Query 031197
Match_columns 164
No_of_seqs 126 out of 970
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 10:38:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031197.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031197hhsearch_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 1.4E-36 3E-41 214.9 10.6 121 20-156 1-121 (121)
2 cd04713 BAH_plant_3 BAH, or Br 100.0 8.2E-36 1.8E-40 217.1 13.3 129 2-133 2-134 (146)
3 cd04717 BAH_polybromo BAH, or 100.0 1.5E-33 3.2E-38 199.6 11.0 115 20-134 1-118 (121)
4 cd04716 BAH_plantDCM_I BAH, or 100.0 5.8E-33 1.3E-37 195.8 12.2 113 20-133 1-118 (122)
5 PF01426 BAH: BAH domain; Int 100.0 1.9E-31 4.2E-36 187.2 12.1 112 21-134 1-117 (119)
6 smart00439 BAH Bromo adjacent 100.0 2E-31 4.4E-36 187.3 12.0 113 22-134 1-118 (120)
7 cd04370 BAH BAH, or Bromo Adja 100.0 2E-31 4.3E-36 187.6 10.8 115 20-134 1-121 (123)
8 cd04709 BAH_MTA BAH, or Bromo 100.0 1.2E-30 2.6E-35 192.3 11.9 114 21-135 2-139 (164)
9 cd04721 BAH_plant_1 BAH, or Br 100.0 7.5E-31 1.6E-35 187.4 10.1 109 19-129 4-118 (130)
10 cd04715 BAH_Orc1p_like BAH, or 100.0 4.5E-30 9.8E-35 188.6 11.8 123 2-128 11-153 (159)
11 cd04710 BAH_fungalPHD BAH, or 100.0 3.7E-29 8.1E-34 179.4 12.5 112 19-132 8-133 (135)
12 cd04718 BAH_plant_2 BAH, or Br 100.0 1.3E-29 2.8E-34 182.0 1.4 96 37-133 50-145 (148)
13 cd04708 BAH_plantDCM_II BAH, o 99.9 2.9E-27 6.3E-32 178.5 11.1 112 20-133 5-143 (202)
14 cd04760 BAH_Dnmt1_I BAH, or Br 99.9 3.9E-27 8.4E-32 165.6 10.8 111 21-133 2-124 (124)
15 cd04720 BAH_Orc1p_Yeast BAH, o 99.9 5.9E-27 1.3E-31 175.6 12.2 116 19-135 49-177 (179)
16 cd04712 BAH_DCM_I BAH, or Brom 99.9 2.4E-26 5.1E-31 164.2 13.1 109 21-133 4-126 (130)
17 cd04719 BAH_Orc1p_animal BAH, 99.9 1E-25 2.3E-30 159.8 9.1 109 21-130 2-123 (128)
18 KOG1886 BAH domain proteins [T 99.9 1.3E-25 2.9E-30 185.8 8.0 161 2-164 31-197 (464)
19 cd04711 BAH_Dnmt1_II BAH, or B 99.9 3.3E-23 7.2E-28 146.5 7.9 99 35-133 22-133 (137)
20 KOG1827 Chromatin remodeling c 99.7 5E-17 1.1E-21 139.6 5.9 126 14-141 184-312 (629)
21 KOG3554 Histone deacetylase co 99.2 8E-13 1.7E-17 109.6 -1.4 113 22-135 5-163 (693)
22 PF00628 PHD: PHD-finger; Int 97.3 0.00011 2.4E-09 43.6 1.3 24 140-164 1-25 (51)
23 smart00249 PHD PHD zinc finger 97.1 0.00029 6.3E-09 40.3 1.5 22 142-164 4-25 (47)
24 KOG1632 Uncharacterized PHD Zn 97.0 0.00025 5.4E-09 58.6 0.6 84 80-164 3-86 (345)
25 KOG4323 Polycomb-like PHD Zn-f 95.4 0.0065 1.4E-07 51.7 1.3 24 140-164 173-196 (464)
26 KOG1973 Chromatin remodeling p 94.7 0.016 3.4E-07 46.5 1.5 27 136-164 217-246 (274)
27 KOG2752 Uncharacterized conser 94.0 0.034 7.4E-07 45.0 2.0 27 138-164 128-159 (345)
28 PF09926 DUF2158: Uncharacteri 93.9 0.12 2.6E-06 31.0 3.8 41 23-67 1-41 (53)
29 COG5076 Transcription factor i 88.9 0.042 9E-07 45.8 -2.8 89 21-109 275-363 (371)
30 PRK10708 hypothetical protein; 88.5 2 4.4E-05 26.0 5.0 44 24-69 2-52 (62)
31 PF10781 DSRB: Dextransucrase 88.4 2.4 5.3E-05 25.7 5.3 45 24-70 2-53 (62)
32 cd05834 HDGF_related The PWWP 88.3 0.88 1.9E-05 29.8 3.8 44 22-67 2-45 (83)
33 cd05835 Dnmt3b_related The PWW 85.9 1.2 2.6E-05 29.3 3.4 41 23-65 1-44 (87)
34 PF08940 DUF1918: Domain of un 84.4 2 4.3E-05 26.2 3.6 40 23-63 3-42 (58)
35 COG5034 TNG2 Chromatin remodel 83.4 0.78 1.7E-05 36.3 1.9 27 136-164 219-248 (271)
36 PF11302 DUF3104: Protein of u 83.4 2.6 5.6E-05 27.1 3.9 31 22-52 5-40 (75)
37 cd06080 MUM1_like Mutated mela 83.3 2.4 5.1E-05 27.7 3.8 39 23-66 1-39 (80)
38 PF11717 Tudor-knot: RNA bindi 82.7 4.4 9.5E-05 24.1 4.7 36 23-61 1-36 (55)
39 PRK13251 transcription attenua 82.5 5.4 0.00012 25.2 5.0 48 58-105 19-66 (75)
40 cd05162 PWWP The PWWP domain, 81.6 2.7 5.9E-05 27.3 3.8 40 23-64 1-46 (87)
41 PF02081 TrpBP: Tryptophan RNA 81.0 3.8 8.3E-05 26.0 4.0 48 58-105 19-66 (75)
42 PF10383 Clr2: Transcription-s 80.9 9.3 0.0002 27.4 6.6 52 10-63 2-70 (139)
43 COG5475 Uncharacterized small 80.5 8.4 0.00018 23.3 5.1 38 21-67 3-40 (60)
44 smart00293 PWWP domain with co 80.4 2.8 6E-05 25.7 3.3 40 23-64 1-47 (63)
45 PF00467 KOW: KOW motif; Inte 79.0 5 0.00011 21.0 3.6 26 25-52 1-26 (32)
46 PF07154 DUF1392: Protein of u 79.0 6.1 0.00013 28.6 5.0 50 8-68 75-124 (150)
47 PF14446 Prok-RING_1: Prokaryo 78.9 1.6 3.5E-05 26.2 1.8 23 142-164 10-32 (54)
48 cd05840 SPBC215_ISWI_like The 76.3 3.9 8.4E-05 27.3 3.3 40 23-64 1-49 (93)
49 PF00855 PWWP: PWWP domain; I 75.2 3.3 7.2E-05 26.5 2.7 40 23-64 1-43 (86)
50 smart00739 KOW KOW (Kyprides, 73.6 6.7 0.00014 19.3 3.1 25 23-49 2-26 (28)
51 cd03703 aeIF5B_II aeIF5B_II: T 70.9 13 0.00029 25.7 4.9 45 3-52 9-53 (110)
52 PF07649 C1_3: C1-like domain; 69.2 2.3 5E-05 22.0 0.7 22 142-164 5-26 (30)
53 PF09871 DUF2098: Uncharacteri 68.7 16 0.00034 24.4 4.7 43 22-70 2-47 (91)
54 COG1370 Prefoldin, molecular c 66.7 4.7 0.0001 29.4 2.1 40 5-46 94-133 (155)
55 KOG1568 Mitochondrial inner me 64.4 37 0.00081 25.3 6.4 76 21-103 67-147 (174)
56 PTZ00112 origin recognition co 63.3 15 0.00032 34.8 5.0 116 9-127 441-602 (1164)
57 PF05180 zf-DNL: DNL zinc fing 63.3 3.6 7.7E-05 25.8 0.8 11 152-162 28-38 (66)
58 PF04322 DUF473: Protein of un 61.0 22 0.00048 24.9 4.6 43 8-50 19-71 (119)
59 PF15057 DUF4537: Domain of un 60.3 19 0.0004 25.3 4.1 40 22-61 55-95 (124)
60 COG4014 Uncharacterized protei 60.2 23 0.00051 23.5 4.2 41 23-69 9-53 (97)
61 PF13913 zf-C2HC_2: zinc-finge 60.1 3.3 7E-05 20.6 0.2 12 152-163 1-12 (25)
62 CHL00141 rpl24 ribosomal prote 60.0 36 0.00078 22.2 5.2 30 21-52 7-36 (83)
63 PRK12281 rplX 50S ribosomal pr 59.2 19 0.00041 23.1 3.7 30 21-52 5-34 (76)
64 PF13832 zf-HC5HC2H_2: PHD-zin 58.2 6.9 0.00015 26.5 1.6 28 134-164 51-81 (110)
65 cd05836 N_Pac_NP60 The PWWP do 57.1 17 0.00037 23.8 3.3 42 23-66 1-46 (86)
66 PF12961 DUF3850: Domain of Un 56.9 9 0.0002 24.4 1.9 24 12-35 18-41 (72)
67 cd06541 ASCH ASC-1 homology or 56.2 26 0.00057 23.6 4.3 43 6-50 14-56 (105)
68 PRK00004 rplX 50S ribosomal pr 52.2 26 0.00056 23.9 3.7 30 21-52 3-32 (105)
69 PF09378 HAS-barrel: HAS barre 52.0 18 0.00039 23.2 2.8 36 13-51 14-49 (91)
70 PF05207 zf-CSL: CSL zinc fing 51.3 5.5 0.00012 23.9 0.2 13 151-163 38-50 (55)
71 cd05837 MSH6_like The PWWP dom 50.9 22 0.00049 24.3 3.2 43 22-66 2-53 (110)
72 PF12503 CMV_1a_C: Cucumber mo 50.6 16 0.00035 23.8 2.3 30 57-90 35-73 (85)
73 PF03144 GTP_EFTU_D2: Elongati 50.6 29 0.00063 21.2 3.5 30 22-51 12-41 (74)
74 PF02591 DUF164: Putative zinc 49.2 10 0.00022 22.6 1.1 13 151-163 44-56 (56)
75 cd06555 ASCH_PF0470_like ASC-1 48.8 48 0.001 22.8 4.6 28 22-50 31-58 (109)
76 TIGR01079 rplX_bact ribosomal 48.4 32 0.0007 23.4 3.7 29 22-52 3-31 (104)
77 KOG1844 PHD Zn-finger proteins 48.2 12 0.00025 32.4 1.8 30 135-164 83-112 (508)
78 cd03702 IF2_mtIF2_II This fami 48.2 47 0.001 22.2 4.4 40 4-52 10-49 (95)
79 smart00743 Agenet Tudor-like d 47.5 27 0.00059 20.7 2.9 28 22-50 2-29 (61)
80 PF07494 Reg_prop: Two compone 47.1 25 0.00054 17.0 2.2 15 44-58 6-20 (24)
81 cd03701 IF2_IF5B_II IF2_IF5B_I 46.7 60 0.0013 21.5 4.8 40 4-52 10-49 (95)
82 COG3257 GlxB Uncharacterized p 45.7 78 0.0017 24.8 5.7 46 16-72 98-143 (264)
83 PF08921 DUF1904: Domain of un 45.3 10 0.00022 26.1 0.8 18 54-71 54-71 (108)
84 smart00652 eIF1a eukaryotic tr 44.7 39 0.00084 22.0 3.5 30 20-51 41-70 (83)
85 COG2956 Predicted N-acetylgluc 43.8 11 0.00023 31.4 0.8 23 140-162 354-377 (389)
86 PF11132 SplA: Transcriptional 43.5 19 0.00041 23.0 1.8 25 22-47 5-29 (75)
87 KOG1473 Nucleosome remodeling 43.4 13 0.00028 35.6 1.4 31 134-164 1119-1149(1414)
88 cd04456 S1_IF1A_like S1_IF1A_l 42.8 47 0.001 21.4 3.6 30 21-51 37-66 (78)
89 cd05793 S1_IF1A S1_IF1A: Trans 42.7 41 0.0009 21.5 3.3 29 20-50 36-64 (77)
90 PRK01191 rpl24p 50S ribosomal 42.2 52 0.0011 23.1 4.0 29 21-51 44-72 (120)
91 PF00667 FAD_binding_1: FAD bi 41.7 37 0.00081 25.9 3.6 25 11-35 30-54 (219)
92 KOG1512 PHD Zn-finger protein 39.9 12 0.00026 30.4 0.6 24 140-164 316-340 (381)
93 PF06940 DUF1287: Domain of un 39.8 30 0.00065 25.6 2.6 41 14-57 98-138 (164)
94 PF13719 zinc_ribbon_5: zinc-r 38.4 18 0.00039 19.7 0.9 11 153-163 2-12 (37)
95 PF11238 DUF3039: Protein of u 37.3 11 0.00025 22.9 0.0 23 141-163 29-54 (58)
96 cd04466 S1_YloQ_GTPase S1_YloQ 37.0 42 0.00092 20.1 2.7 25 22-50 37-61 (68)
97 COG1935 Uncharacterized conser 36.9 66 0.0014 22.5 3.7 42 8-49 19-70 (122)
98 PTZ00194 60S ribosomal protein 36.7 86 0.0019 22.7 4.5 37 21-60 45-81 (143)
99 PF13831 PHD_2: PHD-finger; PD 36.6 14 0.00031 20.0 0.4 13 152-164 3-15 (36)
