Query 031164
Match_columns 164
No_of_seqs 139 out of 939
Neff 8.4
Searched_HMMs 46136
Date Fri Mar 29 10:09:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031164.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031164hhsearch_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 5.1E-36 1.1E-40 210.5 11.5 120 21-157 2-121 (121)
2 cd04713 BAH_plant_3 BAH, or Br 100.0 1.6E-34 3.4E-39 208.9 14.0 129 2-134 2-134 (146)
3 cd04717 BAH_polybromo BAH, or 100.0 2.7E-33 5.8E-38 196.9 11.4 115 21-136 2-119 (121)
4 cd04716 BAH_plantDCM_I BAH, or 100.0 6.2E-32 1.4E-36 189.1 12.1 112 21-134 2-118 (122)
5 PF01426 BAH: BAH domain; Int 100.0 4.2E-31 9E-36 184.4 11.6 113 21-135 1-117 (119)
6 cd04370 BAH BAH, or Bromo Adja 100.0 5.4E-31 1.2E-35 184.3 11.2 114 21-135 2-121 (123)
7 smart00439 BAH Bromo adjacent 100.0 1.4E-30 3.1E-35 181.9 12.5 114 22-135 1-118 (120)
8 cd04709 BAH_MTA BAH, or Bromo 100.0 1.6E-30 3.5E-35 190.2 12.1 115 22-138 3-141 (164)
9 cd04721 BAH_plant_1 BAH, or Br 100.0 2E-30 4.4E-35 183.7 9.9 110 16-130 3-118 (130)
10 cd04710 BAH_fungalPHD BAH, or 100.0 1.6E-29 3.5E-34 180.0 11.6 112 20-133 9-133 (135)
11 cd04715 BAH_Orc1p_like BAH, or 100.0 2.8E-28 6.1E-33 177.8 12.7 121 4-129 13-153 (159)
12 cd04708 BAH_plantDCM_II BAH, o 99.9 2.3E-27 4.9E-32 177.6 11.2 118 14-134 1-143 (202)
13 cd04712 BAH_DCM_I BAH, or Brom 99.9 1.1E-26 2.3E-31 164.7 12.6 110 21-135 4-127 (130)
14 cd04720 BAH_Orc1p_Yeast BAH, o 99.9 1.6E-26 3.5E-31 172.0 13.2 116 20-136 50-177 (179)
15 cd04760 BAH_Dnmt1_I BAH, or Br 99.9 8.8E-27 1.9E-31 162.4 11.0 111 21-134 2-124 (124)
16 cd04718 BAH_plant_2 BAH, or Br 99.9 1.2E-28 2.6E-33 175.6 1.5 96 38-135 51-146 (148)
17 cd04719 BAH_Orc1p_animal BAH, 99.9 8.3E-25 1.8E-29 153.9 8.7 110 21-131 2-123 (128)
18 cd04711 BAH_Dnmt1_II BAH, or B 99.9 2.4E-24 5.2E-29 151.0 8.6 109 26-134 13-133 (137)
19 KOG1886 BAH domain proteins [T 99.9 4.4E-24 9.6E-29 175.5 8.9 160 3-164 32-196 (464)
20 KOG1827 Chromatin remodeling c 99.7 1.5E-17 3.2E-22 141.7 7.3 138 9-149 178-319 (629)
21 KOG3554 Histone deacetylase co 99.1 3.5E-12 7.5E-17 105.0 -1.9 115 22-138 5-165 (693)
22 KOG1632 Uncharacterized PHD Zn 95.6 0.0049 1.1E-07 50.6 1.2 83 81-164 3-85 (345)
23 PF00628 PHD: PHD-finger; Int 95.6 0.0062 1.3E-07 35.6 1.1 23 141-164 1-24 (51)
24 smart00249 PHD PHD zinc finger 95.5 0.009 2E-07 33.6 1.6 21 143-164 4-24 (47)
25 PF09926 DUF2158: Uncharacteri 92.6 0.28 6.1E-06 29.2 3.9 41 23-68 1-41 (53)
26 COG5076 Transcription factor i 92.0 0.024 5.3E-07 46.9 -1.6 95 13-110 269-363 (371)
27 cd05834 HDGF_related The PWWP 90.0 0.66 1.4E-05 30.1 4.1 44 22-68 2-45 (83)
28 PF10781 DSRB: Dextransucrase 89.5 2.1 4.4E-05 25.7 5.5 46 24-72 2-54 (62)
29 PF11302 DUF3104: Protein of u 89.4 1.6 3.5E-05 27.8 5.3 33 22-54 5-42 (75)
30 PF10383 Clr2: Transcription-s 89.1 2.5 5.3E-05 30.2 6.8 55 9-65 1-71 (139)
31 KOG4323 Polycomb-like PHD Zn-f 88.9 0.21 4.6E-06 42.4 1.4 24 140-164 172-195 (464)
32 PRK10708 hypothetical protein; 88.8 2.6 5.6E-05 25.3 5.6 45 24-71 2-53 (62)
33 PF08940 DUF1918: Domain of un 88.3 0.98 2.1E-05 27.3 3.6 39 24-64 4-42 (58)
34 cd05835 Dnmt3b_related The PWW 88.1 0.81 1.8E-05 29.9 3.5 42 23-66 1-44 (87)
35 KOG2752 Uncharacterized conser 87.4 0.39 8.4E-06 38.8 1.9 25 140-164 129-158 (345)
36 cd06080 MUM1_like Mutated mela 86.2 1.7 3.7E-05 28.1 4.2 39 23-67 1-39 (80)
37 PTZ00112 origin recognition co 86.0 1.7 3.7E-05 40.4 5.4 117 9-127 441-601 (1164)
38 cd03703 aeIF5B_II aeIF5B_II: T 85.2 2.7 5.9E-05 28.9 5.0 46 3-53 9-54 (110)
39 COG5475 Uncharacterized small 85.1 4.5 9.7E-05 24.3 5.1 50 22-85 4-53 (60)
40 cd05162 PWWP The PWWP domain, 81.2 3.2 6.8E-05 26.8 3.9 41 23-65 1-46 (87)
41 smart00293 PWWP domain with co 80.5 3.5 7.7E-05 25.0 3.8 42 23-66 1-48 (63)
42 PF00467 KOW: KOW motif; Inte 78.9 6.2 0.00014 20.5 3.9 26 25-52 1-26 (32)
43 PF11717 Tudor-knot: RNA bindi 78.7 8.9 0.00019 22.6 5.0 36 23-62 1-36 (55)
44 cd05840 SPBC215_ISWI_like The 77.1 3.7 8E-05 27.2 3.3 40 23-65 1-49 (93)
45 PF07154 DUF1392: Protein of u 76.7 8.9 0.00019 27.6 5.2 49 8-68 75-123 (150)
46 smart00739 KOW KOW (Kyprides, 74.9 7.2 0.00016 19.0 3.4 26 23-50 2-27 (28)
47 PF00855 PWWP: PWWP domain; I 74.8 3.9 8.5E-05 26.0 2.9 42 23-66 1-44 (86)
48 PF15057 DUF4537: Domain of un 74.2 7.4 0.00016 27.2 4.4 44 22-65 55-98 (124)
49 KOG1568 Mitochondrial inner me 72.7 16 0.00034 27.0 5.8 87 8-104 56-147 (174)
50 PF09871 DUF2098: Uncharacteri 69.5 14 0.0003 24.5 4.6 43 22-71 2-47 (91)
51 COG3257 GlxB Uncharacterized p 69.1 18 0.00039 28.1 5.7 49 14-74 96-144 (264)
52 KOG1973 Chromatin remodeling p 68.9 3.2 7E-05 33.0 1.8 26 137-164 217-245 (274)
53 PF04322 DUF473: Protein of un 66.5 16 0.00035 25.4 4.6 43 8-50 19-71 (119)
54 PF09889 DUF2116: Uncharacteri 63.7 1.1 2.5E-05 27.2 -1.3 23 138-162 2-26 (59)
55 PF13913 zf-C2HC_2: zinc-finge 63.0 2.8 6.1E-05 20.7 0.2 12 153-164 1-12 (25)
56 COG1370 Prefoldin, molecular c 62.2 7.2 0.00016 28.3 2.3 39 5-45 94-132 (155)
57 PRK12281 rplX 50S ribosomal pr 61.4 20 0.00044 22.8 4.1 29 22-52 6-34 (76)
58 COG1188 Ribosome-associated he 61.3 23 0.0005 23.9 4.5 46 5-54 32-77 (100)
59 PF14446 Prok-RING_1: Prokaryo 60.6 8.2 0.00018 23.0 2.0 23 141-163 7-30 (54)
60 PF05180 zf-DNL: DNL zinc fing 60.5 3.7 8E-05 25.5 0.5 16 148-163 23-38 (66)
61 PF02081 TrpBP: Tryptophan RNA 60.2 16 0.00035 23.0 3.3 48 59-106 19-66 (75)
62 CHL00141 rpl24 ribosomal prote 59.6 22 0.00047 23.1 4.0 29 22-52 8-36 (83)
63 PRK13251 transcription attenua 59.3 23 0.0005 22.3 3.9 48 59-106 19-66 (75)
64 COG4014 Uncharacterized protei 58.6 33 0.00071 22.6 4.7 40 24-69 10-52 (97)
65 cd05836 N_Pac_NP60 The PWWP do 58.4 15 0.00033 23.8 3.2 43 23-67 1-46 (86)
66 PF03144 GTP_EFTU_D2: Elongati 58.0 29 0.00062 21.1 4.4 30 22-51 12-41 (74)
67 PF11926 DUF3444: Domain of un 57.2 35 0.00077 26.3 5.5 45 21-68 26-70 (217)
68 cd03702 IF2_mtIF2_II This fami 56.8 29 0.00064 23.0 4.4 41 3-52 9-49 (95)
69 PRK00004 rplX 50S ribosomal pr 56.2 25 0.00053 23.8 4.0 29 22-52 4-32 (105)
70 cd03701 IF2_IF5B_II IF2_IF5B_I 55.9 35 0.00077 22.5 4.7 41 3-52 9-49 (95)
71 COG1935 Uncharacterized conser 55.6 26 0.00055 24.3 4.0 43 8-50 19-71 (122)
72 KOG1512 PHD Zn-finger protein 52.4 5.8 0.00013 31.9 0.5 23 141-164 316-339 (381)
73 TIGR01079 rplX_bact ribosomal 51.8 32 0.00069 23.3 4.0 29 22-52 3-31 (104)
74 cd05837 MSH6_like The PWWP dom 50.9 25 0.00054 23.9 3.4 45 22-68 2-54 (110)
75 PF09378 HAS-barrel: HAS barre 49.7 24 0.00052 22.5 3.1 35 14-51 15-49 (91)
76 smart00743 Agenet Tudor-like d 48.2 31 0.00067 20.3 3.2 28 22-50 2-29 (61)
77 PF11132 SplA: Transcriptional 46.4 17 0.00038 23.0 1.9 25 22-47 5-29 (75)
78 smart00652 eIF1a eukaryotic tr 46.1 42 0.00092 21.7 3.8 28 21-50 42-69 (83)
79 cd05793 S1_IF1A S1_IF1A: Trans 45.9 40 0.00087 21.4 3.6 27 21-49 37-63 (77)
80 COG0662 {ManC} Mannose-6-phosp 45.6 22 0.00047 24.6 2.6 23 14-36 70-92 (127)
81 PRK04980 hypothetical protein; 45.4 55 0.0012 22.1 4.3 38 13-50 21-59 (102)
82 cd06555 ASCH_PF0470_like ASC-1 45.0 74 0.0016 21.7 5.0 30 21-51 30-59 (109)
83 PF07494 Reg_prop: Two compone 44.1 35 0.00075 16.3 2.4 15 44-59 6-20 (24)
84 PF07883 Cupin_2: Cupin domain 43.4 25 0.00053 20.9 2.3 21 15-35 33-53 (71)
85 PRK01191 rpl24p 50S ribosomal 43.4 54 0.0012 22.9 4.1 30 21-52 44-73 (120)
86 cd04456 S1_IF1A_like S1_IF1A_l 42.2 57 0.0012 20.8 3.9 29 21-50 37-65 (78)
87 PF01176 eIF-1a: Translation i 42.2 30 0.00064 21.1 2.5 24 22-47 41-64 (65)
88 COG2956 Predicted N-acetylgluc 42.0 13 0.00028 30.7 1.0 15 149-163 363-377 (389)
89 cd06541 ASCH ASC-1 homology or 41.7 76 0.0016 21.1 4.7 28 22-51 30-57 (105)
90 PF12503 CMV_1a_C: Cucumber mo 40.9 22 0.00048 23.0 1.8 26 59-88 36-70 (85)
91 smart00451 ZnF_U1 U1-like zinc 40.8 15 0.00033 18.9 0.9 10 155-164 4-13 (35)
92 KOG2133 Transcriptional corepr 39.6 21 0.00046 33.4 2.1 111 22-134 145-281 (1229)
93 PF04085 MreC: rod shape-deter 38.6 1.4E+02 0.003 21.4 5.9 47 21-67 92-140 (152)
94 PF13912 zf-C2H2_6: C2H2-type 38.5 8.4 0.00018 18.7 -0.3 10 155-164 2-11 (27)
95 COG4946 Uncharacterized protei 38.4 1.3E+02 0.0028 26.4 6.4 52 4-55 357-414 (668)
96 COG1471 RPS4A Ribosomal protei 37.8 1.3E+02 0.0028 23.5 5.8 14 22-35 152-165 (241)
97 TIGR00100 hypA hydrogenase nic 37.6 16 0.00034 25.1 0.8 27 137-163 68-95 (115)
98 cd03694 GTPBP_II Domain II of 37.2 1.1E+02 0.0024 19.5 5.1 29 22-51 26-54 (87)
99 PF02311 AraC_binding: AraC-li 36.5 90 0.0019 20.5 4.5 22 14-35 36-57 (136)
100 COG4101 Predicted mannose-6-ph 36.3 94 0.002 21.8 4.4 40 22-63 91-136 (142)
101 PF10844 DUF2577: Protein of u 36.1 35 0.00075 22.8 2.3 15 22-36 76-90 (100)
102 KOG1844 PHD Zn-finger proteins 35.4 25 0.00053 30.2 1.8 27 137-163 84-110 (508)
103 cd03698 eRF3_II_like eRF3_II_l 35.4 95 0.0021 19.5 4.2 25 22-51 26-50 (83)
104 PF00667 FAD_binding_1: FAD bi 35.2 67 0.0014 24.3 4.0 24 13-36 32-55 (219)
105 COG1482 ManA Phosphomannose is 35.2 50 0.0011 27.0 3.4 33 22-55 161-193 (312)
106 COG1917 Uncharacterized conser 35.0 50 0.0011 22.6 3.1 22 14-35 77-98 (131)
107 PF09345 DUF1987: Domain of un 34.4 30 0.00065 23.2 1.7 15 57-71 77-91 (99)
108 PLN00036 40S ribosomal protein 34.3 1.7E+02 0.0036 23.3 6.1 14 22-35 153-166 (261)
109 PF05899 Cupin_3: Protein of u 34.3 39 0.00084 21.0 2.2 19 17-35 42-60 (74)
110 cd04466 S1_YloQ_GTPase S1_YloQ 34.2 56 0.0012 19.4 2.9 25 22-50 37-61 (68)
111 TIGR02227 sigpep_I_bact signal 34.1 1.1E+02 0.0023 22.1 4.8 28 22-49 51-78 (163)
112 PF08921 DUF1904: Domain of un 33.9 17 0.00037 24.8 0.5 16 57-72 56-71 (108)
113 COG4127 Uncharacterized conser 33.7 30 0.00066 27.8 1.9 42 22-64 72-117 (318)
114 PRK04012 translation initiatio 33.6 77 0.0017 21.3 3.6 27 21-49 58-84 (100)
115 PF06940 DUF1287: Domain of un 33.5 79 0.0017 23.3 3.9 42 14-59 98-139 (164)
116 TIGR01080 rplX_A_E ribosomal p 33.4 1.2E+02 0.0026 21.0 4.6 38 22-63 41-78 (114)
117 PRK11171 hypothetical protein; 33.3 1.5E+02 0.0033 23.3 5.8 22 15-36 97-118 (266)
118 PRK13922 rod shape-determining 32.9 2.2E+02 0.0047 22.3 6.7 48 21-68 213-262 (276)
119 PRK12380 hydrogenase nickel in 32.9 19 0.00041 24.7 0.6 27 137-163 68-95 (113)
120 TIGR00405 L26e_arch ribosomal 32.6 1.5E+02 0.0033 20.8 5.3 44 22-71 86-129 (145)
121 PTZ00223 40S ribosomal protein 32.4 1.6E+02 0.0034 23.6 5.7 14 22-35 150-163 (273)
122 PRK02935 hypothetical protein; 31.9 26 0.00057 23.9 1.1 10 153-162 69-78 (110)
123 PF05207 zf-CSL: CSL zinc fing 31.8 15 0.00033 21.8 -0.1 12 152-163 38-49 (55)
124 cd03693 EF1_alpha_II EF1_alpha 31.6 1.2E+02 0.0025 19.5 4.2 25 22-51 30-54 (91)
125 PTZ00194 60S ribosomal protein 31.5 94 0.002 22.4 3.9 37 22-62 46-82 (143)
126 PF01079 Hint: Hint module; I 31.4 63 0.0014 24.8 3.3 28 22-50 105-132 (217)
127 cd05792 S1_eIF1AD_like S1_eIF1 31.2 1.1E+02 0.0023 19.6 3.8 14 22-35 38-51 (78)
128 COG0250 NusG Transcription ant 30.8 1.4E+02 0.003 22.2 5.0 45 21-69 122-166 (178)
129 PF02591 DUF164: Putative zinc 30.7 35 0.00076 20.0 1.4 13 152-164 44-56 (56)
130 COG3450 Predicted enzyme of th 30.7 45 0.00096 23.1 2.1 18 18-35 81-98 (116)
131 PF13894 zf-C2H2_4: C2H2-type 30.5 17 0.00037 16.5 0.0 9 156-164 2-10 (24)
132 COG0198 RplX Ribosomal protein 30.3 82 0.0018 21.4 3.3 28 22-51 4-31 (104)
133 cd06530 S26_SPase_I The S26 Ty 30.2 86 0.0019 19.5 3.4 25 23-47 32-56 (85)
134 TIGR03214 ura-cupin putative a 29.8 2.4E+02 0.0051 22.1 6.4 21 15-35 94-114 (260)
135 CHL00010 infA translation init 29.7 1.3E+02 0.0028 19.0 4.1 27 23-51 47-73 (78)
136 COG0375 HybF Zn finger protein 29.3 31 0.00066 23.9 1.1 23 140-162 71-94 (115)
137 smart00734 ZnF_Rad18 Rad18-lik 29.2 23 0.0005 17.6 0.4 10 154-163 1-10 (26)
138 COG1645 Uncharacterized Zn-fin 28.9 24 0.00052 25.0 0.6 23 139-161 28-51 (131)
139 PF12171 zf-C2H2_jaz: Zinc-fin 28.8 24 0.00053 17.2 0.4 9 156-164 3-11 (27)
140 TIGR00523 eIF-1A eukaryotic/ar 28.2 1.1E+02 0.0023 20.6 3.6 28 21-49 56-83 (99)
141 TIGR01956 NusG_myco NusG famil 28.2 1.6E+02 0.0034 23.4 5.0 43 22-68 205-247 (258)
142 PRK12496 hypothetical protein; 28.0 34 0.00073 25.1 1.3 26 137-162 125-151 (164)
143 TIGR00219 mreC rod shape-deter 27.8 2.8E+02 0.0061 22.1 6.6 48 21-68 214-263 (283)
144 cd05838 WHSC1_related The PWWP 27.4 1E+02 0.0023 20.2 3.4 23 24-48 2-24 (95)
145 PRK09943 DNA-binding transcrip 27.3 75 0.0016 23.3 3.1 22 15-36 142-163 (185)
146 PRK15457 ethanolamine utilizat 27.2 67 0.0014 25.1 2.8 22 14-35 188-209 (233)
147 PRK08559 nusG transcription an 27.1 1.7E+02 0.0037 21.0 4.8 43 22-70 94-136 (153)
148 TIGR00074 hypC_hupF hydrogenas 27.0 42 0.0009 21.4 1.4 14 22-35 35-48 (76)
149 PRK03187 tgl transglutaminase; 26.6 52 0.0011 26.2 2.1 19 15-35 160-178 (272)
150 PF13717 zinc_ribbon_4: zinc-r 26.5 35 0.00076 18.3 0.8 8 155-162 3-10 (36)
151 PRK10409 hydrogenase assembly 26.2 45 0.00098 22.0 1.5 14 22-35 41-54 (90)
152 PRK10413 hydrogenase 2 accesso 26.1 46 0.00099 21.6 1.5 14 22-35 42-55 (82)
153 COG0298 HypC Hydrogenase matur 26.0 74 0.0016 20.6 2.4 13 22-34 38-50 (82)
154 PF01155 HypA: Hydrogenase exp 25.9 8.6 0.00019 26.3 -2.1 27 137-163 68-95 (113)
155 TIGR00218 manA mannose-6-phosp 25.9 88 0.0019 25.1 3.4 31 22-53 154-184 (302)
156 PTZ00118 40S ribosomal protein 25.3 3.1E+02 0.0068 21.8 6.2 14 22-35 153-166 (262)
157 PF11023 DUF2614: Protein of u 25.0 41 0.00088 23.2 1.1 11 153-163 68-78 (114)
158 PRK00276 infA translation init 24.7 1.6E+02 0.0036 18.1 3.8 12 22-33 46-57 (72)
159 PRK00420 hypothetical protein; 24.5 41 0.00089 23.2 1.1 24 140-163 24-49 (112)
160 smart00355 ZnF_C2H2 zinc finge 24.4 30 0.00064 15.7 0.3 9 156-164 2-10 (26)
161 cd03696 selB_II selB_II: this 24.2 1.9E+02 0.0041 18.0 4.7 25 22-51 26-50 (83)
162 PF06719 AraC_N: AraC-type tra 23.9 2.6E+02 0.0057 19.8 5.3 19 15-34 29-47 (155)
163 PF08209 Sgf11: Sgf11 (transcr 23.8 61 0.0013 17.2 1.4 11 152-162 2-12 (33)
164 KOG0957 PHD finger protein [Ge 23.7 73 0.0016 27.9 2.6 27 135-161 116-143 (707)
165 cd05701 S1_Rrp5_repeat_hs10 S1 23.5 61 0.0013 20.1 1.6 27 8-35 32-58 (69)
166 PF01050 MannoseP_isomer: Mann 23.4 94 0.002 22.4 2.8 24 13-36 96-119 (151)
167 TIGR00491 aIF-2 translation in 23.1 1.6E+02 0.0035 26.2 4.8 41 7-52 243-283 (590)
168 cd03692 mtIF2_IVc mtIF2_IVc: t 23.0 2.1E+02 0.0045 18.1 4.7 29 22-52 26-54 (84)
169 TIGR00375 conserved hypothetic 22.8 63 0.0014 27.1 2.0 71 87-162 184-266 (374)
170 PF11699 CENP-C_C: Mif2/CENP-C 22.8 97 0.0021 20.1 2.5 23 13-35 45-67 (85)
171 TIGR02754 sod_Ni_protease nick 22.7 1.6E+02 0.0035 18.5 3.7 29 22-50 11-40 (90)
172 cd05841 BS69_related The PWWP 22.7 1.9E+02 0.004 18.8 3.8 38 23-68 7-44 (83)
173 PF13831 PHD_2: PHD-finger; PD 22.4 46 0.00099 17.8 0.8 10 153-162 3-12 (36)
174 TIGR00922 nusG transcription t 21.9 2.5E+02 0.0055 20.1 5.0 45 22-70 119-163 (172)
175 COG1792 MreC Cell shape-determ 21.9 3.1E+02 0.0068 21.9 5.8 32 22-54 212-246 (284)
176 PF01455 HupF_HypC: HupF/HypC 21.9 57 0.0012 20.2 1.3 12 23-34 38-49 (68)
177 PF12961 DUF3850: Domain of Un 21.8 84 0.0018 19.8 2.0 36 14-49 20-58 (72)
178 PF00096 zf-C2H2: Zinc finger, 21.8 26 0.00057 16.1 -0.2 8 156-163 2-9 (23)
179 PF04236 Transp_Tc5_C: Tc5 tra 21.6 85 0.0018 19.2 2.0 21 144-164 30-50 (63)
180 TIGR01665 put_anti_recept phag 21.2 1.5E+02 0.0032 23.7 3.9 31 21-52 276-306 (317)
181 PRK01343 zinc-binding protein; 21.0 54 0.0012 19.7 1.0 14 149-162 4-17 (57)
182 PF03966 Trm112p: Trm112p-like 20.9 40 0.00086 20.7 0.4 16 149-164 48-63 (68)
183 PF13437 HlyD_3: HlyD family s 20.9 2.4E+02 0.0053 18.1 5.3 30 22-51 49-79 (105)
184 KOG1698 Mitochondrial/chloropl 20.8 3E+02 0.0065 21.0 5.1 34 22-55 96-131 (201)
185 PLN00208 translation initiatio 20.8 1.7E+02 0.0036 21.2 3.6 16 57-72 87-102 (145)
186 PF02559 CarD_CdnL_TRCF: CarD- 20.6 1.4E+02 0.0029 19.4 3.0 24 23-52 2-25 (98)
187 PF11012 DUF2850: Protein of u 20.5 1.7E+02 0.0038 18.8 3.3 30 5-34 28-57 (79)
188 PTZ00329 eukaryotic translatio 20.4 1.7E+02 0.0038 21.3 3.7 13 22-34 70-82 (155)
189 KOG1244 Predicted transcriptio 20.2 77 0.0017 25.5 1.9 16 149-164 291-306 (336)
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=100.00 E-value=5.1e-36 Score=210.45 Aligned_cols=120 Identities=44% Similarity=0.819 Sum_probs=108.7
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeecccccCCcccccCCCCeeEEecccccccccceeec
Q 031164 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQSADTIEGK 100 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~s~~~d~~~~~~I~~k 100 (164)
++|++||+|+|.+++++.++|||+|++||++.+|+ ++|+|+|||||+||.++++..++++|||+|++.|.+|+++|+||
T Consensus 2 ~~~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~~g~-~~~~v~WfyrPeEt~~~~~~~~~~~EvF~S~~~d~~~~~~I~gk 80 (121)
T cd04714 2 EIIRVGDCVLFKSPGRPSLPYVARIESLWEDPEGN-MVVRVKWYYRPEETKGGRKPNHGEKELFASDHQDENSVQTIEHK 80 (121)
T ss_pred CEEEcCCEEEEeCCCCCCCCEEEEEEEEEEcCCCC-EEEEEEEEEcHHHccCcccccCCCCceEecCCcccccHHHhCcc
Confidence 59999999999998766789999999999998888 99999999999999999877789999999999999999999999
Q ss_pred cEEEecccccccCCCCCCeEEEeeeeeccCCcccCCCCceEEeeCCCCCCCCceEeC
Q 031164 101 CTVHSFKSYTKLDAVGNDDFFCRFEYNSSSGAFNPDRVAVYCKCEMPYNPDDLMVQC 157 (164)
Q Consensus 101 c~V~~~~~~~~~~~~~~~~ffcr~~yd~~~~~f~p~~~~~~C~c~~~~~pD~~~~~C 157 (164)
|.|++.++|.++.+..+ .+.++..+|+|+.++|||+.||||
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 99999999987643222 455677899999999999999999
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=100.00 E-value=1.6e-34 Score=208.85 Aligned_cols=129 Identities=26% Similarity=0.452 Sum_probs=115.2
Q ss_pred CCCCCCceeeeeEEEcCcCcEEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeecccccCCccc---ccC
Q 031164 2 AKPKAPRRTLESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRR---QFH 78 (164)
Q Consensus 2 ~~~~~~r~~y~~~~i~g~~~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~~~~~---~~~ 78 (164)
.|+.+.|.||++++++|. +|++||+|||.+++. .++|||+|++|+++.+|. ++|+|+|||||+||..... ...
