-||..+-.+ .+.. +-+|++..--...+ -...+-+=
T Consensus 58 ll~k~~v~n--~~~~rGDiVvl~sP~~p~~~~iKRv~alegd----~~~t---~~~k~~~v~vpkghcWVegDn~~hs~D 128 (174)
T KOG1568|consen 58 LLRKWNVKN--RKVSRGDIVVLKSPNDPDKVIIKRVAALEGD----IMVT---EDEKEEPVVVPKGHCWVEGDNQKHSYD 128 (174)
T ss_pred EEEeecccc--ceeccCCEEEEeCCCChhheeeeeeeccccc----Eecc---CCCCCCceecCCCcEEEecCCcccccc
Confidence 334555543 5678999999999987889999999877442 1111 22233321111100 11234455
Q ss_pred eCCceeeeccceEeeeEEE
Q 027093 85 SDHYDVQSAHTIEGKCTVH 103 (228)
Q Consensus 85 S~~~d~i~~~~I~gkc~V~ 103 (228)
|+.+--++...|.|++.-.
T Consensus 129 SntFGPVS~gli~grai~i 147 (174)
T KOG1568|consen 129 SNTFGPVSTGLIVGRAIYI 147 (174)
T ss_pred cCccCCcchhheeeeEEEE
Confidence 5556668889999987543
No 107
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=41.72 E-value=46 Score=24.43 Aligned_cols=34 Identities=24% Similarity=0.271 Sum_probs=26.7
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEE
Q 027093 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKV 58 (228)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v 58 (228)
.++.||-|.|.++. +.--+|.|.++.... +.+.+
T Consensus 3 ~ikkGD~V~Vi~G~--dKGK~G~V~~V~~~~-~~V~V 36 (104)
T TIGR01079 3 KIKKGDTVKVISGK--DKGKRGKVLKVLPKT-NKVIV 36 (104)
T ss_pred cccCCCEEEEeEcC--CCCcEEEEEEEEcCC-CEEEE
Confidence 47899999999997 677899999998754 33444
No 108
>PF00667 FAD_binding_1: FAD binding domain; InterPro: IPR003097 This domain is found in sulphite reductase, NADPH cytochrome P450 reductase, nitric oxide synthase and methionine synthase reductase. Flavoprotein pyridine nucleotide cytochrome reductases [] (FPNCR) catalyse the interchange of reducing equivalents between one-electron carriers and the two-electron-carrying nicotinamide dinucleotides. The enzymes include ferredoxin:NADP+reductases (FNR) [], plant and fungal NAD(P)H:nitrate reductases [, ], NADH:cytochrome b5 reductases [], NADPH:P450 reductases [], NADPH:sulphite reductases [], nitric oxide synthases [], phthalate dioxygenase reductase [], and various other flavoproteins.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3QFR_B 3FJO_A 3QFC_B 3QE2_B 3QFS_A 3QFT_A 2B5O_B 2QTZ_A 2QTL_A 2BPO_B ....
Probab=41.53 E-value=36 Score=28.05 Aligned_cols=23 Identities=17% Similarity=0.429 Sum_probs=13.8
Q ss_pred eEEEcCCCeEEccCCEEEEccCC
Q 027093 13 SYNIKGTNKVVRPGDCVLMRPAD 35 (228)
Q Consensus 13 s~~v~g~~~~~~vGD~V~v~~~~ 35 (228)
.+.+.+.+..|++||.+.|.+.+
T Consensus 32 eldl~~~~l~Y~pGD~l~V~P~N 54 (219)
T PF00667_consen 32 ELDLSDSGLSYQPGDHLGVYPPN 54 (219)
T ss_dssp EEE-TTSTG---TT-EEEEE-SS
T ss_pred EEEeCCCCCcccCCCEEEEEccC
Confidence 44455668999999999999998
No 109
>cd05836 N_Pac_NP60 The PWWP domain is an essential part of the cytokine-like nuclear factor n-pac protein, or NP60, which enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In a variety of cell lines, NP60 has been shown to localize to the nucleus. In addition to the PWWP domain, NP60 also contains an AT-hook and a C-terminal NAD-binding domain. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding proteins, that function as transcription factors regulating a variety of developmental processes.
Probab=41.31 E-value=41 Score=23.67 Aligned_cols=42 Identities=21% Similarity=0.265 Sum_probs=29.1
Q ss_pred EccCCEEEEccCCCCCCCeEEEEeEEEEcC----CCCEEEEEEEEeec
Q 027093 23 VRPGDCVLMRPADSDKPPYVARVEKIEADH----RNNVKVRVRWYYRP 66 (228)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~----~~~~~v~v~WfyRp 66 (228)
+++||.|.-+-.. -+.|-|+|.+-..+. ...-.+.|.||-.+
T Consensus 1 f~~GDlVwaK~~g--~P~WPa~V~~~~~~~~~~~~~~~~~~V~FFG~~ 46 (86)
T cd05836 1 LKLGDLVWAKMKG--FPPWPGRIVKPPKDLKKPRGKAKCFFVFFFGSE 46 (86)
T ss_pred CCCCCEEEEeCCC--CCCCCEEEechhhhcccccCCCCeEEEEEeCCC
Confidence 4789999999886 799999998854321 11244666766644
No 110
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=41.25 E-value=34 Score=18.88 Aligned_cols=26 Identities=19% Similarity=0.393 Sum_probs=18.4
Q ss_pred cCCCCCCCCCceEECCCCCceecCCCC
Q 027093 142 KCEMPYNPDDLMVQCEGCKDWFHPSCM 168 (228)
Q Consensus 142 ~C~~~~~~~~~mi~C~~C~~w~H~~Cv 168 (228)
+|++..++.. ...|+.|.--.|..|+
T Consensus 5 ~C~~~~~~~~-~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 5 VCRRKIDGFY-FYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCcCCCE-eEEeCCCCCeEcCccC
Confidence 5666544333 7888998888888884
No 111
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=40.45 E-value=20 Score=20.90 Aligned_cols=14 Identities=29% Similarity=0.660 Sum_probs=8.5
Q ss_pred CCceEECCCCCcee
Q 027093 150 DDLMVQCEGCKDWF 163 (228)
Q Consensus 150 ~~~mi~C~~C~~w~ 163 (228)
.+..++|..|+.-|
T Consensus 22 ~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 22 KGRKVRCSKCGHVF 35 (36)
T ss_pred CCcEEECCCCCCEe
Confidence 44567777775544
No 112
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=40.43 E-value=28 Score=33.37 Aligned_cols=68 Identities=22% Similarity=0.304 Sum_probs=39.7
Q ss_pred EECCC-CCceecCCCCCCChhhhCCCCeEEcccccccccc---------ccc---CCCCCCCCCc-hhhhccceeeeEEE
Q 027093 154 VQCEG-CKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA---------KRS---LNTFSVSPSV-EAKVRAHMFHFVYV 219 (228)
Q Consensus 154 i~C~~-C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~---------k~~---~~~~~~~~~~-~~~~~~~~~~~~~~ 219 (228)
|.|.. |+..+.+-|.--+.. ..|+|+.|..++.. ..+ .....++-.. .++-..-...|.||
T Consensus 54 v~C~~pC~avlnpyC~id~r~-----~~W~CpfCnqrn~lp~qy~~iS~~~LplellpqssTiey~lskp~~~ppvf~fv 128 (755)
T COG5047 54 VKCTAPCKAVLNPYCHIDERN-----QSWICPFCNQRNTLPPQYRDISNANLPLELLPQSSTIEYTLSKPVILPPVFFFV 128 (755)
T ss_pred ceecccchhhcCcceeeccCC-----ceEecceecCCCCCChhhcCCCcccCCccccCCCceEEEEccCCccCCceEEEE
Confidence 66766 888888888755433 37999999998721 000 1111222222 34434444577788
Q ss_pred Eeeeccc
Q 027093 220 VYILQDK 226 (228)
Q Consensus 220 ~~~~~~~ 226 (228)
+.+-.|.
T Consensus 129 vD~~~D~ 135 (755)
T COG5047 129 VDACCDE 135 (755)
T ss_pred EEeecCH
Confidence 8877763
No 113
>PF03144 GTP_EFTU_D2: Elongation factor Tu domain 2; InterPro: IPR004161 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. EF1A (also known as EF-1alpha or EF-Tu) is a G-protein. It forms a ternary complex of EF1A-GTP-aminoacyltRNA. The binding of aminoacyl-tRNA stimulates GTP hydrolysis by EF1A, causing a conformational change in EF1A that causes EF1A-GDP to detach from the ribosome, leaving the aminoacyl-tRNA attached at the A-site. Only the cognate aminoacyl-tRNA can induce the required conformational change in EF1A through its tight anticodon-codon binding [, ]. EF1A-GDP is returned to its active state, EF1A-GTP, through the action of another elongation factor, EF1B (also known as EF-Ts or EF-1beta/gamma/delta). EF1A consists of three structural domains. This entry represents domain 2 of EF2, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA []. This domain is structurally related to the C-terminal domain of EF2 (IPR004160 from INTERPRO), to which it displays weak sequence matches. This domain is also found in other proteins such as translation initiation factor IF-2 and tetracycline-resistance proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 3MCA_A 3AGJ_E 1SKQ_B 1JNY_A 1S0U_A 1ZUN_B 3SFS_W 3UOQ_W 2H5E_B 2XEX_A ....