100 COG0662 {ManC} Mannose-6-phosp 36.5 22 0.00048 24.8 1.4 23 15-37 71-93 (127)
101 COG1096 Predicted RNA-binding 36.0 20 0.00044 27.2 1.2 22 140-161 152-173 (188)
102 KOG1740 Predicted mitochondria 36.0 29 0.00063 23.6 1.8 30 8-37 35-64 (107)
103 PF01176 eIF-1a: Translation i 35.7 34 0.00073 21.0 2.0 24 21-46 40-63 (65)
104 PF03966 Trm112p: Trm112p-like 34.9 21 0.00045 22.1 1.0 16 148-163 48-63 (68)
105 PF01079 Hint: Hint module; I 34.8 44 0.00096 25.8 3.0 28 22-50 105-132 (217)
106 KOG2133 Transcriptional corepr 34.4 26 0.00056 33.1 1.8 112 21-133 144-281 (1229)
107 PRK04980 hypothetical protein; 33.9 95 0.0021 21.1 4.1 36 14-49 22-58 (102)
108 PF07883 Cupin_2: Cupin domain 33.6 40 0.00087 20.1 2.1 20 16-35 34-53 (71)
109 PRK02935 hypothetical protein; 33.5 22 0.00047 24.4 0.9 10 152-161 69-78 (110)
110 COG0250 NusG Transcription ant 33.2 1.1E+02 0.0024 22.9 4.8 45 21-68 122-166 (178)
111 PF06220 zf-U1: U1 zinc finger 32.9 17 0.00037 20.0 0.3 10 154-163 4-13 (38)
112 cd05838 WHSC1_related The PWWP 32.9 72 0.0016 21.2 3.4 38 24-63 2-46 (95)
113 PF13912 zf-C2H2_6: C2H2-type 32.5 18 0.00039 17.6 0.3 10 154-163 2-11 (27)
114 PF09889 DUF2116: Uncharacteri 32.4 9.6 0.00021 23.3 -0.8 24 138-163 3-28 (59)
115 PRK03187 tgl transglutaminase; 31.9 42 0.00092 26.9 2.4 15 21-35 164-178 (272)
116 COG0198 RplX Ribosomal protein 31.6 99 0.0022 21.1 3.9 30 21-52 3-32 (104)
117 TIGR01080 rplX_A_E ribosomal p 31.6 1.3E+02 0.0028 20.9 4.6 29 21-51 40-68 (114)
118 PF11926 DUF3444: Domain of un 31.5 1.1E+02 0.0023 23.8 4.6 46 20-67 25-70 (217)
119 PF13717 zinc_ribbon_4: zinc-r 31.0 37 0.00081 18.3 1.5 16 149-164 21-36 (36)
120 COG1917 Uncharacterized conser 30.5 70 0.0015 22.0 3.2 21 15-35 78-98 (131)
121 PF07191 zinc-ribbons_6: zinc- 30.4 11 0.00024 23.9 -0.8 21 142-162 6-26 (70)
122 TIGR01956 NusG_myco NusG famil 29.3 1.3E+02 0.0028 24.0 4.8 45 21-68 204-248 (258)
123 COG3450 Predicted enzyme of th 29.1 46 0.001 23.2 2.0 16 20-35 83-98 (116)
124 COG4127 Uncharacterized conser 28.5 41 0.00088 27.3 1.8 41 22-63 72-117 (318)
125 PRK04012 translation initiatio 28.1 1.1E+02 0.0024 20.7 3.7 28 21-50 58-85 (100)
126 CHL00142 rps17 ribosomal prote 27.9 1.8E+02 0.0039 19.0 5.1 29 9-37 37-65 (84)
127 PF05191 ADK_lid: Adenylate ki 27.7 17 0.00038 19.8 -0.3 10 155-164 3-12 (36)
128 PF11012 DUF2850: Protein of u 27.5 84 0.0018 20.4 2.9 30 4-33 27-56 (79)
129 PF13894 zf-C2H2_4: C2H2-type 27.4 26 0.00056 15.9 0.4 9 155-163 2-10 (24)
130 PF11023 DUF2614: Protein of u 27.2 32 0.0007 23.9 0.9 11 152-162 68-78 (114)
131 cd06552 ASCH_yqfb_like ASC-1 h 27.2 1.1E+02 0.0023 20.0 3.5 28 21-50 27-54 (100)
132 cd05792 S1_eIF1AD_like S1_eIF1 27.0 1E+02 0.0022 19.9 3.2 15 21-35 37-51 (78)
133 PF09345 DUF1987: Domain of un 26.7 46 0.001 22.4 1.7 16 55-70 76-91 (99)
134 CHL00010 infA translation init 26.6 1.5E+02 0.0032 18.9 4.0 12 22-33 46-57 (78)
135 PRK09943 DNA-binding transcrip 26.4 74 0.0016 23.4 2.9 40 16-66 143-182 (185)
136 PRK05610 rpsQ 30S ribosomal pr 26.2 1.9E+02 0.0042 18.8 4.9 25 12-36 43-67 (84)
137 PF02311 AraC_binding: AraC-li 26.1 1.6E+02 0.0035 19.3 4.4 21 15-35 37-57 (136)
138 COG2895 CysN GTPases - Sulfate 25.2 90 0.0019 26.5 3.3 25 22-48 249-273 (431)
139 COG1188 Ribosome-associated he 25.2 1.3E+02 0.0029 20.4 3.6 42 6-51 33-74 (100)
140 TIGR02098 MJ0042_CXXC MJ0042 f 25.1 40 0.00086 18.0 0.9 9 154-162 3-11 (38)
141 cd06530 S26_SPase_I The S26 Ty 25.0 1E+02 0.0023 19.2 3.1 25 23-47 32-56 (85)
142 PF05899 Cupin_3: Protein of u 24.9 44 0.00095 20.9 1.2 17 19-35 44-60 (74)
143 smart00734 ZnF_Rad18 Rad18-lik 24.4 27 0.00058 17.5 0.1 10 153-162 1-10 (26)
144 COG4101 Predicted mannose-6-ph 24.0 1.3E+02 0.0027 21.4 3.4 28 21-48 90-123 (142)
145 COG1579 Zn-ribbon protein, pos 24.0 27 0.00058 27.6 0.1 15 150-164 218-232 (239)
146 PF02150 RNA_POL_M_15KD: RNA p 23.8 23 0.00049 19.1 -0.2 11 153-163 1-11 (35)
147 COG0375 HybF Zn finger protein 23.7 37 0.0008 23.7 0.7 20 142-161 75-94 (115)
148 PF00366 Ribosomal_S17: Riboso 23.6 47 0.001 20.8 1.2 27 8-34 29-55 (69)
149 PF12171 zf-C2H2_jaz: Zinc-fin 23.4 38 0.00082 16.6 0.6 9 155-163 3-11 (27)
150 TIGR01665 put_anti_recept phag 23.1 1.1E+02 0.0023 24.7 3.5 31 21-52 276-306 (317)
151 PRK00276 infA translation init 23.1 1.3E+02 0.0028 18.8 3.1 13 21-33 45-57 (72)
152 cd03698 eRF3_II_like eRF3_II_l 23.1 1.8E+02 0.0038 18.3 3.9 25 22-51 26-50 (83)
153 TIGR00922 nusG transcription t 22.7 2.2E+02 0.0047 20.6 4.8 45 22-69 119-163 (172)
154 PF10844 DUF2577: Protein of u 22.7 78 0.0017 21.2 2.2 14 22-35 76-89 (100)
155 smart00451 ZnF_U1 U1-like zinc 22.6 42 0.00091 17.2 0.7 10 154-163 4-13 (35)
156 TIGR00008 infA translation ini 22.5 1.4E+02 0.003 18.8 3.1 25 20-46 42-66 (68)
157 PRK04151 IMP cyclohydrolase; P 22.2 1.9E+02 0.0041 22.2 4.3 42 1-43 9-57 (197)
158 PF01155 HypA: Hydrogenase exp 22.1 11 0.00024 26.0 -2.2 25 138-162 70-95 (113)
159 TIGR00100 hypA hydrogenase nic 22.0 36 0.00077 23.5 0.4 25 138-162 70-95 (115)
160 cd05841 BS69_related The PWWP 22.0 1.7E+02 0.0038 19.0 3.6 35 23-64 7-41 (83)
161 PF06719 AraC_N: AraC-type tra 22.0 2.9E+02 0.0062 19.8 5.2 20 15-35 29-48 (155)
162 TIGR00218 manA mannose-6-phosp 21.8 1.5E+02 0.0033 23.8 4.1 32 21-53 153-184 (302)
163 PF08209 Sgf11: Sgf11 (transcr 21.7 61 0.0013 17.3 1.2 10 152-161 3-12 (33)
164 PTZ00329 eukaryotic translatio 21.1 1.7E+02 0.0037 21.5 3.8 14 21-34 69-82 (155)
165 PLN00208 translation initiatio 21.0 1.7E+02 0.0037 21.3 3.7 16 56-71 87-102 (145)
166 PRK15457 ethanolamine utilizat 21.0 1E+02 0.0022 24.3 2.7 22 14-35 188-209 (233)
167 TIGR03635 S17_bact 30S ribosom 20.8 1.4E+02 0.0031 18.8 3.0 25 12-36 38-62 (71)
168 TIGR00074 hypC_hupF hydrogenas 20.5 63 0.0014 20.7 1.3 14 22-35 35-48 (76)
169 TIGR00405 L26e_arch ribosomal 20.4 2.9E+02 0.0063 19.4 4.9 43 22-69 86-128 (145)
170 TIGR00523 eIF-1A eukaryotic/ar 20.3 1.6E+02 0.0035 19.8 3.3 29 21-50 56-84 (99)
171 TIGR01955 RfaH transcriptional 20.2 1.8E+02 0.0038 20.7 3.8 42 22-67 108-149 (159)
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=1.4e-36 Score=214.86 Aligned_cols=121 Identities=47% Similarity=0.857 Sum_probs=110.1
Q ss_pred CeEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeecccccCcccccCCCceeEEeCCeeeeccceEEEe
Q 031197 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGK 99 (164)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~~~~~~~Elf~s~~~d~i~~~~I~gk 99 (164)
|++|++||+|+|.++++++++|||+|.+||++.+|+++++|+|||||+||+++++..++++|||+|++.|++|+++|+||
T Consensus 1 ~~~~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~~g~~~~~v~WfyrPeEt~~~~~~~~~~~EvF~S~~~d~~~~~~I~gk 80 (121)
T cd04714 1 KEIIRVGDCVLFKSPGRPSLPYVARIESLWEDPEGNMVVRVKWYYRPEETKGGRKPNHGEKELFASDHQDENSVQTIEHK 80 (121)
T ss_pred CCEEEcCCEEEEeCCCCCCCCEEEEEEEEEEcCCCCEEEEEEEEEcHHHccCcccccCCCCceEecCCcccccHHHhCcc
Confidence 35999999999999875578999999999999889999999999999999999888889999999999999999999999
Q ss_pred eEEEeeecccccCCCCcceEEEeeeeecccceecCCCcceeeeecCCCCCCCceEeC
Q 031197 100 CTVHTFKNYTKLENVGAEDYFCRFEYKAATGGFTPDRVAVYCKCEMPYNPDDLMVQC 156 (164)
Q Consensus 100 c~V~~~~~~~~~~~~~~~~f~cr~~yd~~~~~f~p~~~~~~C~C~~p~~pd~~~~~C 156 (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 99999999998775333 455677899999999999999998
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=8.2e-36 Score=217.09 Aligned_cols=129 Identities=29% Similarity=0.474 Sum_probs=115.7
Q ss_pred CCCCCCcceeeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeecccccCccc---ccCC
Q 031197 2 AKTKPGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRR---QFHG 78 (164)
Q Consensus 2 ~~~~~~~~~Y~s~~i~g~~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~---~~~~ 78 (164)
|||++.|++|.+|.++|. +|+|||+|||.+++ +.+||||+|.+||++.+|.++++|+|||||+|+..... ...+
T Consensus 2 ~~~~~~~~~y~s~~~dg~--~y~vgD~Vlv~~~~-~~~pyI~~I~~i~~~~~~~~~v~V~WFyRpeEi~~~~~~~~~~~~ 78 (146)
T cd04713 2 GKGKKKKCHYTSFEKDGN--KYRLEDCVLLVPED-DQKPYIAIIKDIYKQEEGSLKLEVQWLYRPEEIEKKKGGNWKAED 78 (146)
T ss_pred CCCccceeeeeeEEECCE--EEECCCEEEEeCCC-CCCCEEEEEEEEEEcCCCCEEEEEEeeECHHHhccccccccccCC
Confidence 899999999999999975 99999999999987 48999999999999988999999999999999986432 2346
Q ss_pred CceeEEeCCeeeeccceEEEeeEEEeeecccccCCC-CcceEEEeeeeecccceec
Q 031197 79 AKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLENV-GAEDYFCRFEYKAATGGFT 133 (164)
Q Consensus 79 ~~Elf~s~~~d~i~~~~I~gkc~V~~~~~~~~~~~~-~~~~f~cr~~yd~~~~~f~ 133 (164)
+||||+|++.|.+|+++|+|||.|++.+++.+++.. ..++||||+.||+.+++|.