T Consensus 2 ~~~~~~~~~y~s~~~dg~--~y~vgD~Vlv~~~~~-~~pyI~~I~~i~~~~~~~-~~v~V~WFyRpeEi~~~~~~~~~~~ 77 (146)
T cd04713 2 GKGKKKKCHYTSFEKDGN--KYRLEDCVLLVPEDD-QKPYIAIIKDIYKQEEGS-LKLEVQWLYRPEEIEKKKGGNWKAE 77 (146)
T ss_pred CCCccceeeeeeEEECCE--EEECCCEEEEeCCCC-CCCEEEEEEEEEEcCCCC-EEEEEEeeECHHHhccccccccccC
Confidence 588999999999999997 999999999999875 899999999999998887 9999999999999985432 234
Q ss_pred CCCeeEEecccccccccceeeccEEEecccccccCC-CCCCeEEEeeeeeccCCccc
Q 031164 79 GSKEVFLSDHHDIQSADTIEGKCTVHSFKSYTKLDA-VGNDDFFCRFEYNSSSGAFN 134 (164)
Q Consensus 79 ~~~ELf~s~~~d~~~~~~I~~kc~V~~~~~~~~~~~-~~~~~ffcr~~yd~~~~~f~ 134 (164)
++||||+|++.|.+|+++|+|||.|+..+++.+++. ...++||||+.||+.+++|.
T Consensus 78 ~~~ElF~S~~~d~~~~~~I~gkc~V~~~~~~~~~~~~~~~~~F~cr~~yD~~~~~~~ 134 (146)
T cd04713 78 DPRELFYSFHRDEVPAESVLHPCKVAFVPKGKQIPLRKGHSGFIVRRVYDNVNKKLW 134 (146)
T ss_pred CCCeEEEeCCCCcCCHHHCcceeEEEECCccccCCccCCCCeEEEEEEEcCCCCcEe
Confidence 689999999999999999999999999988877654 36789999999999998876
No 3
>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=100.00 E-value=2.7e-33 Score=196.87 Aligned_cols=115 Identities=30% Similarity=0.486 Sum_probs=106.1
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeecccccCCcccccCCCCeeEEecccccccccceeec
Q 031164 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQSADTIEGK 100 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~s~~~d~~~~~~I~~k 100 (164)
..|++||+|+|.+++++.+++||+|.+||++.+|. ++|+|+|||||+||.+++...+++||||+|++.+.+|+++|+||
T Consensus 2 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~-~~~~~~Wf~rP~et~~~~~~~~~~~Evfls~~~d~~~~~~I~~k 80 (121)
T cd04717 2 LQYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGE-KFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGK 80 (121)
T ss_pred CEEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCC-EEEEEEEEeChHHccCCCccccccCceEEcCccccccHHHhcCe
Confidence 48999999999998866889999999999999888 99999999999999987766789999999999999999999999
Q ss_pred cEEEecccccccCCC---CCCeEEEeeeeeccCCcccCC
Q 031164 101 CTVHSFKSYTKLDAV---GNDDFFCRFEYNSSSGAFNPD 136 (164)
Q Consensus 101 c~V~~~~~~~~~~~~---~~~~ffcr~~yd~~~~~f~p~ 136 (164)
|.|++.++|.+.++. ..++||||+.||+..+.|.+.
T Consensus 81 c~Vl~~~~y~~~~p~~~~~~dvy~ce~~y~~~~~~~~~~ 119 (121)
T cd04717 81 CAVMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKI 119 (121)
T ss_pred eEEEehHHHhcCCCCCCCCCCEEEEeEEECcccccEecc
Confidence 999999999988763 468999999999999999864
No 4
>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=99.98 E-value=6.2e-32 Score=189.13 Aligned_cols=112 Identities=21% Similarity=0.368 Sum_probs=102.4
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeecccccCCcc-cccCCCCeeEEecccccccccceee
Q 031164 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGR-RQFHGSKEVFLSDHHDIQSADTIEG 99 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~~~~-~~~~~~~ELf~s~~~d~~~~~~I~~ 99 (164)
..|++||+|+|.+++. .++|||+|++||++.+|. .+++|+|||||+||..++ ...++++|||+|+|.|.+|+++|++
T Consensus 2 ~~~~lgD~V~v~~~~~-~~~yi~rI~~i~e~~~g~-~~~~v~WyyRpeet~~~r~~~~~~~rEvFlS~~~D~~pl~~I~~ 79 (122)
T cd04716 2 ITYNLGDDAYVQGGEG-EEPFICKITEFFEGTDGK-TYFTAQWFYRAEDTVIERQATNHDKKRVFYSEIKNDNPLDCLIS 79 (122)
T ss_pred cEEEcCCEEEEECCCC-CCCEEEEEEEEEEcCCCc-eEEEEEEEEcHHHhccccccccCCCceEEEecccCccchhheee
Confidence 4899999999999975 899999999999999998 999999999999999886 4578899999999999999999999
Q ss_pred ccEEEeccccccc----CCCCCCeEEEeeeeeccCCccc
Q 031164 100 KCTVHSFKSYTKL----DAVGNDDFFCRFEYNSSSGAFN 134 (164)
Q Consensus 100 kc~V~~~~~~~~~----~~~~~~~ffcr~~yd~~~~~f~ 134 (164)
||.|++.+++..+ ...+++.|||++.|+..-.+|.
T Consensus 80 Kc~V~~~~~~~~~~~~~~~~~~~df~c~~~Y~~~~~tF~ 118 (122)
T cd04716 80 KVKILQVPPNVGTKRKKPNSEKCDYYYDMEYCVPYSTFQ 118 (122)
T ss_pred eeEEEEeCCCCCcccccccCCCceEEEeeEeccchhheE
Confidence 9999998888766 3367899999999999988887
No 5
>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=99.97 E-value=4.2e-31 Score=184.45 Aligned_cols=113 Identities=40% Similarity=0.790 Sum_probs=101.0
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEeEEeecCCCC-eEEEEEEEeecccccCCcccccCCCCeeEEecccccccccceee
Q 031164 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGA-NVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQSADTIEG 99 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~-~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~s~~~d~~~~~~I~~ 99 (164)
++|++||+|||.+++++++++||+|++||++.+++ +++++|+|||||+||..+. ...+||||+|++++.+|+++|+|
T Consensus 1 ~~~~vGD~V~v~~~~~~~~~~v~~I~~i~~~~~~~~~~~~~v~Wf~rp~d~~~~~--~~~~~Elf~s~~~~~~~~~~I~g 78 (119)
T PF01426_consen 1 VTYKVGDFVYVKPDDPPEPPYVARIEEIWEDKDGNKEKMVKVRWFYRPEDTSLGK--TFSPRELFLSDHCDDIPVESIRG 78 (119)
T ss_dssp EEEETTSEEEEECTSTTSEEEEEEEEEEEEETTTSEEEEEEEEEEEEGGGSTTGG--HSCTTEEEEEEEEEEEEGGGEEE
T ss_pred CEEeCCCEEEEeCCCCCCCCEEEEEEEEEcCCCCCEEEEEEEEEeECcccccccc--cCCCCEEEEECcEeEEehhhEEe
Confidence 37999999999999977899999999999998775 6999999999999993322 35679999999999999999999
Q ss_pred ccEEEecccccccCCC---CCCeEEEeeeeeccCCcccC
Q 031164 100 KCTVHSFKSYTKLDAV---GNDDFFCRFEYNSSSGAFNP 135 (164)
Q Consensus 100 kc~V~~~~~~~~~~~~---~~~~ffcr~~yd~~~~~f~p 135 (164)
||.|++.+++.+..+. .+++||||+.||+.+++|.+
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 9999999999887652 68999999999999999985
No 6
>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=99.97 E-value=5.4e-31 Score=184.27 Aligned_cols=114 Identities=39% Similarity=0.778 Sum_probs=104.0
Q ss_pred cEEccCCEEEEecCCC--CCCCeEEEEeEEeecCCCCeEEEEEEEeecccccCCcccccCCCCeeEEeccccccccccee
Q 031164 21 KTIKPGDCVLMRPSEP--SKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQSADTIE 98 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~--~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~s~~~d~~~~~~I~ 98 (164)
.+|++||+|+|.+++. .+++|||+|++||++.+|. ++++|+|||||+||+.+....+.+||||+|++++.+++++|.
T Consensus 2 ~~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~~~~~~-~~~~v~wf~rp~e~~~~~~~~~~~~Elf~s~~~~~i~v~~I~ 80 (123)
T cd04370 2 ITYEVGDSVYVEPDDSIKSDPPYIARIEELWEDTNGS-KQVKVRWFYRPEETPKGLSPFALRRELFLSDHLDEIPVESII 80 (123)
T ss_pred CEEecCCEEEEecCCcCCCCCCEEEEEeeeeECCCCC-EEEEEEEEEchhHhccccccccccceeEEecCccccCHHHhc
Confidence 4899999999999874 4789999999999998888 999999999999999987767899999999999999999999
Q ss_pred eccEEEecccccccC----CCCCCeEEEeeeeeccCCcccC
Q 031164 99 GKCTVHSFKSYTKLD----AVGNDDFFCRFEYNSSSGAFNP 135 (164)
Q Consensus 99 ~kc~V~~~~~~~~~~----~~~~~~ffcr~~yd~~~~~f~p 135 (164)
|+|.|++.+++.+.. ....++||||+.||+.+++|.+
T Consensus 81 gkc~V~~~~~~~~~~~~~~~~~~~~f~~r~~yd~~~~~fk~ 121 (123)
T cd04370 81 GKCKVLFVSEFEGLKQRPNKIDTDDFFCRLAYDPTTKEFKA 121 (123)
T ss_pred cccEEEechHhhccccccccCCCCeEEEEEEECcCcceEEe
Confidence 999999999998764 2457899999999999988875
No 7
>smart00439 BAH Bromo adjacent homology domain.
Probab=99.97 E-value=1.4e-30 Score=181.89 Aligned_cols=114 Identities=39% Similarity=0.697 Sum_probs=103.1
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeecccccCCcccccCCCCeeEEecccccccccceeecc
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQSADTIEGKC 101 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~s~~~d~~~~~~I~~kc 101 (164)
.|++||+|+|.+++.+++++||+|.+||++.+|..++++|+|||||+||+++....+.+||||+|++.+.+++++|.|||
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 37899999999998657999999999999987764799999999999999987766789999999999999999999999
Q ss_pred EEEecccccccCCC----CCCeEEEeeeeeccCCcccC
Q 031164 102 TVHSFKSYTKLDAV----GNDDFFCRFEYNSSSGAFNP 135 (164)
Q Consensus 102 ~V~~~~~~~~~~~~----~~~~ffcr~~yd~~~~~f~p 135 (164)
.|++.+++.+..+. ..++||||+.||..+++|.+
T Consensus 81 ~V~~~~~~~~~~~~~~~~~~~~f~cr~~yd~~~~~f~~ 118 (120)
T smart00439 81 NVLSKSDYPGLRPEGKIGEPDVFFCESLYDPEKGAFKK 118 (120)
T ss_pred EEEEcchhcccccccCCCCCCeEEEEEEEccccCcccC
Confidence 99999999877652 47899999999999999974
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=99.97 E-value=1.6e-30 Score=190.19 Aligned_cols=115 Identities=27% Similarity=0.466 Sum_probs=101.9
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeecccccCCcc----------------------cccCC
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGR----------------------RQFHG 79 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~~~~----------------------~~~~~ 79 (164)
.|++||+|||.++. ..+++||+|++|+++.+|. ++++|+|||||+|++... ...+.
T Consensus 3 ~yrvGD~Vy~~~~~-~~Py~I~rI~e~~~~~~~~-~~vkV~wfYRp~DI~~~~~~l~~~~r~~~~~~~~~~~~~~~~~~~ 80 (164)
T cd04709 3 MYRVGDYVYFESSP-NNPYLIRRIEELNKTARGH-VEAKVVCYYRRRDIPDSLYQLADQHRRELEEKSDDLTPKQRHQLR 80 (164)
T ss_pred EEecCCEEEEECCC-CCCCEEEEEEEEEeCCCCC-EEEEEEEEEChhHccchhhhhcccccccccccccccchhhhhccC
Confidence 89999999999984 4688999999999999998 999999999999986421 12357
Q ss_pred CCeeEEecccccccccceeeccEEEecccccccCC--CCCCeEEEeeeeeccCCcccCCCC
Q 031164 80 SKEVFLSDHHDIQSADTIEGKCTVHSFKSYTKLDA--VGNDDFFCRFEYNSSSGAFNPDRV 138 (164)
Q Consensus 80 ~~ELf~s~~~d~~~~~~I~~kc~V~~~~~~~~~~~--~~~~~ffcr~~yd~~~~~f~p~~~ 138 (164)
.+|||+|+|.+.+|+++|+|||.|++..++.++.. ..+++|||+..||+.+++|...+.
T Consensus 81 ~rELF~S~~~d~~p~~~IrGKC~V~~~~d~~~l~~~~~~~d~Ff~~~~YDP~~k~l~~~~g 141 (164)
T cd04709 81 HRELFLSRQVETLPATHIRGKCSVTLLNDTESARSYLAREDTFFYSLVYDPEQKTLLADQG 141 (164)
T ss_pred cceeEEecccccccHHHeeeeEEEEEehhhhhhhhccCCCCEEEEEEEECCCCCeecccce
Confidence 99999999999999999999999999999988754 468999999999999999998643
No 9
>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=99.97 E-value=2e-30 Score=183.75 Aligned_cols=110 Identities=28% Similarity=0.461 Sum_probs=98.5
Q ss_pred EcCcCcEEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeecccccCCccccc-CCCCeeEEecccccccc
Q 031164 16 VKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQF-HGSKEVFLSDHHDIQSA 94 (164)
Q Consensus 16 i~g~~~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~~~~~~~-~~~~ELf~s~~~d~~~~ 94 (164)
.+|. ++++||+|||.+++ +++|||+|++||++.+|. ++++|+||+||+|+.++.++. +.+||||+|++.+.+|+
T Consensus 3 r~~~--~i~vGD~V~v~~~~--~~~~va~Ie~i~ed~~g~-~~v~v~WF~~p~E~~~~~~~~~~~~~EvFlS~~~d~i~~ 77 (130)
T cd04721 3 RNGV--TISVHDFVYVLSEE--EDRYVAYIEDLYEDKKGS-KMVKVRWFHTTDEVGAALSPDSVNPREIFLSPNLQVISV 77 (130)
T ss_pred cCCE--EEECCCEEEEeCCC--CCcEEEEEEEEEEcCCCC-EEEEEEEecCHHHhccccCCCCCCCCeEEEcCCccccch
Confidence 4554 89999999999887 678999999999998898 999999999999999876554 89999999999999999
Q ss_pred cceeeccEEEecccccccCCC-----CCCeEEEeeeeeccC
Q 031164 95 DTIEGKCTVHSFKSYTKLDAV-----GNDDFFCRFEYNSSS 130 (164)
Q Consensus 95 ~~I~~kc~V~~~~~~~~~~~~-----~~~~ffcr~~yd~~~ 130 (164)
++|.|||.|++.++|.++... ..++|+||+.||...
T Consensus 78 ~~I~gk~~Vls~~~y~k~~~~~~~~~~~~~f~C~~~~d~~~ 118 (130)
T cd04721 78 ECIDGLATVLTREHYEKFQSVPKNSSELQAYFCYRQIDNNK 118 (130)
T ss_pred HHeeeeeEECCHHHHhhhhccccCccccccEEEEEEecCCC
Confidence 999999999999999987642 256999999999875
No 10
>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=99.96 E-value=1.6e-29 Score=179.97 Aligned_cols=112 Identities=22% Similarity=0.443 Sum_probs=97.9
Q ss_pred CcEEccCCEEEEecCCCCCCCeEEEEeEEeecCCCC-----------eEEEEEEEeecccccCCcccccCCCCeeEEecc
Q 031164 20 SKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGA-----------NVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDH 88 (164)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~-----------~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~s~~ 88 (164)
|..|++||+|||.++++++|++||+|++|+..+++. ..+++|+|||||+|+.... ..+.+|||+|+|
T Consensus 9 g~~~~vgD~Vyv~~~~~~ePyyIgrI~e~~~~~~~~~~~~~~~~~~~~~~vrV~wfYRp~Di~~~~--~~d~relf~S~h 86 (135)
T cd04710 9 GELLKVNDHIYMSSEPPGEPYYIGRIMEFVPKHEFPSGIHARVFPASYFQVRLNWYYRPRDISRRV--VADSRLLYASMH 86 (135)
T ss_pred CeEEeCCCEEEEecCCCCCCCEEEEEEEEEecCCCCccccccccCCCcEEEEEEEEeCHHHcCCcc--cCCceEEEEEee
Confidence 459999999999999888999999999999864322 2689999999999996544 468999999999
Q ss_pred cccccccceeeccEEEecccccccCC--CCCCeEEEeeeeeccCCcc
Q 031164 89 HDIQSADTIEGKCTVHSFKSYTKLDA--VGNDDFFCRFEYNSSSGAF 133 (164)
Q Consensus 89 ~d~~~~~~I~~kc~V~~~~~~~~~~~--~~~~~ffcr~~yd~~~~~f 133 (164)
.|.+|+++|+|||+|.+.+++..+.. ..+++|||.+.||+.+++|
T Consensus 87 ~d~~p~~si~gKC~V~~~~di~~l~~~~~~~~~Fyf~~lyD~~~~r~ 133 (135)
T cd04710 87 SDICPIGSVRGKCTVRHRDQIPDLEEYKKRPNHFYFDQLFDRYILRY 133 (135)
T ss_pred EeeechHHEEeEEEEEEecccchhhhhccCCCEEEEEeeeCcchhhc
Confidence 99999999999999999998876543 4689999999999999887
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=99.96 E-value=2.8e-28 Score=177.81 Aligned_cols=121 Identities=24% Similarity=0.295 Sum_probs=99.3
Q ss_pred CCCCceeeeeEEEcCcCcEEccCCEEEEecCCCCCCCeEEEEeEEeecCC--CCeEEEEEEEeecccccCCccc--ccCC
Q 031164 4 PKAPRRTLESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDAR--GANVKVHVRWYYRPEESIGGRR--QFHG 79 (164)
Q Consensus 4 ~~~~r~~y~~~~i~g~~~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~--g~~~~v~v~Wfyrp~e~~~~~~--~~~~ 79 (164)
++++++||++++++|. .|++||+|+|.+++ .++|||+|.+||++.+ |. ++++|+|||||+||..+.. +.+.
T Consensus 13 ~~~~~~~Y~s~~~~g~--~y~lGD~Vlv~s~~--~~~yIgkI~~iwe~~~~~g~-~~~~v~WfyRp~E~~~~~~~~~~~~ 87 (159)
T cd04715 13 KKKDGQFYRSFTYDGV--EYRLYDDVYVHNGD--SEPYIGKIIKIYETAIDSGK-KKVKVIWFFRPSEIRMELKGEPKRH 87 (159)
T ss_pred ccCCceEEEEEEECCE--EEeCCCEEEEeCCC--CCCEEEEEEEEEEcCCcCCc-eEEEEEeeeCHHHhccccccCcccC
Confidence 4567779999999987 99999999999865 7999999999999865 77 9999999999999985432 3478
Q ss_pred CCeeEEeccc-----ccccccceeeccEEEecccccccCCC-----C------CCeEEEeeeeecc
Q 031164 80 SKEVFLSDHH-----DIQSADTIEGKCTVHSFKSYTKLDAV-----G------NDDFFCRFEYNSS 129 (164)
Q Consensus 80 ~~ELf~s~~~-----d~~~~~~I~~kc~V~~~~~~~~~~~~-----~------~~~ffcr~~yd~~ 129 (164)
+||||+|+|. +.+|+++|.|||.|++.++|....+. . ..+|.||++-+..
T Consensus 88 ~nEvFlS~~~d~~~~~~n~l~sI~gKC~Vl~~~ey~~~~~~s~~~~~~~~~~f~~~f~~~~~~~~~ 153 (159)
T cd04715 88 INEVFLACGRGEGLANINLLESIIGKCNVVCISEDFRNPQPSDGIPTSADFLFPCNFDVGRCVIVD 153 (159)
T ss_pred CCcEEEecCcCccccccCcHHHccceeEEEEehHhhhCCCCcCCccccCcceeeeEEEecCceecc
Confidence 9999999986 66889999999999999999765432 1 2455566655554
No 12
>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=99.95 E-value=2.3e-27 Score=177.64 Aligned_cols=118 Identities=25% Similarity=0.474 Sum_probs=101.4
Q ss_pred EEEcCcCcEEccCCEEEEecC------------------CCCCCCeEEEEeEEeecCCCC-----eEEEEEEEeeccccc
Q 031164 14 YTVKSISKTIKPGDCVLMRPS------------------EPSKPSYVAKIERIESDARGA-----NVKVHVRWYYRPEES 70 (164)
Q Consensus 14 ~~i~g~~~~~~vGD~V~v~~~------------------~~~~~~~i~~I~~i~~~~~g~-----~~~v~v~Wfyrp~e~ 70 (164)
|+++|. +|++||+|||.++ +. .++.||+|.+|+..+++. ...++|+|||||+||
T Consensus 1 f~~~Gv--~Y~vgD~VYv~p~~f~~~~~~~~~~~~G~N~~~-~p~~I~qI~ei~~~k~~~~~~~~~~~vrVrwFYRPEdt 77 (202)
T cd04708 1 FVYDGV--TYSVGDFLYVSPDAFAEEERERATFKAGRNVGL-KAFVVCQVLEIVVEKESKQADVASTQVKVRRFYRPEDV 77 (202)
T ss_pred CcCCCE--EEecCCeEEECcccccccccccccccccccCCC-CCcEEEEEEEEEecccCCCCCCcceEEEEEEEechhhc
Confidence 356776 9999999999999 22 588999999999876552 389999999999998
Q ss_pred CCcccccCCCCeeEEecccccccccceeeccEEEecccccccCC--CCCCeEEEeeeeeccCCccc
Q 031164 71 IGGRRQFHGSKEVFLSDHHDIQSADTIEGKCTVHSFKSYTKLDA--VGNDDFFCRFEYNSSSGAFN 134 (164)
Q Consensus 71 ~~~~~~~~~~~ELf~s~~~d~~~~~~I~~kc~V~~~~~~~~~~~--~~~~~ffcr~~yd~~~~~f~ 134 (164)
........+.+|||+|++.+++|+++|.|||+|....++.++.. ..++.|||+..||+.++.|+
T Consensus 78 ~~~~~y~sd~rely~Sde~~~~~~~~I~GKC~V~~~~d~~~~~~~~~~~~~Ffc~~~Yd~~tg~f~ 143 (202)
T cd04708 78 SPEKAYASDIREVYYSEDTLTVPVEAVEGKCEVRKKSDLPDSDAPVIFEHVFFCELLYDPAKGSLK 143 (202)
T ss_pred CcccceecCceeEEEeccceeechhHcceEEEEEecCcchhhhccccCCCceEEEEEEcCCCCccC
Confidence 65333334899999999999999999999999999999887654 56899999999999999999
No 13
>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=99.95 E-value=1.1e-26 Score=164.71 Aligned_cols=110 Identities=24% Similarity=0.334 Sum_probs=94.4
Q ss_pred cEEccCCEEEEecCCCC----------CCCeEEEEeEEeecCCCCeEEEEEEEeecccccCCcccccCCCCeeEEecccc
Q 031164 21 KTIKPGDCVLMRPSEPS----------KPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHD 90 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~----------~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~s~~~d 90 (164)
..|++||+|+|.+++++ .+++|++|+.|+++.+|. +|++++|||||+||.+++ ++++||||+|+|++
T Consensus 4 ~~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~~~g~-~~~h~~W~yrp~eTv~g~--~~~~~ElFLSd~c~ 80 (130)
T cd04712 4 LTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKGSDGS-KMFHGRWLYRGCDTVLGN--YANERELFLTNECT 80 (130)
T ss_pred CEEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeecCCCc-eEEEEEEEEcchhccccc--cCCCceEEEecccc
Confidence 48999999999998865 388999999999999998 999999999999999998 58899999999999
Q ss_pred ccccc----ceeeccEEEecccccccCCCCCCeEEEeeeeeccCCcccC
Q 031164 91 IQSAD----TIEGKCTVHSFKSYTKLDAVGNDDFFCRFEYNSSSGAFNP 135 (164)
Q Consensus 91 ~~~~~----~I~~kc~V~~~~~~~~~~~~~~~~ffcr~~yd~~~~~f~p 135 (164)
.++++ +|.+||.|........ ...++.|+|+..|+++++.|+.