Probab=39.83 E-value=61 Score=21.28 Aligned_cols=30 Identities=23% Similarity=0.299 Sum_probs=22.6
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEeEEEEc
Q 027093 22 VVRPGDCVLMRPADSDKPPYVARVEKIEAD 51 (228)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~ 51 (228)
++++||.|++.+...+..+..++|.+|+..
T Consensus 12 ~l~~gd~v~~~~~~~~~~~~~~~I~~i~~~ 41 (74)
T PF03144_consen 12 TLKKGDKVRVLPNGTGKKGQVVKIKSIFMF 41 (74)
T ss_dssp EEETTEEEEEESTTTTEECEEEEEEEEEET
T ss_pred EEcCCCEEEECccCCcceeeeeeccccccc
Confidence 899999999977322234577899888874
No 114
>KOG2133 consensus Transcriptional corepressor Atrophin-1/DRPLA [General function prediction only]
Probab=38.96 E-value=19 Score=36.33 Aligned_cols=113 Identities=16% Similarity=0.200 Sum_probs=78.8
Q ss_pred CeEEccCCEEEEccCCCCCCCeEEEEeEEEEcCC-CCEEEEEEEEeeccccc-CC---c-------c-------ccCCCC
Q 027093 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEADHR-NNVKVRVRWYYRPEESI-GG---R-------R-------QFHGAK 80 (228)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~-~~~~v~v~WfyRp~d~~-~~---~-------~-------~~~~~~ 80 (228)
+..|.++|.|.+....+ .++.|+.|-.+...++ ..+.++.-.+.|++|++ .+ . . .-...+
T Consensus 143 e~~y~~~~~l~~~v~~~-~p~lia~~~~~~~~Kr~~~~~~k~s~~~r~~d~Pet~y~~~m~pe~Ar~e~~P~~~pq~~sq 221 (1229)
T KOG2133|consen 143 ETLYDLRDSLFVEVSQP-EPYLIAAICGFKYTKRDDRQVVKLSFYFRADDIPETGYLNLMKPERARLEINPHLCPQPLSQ 221 (1229)
T ss_pred chhhhhhhhhhhhhccC-CccccccccCccccccccccccccccccccccCcccccccccCchhhhhccCCccCCCcchh
Confidence 46789999999998873 6777787776666664 46778888999999987 22 0 0 012457
Q ss_pred eEEeeCCcee-eeccceEeeeEEEeecccccccC------CCCcceEEeecccccccccc
Q 027093 81 ELFLSDHYDV-QSAHTIEGKCTVHTFKNYTKLEN------VGAEDYFCRFEYKAATGGFT 133 (228)
Q Consensus 81 ELFlS~~~d~-i~~~~I~gkc~V~~~~~~~~~~~------~~~~~Ffcr~~Yd~~~~~f~ 133 (228)
|||.+...++ .|..+..|||.+....++..... ...++||....|.+.+....
T Consensus 222 ~l~~s~l~~i~qppscp~gk~~~~~skd~~h~~~~n~p~~ld~~i~fk~agglpps~k~a 281 (1229)
T KOG2133|consen 222 ELFNSELQGITQPPSCPRGKGIAEYSKDVRHGGNTNAPFSLDNDIFFKCAGGLPPSTKPA 281 (1229)
T ss_pred hhhcccccCCCCCCcCCCCCceEEeecccccCCccCCCCcccceeeeecccCCCCCCCCC
Confidence 8999887744 88999999999986655532221 23466776788877766544
No 115
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF06940 DUF1287: Domain of unknown function (DUF1287); InterPro: IPR009706 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=38.48 E-value=45 Score=26.59 Aligned_cols=43 Identities=21% Similarity=0.165 Sum_probs=30.9
Q ss_pred eEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEE
Q 027093 13 SYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKV 58 (228)
Q Consensus 13 s~~v~g~~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v 58 (228)
+..+..+...|+.||.|...-+. ..++||.|.+-.. .+|..++
T Consensus 97 ~L~~~~~~~~~q~GDIVtw~l~~--~~~HIgIVSd~r~-~~G~p~v 139 (164)
T PF06940_consen 97 SLTTDINPEDWQPGDIVTWRLPG--GLPHIGIVSDRRS-KDGVPLV 139 (164)
T ss_pred eccCCCChhhcCCCCEEEEeCCC--CCCeEEEEeCCcC-CCCCEEE
Confidence 34444445789999999998775 5889999988765 4564443
No 117
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=37.68 E-value=32 Score=30.38 Aligned_cols=54 Identities=13% Similarity=0.149 Sum_probs=41.7
Q ss_pred ceeeecCCCCCCCCCceEECCCCCceecCCCCCCChhhhCCCCeEEccccccccccc
Q 027093 137 VAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 193 (228)
Q Consensus 137 ~~~~C~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~k 193 (228)
-+.+|.|-.+....+.|..|-.|.-|+|..-..+..-.. ..|-|.-|..+.+..
T Consensus 52 rQ~l~sClTC~P~~~~agvC~~C~~~CH~~H~lveL~tK---R~FrCDCg~sk~g~~ 105 (345)
T KOG2752|consen 52 RQALFSCLTCTPAPEMAGVCYACSLSCHDGHELVELYTK---RNFRCDCGNSKFGRC 105 (345)
T ss_pred ccceeEeecccCChhhceeEEEeeeeecCCceeeecccc---CCccccccccccccc
Confidence 356777877775566889999999999999888865443 468899888877644
No 118
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=37.55 E-value=1.3e+02 Score=20.32 Aligned_cols=26 Identities=23% Similarity=0.408 Sum_probs=16.3
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEeE
Q 027093 22 VVRPGDCVLMRPADSDKPPYVARVEK 47 (228)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~rI~~ 47 (228)
.++.||.|.+.........++.||..
T Consensus 31 ~~~~GDiv~~~~~~~~~~~~vkRv~~ 56 (85)
T cd06530 31 EPKRGDVVVFKSPGDPGKPIIKRVIG 56 (85)
T ss_pred CCCCCCEEEEeCCCCCCCEEEEEEEE
Confidence 35667777777665224566677766
No 119
>cd05837 MSH6_like The PWWP domain is present in MSH6, a mismatch repair protein homologous to bacterial MutS. The PWWP domain of histone-lysine N-methyltransferase, also known as Nuclear SET domain-containing protein 3, is also included. Mutations in MSH6 have been linked to increased cancer susceptibility, particularly in hereditary nonpolyposis colorectal cancer in humans. The role of the PWWP domain in MSH6 is not clear; MSH6 orthologs found in S. cerevisiae, Caenorhabditis elegans and Arabidopsis thaliana lack the PWWP domain. Histone methyltransferases (HMTases) induce the posttranslational methylation of lysine residues in histones and play a role in apoptosis. In the HMTase Whistle, the PWWP domain is necessary for HMTase activity. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain pro
Probab=37.32 E-value=44 Score=24.64 Aligned_cols=44 Identities=16% Similarity=0.166 Sum_probs=32.0
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEeEEEE---------cCCCCEEEEEEEEeecc
Q 027093 22 VVRPGDCVLMRPADSDKPPYVARVEKIEA---------DHRNNVKVRVRWYYRPE 67 (228)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~rI~~i~~---------~~~~~~~v~v~WfyRp~ 67 (228)
.|.+||.|...-.. -+.|-|.|.+--. .......+.|++|....
T Consensus 2 ~~~~GdlVWaK~~g--~PwWPa~V~~~~~~~~~~~~~~~~~~~~~~~V~FFG~~~ 54 (110)
T cd05837 2 KYQVGDLVWAKVSG--YPWWPCMVCSDPLLGTYTKTKRNKRKPRQYHVQFFGDNP 54 (110)
T ss_pred CCCCCCEEEEeCCC--CCCCCEEEecccccchhhhhhhccCCCCeEEEEEcCCCC
Confidence 58899999999986 7899999985311 12234678888887543
No 120
>COG3257 GlxB Uncharacterized protein, possibly involved in glyoxylate utilization [General function prediction only]
Probab=37.28 E-value=90 Score=26.32 Aligned_cols=60 Identities=17% Similarity=0.343 Sum_probs=36.3
Q ss_pred EEEcCCCeEEccCCEEEEccCCCCCCCeEEEEeEEEEcCC-CCEEEEEEEEeecccccCCccccCCCCeEEeeCCce
Q 027093 14 YNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHR-NNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYD 89 (228)
Q Consensus 14 ~~v~g~~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~-~~~~v~v~WfyRp~d~~~~~~~~~~~~ELFlS~~~d 89 (228)
+.+.|+-..++-|+++|+.++.. |.-.+ ..--.++.|+-++-+...|.. .-|+|.++..+
T Consensus 96 v~~~G~th~l~eggyaylPpgs~------------~~~~N~~~~~~rfhw~rk~Y~~VdG~~----~P~~~~~Ne~e 156 (264)
T COG3257 96 VKAEGKTHALREGGYAYLPPGSG------------WTLRNAQKEDSRFHWIRKRYQPVEGVQ----APELVSGNESE 156 (264)
T ss_pred EEEcCeEEEeccCCeEEeCCCCc------------ceEeeccCCceEEEEEeecceeecCcc----CCcceecChhh
Confidence 44555556678899999998861 22121 123477888888888765532 34555555443
No 121
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=36.85 E-value=75 Score=24.80 Aligned_cols=40 Identities=13% Similarity=0.067 Sum_probs=29.3
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEE
Q 027093 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWY 63 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~Wf 63 (228)
..++.||.|.|.++. +.--.|+|.++... ++.+.|.+.=.