T Consensus 79 ~~ElF~S~~~d~~~~~~I~gkc~V~~~~~~~~~~~~~~~~~F~cr~~yD~~~~~~~ 134 (146)
T cd04713 79 PRELFYSFHRDEVPAESVLHPCKVAFVPKGKQIPLRKGHSGFIVRRVYDNVNKKLW 134 (146)
T ss_pred CCeEEEeCCCCcCCHHHCcceeEEEECCccccCCccCCCCeEEEEEEEcCCCCcEe
Confidence 899999999999999999999999999988877654 5789999999999988765
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=1.5e-33 Score=199.57 Aligned_cols=115 Identities=27% Similarity=0.491 Sum_probs=105.8
Q ss_pred CeEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeecccccCcccccCCCceeEEeCCeeeeccceEEEe
Q 031197 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGK 99 (164)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~~~~~~~Elf~s~~~d~i~~~~I~gk 99 (164)
|..|++||+|+|.+++.+++++||+|.+||++.+|..+++|+|||||+||.+++...+.+||||+|++.|.+|+++|+||
T Consensus 1 g~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~Wf~rP~et~~~~~~~~~~~Evfls~~~d~~~~~~I~~k 80 (121)
T cd04717 1 GLQYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGK 80 (121)
T ss_pred CCEEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEEEEEeChHHccCCCccccccCceEEcCccccccHHHhcCe
Confidence 35899999999999875588999999999999999999999999999999988776788999999999999999999999
Q ss_pred eEEEeeecccccCCC---CcceEEEeeeeecccceecC
Q 031197 100 CTVHTFKNYTKLENV---GAEDYFCRFEYKAATGGFTP 134 (164)
Q Consensus 100 c~V~~~~~~~~~~~~---~~~~f~cr~~yd~~~~~f~p 134 (164)
|.|++.++|.+.++. ..++|+||+.||+..+.|.+
T Consensus 81 c~Vl~~~~y~~~~p~~~~~~dvy~ce~~y~~~~~~~~~ 118 (121)
T cd04717 81 CAVMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKK 118 (121)
T ss_pred eEEEehHHHhcCCCCCCCCCCEEEEeEEECcccccEec
Confidence 999999999998763 46899999999999998875
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=100.00 E-value=5.8e-33 Score=195.85 Aligned_cols=113 Identities=17% Similarity=0.342 Sum_probs=103.4
Q ss_pred CeEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeecccccCcc-cccCCCceeEEeCCeeeeccceEEE
Q 031197 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGR-RQFHGAKELFLSDHYDVQSAHTIEG 98 (164)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~-~~~~~~~Elf~s~~~d~i~~~~I~g 98 (164)
|..|++||+|+|.+++ ..++|||+|.+||++.+|..+++|+|||||+||..++ ...++++|||+|++.|++|+++|+|
T Consensus 1 g~~~~lgD~V~v~~~~-~~~~yi~rI~~i~e~~~g~~~~~v~WyyRpeet~~~r~~~~~~~rEvFlS~~~D~~pl~~I~~ 79 (122)
T cd04716 1 GITYNLGDDAYVQGGE-GEEPFICKITEFFEGTDGKTYFTAQWFYRAEDTVIERQATNHDKKRVFYSEIKNDNPLDCLIS 79 (122)
T ss_pred CcEEEcCCEEEEECCC-CCCCEEEEEEEEEEcCCCceEEEEEEEEcHHHhccccccccCCCceEEEecccCccchhheee
Confidence 3589999999999997 4899999999999999999999999999999999987 4467899999999999999999999
Q ss_pred eeEEEeeeccccc----CCCCcceEEEeeeeecccceec
Q 031197 99 KCTVHTFKNYTKL----ENVGAEDYFCRFEYKAATGGFT 133 (164)
Q Consensus 99 kc~V~~~~~~~~~----~~~~~~~f~cr~~yd~~~~~f~ 133 (164)
||.|++++++..+ ...+.++|||++.|+....+|.
T Consensus 80 Kc~V~~~~~~~~~~~~~~~~~~~df~c~~~Y~~~~~tF~ 118 (122)
T cd04716 80 KVKILQVPPNVGTKRKKPNSEKCDYYYDMEYCVPYSTFQ 118 (122)
T ss_pred eeEEEEeCCCCCcccccccCCCceEEEeeEeccchhheE
Confidence 9999999988876 3357889999999999998887
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=1.9e-31 Score=187.24 Aligned_cols=112 Identities=38% Similarity=0.789 Sum_probs=100.8
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCc--EEEEEEEeeecccccCcccccCCCceeEEeCCeeeeccceEEE
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNN--VKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEG 98 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~--~~v~v~Wfyrp~e~~~~~~~~~~~~Elf~s~~~d~i~~~~I~g 98 (164)
++|++||+|||.+++++++++||+|++||++.++. ++++|+|||||+||..++. ..+||||+|++++++|+++|.|
T Consensus 1 ~~~~vGD~V~v~~~~~~~~~~v~~I~~i~~~~~~~~~~~~~v~Wf~rp~d~~~~~~--~~~~Elf~s~~~~~~~~~~I~g 78 (119)
T PF01426_consen 1 VTYKVGDFVYVKPDDPPEPPYVARIEEIWEDKDGNKEKMVKVRWFYRPEDTSLGKT--FSPRELFLSDHCDDIPVESIRG 78 (119)
T ss_dssp EEEETTSEEEEECTSTTSEEEEEEEEEEEEETTTSEEEEEEEEEEEEGGGSTTGGH--SCTTEEEEEEEEEEEEGGGEEE
T ss_pred CEEeCCCEEEEeCCCCCCCCEEEEEEEEEcCCCCCEEEEEEEEEeECccccccccc--CCCCEEEEECcEeEEehhhEEe
Confidence 48999999999999877999999999999998877 9999999999999933333 4579999999999999999999
Q ss_pred eeEEEeeecccccCCC---CcceEEEeeeeecccceecC
Q 031197 99 KCTVHTFKNYTKLENV---GAEDYFCRFEYKAATGGFTP 134 (164)
Q Consensus 99 kc~V~~~~~~~~~~~~---~~~~f~cr~~yd~~~~~f~p 134 (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 9999999999987653 68999999999999999985
No 6
>smart00439 BAH Bromo adjacent homology domain.
Probab=99.97 E-value=2e-31 Score=187.27 Aligned_cols=113 Identities=38% Similarity=0.744 Sum_probs=103.5
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEcEEeeccCCc-EEEEEEEeeecccccCcccccCCCceeEEeCCeeeeccceEEEee
Q 031197 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNN-VKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKC 100 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~-~~v~v~Wfyrp~e~~~~~~~~~~~~Elf~s~~~d~i~~~~I~gkc 100 (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 4789999999998855789999999999999888 899999999999999987777789999999999999999999999
Q ss_pred EEEeeecccccCCC----CcceEEEeeeeecccceecC
Q 031197 101 TVHTFKNYTKLENV----GAEDYFCRFEYKAATGGFTP 134 (164)
Q Consensus 101 ~V~~~~~~~~~~~~----~~~~f~cr~~yd~~~~~f~p 134 (164)
.|++.+++.+..+. ..++||||+.||..+++|.+
T Consensus 81 ~V~~~~~~~~~~~~~~~~~~~~f~cr~~yd~~~~~f~~ 118 (120)
T smart00439 81 NVLSKSDYPGLRPEGKIGEPDVFFCESLYDPEKGAFKK 118 (120)
T ss_pred EEEEcchhcccccccCCCCCCeEEEEEEEccccCcccC
Confidence 99999999887653 46899999999999999874
No 7
>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=2e-31 Score=187.55 Aligned_cols=115 Identities=39% Similarity=0.767 Sum_probs=104.5
Q ss_pred CeEEccCCEEEEccCCC--CCCCeEEEEcEEeeccCCcEEEEEEEeeecccccCcccccCCCceeEEeCCeeeeccceEE
Q 031197 20 NKVVRPGDCVLMRPADS--DKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIE 97 (164)
Q Consensus 20 ~~~~~vGD~V~v~~~~~--~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~~~~~~~Elf~s~~~d~i~~~~I~ 97 (164)
|.+|++||+|+|.+++. .+++|||+|.+||++.+|.++++|+|||||+||+.+....+.+||||+|++.+++++++|.