T Consensus 81 ~~~~~~~~~~I~~k~~V~~~~~~~~--~~~~~~F~r~syy~~e~~~F~~ 127 (130)
T cd04712 81 CLELDLLSTEIKGVHKVDWSGTPWG--KGLPEFFVRQSYYWPERGAFTS 127 (130)
T ss_pred ccccccccceeEEEEEEEEecCcCC--cCCCCEEEEEEEECccCCceEc
Confidence 99999 9999999998766532 1234556666666669999983
No 14
>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=99.94 E-value=1.6e-26 Score=172.03 Aligned_cols=116 Identities=22% Similarity=0.327 Sum_probs=102.2
Q ss_pred CcEEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeecccccCCccc--c-------cCCCCeeEEecccc
Q 031164 20 SKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRR--Q-------FHGSKEVFLSDHHD 90 (164)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~~~~~--~-------~~~~~ELf~s~~~d 90 (164)
++++++||+|+|.+++. .++|||.|.+|+.+..++.+.+.|+|||||.|+.+++. . ...+||||+|.|.+
T Consensus 50 ~~~~~vGD~Vlik~~~~-~~~~V~iI~ei~~~~~~~~v~i~v~Wy~r~~Ei~~~~~~~~~~~~~~~~~~~nElflT~~~d 128 (179)
T cd04720 50 GLELSVGDTILVKDDVA-NSPSVYLIHEIRLNTLNNEVELWVMWFLRWFEINPARYYKQFDPEFRSESNKNELYLTAELS 128 (179)
T ss_pred CeEEeCCCEEEEeCCCC-CCCEEEEEEEEEeCCCCCEEEEEEEEcCCHHHcccccccccccchhcccCCCceEEEecccc
Confidence 46999999999999875 89999999999998765558999999999999987552 2 23379999999999
Q ss_pred cccccceeeccEEEecccccccCCC---CCCeEEEeeeeeccCCcccCC
Q 031164 91 IQSADTIEGKCTVHSFKSYTKLDAV---GNDDFFCRFEYNSSSGAFNPD 136 (164)
Q Consensus 91 ~~~~~~I~~kc~V~~~~~~~~~~~~---~~~~ffcr~~yd~~~~~f~p~ 136 (164)
.+++.+|+++|.|++.++|.++.+. +..+||||++||+.++.|+|+
T Consensus 129 ~i~l~~Ii~k~~Vls~~ef~~~~~~~~~~~~~F~cR~~~d~~~~~F~~~ 177 (179)
T cd04720 129 EIKLKDIIDKANVLSESEFNDLSTDDKNGERTFFCRYACEPDGEEFVWI 177 (179)
T ss_pred eEEhhheeeeEEEecHHHhhhhcccccCCCceEEEEEEEeCCCCeEccc
Confidence 9999999999999999999877643 678999999999999999985
No 15
>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=99.94 E-value=8.8e-27 Score=162.44 Aligned_cols=111 Identities=25% Similarity=0.512 Sum_probs=97.0
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeecccccCCcccccCCCCeeEEecccccccccceeec
Q 031164 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQSADTIEGK 100 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~s~~~d~~~~~~I~~k 100 (164)
.+|++||+|+|.++++..+++||+|+.||++.+|. +|++|+|||||+||.+++. +.++|||+|++++.+++++|.+|
T Consensus 2 ~~i~vGD~V~v~~~~~~~p~~I~rV~~mfe~~~g~-k~~h~rWf~Rg~dTVlG~~--~~~kEvFlsd~c~d~~l~~I~~K 78 (124)
T cd04760 2 EELEAGDCVSVKPDDPTKPLYIARVTYMWKDSIGG-KMFHAHWFCRGSDTVLGET--SDPLELFLVDECEDMALSSIHGK 78 (124)
T ss_pred CEEecCCEEEEecCCCCCCcEEEEEhhheecCCCC-cEEEEEEEEECCccccccc--CCCcEEEeecccCCcchHHheee
Confidence 48999999999998777899999999999999998 9999999999999999986 78999999999999999999999
Q ss_pred cEEEecccccc----cC---C-----CCCCeEEEeeeeeccCCccc
Q 031164 101 CTVHSFKSYTK----LD---A-----VGNDDFFCRFEYNSSSGAFN 134 (164)
Q Consensus 101 c~V~~~~~~~~----~~---~-----~~~~~ffcr~~yd~~~~~f~ 134 (164)
|.|...+.-.. .. + .+.++|||+.-||+...+|.
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 99998654311 11 1 23589999999999888774
No 16
>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=99.94 E-value=1.2e-28 Score=175.59 Aligned_cols=96 Identities=26% Similarity=0.522 Sum_probs=91.9
Q ss_pred CCCeEEEEeEEeecCCCCeEEEEEEEeecccccCCcccccCCCCeeEEecccccccccceeeccEEEecccccccCCCCC
Q 031164 38 KPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQSADTIEGKCTVHSFKSYTKLDAVGN 117 (164)
Q Consensus 38 ~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~s~~~d~~~~~~I~~kc~V~~~~~~~~~~~~~~ 117 (164)
.++|||+|++||.+. |+ .+++|+|||||+||.+|+++.++.+|||+|++.|++++++|.|||.|+++++|.++.+.+.
T Consensus 51 ~~~~vArIekiW~~~-G~-~~~~grWy~rPEET~~gr~~~~~~kEvFlS~~~d~~~~~~I~gkC~V~~~keY~k~e~~g~ 128 (148)
T cd04718 51 GDLWLARIEKLWEEN-GT-YWYAARWYTLPEETHMGRQPHNLRRELYLTNDFADIEMECILRHCSVKCPKEFRDASNDGD 128 (148)
T ss_pred CchHHHHHHHHHhcc-Cc-eEEEEEEEeCchhccCccccccccceeeeccccccccHHHHhcccEEcCHHHcccccCCCC
Confidence 678999999999986 88 9999999999999999999989999999999999999999999999999999999888899
Q ss_pred CeEEEeeeeeccCCcccC
Q 031164 118 DDFFCRFEYNSSSGAFNP 135 (164)
Q Consensus 118 ~~ffcr~~yd~~~~~f~p 135 (164)
|+|||++.||..+++|..
T Consensus 129 Dvy~Ce~~Yd~~~~~Fkr 146 (148)
T cd04718 129 DVFLCEYEYDVHWQSFKR 146 (148)
T ss_pred ceEEEEEEEhhhcCceee
Confidence 999999999999999974
No 17
>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=99.92 E-value=8.3e-25 Score=153.94 Aligned_cols=110 Identities=25% Similarity=0.354 Sum_probs=93.6
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEeEEeecCCC--CeEEEEEEEeecccccCCcc----cccCCCCeeEEecccc---c
Q 031164 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDARG--ANVKVHVRWYYRPEESIGGR----RQFHGSKEVFLSDHHD---I 91 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g--~~~~v~v~Wfyrp~e~~~~~----~~~~~~~ELf~s~~~d---~ 91 (164)
.+|++||+|+|.++++ +++|||+|+.|+++.+| ....++|||||||+|++... ....+++|||+|++.+ .
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 3799999999999986 78899999999999776 22799999999999997432 1236899999999974 8
Q ss_pred ccccceeeccEEEecccccccCC---CCCCeEEEeeeeeccCC
Q 031164 92 QSADTIEGKCTVHSFKSYTKLDA---VGNDDFFCRFEYNSSSG 131 (164)
Q Consensus 92 ~~~~~I~~kc~V~~~~~~~~~~~---~~~~~ffcr~~yd~~~~ 131 (164)
+++++|.|+|.|++.++|.++.. ....+||.|+.++.+..
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 99999999999999999988763 24688999999998873
No 18
>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=99.91 E-value=2.4e-24 Score=150.97 Aligned_cols=109 Identities=22% Similarity=0.471 Sum_probs=89.2
Q ss_pred CCEEEEecCCCCCCCeEEEEeEEeecCCCC------eEEEEEEEeecccccCCcccc-cCCC-CeeEEecccccccccce
Q 031164 26 GDCVLMRPSEPSKPSYVAKIERIESDARGA------NVKVHVRWYYRPEESIGGRRQ-FHGS-KEVFLSDHHDIQSADTI 97 (164)
Q Consensus 26 GD~V~v~~~~~~~~~~i~~I~~i~~~~~g~------~~~v~v~Wfyrp~e~~~~~~~-~~~~-~ELf~s~~~d~~~~~~I 97 (164)
+|.|-=.+-+.+.|++||||++|...+++. +++|+|+|||||+|+..++.. ++.. ||||+|+|.+.+|+++|
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 344443455667899999999999876543 478999999999999998644 4444 99999999999999999
Q ss_pred eeccEEEecccccc-c---CCCCCCeEEEeeeeeccCCccc
Q 031164 98 EGKCTVHSFKSYTK-L---DAVGNDDFFCRFEYNSSSGAFN 134 (164)
Q Consensus 98 ~~kc~V~~~~~~~~-~---~~~~~~~ffcr~~yd~~~~~f~ 134 (164)
.|||+|.+.++..+ + ...+++.|||+.+||.++|.|+
T Consensus 93 ~GKC~V~~~~di~~s~~~y~~~gpd~Fyf~~~Y~a~t~~F~ 133 (137)
T cd04711 93 QGRCTVEYGEDLPESVQEYSGGGPDRFYFLEAYNAKTKSFE 133 (137)
T ss_pred cceEEEEeccccchhHHHHhcCCCcceEEhhhhccccCccc
Confidence 99999997766543 2 2257899999999999999998
No 19
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=99.90 E-value=4.4e-24 Score=175.47 Aligned_cols=160 Identities=33% Similarity=0.499 Sum_probs=141.6
Q ss_pred CCCCCceeeeeEEEcCcCcEEcc-CCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeecccccCCccc---ccC
Q 031164 3 KPKAPRRTLESYTVKSISKTIKP-GDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRR---QFH 78 (164)
Q Consensus 3 ~~~~~r~~y~~~~i~g~~~~~~v-GD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~~~~~---~~~ 78 (164)
|++..+.||.++.+.|+ .+.. ||.|++.+++.+.++|||+|+.|+.+..|..+.+.|+|||||+|+..+.. ...
T Consensus 32 v~~~k~~h~~t~~~~~g--~~~~~~d~vllvped~~~pPyvaii~~i~a~~~g~~~k~ev~W~YrPee~~~~~~~~~~a~ 109 (464)
T KOG1886|consen 32 VGGVKSLHFETFIYRGG--RYINYGDSVLLVPEDPGKPPYVAIIEDIYAQERGGNVKVEVQWFYRPEESEGGGSGKWGAK 109 (464)
T ss_pred ccccccccccceeeccC--cccccCcceeecCCCCCCCCeeEEEeeeeccccCCCcceecccccCCCccCCCCCCCcccC
Confidence 45556899999999986 6666 99999999998899999999999999876449999999999999997643 234
Q ss_pred CCCeeEEecccccccccceeeccEEEecccccccCC-CCCCeEEEeeeeeccCCcccCCCCceEEeeCCCCCCCCceEeC
Q 031164 79 GSKEVFLSDHHDIQSADTIEGKCTVHSFKSYTKLDA-VGNDDFFCRFEYNSSSGAFNPDRVAVYCKCEMPYNPDDLMVQC 157 (164)
Q Consensus 79 ~~~ELf~s~~~d~~~~~~I~~kc~V~~~~~~~~~~~-~~~~~ffcr~~yd~~~~~f~p~~~~~~C~c~~~~~pD~~~~~C 157 (164)
.++|||+|.|.|.+++++|.++|.|.++..+.++.. .+.+.|+||..||..++.+.+.-....|.|.+..+|++...+|
T Consensus 110 ~~relF~SfH~De~~A~ti~~rC~V~fvp~~kqlp~~~~~~~f~~r~vYd~~~~~~~~~~~~~~~~~~k~e~d~~~~kt~ 189 (464)
T KOG1886|consen 110 QPRELFLSFHEDEAFAETILHRCKVHFVPAYKQLPNRVGHESFICRRVYDAVTSKLRKLRDGDFGDGQKLEIDMLVPKTG 189 (464)
T ss_pred CCccccccccccchhhhhhcccceeeeccccccccccCCCCCcccccccccccccccCccccchhcccccCCccchhhhc
Confidence 578999999999999999999999999999998876 6789999999999999999976666788999999999999999
Q ss_pred CccCCCC
Q 031164 158 EGCSDWS 164 (164)
Q Consensus 158 ~~C~~~~ 164 (164)
..|+.|+
T Consensus 190 ~~~~~~~ 196 (464)
T KOG1886|consen 190 PRRGTLP 196 (464)
T ss_pred ccCCCCC
Confidence 9998874
No 20
>KOG1827 consensus Chromatin remodeling complex RSC, subunit RSC1/Polybromo and related proteins [Chromatin structure and dynamics; Transcription]
Probab=99.71 E-value=1.5e-17 Score=141.72 Aligned_cols=138 Identities=24% Similarity=0.248 Sum_probs=121.6
Q ss_pred eeeee-EEEcCcCcEEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeecccccCCcccccCCCCeeEEec
Q 031164 9 RTLES-YTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVFLSD 87 (164)
Q Consensus 9 ~~y~~-~~i~g~~~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~s~ 87 (164)
.|... +.|+|. .+.+||.||+.+.++...+.|++|.++|.+.+|. .+..+.|||||++|.+-..+.+..+|+|.|.
T Consensus 178 ~~~~~~~~i~~~--~~~~gd~vlv~~~~d~~~p~v~~Ier~w~~~dg~-k~~~~~w~~rP~~T~H~a~r~F~k~Evfkt~ 254 (629)
T KOG1827|consen 178 YHELGPVEIDGT--KYIVGDYVLVQNPADNLKPIVAQIERLWKLPDGE-KWPQGCWIYRPEETVHRADRKFYKQEVFKTS 254 (629)
T ss_pred cccCCCccccCc--ccccCceeeecCcccccCCceeeecccccCcccc-cccceeEeeCCccCccccccchhcccceecc
Confidence 34444 678887 9999999999998876899999999999999999 9999999999999998766668899999999
Q ss_pred ccccccccceeeccEEEecccccccCC---CCCCeEEEeeeeeccCCcccCCCCceEEeeCCCCC
Q 031164 88 HHDIQSADTIEGKCTVHSFKSYTKLDA---VGNDDFFCRFEYNSSSGAFNPDRVAVYCKCEMPYN 149 (164)
Q Consensus 88 ~~d~~~~~~I~~kc~V~~~~~~~~~~~---~~~~~ffcr~~yd~~~~~f~p~~~~~~C~c~~~~~ 149 (164)
.....+++.|+|+|.|+++.+|...++ ...++|+|.+.|+.+.+.|.+.+.|..|.-....+
T Consensus 255 ~~~~~~~q~l~g~c~v~~~~~yi~~~p~~ls~~dv~lcesRyn~~~K~f~kirsw~~~~p~E~~~ 319 (629)
T KOG1827|consen 255 LYRDDLVQRLLGKCYVMKPTEYISGDPENLSEEDVFLCESRYNEQLKKFNKIRSWKAFLPREVPL 319 (629)
T ss_pred cccccHHHHhhcceEEeehhHhhhcCcccccccceeeEEeeeccchhhhccccCchhcCccccCC
Confidence 999999999999999999999998877 35799999999999999999987777775444333
No 21
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=99.13 E-value=3.5e-12 Score=105.05 Aligned_cols=115 Identities=27% Similarity=0.466 Sum_probs=96.9
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeecccccCCc---------c------------------
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGG---------R------------------ 74 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~~~---------~------------------ 74 (164)
.|++||+||+..... .++.|-+|+++..+.+|+ +.++|-.|||..|++.. +
T Consensus 5 ~y~vgd~vYf~~sss-~PYliRrIEELnKTa~Gn-VeAkvVc~~RRRDIs~~L~~lAD~~ar~~~~y~a~~~a~~~~e~e 82 (693)
T KOG3554|consen 5 MYRVGDYVYFENSSS-NPYLIRRIEELNKTANGN-VEAKVVCYLRRRDISSHLLKLADKHARRFDNYAAPEAAPEATEAE 82 (693)
T ss_pred cceecceEEEecCCC-ChHHHHHHHHHhccccCC-cceEEEEEEEccchHHHHHHHHHHHhhhcccccCcccCcccchhh
Confidence 789999999999875 688899999999999999 99999999999998520 0
Q ss_pred -----------------cccCCCCeeEEecccccccccceeeccEEEecccccccCC--CCCCeEEEeeeeeccCCcccC
Q 031164 75 -----------------RQFHGSKEVFLSDHHDIQSADTIEGKCTVHSFKSYTKLDA--VGNDDFFCRFEYNSSSGAFNP 135 (164)
Q Consensus 75 -----------------~~~~~~~ELf~s~~~d~~~~~~I~~kc~V~~~~~~~~~~~--~~~~~ffcr~~yd~~~~~f~p 135 (164)
+.-...+|||+|.+.+..|+..|+|||.|.-+.+-+.+.. ..+|+||+-..||+..+.+..
T Consensus 83 ~EEe~e~p~~vdlt~~qrhqLrhrElFlsRQ~EsLPAthIRGKCsV~LLnete~~~~YL~~eDtFfySLVyDP~~kTLLA 162 (693)
T KOG3554|consen 83 IEEESECPAPVDLTEKQRHQLRHRELFLSRQSESLPATHIRGKCSVTLLNETESLQSYLEKEDTFFYSLVYDPNQKTLLA 162 (693)
T ss_pred hhhhccCCCcCCCCHHHHHHHHHHHHHHhhhhccCchhhhccceeEEEecChHHHHhhccccceeEEEeeeccchhhhhc
Confidence 0012358999999999999999999999999887665543 578999999999999998876
Q ss_pred CCC
Q 031164 136 DRV 138 (164)
Q Consensus 136 ~~~ 138 (164)
++.
T Consensus 163 DkG 165 (693)
T KOG3554|consen 163 DKG 165 (693)
T ss_pred cCc
Confidence 543
No 22
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=95.63 E-value=0.0049 Score=50.60 Aligned_cols=83 Identities=23% Similarity=0.312 Sum_probs=66.1
Q ss_pred CeeEEecccccccccceeeccEEEecccccccCCCCCCeEEEeeeeeccCCcccCCCCceEEeeCCCCCCCCceEeCCcc
Q 031164 81 KEVFLSDHHDIQSADTIEGKCTVHSFKSYTKLDAVGNDDFFCRFEYNSSSGAFNPDRVAVYCKCEMPYNPDDLMVQCEGC 160 (164)
Q Consensus 81 ~ELf~s~~~d~~~~~~I~~kc~V~~~~~~~~~~~~~~~~ffcr~~yd~~~~~f~p~~~~~~C~c~~~~~pD~~~~~C~~C 160 (164)
.+.+++.+...-....+.+++.......+... +....+..++..+....+.+.+......|.|.++.+||..+++|+.|
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~k~~~~~~~~a~~~~~~~~~~~~~p~~~~~~cd~C 81 (345)
T KOG1632|consen 3 KIPKTSKTFSKTESDRRAPIAQKTTKPPKEPV-PIERPVPDVFRGRKGRRGGLLKALTQRYCKCYKPCDPDDLMEQCDLC 81 (345)
T ss_pred CcccccceecccccccccccccccccCCcCCC-CCCCCCcccccccccccccccHhhhhchhhcccccCchhhhhccccc
Confidence 34556666667777777777777776666543 45677788888888888888887777899999999999889999999
Q ss_pred CCCC
Q 031164 161 SDWS 164 (164)
Q Consensus 161 ~~~~ 164 (164)
..||
T Consensus 82 ~~~~ 85 (345)
T KOG1632|consen 82 EDWY 85 (345)
T ss_pred cccc
Confidence 9997
No 23
>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=95.55 E-value=0.0062 Score=35.61 Aligned_cols=23 Identities=39% Similarity=1.112 Sum_probs=18.6
Q ss_pred EE-eeCCCCCCCCceEeCCccCCCC
Q 031164 141 YC-KCEMPYNPDDLMVQCEGCSDWS 164 (164)
Q Consensus 141 ~C-~c~~~~~pD~~~~~C~~C~~~~ 164 (164)
.| +|.+ .+++..+++|+.|++||
T Consensus 1 ~C~vC~~-~~~~~~~i~C~~C~~~~ 24 (51)
T PF00628_consen 1 YCPVCGQ-SDDDGDMIQCDSCNRWY 24 (51)
T ss_dssp EBTTTTS-SCTTSSEEEBSTTSCEE
T ss_pred eCcCCCC-cCCCCCeEEcCCCChhh
Confidence 36 6788 55667899999999997
No 24
>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 PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=92.57 E-value=0.28 Score=29.18 Aligned_cols=41 Identities=20% Similarity=0.327 Sum_probs=27.9
Q ss_pred EccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeeccc
Q 031164 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPE 68 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~ 68 (164)
|++||.|.++++++ ...|..|..- ..... .++..+||---.
T Consensus 1 f~~GDvV~LKSGGp--~MTV~~v~~~--~~~~~-~~v~C~WFd~~~ 41 (53)
T PF09926_consen 1 FKIGDVVQLKSGGP--RMTVTEVGPN--AGASG-GWVECQWFDGHG 41 (53)
T ss_pred CCCCCEEEEccCCC--CeEEEEcccc--ccCCC-CeEEEEeCCCCC
Confidence 57999999999995 5555555433 11122 689999996433
No 26
>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]
Probab=91.98 E-value=0.024 Score=46.92 Aligned_cols=95 Identities=16% Similarity=0.037 Sum_probs=79.8
Q ss_pred eEEEcCcCcEEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeecccccCCcccccCCCCeeEEecccccc
Q 031164 13 SYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQ 92 (164)
Q Consensus 13 ~~~i~g~~~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~s~~~d~~ 92 (164)
++.+.+. ...+|+.+.+.+..+...+.++.+...+.+.++. .+.-+.|||+|+++.......+..+++......+.+
T Consensus 269 ~~~i~~~--~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 345 (371)
T COG5076 269 SVLITNS--QAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTK-ELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTDY 345 (371)
T ss_pred hhccccc--ccccccccccccCCcccccchhhhhhcccccccc-hhhhhcccCCCccccccccchhhhcccccchhhhhh
Confidence 4455654 7899999999998877899999999999998888 777999999999887776666788999999889999
Q ss_pred cccceeeccEEEeccccc
Q 031164 93 SADTIEGKCTVHSFKSYT 110 (164)
Q Consensus 93 ~~~~I~~kc~V~~~~~~~ 110 (164)
......+.|.|....++.
T Consensus 346 ~~~~~~~~~~~~~~~~~~ 363 (371)
T COG5076 346 YKNANVLEDFVIKKTRLI 363 (371)
T ss_pred hhhccchhhhHhhhhhhh
Confidence 999998888887765543
No 27
>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=90.01 E-value=0.66 Score=30.13 Aligned_cols=44 Identities=23% Similarity=0.314 Sum_probs=35.3
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeeccc
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPE 68 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~ 68 (164)
.+++||.|...-.+ -++|-|+|.+.-...... ..+.|+||-..+
T Consensus 2 ~f~~GdlVwaK~kG--yp~WPa~I~~~~~~~~~~-~~~~V~FfGt~~ 45 (83)
T cd05834 2 QFKAGDLVFAKVKG--YPAWPARVDEPEDWKPPG-KKYPVYFFGTHE 45 (83)
T ss_pred CCCCCCEEEEecCC--CCCCCEEEecccccCCCC-CEEEEEEeCCCC
Confidence 57899999999877 699999999987653333 679999998543
No 28
>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=89.54 E-value=2.1 Score=25.73 Aligned_cols=46 Identities=20% Similarity=0.328 Sum_probs=34.3
Q ss_pred ccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEE-------EEEEeecccccCC
Q 031164 24 KPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKV-------HVRWYYRPEESIG 72 (164)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v-------~v~Wfyrp~e~~~ 72 (164)
+++|.|.|+.++ .+..-|.|..+..-..|- +++ .+.||+.-.+-+.