T Consensus 45 ~~IkkGD~V~Vi~Gk--~KGk~GkV~~V~~k-~~~ViVEgvn~ 84 (143)
T PTZ00194 45 MPVRKDDEVMVVRGH--HKGREGKVTAVYRK-KWVIHIEKITR 84 (143)
T ss_pred ceeecCCEEEEecCC--CCCCceEEEEEEcC-CCEEEEeCeEE
Confidence 578999999999997 45567999999773 34455555433
No 122
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=35.54 E-value=46 Score=20.76 Aligned_cols=37 Identities=22% Similarity=0.449 Sum_probs=17.9
Q ss_pred EECCCCCceecCCCC----CCCh--hhhCCCCeEEcccccccc
Q 027093 154 VQCEGCKDWFHPSCM----GMTI--EEAKKLDHFLCSDCSSDV 190 (228)
Q Consensus 154 i~C~~C~~w~H~~Cv----~~~~--~~~~~~~~~~C~~C~~~~ 190 (228)
.+|..|+--|...=- ++++ ...+.++.|.|+.|....
T Consensus 2 y~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~K 44 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAPK 44 (47)
T ss_dssp EEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSBG
T ss_pred cCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCcc
Confidence 356666666654321 2221 122345789999998753
No 123
>PHA02862 5L protein; Provisional
Probab=34.79 E-value=7.7 Score=30.31 Aligned_cols=49 Identities=18% Similarity=0.356 Sum_probs=30.3
Q ss_pred cCCCCCCCCCceEECCCCCceecCCCCCCChhhhCCCCeEEccccccccccc
Q 027093 142 KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 193 (228)
Q Consensus 142 ~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~k 193 (228)
+|.+..+++...=.|.+--+|-|.+|+..=.... ..-.|+.|......|
T Consensus 7 IC~~~~~e~~~PC~C~GS~K~VHq~CL~~WIn~S---~k~~CeLCkteY~Ik 55 (156)
T PHA02862 7 ICNDVCDERNNFCGCNEEYKVVHIKCMQLWINYS---KKKECNLCKTKYNIK 55 (156)
T ss_pred EecCcCCCCcccccccCcchhHHHHHHHHHHhcC---CCcCccCCCCeEEEE
Confidence 5655544333333455678999999975422221 345799999887654
No 124
>cd06541 ASCH ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery.
Probab=34.22 E-value=84 Score=22.74 Aligned_cols=28 Identities=25% Similarity=0.501 Sum_probs=22.2
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEeEEEE
Q 027093 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~ 50 (228)
..+++||.+.|...+ .+.-+.+|.++..
T Consensus 29 ~~~k~Gd~~i~~~~~--~~~~~i~v~~V~~ 56 (105)
T cd06541 29 QLPKAGDYLIILDGQ--QPLAIAEVVKVEI 56 (105)
T ss_pred cCCCCCCEEEEecCC--CcEEEEEEEEEEE
Confidence 578999999998876 5666788887765
No 125
>PF11132 SplA: Transcriptional regulator protein (SplA); InterPro: IPR022608 The SplA protein functions in trans as a negative regulator of the level of splB-lacZ expression in the developing forespore [].
Probab=33.85 E-value=29 Score=23.77 Aligned_cols=25 Identities=20% Similarity=0.247 Sum_probs=18.8
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEeE
Q 027093 22 VVRPGDCVLMRPADSDKPPYVARVEK 47 (228)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~rI~~ 47 (228)
.|++||.|||.=-+ +..+-|+-|.+
T Consensus 5 ~~~~GD~VyViYrN-PHt~~VanIqe 29 (75)
T PF11132_consen 5 PYHAGDIVYVIYRN-PHTQDVANIQE 29 (75)
T ss_pred ccCCCCEEEEEEcC-CCCccccccch
Confidence 68999999998876 34556666654
No 126
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=33.29 E-value=79 Score=21.77 Aligned_cols=28 Identities=25% Similarity=0.158 Sum_probs=18.7
Q ss_pred CeEEccCCEEEEccCCCCCCCeEEEEeEEE
Q 027093 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIE 49 (228)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~ 49 (228)
...++.||+|.|...+ ...--|+|+..+
T Consensus 36 ~iwI~~GD~V~Ve~~~--~d~~kg~Iv~r~ 63 (77)
T cd05793 36 RVWINEGDIVLVAPWD--FQDDKADIIYKY 63 (77)
T ss_pred cEEEcCCCEEEEEecc--ccCCEEEEEEEc
Confidence 3678889999998665 234456665544
No 127
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=32.85 E-value=87 Score=23.07 Aligned_cols=36 Identities=22% Similarity=0.171 Sum_probs=27.9
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEE
Q 027093 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVR 61 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~ 61 (228)
..++.||.|+|.++. +.---|+|.++.... +.|.+-
T Consensus 3 ~~IrkGD~V~Vi~Gk--dKGk~GkVl~v~~k~---V~VEGv 38 (104)
T COG0198 3 MKVKKGDTVKVIAGK--DKGKEGKVLKVLPKK---VVVEGV 38 (104)
T ss_pred cceecCCEEEEEecC--CCCcceEEEEEecCe---EEEECc
Confidence 357889999999997 666789999998754 555544
No 128
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=32.54 E-value=89 Score=21.86 Aligned_cols=29 Identities=28% Similarity=0.240 Sum_probs=19.0
Q ss_pred CeEEccCCEEEEccCCCCCCCeEEEEeEEEE
Q 027093 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (228)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~ 50 (228)
...++.||+|.|...+. ..--|+|+....
T Consensus 41 ~iwI~~GD~VlVe~~~~--~~~kg~Iv~r~~ 69 (83)
T smart00652 41 KVWIRRGDIVLVDPWDF--QDVKADIIYKYT 69 (83)
T ss_pred cEEEcCCCEEEEEecCC--CCCEEEEEEEeC
Confidence 46788899999987642 244566655543
No 129
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=31.62 E-value=21 Score=31.34 Aligned_cols=36 Identities=25% Similarity=0.447 Sum_probs=23.8
Q ss_pred CCCceEECCCCCceecCCCCCCChhhhCCCCeEEcccccccccc
Q 027093 149 PDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (228)
Q Consensus 149 ~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (228)
|++.++.|+.|+...+. .+.+. ..++|+.|-.-.++
T Consensus 34 p~~lw~kc~~C~~~~~~-------~~l~~-~~~vcp~c~~h~rl 69 (296)
T CHL00174 34 YKHLWVQCENCYGLNYK-------KFLKS-KMNICEQCGYHLKM 69 (296)
T ss_pred CCCCeeECCCccchhhH-------HHHHH-cCCCCCCCCCCcCC
Confidence 67789999999763322 22211 46899999876653
No 130
>PF12503 CMV_1a_C: Cucumber mosaic virus 1a protein C terminal ; InterPro: IPR022184 This domain family is found in viruses, and is approximately 90 amino acids in length. The family is found in association with PF01443 from PFAM, PF01660 from PFAM. There is a conserved GLG sequence motif. 1a protein is the major virulence factor of the (Cucumber mosaic virus. The Ns strain of CMV causes necrotic lesions to Nicotiana spp. while other strains cause systemic mosaic. The determinant of the pathogenesis of these different strains is the specific amino acid residue at the 461 residue of the 1a protein. ; GO: 0008168 methyltransferase activity, 0016817 hydrolase activity, acting on acid anhydrides
Probab=31.43 E-value=1.8e+02 Score=20.51 Aligned_cols=44 Identities=25% Similarity=0.255 Sum_probs=26.1
Q ss_pred EeEEEEcCCCCEE---EEEEEEeeccccc-------CCccccCCCCeEEeeCCcee
Q 027093 45 VEKIEADHRNNVK---VRVRWYYRPEESI-------GGRRQFHGAKELFLSDHYDV 90 (228)
Q Consensus 45 I~~i~~~~~~~~~---v~v~WfyRp~d~~-------~~~~~~~~~~ELFlS~~~d~ 90 (228)
|.+.+...|.-+- -.++|+| |.++. .|-.+ -.++|||+-+..-.
T Consensus 20 V~dTY~~vD~lVNvHf~~GrWm~-P~~~~Y~VGyNe~GLGp-K~~~ElyiVnk~Cv 73 (85)
T PF12503_consen 20 VFDTYHRVDPLVNVHFPNGRWMY-PEGYEYMVGYNESGLGP-KFDGELYIVNKDCV 73 (85)
T ss_pred eEEEEeeccccEEEEecCCceec-CCCeEEEeeecCCCCCc-CcCCeEEEEcCcEE
Confidence 5555555555433 3467999 88763 11111 24789999887543
No 131
>cd03701 IF2_IF5B_II IF2_IF5B_II: This family represents the domain II of prokaryotic Initiation Factor 2 (IF2) and its archeal and eukaryotic homologue aeIF5B. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of the 60S ribosomal subunit. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains in EF1A, eEF1A and aeIF2gamma.
Probab=31.27 E-value=1.4e+02 Score=21.20 Aligned_cols=41 Identities=10% Similarity=0.323 Sum_probs=29.3
Q ss_pred CCCCCceeeeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEeEEEEcC
Q 027093 3 KTKPGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADH 52 (228)
Q Consensus 3 ~~~~~~~~y~s~~v~g~~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~ 52 (228)
+..+++-.+-..+|.. -++++||++.+-.. .|+|..|+.+.