T Consensus 1 g~~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~~~~~~~~~~v~wf~rp~e~~~~~~~~~~~~Elf~s~~~~~i~v~~I~ 80 (123)
T cd04370 1 GITYEVGDSVYVEPDDSIKSDPPYIARIEELWEDTNGSKQVKVRWFYRPEETPKGLSPFALRRELFLSDHLDEIPVESII 80 (123)
T ss_pred CCEEecCCEEEEecCCcCCCCCCEEEEEeeeeECCCCCEEEEEEEEEchhHhccccccccccceeEEecCccccCHHHhc
Confidence 35899999999999873 3789999999999999999999999999999999987767899999999999999999999
Q ss_pred EeeEEEeeecccccC--C--CCcceEEEeeeeecccceecC
Q 031197 98 GKCTVHTFKNYTKLE--N--VGAEDYFCRFEYKAATGGFTP 134 (164)
Q Consensus 98 gkc~V~~~~~~~~~~--~--~~~~~f~cr~~yd~~~~~f~p 134 (164)
|||.|++.+++.+.. . ...++||||+.||+.+++|.+
T Consensus 81 gkc~V~~~~~~~~~~~~~~~~~~~~f~~r~~yd~~~~~fk~ 121 (123)
T cd04370 81 GKCKVLFVSEFEGLKQRPNKIDTDDFFCRLAYDPTTKEFKA 121 (123)
T ss_pred cccEEEechHhhccccccccCCCCeEEEEEEECcCcceEEe
Confidence 999999999998764 1 357899999999999998875
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=1.2e-30 Score=192.32 Aligned_cols=114 Identities=25% Similarity=0.491 Sum_probs=101.2
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeecccccCc--------c--------------cccCC
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGG--------R--------------RQFHG 78 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~--------~--------------~~~~~ 78 (164)
..|++||+|||.++. ..+++||+|++|+++.+|.+.++|+|||||+|++.. + +...+
T Consensus 2 ~~yrvGD~Vy~~~~~-~~Py~I~rI~e~~~~~~~~~~vkV~wfYRp~DI~~~~~~l~~~~r~~~~~~~~~~~~~~~~~~~ 80 (164)
T cd04709 2 NMYRVGDYVYFESSP-NNPYLIRRIEELNKTARGHVEAKVVCYYRRRDIPDSLYQLADQHRRELEEKSDDLTPKQRHQLR 80 (164)
T ss_pred cEEecCCEEEEECCC-CCCCEEEEEEEEEeCCCCCEEEEEEEEEChhHccchhhhhcccccccccccccccchhhhhccC
Confidence 489999999999885 567889999999999999999999999999998652 1 12357
Q ss_pred CceeEEeCCeeeeccceEEEeeEEEeeecccccCC--CCcceEEEeeeeecccceecCC
Q 031197 79 AKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLEN--VGAEDYFCRFEYKAATGGFTPD 135 (164)
Q Consensus 79 ~~Elf~s~~~d~i~~~~I~gkc~V~~~~~~~~~~~--~~~~~f~cr~~yd~~~~~f~p~ 135 (164)
.+|||+|+|.|.+|+++|+|||.|++++++.++.. ..+++|||+..||+.+++|.+.
T Consensus 81 ~rELF~S~~~d~~p~~~IrGKC~V~~~~d~~~l~~~~~~~d~Ff~~~~YDP~~k~l~~~ 139 (164)
T cd04709 81 HRELFLSRQVETLPATHIRGKCSVTLLNDTESARSYLAREDTFFYSLVYDPEQKTLLAD 139 (164)
T ss_pred cceeEEecccccccHHHeeeeEEEEEehhhhhhhhccCCCCEEEEEEEECCCCCeeccc
Confidence 99999999999999999999999999999998764 3589999999999999999974
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=7.5e-31 Score=187.36 Aligned_cols=109 Identities=27% Similarity=0.438 Sum_probs=98.8
Q ss_pred CCeEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeecccccCccccc-CCCceeEEeCCeeeeccceEE
Q 031197 19 TNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQF-HGAKELFLSDHYDVQSAHTIE 97 (164)
Q Consensus 19 ~~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~~~-~~~~Elf~s~~~d~i~~~~I~ 97 (164)
+++++++||+|||++++ +++|||+|++||++.+|.++++|+||+||+|+.++.++. +.+||||+|++.+++|+++|.
T Consensus 4 ~~~~i~vGD~V~v~~~~--~~~~va~Ie~i~ed~~g~~~v~v~WF~~p~E~~~~~~~~~~~~~EvFlS~~~d~i~~~~I~ 81 (130)
T cd04721 4 NGVTISVHDFVYVLSEE--EDRYVAYIEDLYEDKKGSKMVKVRWFHTTDEVGAALSPDSVNPREIFLSPNLQVISVECID 81 (130)
T ss_pred CCEEEECCCEEEEeCCC--CCcEEEEEEEEEEcCCCCEEEEEEEecCHHHhccccCCCCCCCCeEEEcCCccccchHHee
Confidence 45799999999999887 788999999999999999999999999999999976554 899999999999999999999
Q ss_pred EeeEEEeeecccccCCCC-----cceEEEeeeeeccc
Q 031197 98 GKCTVHTFKNYTKLENVG-----AEDYFCRFEYKAAT 129 (164)
Q Consensus 98 gkc~V~~~~~~~~~~~~~-----~~~f~cr~~yd~~~ 129 (164)
|||+|++.++|.++.... .++|+||+.||...
T Consensus 82 gk~~Vls~~~y~k~~~~~~~~~~~~~f~C~~~~d~~~ 118 (130)
T cd04721 82 GLATVLTREHYEKFQSVPKNSSELQAYFCYRQIDNNK 118 (130)
T ss_pred eeeEECCHHHHhhhhccccCccccccEEEEEEecCCC
Confidence 999999999999876432 56899999999974
No 10
>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=99.97 E-value=4.5e-30 Score=188.63 Aligned_cols=123 Identities=21% Similarity=0.281 Sum_probs=101.6
Q ss_pred CCCCCCcceeeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEcEEeeccC--CcEEEEEEEeeecccccCccc--ccC
Q 031197 2 AKTKPGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHR--NNVKVRVRWYYRPEESIGGRR--QFH 77 (164)
Q Consensus 2 ~~~~~~~~~Y~s~~i~g~~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~--g~~~v~v~Wfyrp~e~~~~~~--~~~ 77 (164)
+..++++++|+++.++|. +|++||+|+|.+++ .++|||+|.+||++.+ |.++++|+|||||+||..+.. +.+
T Consensus 11 ~~~~~~~~~Y~s~~~~g~--~y~lGD~Vlv~s~~--~~~yIgkI~~iwe~~~~~g~~~~~v~WfyRp~E~~~~~~~~~~~ 86 (159)
T cd04715 11 GGKKKDGQFYRSFTYDGV--EYRLYDDVYVHNGD--SEPYIGKIIKIYETAIDSGKKKVKVIWFFRPSEIRMELKGEPKR 86 (159)
T ss_pred ccccCCceEEEEEEECCE--EEeCCCEEEEeCCC--CCCEEEEEEEEEEcCCcCCceEEEEEeeeCHHHhccccccCccc
Confidence 445678889999999974 99999999999865 8999999999999875 899999999999999986432 357
Q ss_pred CCceeEEeCCe-----eeeccceEEEeeEEEeeecccccCCC-----C------cceEEEeeeeecc
Q 031197 78 GAKELFLSDHY-----DVQSAHTIEGKCTVHTFKNYTKLENV-----G------AEDYFCRFEYKAA 128 (164)
Q Consensus 78 ~~~Elf~s~~~-----d~i~~~~I~gkc~V~~~~~~~~~~~~-----~------~~~f~cr~~yd~~ 128 (164)
.+||||+|+|. +++|+++|.|||.|+++++|.+..+. . ..+|.||++-+..
T Consensus 87 ~~nEvFlS~~~d~~~~~~n~l~sI~gKC~Vl~~~ey~~~~~~s~~~~~~~~~~f~~~f~~~~~~~~~ 153 (159)
T cd04715 87 HINEVFLACGRGEGLANINLLESIIGKCNVVCISEDFRNPQPSDGIPTSADFLFPCNFDVGRCVIVD 153 (159)
T ss_pred CCCcEEEecCcCccccccCcHHHccceeEEEEehHhhhCCCCcCCccccCcceeeeEEEecCceecc
Confidence 89999999986 66899999999999999999976442 1 3455566655554
No 11
>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=3.7e-29 Score=179.42 Aligned_cols=112 Identities=21% Similarity=0.464 Sum_probs=98.1
Q ss_pred CCeEEccCCEEEEccCCCCCCCeEEEEcEEeeccC------------CcEEEEEEEeeecccccCcccccCCCceeEEeC
Q 031197 19 TNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHR------------NNVKVRVRWYYRPEESIGGRRQFHGAKELFLSD 86 (164)
Q Consensus 19 ~~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~------------g~~~v~v~Wfyrp~e~~~~~~~~~~~~Elf~s~ 86 (164)
+|..|++||+|||.++++.++++||||++|+...+ +..+++|+|||||+|+..+. ..+.+|||+|.
T Consensus 8 ~g~~~~vgD~Vyv~~~~~~ePyyIgrI~e~~~~~~~~~~~~~~~~~~~~~~vrV~wfYRp~Di~~~~--~~d~relf~S~ 85 (135)
T cd04710 8 NGELLKVNDHIYMSSEPPGEPYYIGRIMEFVPKHEFPSGIHARVFPASYFQVRLNWYYRPRDISRRV--VADSRLLYASM 85 (135)
T ss_pred CCeEEeCCCEEEEecCCCCCCCEEEEEEEEEecCCCCccccccccCCCcEEEEEEEEeCHHHcCCcc--cCCceEEEEEe
Confidence 46799999999999998788999999999998642 33689999999999985444 46899999999
Q ss_pred CeeeeccceEEEeeEEEeeecccccCC--CCcceEEEeeeeeccccee
Q 031197 87 HYDVQSAHTIEGKCTVHTFKNYTKLEN--VGAEDYFCRFEYKAATGGF 132 (164)
Q Consensus 87 ~~d~i~~~~I~gkc~V~~~~~~~~~~~--~~~~~f~cr~~yd~~~~~f 132 (164)
|.|++|+++|+|||+|.+.++..++.. ..+++|||.+.||+..++|
T Consensus 86 h~d~~p~~si~gKC~V~~~~di~~l~~~~~~~~~Fyf~~lyD~~~~r~ 133 (135)
T cd04710 86 HSDICPIGSVRGKCTVRHRDQIPDLEEYKKRPNHFYFDQLFDRYILRY 133 (135)
T ss_pred eEeeechHHEEeEEEEEEecccchhhhhccCCCEEEEEeeeCcchhhc
Confidence 999999999999999999999877654 4589999999999998776
No 12
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.95 E-value=1.3e-29 Score=182.02 Aligned_cols=96 Identities=26% Similarity=0.516 Sum_probs=92.4
Q ss_pred CCCCeEEEEcEEeeccCCcEEEEEEEeeecccccCcccccCCCceeEEeCCeeeeccceEEEeeEEEeeecccccCCCCc
Q 031197 37 DKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLENVGA 116 (164)
Q Consensus 37 ~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~~~~~~~Elf~s~~~d~i~~~~I~gkc~V~~~~~~~~~~~~~~ 116 (164)
..++|||+|++||++. |+.+++|+|||||+||.+|+++.++.+|||+|++.|++++++|+|||.|+++++|.++.+.+.