T Consensus 2 kvnD~VtVKTDG--~~rR~G~ilavE~F~EG~-MYLvaL~dYP~GiWFFNE~~~~d 54 (62)
T PF10781_consen 2 KVNDRVTVKTDG--GPRREGVILAVEPFNEGT-MYLVALEDYPAGIWFFNEKDSPD 54 (62)
T ss_pred ccccEEEEecCC--cccccceEEEEeeccCcE-EEEEEcCcCCcceEEEecCCCCC
Confidence 689999999988 578888888888776775 443 3568887655443
No 29
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=89.44 E-value=1.6 Score=27.82 Aligned_cols=33 Identities=27% Similarity=0.557 Sum_probs=25.8
Q ss_pred EEccCCEEEEecCC-----CCCCCeEEEEeEEeecCCC
Q 031164 22 TIKPGDCVLMRPSE-----PSKPSYVAKIERIESDARG 54 (164)
Q Consensus 22 ~~~vGD~V~v~~~~-----~~~~~~i~~I~~i~~~~~g 54 (164)
.++.||+|.|..+. .+..-|+|+|.......++
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ggaR~ 42 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGARD 42 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEeccccC
Confidence 46899999999876 2367899999998875433
No 30
>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=89.12 E-value=2.5 Score=30.23 Aligned_cols=55 Identities=18% Similarity=0.209 Sum_probs=38.7
Q ss_pred eeeeeEEEcCcCcEEccCCEEEEecCC----------CCCCCeEEEEeEEeecCCCC------eEEEEEEEee
Q 031164 9 RTLESYTVKSISKTIKPGDCVLMRPSE----------PSKPSYVAKIERIESDARGA------NVKVHVRWYY 65 (164)
Q Consensus 9 ~~y~~~~i~g~~~~~~vGD~V~v~~~~----------~~~~~~i~~I~~i~~~~~g~------~~~v~v~Wfy 65 (164)
.||.++.+.. |.+.+||.|-|.+.. .++..-|..|.+|....... ..+|++.-|-
T Consensus 1 i~y~GiflGA--E~I~vGD~VRl~~~~~~~~~~~~~~~~~~tdvMvI~~I~~~~~~~~~~~~~~v~~~G~lY~ 71 (139)
T PF10383_consen 1 IYYRGIFLGA--EMIWVGDAVRLKPLNASPSPNQSDGNPDVTDVMVIDEIQLRLINCDPDSPSTVRFRGDLYT 71 (139)
T ss_pred CeECeEEEee--EEEEeCCEEEECccCCCcccccccCCCCceeEEEEeEEEEecccCCCCCCceEEEEeEece
Confidence 3889998875 599999999995432 22455789999998764331 2677777643
No 31
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=88.88 E-value=0.21 Score=42.40 Aligned_cols=24 Identities=33% Similarity=0.869 Sum_probs=18.6
Q ss_pred eEEeeCCCCCCCCceEeCCccCCCC
Q 031164 140 VYCKCEMPYNPDDLMVQCEGCSDWS 164 (164)
Q Consensus 140 ~~C~c~~~~~pD~~~~~C~~C~~~~ 164 (164)
-.|-|.++..=+ +++||++|+.||
T Consensus 172 ~vC~~g~~~~~N-rmlqC~~C~~~f 195 (464)
T KOG4323|consen 172 SVCYCGGPGAGN-RMLQCDKCRQWY 195 (464)
T ss_pred eeeecCCcCccc-eeeeecccccHH
Confidence 355566666555 899999999998
No 32
>PRK10708 hypothetical protein; Provisional
Probab=88.84 E-value=2.6 Score=25.32 Aligned_cols=45 Identities=16% Similarity=0.282 Sum_probs=33.8
Q ss_pred ccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEE-------EEEEeecccccC
Q 031164 24 KPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKV-------HVRWYYRPEESI 71 (164)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v-------~v~Wfyrp~e~~ 71 (164)
+++|.|.|+.++ .+...|.|..+..-..|. +++ .+.||+.-.+-+
T Consensus 2 kvnD~VtVKTDG--~~rR~G~iLavE~F~EG~-MyLvaL~dYP~GiWFFNE~~~~ 53 (62)
T PRK10708 2 KVNDRVTVKTDG--GPRRPGVVLAVEEFSEGT-MYLVSLEDYPLGIWFFNEAGHQ 53 (62)
T ss_pred ccccEEEEecCC--CccccceEEEEeeccCcE-EEEEEcCcCCCceEEEeccCCC
Confidence 689999999988 578889998888776775 443 356888755444
No 33
>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=88.33 E-value=0.98 Score=27.31 Aligned_cols=39 Identities=21% Similarity=0.382 Sum_probs=26.9
Q ss_pred ccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEe
Q 031164 24 KPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWY 64 (164)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wf 64 (164)
++||.+.+.......+...|.|.++... +|. +-..|+|-
T Consensus 4 ~vGD~lvv~g~~vg~~~r~GeIveV~g~-dG~-PPY~VRw~ 42 (58)
T PF08940_consen 4 SVGDRLVVHGRTVGQPDRHGEIVEVRGP-DGS-PPYLVRWD 42 (58)
T ss_dssp -TTEEEEES-TTTS--EEEEEEEE-S-S-SS--S-EEEEET
T ss_pred CCCCEEEEcCCcCCCCCcEeEEEEEECC-CCC-CCEEEEec
Confidence 6899999999876689999999999975 566 78889994
No 34
>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=88.05 E-value=0.81 Score=29.92 Aligned_cols=42 Identities=17% Similarity=0.237 Sum_probs=32.3
Q ss_pred EccCCEEEEecCCCCCCCeEEEEeEEeecCC--CCeEEEEEEEeec
Q 031164 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDAR--GANVKVHVRWYYR 66 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~--g~~~~v~v~Wfyr 66 (164)
+++||.|...-.+ -+.|-|+|.+...+.. ....++.|+||=.
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 4789999999877 5899999999876531 1126799999864
No 35
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=87.41 E-value=0.39 Score=38.77 Aligned_cols=25 Identities=44% Similarity=1.208 Sum_probs=21.9
Q ss_pred eEEeeCCCCCC-----CCceEeCCccCCCC
Q 031164 140 VYCKCEMPYNP-----DDLMVQCEGCSDWS 164 (164)
Q Consensus 140 ~~C~c~~~~~p-----D~~~~~C~~C~~~~ 164 (164)
..|.|+.|+++ +..++||..|..||
T Consensus 129 ~~C~Cd~~Ypdp~~~~e~~m~QC~iCEDWF 158 (345)
T KOG2752|consen 129 LFCKCDTPYPDPVRTEEGEMLQCVICEDWF 158 (345)
T ss_pred eeEEecCCCCCccccccceeeeEEeccchh
Confidence 59999999986 33899999999997
No 36
>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=86.21 E-value=1.7 Score=28.08 Aligned_cols=39 Identities=21% Similarity=0.214 Sum_probs=32.0
Q ss_pred EccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeecc
Q 031164 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRP 67 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp 67 (164)
+.+||.|.-.-.+ -|.|.|+|.++... . ..+.|.||=..
T Consensus 1 f~~gdlVWaK~~g--~P~WPa~I~~~~~~---~-~k~~V~FfG~~ 39 (80)
T cd06080 1 FEKNDLVWAKIQG--YPWWPAVIKSISRK---K-QKARVNFIGDN 39 (80)
T ss_pred CCCCCEEEEeCCC--CCCCCEEEeeecCC---C-CEEEEEEeCCC
Confidence 4689999999887 58999999998643 4 67999998766
No 37
>PTZ00112 origin recognition complex 1 protein; Provisional
Probab=86.01 E-value=1.7 Score=40.43 Aligned_cols=117 Identities=24% Similarity=0.293 Sum_probs=73.6
Q ss_pred eeeeeEEEcCcCcEEccCCEEEEecCCCCC----------------------CCeEEEEeEEeecCCCCeEEEEEEEeec
Q 031164 9 RTLESYTVKSISKTIKPGDCVLMRPSEPSK----------------------PSYVAKIERIESDARGANVKVHVRWYYR 66 (164)
Q Consensus 9 ~~y~~~~i~g~~~~~~vGD~V~v~~~~~~~----------------------~~~i~~I~~i~~~~~g~~~~v~v~Wfyr 66 (164)
.-|+++.|++. .|.+||.|+|.-+.... ..--|+|.+|+.+...+.+.+.|..||-
T Consensus 441 ~iye~~~in~~--~ys~g~dv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~kg~is~fy~~~~~~~~~~e~c~y~d 518 (1164)
T PTZ00112 441 VIYESIQINDV--EYSIGDDVLIFCTGNGNTYNGKSGTKKNQNNKNIKENIYQLRKGKISSFYKNTNSNQVEAEVCIYYD 518 (1164)
T ss_pred eEEEEEEEcce--eeccCCcEEEEEcCCCCccccccCccccccccchhhhhheecccccchhhhcCCCceeeEEEEEEEc
Confidence 46999999986 99999999998664320 1236899999988655558899999999
Q ss_pred ccccCC------c--ccccCCCCeeEE---------ecc--cccccccceeeccEEEeccc-cccc--CCCCCCeEEEee
Q 031164 67 PEESIG------G--RRQFHGSKEVFL---------SDH--HDIQSADTIEGKCTVHSFKS-YTKL--DAVGNDDFFCRF 124 (164)
Q Consensus 67 p~e~~~------~--~~~~~~~~ELf~---------s~~--~d~~~~~~I~~kc~V~~~~~-~~~~--~~~~~~~ffcr~ 124 (164)
-.|.+- . ....-..-|+|+ -.. +-.+.+.-|..|..|..... |.+- ...|.+-|.|-+
T Consensus 519 ~~d~~~i~~~~~~~~~rr~~~~f~~~~d~~~~~~~llgni~f~~~~~~~i~kki~~~ne~~~~~~d~~~~~g~~kflc~~ 598 (1164)
T PTZ00112 519 QHDAQYIKELEEKQKSRRCKADFEVFLDDDTKNFYLLGNIHFKILDAKMILKKIYVYNEKELYDEDKTAKQGKDKFLCTH 598 (1164)
T ss_pred cccHHHHHHHHHHHHhhhhhhhhhHhcccccceeEEecceeEEEechHhhhhhheeecchhhcccchhhhcccchhhhhH
Confidence 887641 0 011112334444 332 23445555777777776433 2211 114567777765
Q ss_pred eee
Q 031164 125 EYN 127 (164)
Q Consensus 125 ~yd 127 (164)
..-
T Consensus 599 ~~k 601 (1164)
T PTZ00112 599 YLK 601 (1164)
T ss_pred hhh
Confidence 443
No 38
>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=85.22 E-value=2.7 Score=28.85 Aligned_cols=46 Identities=15% Similarity=0.135 Sum_probs=35.8
Q ss_pred CCCCCceeeeeEEEcCcCcEEccCCEEEEecCCCCCCCeEEEEeEEeecCC
Q 031164 3 KPKAPRRTLESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDAR 53 (164)
Q Consensus 3 ~~~~~r~~y~~~~i~g~~~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~ 53 (164)
|-.+|+-..-.+.+... ++++||.|.+-... .|-+++|..|.....
T Consensus 9 k~~~G~G~t~dvIl~~G--tL~~GD~Iv~g~~~---Gpi~tkVRaLl~~~~ 54 (110)
T cd03703 9 KEEEGLGTTIDVILYDG--TLREGDTIVVCGLN---GPIVTKVRALLKPQP 54 (110)
T ss_pred EEcCCCceEEEEEEECC--eEecCCEEEEccCC---CCceEEEeEecCCCC
Confidence 45567777777666443 99999999998765 588999999998754
No 39
>COG5475 Uncharacterized small protein [Function unknown]
Probab=85.09 E-value=4.5 Score=24.26 Aligned_cols=50 Identities=18% Similarity=0.368 Sum_probs=30.8
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeecccccCCcccccCCCCeeEE
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVFL 85 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~ 85 (164)
.+++||.|.|+++++ .|..+.-..+-|+..+||-+-. .....+.++||..
T Consensus 4 ~FstgdvV~lKsGGP----------~Mtvs~~ss~Gmy~C~Wf~g~g----~~~~~F~ed~Lvp 53 (60)
T COG5475 4 SFSTGDVVTLKSGGP----------RMTVSGYSSDGMYECRWFDGYG----VKREAFHEDELVP 53 (60)
T ss_pred eeecCcEEEeecCCc----------eEEEeccccCCeEEEEEecCCC----cccccccccceec
Confidence 789999999999985 2222110111479999997754 2222355666653
No 40
>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=81.20 E-value=3.2 Score=26.81 Aligned_cols=41 Identities=24% Similarity=0.344 Sum_probs=31.6
Q ss_pred EccCCEEEEecCCCCCCCeEEEEeEEeecCC-----CCeEEEEEEEee
Q 031164 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDAR-----GANVKVHVRWYY 65 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~-----g~~~~v~v~Wfy 65 (164)
|++||.|...-.+ -+.|-|+|.+...... ..+..+.|++|-
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 4789999999987 5899999999887532 112578888885
No 41
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=80.52 E-value=3.5 Score=25.04 Aligned_cols=42 Identities=19% Similarity=0.187 Sum_probs=31.0
Q ss_pred EccCCEEEEecCCCCCCCeEEEEeEEeecCC------CCeEEEEEEEeec
Q 031164 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDAR------GANVKVHVRWYYR 66 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~------g~~~~v~v~Wfyr 66 (164)
|++||.|..+-.+ -+.|-|+|.+-....+ ..+..+.|++|-.
T Consensus 1 f~~GdlVwaK~~G--~p~WPa~V~~~~~~~~~~~~~~~~~~~~~V~Ffg~ 48 (63)
T smart00293 1 FKPGDLVWAKMKG--FPWWPALVVSPKETPDNIRKRKRFENLYPVLFFGD 48 (63)
T ss_pred CCCCCEEEEECCC--CCCCCeEEcCcccCChhHhhccCCCCEEEEEEeCC
Confidence 5789999999988 5899999988875431 1125677777653
No 42
>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=78.85 E-value=6.2 Score=20.51 Aligned_cols=26 Identities=23% Similarity=0.259 Sum_probs=22.4
Q ss_pred cCCEEEEecCCCCCCCeEEEEeEEeecC
Q 031164 25 PGDCVLMRPSEPSKPSYVAKIERIESDA 52 (164)
Q Consensus 25 vGD~V~v~~~~~~~~~~i~~I~~i~~~~ 52 (164)
+||.|.|.++. ..-.+|+|.++..+.
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 59999999988 578999999998764
No 43
>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=78.70 E-value=8.9 Score=22.60 Aligned_cols=36 Identities=28% Similarity=0.326 Sum_probs=25.4
Q ss_pred EccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEE
Q 031164 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVR 62 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~ 62 (164)
+.+|+.|++.-.+ ...+-|+|.++.... |. ....|.
T Consensus 1 ~~vG~~v~~~~~~--~~~y~A~I~~~r~~~-~~-~~YyVH 36 (55)
T PF11717_consen 1 FEVGEKVLCKYKD--GQWYEAKILDIREKN-GE-PEYYVH 36 (55)
T ss_dssp --TTEEEEEEETT--TEEEEEEEEEEEECT-TC-EEEEEE
T ss_pred CCcCCEEEEEECC--CcEEEEEEEEEEecC-CC-EEEEEE
Confidence 4689999999833 589999999999953 43 344443
No 44
>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=77.10 E-value=3.7 Score=27.22 Aligned_cols=40 Identities=23% Similarity=0.346 Sum_probs=29.3
Q ss_pred EccCCEEEEecCCCCCCCeEEEEeEEe---------ecCCCCeEEEEEEEee
Q 031164 23 IKPGDCVLMRPSEPSKPSYVAKIERIE---------SDARGANVKVHVRWYY 65 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~i~~I~~i~---------~~~~g~~~~v~v~Wfy 65 (164)
|++||.|...-.+ -+.|-|+|.+=. ....+. ..+.|++|-
T Consensus 1 f~~GDlVwaK~~G--yPwWPA~V~~~~~~p~~~l~~~~~~~~-~~~~V~FFg 49 (93)
T cd05840 1 FQPGDRVLAKVKG--FPAWPAIVVPEEMLPDSVLKGKKKKNK-RTYPVMFFP 49 (93)
T ss_pred CCCCCEEEEeCCC--CCCCCEEECChHHCCHHHHhcccCCCC-CeEEEEEeC
Confidence 5789999999987 589999997632 111223 678888884
No 45
>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=76.66 E-value=8.9 Score=27.55 Aligned_cols=49 Identities=27% Similarity=0.307 Sum_probs=31.1
Q ss_pred ceeeeeEEEcCcCcEEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeeccc
Q 031164 8 RRTLESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPE 68 (164)
Q Consensus 8 r~~y~~~~i~g~~~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~ 68 (164)
...+++.++... .+++||.|.+...+ +.+-.-.|..|. .++-.|||--+
T Consensus 75 tg~~q~~tv~kp--~F~LGd~V~~~f~~--~~pkqRlIlGv~--------lv~~~W~Y~VE 123 (150)
T PF07154_consen 75 TGQLQSLTVQKP--AFRLGDRVEFRFYS--DGPKQRLILGVF--------LVNNSWFYAVE 123 (150)
T ss_pred cCccceeeccCC--ceecCCEEEEEecC--CCCceEEEEEEE--------EecCceEEEEE
Confidence 345666677765 78999999998865 244444555443 35556777544
No 46
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=74.92 E-value=7.2 Score=19.04 Aligned_cols=26 Identities=19% Similarity=0.261 Sum_probs=20.7
Q ss_pred EccCCEEEEecCCCCCCCeEEEEeEEee
Q 031164 23 IKPGDCVLMRPSEPSKPSYVAKIERIES 50 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~i~~I~~i~~ 50 (164)
+.+||.|.|..+. ..-.+|.|.++..
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 4789999999876 4677898888753
No 47
>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=74.76 E-value=3.9 Score=26.02 Aligned_cols=42 Identities=21% Similarity=0.389 Sum_probs=30.3
Q ss_pred EccCCEEEEecCCCCCCCeEEEEeEEeecC--CCCeEEEEEEEeec
Q 031164 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDA--RGANVKVHVRWYYR 66 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~--~g~~~~v~v~Wfyr 66 (164)
|++||.|...-.+ -+.|-|+|....... ......+.|.||-.
T Consensus 1 f~~GdlVWaK~~g--~pwWPa~V~~~~~~~~~~~~~~~~~V~Ffg~ 44 (86)
T PF00855_consen 1 FRPGDLVWAKLKG--YPWWPARVCDPDEKSKKKRKDGHVLVRFFGD 44 (86)
T ss_dssp -STTEEEEEEETT--SEEEEEEEEECCHCTSCSSSSTEEEEEETTT
T ss_pred CCCCCEEEEEeCC--CCCCceEEeecccccccCCCCCEEEEEecCC
Confidence 5789999999877 589999999987532 11126677877654
No 48
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=74.20 E-value=7.4 Score=27.17 Aligned_cols=44 Identities=16% Similarity=0.111 Sum_probs=29.2
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEee
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYY 65 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfy 65 (164)
.+++||.|+...+..+..+.-|.|+...+.....+..+.|.-+-
T Consensus 55 ~L~~GD~VLA~~~~~~~~Y~Pg~V~~~~~~~~~~~~~~~V~f~n 98 (124)
T PF15057_consen 55 SLQVGDKVLAPWEPDDCRYGPGTVIAGPERRASEDKEYTVRFYN 98 (124)
T ss_pred cCCCCCEEEEecCcCCCEEeCEEEEECccccccCCceEEEEEEC
Confidence 68999999999765434455699998765542222556665443
No 49
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=72.67 E-value=16 Score=27.02 Aligned_cols=87 Identities=20% Similarity=0.301 Sum_probs=52.6
Q ss_pred ceeeeeEEEcCcCcEEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeecccccC---Ccc-c-ccCCCCe
Q 031164 8 RRTLESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESI---GGR-R-QFHGSKE 82 (164)
Q Consensus 8 r~~y~~~~i~g~~~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~---~~~-~-~~~~~~E 82 (164)
......+-+... .+..||.|.+.+..++++.+|-||..+.-+ .+.. +-++++.. .|. . .--...+
T Consensus 56 ~Vll~k~~v~n~--~~~rGDiVvl~sP~~p~~~~iKRv~alegd-----~~~t---~~~k~~~v~vpkghcWVegDn~~h 125 (174)
T KOG1568|consen 56 TVLLRKWNVKNR--KVSRGDIVVLKSPNDPDKVIIKRVAALEGD-----IMVT---EDEKEEPVVVPKGHCWVEGDNQKH 125 (174)
T ss_pred EEEEEeeccccc--eeccCCEEEEeCCCChhheeeeeeeccccc-----Eecc---CCCCCCceecCCCcEEEecCCccc
Confidence 344455555543 678999999999887789999999887643 2221 22233322 111 0 0012344
Q ss_pred eEEecccccccccceeeccEEE
Q 031164 83 VFLSDHHDIQSADTIEGKCTVH 104 (164)
Q Consensus 83 Lf~s~~~d~~~~~~I~~kc~V~ 104 (164)
=+=|+..--++...|.|++.-.
T Consensus 126 s~DSntFGPVS~gli~grai~i 147 (174)
T KOG1568|consen 126 SYDSNTFGPVSTGLIVGRAIYI 147 (174)
T ss_pred ccccCccCCcchhheeeeEEEE
Confidence 5556666778888899987443
No 50
>PF09871 DUF2098: Uncharacterized protein conserved in archaea (DUF2098); InterPro: IPR019209 This family of proteins have no known function.
Probab=69.47 E-value=14 Score=24.50 Aligned_cols=43 Identities=30% Similarity=0.411 Sum_probs=31.5
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEE---EEeecccccC
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHV---RWYYRPEESI 71 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v---~Wfyrp~e~~ 71 (164)
.|.+|++|--.+.+ .+|+|.+|... +|. .||.+ .-||||.-+.
T Consensus 2 ~I~vGs~VRY~~TG-----T~G~V~diK~e-d~~-~wv~LD~t~L~Yr~~~Le 47 (91)
T PF09871_consen 2 PIKVGSYVRYINTG-----TVGKVVDIKEE-DGE-TWVLLDSTDLYYRPDYLE 47 (91)
T ss_pred cceeCCEEEECCCC-----eEEEEEEEEEe-CCC-eEEEEccCCceeecceeE
Confidence 57888888665443 58999999554 566 88888 5778888554
No 51
>COG3257 GlxB Uncharacterized protein, possibly involved in glyoxylate utilization [General function prediction only]
Probab=69.05 E-value=18 Score=28.10 Aligned_cols=49 Identities=8% Similarity=0.330 Sum_probs=31.9
Q ss_pred EEEcCcCcEEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeecccccCCcc
Q 031164 14 YTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGR 74 (164)
Q Consensus 14 ~~i~g~~~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~~~~ 74 (164)
+++.|....++.|+++|+.++.. | .+. +.+.--.++.|+-++-+...|.
T Consensus 96 v~~~G~th~l~eggyaylPpgs~----~-----~~~---N~~~~~~rfhw~rk~Y~~VdG~ 144 (264)
T COG3257 96 VKAEGKTHALREGGYAYLPPGSG----W-----TLR---NAQKEDSRFHWIRKRYQPVEGV 144 (264)
T ss_pred EEEcCeEEEeccCCeEEeCCCCc----c-----eEe---eccCCceEEEEEeecceeecCc
Confidence 34456556689999999998762 1 111 1221457888998888877654
No 52
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=68.92 E-value=3.2 Score=33.03 Aligned_cols=26 Identities=27% Similarity=0.853 Sum_probs=20.0
Q ss_pred CCceEEeeCCCCCCCCceEeCCc--cC-CCC
Q 031164 137 RVAVYCKCEMPYNPDDLMVQCEG--CS-DWS 164 (164)
Q Consensus 137 ~~~~~C~c~~~~~pD~~~~~C~~--C~-~~~ 164 (164)
.-+..|+|.+..- ..||.||. |. .||
T Consensus 217 ~e~~yC~Cnqvsy--g~Mi~CDn~~C~~eWF 245 (274)
T KOG1973|consen 217 DEPTYCICNQVSY--GKMIGCDNPGCPIEWF 245 (274)
T ss_pred CCCEEEEeccccc--ccccccCCCCCCcceE
Confidence 4568999993332 47999996 99 997
No 53
>PF04322 DUF473: Protein of unknown function (DUF473); InterPro: IPR007417 This is a family of uncharacterised archaeal proteins.
Probab=66.55 E-value=16 Score=25.44 Aligned_cols=43 Identities=19% Similarity=0.472 Sum_probs=29.5
Q ss_pred ceeeeeEEEcCcC-----cEEccCCEEEEecCCC-----CCCCeEEEEeEEee
Q 031164 8 RRTLESYTVKSIS-----KTIKPGDCVLMRPSEP-----SKPSYVAKIERIES 50 (164)
Q Consensus 8 r~~y~~~~i~g~~-----~~~~vGD~V~v~~~~~-----~~~~~i~~I~~i~~ 50 (164)
|.+++.++++... ..+.+||+|++.+... +..-.||+|.++.-
T Consensus 19 ~~~~RTiEirSa~N~~~~~~~~~Gd~VFlT~~~~~Dl~~Gt~GiIa~V~~~~i 71 (119)
T PF04322_consen 19 KNHIRTIEIRSAHNVIALESLDPGDRVFLTSVSLEDLTPGTEGIIAEVKKIEI 71 (119)
T ss_pred hCCceEEEEEcchheeeeecCCCCCEEEEecCCHHHCCCCCCeEEEEEEEEEE
Confidence 3466777666431 3469999999998753 34667888877754
No 54
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=63.72 E-value=1.1 Score=27.20 Aligned_cols=23 Identities=30% Similarity=0.807 Sum_probs=18.0
Q ss_pred CceEEe-eCCCCCCCCceEeCC-ccCC
Q 031164 138 VAVYCK-CEMPYNPDDLMVQCE-GCSD 162 (164)
Q Consensus 138 ~~~~C~-c~~~~~pD~~~~~C~-~C~~ 162 (164)
.+++|. |.+|..||. .+|+ .|++
T Consensus 2 ~HkHC~~CG~~Ip~~~--~fCS~~C~~ 26 (59)
T PF09889_consen 2 PHKHCPVCGKPIPPDE--SFCSPKCRE 26 (59)
T ss_pred CCCcCCcCCCcCCcch--hhhCHHHHH
Confidence 467895 999999985 7895 8864
No 55
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=63.00 E-value=2.8 Score=20.69 Aligned_cols=12 Identities=25% Similarity=0.418 Sum_probs=9.3
Q ss_pred ceEeCCccCCCC
Q 031164 153 LMVQCEGCSDWS 164 (164)
Q Consensus 153 ~~~~C~~C~~~~ 164 (164)
.+++|+.|+..|
T Consensus 1 ~l~~C~~CgR~F 12 (25)
T PF13913_consen 1 ELVPCPICGRKF 12 (25)
T ss_pred CCCcCCCCCCEE
Confidence 368899998764
No 56
>COG1370 Prefoldin, molecular chaperone implicated in de novo protein folding, alpha subunit [Posttranslational modification, protein turnover, chaperones]
Probab=62.24 E-value=7.2 Score=28.25 Aligned_cols=39 Identities=15% Similarity=0.295 Sum_probs=32.4
Q ss_pred CCCceeeeeEEEcCcCcEEccCCEEEEecCCCCCCCeEEEE
Q 031164 5 KAPRRTLESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKI 45 (164)
Q Consensus 5 ~~~r~~y~~~~i~g~~~~~~vGD~V~v~~~~~~~~~~i~~I 45 (164)
++||.-|.++.+.+. +.++.||-|+|-++++ ...-+|+.
T Consensus 94 r~Gk~VFaKfVi~~D-~~iR~~dEvlVVne~d-~LlAvGra 132 (155)
T COG1370 94 RKGKSVFAKFVIDVD-EEIRAGDEVLVVNEDD-ELLAVGRA 132 (155)
T ss_pred HhccchhhhheeccC-cccCCCCeEEEECCCC-cEEEeeeE
Confidence 578999999999884 7999999999999885 56666664
No 57
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=61.42 E-value=20 Score=22.82 Aligned_cols=29 Identities=17% Similarity=0.260 Sum_probs=24.8
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecC
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDA 52 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~ 52 (164)
.++.||-|.|.++. +.--+|.|.++....