T Consensus 9 ~~~~g~G~vatviV~~--GtL~~Gd~iv~G~~-------~GkVr~~~d~~ 49 (95)
T cd03701 9 KLDKGRGPVATVIVQN--GTLKKGDVIVAGGT-------YGKIRTMVDEN 49 (95)
T ss_pred EecCCCCeeEEEEEEc--CeEecCCEEEECCc-------cceEEEEECCC
Confidence 3445655666666653 39999999988665 48898888754
No 132
>cd03702 IF2_mtIF2_II This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2 is structurally and functionally related to eukaryotic mitochondrial mtIF-2.
Probab=30.75 E-value=1.2e+02 Score=21.68 Aligned_cols=41 Identities=10% Similarity=0.263 Sum_probs=29.4
Q ss_pred CCCCceeeeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEeEEEEcCC
Q 027093 4 TKPGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHR 53 (228)
Q Consensus 4 ~~~~~~~y~s~~v~g~~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~ 53 (228)
..++.-.+..++|.. -++++||++.+-.. .|||..|+.+..
T Consensus 10 ~~~g~G~vatviV~~--GtL~~Gd~iv~G~~-------~gkVr~l~d~~g 50 (95)
T cd03702 10 LDKGRGPVATVLVQN--GTLKVGDVLVAGTT-------YGKVRAMFDENG 50 (95)
T ss_pred ecCCCCccEEEEEEc--CeEeCCCEEEEccc-------ccEEEEEECCCC
Confidence 345555666676753 38999999988655 469999988643
No 133
>PRK08359 transcription factor; Validated
Probab=30.70 E-value=5.8 Score=32.07 Aligned_cols=36 Identities=22% Similarity=0.421 Sum_probs=23.2
Q ss_pred EECCCCCceecCCCCCCChhhhCCCCeEEcccccccccc
Q 027093 154 VQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (228)
Q Consensus 154 i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (228)
.+|+.|+.-..+....+.-..+ ...+|..|..+.+.
T Consensus 7 ~~CEiCG~~i~g~~~~v~ieGa---el~VC~~Ca~k~G~ 42 (176)
T PRK08359 7 RYCEICGAEIRGPGHRIRIEGA---ELLVCDRCYEKYGR 42 (176)
T ss_pred ceeecCCCccCCCCeEEEEcCe---EEehHHHHHHHhCC
Confidence 3488888777665444333322 46899999966665
No 134
>PF07494 Reg_prop: Two component regulator propeller; InterPro: IPR011110 A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats. These repeats show homology to members of IPR002372 from INTERPRO and IPR001680 from INTERPRO indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=30.26 E-value=72 Score=16.49 Aligned_cols=15 Identities=20% Similarity=0.266 Sum_probs=10.7
Q ss_pred EEeEEEEcCCCCEEE
Q 027093 44 RVEKIEADHRNNVKV 58 (228)
Q Consensus 44 rI~~i~~~~~~~~~v 58 (228)
.|..|.++++|.+|+
T Consensus 6 ~I~~i~~D~~G~lWi 20 (24)
T PF07494_consen 6 NIYSIYEDSDGNLWI 20 (24)
T ss_dssp CEEEEEE-TTSCEEE
T ss_pred eEEEEEEcCCcCEEE
Confidence 367888888888775
No 135
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=30.05 E-value=96 Score=22.68 Aligned_cols=45 Identities=20% Similarity=0.356 Sum_probs=35.2
Q ss_pred CCceeeeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCC
Q 027093 6 PGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRN 54 (228)
Q Consensus 6 ~~~~~y~s~~v~g~~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~ 54 (228)
.|+.++++..++. ...+++||.+.|.-+. ..+..+|..+-....+
T Consensus 33 ~GrV~vNG~~aKp-S~~VK~GD~l~i~~~~---~~~~v~Vl~~~~~r~~ 77 (100)
T COG1188 33 GGRVKVNGQRAKP-SKEVKVGDILTIRFGN---KEFTVKVLALGEQRRP 77 (100)
T ss_pred CCeEEECCEEccc-ccccCCCCEEEEEeCC---cEEEEEEEecccccCc
Confidence 4788888888864 5899999999999886 6678888888664433
No 136
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=30.02 E-value=24 Score=30.71 Aligned_cols=37 Identities=16% Similarity=0.540 Sum_probs=24.4
Q ss_pred CCCCceEECCCCCceecCCCCCCChhhhCCCCeEEcccccccccc
Q 027093 148 NPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (228)
Q Consensus 148 ~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (228)
-|++.++.|+.|+...+. .+... ..++|+.|-.-.++
T Consensus 21 ~~~~~~~~c~~c~~~~~~-------~~l~~-~~~vc~~c~~h~rl 57 (285)
T TIGR00515 21 VPEGVWTKCPKCGQVLYT-------KELER-NLEVCPKCDHHMRM 57 (285)
T ss_pred CCCCCeeECCCCcchhhH-------HHHHh-hCCCCCCCCCcCcC
Confidence 367789999999774432 22211 35899999876553
No 137
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=29.47 E-value=1.2e+02 Score=23.72 Aligned_cols=40 Identities=25% Similarity=0.419 Sum_probs=26.0
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEeEEEEc----CCCCEEEEEE
Q 027093 22 VVRPGDCVLMRPADSDKPPYVARVEKIEAD----HRNNVKVRVR 61 (228)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~----~~~~~~v~v~ 61 (228)
.++.||.|.+..+......+|.||..+-.+ .++.+++.++
T Consensus 51 ~~~rGDiVvf~~~~~~~~~~iKRVig~pGd~v~i~~~~l~vNg~ 94 (163)
T TIGR02227 51 DPKRGDIVVFKDPDDNKNIYVKRVIGLPGDKVEFRDGKLYINGK 94 (163)
T ss_pred CCCCCcEEEEecCCCCCceeEEEEEecCCCEEEEECCEEEECCE
Confidence 578899999887654456788888876332 2444444443
No 138
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=29.16 E-value=48 Score=33.63 Aligned_cols=48 Identities=19% Similarity=0.629 Sum_probs=36.4
Q ss_pred cCCCCCCCCCceEECCCCCceecCCCCCCChhhhCCCCeEEcccccccccc
Q 027093 142 KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (228)
Q Consensus 142 ~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (228)
.|.+..++ ... +|+.|.+-+|..|.+.+.....+ ..|.|+.|......
T Consensus 160 ~~~k~~~~-~~~-~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 207 (904)
T KOG1246|consen 160 TCSKGKEE-KLL-LCDSCDDSYHTYCLRPPLTRVPD-GDWRCPKCIPTPES 207 (904)
T ss_pred ccccCCCc-cce-ecccccCcccccccCCCCCcCCc-CcccCCcccccccC
Confidence 45555544 444 99999999999999998777655 46779999987443
No 139
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=29.15 E-value=25 Score=30.74 Aligned_cols=37 Identities=19% Similarity=0.542 Sum_probs=24.8
Q ss_pred CCCCceEECCCCCceecCCCCCCChhhhCCCCeEEcccccccccc
Q 027093 148 NPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (228)
Q Consensus 148 ~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (228)
-|++.|+.|+.|+...+. .+.+. +.++|+.|-.-.++
T Consensus 22 ~~~~~~~~c~~c~~~~~~-------~~l~~-~~~vc~~c~~h~rl 58 (292)
T PRK05654 22 VPEGLWTKCPSCGQVLYR-------KELEA-NLNVCPKCGHHMRI 58 (292)
T ss_pred CCCCCeeECCCccchhhH-------HHHHh-cCCCCCCCCCCeeC
Confidence 367789999999774432 22212 35799999877654
No 140
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=28.83 E-value=1.3e+02 Score=22.43 Aligned_cols=39 Identities=26% Similarity=0.204 Sum_probs=28.8
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEE
Q 027093 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRW 62 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~W 62 (228)
..++.||-|.|.++. +.-..|.|.+|.. .++.+.|.+.-
T Consensus 40 ~~IkkGD~V~Vi~Gk--~KGk~GkV~~V~~-~~~~V~Vegvn 78 (114)
T TIGR01080 40 LPVRKGDKVRIMRGD--FKGHEGKVSKVDL-KRYRIYVEGVT 78 (114)
T ss_pred ceeecCCEEEEecCC--CCCCEEEEEEEEc-CCCEEEEcCeE
Confidence 478999999999997 5667899999974 33445544443
No 141
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=28.74 E-value=75 Score=20.21 Aligned_cols=28 Identities=21% Similarity=0.223 Sum_probs=22.3
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEeEEEE
Q 027093 22 VVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (228)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~rI~~i~~ 50 (228)
.+++||.|.+...+ .+.-|-|+|.++..
T Consensus 2 ~~~~G~~Ve~~~~~-~~~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKE-EDSWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECC-CCEEEEEEEEEECC
Confidence 47899999999865 35667799999865
No 142
>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.81 E-value=51 Score=32.27 Aligned_cols=34 Identities=18% Similarity=0.498 Sum_probs=24.9
Q ss_pred EECCCCCceecCCCCCCChhhhCCCCeEEcccccccccc
Q 027093 154 VQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (228)
Q Consensus 154 i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (228)
+.|..|+..+.+-|.-.... ..|.|+.|..++..