T Consensus 50 ~~~~~vArIekiW~~~-G~~~~~grWy~rPEET~~gr~~~~~~kEvFlS~~~d~~~~~~I~gkC~V~~~keY~k~e~~g~ 128 (148)
T cd04718 50 SGDLWLARIEKLWEEN-GTYWYAARWYTLPEETHMGRQPHNLRRELYLTNDFADIEMECILRHCSVKCPKEFRDASNDGD 128 (148)
T ss_pred cCchHHHHHHHHHhcc-CceEEEEEEEeCchhccCccccccccceeeeccccccccHHHHhcccEEcCHHHcccccCCCC
Confidence 4689999999999986 999999999999999999999999999999999999999999999999999999999888899
Q ss_pred ceEEEeeeeecccceec
Q 031197 117 EDYFCRFEYKAATGGFT 133 (164)
Q Consensus 117 ~~f~cr~~yd~~~~~f~ 133 (164)
|+|||++.||..+++|+
T Consensus 129 Dvy~Ce~~Yd~~~~~Fk 145 (148)
T cd04718 129 DVFLCEYEYDVHWQSFK 145 (148)
T ss_pred ceEEEEEEEhhhcCcee
Confidence 99999999999999996
No 13
>cd04708 BAH_plantDCM_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.95 E-value=2.9e-27 Score=178.48 Aligned_cols=112 Identities=23% Similarity=0.471 Sum_probs=98.3
Q ss_pred CeEEccCCEEEEccC------------------CCCCCCeEEEEcEEeeccCC------cEEEEEEEeeecccccCcccc
Q 031197 20 NKVVRPGDCVLMRPA------------------DSDKPPYVARVEKIEADHRN------NVKVRVRWYYRPEESIGGRRQ 75 (164)
Q Consensus 20 ~~~~~vGD~V~v~~~------------------~~~~~~~ig~I~~i~~~~~g------~~~v~v~Wfyrp~e~~~~~~~ 75 (164)
|++|++||+|||.++ + ..++.||+|.+|+...++ ...++|+|||||+||.. +.+
T Consensus 5 Gv~Y~vgD~VYv~p~~f~~~~~~~~~~~~G~N~~-~~p~~I~qI~ei~~~k~~~~~~~~~~~vrVrwFYRPEdt~~-~~~ 82 (202)
T cd04708 5 GVTYSVGDFLYVSPDAFAEEERERATFKAGRNVG-LKAFVVCQVLEIVVEKESKQADVASTQVKVRRFYRPEDVSP-EKA 82 (202)
T ss_pred CEEEecCCeEEECcccccccccccccccccccCC-CCCcEEEEEEEEEecccCCCCCCcceEEEEEEEechhhcCc-ccc
Confidence 469999999999998 2 358889999999986544 68999999999999855 444
Q ss_pred c-CCCceeEEeCCeeeeccceEEEeeEEEeeecccccCC--CCcceEEEeeeeecccceec
Q 031197 76 F-HGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLEN--VGAEDYFCRFEYKAATGGFT 133 (164)
Q Consensus 76 ~-~~~~Elf~s~~~d~i~~~~I~gkc~V~~~~~~~~~~~--~~~~~f~cr~~yd~~~~~f~ 133 (164)
+ .+.+|||+|++.+++|+++|.|||+|...+++.++.. ..+++|||+..||+.++.|+
T Consensus 83 y~sd~rely~Sde~~~~~~~~I~GKC~V~~~~d~~~~~~~~~~~~~Ffc~~~Yd~~tg~f~ 143 (202)
T cd04708 83 YASDIREVYYSEDTLTVPVEAVEGKCEVRKKSDLPDSDAPVIFEHVFFCELLYDPAKGSLK 143 (202)
T ss_pred eecCceeEEEeccceeechhHcceEEEEEecCcchhhhccccCCCceEEEEEEcCCCCccC
Confidence 4 4899999999999999999999999999999887654 56899999999999999999
No 14
>cd04760 BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.95 E-value=3.9e-27 Score=165.57 Aligned_cols=111 Identities=25% Similarity=0.449 Sum_probs=97.7
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeecccccCcccccCCCceeEEeCCeeeeccceEEEee
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKC 100 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~~~~~~~Elf~s~~~d~i~~~~I~gkc 100 (164)
.+|++||+|+|+++++..+++||+|+.||++.+|.++++|+||+||+||.+|++ ++++|||+|++++++++++|.+||
T Consensus 2 ~~i~vGD~V~v~~~~~~~p~~I~rV~~mfe~~~g~k~~h~rWf~Rg~dTVlG~~--~~~kEvFlsd~c~d~~l~~I~~Kv 79 (124)
T cd04760 2 EELEAGDCVSVKPDDPTKPLYIARVTYMWKDSIGGKMFHAHWFCRGSDTVLGET--SDPLELFLVDECEDMALSSIHGKV 79 (124)
T ss_pred CEEecCCEEEEecCCCCCCcEEEEEhhheecCCCCcEEEEEEEEECCccccccc--CCCcEEEeecccCCcchHHheeee
Confidence 489999999999987788999999999999999999999999999999999986 689999999999999999999999
Q ss_pred EEEeeecccc---c---C-C-----CCcceEEEeeeeecccceec
Q 031197 101 TVHTFKNYTK---L---E-N-----VGAEDYFCRFEYKAATGGFT 133 (164)
Q Consensus 101 ~V~~~~~~~~---~---~-~-----~~~~~f~cr~~yd~~~~~f~ 133 (164)
.|...+.-.. . . + -+.++|||+.-||+...+|+
T Consensus 80 ~V~~~~p~~~w~~~~g~~~~~~~~~ddg~tffyq~~yd~~~arf~ 124 (124)
T cd04760 80 NVIYKAPSENWSMEGGMDEEDEIFEDDGKTFFYQKWYDPECARFE 124 (124)
T ss_pred EEEEeCCCcchhhhcCCCCccccccCCCCeEEEEEeeChhhhccC
Confidence 9999664321 1 1 1 23679999999999888774
No 15
>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=99.95 E-value=5.9e-27 Score=175.64 Aligned_cols=116 Identities=22% Similarity=0.343 Sum_probs=102.4
Q ss_pred CCeEEccCCEEEEccCCCCCCCeEEEEcEEeeccC-CcEEEEEEEeeecccccCccc--c-------cCCCceeEEeCCe
Q 031197 19 TNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHR-NNVKVRVRWYYRPEESIGGRR--Q-------FHGAKELFLSDHY 88 (164)
Q Consensus 19 ~~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~-g~~~v~v~Wfyrp~e~~~~~~--~-------~~~~~Elf~s~~~ 88 (164)
+++++++||+|+|++++ .+++|||.|.+|+.+.. +.+.+.|+|||||.|+.+++. . ...+||||+|.|.
T Consensus 49 d~~~~~vGD~Vlik~~~-~~~~~V~iI~ei~~~~~~~~v~i~v~Wy~r~~Ei~~~~~~~~~~~~~~~~~~~nElflT~~~ 127 (179)
T cd04720 49 DGLELSVGDTILVKDDV-ANSPSVYLIHEIRLNTLNNEVELWVMWFLRWFEINPARYYKQFDPEFRSESNKNELYLTAEL 127 (179)
T ss_pred CCeEEeCCCEEEEeCCC-CCCCEEEEEEEEEeCCCCCEEEEEEEEcCCHHHcccccccccccchhcccCCCceEEEeccc
Confidence 56899999999999987 48999999999998865 558999999999999987653 2 2348999999999
Q ss_pred eeeccceEEEeeEEEeeecccccCCC---CcceEEEeeeeecccceecCC
Q 031197 89 DVQSAHTIEGKCTVHTFKNYTKLENV---GAEDYFCRFEYKAATGGFTPD 135 (164)
Q Consensus 89 d~i~~~~I~gkc~V~~~~~~~~~~~~---~~~~f~cr~~yd~~~~~f~p~ 135 (164)
+.|++.+|++||.|++.++|.++.+. +..+||||++||+.++.|+|.
T Consensus 128 d~i~l~~Ii~k~~Vls~~ef~~~~~~~~~~~~~F~cR~~~d~~~~~F~~~ 177 (179)
T cd04720 128 SEIKLKDIIDKANVLSESEFNDLSTDDKNGERTFFCRYACEPDGEEFVWI 177 (179)
T ss_pred ceEEhhheeeeEEEecHHHhhhhcccccCCCceEEEEEEEeCCCCeEccc
Confidence 99999999999999999999987653 578999999999999999875
No 16
>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=99.94 E-value=2.4e-26 Score=164.16 Aligned_cols=109 Identities=25% Similarity=0.330 Sum_probs=94.2
Q ss_pred eEEccCCEEEEccCCCC----------CCCeEEEEcEEeeccCCcEEEEEEEeeecccccCcccccCCCceeEEeCCeee
Q 031197 21 KVVRPGDCVLMRPADSD----------KPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDV 90 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~----------~~~~ig~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~~ 81 (130)
T cd04712 4 LTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKGSDGSKMFHGRWLYRGCDTVLGN--YANERELFLTNECTC 81 (130)
T ss_pred CEEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeecCCCceEEEEEEEEcchhccccc--cCCCceEEEeccccc
Confidence 48999999999998854 389999999999999999999999999999999998 578999999999999
Q ss_pred eccc----eEEEeeEEEeeecccccCCCCcceEEEeeeeecccceec
Q 031197 91 QSAH----TIEGKCTVHTFKNYTKLENVGAEDYFCRFEYKAATGGFT 133 (164)
Q Consensus 91 i~~~----~I~gkc~V~~~~~~~~~~~~~~~~f~cr~~yd~~~~~f~ 133 (164)
++++ .|.+||.|........ ...++.|||+..|+++.+.|+
T Consensus 82 ~~~~~~~~~I~~k~~V~~~~~~~~--~~~~~~F~r~syy~~e~~~F~ 126 (130)
T cd04712 82 LELDLLSTEIKGVHKVDWSGTPWG--KGLPEFFVRQSYYWPERGAFT 126 (130)
T ss_pred cccccccceeEEEEEEEEecCcCC--cCCCCEEEEEEEECccCCceE
Confidence 9999 9999999998776543 113455666666666999987
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=99.93 E-value=1e-25 Score=159.76 Aligned_cols=109 Identities=26% Similarity=0.370 Sum_probs=93.4
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeeccCC---cEEEEEEEeeecccccCccc----ccCCCceeEEeCCe---ee
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRN---NVKVRVRWYYRPEESIGGRR----QFHGAKELFLSDHY---DV 90 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g---~~~v~v~Wfyrp~e~~~~~~----~~~~~~Elf~s~~~---d~ 90 (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 4899999999999984 88999999999998765 56999999999999974321 12589999999987 48
Q ss_pred eccceEEEeeEEEeeecccccCCC---CcceEEEeeeeecccc
Q 031197 91 QSAHTIEGKCTVHTFKNYTKLENV---GAEDYFCRFEYKAATG 130 (164)
Q Consensus 91 i~~~~I~gkc~V~~~~~~~~~~~~---~~~~f~cr~~yd~~~~ 130 (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 999999999999999999988742 4678999999998874
No 18
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=99.92 E-value=1.3e-25 Score=185.83 Aligned_cols=161 Identities=35% Similarity=0.478 Sum_probs=144.8
Q ss_pred CCCCCCcceeeeEEEcCCCeEEcc-CCEEEEccCCCCCCCeEEEEcEEeeccC-CcEEEEEEEeeecccccCccc---cc
Q 031197 2 AKTKPGKKDLDSYNIKGTNKVVRP-GDCVLMRPADSDKPPYVARVEKIEADHR-NNVKVRVRWYYRPEESIGGRR---QF 76 (164)
Q Consensus 2 ~~~~~~~~~Y~s~~i~g~~~~~~v-GD~V~v~~~~~~~~~~ig~I~~i~~~~~-g~~~v~v~Wfyrp~e~~~~~~---~~ 76 (164)
||+++.+.+|.+|..+++ .+.. ||.|++.++++..+||||+|+.|+.+.. +.+.+.|+|||||+|+..+.. ..