T Consensus 6 ~I~kGD~V~Vi~G~--dKGK~G~V~~V~~~~ 34 (76)
T PRK12281 6 KVKKGDMVKVIAGD--DKGKTGKVLAVLPKK 34 (76)
T ss_pred cccCCCEEEEeEcC--CCCcEEEEEEEEcCC
Confidence 57999999999987 577889999998753
No 58
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=61.27 E-value=23 Score=23.88 Aligned_cols=46 Identities=22% Similarity=0.337 Sum_probs=35.8
Q ss_pred CCCceeeeeEEEcCcCcEEccCCEEEEecCCCCCCCeEEEEeEEeecCCC
Q 031164 5 KAPRRTLESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARG 54 (164)
Q Consensus 5 ~~~r~~y~~~~i~g~~~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g 54 (164)
..||.+++.-..+. +..+++||.+-|.-+. ..+..+|..+-....+
T Consensus 32 ~~GrV~vNG~~aKp-S~~VK~GD~l~i~~~~---~~~~v~Vl~~~~~r~~ 77 (100)
T COG1188 32 EGGRVKVNGQRAKP-SKEVKVGDILTIRFGN---KEFTVKVLALGEQRRP 77 (100)
T ss_pred HCCeEEECCEEccc-ccccCCCCEEEEEeCC---cEEEEEEEecccccCc
Confidence 36899999887765 4699999999999877 5778888888765433
No 59
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=60.58 E-value=8.2 Score=23.01 Aligned_cols=23 Identities=26% Similarity=0.632 Sum_probs=19.3
Q ss_pred EE-eeCCCCCCCCceEeCCccCCC
Q 031164 141 YC-KCEMPYNPDDLMVQCEGCSDW 163 (164)
Q Consensus 141 ~C-~c~~~~~pD~~~~~C~~C~~~ 163 (164)
-| +|.++..|....+.|+.|+.=
T Consensus 7 ~C~~Cg~~~~~~dDiVvCp~Cgap 30 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDIVVCPECGAP 30 (54)
T ss_pred cChhhCCcccCCCCEEECCCCCCc
Confidence 45 489999988889999999864
No 60
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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 DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=60.47 E-value=3.7 Score=25.55 Aligned_cols=16 Identities=38% Similarity=0.954 Sum_probs=9.2
Q ss_pred CCCCCceEeCCccCCC
Q 031164 148 YNPDDLMVQCEGCSDW 163 (164)
Q Consensus 148 ~~pD~~~~~C~~C~~~ 163 (164)
++--..+++|++|+.|
T Consensus 23 Y~~GvViv~C~gC~~~ 38 (66)
T PF05180_consen 23 YHKGVVIVQCPGCKNR 38 (66)
T ss_dssp HHTSEEEEE-TTS--E
T ss_pred HhCCeEEEECCCCcce
Confidence 3334489999999875
No 61
>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=60.18 E-value=16 Score=22.98 Aligned_cols=48 Identities=21% Similarity=0.149 Sum_probs=32.9
Q ss_pred EEEEEeecccccCCcccccCCCCeeEEecccccccccceeeccEEEec
Q 031164 59 VHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQSADTIEGKCTVHSF 106 (164)
Q Consensus 59 v~v~Wfyrp~e~~~~~~~~~~~~ELf~s~~~d~~~~~~I~~kc~V~~~ 106 (164)
|.|.=+-|..||.-.-..-.+..|+.+....+..++--|+|++.|++.
T Consensus 19 V~ViGlTRG~dtkfhHtEkLDkGEVmIaQFTehtsaiKiRGkA~I~t~ 66 (75)
T PF02081_consen 19 VTVIGLTRGTDTKFHHTEKLDKGEVMIAQFTEHTSAIKIRGKAEILTK 66 (75)
T ss_dssp EEEEEEESSSSSSEEEEEEE-TT-EEEEE-BSSEEEEEEESSEEEEET
T ss_pred eEEEEEecCCcccchhhhccCCCcEEEEEeecceEEEEEeeeEEEEec
Confidence 444455566666533222357899999999999999999999999874
No 62
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=59.56 E-value=22 Score=23.07 Aligned_cols=29 Identities=17% Similarity=0.296 Sum_probs=24.7
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecC
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDA 52 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~ 52 (164)
.++.||.|.|.++. +.--+|.|.++....
T Consensus 8 ~I~~GD~V~Vi~G~--dKGK~G~V~~V~~~~ 36 (83)
T CHL00141 8 HVKIGDTVKIISGS--DKGKIGEVLKIIKKS 36 (83)
T ss_pred cccCCCEEEEeEcC--CCCcEEEEEEEEcCC
Confidence 67999999999987 467889999998753
No 63
>PRK13251 transcription attenuation protein MtrB; Provisional
Probab=59.35 E-value=23 Score=22.25 Aligned_cols=48 Identities=21% Similarity=0.189 Sum_probs=35.8
Q ss_pred EEEEEeecccccCCcccccCCCCeeEEecccccccccceeeccEEEec
Q 031164 59 VHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQSADTIEGKCTVHSF 106 (164)
Q Consensus 59 v~v~Wfyrp~e~~~~~~~~~~~~ELf~s~~~d~~~~~~I~~kc~V~~~ 106 (164)
|.|.=+-|..|+.---..-.+..|+.+....+..++-.|+|++.+++.
T Consensus 19 V~vIgltrg~dtkfhhtEkLDkGEVmiaqftehtsaiKirGkA~I~t~ 66 (75)
T PRK13251 19 VNVIGLTRGKDTKFHHTEKLDKGEVMIAQFTEHTSAIKIRGKAEIQTK 66 (75)
T ss_pred eEEEEEecCCCccchhhhhcCCCcEEEEEeecceeEEEEeceEEEEee
Confidence 445555666666432222367899999999999999999999999874
No 64
>COG4014 Uncharacterized protein conserved in archaea [Function unknown]
Probab=58.55 E-value=33 Score=22.63 Aligned_cols=40 Identities=28% Similarity=0.411 Sum_probs=29.2
Q ss_pred ccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEE---Eeecccc
Q 031164 24 KPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVR---WYYRPEE 69 (164)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~---Wfyrp~e 69 (164)
.+||.|---+.+ .+|+|..|.++.+|. .|+.+- -+||+.=
T Consensus 10 ~VG~avrYvnTg-----TvgrV~dIkkdEdG~-~WV~LdstdLwYre~~ 52 (97)
T COG4014 10 KVGDAVRYVNTG-----TVGRVVDIKKDEDGD-IWVVLDSTDLWYREHY 52 (97)
T ss_pred hhcceEEEeecC-----ceeeEEEEEeecCCc-eEEEEecCCceecccc
Confidence 478876544333 489999999999999 998874 4567663
No 65
>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=58.43 E-value=15 Score=23.81 Aligned_cols=43 Identities=21% Similarity=0.303 Sum_probs=30.2
Q ss_pred EccCCEEEEecCCCCCCCeEEEEeEEeecCC---CCeEEEEEEEeecc
Q 031164 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDAR---GANVKVHVRWYYRP 67 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~---g~~~~v~v~Wfyrp 67 (164)
+++||.|.-.-.+ -+.|-|+|.+-..+.. +....+.|.||=.+
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 4789999999887 6899999988543311 11145777777654
No 66
>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=58.04 E-value=29 Score=21.10 Aligned_cols=30 Identities=37% Similarity=0.361 Sum_probs=22.8
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeec
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESD 51 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~ 51 (164)
+++.||.|++.+...+..+..++|.+|+..
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 899999999977322234578888888875
No 67
>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=57.15 E-value=35 Score=26.27 Aligned_cols=45 Identities=20% Similarity=0.473 Sum_probs=36.5
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeeccc
Q 031164 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPE 68 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~ 68 (164)
..+++|+.=.+..+.+.-|.+.|+|..+... +. -.+++.|+-.-.
T Consensus 26 ~~F~~gQIWAlYd~~D~mPR~Ya~I~kV~~~--~~-Fkl~i~wLe~~~ 70 (217)
T PF11926_consen 26 EKFQVGQIWALYDDDDGMPRYYARIKKVDSS--NP-FKLHITWLEPCP 70 (217)
T ss_pred HhCCCCCEEEEeeCCCCCeeeEEEEEEEecC--CC-eEEEEEEccccC
Confidence 4789999999998877789999999999975 23 689999985433
No 68
>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=56.76 E-value=29 Score=22.97 Aligned_cols=41 Identities=20% Similarity=0.277 Sum_probs=30.2
Q ss_pred CCCCCceeeeeEEEcCcCcEEccCCEEEEecCCCCCCCeEEEEeEEeecC
Q 031164 3 KPKAPRRTLESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDA 52 (164)
Q Consensus 3 ~~~~~r~~y~~~~i~g~~~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~ 52 (164)
+..+|+-..-.+.+... ++++||++..-.. .|+|..|+.+.
T Consensus 9 ~~~~g~G~vatviV~~G--tL~~Gd~iv~G~~-------~gkVr~l~d~~ 49 (95)
T cd03702 9 KLDKGRGPVATVLVQNG--TLKVGDVLVAGTT-------YGKVRAMFDEN 49 (95)
T ss_pred EecCCCCccEEEEEEcC--eEeCCCEEEEccc-------ccEEEEEECCC
Confidence 34566667777777654 9999999988644 35999999764
No 69
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=56.21 E-value=25 Score=23.84 Aligned_cols=29 Identities=21% Similarity=0.329 Sum_probs=25.1
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecC
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDA 52 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~ 52 (164)
.++.||.|.|.++. +.--+|.|.++....
T Consensus 4 ~i~kGD~V~Vi~G~--dKGk~G~V~~V~~~~ 32 (105)
T PRK00004 4 KIKKGDTVIVIAGK--DKGKRGKVLKVLPKK 32 (105)
T ss_pred cccCCCEEEEeEcC--CCCcEEEEEEEEcCC
Confidence 57899999999987 578899999998763
No 70
>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=55.89 E-value=35 Score=22.46 Aligned_cols=41 Identities=22% Similarity=0.316 Sum_probs=30.5
Q ss_pred CCCCCceeeeeEEEcCcCcEEccCCEEEEecCCCCCCCeEEEEeEEeecC
Q 031164 3 KPKAPRRTLESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDA 52 (164)
Q Consensus 3 ~~~~~r~~y~~~~i~g~~~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~ 52 (164)
|..+|+-..-.+.+... ++++||++.+-.. .|+|..|+.+.
T Consensus 9 ~~~~g~G~vatviV~~G--tL~~Gd~iv~G~~-------~GkVr~~~d~~ 49 (95)
T cd03701 9 KLDKGRGPVATVIVQNG--TLKKGDVIVAGGT-------YGKIRTMVDEN 49 (95)
T ss_pred EecCCCCeeEEEEEEcC--eEecCCEEEECCc-------cceEEEEECCC
Confidence 44567777777777765 9999999988644 47888888763
No 71
>COG1935 Uncharacterized conserved protein [Function unknown]
Probab=55.57 E-value=26 Score=24.32 Aligned_cols=43 Identities=21% Similarity=0.446 Sum_probs=29.1
Q ss_pred ceeeeeEEEcCcC-----cEEccCCEEEEecCCC-----CCCCeEEEEeEEee
Q 031164 8 RRTLESYTVKSIS-----KTIKPGDCVLMRPSEP-----SKPSYVAKIERIES 50 (164)
Q Consensus 8 r~~y~~~~i~g~~-----~~~~vGD~V~v~~~~~-----~~~~~i~~I~~i~~ 50 (164)
|.+++.+++.... +..+.||.|++.+... +..-.||+|.++..
T Consensus 19 ~~~~rTieiRsa~N~~tv~rl~~GDlVFlT~~~~~Dl~~GtsGiiAkV~~vev 71 (122)
T COG1935 19 RNPIRTIEIRSARNLLTVLRLHEGDLVFLTSTSLEDLTKGTSGIIAKVRRVEV 71 (122)
T ss_pred hCCceEEEEEcccchHHhhcCCCCCEEEEehhHhhHhhcCcceeEEEEEEEEE
Confidence 4567777776431 4579999999998642 23557887776653
No 72
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=52.44 E-value=5.8 Score=31.88 Aligned_cols=23 Identities=22% Similarity=0.550 Sum_probs=18.5
Q ss_pred EE-eeCCCCCCCCceEeCCccCCCC
Q 031164 141 YC-KCEMPYNPDDLMVQCEGCSDWS 164 (164)
Q Consensus 141 ~C-~c~~~~~pD~~~~~C~~C~~~~ 164 (164)
+| +|.+|..-|. +++||.|...|
T Consensus 316 lC~IC~~P~~E~E-~~FCD~CDRG~ 339 (381)
T KOG1512|consen 316 LCRICLGPVIESE-HLFCDVCDRGP 339 (381)
T ss_pred hhhccCCcccchh-eeccccccCCC
Confidence 55 4888888777 99999998764
No 73
>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=51.80 E-value=32 Score=23.30 Aligned_cols=29 Identities=21% Similarity=0.286 Sum_probs=24.8
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecC
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDA 52 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~ 52 (164)
.++.||-|.|.++. +.--+|.|.++....
T Consensus 3 ~ikkGD~V~Vi~G~--dKGK~G~V~~V~~~~ 31 (104)
T TIGR01079 3 KIKKGDTVKVISGK--DKGKRGKVLKVLPKT 31 (104)
T ss_pred cccCCCEEEEeEcC--CCCcEEEEEEEEcCC
Confidence 47899999999987 578899999998653
No 74
>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=50.93 E-value=25 Score=23.93 Aligned_cols=45 Identities=16% Similarity=0.140 Sum_probs=32.0
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeec--------CCCCeEEEEEEEeeccc
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESD--------ARGANVKVHVRWYYRPE 68 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~--------~~g~~~~v~v~Wfyrp~ 68 (164)
+|.+||.|...-.+ -+.|-|+|.+--.. .......+.|++|-...
T Consensus 2 ~~~~GdlVWaK~~g--~PwWPa~V~~~~~~~~~~~~~~~~~~~~~~~V~FFG~~~ 54 (110)
T cd05837 2 KYQVGDLVWAKVSG--YPWWPCMVCSDPLLGTYTKTKRNKRKPRQYHVQFFGDNP 54 (110)
T ss_pred CCCCCCEEEEeCCC--CCCCCEEEecccccchhhhhhhccCCCCeEEEEEcCCCC
Confidence 58899999999887 58999999853211 11112678999988643
No 75
>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=49.65 E-value=24 Score=22.46 Aligned_cols=35 Identities=14% Similarity=0.355 Sum_probs=23.2
Q ss_pred EEEcCcCcEEccCCEEEEecCCCCCCCeEEEEeEEeec
Q 031164 14 YTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESD 51 (164)
Q Consensus 14 ~~i~g~~~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~ 51 (164)
|.+++. ...++||+|.+...+ ...-+|+|.++...
T Consensus 15 f~~~~~-~~v~~GeyV~i~~~~--~~~vlG~V~~i~~~ 49 (91)
T PF09378_consen 15 FIVEPS-KDVRVGEYVVIEYDD--GEKVLGMVTSISRG 49 (91)
T ss_dssp EEEEE--TT-BTTEEEEES------TTEEEEEEEEES-
T ss_pred EEEeCC-CCCCcCeEEEEEEec--hhhhhhhhheeEEc
Confidence 445442 368999999999884 57899999999874
No 76
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=48.22 E-value=31 Score=20.33 Aligned_cols=28 Identities=21% Similarity=0.274 Sum_probs=22.6
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEee
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIES 50 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~ 50 (164)
.+++||.|.+...+ +..-|-|+|.++..
T Consensus 2 ~~~~G~~Ve~~~~~-~~~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKE-EDSWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECC-CCEEEEEEEEEECC
Confidence 47899999999865 25677899998875
No 77
>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=46.36 E-value=17 Score=22.97 Aligned_cols=25 Identities=28% Similarity=0.389 Sum_probs=20.0
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeE
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIER 47 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~ 47 (164)
.++.||.|||-=.++ .-+.|+.|++
T Consensus 5 ~~~~GD~VyViYrNP-Ht~~VanIqe 29 (75)
T PF11132_consen 5 PYHAGDIVYVIYRNP-HTQDVANIQE 29 (75)
T ss_pred ccCCCCEEEEEEcCC-CCccccccch
Confidence 789999999987775 5677887754
No 78
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=46.07 E-value=42 Score=21.66 Aligned_cols=28 Identities=29% Similarity=0.232 Sum_probs=19.5
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEeEEee
Q 031164 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIES 50 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~ 50 (164)
.-++.||+|+|...+- ..--|.|.....
T Consensus 42 iwI~~GD~VlVe~~~~--~~~kg~Iv~r~~ 69 (83)
T smart00652 42 VWIRRGDIVLVDPWDF--QDVKADIIYKYT 69 (83)
T ss_pred EEEcCCCEEEEEecCC--CCCEEEEEEEeC
Confidence 4689999999987653 355666665553
No 79
>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=45.90 E-value=40 Score=21.44 Aligned_cols=27 Identities=30% Similarity=0.178 Sum_probs=19.2
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEeEEe
Q 031164 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIE 49 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~ 49 (164)
..++.||.|.|...+- ..--|.|...+
T Consensus 37 iwI~~GD~V~Ve~~~~--d~~kg~Iv~r~ 63 (77)
T cd05793 37 VWINEGDIVLVAPWDF--QDDKADIIYKY 63 (77)
T ss_pred EEEcCCCEEEEEeccc--cCCEEEEEEEc
Confidence 4689999999987653 45566666554
No 80
>COG0662 {ManC} Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=45.63 E-value=22 Score=24.61 Aligned_cols=23 Identities=26% Similarity=0.446 Sum_probs=18.1
Q ss_pred EEEcCcCcEEccCCEEEEecCCC
Q 031164 14 YTVKSISKTIKPGDCVLMRPSEP 36 (164)
Q Consensus 14 ~~i~g~~~~~~vGD~V~v~~~~~ 36 (164)
++++|....++.||+++|.++..
T Consensus 70 v~~~~~~~~v~~gd~~~iP~g~~ 92 (127)
T COG0662 70 VTIGGEEVEVKAGDSVYIPAGTP 92 (127)
T ss_pred EEECCEEEEecCCCEEEECCCCc
Confidence 45556557889999999999874
No 81
>PRK04980 hypothetical protein; Provisional
Probab=45.44 E-value=55 Score=22.14 Aligned_cols=38 Identities=16% Similarity=0.277 Sum_probs=23.6
Q ss_pred eEEEcCc-CcEEccCCEEEEecCCCCCCCeEEEEeEEee
Q 031164 13 SYTVKSI-SKTIKPGDCVLMRPSEPSKPSYVAKIERIES 50 (164)
Q Consensus 13 ~~~i~g~-~~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~ 50 (164)
.+|++.. .-.+++||.|.|...+.+.+....+|.++..
T Consensus 21 TiTiRd~se~~~~~G~~~~V~~~e~g~~~c~ieI~sV~~ 59 (102)
T PRK04980 21 TITIRDESESHFKPGDVLRVGTFEDDRYFCTIEVLSVSP 59 (102)
T ss_pred eEEeeCCcccCCCCCCEEEEEECCCCcEEEEEEEEEEEE
Confidence 4566542 2368999999997554334455556666654
No 82
>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=44.97 E-value=74 Score=21.74 Aligned_cols=30 Identities=23% Similarity=0.346 Sum_probs=22.0
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEeEEeec
Q 031164 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESD 51 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~ 51 (164)
..+++||.+.+..-+. .....++|..|..=
T Consensus 30 ~~ikvGD~I~f~~~~~-~~~l~v~V~~i~~Y 59 (109)
T cd06555 30 QQIKVGDKILFNDLDT-GQQLLVKVVDIRKY 59 (109)
T ss_pred hcCCCCCEEEEEEcCC-CcEEEEEEEEEEec
Confidence 3699999999987653 45667777777653
No 83
>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=44.15 E-value=35 Score=16.33 Aligned_cols=15 Identities=27% Similarity=0.370 Sum_probs=10.7
Q ss_pred EEeEEeecCCCCeEEE
Q 031164 44 KIERIESDARGANVKV 59 (164)
Q Consensus 44 ~I~~i~~~~~g~~~~v 59 (164)
.|..|.++++|. +|+
T Consensus 6 ~I~~i~~D~~G~-lWi 20 (24)
T PF07494_consen 6 NIYSIYEDSDGN-LWI 20 (24)
T ss_dssp CEEEEEE-TTSC-EEE
T ss_pred eEEEEEEcCCcC-EEE
Confidence 377888888888 765
No 84
>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=43.42 E-value=25 Score=20.92 Aligned_cols=21 Identities=33% Similarity=0.608 Sum_probs=15.5
Q ss_pred EEcCcCcEEccCCEEEEecCC
Q 031164 15 TVKSISKTIKPGDCVLMRPSE 35 (164)
Q Consensus 15 ~i~g~~~~~~vGD~V~v~~~~ 35 (164)
+++|....++.||.+++.+..
T Consensus 33 ~~~~~~~~l~~Gd~~~i~~~~ 53 (71)
T PF07883_consen 33 TVDGERVELKPGDAIYIPPGV 53 (71)
T ss_dssp EETTEEEEEETTEEEEEETTS
T ss_pred EEccEEeEccCCEEEEECCCC
Confidence 355555678889999888775
No 85
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=43.36 E-value=54 Score=22.89 Aligned_cols=30 Identities=13% Similarity=0.204 Sum_probs=24.8
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEeEEeecC
Q 031164 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDA 52 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~ 52 (164)
..|+.||-|.|-++. +.--.|+|.++....
T Consensus 44 ~~IkkGD~V~VisG~--~KGk~GkV~~V~~~~ 73 (120)
T PRK01191 44 LPVRKGDTVKVMRGD--FKGEEGKVVEVDLKR 73 (120)
T ss_pred ceEeCCCEEEEeecC--CCCceEEEEEEEcCC
Confidence 368999999999998 466779999997653
No 86
>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=42.24 E-value=57 Score=20.79 Aligned_cols=29 Identities=28% Similarity=0.273 Sum_probs=19.0
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEeEEee
Q 031164 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIES 50 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~ 50 (164)
.-++.||+|+|.+.+- +..--|.|.....
T Consensus 37 iwI~~GD~VlV~~~~~-~~~~kg~Iv~r~~ 65 (78)
T cd04456 37 IWIKRGDFLIVDPIEE-GEDVKADIIFVYC 65 (78)
T ss_pred EEEcCCCEEEEEeccc-CCCceEEEEEEeC
Confidence 4689999999987652 2345555555443
No 87
>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=42.24 E-value=30 Score=21.11 Aligned_cols=24 Identities=38% Similarity=0.393 Sum_probs=15.7
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeE
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIER 47 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~ 47 (164)
.++.||+|+|...+. +.--|.|..
T Consensus 41 wI~~GD~V~V~~~~~--d~~kG~Ii~ 64 (65)
T PF01176_consen 41 WIKRGDFVLVEPSPY--DKVKGRIIY 64 (65)
T ss_dssp ---TTEEEEEEESTT--CTTEEEEEE
T ss_pred ecCCCCEEEEEeccc--CCCeEEEEE
Confidence 589999999998663 366677653
No 88
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=41.99 E-value=13 Score=30.72 Aligned_cols=15 Identities=27% Similarity=0.893 Sum_probs=12.4
Q ss_pred CCCCceEeCCccCCC
Q 031164 149 NPDDLMVQCEGCSDW 163 (164)
Q Consensus 149 ~pD~~~~~C~~C~~~ 163 (164)
.-...|-+|++|++|
T Consensus 363 ~a~~l~W~CPsC~~W 377 (389)
T COG2956 363 TAHTLYWHCPSCRAW 377 (389)
T ss_pred cceeeeeeCCCcccc
Confidence 344679999999999
No 89
>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=41.71 E-value=76 Score=21.14 Aligned_cols=28 Identities=21% Similarity=0.406 Sum_probs=22.7
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeec
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESD 51 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~ 51 (164)
.+++||.+.|...+ .+..+.+|.++..-
T Consensus 30 ~~k~Gd~~i~~~~~--~~~~~i~v~~V~~~ 57 (105)
T cd06541 30 LPKAGDYLIILDGQ--QPLAIAEVVKVEIM 57 (105)
T ss_pred CCCCCCEEEEecCC--CcEEEEEEEEEEEE
Confidence 68999999998776 56778888887653
No 90
>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=40.87 E-value=22 Score=23.03 Aligned_cols=26 Identities=27% Similarity=0.535 Sum_probs=17.4
Q ss_pred EEEEEeecccccC---------CcccccCCCCeeEEecc
Q 031164 59 VHVRWYYRPEESI---------GGRRQFHGSKEVFLSDH 88 (164)
Q Consensus 59 v~v~Wfyrp~e~~---------~~~~~~~~~~ELf~s~~ 88 (164)
..++|+| |.++. +|++ .++|||+-+.