T Consensus 54 ~~C~~C~AvlNPyc~vd~~a-----~~W~CpfC~qrN~~ 87 (745)
T KOG1986|consen 54 LRCSKCGAVLNPYCSVDFRA-----KSWICPFCNQRNPF 87 (745)
T ss_pred chhccchhhcCcceeecccC-----ceEeccccccCCCC
Confidence 66777877777777655433 36999999998753
No 143
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=27.64 E-value=17 Score=27.14 Aligned_cols=52 Identities=23% Similarity=0.489 Sum_probs=35.5
Q ss_pred eeee-cCCCCCCC-CCceEECCCCCceecCCCCCCChhhhCCCCeEEccccccccccc
Q 027093 138 AVYC-KCEMPYNP-DDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 193 (228)
Q Consensus 138 ~~~C-~C~~~~~~-~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~k 193 (228)
...| +|+.+..- ...-..|..|+......|-...... ..|+|..|......+
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~~~~----~~WlC~vC~k~rel~ 107 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYSKKE----PIWLCKVCQKQRELK 107 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEETSSS----CCEEEHHHHHHHHHH
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCcCCCC----CCEEChhhHHHHHHH
Confidence 3456 67765421 2234889999999999998873222 579999999877655
No 144
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=27.34 E-value=1.3e+02 Score=20.72 Aligned_cols=30 Identities=17% Similarity=0.280 Sum_probs=19.0
Q ss_pred CeEEccCCEEEEccCCCCCCCeEEEEeEEEE
Q 027093 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (228)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~ 50 (228)
...++.||+|.|.+.+. +..-=|.|+....
T Consensus 36 ~iwI~~GD~VlV~~~~~-~~~~kg~Iv~r~~ 65 (78)
T cd04456 36 NIWIKRGDFLIVDPIEE-GEDVKADIIFVYC 65 (78)
T ss_pred CEEEcCCCEEEEEeccc-CCCceEEEEEEeC
Confidence 36789999999977652 1234455555443
No 145
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=27.26 E-value=31 Score=27.22 Aligned_cols=19 Identities=26% Similarity=0.747 Sum_probs=14.1
Q ss_pred CCceEECCCCCceecCCCC
Q 027093 150 DDLMVQCEGCKDWFHPSCM 168 (228)
Q Consensus 150 ~~~mi~C~~C~~w~H~~Cv 168 (228)
..-.++|..|++||.-.=-
T Consensus 11 p~~vv~C~~c~kWFCNg~~ 29 (152)
T PF09416_consen 11 PSCVVKCNTCNKWFCNGRG 29 (152)
T ss_dssp CCCEEEETTTTEEEES--T
T ss_pred cccEeEcCCCCcEeecCCC
Confidence 3578999999999985443
No 146
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=27.04 E-value=24 Score=31.14 Aligned_cols=31 Identities=23% Similarity=0.647 Sum_probs=19.6
Q ss_pred eee-cCCCCCCCCCceEECCCCCceecCCCCCCCh
Q 027093 139 VYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTI 172 (228)
Q Consensus 139 ~~C-~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~ 172 (228)
-+| .|+.|-.-.+.||-|+ .-|..+|.....
T Consensus 91 HfCd~Cd~PI~IYGRmIPCk---HvFCl~CAr~~~ 122 (389)
T KOG2932|consen 91 HFCDRCDFPIAIYGRMIPCK---HVFCLECARSDS 122 (389)
T ss_pred EeecccCCcceeeecccccc---hhhhhhhhhcCc
Confidence 345 6776665577888765 456666666544
No 147
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=26.77 E-value=1.6e+02 Score=21.85 Aligned_cols=28 Identities=21% Similarity=0.399 Sum_probs=19.7
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEeEEEE
Q 027093 22 VVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (228)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~rI~~i~~ 50 (228)
.+++||.+.+..-+. .....++|..|..
T Consensus 31 ~ikvGD~I~f~~~~~-~~~l~v~V~~i~~ 58 (109)
T cd06555 31 QIKVGDKILFNDLDT-GQQLLVKVVDIRK 58 (109)
T ss_pred cCCCCCEEEEEEcCC-CcEEEEEEEEEEe
Confidence 699999999987652 3445566666654
No 148
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=26.70 E-value=71 Score=20.63 Aligned_cols=25 Identities=32% Similarity=0.369 Sum_probs=16.2
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEeEEEE
Q 027093 22 VVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (228)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~rI~~i~~ 50 (228)
...+||.|.+...+ ++ -+.|.++.+
T Consensus 37 ~~~VGD~V~~~~~~-~~---~~~I~~vl~ 61 (68)
T cd04466 37 PPAVGDRVEFEPED-DG---EGVIEEILP 61 (68)
T ss_pred CCCCCcEEEEEECC-CC---cEEEEEEec
Confidence 36899999997543 12 255666654
No 149
>KOG1740 consensus Predicted mitochondrial/chloroplast ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=26.53 E-value=46 Score=24.33 Aligned_cols=28 Identities=21% Similarity=0.342 Sum_probs=23.4
Q ss_pred eeeeeEEEcCCCeEEccCCEEEEccCCC
Q 027093 9 KDLDSYNIKGTNKVVRPGDCVLMRPADS 36 (228)
Q Consensus 9 ~~y~s~~v~g~~~~~~vGD~V~v~~~~~ 36 (228)
+++..+.+++++...++||-|-+.+.-+
T Consensus 36 ~~~~kymahD~~n~cnvGD~VrlepsRP 63 (107)
T KOG1740|consen 36 KRTSKYMAHDDKNQCNVGDRVRLEPSRP 63 (107)
T ss_pred HHhhheeecCccccccccceEEeccCCc
Confidence 4566788888888899999999999864
No 150
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.39 E-value=28 Score=26.91 Aligned_cols=77 Identities=17% Similarity=0.234 Sum_probs=48.7
Q ss_pred eeeecCCCCCCCCCceEECCCCCceecCCCCCCChhhhCCCCeEEcccccccccc------cccCCCCCCCCCchhhhcc
Q 027093 138 AVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA------KRSLNTFSVSPSVEAKVRA 211 (228)
Q Consensus 138 ~~~C~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~------k~~~~~~~~~~~~~~~~~~ 211 (228)
++.-||.+.--.|+---.|--|+--|...|-|--...... -.|+|..|....+. +--.+.+.+++++..+|..
T Consensus 66 atC~IC~KTKFADG~GH~C~YCq~r~CARCGGrv~lrsNK-v~wvcnlc~k~q~il~ksg~wf~~sgs~~~~~pd~~v~~ 144 (169)
T KOG3799|consen 66 ATCGICHKTKFADGCGHNCSYCQTRFCARCGGRVSLRSNK-VMWVCNLCRKQQEILTKSGAWFYNSGSNTPQQPDQKVLR 144 (169)
T ss_pred cchhhhhhcccccccCcccchhhhhHHHhcCCeeeeccCc-eEEeccCCcHHHHHHHhcchHHHhcCCCCCCCccccccc
Confidence 4444887655455555667788999999998875444322 47999999987652 1113334455555566666
Q ss_pred ceee
Q 027093 212 HMFH 215 (228)
Q Consensus 212 ~~~~ 215 (228)
+.++
T Consensus 145 ~~~~ 148 (169)
T KOG3799|consen 145 GLRN 148 (169)
T ss_pred chhc
Confidence 6554
No 151
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=26.35 E-value=10 Score=36.31 Aligned_cols=32 Identities=22% Similarity=0.560 Sum_probs=24.9
Q ss_pred ceEECCCCCceecCCCCCCChhhhCCCCeEEccccccccc
Q 027093 152 LMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 191 (228)
Q Consensus 152 ~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 191 (228)
.-..|+.|..|||..|......- ||.|.+-..
T Consensus 530 ~~~rC~~C~avfH~~C~~r~s~~--------CPrC~R~q~ 561 (580)
T KOG1829|consen 530 NTRRCSTCLAVFHKKCLRRKSPC--------CPRCERRQK 561 (580)
T ss_pred cceeHHHHHHHHHHHHHhccCCC--------CCchHHHHH
Confidence 34779999999999998774321 999987554
No 152
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=25.53 E-value=52 Score=22.54 Aligned_cols=37 Identities=19% Similarity=0.369 Sum_probs=24.9
Q ss_pred eEEEcCCCeEEccCCEEEEccCCCC---CCCeEEEEeEEE
Q 027093 13 SYNIKGTNKVVRPGDCVLMRPADSD---KPPYVARVEKIE 49 (228)
Q Consensus 13 s~~v~g~~~~~~vGD~V~v~~~~~~---~~~~I~rI~~i~ 49 (228)
.|.+..|+..|++||.+.+..=+++ .....++|..|.
T Consensus 19 tfEiRkNDRdf~VGD~L~L~E~~~~~YTGr~~~~~Ityi~ 58 (72)
T PF12961_consen 19 TFEIRKNDRDFQVGDILVLREWDNGEYTGREIEAEITYIT 58 (72)
T ss_pred eEEEEecCCCCCCCCEEEEEEecCCCccccEEEEEEEEEe
Confidence 5667777789999999998775421 223446666664
No 153
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=25.49 E-value=37 Score=28.17 Aligned_cols=39 Identities=15% Similarity=0.348 Sum_probs=26.4
Q ss_pred eEECCCCCceecCCCCCCChhhh-----------CC-----CCeEEccccccccc
Q 027093 153 MVQCEGCKDWFHPSCMGMTIEEA-----------KK-----LDHFLCSDCSSDVD 191 (228)
Q Consensus 153 mi~C~~C~~w~H~~Cv~~~~~~~-----------~~-----~~~~~C~~C~~~~~ 191 (228)
-+.|+.|++-|...-|....... +. -+.|+||.|--..-
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~ 59 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAF 59 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccc
Confidence 37899999888887775543221 01 15799999987654
No 154
>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=25.47 E-value=22 Score=21.26 Aligned_cols=32 Identities=22% Similarity=0.446 Sum_probs=21.8
Q ss_pred eeee-cCCCCCCCCC-ceEECCCCCceecCCCCCC
Q 027093 138 AVYC-KCEMPYNPDD-LMVQCEGCKDWFHPSCMGM 170 (228)
Q Consensus 138 ~~~C-~C~~~~~~~~-~mi~C~~C~~w~H~~Cv~~ 170 (228)
+.+| .|++..- .. ....|..|+.-.|..|+..