T Consensus 31 Gv~~~k~~h~~t~~~~~g--~~~~~~d~vllvped~~~pPyvaii~~i~a~~~g~~~k~ev~W~YrPee~~~~~~~~~~a 108 (464)
T KOG1886|consen 31 GVGGVKSLHFETFIYRGG--RYINYGDSVLLVPEDPGKPPYVAIIEDIYAQERGGNVKVEVQWFYRPEESEGGGSGKWGA 108 (464)
T ss_pred cccccccccccceeeccC--cccccCcceeecCCCCCCCCeeEEEeeeeccccCCCcceecccccCCCccCCCCCCCccc
Confidence 566666999999999975 5555 9999999999889999999999999886 589999999999999997643 33
Q ss_pred CCCceeEEeCCeeeeccceEEEeeEEEeeecccccCC-CCcceEEEeeeeecccceecCCCcceeeeecCCCCCCCceEe
Q 031197 77 HGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLEN-VGAEDYFCRFEYKAATGGFTPDRVAVYCKCEMPYNPDDLMVQ 155 (164)
Q Consensus 77 ~~~~Elf~s~~~d~i~~~~I~gkc~V~~~~~~~~~~~-~~~~~f~cr~~yd~~~~~f~p~~~~~~C~C~~p~~pd~~~~~ 155 (164)
..++|||+|.|.|.+++++|.++|.|.++..+.+++. .+-+.|+||..||..++.|.+-...-.|.|++..+|++...+
T Consensus 109 ~~~relF~SfH~De~~A~ti~~rC~V~fvp~~kqlp~~~~~~~f~~r~vYd~~~~~~~~~~~~~~~~~~k~e~d~~~~kt 188 (464)
T KOG1886|consen 109 KQPRELFLSFHEDEAFAETILHRCKVHFVPAYKQLPNRVGHESFICRRVYDAVTSKLRKLRDGDFGDGQKLEIDMLVPKT 188 (464)
T ss_pred CCCccccccccccchhhhhhcccceeeeccccccccccCCCCCcccccccccccccccCccccchhcccccCCccchhhh
Confidence 4678999999999999999999999999999999876 678899999999999999998788889999999999999999
Q ss_pred CcccccccC
Q 031197 156 CEGCKDWIY 164 (164)
Q Consensus 156 C~~C~~w~h 164 (164)
|..|..|+|
T Consensus 189 ~~~~~~~~~ 197 (464)
T KOG1886|consen 189 GPRRGTLPD 197 (464)
T ss_pred cccCCCCCC
Confidence 999999976
No 19
>cd04711 BAH_Dnmt1_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.89 E-value=3.3e-23 Score=146.47 Aligned_cols=99 Identities=25% Similarity=0.530 Sum_probs=82.5
Q ss_pred CCCCCCeEEEEcEEeeccCC-------cEEEEEEEeeecccccCcccc-cCC-CceeEEeCCeeeeccceEEEeeEEEee
Q 031197 35 DSDKPPYVARVEKIEADHRN-------NVKVRVRWYYRPEESIGGRRQ-FHG-AKELFLSDHYDVQSAHTIEGKCTVHTF 105 (164)
Q Consensus 35 ~~~~~~~ig~I~~i~~~~~g-------~~~v~v~Wfyrp~e~~~~~~~-~~~-~~Elf~s~~~d~i~~~~I~gkc~V~~~ 105 (164)
+.+.+++||||.+|....++ .++|+|+|||||+|+..+++. ++. -||||+|+|.+++|+++|.|||+|...
T Consensus 22 d~~ePy~VgrI~eI~~~k~~~~k~~~~~ikvrV~~fYRPEdi~~g~~~ayhsDirevy~Sd~~~~~~~~~I~GKC~V~~~ 101 (137)
T cd04711 22 DAPEPFRIGRIKEIFCAKRSNGKPNESDIKLRINKFYRPENTHKGFKATYHADINMLYWSDEEATVDFSAVQGRCTVEYG 101 (137)
T ss_pred CCCCCcEEEEEEEEecCCCCCCCCCccceEEEEEEEecccccccccccccccceeeEEeecceeecChhhccceEEEEec
Confidence 44589999999999886532 478999999999999998654 444 499999999999999999999999965
Q ss_pred ecccc-c---CCCCcceEEEeeeeecccceec
Q 031197 106 KNYTK-L---ENVGAEDYFCRFEYKAATGGFT 133 (164)
Q Consensus 106 ~~~~~-~---~~~~~~~f~cr~~yd~~~~~f~ 133 (164)
++... + ...+++.|||+..||..++.|+
T Consensus 102 ~di~~s~~~y~~~gpd~Fyf~~~Y~a~t~~F~ 133 (137)
T cd04711 102 EDLPESVQEYSGGGPDRFYFLEAYNAKTKSFE 133 (137)
T ss_pred cccchhHHHHhcCCCcceEEhhhhccccCccc
Confidence 55432 1 2257899999999999999998
No 20
>KOG1827 consensus Chromatin remodeling complex RSC, subunit RSC1/Polybromo and related proteins [Chromatin structure and dynamics; Transcription]
Probab=99.67 E-value=5e-17 Score=139.56 Aligned_cols=126 Identities=23% Similarity=0.335 Sum_probs=112.7
Q ss_pred EEEcCCCeEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeecccccCcccccCCCceeEEeCCeeeecc
Q 031197 14 YNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSA 93 (164)
Q Consensus 14 ~~i~g~~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~~~~~~~Elf~s~~~d~i~~ 93 (164)
..|+|. .|.+||.||+.+.++..++.|++|.++|++.+|+.++.+.|||||++|.+-..+.+..+|+|.|......++
T Consensus 184 ~~i~~~--~~~~gd~vlv~~~~d~~~p~v~~Ier~w~~~dg~k~~~~~w~~rP~~T~H~a~r~F~k~Evfkt~~~~~~~~ 261 (629)
T KOG1827|consen 184 VEIDGT--KYIVGDYVLVQNPADNLKPIVAQIERLWKLPDGEKWPQGCWIYRPEETVHRADRKFYKQEVFKTSLYRDDLV 261 (629)
T ss_pred ccccCc--ccccCceeeecCcccccCCceeeecccccCcccccccceeEeeCCccCccccccchhcccceecccccccHH
Confidence 456654 899999999999885689999999999999999999999999999999987666678999999999999999
Q ss_pred ceEEEeeEEEeeecccccCCC---CcceEEEeeeeecccceecCCCcceee
Q 031197 94 HTIEGKCTVHTFKNYTKLENV---GAEDYFCRFEYKAATGGFTPDRVAVYC 141 (164)
Q Consensus 94 ~~I~gkc~V~~~~~~~~~~~~---~~~~f~cr~~yd~~~~~f~p~~~~~~C 141 (164)
..|+|+|.|+.+.+|...++. ..++|+|.+.|+...+.|.....+..|
T Consensus 262 q~l~g~c~v~~~~~yi~~~p~~ls~~dv~lcesRyn~~~K~f~kirsw~~~ 312 (629)
T KOG1827|consen 262 QRLLGKCYVMKPTEYISGDPENLSEEDVFLCESRYNEQLKKFNKIRSWKAF 312 (629)
T ss_pred HHhhcceEEeehhHhhhcCcccccccceeeEEeeeccchhhhccccCchhc
Confidence 999999999999999998773 588999999999999999976555544
No 21
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=99.23 E-value=8e-13 Score=109.60 Aligned_cols=113 Identities=25% Similarity=0.436 Sum_probs=95.7
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeecccccCc---------c-------------------
Q 031197 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGG---------R------------------- 73 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~---------~------------------- 73 (164)
.|++||+||+.... ..++.|-+|+++-.+.+|++.++|--|||..|++.. +
T Consensus 5 ~y~vgd~vYf~~ss-s~PYliRrIEELnKTa~GnVeAkvVc~~RRRDIs~~L~~lAD~~ar~~~~y~a~~~a~~~~e~e~ 83 (693)
T KOG3554|consen 5 MYRVGDYVYFENSS-SNPYLIRRIEELNKTANGNVEAKVVCYLRRRDISSHLLKLADKHARRFDNYAAPEAAPEATEAEI 83 (693)
T ss_pred cceecceEEEecCC-CChHHHHHHHHHhccccCCcceEEEEEEEccchHHHHHHHHHHHhhhcccccCcccCcccchhhh
Confidence 79999999999887 467789999999999999999999999999987521 1
Q ss_pred -----cc-----------cCCCceeEEeCCeeeeccceEEEeeEEEeeecccccCC--CCcceEEEeeeeecccceecCC
Q 031197 74 -----RQ-----------FHGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLEN--VGAEDYFCRFEYKAATGGFTPD 135 (164)
Q Consensus 74 -----~~-----------~~~~~Elf~s~~~d~i~~~~I~gkc~V~~~~~~~~~~~--~~~~~f~cr~~yd~~~~~f~p~ 135 (164)
.+ ..-.+|||+|.+.+..|+..|+|||.|..+.+-+.+.. ..+|+||+...||+..+++..+
T Consensus 84 EEe~e~p~~vdlt~~qrhqLrhrElFlsRQ~EsLPAthIRGKCsV~LLnete~~~~YL~~eDtFfySLVyDP~~kTLLAD 163 (693)
T KOG3554|consen 84 EEESECPAPVDLTEKQRHQLRHRELFLSRQSESLPATHIRGKCSVTLLNETESLQSYLEKEDTFFYSLVYDPNQKTLLAD 163 (693)
T ss_pred hhhccCCCcCCCCHHHHHHHHHHHHHHhhhhccCchhhhccceeEEEecChHHHHhhccccceeEEEeeeccchhhhhcc
Confidence 00 12368999999999999999999999999988766543 3689999999999999888763
No 22
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=97.30 E-value=0.00011 Score=43.58 Aligned_cols=24 Identities=38% Similarity=1.050 Sum_probs=21.0
Q ss_pred ee-eecCCCCCCCceEeCcccccccC
Q 031197 140 YC-KCEMPYNPDDLMVQCEGCKDWIY 164 (164)
Q Consensus 140 ~C-~C~~p~~pd~~~~~C~~C~~w~h 164 (164)
.| +|.+ .+++..+|+|++|++|||
T Consensus 1 ~C~vC~~-~~~~~~~i~C~~C~~~~H 25 (51)
T PF00628_consen 1 YCPVCGQ-SDDDGDMIQCDSCNRWYH 25 (51)
T ss_dssp EBTTTTS-SCTTSSEEEBSTTSCEEE
T ss_pred eCcCCCC-cCCCCCeEEcCCCChhhC
Confidence 36 7888 678889999999999999
No 23
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=96.95 E-value=0.00025 Score=58.55 Aligned_cols=84 Identities=25% Similarity=0.345 Sum_probs=68.1
Q ss_pred ceeEEeCCeeeeccceEEEeeEEEeeecccccCCCCcceEEEeeeeecccceecCCCcceeeeecCCCCCCCceEeCccc
Q 031197 80 KELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLENVGAEDYFCRFEYKAATGGFTPDRVAVYCKCEMPYNPDDLMVQCEGC 159 (164)
Q Consensus 80 ~Elf~s~~~d~i~~~~I~gkc~V~~~~~~~~~~~~~~~~f~cr~~yd~~~~~f~p~~~~~~C~C~~p~~pd~~~~~C~~C 159 (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 34566666667777777788877777766654 44567788888888888888887778899999999999999999999
Q ss_pred ccccC
Q 031197 160 KDWIY 164 (164)
Q Consensus 160 ~~w~h 164 (164)
..|||
T Consensus 82 ~~~~~ 86 (345)
T KOG1632|consen 82 EDWYH 86 (345)
T ss_pred ccccc
Confidence 99998
No 25
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=95.44 E-value=0.0065 Score=51.68 Aligned_cols=24 Identities=33% Similarity=0.909 Sum_probs=19.5
Q ss_pred eeeecCCCCCCCceEeCcccccccC
Q 031197 140 YCKCEMPYNPDDLMVQCEGCKDWIY 164 (164)
Q Consensus 140 ~C~C~~p~~pd~~~~~C~~C~~w~h 164 (164)
+|.|-+|..-. .|+||++|+.|||
T Consensus 173 vC~~g~~~~~N-rmlqC~~C~~~fH 196 (464)
T KOG4323|consen 173 VCYCGGPGAGN-RMLQCDKCRQWYH 196 (464)
T ss_pred eeecCCcCccc-eeeeecccccHHH
Confidence 55666665555 9999999999999
No 26
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=94.70 E-value=0.016 Score=46.49 Aligned_cols=27 Identities=26% Similarity=0.827 Sum_probs=22.3
Q ss_pred CcceeeeecCCCCCCCceEeCcc--cc-cccC
Q 031197 136 RVAVYCKCEMPYNPDDLMVQCEG--CK-DWIY 164 (164)
Q Consensus 136 ~~~~~C~C~~p~~pd~~~~~C~~--C~-~w~h 164 (164)
.-+.+|+|+ ..--..||.||+ |. .|||
T Consensus 217 ~e~~yC~Cn--qvsyg~Mi~CDn~~C~~eWFH 246 (274)
T KOG1973|consen 217 DEPTYCICN--QVSYGKMIGCDNPGCPIEWFH 246 (274)
T ss_pred CCCEEEEec--ccccccccccCCCCCCcceEE
Confidence 456899999 345568999996 99 9999
No 27
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=94.00 E-value=0.034 Score=44.98 Aligned_cols=27 Identities=41% Similarity=1.157 Sum_probs=23.9
Q ss_pred ceeeeecCCCCC-----CCceEeCcccccccC
Q 031197 138 AVYCKCEMPYNP-----DDLMVQCEGCKDWIY 164 (164)
Q Consensus 138 ~~~C~C~~p~~p-----d~~~~~C~~C~~w~h 164 (164)
-+.|+|+-|+++ +..|+||-.|..|||
T Consensus 128 G~~C~Cd~~Ypdp~~~~e~~m~QC~iCEDWFH 159 (345)
T KOG2752|consen 128 GLFCKCDTPYPDPVRTEEGEMLQCVICEDWFH 159 (345)
T ss_pred ceeEEecCCCCCccccccceeeeEEeccchhc
Confidence 469999999985 348999999999999
No 28
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=93.94 E-value=0.12 Score=31.04 Aligned_cols=41 Identities=17% Similarity=0.235 Sum_probs=29.0
Q ss_pred EccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeecc
Q 031197 23 VRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPE 67 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~ 67 (164)
+++||.|.+++++ ...-|..|..- ......++..+||---.