T Consensus 36 ~~GrWm~-P~~~~Y~VGyNe~GLGpK---~~~ElyiVnk 70 (85)
T PF12503_consen 36 PNGRWMY-PEGYEYMVGYNESGLGPK---FDGELYIVNK 70 (85)
T ss_pred cCCceec-CCCeEEEeeecCCCCCcC---cCCeEEEEcC
Confidence 3457998 88764 2233 4899999764
No 91
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=40.78 E-value=15 Score=18.92 Aligned_cols=10 Identities=20% Similarity=0.331 Sum_probs=8.0
Q ss_pred EeCCccCCCC
Q 031164 155 VQCEGCSDWS 164 (164)
Q Consensus 155 ~~C~~C~~~~ 164 (164)
..|+.|++||
T Consensus 4 ~~C~~C~~~~ 13 (35)
T smart00451 4 FYCKLCNVTF 13 (35)
T ss_pred eEccccCCcc
Confidence 4699998886
No 92
>KOG2133 consensus Transcriptional corepressor Atrophin-1/DRPLA [General function prediction only]
Probab=39.63 E-value=21 Score=33.45 Aligned_cols=111 Identities=22% Similarity=0.207 Sum_probs=79.7
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecCC-CCeEEEEEEEeecccccC-Cc---cc--------------ccCCCCe
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDAR-GANVKVHVRWYYRPEESI-GG---RR--------------QFHGSKE 82 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~-g~~~~v~v~Wfyrp~e~~-~~---~~--------------~~~~~~E 82 (164)
.|.++|.+.+....+ .++.|+.|-.+-..++ .. ..++...+.|+++++ .+ .+ .-...+|
T Consensus 145 ~y~~~~~l~~~v~~~-~p~lia~~~~~~~~Kr~~~-~~~k~s~~~r~~d~Pet~y~~~m~pe~Ar~e~~P~~~pq~~sq~ 222 (1229)
T KOG2133|consen 145 LYDLRDSLFVEVSQP-EPYLIAAICGFKYTKRDDR-QVVKLSFYFRADDIPETGYLNLMKPERARLEINPHLCPQPLSQE 222 (1229)
T ss_pred hhhhhhhhhhhhccC-CccccccccCccccccccc-cccccccccccccCcccccccccCchhhhhccCCccCCCcchhh
Confidence 688899999888875 6777887776666554 34 677888999999998 22 00 0135688
Q ss_pred eEEeccc-ccccccceeeccEEEecccccccCC------CCCCeEEEeeeeeccCCccc
Q 031164 83 VFLSDHH-DIQSADTIEGKCTVHSFKSYTKLDA------VGNDDFFCRFEYNSSSGAFN 134 (164)
Q Consensus 83 Lf~s~~~-d~~~~~~I~~kc~V~~~~~~~~~~~------~~~~~ffcr~~yd~~~~~f~ 134 (164)
||.+... -.-|..+-.++|.+.+..+...... .+.++||...++.+-.+...
T Consensus 223 l~~s~l~~i~qppscp~gk~~~~~skd~~h~~~~n~p~~ld~~i~fk~agglpps~k~a 281 (1229)
T KOG2133|consen 223 LFNSELQGITQPPSCPRGKGIAEYSKDVRHGGNTNAPFSLDNDIFFKCAGGLPPSTKPA 281 (1229)
T ss_pred hhcccccCCCCCCcCCCCCceEEeecccccCCccCCCCcccceeeeecccCCCCCCCCC
Confidence 8988877 5678899999999997666544331 24577777788887766555
No 93
>PF04085 MreC: rod shape-determining protein MreC; InterPro: IPR007221 MreC (murein formation C) is involved in the rod shape determination in Escherichia coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped.; GO: 0008360 regulation of cell shape; PDB: 2J5U_B 2QF4_B 2QF5_A.
Probab=38.65 E-value=1.4e+02 Score=21.35 Aligned_cols=47 Identities=23% Similarity=0.165 Sum_probs=27.5
Q ss_pred cEEccCCEEEEecCCC--CCCCeEEEEeEEeecCCCCeEEEEEEEeecc
Q 031164 21 KTIKPGDCVLMRPSEP--SKPSYVAKIERIESDARGANVKVHVRWYYRP 67 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~--~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp 67 (164)
..++.||.|+-...+. +....||+|.++..+.++....+.+.=+...
T Consensus 92 ~~i~~GD~V~TSG~~~~fP~Gi~VG~V~~v~~~~~~~~~~~~v~p~~d~ 140 (152)
T PF04085_consen 92 ADIKKGDIVVTSGLGGIFPPGIPVGTVSSVEPDKSGLFKEVYVKPAVDF 140 (152)
T ss_dssp S---TT-EEEEE-TTSSS-CCEEEEEEEEEECTTTCCCEEEEEEESS--
T ss_pred CCCCCCCEEEECCCCCcCCCCCEEEEEEEEEeCCCCcEEEEEEEECCCc
Confidence 4789999998764332 3456899999999887655455666544443
No 94
>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=38.46 E-value=8.4 Score=18.73 Aligned_cols=10 Identities=20% Similarity=0.710 Sum_probs=7.6
Q ss_pred EeCCccCCCC
Q 031164 155 VQCEGCSDWS 164 (164)
Q Consensus 155 ~~C~~C~~~~ 164 (164)
.+|+.|++.|
T Consensus 2 ~~C~~C~~~F 11 (27)
T PF13912_consen 2 FECDECGKTF 11 (27)
T ss_dssp EEETTTTEEE
T ss_pred CCCCccCCcc
Confidence 5788998765
No 95
>COG4946 Uncharacterized protein related to the periplasmic component of the Tol biopolymer transport system [Function unknown]
Probab=38.38 E-value=1.3e+02 Score=26.37 Aligned_cols=52 Identities=15% Similarity=0.161 Sum_probs=41.0
Q ss_pred CCCCceeeeeEEEcCcCcEE--ccCCEEEEecCCCC----CCCeEEEEeEEeecCCCC
Q 031164 4 PKAPRRTLESYTVKSISKTI--KPGDCVLMRPSEPS----KPSYVAKIERIESDARGA 55 (164)
Q Consensus 4 ~~~~r~~y~~~~i~g~~~~~--~vGD~V~v~~~~~~----~~~~i~~I~~i~~~~~g~ 55 (164)
+++|+..|..+..++++.++ +-||.+-|...+.. -..-+|.|+++-.+++|.
T Consensus 357 ~~~~~VrY~r~~~~~e~~vigt~dgD~l~iyd~~~~e~kr~e~~lg~I~av~vs~dGK 414 (668)
T COG4946 357 GKKGGVRYRRIQVDPEGDVIGTNDGDKLGIYDKDGGEVKRIEKDLGNIEAVKVSPDGK 414 (668)
T ss_pred CCCCceEEEEEccCCcceEEeccCCceEEEEecCCceEEEeeCCccceEEEEEcCCCc
Confidence 67889999999888775554 66889998876543 256789999999998886
No 96
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=37.77 E-value=1.3e+02 Score=23.54 Aligned_cols=14 Identities=36% Similarity=0.458 Sum_probs=12.7
Q ss_pred EEccCCEEEEecCC
Q 031164 22 TIKPGDCVLMRPSE 35 (164)
Q Consensus 22 ~~~vGD~V~v~~~~ 35 (164)
.|++||.|.+.-++
T Consensus 152 ~~k~~Dtv~i~lp~ 165 (241)
T COG1471 152 NYKTGDTVKISLPE 165 (241)
T ss_pred ccccccEEEEeCCC
Confidence 79999999999877
No 97
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=37.61 E-value=16 Score=25.12 Aligned_cols=27 Identities=22% Similarity=0.577 Sum_probs=20.1
Q ss_pred CCceEEe-eCCCCCCCCceEeCCccCCC
Q 031164 137 RVAVYCK-CEMPYNPDDLMVQCEGCSDW 163 (164)
Q Consensus 137 ~~~~~C~-c~~~~~pD~~~~~C~~C~~~ 163 (164)
.....|. |.....++.....|+.|+..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (115)
T TIGR00100 68 PVECECEDCSEEVSPEIDLYRCPKCHGI 95 (115)
T ss_pred CcEEEcccCCCEEecCCcCccCcCCcCC
Confidence 3445774 88888887777889999864
No 98
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=37.24 E-value=1.1e+02 Score=19.46 Aligned_cols=29 Identities=21% Similarity=0.409 Sum_probs=22.5
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeec
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESD 51 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~ 51 (164)
.+++||.|++.|... .....++|.+|...
T Consensus 26 ~v~~g~~v~~~P~~~-g~~~~~~V~sI~~~ 54 (87)
T cd03694 26 VIRLGDTLLLGPDQD-GSFRPVTVKSIHRN 54 (87)
T ss_pred EEeCCCEEEECCCCC-CCEeEEEEEEEEEC
Confidence 789999999998752 23467899988754
No 99
>PF02311 AraC_binding: AraC-like ligand binding domain; InterPro: IPR003313 This entry defines the arabinose-binding and dimerisation domain of the bacterial gene regulatory protein AraC. The crystal structure of the arabinose-binding and dimerization domain of the Escherichia coli gene regulatory protein AraC was determined in the presence and absence of L-arabinose. The arabinose-bound molecule shows that the protein adopts an unusual fold, binding sugar within a beta barrel and completely burying the arabinose with the amino-terminal arm of the protein. Dimer contacts in the presence of arabinose are mediated by an antiparallel coiled-coil. In the uncomplexed protein, the amino-terminal arm is disordered, uncovering the sugar-binding pocket and allowing it to serve as an oligomerization interface [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 1XJA_B 2ARA_A 2AAC_B 2ARC_A.
Probab=36.48 E-value=90 Score=20.49 Aligned_cols=22 Identities=27% Similarity=0.588 Sum_probs=13.7
Q ss_pred EEEcCcCcEEccCCEEEEecCC
Q 031164 14 YTVKSISKTIKPGDCVLMRPSE 35 (164)
Q Consensus 14 ~~i~g~~~~~~vGD~V~v~~~~ 35 (164)
+.++|....++.||.+++.++.
T Consensus 36 ~~~~~~~~~l~~g~~~li~p~~ 57 (136)
T PF02311_consen 36 LHIDGQEYPLKPGDLFLIPPGQ 57 (136)
T ss_dssp EEETTEEEEE-TT-EEEE-TTS
T ss_pred EEECCEEEEEECCEEEEecCCc
Confidence 3456655677889999988877
No 100
>COG4101 Predicted mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=36.31 E-value=94 Score=21.83 Aligned_cols=40 Identities=23% Similarity=0.307 Sum_probs=24.0
Q ss_pred EEccCCEEEEecCCCC------CCCeEEEEeEEeecCCCCeEEEEEEE
Q 031164 22 TIKPGDCVLMRPSEPS------KPSYVAKIERIESDARGANVKVHVRW 63 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~------~~~~i~~I~~i~~~~~g~~~~v~v~W 63 (164)
+...||+.||.+.-+. ..+..+.|.+- |.++++.-+.+.|
T Consensus 91 ~~~pGDf~YiPpgVPHqp~N~S~ep~s~vIaRs--Dp~~~Esv~~lpe 136 (142)
T COG4101 91 EVGPGDFFYIPPGVPHQPANLSTEPLSAVIARS--DPNPQESVQLLPE 136 (142)
T ss_pred EecCCCeEEcCCCCCCcccccCCCCeEEEEEcc--CCCCCcCcEEecc
Confidence 4689999999987643 45566666443 4444433333333
No 101
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=36.07 E-value=35 Score=22.76 Aligned_cols=15 Identities=33% Similarity=0.397 Sum_probs=12.5
Q ss_pred EEccCCEEEEecCCC
Q 031164 22 TIKPGDCVLMRPSEP 36 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~ 36 (164)
.+++||.|++.+...
T Consensus 76 ~Lk~GD~V~ll~~~~ 90 (100)
T PF10844_consen 76 GLKVGDKVLLLRVQG 90 (100)
T ss_pred CCcCCCEEEEEEecC
Confidence 569999999999654
No 102
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=35.44 E-value=25 Score=30.24 Aligned_cols=27 Identities=33% Similarity=0.914 Sum_probs=23.4
Q ss_pred CCceEEeeCCCCCCCCceEeCCccCCC
Q 031164 137 RVAVYCKCEMPYNPDDLMVQCEGCSDW 163 (164)
Q Consensus 137 ~~~~~C~c~~~~~pD~~~~~C~~C~~~ 163 (164)
.....|.|..-..+|..++||+.|..|
T Consensus 84 ~~~~~c~c~~~~~~~g~~i~c~~c~~W 110 (508)
T KOG1844|consen 84 REISRCDCGLEDDMEGLMIQCDWCGRW 110 (508)
T ss_pred CcccccccccccCCCceeeCCcccCcc
Confidence 466789998877778899999999999
No 103
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=35.39 E-value=95 Score=19.48 Aligned_cols=25 Identities=32% Similarity=0.594 Sum_probs=19.5
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeec
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESD 51 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~ 51 (164)
.+++||.|++.|.+ . .++|.+|...
T Consensus 26 ~i~~Gd~v~i~P~~--~---~~~V~si~~~ 50 (83)
T cd03698 26 SIQKGDTLLVMPSK--E---SVEVKSIYVD 50 (83)
T ss_pred EEeCCCEEEEeCCC--c---EEEEEEEEEC
Confidence 79999999999876 2 4677777643
No 104
>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=35.19 E-value=67 Score=24.33 Aligned_cols=24 Identities=17% Similarity=0.340 Sum_probs=14.0
Q ss_pred eEEEcCcCcEEccCCEEEEecCCC
Q 031164 13 SYTVKSISKTIKPGDCVLMRPSEP 36 (164)
Q Consensus 13 ~~~i~g~~~~~~vGD~V~v~~~~~ 36 (164)
.+.+.+.+..|++||.+.|.+.++
T Consensus 32 eldl~~~~l~Y~pGD~l~V~P~N~ 55 (219)
T PF00667_consen 32 ELDLSDSGLSYQPGDHLGVYPPND 55 (219)
T ss_dssp EEE-TTSTG---TT-EEEEE-SSE
T ss_pred EEEeCCCCCcccCCCEEEEEccCC
Confidence 444566678999999999999984
No 105
>COG1482 ManA Phosphomannose isomerase [Carbohydrate transport and metabolism]
Probab=35.18 E-value=50 Score=26.97 Aligned_cols=33 Identities=12% Similarity=0.379 Sum_probs=26.8
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecCCCC
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGA 55 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~ 55 (164)
.++.||+++|.++.. .-+-=|.|.++-++.+.-
T Consensus 161 ~lkpGe~~fl~Agt~-HA~~~G~~lEvmqnSDnt 193 (312)
T COG1482 161 KLKPGEAFFLPAGTP-HAYLKGLVLEVMQNSDNT 193 (312)
T ss_pred ecCCCCEEEecCCCc-eeeccceEEEEEecCccE
Confidence 789999999999985 455667899998876654
No 106
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=35.04 E-value=50 Score=22.61 Aligned_cols=22 Identities=23% Similarity=0.516 Sum_probs=17.5
Q ss_pred EEEcCcCcEEccCCEEEEecCC
Q 031164 14 YTVKSISKTIKPGDCVLMRPSE 35 (164)
Q Consensus 14 ~~i~g~~~~~~vGD~V~v~~~~ 35 (164)
++++|...+++.||++++.++.
T Consensus 77 ~~~~g~~~~l~~Gd~i~ip~g~ 98 (131)
T COG1917 77 VQLEGEKKELKAGDVIIIPPGV 98 (131)
T ss_pred EEecCCceEecCCCEEEECCCC
Confidence 3455666789999999999975
No 107
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=34.40 E-value=30 Score=23.21 Aligned_cols=15 Identities=40% Similarity=0.833 Sum_probs=12.6
Q ss_pred EEEEEEEeecccccC
Q 031164 57 VKVHVRWYYRPEESI 71 (164)
Q Consensus 57 ~~v~v~Wfyrp~e~~ 71 (164)
..|+|.|||.++|..
T Consensus 77 ~~V~v~Wyyd~dD~~ 91 (99)
T PF09345_consen 77 GKVTVNWYYDEDDED 91 (99)
T ss_pred CcEEEEEEECCCCch
Confidence 679999999988653
No 108
>PLN00036 40S ribosomal protein S4; Provisional
Probab=34.35 E-value=1.7e+02 Score=23.33 Aligned_cols=14 Identities=21% Similarity=0.283 Sum_probs=11.3
Q ss_pred EEccCCEEEEecCC
Q 031164 22 TIKPGDCVLMRPSE 35 (164)
Q Consensus 22 ~~~vGD~V~v~~~~ 35 (164)
.|++||+|.|.-++
T Consensus 153 ~~k~~Dtv~i~l~~ 166 (261)
T PLN00036 153 LIKANDTIKIDLET 166 (261)
T ss_pred ccccCCEEEEeCCC
Confidence 68899999998544
No 109
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=34.35 E-value=39 Score=21.03 Aligned_cols=19 Identities=21% Similarity=0.288 Sum_probs=13.8
Q ss_pred cCcCcEEccCCEEEEecCC
Q 031164 17 KSISKTIKPGDCVLMRPSE 35 (164)
Q Consensus 17 ~g~~~~~~vGD~V~v~~~~ 35 (164)
+|...+++.||.+++..+.
T Consensus 42 ~G~~~~~~aGD~~~~p~G~ 60 (74)
T PF05899_consen 42 DGETVTFKAGDAFFLPKGW 60 (74)
T ss_dssp TTEEEEEETTEEEEE-TTE
T ss_pred CCCEEEEcCCcEEEECCCC
Confidence 3444678999999998775
No 110
>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=34.18 E-value=56 Score=19.44 Aligned_cols=25 Identities=28% Similarity=0.316 Sum_probs=15.9
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEee
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIES 50 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~ 50 (164)
...+||.|.+...+. +. +.|..+.+
T Consensus 37 ~~~VGD~V~~~~~~~-~~---~~I~~vl~ 61 (68)
T cd04466 37 PPAVGDRVEFEPEDD-GE---GVIEEILP 61 (68)
T ss_pred CCCCCcEEEEEECCC-Cc---EEEEEEec
Confidence 357999999975442 22 45666654
No 111
>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=34.09 E-value=1.1e+02 Score=22.09 Aligned_cols=28 Identities=25% Similarity=0.450 Sum_probs=19.6
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEe
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIE 49 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~ 49 (164)
.++.||.|.+.++......+|.||..+-
T Consensus 51 ~~~rGDiVvf~~~~~~~~~~iKRVig~p 78 (163)
T TIGR02227 51 DPKRGDIVVFKDPDDNKNIYVKRVIGLP 78 (163)
T ss_pred CCCCCcEEEEecCCCCCceeEEEEEecC
Confidence 5677888888765434567788887764
No 112
>PF08921 DUF1904: Domain of unknown function (DUF1904); InterPro: IPR015017 This entry represents a family of hypothetical bacterial proteins. ; PDB: 1U9D_B.
Probab=33.92 E-value=17 Score=24.81 Aligned_cols=16 Identities=31% Similarity=0.459 Sum_probs=10.8
Q ss_pred EEEEEEEeecccccCC
Q 031164 57 VKVHVRWYYRPEESIG 72 (164)
Q Consensus 57 ~~v~v~Wfyrp~e~~~ 72 (164)
++|.|.||-|+.|+..
T Consensus 56 pfVEV~WF~R~qe~qd 71 (108)
T PF08921_consen 56 PFVEVLWFDRGQEVQD 71 (108)
T ss_dssp -EEEEEES---HHHHH
T ss_pred eeEEEEEecCCHHHHH
Confidence 6899999999999874
No 113
>COG4127 Uncharacterized conserved protein [Function unknown]
Probab=33.68 E-value=30 Score=27.80 Aligned_cols=42 Identities=19% Similarity=0.328 Sum_probs=30.0
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecCC----CCeEEEEEEEe
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDAR----GANVKVHVRWY 64 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~----g~~~~v~v~Wf 64 (164)
+++.||.|.+.+... ..++||+|.+=++-.. |-.....|.|+
T Consensus 72 eI~KGDlvi~y~k~~-r~y~IGkVtsdYEy~p~~~~~i~hTrkVkWL 117 (318)
T COG4127 72 EIQKGDLVITYSKSN-RTYLIGKVTSDYEYHPEWLEGIGHTRKVKWL 117 (318)
T ss_pred HhccCcEEEeecccC-ceEEEEEecCCcccCccccccCchhhHhHHh
Confidence 589999999998875 7899999987665311 11134567776
No 114
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=33.62 E-value=77 Score=21.30 Aligned_cols=27 Identities=26% Similarity=0.204 Sum_probs=17.8
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEeEEe
Q 031164 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIE 49 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~ 49 (164)
..++.||.|+|...+- ..--|.|...+
T Consensus 58 IwI~~GD~VlVe~~~~--~~~kg~Iv~r~ 84 (100)
T PRK04012 58 MWIREGDVVIVAPWDF--QDEKADIIWRY 84 (100)
T ss_pred EEecCCCEEEEEeccc--CCCEEEEEEEc
Confidence 3578899999987553 24456665554
No 115
>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=33.47 E-value=79 Score=23.29 Aligned_cols=42 Identities=21% Similarity=0.212 Sum_probs=29.6
Q ss_pred EEEcCcCcEEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEE
Q 031164 14 YTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKV 59 (164)
Q Consensus 14 ~~i~g~~~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v 59 (164)
+++......++.||-|...-.+ ..+.||.|.+-... +|. +++
T Consensus 98 L~~~~~~~~~q~GDIVtw~l~~--~~~HIgIVSd~r~~-~G~-p~v 139 (164)
T PF06940_consen 98 LTTDINPEDWQPGDIVTWRLPG--GLPHIGIVSDRRSK-DGV-PLV 139 (164)
T ss_pred ccCCCChhhcCCCCEEEEeCCC--CCCeEEEEeCCcCC-CCC-EEE
Confidence 3344334589999999998666 48999999877653 565 443
No 116
>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=33.41 E-value=1.2e+02 Score=20.96 Aligned_cols=38 Identities=16% Similarity=0.181 Sum_probs=27.7
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEE
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRW 63 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~W 63 (164)
.++.||-|.|.++. +.--.|.|.++... ++. +.|.+.-
T Consensus 41 ~IkkGD~V~Vi~Gk--~KGk~GkV~~V~~~-~~~-V~Vegvn 78 (114)
T TIGR01080 41 PVRKGDKVRIMRGD--FKGHEGKVSKVDLK-RYR-IYVEGVT 78 (114)
T ss_pred eeecCCEEEEecCC--CCCCEEEEEEEEcC-CCE-EEEcCeE
Confidence 68999999999998 46778999999743 233 4444433
No 117
>PRK11171 hypothetical protein; Provisional
Probab=33.34 E-value=1.5e+02 Score=23.33 Aligned_cols=22 Identities=14% Similarity=0.374 Sum_probs=15.7
Q ss_pred EEcCcCcEEccCCEEEEecCCC
Q 031164 15 TVKSISKTIKPGDCVLMRPSEP 36 (164)
Q Consensus 15 ~i~g~~~~~~vGD~V~v~~~~~ 36 (164)
.++|...++..||++++.+..+
T Consensus 97 ~~~g~~~~L~~GDsi~~p~~~~ 118 (266)
T PRK11171 97 TLEGKTHALSEGGYAYLPPGSD 118 (266)
T ss_pred EECCEEEEECCCCEEEECCCCC
Confidence 4455545678899999988763
No 118
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=32.90 E-value=2.2e+02 Score=22.33 Aligned_cols=48 Identities=25% Similarity=0.169 Sum_probs=32.3
Q ss_pred cEEccCCEEEEecCCC--CCCCeEEEEeEEeecCCCCeEEEEEEEeeccc
Q 031164 21 KTIKPGDCVLMRPSEP--SKPSYVAKIERIESDARGANVKVHVRWYYRPE 68 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~--~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~ 68 (164)
..+++||-|+-..-+. +....||+|.++..+.++....+.+.=+..+.
T Consensus 213 ~~i~~GD~VvTSGl~g~fP~Gi~VG~V~~v~~~~~~~~~~~~v~p~~d~~ 262 (276)
T PRK13922 213 ADIKVGDLVVTSGLGGIFPAGLPVGKVTSVERDDYGLFKTVYVKPAADLD 262 (276)
T ss_pred CCCCCCCEEEECCCCCcCCCCCEEEEEEEEEeCCCCCeeEEEEEECcccC
Confidence 3689999987776542 35678999999977765533555555444433
No 119
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=32.87 E-value=19 Score=24.67 Aligned_cols=27 Identities=19% Similarity=0.411 Sum_probs=19.7
Q ss_pred CCceEEe-eCCCCCCCCceEeCCccCCC
Q 031164 137 RVAVYCK-CEMPYNPDDLMVQCEGCSDW 163 (164)
Q Consensus 137 ~~~~~C~-c~~~~~pD~~~~~C~~C~~~ 163 (164)
...-.|. |.....++.....|+.|+..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQHDAQCPHCHGE 95 (113)
T ss_pred CcEEEcccCCCEEecCCcCccCcCCCCC
Confidence 3445774 88888887666679999853
No 120
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=32.62 E-value=1.5e+02 Score=20.79 Aligned_cols=44 Identities=20% Similarity=0.163 Sum_probs=32.0
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeecccccC
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESI 71 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~~ 71 (164)
.++.||.|.|..+. -.-+.|+|.++...+ ..+.+...-+.-.|+
T Consensus 86 ~~~~Gd~V~I~~GP--f~G~~g~v~~~d~~k----~~v~v~l~~~~~~~~ 129 (145)
T TIGR00405 86 SIKKGDIVEIISGP--FKGERAKVIRVDESK----EEVTLELIEAAVPIP 129 (145)
T ss_pred ccCCCCEEEEeecC--CCCCeEEEEEEcCCC----CEEEEEEEEcCccce
Confidence 58999999999877 578899999886422 456666666555533
No 121
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=32.43 E-value=1.6e+02 Score=23.63 Aligned_cols=14 Identities=21% Similarity=0.354 Sum_probs=11.0
Q ss_pred EEccCCEEEEecCC
Q 031164 22 TIKPGDCVLMRPSE 35 (164)
Q Consensus 22 ~~~vGD~V~v~~~~ 35 (164)
.|++||.|.|.-++
T Consensus 150 ~~k~~Dtv~i~l~~ 163 (273)
T PTZ00223 150 RTSRGDTLVYNVKE 163 (273)
T ss_pred cccCCCEEEEECCC
Confidence 67899999998554
No 122
>PRK02935 hypothetical protein; Provisional
Probab=31.88 E-value=26 Score=23.86 Aligned_cols=10 Identities=30% Similarity=0.863 Sum_probs=8.3
Q ss_pred ceEeCCccCC
Q 031164 153 LMVQCEGCSD 162 (164)
Q Consensus 153 ~~~~C~~C~~ 162 (164)
..++|++|+|
T Consensus 69 vqV~CP~C~K 78 (110)
T PRK02935 69 VQVICPSCEK 78 (110)
T ss_pred eeeECCCCCc
Confidence 5689999987
No 123
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 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 probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=31.79 E-value=15 Score=21.80 Aligned_cols=12 Identities=50% Similarity=1.431 Sum_probs=8.9
Q ss_pred CceEeCCccCCC
Q 031164 152 DLMVQCEGCSDW 163 (164)
Q Consensus 152 ~~~~~C~~C~~~ 163 (164)
..+++|++|.-|
T Consensus 38 ~~iv~C~sCSL~ 49 (55)
T PF05207_consen 38 EVIVQCDSCSLW 49 (55)
T ss_dssp --EEEETTTTEE
T ss_pred CEEEECCCCccE
Confidence 478999999866
No 124
>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.