T Consensus 11 ~~~C~~C~~~i~-~~~~~~~C~~C~~~~H~~C~~~ 44 (49)
T smart00109 11 PTKCCVCRKSIW-GSFQGLRCSWCKVKCHKKCAEK 44 (49)
T ss_pred CCCccccccccC-cCCCCcCCCCCCchHHHHHHhh
Confidence 3444 6766542 22 3678999999999999865
No 155
>PF02559 CarD_CdnL_TRCF: CarD-like/TRCF domain; InterPro: IPR003711 The bacterium Myxococcus xanthus responds to blue light by producing carotenoids. It also responds to starvation conditions by developing fruiting bodies, where the cells differentiate into myxospores. Each response entails the transcriptional activation of a separate set of genes. A single gene, carD, is required for the activation of both light- and starvation-inducible genes []. The predicted protein contains four repeats of a DNA-binding domain present in mammalian high mobility group I(Y) proteins and other nuclear proteins from animals and plants. Other peptide stretches on CarD also resemble functional domains typical of eukaryotic transcription factors, including a very acidic region and a leucine zipper. High mobility group yI(Y) proteins are known to bind the minor groove of A+T-rich DNA [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3MLQ_H 2EYQ_A.
Probab=25.31 E-value=94 Score=21.98 Aligned_cols=24 Identities=33% Similarity=0.429 Sum_probs=18.3
Q ss_pred EccCCEEEEccCCCCCCCeEEEEeEEEEcC
Q 027093 23 VRPGDCVLMRPADSDKPPYVARVEKIEADH 52 (228)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~ 52 (228)
|++||.|.=.... ||+|..|....
T Consensus 2 f~~GD~VVh~~~G------v~~i~~i~~~~ 25 (98)
T PF02559_consen 2 FKIGDYVVHPNHG------VGRIEGIEEIE 25 (98)
T ss_dssp --TTSEEEETTTE------EEEEEEEEEEE
T ss_pred CCCCCEEEECCCc------eEEEEEEEEEe
Confidence 6789999877766 99999997754
No 156
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=25.07 E-value=77 Score=20.76 Aligned_cols=57 Identities=23% Similarity=0.417 Sum_probs=29.1
Q ss_pred cCCCceeee-cCCCCCCCCCceEECCCCCceecCCCCCCChhh-----hCCCCeEEccccccc
Q 027093 133 TPDRVAVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEE-----AKKLDHFLCSDCSSD 189 (228)
Q Consensus 133 ~p~~~~~~C-~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~~~-----~~~~~~~~C~~C~~~ 189 (228)
.|+.....| +|..+.+--..=..|..|+..|..+|....... ......-+|..|...
T Consensus 4 ~~d~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~~~~~~~~~~~~~~RvC~~C~~~ 66 (69)
T PF01363_consen 4 VPDSEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRIPLPTPSSGSGEPVRVCDSCYSK 66 (69)
T ss_dssp SSGGG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEEEET--GGTESEEEEE-HHHHHH
T ss_pred CCCCCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEEcccccccCCCCcCEECHHHHHH
Confidence 455566677 688776544455789999999999999754321 111246788888754
No 157
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=25.01 E-value=29 Score=27.33 Aligned_cols=34 Identities=21% Similarity=0.531 Sum_probs=21.5
Q ss_pred ECCCCCceecCCCCCCChhhhCCCCeEEcccccccccc
Q 027093 155 QCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (228)
Q Consensus 155 ~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (228)
+|+.|+.-..+....+.-..+ ...+|..|. +.+.
T Consensus 2 ~CEiCG~~i~~~~~~v~iega---~l~vC~~C~-k~G~ 35 (154)
T TIGR00270 2 NCEICGRKIKGKGFKIVIEGS---EMTVCGECR-KFGK 35 (154)
T ss_pred ccccCCCccCCCCeEEEEcCe---EEehhhhHH-hcCC
Confidence 388888766665444333332 468899999 5554
No 158
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=24.71 E-value=52 Score=23.91 Aligned_cols=16 Identities=38% Similarity=0.792 Sum_probs=13.1
Q ss_pred CEEEEEEEEeeccccc
Q 027093 55 NVKVRVRWYYRPEESI 70 (228)
Q Consensus 55 ~~~v~v~WfyRp~d~~ 70 (228)
...|+|.|||.++|-.
T Consensus 76 g~~V~v~Wyyd~dD~~ 91 (99)
T PF09345_consen 76 GGKVTVNWYYDEDDED 91 (99)
T ss_pred CCcEEEEEEECCCCch
Confidence 3779999999988753
No 159
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=24.67 E-value=1.7e+02 Score=23.65 Aligned_cols=45 Identities=27% Similarity=0.465 Sum_probs=35.2
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeeccc
Q 027093 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEE 68 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~d 68 (228)
..+.+||.|-|.++. -..+.|+|+++..+ .+.+.+.|.-|-|+--
T Consensus 122 ~~~e~Gd~VrI~~Gp--Fa~f~g~V~evd~e-k~~~~v~v~ifgr~tP 166 (178)
T COG0250 122 VDFEPGDVVRIIDGP--FAGFKAKVEEVDEE-KGKLKVEVSIFGRPTP 166 (178)
T ss_pred ccCCCCCEEEEeccC--CCCccEEEEEEcCc-CcEEEEEEEEeCCceE
Confidence 578999999999996 46689999999874 3557777777777654
No 160
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=24.43 E-value=84 Score=20.70 Aligned_cols=25 Identities=24% Similarity=0.343 Sum_probs=16.0
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEeE
Q 027093 21 KVVRPGDCVLMRPADSDKPPYVARVEK 47 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~rI~~ 47 (228)
..++.||+|.|...+. ..--|+|+.
T Consensus 40 iwI~~GD~V~V~~~~~--d~~kG~Ii~ 64 (65)
T PF01176_consen 40 IWIKRGDFVLVEPSPY--DKVKGRIIY 64 (65)
T ss_dssp C---TTEEEEEEESTT--CTTEEEEEE
T ss_pred EecCCCCEEEEEeccc--CCCeEEEEE
Confidence 5678999999998652 256677764
No 161
>COG0662 {ManC} Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=24.25 E-value=71 Score=23.91 Aligned_cols=22 Identities=27% Similarity=0.451 Sum_probs=17.5
Q ss_pred EEEcCCCeEEccCCEEEEccCC
Q 027093 14 YNIKGTNKVVRPGDCVLMRPAD 35 (228)
Q Consensus 14 ~~v~g~~~~~~vGD~V~v~~~~ 35 (228)
+.+++.-..++.||+++|.++.
T Consensus 70 v~~~~~~~~v~~gd~~~iP~g~ 91 (127)
T COG0662 70 VTIGGEEVEVKAGDSVYIPAGT 91 (127)
T ss_pred EEECCEEEEecCCCEEEECCCC
Confidence 4455556788999999999986
No 162
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=23.99 E-value=37 Score=29.50 Aligned_cols=37 Identities=19% Similarity=0.586 Sum_probs=25.9
Q ss_pred CCCceEECCCCCceecCCCCCCChhhhCCCCeEEccccccccccc
Q 027093 149 PDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 193 (228)
Q Consensus 149 ~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~k 193 (228)
+++.|++|..|+...|.+ +... +.++|+.|..-.++.
T Consensus 24 ~e~lw~KCp~c~~~~y~~-------eL~~-n~~vcp~c~~h~ri~ 60 (294)
T COG0777 24 PEGLWTKCPSCGEMLYRK-------ELES-NLKVCPKCGHHMRIS 60 (294)
T ss_pred CCCceeECCCccceeeHH-------HHHh-hhhcccccCcccccC
Confidence 478999999997654432 2211 579999999877654
No 163
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=23.98 E-value=1.4e+02 Score=21.78 Aligned_cols=27 Identities=26% Similarity=0.224 Sum_probs=14.3
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEeEEE
Q 027093 21 KVVRPGDCVLMRPADSDKPPYVARVEKIE 49 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~rI~~i~ 49 (228)
..++.||+|.|...+. + .-=|+|+..+
T Consensus 58 IwI~~GD~VlVe~~~~-~-~~kg~Iv~r~ 84 (100)
T PRK04012 58 MWIREGDVVIVAPWDF-Q-DEKADIIWRY 84 (100)
T ss_pred EEecCCCEEEEEeccc-C-CCEEEEEEEc
Confidence 4566777777766442 1 3344444433
No 164
>KOG3896 consensus Dynactin, subunit p62 [Cell motility]
Probab=23.61 E-value=56 Score=29.25 Aligned_cols=9 Identities=33% Similarity=0.874 Sum_probs=4.2
Q ss_pred eecCCCCCC
Q 027093 162 WFHPSCMGM 170 (228)
Q Consensus 162 w~H~~Cv~~ 170 (228)
.|.+.|+..