T Consensus 1 f~~GDvV~LKSGG--p~MTV~~v~~~--~~~~~~~v~C~WFd~~~ 41 (53)
T PF09926_consen 1 FKIGDVVQLKSGG--PRMTVTEVGPN--AGASGGWVECQWFDGHG 41 (53)
T ss_pred CCCCCEEEEccCC--CCeEEEEcccc--ccCCCCeEEEEeCCCCC
Confidence 4799999999998 45666655544 12344689999997443
No 29
>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]
Probab=88.87 E-value=0.042 Score=45.83 Aligned_cols=89 Identities=13% Similarity=0.075 Sum_probs=76.3
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeecccccCcccccCCCceeEEeCCeeeeccceEEEee
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKC 100 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~~~~~~~Elf~s~~~d~i~~~~I~gkc 100 (164)
....+|+.+.+.+..+...+.++++...|.+.++..+.-+.|||+|.++.......+..+++......+........+.|
T Consensus 275 ~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 (371)
T COG5076 275 SQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTDYYKNANVLED 354 (371)
T ss_pred cccccccccccccCCcccccchhhhhhcccccccchhhhhcccCCCccccccccchhhhcccccchhhhhhhhhccchhh
Confidence 37899999999988777899999999999998888888999999999777766666778999999989999999999988
Q ss_pred EEEeeeccc
Q 031197 101 TVHTFKNYT 109 (164)
Q Consensus 101 ~V~~~~~~~ 109 (164)
.|....++.
T Consensus 355 ~~~~~~~~~ 363 (371)
T COG5076 355 FVIKKTRLI 363 (371)
T ss_pred hHhhhhhhh
Confidence 887765544
No 30
>PRK10708 hypothetical protein; Provisional
Probab=88.49 E-value=2 Score=25.97 Aligned_cols=44 Identities=14% Similarity=0.234 Sum_probs=32.4
Q ss_pred ccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEE-------EEEEeeecccc
Q 031197 24 RPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKV-------RVRWYYRPEES 69 (164)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v-------~v~Wfyrp~e~ 69 (164)
+++|.|.|++++ .+...|.|..+-.=..|.+++ .+.||+.-.+-
T Consensus 2 kvnD~VtVKTDG--~~rR~G~iLavE~F~EG~MyLvaL~dYP~GiWFFNE~~~ 52 (62)
T PRK10708 2 KVNDRVTVKTDG--GPRRPGVVLAVEEFSEGTMYLVSLEDYPLGIWFFNEAGH 52 (62)
T ss_pred ccccEEEEecCC--CccccceEEEEeeccCcEEEEEEcCcCCCceEEEeccCC
Confidence 689999999997 778889998887666676554 35677655443
No 31
>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=88.40 E-value=2.4 Score=25.65 Aligned_cols=45 Identities=13% Similarity=0.284 Sum_probs=32.6
Q ss_pred ccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEE-------EEEEeeeccccc
Q 031197 24 RPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKV-------RVRWYYRPEESI 70 (164)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v-------~v~Wfyrp~e~~ 70 (164)
+++|.|.|++++ .+..-|.|..+.+=..|.+++ .+.||+.-.+-+
T Consensus 2 kvnD~VtVKTDG--~~rR~G~ilavE~F~EG~MYLvaL~dYP~GiWFFNE~~~~ 53 (62)
T PF10781_consen 2 KVNDRVTVKTDG--GPRREGVILAVEPFNEGTMYLVALEDYPAGIWFFNEKDSP 53 (62)
T ss_pred ccccEEEEecCC--cccccceEEEEeeccCcEEEEEEcCcCCcceEEEecCCCC
Confidence 689999999997 677888888887666675544 356776655433
No 32
>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=88.31 E-value=0.88 Score=29.76 Aligned_cols=44 Identities=25% Similarity=0.320 Sum_probs=35.3
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeecc
Q 031197 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPE 67 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~ 67 (164)
.+++||.|.-+-.+ -++|-|+|.+.-+.......+.|+||-..+
T Consensus 2 ~f~~GdlVwaK~kG--yp~WPa~I~~~~~~~~~~~~~~V~FfGt~~ 45 (83)
T cd05834 2 QFKAGDLVFAKVKG--YPAWPARVDEPEDWKPPGKKYPVYFFGTHE 45 (83)
T ss_pred CCCCCCEEEEecCC--CCCCCEEEecccccCCCCCEEEEEEeCCCC
Confidence 57899999999876 799999999987653445679999988543
No 33
>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=85.89 E-value=1.2 Score=29.34 Aligned_cols=41 Identities=22% Similarity=0.199 Sum_probs=32.1
Q ss_pred EccCCEEEEccCCCCCCCeEEEEcEEeecc---CCcEEEEEEEeee
Q 031197 23 VRPGDCVLMRPADSDKPPYVARVEKIEADH---RNNVKVRVRWYYR 65 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~---~g~~~v~v~Wfyr 65 (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 4689999999876 789999999986553 1235789999863
No 34
>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=84.43 E-value=2 Score=26.20 Aligned_cols=40 Identities=15% Similarity=0.297 Sum_probs=26.5
Q ss_pred EccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEe
Q 031197 23 VRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWY 63 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wf 63 (164)
-++||.+.|.+..-..+...|.|+++.- ++|..-..|+|-
T Consensus 3 A~vGD~lvv~g~~vg~~~r~GeIveV~g-~dG~PPY~VRw~ 42 (58)
T PF08940_consen 3 ASVGDRLVVHGRTVGQPDRHGEIVEVRG-PDGSPPYLVRWD 42 (58)
T ss_dssp --TTEEEEES-TTTS--EEEEEEEE-S--SSS-S-EEEEET
T ss_pred CCCCCEEEEcCCcCCCCCcEeEEEEEEC-CCCCCCEEEEec
Confidence 3689999999876668899999999987 467778889985
No 35
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=83.44 E-value=0.78 Score=36.25 Aligned_cols=27 Identities=33% Similarity=0.912 Sum_probs=21.2
Q ss_pred CcceeeeecCCCCCCCceEeCc--ccc-cccC
Q 031197 136 RVAVYCKCEMPYNPDDLMVQCE--GCK-DWIY 164 (164)
Q Consensus 136 ~~~~~C~C~~p~~pd~~~~~C~--~C~-~w~h 164 (164)
.-..+|-|+|+ .-..||.|| .|. .|||
T Consensus 219 ~e~lYCfCqqv--SyGqMVaCDn~nCkrEWFH 248 (271)
T COG5034 219 GEELYCFCQQV--SYGQMVACDNANCKREWFH 248 (271)
T ss_pred CceeEEEeccc--ccccceecCCCCCchhhee
Confidence 34679999998 346899997 786 5998
No 36
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=83.39 E-value=2.6 Score=27.11 Aligned_cols=31 Identities=29% Similarity=0.503 Sum_probs=24.7
Q ss_pred EEccCCEEEEccCC-----CCCCCeEEEEcEEeecc
Q 031197 22 VVRPGDCVLMRPAD-----SDKPPYVARVEKIEADH 52 (164)
Q Consensus 22 ~~~vGD~V~v~~~~-----~~~~~~ig~I~~i~~~~ 52 (164)
.++.||+|.|..++ .+..-|+|+|...-...
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~gga 40 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGA 40 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEeccc
Confidence 47899999998865 24678999999987653
No 37
>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=83.30 E-value=2.4 Score=27.66 Aligned_cols=39 Identities=21% Similarity=0.226 Sum_probs=31.8
Q ss_pred EccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeec
Q 031197 23 VRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRP 66 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp 66 (164)
+.+||.|.-+-.+ -+.|.|+|.++.. +...+.|.||=..
T Consensus 1 f~~gdlVWaK~~g--~P~WPa~I~~~~~---~~~k~~V~FfG~~ 39 (80)
T cd06080 1 FEKNDLVWAKIQG--YPWWPAVIKSISR---KKQKARVNFIGDN 39 (80)
T ss_pred CCCCCEEEEeCCC--CCCCCEEEeeecC---CCCEEEEEEeCCC
Confidence 4689999998876 7899999999864 3567889988766
No 38
>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=82.67 E-value=4.4 Score=24.14 Aligned_cols=36 Identities=22% Similarity=0.262 Sum_probs=25.7
Q ss_pred EccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEE
Q 031197 23 VRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVR 61 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~ 61 (164)
+.+|+.|++.-.+ ...+-|+|+++... .|.....|.
T Consensus 1 ~~vG~~v~~~~~~--~~~y~A~I~~~r~~-~~~~~YyVH 36 (55)
T PF11717_consen 1 FEVGEKVLCKYKD--GQWYEAKILDIREK-NGEPEYYVH 36 (55)
T ss_dssp --TTEEEEEEETT--TEEEEEEEEEEEEC-TTCEEEEEE
T ss_pred CCcCCEEEEEECC--CcEEEEEEEEEEec-CCCEEEEEE
Confidence 4689999999843 78999999999984 444444443
No 39
>PRK13251 transcription attenuation protein MtrB; Provisional
Probab=82.53 E-value=5.4 Score=25.25 Aligned_cols=48 Identities=21% Similarity=0.177 Sum_probs=38.6
Q ss_pred EEEEEeeecccccCcccccCCCceeEEeCCeeeeccceEEEeeEEEee
Q 031197 58 VRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHTF 105 (164)
Q Consensus 58 v~v~Wfyrp~e~~~~~~~~~~~~Elf~s~~~d~i~~~~I~gkc~V~~~ 105 (164)
|.|.=+-|..|+.-......+..||.+...++..++-.|+||+.+++.