Probab=31.58 E-value=1.2e+02 Score=19.51 Aligned_cols=25 Identities=24% Similarity=0.515 Sum_probs=19.9
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeec
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESD 51 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~ 51 (164)
.+++||.|++.|.. ..+.|.+|+..
T Consensus 30 ~i~~gd~v~i~P~~-----~~~~V~sI~~~ 54 (91)
T cd03693 30 VLKPGMVVTFAPAG-----VTGEVKSVEMH 54 (91)
T ss_pred eeecCCEEEECCCC-----cEEEEEEEEEC
Confidence 78999999999875 34778777654
No 125
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=31.50 E-value=94 Score=22.38 Aligned_cols=37 Identities=8% Similarity=0.123 Sum_probs=27.2
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEE
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVR 62 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~ 62 (164)
.|+.||-|.|.++.+ .--.|+|.++.... +. +.|.+.
T Consensus 46 ~IkkGD~V~Vi~Gk~--KGk~GkV~~V~~k~-~~-ViVEgv 82 (143)
T PTZ00194 46 PVRKDDEVMVVRGHH--KGREGKVTAVYRKK-WV-IHIEKI 82 (143)
T ss_pred eeecCCEEEEecCCC--CCCceEEEEEEcCC-CE-EEEeCe
Confidence 789999999999984 55669999997643 33 444443
No 126
>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=31.38 E-value=63 Score=24.83 Aligned_cols=28 Identities=21% Similarity=0.475 Sum_probs=15.7
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEee
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIES 50 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~ 50 (164)
.+++||+|++...+. ......+|.++..
T Consensus 105 ~V~~Gd~v~~~~~~~-~~~~~~~V~~v~~ 132 (217)
T PF01079_consen 105 DVRVGDCVLVSDEGG-GKLRPSRVVRVST 132 (217)
T ss_dssp G--TT-EEEEE-TTT---EEEEEEEEEEE
T ss_pred hCCCCCEEEEEEcCC-CcEEEEEEEEEEE
Confidence 579999999944442 5667777777754
No 127
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A 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.
Probab=31.24 E-value=1.1e+02 Score=19.63 Aligned_cols=14 Identities=57% Similarity=0.764 Sum_probs=11.7
Q ss_pred EEccCCEEEEecCC
Q 031164 22 TIKPGDCVLMRPSE 35 (164)
Q Consensus 22 ~~~vGD~V~v~~~~ 35 (164)
-++.||+|+|.+-+
T Consensus 38 WIkrGd~VlV~p~~ 51 (78)
T cd05792 38 WIKRGDFVLVEPIE 51 (78)
T ss_pred EEEeCCEEEEEecc
Confidence 48999999998755
No 128
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=30.80 E-value=1.4e+02 Score=22.21 Aligned_cols=45 Identities=29% Similarity=0.526 Sum_probs=34.7
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeecccc
Q 031164 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEE 69 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e 69 (164)
..+.+||.|-|.++. -..+.|+|+++..++ +. ..+.+.-|-|+--
T Consensus 122 ~~~e~Gd~VrI~~Gp--Fa~f~g~V~evd~ek-~~-~~v~v~ifgr~tP 166 (178)
T COG0250 122 VDFEPGDVVRIIDGP--FAGFKAKVEEVDEEK-GK-LKVEVSIFGRPTP 166 (178)
T ss_pred ccCCCCCEEEEeccC--CCCccEEEEEEcCcC-cE-EEEEEEEeCCceE
Confidence 478999999999887 477999999998764 33 6666766666543
No 129
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=30.69 E-value=35 Score=20.00 Aligned_cols=13 Identities=31% Similarity=0.624 Sum_probs=10.1
Q ss_pred CceEeCCccCCCC
Q 031164 152 DLMVQCEGCSDWS 164 (164)
Q Consensus 152 ~~~~~C~~C~~~~ 164 (164)
...++|+.|+..+
T Consensus 44 ~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 44 DEIVFCPNCGRIL 56 (56)
T ss_pred CCeEECcCCCccC
Confidence 3589999998753
No 130
>COG3450 Predicted enzyme of the cupin superfamily [General function prediction only]
Probab=30.69 E-value=45 Score=23.13 Aligned_cols=18 Identities=11% Similarity=0.246 Sum_probs=14.1
Q ss_pred CcCcEEccCCEEEEecCC
Q 031164 18 SISKTIKPGDCVLMRPSE 35 (164)
Q Consensus 18 g~~~~~~vGD~V~v~~~~ 35 (164)
|+...|+.||.+++.++-
T Consensus 81 Ge~v~~~aGD~~~~~~G~ 98 (116)
T COG3450 81 GEPVEVRAGDSFVFPAGF 98 (116)
T ss_pred CeEEEEcCCCEEEECCCC
Confidence 444578999999998876
No 131
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=30.52 E-value=17 Score=16.47 Aligned_cols=9 Identities=33% Similarity=0.574 Sum_probs=4.9
Q ss_pred eCCccCCCC
Q 031164 156 QCEGCSDWS 164 (164)
Q Consensus 156 ~C~~C~~~~ 164 (164)
+|+.|++.|
T Consensus 2 ~C~~C~~~~ 10 (24)
T PF13894_consen 2 QCPICGKSF 10 (24)
T ss_dssp E-SSTS-EE
T ss_pred CCcCCCCcC
Confidence 688887653
No 132
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=30.31 E-value=82 Score=21.41 Aligned_cols=28 Identities=18% Similarity=0.278 Sum_probs=22.5
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeec
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESD 51 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~ 51 (164)
.++.||.|+|.++. +.---|+|.++...
T Consensus 4 ~IrkGD~V~Vi~Gk--dKGk~GkVl~v~~k 31 (104)
T COG0198 4 KVKKGDTVKVIAGK--DKGKEGKVLKVLPK 31 (104)
T ss_pred ceecCCEEEEEecC--CCCcceEEEEEecC
Confidence 57899999999998 46667888777654
No 133
>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=30.19 E-value=86 Score=19.50 Aligned_cols=25 Identities=16% Similarity=0.308 Sum_probs=11.3
Q ss_pred EccCCEEEEecCCCCCCCeEEEEeE
Q 031164 23 IKPGDCVLMRPSEPSKPSYVAKIER 47 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~i~~I~~ 47 (164)
++.||.|.+...+.....++.||..
T Consensus 32 ~~~GDiv~~~~~~~~~~~~vkRv~~ 56 (85)
T cd06530 32 PKRGDVVVFKSPGDPGKPIIKRVIG 56 (85)
T ss_pred CCCCCEEEEeCCCCCCCEEEEEEEE
Confidence 4445555555443222344555544
No 134
>TIGR03214 ura-cupin putative allantoin catabolism protein. This model represents a protein containing a tandem arrangement of cupin domains (N-terminal part of pfam07883 and C-terminal more distantly related to pfam00190). This protein is found in the vicinity of genes involved in the catabolism of allantoin, a breakdown product of urate and sometimes of urate iteslf. The distribution of pathway components in the genomes in which this family is observed suggests that the function is linked to the allantoate catabolism to glyoxylate pathway (GenProp0686) since it is sometimes found in genomes lacking any elements of the xanthine-to-allantoin pathways (e.g. in Enterococcus faecalis).
Probab=29.85 E-value=2.4e+02 Score=22.14 Aligned_cols=21 Identities=14% Similarity=0.397 Sum_probs=15.3
Q ss_pred EEcCcCcEEccCCEEEEecCC
Q 031164 15 TVKSISKTIKPGDCVLMRPSE 35 (164)
Q Consensus 15 ~i~g~~~~~~vGD~V~v~~~~ 35 (164)
+++|...+++.||++++.++.
T Consensus 94 ~~~g~~~~L~~Gd~~y~pa~~ 114 (260)
T TIGR03214 94 TAEGETHELREGGYAYLPPGS 114 (260)
T ss_pred EECCEEEEECCCCEEEECCCC
Confidence 445554577889999998876
No 135
>CHL00010 infA translation initiation factor 1
Probab=29.68 E-value=1.3e+02 Score=19.03 Aligned_cols=27 Identities=26% Similarity=0.142 Sum_probs=14.4
Q ss_pred EccCCEEEEecCCCCCCCeEEEEeEEeec
Q 031164 23 IKPGDCVLMRPSEPSKPSYVAKIERIESD 51 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~i~~I~~i~~~ 51 (164)
+.+||.|.|.+... ...-|.|+.=+.+
T Consensus 47 ~~vGD~V~ve~~~~--~~~~g~Ii~r~~~ 73 (78)
T CHL00010 47 ILPGDRVKVELSPY--DLTKGRIIYRLRN 73 (78)
T ss_pred cCCCCEEEEEEccc--CCCeEEEEEEecC
Confidence 56788888874331 1223566544444
No 136
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=29.34 E-value=31 Score=23.91 Aligned_cols=23 Identities=22% Similarity=0.715 Sum_probs=17.4
Q ss_pred eEEe-eCCCCCCCCceEeCCccCC
Q 031164 140 VYCK-CEMPYNPDDLMVQCEGCSD 162 (164)
Q Consensus 140 ~~C~-c~~~~~pD~~~~~C~~C~~ 162 (164)
--|. |.++..|+.....|+.|+.
T Consensus 71 ~~C~~C~~~~~~e~~~~~CP~C~s 94 (115)
T COG0375 71 CWCLDCGQEVELEELDYRCPKCGS 94 (115)
T ss_pred EEeccCCCeecchhheeECCCCCC
Confidence 4554 6788888887677999984
No 137
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=29.24 E-value=23 Score=17.56 Aligned_cols=10 Identities=40% Similarity=0.690 Sum_probs=7.4
Q ss_pred eEeCCccCCC
Q 031164 154 MVQCEGCSDW 163 (164)
Q Consensus 154 ~~~C~~C~~~ 163 (164)
++.|+.|.+-
T Consensus 1 ~v~CPiC~~~ 10 (26)
T smart00734 1 LVQCPVCFRE 10 (26)
T ss_pred CCcCCCCcCc
Confidence 4689999763
No 138
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=28.92 E-value=24 Score=25.00 Aligned_cols=23 Identities=39% Similarity=0.668 Sum_probs=18.4
Q ss_pred ceEE-eeCCCCCCCCceEeCCccC
Q 031164 139 AVYC-KCEMPYNPDDLMVQCEGCS 161 (164)
Q Consensus 139 ~~~C-~c~~~~~pD~~~~~C~~C~ 161 (164)
..+| .|..|.=--..-++|+.|+
T Consensus 28 ~~hCp~Cg~PLF~KdG~v~CPvC~ 51 (131)
T COG1645 28 AKHCPKCGTPLFRKDGEVFCPVCG 51 (131)
T ss_pred HhhCcccCCcceeeCCeEECCCCC
Confidence 4578 5888875566899999998
No 139
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=28.81 E-value=24 Score=17.21 Aligned_cols=9 Identities=22% Similarity=0.992 Sum_probs=6.8
Q ss_pred eCCccCCCC
Q 031164 156 QCEGCSDWS 164 (164)
Q Consensus 156 ~C~~C~~~~ 164 (164)
.|+.|+++|
T Consensus 3 ~C~~C~k~f 11 (27)
T PF12171_consen 3 YCDACDKYF 11 (27)
T ss_dssp BBTTTTBBB
T ss_pred CcccCCCCc
Confidence 588888765
No 140
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=28.22 E-value=1.1e+02 Score=20.58 Aligned_cols=28 Identities=25% Similarity=0.226 Sum_probs=16.3
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEeEEe
Q 031164 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIE 49 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~ 49 (164)
.-++.||+|+|.+-+. +..--|.|...+
T Consensus 56 iwI~~GD~VlVsp~d~-~~~~kg~Iv~r~ 83 (99)
T TIGR00523 56 IWIREGDVVIVKPWEF-QGDDKCDIVWRY 83 (99)
T ss_pred EEecCCCEEEEEEccC-CCCccEEEEEEc
Confidence 3578899999965442 212235555544
No 141
>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=28.16 E-value=1.6e+02 Score=23.44 Aligned_cols=43 Identities=19% Similarity=0.262 Sum_probs=34.3
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeeccc
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPE 68 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~ 68 (164)
.+.+||.|.|..+. -.-+.|.|.++..+ .+. ..|.+.+|-|.-
T Consensus 205 ~f~vGd~VrI~dGP--F~GfeG~I~eid~~-k~R-v~VlV~IfGR~T 247 (258)
T TIGR01956 205 KFRVGNFVKIVDGP--FKGIVGKIKKIDQE-KKK-AIVEVEILGKSV 247 (258)
T ss_pred CCCCCCEEEEEecC--CCCcEEEEEEEeCC-CCE-EEEEEEecCCcE
Confidence 47899999999887 57889999999753 234 788888887764
No 142
>PRK12496 hypothetical protein; Provisional
Probab=28.00 E-value=34 Score=25.06 Aligned_cols=26 Identities=31% Similarity=0.561 Sum_probs=19.6
Q ss_pred CCceEEe-eCCCCCCCCceEeCCccCC
Q 031164 137 RVAVYCK-CEMPYNPDDLMVQCEGCSD 162 (164)
Q Consensus 137 ~~~~~C~-c~~~~~pD~~~~~C~~C~~ 162 (164)
.|...|. |.+.++-+...-.|+.|+.
T Consensus 125 ~w~~~C~gC~~~~~~~~~~~~C~~CG~ 151 (164)
T PRK12496 125 KWRKVCKGCKKKYPEDYPDDVCEICGS 151 (164)
T ss_pred eeeEECCCCCccccCCCCCCcCCCCCC
Confidence 6778898 9988864444458999985
No 143
>TIGR00219 mreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.
Probab=27.83 E-value=2.8e+02 Score=22.12 Aligned_cols=48 Identities=15% Similarity=0.142 Sum_probs=32.6
Q ss_pred cEEccCCEEEEecCCC--CCCCeEEEEeEEeecCCCCeEEEEEEEeeccc
Q 031164 21 KTIKPGDCVLMRPSEP--SKPSYVAKIERIESDARGANVKVHVRWYYRPE 68 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~--~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~ 68 (164)
..+++||-|+-..-+. +....||+|.++..+.++....+.+.=+....
T Consensus 214 ~~v~~GD~VvTSGlgg~fP~Gl~VG~V~~v~~~~~~~~~~v~v~P~ad~~ 263 (283)
T TIGR00219 214 KDIKKGDLIVTSGLGGRFPEGYPIGVVTSVHIDSYNSLLVIEVKPAAVLD 263 (283)
T ss_pred CCCCCCCEEEECCCCCcCCCCCEEEEEEEEEeCCCCceEEEEEEECCCcc
Confidence 3789999887765442 35678999999998776654555555444433
No 144
>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=27.35 E-value=1e+02 Score=20.21 Aligned_cols=23 Identities=22% Similarity=0.030 Sum_probs=19.6
Q ss_pred ccCCEEEEecCCCCCCCeEEEEeEE
Q 031164 24 KPGDCVLMRPSEPSKPSYVAKIERI 48 (164)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~i~~I~~i 48 (164)
.+||.|...-.. -+.|-|+|.+-
T Consensus 2 ~~GdlVWaK~~g--~pwWPa~V~~~ 24 (95)
T cd05838 2 LYGDIVWAKLGN--FRWWPAIICDP 24 (95)
T ss_pred CcCCEEEEECCC--CCCCCeEEcCh
Confidence 579999999887 58999999864
No 145
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=27.35 E-value=75 Score=23.27 Aligned_cols=22 Identities=14% Similarity=0.273 Sum_probs=15.7
Q ss_pred EEcCcCcEEccCCEEEEecCCC
Q 031164 15 TVKSISKTIKPGDCVLMRPSEP 36 (164)
Q Consensus 15 ~i~g~~~~~~vGD~V~v~~~~~ 36 (164)
.++|....++.||++++.++.+
T Consensus 142 ~~~~~~~~l~~Gd~~~~~~~~~ 163 (185)
T PRK09943 142 TINGQDYHLVAGQSYAINTGIP 163 (185)
T ss_pred EECCEEEEecCCCEEEEcCCCC
Confidence 4555556678888888888763
No 146
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=27.16 E-value=67 Score=25.09 Aligned_cols=22 Identities=14% Similarity=0.218 Sum_probs=18.0
Q ss_pred EEEcCcCcEEccCCEEEEecCC
Q 031164 14 YTVKSISKTIKPGDCVLMRPSE 35 (164)
Q Consensus 14 ~~i~g~~~~~~vGD~V~v~~~~ 35 (164)
++++|...+++.||+++|.++.
T Consensus 188 l~IdG~t~~l~pGDvlfIPkGs 209 (233)
T PRK15457 188 VRHEGETMIAKAGDVMFIPKGS 209 (233)
T ss_pred EEECCEEEEeCCCcEEEECCCC
Confidence 4567776778999999999887
No 147
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=27.07 E-value=1.7e+02 Score=20.95 Aligned_cols=43 Identities=21% Similarity=0.192 Sum_probs=32.9
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeeccccc
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEES 70 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~ 70 (164)
.+++||.|.|..+. -..+.|+|.++...+ ..+.+..+-+.-.|
T Consensus 94 ~~~~G~~V~I~~Gp--f~g~~g~V~~vd~~k----~~v~v~ll~~~~~~ 136 (153)
T PRK08559 94 GIKEGDIVELIAGP--FKGEKARVVRVDESK----EEVTVELLEAAVPI 136 (153)
T ss_pred CCCCCCEEEEeccC--CCCceEEEEEEcCCC----CEEEEEEECCccee
Confidence 58999999999887 477899999997642 34777777766543
No 148
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=26.98 E-value=42 Score=21.39 Aligned_cols=14 Identities=36% Similarity=0.465 Sum_probs=11.6
Q ss_pred EEccCCEEEEecCC
Q 031164 22 TIKPGDCVLMRPSE 35 (164)
Q Consensus 22 ~~~vGD~V~v~~~~ 35 (164)
..++||+|+|..+-
T Consensus 35 ~~~vGD~VLVH~G~ 48 (76)
T TIGR00074 35 EVKVGDYVLVHVGF 48 (76)
T ss_pred CCCCCCEEEEecCh
Confidence 46999999999763
No 149
>PRK03187 tgl transglutaminase; Provisional
Probab=26.60 E-value=52 Score=26.22 Aligned_cols=19 Identities=32% Similarity=0.632 Sum_probs=15.4
Q ss_pred EEcCcCcEEccCCEEEEecCC
Q 031164 15 TVKSISKTIKPGDCVLMRPSE 35 (164)
Q Consensus 15 ~i~g~~~~~~vGD~V~v~~~~ 35 (164)
+..|. .+-+||+||+++++
T Consensus 160 t~~g~--~~~PGD~vYFkNPd 178 (272)
T PRK03187 160 TKTGG--DFLPGDCVYFKNPD 178 (272)
T ss_pred EecCC--CCCCCcEEEecCCC
Confidence 34555 89999999999876
No 150
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=26.49 E-value=35 Score=18.27 Aligned_cols=8 Identities=25% Similarity=1.078 Sum_probs=4.8
Q ss_pred EeCCccCC
Q 031164 155 VQCEGCSD 162 (164)
Q Consensus 155 ~~C~~C~~ 162 (164)
|.|+.|+.
T Consensus 3 i~Cp~C~~ 10 (36)
T PF13717_consen 3 ITCPNCQA 10 (36)
T ss_pred EECCCCCC
Confidence 55666654
No 151
>PRK10409 hydrogenase assembly chaperone; Provisional
Probab=26.17 E-value=45 Score=22.01 Aligned_cols=14 Identities=21% Similarity=0.218 Sum_probs=11.7
Q ss_pred EEccCCEEEEecCC
Q 031164 22 TIKPGDCVLMRPSE 35 (164)
Q Consensus 22 ~~~vGD~V~v~~~~ 35 (164)
..++||+|+|..+-
T Consensus 41 ~~~vGDyVLVHaGf 54 (90)
T PRK10409 41 QPRVGQWVLVHVGF 54 (90)
T ss_pred ccCCCCEEEEecCh
Confidence 47999999999764
No 152
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=26.06 E-value=46 Score=21.55 Aligned_cols=14 Identities=21% Similarity=0.078 Sum_probs=11.3
Q ss_pred EEccCCEEEEecCC
Q 031164 22 TIKPGDCVLMRPSE 35 (164)
Q Consensus 22 ~~~vGD~V~v~~~~ 35 (164)
..++||+|+|..+-
T Consensus 42 ~~~vGDyVLVHaGf 55 (82)
T PRK10413 42 ADLLGQWVLVHVGF 55 (82)
T ss_pred ccccCCEEEEecch
Confidence 45789999999764
No 153
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=26.04 E-value=74 Score=20.58 Aligned_cols=13 Identities=38% Similarity=0.601 Sum_probs=11.2
Q ss_pred EEccCCEEEEecC
Q 031164 22 TIKPGDCVLMRPS 34 (164)
Q Consensus 22 ~~~vGD~V~v~~~ 34 (164)
..++||+|+|..+
T Consensus 38 ~v~~GdyVLVHvG 50 (82)
T COG0298 38 EVKVGDYVLVHVG 50 (82)
T ss_pred ccccCCEEEEEee
Confidence 6799999999865
No 154
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=25.93 E-value=8.6 Score=26.33 Aligned_cols=27 Identities=22% Similarity=0.685 Sum_probs=18.6
Q ss_pred CCceEE-eeCCCCCCCCceEeCCccCCC
Q 031164 137 RVAVYC-KCEMPYNPDDLMVQCEGCSDW 163 (164)
Q Consensus 137 ~~~~~C-~c~~~~~pD~~~~~C~~C~~~ 163 (164)
.....| .|...+.|+.....|+.|+..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PF01155_consen 68 PARARCRDCGHEFEPDEFDFSCPRCGSP 95 (113)
T ss_dssp --EEEETTTS-EEECHHCCHH-SSSSSS
T ss_pred CCcEECCCCCCEEecCCCCCCCcCCcCC
Confidence 344578 588999888888889999874
No 155
>TIGR00218 manA mannose-6-phosphate isomerase, class I. The names phosphomannose isomerase and mannose-6-phosphate isomerase are synonomous. This family contains two rather deeply branched groups. One group contains an experimentally determined phosphomannose isomerase of Streptococcus mutans as well as three uncharacterized paralogous proteins of Bacillus subtilis, all at more than 50 % identity to each other, plus a more distant homolog from Archaeoglobus fulgidus. The other group contains members from E. coli, budding yeast, Borrelia burgdorferi, etc.
Probab=25.88 E-value=88 Score=25.06 Aligned_cols=31 Identities=16% Similarity=0.311 Sum_probs=24.4
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecCC
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDAR 53 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~ 53 (164)
.++.||+++|.++..+. +-=+.|.+|-+..+
T Consensus 154 ~v~~Gd~i~ipaGt~HA-~~g~~~~Eiq~~SD 184 (302)
T TIGR00218 154 KLKPGDFFYVPSGTPHA-YKGGLVLEVMQNSD 184 (302)
T ss_pred ccCCCCEEEeCCCCccc-ccCceEEEEEcCCC
Confidence 68999999999998755 55557888887654
No 156
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=25.26 E-value=3.1e+02 Score=21.82 Aligned_cols=14 Identities=21% Similarity=0.377 Sum_probs=11.4
Q ss_pred EEccCCEEEEecCC
Q 031164 22 TIKPGDCVLMRPSE 35 (164)
Q Consensus 22 ~~~vGD~V~v~~~~ 35 (164)
.|++||+|.+.-++
T Consensus 153 ~ik~~Dtv~i~l~~ 166 (262)
T PTZ00118 153 DVKVGDSLRLDLET 166 (262)
T ss_pred cccCCCEEEEECCC
Confidence 68899999998544
No 157
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=24.97 E-value=41 Score=23.21 Aligned_cols=11 Identities=27% Similarity=0.818 Sum_probs=8.9
Q ss_pred ceEeCCccCCC
Q 031164 153 LMVQCEGCSDW 163 (164)
Q Consensus 153 ~~~~C~~C~~~ 163 (164)
..+.|++|+|.
T Consensus 68 v~V~CP~C~K~ 78 (114)
T PF11023_consen 68 VQVECPNCGKQ 78 (114)
T ss_pred eeeECCCCCCh
Confidence 57889999874
No 158
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=24.70 E-value=1.6e+02 Score=18.13 Aligned_cols=12 Identities=42% Similarity=0.545 Sum_probs=8.2
Q ss_pred EEccCCEEEEec
Q 031164 22 TIKPGDCVLMRP 33 (164)
Q Consensus 22 ~~~vGD~V~v~~ 33 (164)
.+.+||.|.+..
T Consensus 46 ~i~vGD~V~ve~ 57 (72)
T PRK00276 46 RILPGDKVTVEL 57 (72)
T ss_pred ccCCCCEEEEEE
Confidence 356777777774
No 159
>PRK00420 hypothetical protein; Validated
Probab=24.47 E-value=41 Score=23.17 Aligned_cols=24 Identities=25% Similarity=0.401 Sum_probs=17.5
Q ss_pred eEE-eeCCCCCC-CCceEeCCccCCC
Q 031164 140 VYC-KCEMPYNP-DDLMVQCEGCSDW 163 (164)
Q Consensus 140 ~~C-~c~~~~~p-D~~~~~C~~C~~~ 163 (164)
.+| .|..|.-- -...++|+.|+.-
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCe
Confidence 577 68887753 3468999999863
No 160
>smart00355 ZnF_C2H2 zinc finger.
Probab=24.44 E-value=30 Score=15.73 Aligned_cols=9 Identities=22% Similarity=0.693 Sum_probs=6.1
Q ss_pred eCCccCCCC
Q 031164 156 QCEGCSDWS 164 (164)
Q Consensus 156 ~C~~C~~~~ 164 (164)
.|+.|++.|
T Consensus 2 ~C~~C~~~f 10 (26)
T smart00355 2 RCPECGKVF 10 (26)
T ss_pred CCCCCcchh
Confidence 577787654
No 161
>cd03696 selB_II selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.