T Consensus 46 hfCp~CLEn 54 (449)
T KOG3896|consen 46 HFCPRCLEN 54 (449)
T ss_pred ccchhhccC
Confidence 344555533
No 165
>cd05838 WHSC1_related The PWWP domain was first identified in the WHSC1 (Wolf-Hirschhorn syndrome candidate 1) protein, a protein implicated in Wolf-Hirschhorn syndrome (WHS). When translocated, WHSC1 plays a role in lymphoid multiple myeloma (MM) disease, also known as plasmacytoma. WHCS1 proteins typically contain two copies of the PWWP domain. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=23.19 E-value=1.1e+02 Score=21.76 Aligned_cols=23 Identities=17% Similarity=0.018 Sum_probs=19.9
Q ss_pred ccCCEEEEccCCCCCCCeEEEEeEE
Q 027093 24 RPGDCVLMRPADSDKPPYVARVEKI 48 (228)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~I~rI~~i 48 (228)
++||.|..+-.. .+.|-|+|.+-
T Consensus 2 ~~GdlVWaK~~g--~pwWPa~V~~~ 24 (95)
T cd05838 2 LYGDIVWAKLGN--FRWWPAIICDP 24 (95)
T ss_pred CcCCEEEEECCC--CCCCCeEEcCh
Confidence 579999999887 78999999874
No 166
>PF14353 CpXC: CpXC protein
Probab=23.13 E-value=64 Score=24.12 Aligned_cols=38 Identities=18% Similarity=0.476 Sum_probs=23.0
Q ss_pred EECCCCCceecC---CCCCCChhh-------hCCCCeEEccccccccc
Q 027093 154 VQCEGCKDWFHP---SCMGMTIEE-------AKKLDHFLCSDCSSDVD 191 (228)
Q Consensus 154 i~C~~C~~w~H~---~Cv~~~~~~-------~~~~~~~~C~~C~~~~~ 191 (228)
|.|..|+.-|.. .-|+....+ ...+..+.||.|-....
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFR 49 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCcee
Confidence 567788766654 334432221 23346899999988765
No 167
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=23.13 E-value=1.7e+02 Score=25.20 Aligned_cols=46 Identities=17% Similarity=0.234 Sum_probs=36.0
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeecccc
Q 027093 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEES 69 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~d~ 69 (228)
..+.+||.|.|..+. -.-+.|.|.++.. ..+.+.|.+.+|-|.--+
T Consensus 204 ~~f~vGd~VrI~dGP--F~GfeG~I~eid~-~k~Rv~VlV~IfGR~TpV 249 (258)
T TIGR01956 204 SKFRVGNFVKIVDGP--FKGIVGKIKKIDQ-EKKKAIVEVEILGKSVDV 249 (258)
T ss_pred cCCCCCCEEEEEecC--CCCcEEEEEEEeC-CCCEEEEEEEecCCcEEE
Confidence 347899999999986 5668899999975 356688888888876543
No 168
>PF08921 DUF1904: Domain of unknown function (DUF1904); InterPro: IPR015017 This entry represents a family of hypothetical bacterial proteins. ; PDB: 1U9D_B.
Probab=22.88 E-value=35 Score=25.27 Aligned_cols=17 Identities=29% Similarity=0.411 Sum_probs=10.0
Q ss_pred CCEEEEEEEEeeccccc
Q 027093 54 NNVKVRVRWYYRPEESI 70 (228)
Q Consensus 54 ~~~~v~v~WfyRp~d~~ 70 (228)
+..+|.|.||-|+.|+.
T Consensus 54 ~~pfVEV~WF~R~qe~q 70 (108)
T PF08921_consen 54 GYPFVEVLWFDRGQEVQ 70 (108)
T ss_dssp ---EEEEEES---HHHH
T ss_pred cceeEEEEEecCCHHHH
Confidence 34689999999999975
No 169
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.88 E-value=43 Score=26.55 Aligned_cols=34 Identities=26% Similarity=0.391 Sum_probs=24.2
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCC
Q 027093 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNN 55 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~ 55 (228)
..+++||.|..+-++ .+-|.|-|+++.++..+|+
T Consensus 76 ~p~~vGdivVf~veg-R~IPiVHRviK~he~~~~~ 109 (180)
T KOG3342|consen 76 DPIRVGDIVVFKVEG-REIPIVHRVIKQHEKSNGH 109 (180)
T ss_pred CcceeccEEEEEECC-ccCchhHHHHHHhcccCCc
Confidence 457788888887776 3667778888777755443
No 170
>PF04322 DUF473: Protein of unknown function (DUF473); InterPro: IPR007417 This is a family of uncharacterised archaeal proteins.
Probab=22.32 E-value=1.4e+02 Score=22.59 Aligned_cols=29 Identities=31% Similarity=0.512 Sum_probs=21.9
Q ss_pred EEccCCEEEEccCC-----CCCCCeEEEEeEEEE
Q 027093 22 VVRPGDCVLMRPAD-----SDKPPYVARVEKIEA 50 (228)
Q Consensus 22 ~~~vGD~V~v~~~~-----~~~~~~I~rI~~i~~ 50 (228)
.+.+||+|++.+.. ++..-.||+|.++.-
T Consensus 38 ~~~~Gd~VFlT~~~~~Dl~~Gt~GiIa~V~~~~i 71 (119)
T PF04322_consen 38 SLDPGDRVFLTSVSLEDLTPGTEGIIAEVKKIEI 71 (119)
T ss_pred cCCCCCEEEEecCCHHHCCCCCCeEEEEEEEEEE
Confidence 35899999999875 245567888887754
No 171
>COG4127 Uncharacterized conserved protein [Function unknown]
Probab=22.27 E-value=56 Score=28.50 Aligned_cols=41 Identities=17% Similarity=0.359 Sum_probs=29.6
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEeEEEEcCCC-----CEEEEEEEE
Q 027093 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRN-----NVKVRVRWY 63 (228)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~-----~~~v~v~Wf 63 (228)
+++.||-|.+.+.. ...++||+|.+=++=.-. .....|.|+
T Consensus 72 eI~KGDlvi~y~k~-~r~y~IGkVtsdYEy~p~~~~~i~hTrkVkWL 117 (318)
T COG4127 72 EIQKGDLVITYSKS-NRTYLIGKVTSDYEYHPEWLEGIGHTRKVKWL 117 (318)
T ss_pred HhccCcEEEeeccc-CceEEEEEecCCcccCccccccCchhhHhHHh
Confidence 57899999999987 578999999876652111 133567776
No 172
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.18 E-value=14 Score=31.89 Aligned_cols=55 Identities=22% Similarity=0.338 Sum_probs=34.1
Q ss_pred eeeecCCCCCCCCC---ceE---ECCCCCceecCCCCCCChhhhCCCCeEEccccccccccccc
Q 027093 138 AVYCKCEMPYNPDD---LMV---QCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAKRS 195 (228)
Q Consensus 138 ~~~C~C~~~~~~~~---~mi---~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~k~~ 195 (228)
.++-+|++..+.+. ..| -=-+|+.-||..|++-=-.-. .+=+||-|.++...+++
T Consensus 225 ~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivG---KkqtCPYCKekVdl~rm 285 (328)
T KOG1734|consen 225 SVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVG---KKQTCPYCKEKVDLKRM 285 (328)
T ss_pred chhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeec---CCCCCchHHHHhhHhhh
Confidence 34448988665332 111 112799999999996532211 23469999999887654
No 173
>PF07883 Cupin_2: Cupin domain; InterPro: IPR013096 This family represents the conserved barrel domain of the cupin superfamily [] (cupa is the Latin term for a small barrel). ; PDB: 2OPK_C 3BU7_B 2PHD_D 3NVC_A 3NKT_A 3NJZ_A 3NW4_A 3NST_A 3NL1_A 2H0V_A ....
Probab=22.03 E-value=76 Score=20.31 Aligned_cols=21 Identities=24% Similarity=0.653 Sum_probs=15.0
Q ss_pred EEcCCCeEEccCCEEEEccCC
Q 027093 15 NIKGTNKVVRPGDCVLMRPAD 35 (228)
Q Consensus 15 ~v~g~~~~~~vGD~V~v~~~~ 35 (228)
.+++.-..++.||.+++.++.
T Consensus 33 ~~~~~~~~l~~Gd~~~i~~~~ 53 (71)
T PF07883_consen 33 TVDGERVELKPGDAIYIPPGV 53 (71)
T ss_dssp EETTEEEEEETTEEEEEETTS
T ss_pred EEccEEeEccCCEEEEECCCC
Confidence 355556677888888888875
No 174
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=22.02 E-value=65 Score=17.17 Aligned_cols=9 Identities=33% Similarity=0.988 Sum_probs=7.5
Q ss_pred CeEEccccc
Q 027093 179 DHFLCSDCS 187 (228)
Q Consensus 179 ~~~~C~~C~ 187 (228)
..|.||+|-
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 589999994
No 175
>PF01079 Hint: Hint module; InterPro: IPR001767 This domain identifies a group of cysteine peptidases correspond to MEROPS peptidase family C46 (clan CH). The type example is the Hedgehog protein from Drosophila melanogaster (Fruit fly). These are involved in intracellular signalling required for a variety of patterning events during development. The hedgehog family of proteins self process by a cysteine-dependent mechanism, which is a one-time autolytic cleavage. It is differentiated from a typical peptidase reaction by the fact that the newly-formed carboxyl group is esterified with cholesterol, rather than being left free. The three-dimensional structure of the autolytic domain of the hedgehog protein of D. melanogaster shows that it is formed from two divergent copies of a module that also occurs in inteins, called a Hint domain [,].; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3K7H_B 3K7I_B 3K7G_B 1AT0_A 3MXW_A 3M1N_B 3HO5_H 2WFR_A 2WFQ_A 2WG3_B ....
Probab=22.00 E-value=2.3e+02 Score=23.64 Aligned_cols=28 Identities=32% Similarity=0.487 Sum_probs=16.8
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEeEEEE
Q 027093 22 VVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (228)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~rI~~i~~ 50 (228)
.+++||+|++.... .......+|.+|..
T Consensus 105 ~V~~Gd~v~~~~~~-~~~~~~~~V~~v~~ 132 (217)
T PF01079_consen 105 DVRVGDCVLVSDEG-GGKLRPSRVVRVST 132 (217)
T ss_dssp G--TT-EEEEE-TT-T--EEEEEEEEEEE
T ss_pred hCCCCCEEEEEEcC-CCcEEEEEEEEEEE
Confidence 47999999994443 36677888888866
No 176
>PF14047 DCR: Dppa2/4 conserved region
Probab=21.58 E-value=35 Score=22.94 Aligned_cols=23 Identities=26% Similarity=0.626 Sum_probs=15.4
Q ss_pred CCCCCCChhhhCCCCeEEcccccccc
Q 027093 165 PSCMGMTIEEAKKLDHFLCSDCSSDV 190 (228)
Q Consensus 165 ~~Cv~~~~~~~~~~~~~~C~~C~~~~ 190 (228)
+.|+-.++... |..+|+.|..++
T Consensus 43 Pac~fpppgle---DNmLCp~Cv~rN 65 (66)
T PF14047_consen 43 PACIFPPPGLE---DNMLCPECVKRN 65 (66)
T ss_pred ccccCCCCCcc---ccccCHhHhhcc
Confidence 45655554433 689999998754
No 177
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=21.27 E-value=1.1e+02 Score=22.67 Aligned_cols=22 Identities=23% Similarity=0.622 Sum_probs=17.9
Q ss_pred EEEcCCCeEEccCCEEEEccCC
Q 027093 14 YNIKGTNKVVRPGDCVLMRPAD 35 (228)
Q Consensus 14 ~~v~g~~~~~~vGD~V~v~~~~ 35 (228)
+.++|.-.+++.||+|++.++.
T Consensus 77 ~~~~g~~~~l~~Gd~i~ip~g~ 98 (131)
T COG1917 77 VQLEGEKKELKAGDVIIIPPGV 98 (131)
T ss_pred EEecCCceEecCCCEEEECCCC
Confidence 3455677899999999999975
No 178
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=21.00 E-value=2.1e+02 Score=22.38 Aligned_cols=45 Identities=18% Similarity=0.271 Sum_probs=34.9
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEEeecccc
Q 027093 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEES 69 (228)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~rI~~i~~~~~~~~~v~v~WfyRp~d~ 69 (228)
.+++||-|.|..+. -.-+.|.|.++.. .++...+.+.+|-|...+
T Consensus 119 ~~~~G~~V~I~~Gp--f~G~~g~v~~~~~-~~~r~~V~v~~~g~~~~v 163 (172)
T TIGR00922 119 DFEVGEQVRVNDGP--FANFTGTVEEVDY-EKSKLKVSVSIFGRETPV 163 (172)
T ss_pred CCCCCCEEEEeecC--CCCcEEEEEEEcC-CCCEEEEEEEECCCceEE
Confidence 47899999999886 5667899999854 455688888888876544
No 179
>COG4101 Predicted mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=20.90 E-value=1.7e+02 Score=22.32 Aligned_cols=28 Identities=25% Similarity=0.437 Sum_probs=19.8
Q ss_pred eEEccCCEEEEccCCC------CCCCeEEEEeEE
Q 027093 21 KVVRPGDCVLMRPADS------DKPPYVARVEKI 48 (228)
Q Consensus 21 ~~~~vGD~V~v~~~~~------~~~~~I~rI~~i 48 (228)
.+...||+.||.++-+ +..+..+.|.+-
T Consensus 90 a~~~pGDf~YiPpgVPHqp~N~S~ep~s~vIaRs 123 (142)
T COG4101 90 AEVGPGDFFYIPPGVPHQPANLSTEPLSAVIARS 123 (142)
T ss_pred EEecCCCeEEcCCCCCCcccccCCCCeEEEEEcc
Confidence 4678999999999864 345566666543
No 180
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=20.81 E-value=51 Score=19.53 Aligned_cols=9 Identities=22% Similarity=0.818 Sum_probs=4.4
Q ss_pred CeEEccccc
Q 027093 179 DHFLCSDCS 187 (228)
Q Consensus 179 ~~~~C~~C~ 187 (228)
....|+.|-
T Consensus 18 ~id~C~~C~ 26 (41)
T PF13453_consen 18 EIDVCPSCG 26 (41)
T ss_pred EEEECCCCC
Confidence 345555553
No 181
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=20.75 E-value=20 Score=25.37 Aligned_cols=62 Identities=21% Similarity=0.424 Sum_probs=36.4
Q ss_pred CcceEEeeccccccccccCCCceeeecCCCCCCCCCceEECCCCCceecCCCCCCChhhhCCCCeEEcccccccccc
Q 027093 116 AEDYFCRFEYKAATGGFTPDRVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (228)
Q Consensus 116 ~~~Ffcr~~Yd~~~~~f~p~~~~~~C~C~~~~~~~~~mi~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (228)
+.--+||..||..- | .|.-|.+ +-..+.+ .|+.-||+.|+..=..... ..-.||.|++.-..
T Consensus 22 d~CgICr~~fdg~C----p-------~Ck~Pgd-~Cplv~g-~C~H~FH~hCI~kWl~~~~--~~~~CPmCR~~w~~ 83 (85)
T PF12861_consen 22 DVCGICRMPFDGCC----P-------DCKFPGD-DCPLVWG-KCSHNFHMHCILKWLSTQS--SKGQCPMCRQPWKF 83 (85)
T ss_pred CceeeEecccccCC----C-------CccCCCC-CCceeec-cCccHHHHHHHHHHHcccc--CCCCCCCcCCeeee
Confidence 34467888877431 1 2555543 2233333 5999999999854222111 13479999986554
No 182
>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=20.59 E-value=16 Score=24.77 Aligned_cols=26 Identities=23% Similarity=0.586 Sum_probs=16.8
Q ss_pred CCCCceecCCCCCCChhhhCCCCeEEccccc
Q 027093 157 EGCKDWFHPSCMGMTIEEAKKLDHFLCSDCS 187 (228)
Q Consensus 157 ~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~ 187 (228)
..|+..||..|+..=.... -.||.|+
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 4699999999995322221 2688885
No 183
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=20.17 E-value=55 Score=18.40 Aligned_cols=10 Identities=20% Similarity=1.029 Sum_probs=7.6
Q ss_pred CeEEcccccc
Q 027093 179 DHFLCSDCSS 188 (228)
Q Consensus 179 ~~~~C~~C~~ 188 (228)
..++|+.|..
T Consensus 18 ~~~vCp~C~~ 27 (30)
T PF08274_consen 18 ELLVCPECGH 27 (30)
T ss_dssp SSEEETTTTE
T ss_pred CEEeCCcccc
Confidence 5788888864
No 184
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=20.12 E-value=50 Score=17.18 Aligned_cols=10 Identities=30% Similarity=0.976 Sum_probs=7.1
Q ss_pred ECCCCCceec
Q 027093 155 QCEGCKDWFH 164 (228)
Q Consensus 155 ~C~~C~~w~H 164 (228)
.|+.|++.|.
T Consensus 3 ~C~~C~~~F~ 12 (27)
T PF13912_consen 3 ECDECGKTFS 12 (27)
T ss_dssp EETTTTEEES
T ss_pred CCCccCCccC
Confidence 5777777774
No 185
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=20.05 E-value=81 Score=22.77 Aligned_cols=21 Identities=24% Similarity=0.271 Sum_probs=15.5
Q ss_pred EEccCCEEEEccCCCCCCCeE
Q 027093 22 VVRPGDCVLMRPADSDKPPYV 42 (228)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I 42 (228)
.+++||.|.+.+...++.++|
T Consensus 76 ~Lk~GD~V~ll~~~~gQ~yiV 96 (100)
T PF10844_consen 76 GLKVGDKVLLLRVQGGQKYIV 96 (100)
T ss_pred CCcCCCEEEEEEecCCCEEEE
Confidence 579999999999654444443
No 186
>cd06203 methionine_synthase_red Human methionine synthase reductase (MSR) restores methionine sythase which is responsible for the regeneration of methionine from homocysteine, as well as the coversion of methyltetrahydrofolate to tetrahydrofolate. In MSR, electrons are transferred from NADPH to FAD to FMN to cob(II)alamin. MSR resembles proteins of the cytochrome p450 family including nitric oxide synthase, the alpha subunit of sulfite reductase, but contains an extended hinge region. NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. CYPORs resemble ferredoxin reductase (FNR) but have a connecting subdomain inserted within the flavin binding region, which helps orient the FMN binding doamin with the FNR module. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme
Probab=20.03 E-value=1.2e+02 Score=27.46 Aligned_cols=22 Identities=23% Similarity=0.449 Sum_probs=17.6
Q ss_pred EEcCCCeEEccCCEEEEccCCC
Q 027093 15 NIKGTNKVVRPGDCVLMRPADS 36 (228)
Q Consensus 15 ~v~g~~~~~~vGD~V~v~~~~~ 36 (228)
-+.+.|..|++||.+.|.+.++
T Consensus 23 ~~~~~~~~y~~GD~l~V~p~N~ 44 (398)
T cd06203 23 DLSPTGFDYQPGDTIGILPPNT 44 (398)
T ss_pred ecCCCCCcCCCCCEEEEeCCCC
Confidence 3435678899999999999873
Done!