Probab=24.22 E-value=1.9e+02 Score=18.00 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=20.2
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeec
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESD 51 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~ 51 (164)
.+++||-|.+.|.. ..+.|.+|...
T Consensus 26 ~i~~g~~v~~~p~~-----~~~~V~sI~~~ 50 (83)
T cd03696 26 SVKVGDKVEILPLG-----EETRVRSIQVH 50 (83)
T ss_pred EEeCCCEEEECCCC-----ceEEEEEEEEC
Confidence 79999999999865 36888888754
No 162
>PF06719 AraC_N: AraC-type transcriptional regulator N-terminus; InterPro: IPR009594 This entry represents the N terminus of bacterial ARAC-type transcriptional regulators. In Escherichia coli these regulate the L-arabinose operon through sensing the presence of arabinose, and when the sugar is present, transmitting this information from the arabinose-binding domains to the protein s DNA-binding domains []. This family might represent the N-terminal arm of the protein, which binds to the C-terminal DNA binding domains to hold them in a state where the protein prefers to loop and remain non-activating []. This domain is associated with the IPR000005 from INTERPRO domain.
Probab=23.90 E-value=2.6e+02 Score=19.84 Aligned_cols=19 Identities=21% Similarity=0.303 Sum_probs=8.9
Q ss_pred EEcCcCcEEccCCEEEEecC
Q 031164 15 TVKSISKTIKPGDCVLMRPS 34 (164)
Q Consensus 15 ~i~g~~~~~~vGD~V~v~~~ 34 (164)
.+.|. +.+.+|+-++....
T Consensus 29 vlQG~-K~~~~g~~~~~Y~~ 47 (155)
T PF06719_consen 29 VLQGS-KRVHLGDQVFEYDA 47 (155)
T ss_pred EEeee-EEEEECCceEEecC
Confidence 34443 45555555544443
No 163
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=23.83 E-value=61 Score=17.16 Aligned_cols=11 Identities=27% Similarity=0.791 Sum_probs=7.2
Q ss_pred CceEeCCccCC
Q 031164 152 DLMVQCEGCSD 162 (164)
Q Consensus 152 ~~~~~C~~C~~ 162 (164)
..++.|+.|++
T Consensus 2 ~~~~~C~nC~R 12 (33)
T PF08209_consen 2 SPYVECPNCGR 12 (33)
T ss_dssp S-EEE-TTTSS
T ss_pred CCeEECCCCcC
Confidence 35889999975
No 164
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=23.67 E-value=73 Score=27.92 Aligned_cols=27 Identities=26% Similarity=0.732 Sum_probs=19.3
Q ss_pred CCCCceEEeeCCCCCCCC-ceEeCCccC
Q 031164 135 PDRVAVYCKCEMPYNPDD-LMVQCEGCS 161 (164)
Q Consensus 135 p~~~~~~C~c~~~~~pD~-~~~~C~~C~ 161 (164)
|.+|-.-|+|..-.--|- .++||++|+
T Consensus 116 pkk~~iCcVClg~rs~da~ei~qCd~CG 143 (707)
T KOG0957|consen 116 PKKAVICCVCLGQRSVDAGEILQCDKCG 143 (707)
T ss_pred cccceEEEEeecCccccccceeeccccC
Confidence 446667789976554333 699999997
No 165
>cd05701 S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=23.52 E-value=61 Score=20.08 Aligned_cols=27 Identities=19% Similarity=0.298 Sum_probs=19.6
Q ss_pred ceeeeeEEEcCcCcEEccCCEEEEecCC
Q 031164 8 RRTLESYTVKSISKTIKPGDCVLMRPSE 35 (164)
Q Consensus 8 r~~y~~~~i~g~~~~~~vGD~V~v~~~~ 35 (164)
+.|++....-+ .+.+++|.++.|.-.+
T Consensus 32 ~sHLNdtfrf~-seklkvG~~l~v~lk~ 58 (69)
T cd05701 32 RSHLNDTFRFD-SEKLSVGQCLDVTLKD 58 (69)
T ss_pred hhhcccccccc-ceeeeccceEEEEEec
Confidence 45666665555 3789999999988655
No 166
>PF01050 MannoseP_isomer: Mannose-6-phosphate isomerase; InterPro: IPR001538 Mannose-6-phosphate isomerase or phosphomannose isomerase (5.3.1.8 from EC) (PMI) is the enzyme that catalyses the interconversion of mannose-6-phosphate and fructose-6-phosphate. In eukaryotes PMI is involved in the synthesis of GDP-mannose, a constituent of N- and O-linked glycans and GPI anchors and in prokaryotes it participates in a variety of pathways, including capsular polysaccharide biosynthesis and D-mannose metabolism. PMI's belong to the cupin superfamily whose functions range from isomerase and epimerase activities involved in the modification of cell wall carbohydrates in bacteria and plants, to non-enzymatic storage proteins in plant seeds, and transcription factors linked to congenital baldness in mammals []. Three classes of PMI have been defined []. The type II phosphomannose isomerases are bifunctional enzymes 5.3.1.8 from EC. This entry covers the isomerase region of the protein []. The guanosine diphospho-D-mannose pyrophosphorylase region is described in another InterPro entry (see IPR005836 from INTERPRO).; GO: 0016779 nucleotidyltransferase activity, 0005976 polysaccharide metabolic process
Probab=23.41 E-value=94 Score=22.41 Aligned_cols=24 Identities=25% Similarity=0.306 Sum_probs=17.8
Q ss_pred eEEEcCcCcEEccCCEEEEecCCC
Q 031164 13 SYTVKSISKTIKPGDCVLMRPSEP 36 (164)
Q Consensus 13 ~~~i~g~~~~~~vGD~V~v~~~~~ 36 (164)
.+++++....++.||.|+|..+..
T Consensus 96 ~v~~~~~~~~~~~g~sv~Ip~g~~ 119 (151)
T PF01050_consen 96 EVTLDDEEFTLKEGDSVYIPRGAK 119 (151)
T ss_pred EEEECCEEEEEcCCCEEEECCCCE
Confidence 345666666789999999988763
No 167
>TIGR00491 aIF-2 translation initiation factor aIF-2/yIF-2. This model describes archaeal and eukaryotic orthologs of bacterial IF-2. Like IF-2, it helps convey the initiator tRNA to the ribosome, although the initiator is N-formyl-Met in bacteria and Met here. This protein is not closely related to the subunits of eIF-2 of eukaryotes, which is also involved in the initiation of translation. The aIF-2 of Methanococcus jannaschii contains a large intein interrupting a region of very strongly conserved sequence very near the amino end; this model does not correctly align the sequences from Methanococcus jannaschii and Pyrococcus horikoshii in this region.
Probab=23.14 E-value=1.6e+02 Score=26.21 Aligned_cols=41 Identities=12% Similarity=0.131 Sum_probs=29.2
Q ss_pred CceeeeeEEEcCcCcEEccCCEEEEecCCCCCCCeEEEEeEEeecC
Q 031164 7 PRRTLESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDA 52 (164)
Q Consensus 7 ~r~~y~~~~i~g~~~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~ 52 (164)
|+-..-..++... ++++||.|.+.+.. .+.+++|..|....
T Consensus 243 G~G~v~t~~v~~G--~l~~GD~iv~~~~~---~~i~~kVr~l~~~~ 283 (590)
T TIGR00491 243 GLGMTIDAVIYDG--ILRKGDTIAMAGSD---DVIVTRVRALLKPR 283 (590)
T ss_pred CCceEEEEEEEcC--EEeCCCEEEEccCC---CcccEEEEEecCCC
Confidence 4434444444433 89999999999876 47789999998654
No 168
>cd03692 mtIF2_IVc mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor EF-Tu. The C-terminal part of mtIF2 contains the entire fMet-tRNAfmet binding site of IF-2 and is resistant to proteolysis. This C-terminal portion consists of two domains, IF2 C1 and IF2 C2. IF2 C2 been shown to contain all molecular determinants necessary and sufficient for the recognition and binding of fMet-tRNAfMet. Like IF2 from certain prokaryotes such as Thermus thermophilus, mtIF2lacks domain II which is thought to be involved in binding of E.coli IF-2 to 30S subunits.
Probab=22.98 E-value=2.1e+02 Score=18.06 Aligned_cols=29 Identities=21% Similarity=0.158 Sum_probs=24.2
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecC
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDA 52 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~ 52 (164)
.++.|+.|.|.+.+ ...+-|+|.+|+..+
T Consensus 26 ~l~~g~~v~vlr~~--~~~~~g~i~sl~~~~ 54 (84)
T cd03692 26 KIKRNAKVRVLRNG--EVIYEGKISSLKRFK 54 (84)
T ss_pred EEeCCCEEEEEcCC--CEEEEEEEEEEEEcC
Confidence 89999999999986 356789999998653
No 169
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=22.85 E-value=63 Score=27.08 Aligned_cols=71 Identities=15% Similarity=0.419 Sum_probs=45.0
Q ss_pred ccccccccc--ceeeccEEEeccc-----cccc-CCCCCCeEEEeeeeeccCCcccCCCCceEEe-eCCCCCCCCce---
Q 031164 87 DHHDIQSAD--TIEGKCTVHSFKS-----YTKL-DAVGNDDFFCRFEYNSSSGAFNPDRVAVYCK-CEMPYNPDDLM--- 154 (164)
Q Consensus 87 ~~~d~~~~~--~I~~kc~V~~~~~-----~~~~-~~~~~~~ffcr~~yd~~~~~f~p~~~~~~C~-c~~~~~pD~~~--- 154 (164)
..+|..++. .|-...+++..++ +... .........--..++|+.+++-- ..|. |..+.+|....
T Consensus 184 SnSDAHsl~p~~IGre~n~~~~~~~sf~~~~~~l~ai~~~~i~~~~g~~P~~GKYh~----~~c~~C~~~~~~~~~~~~~ 259 (374)
T TIGR00375 184 TNSDAHSLGPHRLGREFNQLEVQSADFTEFALALKAIDDRKIIANYGLDPLLGKYHQ----TACEACGEPAVSEDAETAC 259 (374)
T ss_pred eecCCCCCChhHhCCceEEEecCCCCHHHHHHHHHHhhCCceEeeeeECcCCCccch----hhhcccCCcCCchhhhhcC
Confidence 345777777 7777777776543 2211 11222334556777888777764 4674 88888888744
Q ss_pred EeCCccCC
Q 031164 155 VQCEGCSD 162 (164)
Q Consensus 155 ~~C~~C~~ 162 (164)
-.|+ |++
T Consensus 260 ~~Cp-CG~ 266 (374)
T TIGR00375 260 ANCP-CGG 266 (374)
T ss_pred CCCC-CCC
Confidence 7799 986
No 170
>PF11699 CENP-C_C: Mif2/CENP-C like; PDB: 2VPV_B.
Probab=22.83 E-value=97 Score=20.11 Aligned_cols=23 Identities=13% Similarity=0.187 Sum_probs=15.0
Q ss_pred eEEEcCcCcEEccCCEEEEecCC
Q 031164 13 SYTVKSISKTIKPGDCVLMRPSE 35 (164)
Q Consensus 13 ~~~i~g~~~~~~vGD~V~v~~~~ 35 (164)
+++++++..++..||..+|.+++
T Consensus 45 ~Vti~~~~f~v~~G~~F~VP~gN 67 (85)
T PF11699_consen 45 EVTIHETSFVVTKGGSFQVPRGN 67 (85)
T ss_dssp EEEETTEEEEEETT-EEEE-TT-
T ss_pred EEEEcCcEEEEeCCCEEEECCCC
Confidence 35666766778889988888876
No 171
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease. Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad.
Probab=22.74 E-value=1.6e+02 Score=18.52 Aligned_cols=29 Identities=17% Similarity=0.324 Sum_probs=14.9
Q ss_pred EEccCCEEEEecCC-CCCCCeEEEEeEEee
Q 031164 22 TIKPGDCVLMRPSE-PSKPSYVAKIERIES 50 (164)
Q Consensus 22 ~~~vGD~V~v~~~~-~~~~~~i~~I~~i~~ 50 (164)
+++.||.|+|.+.. ....+..|.|.-+..
T Consensus 11 ~l~~GD~vlv~~~~~~~~~~~~Gdivv~~~ 40 (90)
T TIGR02754 11 TLPPGDRIIVVPWLKIFRVPPIGNVVVVRH 40 (90)
T ss_pred ccCCCCEEEEEEccccCCCCCCCeEEEEec
Confidence 56777777777521 112223455555543
No 172
>cd05841 BS69_related The PWWP domain is part of BS69 protein, a nuclear protein that specifically binds adenoviral E1A and Epstein-Barr viral EBNA2 proteins, suppressing their transactivation functions. BS69 is a multi-domain protein, containing bromo, PHD, PWWP, and MYND domains. The specific role of the PWWP domain within BS69 is not clearly identified, but BS69 functions in chromatin remodeling, consistent with other PWWP-containing proteins. 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=22.71 E-value=1.9e+02 Score=18.75 Aligned_cols=38 Identities=26% Similarity=0.388 Sum_probs=28.7
Q ss_pred EccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeeccc
Q 031164 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPE 68 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~ 68 (164)
...||.|.-.-.+ -++|-|+|.+.. + ..+.|++|-...
T Consensus 7 ~~p~dLVwAK~kG--yp~WPAkV~~~~----~--~~~~V~FFG~t~ 44 (83)
T cd05841 7 RPPHELVWAKLKG--FPYWPAKVMRVE----D--NQVDVRFFGGQH 44 (83)
T ss_pred CCCCCEEEEeCCC--CCCCCEEEeecC----C--CeEEEEEcCCCC
Confidence 4689999999877 589999998642 2 468888887333
No 173
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=22.39 E-value=46 Score=17.84 Aligned_cols=10 Identities=20% Similarity=0.793 Sum_probs=5.9
Q ss_pred ceEeCCccCC
Q 031164 153 LMVQCEGCSD 162 (164)
Q Consensus 153 ~~~~C~~C~~ 162 (164)
.+++|++|+-
T Consensus 3 ~ll~C~~C~v 12 (36)
T PF13831_consen 3 PLLFCDNCNV 12 (36)
T ss_dssp EEEE-SSS--
T ss_pred ceEEeCCCCC
Confidence 5889999974
No 174
>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=21.91 E-value=2.5e+02 Score=20.12 Aligned_cols=45 Identities=16% Similarity=0.319 Sum_probs=33.6
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEeEEeecCCCCeEEEEEEEeeccccc
Q 031164 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEES 70 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~v~v~Wfyrp~e~ 70 (164)
.++.||.|.|..+. -.-+.|.|.++... ++. ..+.+.+|-|...+
T Consensus 119 ~~~~G~~V~I~~Gp--f~G~~g~v~~~~~~-~~r-~~V~v~~~g~~~~v 163 (172)
T TIGR00922 119 DFEVGEQVRVNDGP--FANFTGTVEEVDYE-KSK-LKVSVSIFGRETPV 163 (172)
T ss_pred CCCCCCEEEEeecC--CCCcEEEEEEEcCC-CCE-EEEEEEECCCceEE
Confidence 47899999999877 57789999998542 234 77888888775443
No 175
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=21.89 E-value=3.1e+02 Score=21.89 Aligned_cols=32 Identities=22% Similarity=0.337 Sum_probs=24.4
Q ss_pred EEccCCEEEEecCCC---CCCCeEEEEeEEeecCCC
Q 031164 22 TIKPGDCVLMRPSEP---SKPSYVAKIERIESDARG 54 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~---~~~~~i~~I~~i~~~~~g 54 (164)
.++.|| ..+.++-. +....||+|.++..+..+
T Consensus 212 ~i~~GD-~vvTSGlgg~fP~Gl~Vg~V~~v~~~~~~ 246 (284)
T COG1792 212 DIKEGD-LVVTSGLGGVFPAGLPVGEVSSVKLDDYG 246 (284)
T ss_pred CccCCC-EEEecCCCCcCCCCcEEEEEEEEEeCCCc
Confidence 789999 55665532 467899999999988644
No 176
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=21.87 E-value=57 Score=20.21 Aligned_cols=12 Identities=42% Similarity=0.711 Sum_probs=8.7
Q ss_pred EccCCEEEEecC
Q 031164 23 IKPGDCVLMRPS 34 (164)
Q Consensus 23 ~~vGD~V~v~~~ 34 (164)
.++||+|+|..+
T Consensus 38 v~~Gd~VLVHaG 49 (68)
T PF01455_consen 38 VKVGDYVLVHAG 49 (68)
T ss_dssp B-TT-EEEEETT
T ss_pred CCCCCEEEEecC
Confidence 689999999876
No 177
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=21.78 E-value=84 Score=19.84 Aligned_cols=36 Identities=17% Similarity=0.343 Sum_probs=20.6
Q ss_pred EEEcCcCcEEccCCEEEEecCCCC---CCCeEEEEeEEe
Q 031164 14 YTVKSISKTIKPGDCVLMRPSEPS---KPSYVAKIERIE 49 (164)
Q Consensus 14 ~~i~g~~~~~~vGD~V~v~~~~~~---~~~~i~~I~~i~ 49 (164)
+++.-+...|++||.+.+.--++. .....++|..|.
T Consensus 20 fEiRkNDRdf~VGD~L~L~E~~~~~YTGr~~~~~Ityi~ 58 (72)
T PF12961_consen 20 FEIRKNDRDFQVGDILVLREWDNGEYTGREIEAEITYIT 58 (72)
T ss_pred EEEEecCCCCCCCCEEEEEEecCCCccccEEEEEEEEEe
Confidence 334433348999999998764421 122345555553
No 178
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=21.76 E-value=26 Score=16.07 Aligned_cols=8 Identities=25% Similarity=0.712 Sum_probs=5.7
Q ss_pred eCCccCCC
Q 031164 156 QCEGCSDW 163 (164)
Q Consensus 156 ~C~~C~~~ 163 (164)
.|+.|++-
T Consensus 2 ~C~~C~~~ 9 (23)
T PF00096_consen 2 KCPICGKS 9 (23)
T ss_dssp EETTTTEE
T ss_pred CCCCCCCc
Confidence 68888764
No 179
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.61 E-value=85 Score=19.22 Aligned_cols=21 Identities=14% Similarity=0.486 Sum_probs=16.4
Q ss_pred eCCCCCCCCceEeCCccCCCC
Q 031164 144 CEMPYNPDDLMVQCEGCSDWS 164 (164)
Q Consensus 144 c~~~~~pD~~~~~C~~C~~~~ 164 (164)
|..+.-.....|.|.-|++++
T Consensus 30 C~~~gC~~~s~I~C~~Ckk~~ 50 (63)
T PF04236_consen 30 CDITGCNNTSFIRCAYCKKSL 50 (63)
T ss_pred CCCCCCCCcCEEEccccCCcc
Confidence 455566778899999999874
No 180
>TIGR01665 put_anti_recept phage minor structural protein, N-terminal region. This model represents the conserved N-terminal region, typically from about residue 25 to about residue 350, of a family of uncharacterized phage proteins 500 to 1700 residues in length.
Probab=21.18 E-value=1.5e+02 Score=23.74 Aligned_cols=31 Identities=19% Similarity=0.306 Sum_probs=24.6
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEeEEeecC
Q 031164 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDA 52 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~ 52 (164)
+.+.+||.|.|...+- ....-+||.++..+.
T Consensus 276 e~v~lGDtV~v~~~~~-~i~~~~RVi~~~~~~ 306 (317)
T TIGR01665 276 EPIGIGDTVRLKHTDF-NIKVYARVIKVEYSP 306 (317)
T ss_pred ccccCCCEEEEEcCCC-CceeEEEEEEEeccc
Confidence 4789999999998875 455569999887664
No 181
>PRK01343 zinc-binding protein; Provisional
Probab=21.00 E-value=54 Score=19.75 Aligned_cols=14 Identities=21% Similarity=0.517 Sum_probs=9.5
Q ss_pred CCCCceEeCCccCC
Q 031164 149 NPDDLMVQCEGCSD 162 (164)
Q Consensus 149 ~pD~~~~~C~~C~~ 162 (164)
++.+..+.|+.|++
T Consensus 4 ~~~~p~~~CP~C~k 17 (57)
T PRK01343 4 EPLRPTRPCPECGK 17 (57)
T ss_pred ccCCCCCcCCCCCC
Confidence 34556677888876
No 182
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=20.91 E-value=40 Score=20.65 Aligned_cols=16 Identities=13% Similarity=0.152 Sum_probs=12.2
Q ss_pred CCCCceEeCCccCCCC
Q 031164 149 NPDDLMVQCEGCSDWS 164 (164)
Q Consensus 149 ~pD~~~~~C~~C~~~~ 164 (164)
........|+.|+.||
T Consensus 48 ~i~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 48 EIVEGELICPECGREY 63 (68)
T ss_dssp ETTTTEEEETTTTEEE
T ss_pred cccCCEEEcCCCCCEE
Confidence 3555788899998886
No 183
>PF13437 HlyD_3: HlyD family secretion protein
Probab=20.90 E-value=2.4e+02 Score=18.07 Aligned_cols=30 Identities=27% Similarity=0.397 Sum_probs=19.4
Q ss_pred EEc-cCCEEEEecCCCCCCCeEEEEeEEeec
Q 031164 22 TIK-PGDCVLMRPSEPSKPSYVAKIERIESD 51 (164)
Q Consensus 22 ~~~-vGD~V~v~~~~~~~~~~i~~I~~i~~~ 51 (164)
.++ .|+-|.+...+.....+-|+|.+|...
T Consensus 49 ~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~~ 79 (105)
T PF13437_consen 49 RIKDPGQKVTVRLDPGPEKTIEGKVSSISPS 79 (105)
T ss_pred ceEeCCCEEEEEECCCCCcEEEEEEEEEeCc
Confidence 455 777777776532345777777777664
No 184
>KOG1698 consensus Mitochondrial/chloroplast ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=20.79 E-value=3e+02 Score=20.99 Aligned_cols=34 Identities=21% Similarity=0.171 Sum_probs=24.0
Q ss_pred EEccCCEEEEecCCCCC--CCeEEEEeEEeecCCCC
Q 031164 22 TIKPGDCVLMRPSEPSK--PSYVAKIERIESDARGA 55 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~--~~~i~~I~~i~~~~~g~ 55 (164)
.+++||.|.|.++++.. .-.++.+..|.....|.
T Consensus 96 e~~~G~Iv~V~s~~p~~k~k~s~f~Gi~I~R~~~Gl 131 (201)
T KOG1698|consen 96 EFKVGSIVRVTSEDPENKRKVSRFKGICIRRRNAGL 131 (201)
T ss_pred ccccccEEEEEecCCccCCceeEEEEEEEEecccCC
Confidence 68999999999988643 34566666666555553
No 185
>PLN00208 translation initiation factor (eIF); Provisional
Probab=20.78 E-value=1.7e+02 Score=21.15 Aligned_cols=16 Identities=31% Similarity=0.279 Sum_probs=9.2
Q ss_pred EEEEEEEeecccccCC
Q 031164 57 VKVHVRWYYRPEESIG 72 (164)
Q Consensus 57 ~~v~v~Wfyrp~e~~~ 72 (164)
....+.|=|.+.++..
T Consensus 87 ~KgdIv~ry~~dqvr~ 102 (145)
T PLN00208 87 DKADVILKYMPDEARL 102 (145)
T ss_pred CEEEEEEEcCHHHHHH
Confidence 4455666666666553
No 186
>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=20.60 E-value=1.4e+02 Score=19.44 Aligned_cols=24 Identities=38% Similarity=0.428 Sum_probs=16.2
Q ss_pred EccCCEEEEecCCCCCCCeEEEEeEEeecC
Q 031164 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDA 52 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~ 52 (164)
|++||.|.=...+ ||+|..|....
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 6889999865444 88888887643
No 187
>PF11012 DUF2850: Protein of unknown function (DUF2850); InterPro: IPR021271 This family of proteins with unknown function appear to be restricted to Vibrionaceae.
Probab=20.53 E-value=1.7e+02 Score=18.77 Aligned_cols=30 Identities=10% Similarity=0.103 Sum_probs=23.8
Q ss_pred CCCceeeeeEEEcCcCcEEccCCEEEEecC
Q 031164 5 KAPRRTLESYTVKSISKTIKPGDCVLMRPS 34 (164)
Q Consensus 5 ~~~r~~y~~~~i~g~~~~~~vGD~V~v~~~ 34 (164)
.+||.-=.++..+|...+|++|+-+++..-
T Consensus 28 ~ngrlV~T~F~fDG~~l~~~~G~~~~~y~~ 57 (79)
T PF11012_consen 28 RNGRLVATSFEFDGKTLEYRTGSGTYRYQI 57 (79)
T ss_pred ECCCEEeeEEEECCCEEEEEECCeEEEEEE
Confidence 367777778889998888999998887753
No 188
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=20.37 E-value=1.7e+02 Score=21.32 Aligned_cols=13 Identities=31% Similarity=0.383 Sum_probs=8.3
Q ss_pred EEccCCEEEEecC
Q 031164 22 TIKPGDCVLMRPS 34 (164)
Q Consensus 22 ~~~vGD~V~v~~~ 34 (164)
.|+.||.|+|...
T Consensus 70 WI~~GD~VlVel~ 82 (155)
T PTZ00329 70 WINIGDIILVSLR 82 (155)
T ss_pred EecCCCEEEEecc
Confidence 4667777777553
No 189
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=20.22 E-value=77 Score=25.49 Aligned_cols=16 Identities=25% Similarity=0.623 Sum_probs=13.0
Q ss_pred CCCCceEeCCccCCCC
Q 031164 149 NPDDLMVQCEGCSDWS 164 (164)
Q Consensus 149 ~pD~~~~~C~~C~~~~ 164 (164)
..|.++.|||.|...|
T Consensus 291 enddqllfcddcdrgy 306 (336)
T KOG1244|consen 291 ENDDQLLFCDDCDRGY 306 (336)
T ss_pred CCCceeEeecccCCce
Confidence 4567799999998865
Done!