T Consensus 19 V~vIgltrg~dtkfhhtEkLDkGEVmiaqftehtsaiKirGkA~I~t~ 66 (75)
T PRK13251 19 VNVIGLTRGKDTKFHHTEKLDKGEVMIAQFTEHTSAIKIRGKAEIQTK 66 (75)
T ss_pred eEEEEEecCCCccchhhhhcCCCcEEEEEeecceeEEEEeceEEEEee
Confidence 666667778887644333468999999999999999999999999874
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=81.64 E-value=2.7 Score=27.32 Aligned_cols=40 Identities=30% Similarity=0.321 Sum_probs=31.5
Q ss_pred EccCCEEEEccCCCCCCCeEEEEcEEeecc------CCcEEEEEEEee
Q 031197 23 VRPGDCVLMRPADSDKPPYVARVEKIEADH------RNNVKVRVRWYY 64 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~------~g~~~v~v~Wfy 64 (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 4789999999986 689999999988753 223577888775
No 41
>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=80.99 E-value=3.8 Score=25.96 Aligned_cols=48 Identities=21% Similarity=0.143 Sum_probs=35.6
Q ss_pred EEEEEeeecccccCcccccCCCceeEEeCCeeeeccceEEEeeEEEee
Q 031197 58 VRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHTF 105 (164)
Q Consensus 58 v~v~Wfyrp~e~~~~~~~~~~~~Elf~s~~~d~i~~~~I~gkc~V~~~ 105 (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 666667777777644333468999999999999999999999999873
No 42
>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=80.86 E-value=9.3 Score=27.42 Aligned_cols=52 Identities=19% Similarity=0.308 Sum_probs=37.0
Q ss_pred eeeeEEEcCCCeEEccCCEEEEccCC----------CCCCCeEEEEcEEeeccCC-------cEEEEEEEe
Q 031197 10 DLDSYNIKGTNKVVRPGDCVLMRPAD----------SDKPPYVARVEKIEADHRN-------NVKVRVRWY 63 (164)
Q Consensus 10 ~Y~s~~i~g~~~~~~vGD~V~v~~~~----------~~~~~~ig~I~~i~~~~~g-------~~~v~v~Wf 63 (164)
||.++.+.. +.+.+||.|-|++.. ..+..-|-.|.+|...... .+.+++.-|
T Consensus 2 ~y~GiflGA--E~I~vGD~VRl~~~~~~~~~~~~~~~~~~tdvMvI~~I~~~~~~~~~~~~~~v~~~G~lY 70 (139)
T PF10383_consen 2 YYRGIFLGA--EMIWVGDAVRLKPLNASPSPNQSDGNPDVTDVMVIDEIQLRLINCDPDSPSTVRFRGDLY 70 (139)
T ss_pred eECeEEEee--EEEEeCCEEEECccCCCcccccccCCCCceeEEEEeEEEEecccCCCCCCceEEEEeEec
Confidence 788887774 699999999995432 2356678888888876422 477777743
No 43
>COG5475 Uncharacterized small protein [Function unknown]
Probab=80.51 E-value=8.4 Score=23.30 Aligned_cols=38 Identities=13% Similarity=0.156 Sum_probs=25.9
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeecc
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPE 67 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~ 67 (164)
..+++||.|.+++++| ... ++=+ ...-++..+||-+..
T Consensus 3 ~~FstgdvV~lKsGGP--~Mt----vs~~---ss~Gmy~C~Wf~g~g 40 (60)
T COG5475 3 MSFSTGDVVTLKSGGP--RMT----VSGY---SSDGMYECRWFDGYG 40 (60)
T ss_pred ceeecCcEEEeecCCc--eEE----Eecc---ccCCeEEEEEecCCC
Confidence 4789999999999984 111 1111 122589999998766
No 44
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=80.40 E-value=2.8 Score=25.69 Aligned_cols=40 Identities=20% Similarity=0.170 Sum_probs=30.0
Q ss_pred EccCCEEEEccCCCCCCCeEEEEcEEeeccC-------CcEEEEEEEee
Q 031197 23 VRPGDCVLMRPADSDKPPYVARVEKIEADHR-------NNVKVRVRWYY 64 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~-------g~~~v~v~Wfy 64 (164)
|++||.|..+-.+ -+.|-|+|..-....+ ....+.|++|-
T Consensus 1 f~~GdlVwaK~~G--~p~WPa~V~~~~~~~~~~~~~~~~~~~~~V~Ffg 47 (63)
T smart00293 1 FKPGDLVWAKMKG--FPWWPALVVSPKETPDNIRKRKRFENLYPVLFFG 47 (63)
T ss_pred CCCCCEEEEECCC--CCCCCeEEcCcccCChhHhhccCCCCEEEEEEeC
Confidence 5789999999987 7899999998875432 23566677664
No 45
>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=79.03 E-value=5 Score=21.04 Aligned_cols=26 Identities=15% Similarity=0.233 Sum_probs=22.1
Q ss_pred cCCEEEEccCCCCCCCeEEEEcEEeecc
Q 031197 25 PGDCVLMRPADSDKPPYVARVEKIEADH 52 (164)
Q Consensus 25 vGD~V~v~~~~~~~~~~ig~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 59999999997 677999999998653
No 46
>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=79.00 E-value=6.1 Score=28.58 Aligned_cols=50 Identities=24% Similarity=0.314 Sum_probs=35.1
Q ss_pred cceeeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeeccc
Q 031197 8 KKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEE 68 (164)
Q Consensus 8 ~~~Y~s~~i~g~~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~e 68 (164)
....++.++.+- .+++||.|.+...+ +.+-.-.|..|.. ++-.|||-=+-
T Consensus 75 tg~~q~~tv~kp--~F~LGd~V~~~f~~--~~pkqRlIlGv~l-------v~~~W~Y~VE~ 124 (150)
T PF07154_consen 75 TGQLQSLTVQKP--AFRLGDRVEFRFYS--DGPKQRLILGVFL-------VNNSWFYAVEW 124 (150)
T ss_pred cCccceeeccCC--ceecCCEEEEEecC--CCCceEEEEEEEE-------ecCceEEEEEE
Confidence 344556666654 78999999998865 4666777777754 66678887664
No 47
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=78.95 E-value=1.6 Score=26.24 Aligned_cols=23 Identities=22% Similarity=0.433 Sum_probs=21.4
Q ss_pred eecCCCCCCCceEeCcccccccC
Q 031197 142 KCEMPYNPDDLMVQCEGCKDWIY 164 (164)
Q Consensus 142 ~C~~p~~pd~~~~~C~~C~~w~h 164 (164)
.|.++..|.+.++.|+.|..=||
T Consensus 10 ~Cg~~~~~~dDiVvCp~CgapyH 32 (54)
T PF14446_consen 10 VCGKKFKDGDDIVVCPECGAPYH 32 (54)
T ss_pred hhCCcccCCCCEEECCCCCCccc
Confidence 68999999999999999999888
No 48
>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=76.26 E-value=3.9 Score=27.31 Aligned_cols=40 Identities=28% Similarity=0.382 Sum_probs=29.8
Q ss_pred EccCCEEEEccCCCCCCCeEEEEcEEe---------eccCCcEEEEEEEee
Q 031197 23 VRPGDCVLMRPADSDKPPYVARVEKIE---------ADHRNNVKVRVRWYY 64 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~ig~I~~i~---------~~~~g~~~v~v~Wfy 64 (164)
+++||.|..+-.+ -+.|-|+|..-. ....+...+.|++|-
T Consensus 1 f~~GDlVwaK~~G--yPwWPA~V~~~~~~p~~~l~~~~~~~~~~~~V~FFg 49 (93)
T cd05840 1 FQPGDRVLAKVKG--FPAWPAIVVPEEMLPDSVLKGKKKKNKRTYPVMFFP 49 (93)
T ss_pred CCCCCEEEEeCCC--CCCCCEEECChHHCCHHHHhcccCCCCCeEEEEEeC
Confidence 4789999999887 799999998622 112345678888884
No 49
>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=75.18 E-value=3.3 Score=26.54 Aligned_cols=40 Identities=33% Similarity=0.455 Sum_probs=29.5
Q ss_pred EccCCEEEEccCCCCCCCeEEEEcEEeecc---CCcEEEEEEEee
Q 031197 23 VRPGDCVLMRPADSDKPPYVARVEKIEADH---RNNVKVRVRWYY 64 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~---~g~~~v~v~Wfy 64 (164)
|++||.|..+-.+ -+.|-|+|....... .....+.|+||-
T Consensus 1 f~~GdlVWaK~~g--~pwWPa~V~~~~~~~~~~~~~~~~~V~Ffg 43 (86)
T PF00855_consen 1 FRPGDLVWAKLKG--YPWWPARVCDPDEKSKKKRKDGHVLVRFFG 43 (86)
T ss_dssp -STTEEEEEEETT--SEEEEEEEEECCHCTSCSSSSTEEEEEETT
T ss_pred CCCCCEEEEEeCC--CCCCceEEeecccccccCCCCCEEEEEecC
Confidence 5789999999876 689999999987432 234566777664
No 50
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=73.64 E-value=6.7 Score=19.32 Aligned_cols=25 Identities=20% Similarity=0.223 Sum_probs=20.3
Q ss_pred EccCCEEEEccCCCCCCCeEEEEcEEe
Q 031197 23 VRPGDCVLMRPADSDKPPYVARVEKIE 49 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~ig~I~~i~ 49 (164)
+.+||.|.|..+. ..-.+|.|.++.
T Consensus 2 ~~~G~~V~I~~G~--~~g~~g~i~~i~ 26 (28)
T smart00739 2 FEVGDTVRVIAGP--FKGKVGKVLEVD 26 (28)
T ss_pred CCCCCEEEEeECC--CCCcEEEEEEEc
Confidence 4689999999986 566788888875
No 51
>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=70.95 E-value=13 Score=25.68 Aligned_cols=45 Identities=18% Similarity=0.257 Sum_probs=34.2
Q ss_pred CCCCCcceeeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEcEEeecc
Q 031197 3 KTKPGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADH 52 (164)
Q Consensus 3 ~~~~~~~~Y~s~~i~g~~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~ 52 (164)
|--+|+-..-.+.+..+ ++++||.+.+-..+ .|-+++|..|..+.
T Consensus 9 k~~~G~G~t~dvIl~~G--tL~~GD~Iv~g~~~---Gpi~tkVRaLl~~~ 53 (110)
T cd03703 9 KEEEGLGTTIDVILYDG--TLREGDTIVVCGLN---GPIVTKVRALLKPQ 53 (110)
T ss_pred EEcCCCceEEEEEEECC--eEecCCEEEEccCC---CCceEEEeEecCCC
Confidence 33466667767766533 99999999998764 68899999998753
No 52
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=69.22 E-value=2.3 Score=22.01 Aligned_cols=22 Identities=18% Similarity=0.480 Sum_probs=7.7
Q ss_pred eecCCCCCCCceEeCcccccccC
Q 031197 142 KCEMPYNPDDLMVQCEGCKDWIY 164 (164)
Q Consensus 142 ~C~~p~~pd~~~~~C~~C~~w~h 164 (164)
.|.++... ...+.|..|+..+|
T Consensus 5 ~C~~~~~~-~~~Y~C~~Cdf~lH 26 (30)
T PF07649_consen 5 ACGKPIDG-GWFYRCSECDFDLH 26 (30)
T ss_dssp TTS----S---EEE-TTT-----
T ss_pred cCCCcCCC-CceEECccCCCccC
Confidence 45666555 57888999999887
No 53
>PF09871 DUF2098: Uncharacterized protein conserved in archaea (DUF2098); InterPro: IPR019209 This family of proteins have no known function.
Probab=68.66 E-value=16 Score=24.43 Aligned_cols=43 Identities=23% Similarity=0.336 Sum_probs=31.9
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEE---EEeeeccccc
Q 031197 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRV---RWYYRPEESI 70 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v---~Wfyrp~e~~ 70 (164)
.|.+|++|-=.+.+ -+|+|.+| ...++..||.+ .-||||+-+.
T Consensus 2 ~I~vGs~VRY~~TG-----T~G~V~di-K~ed~~~wv~LD~t~L~Yr~~~Le 47 (91)
T PF09871_consen 2 PIKVGSYVRYINTG-----TVGKVVDI-KEEDGETWVLLDSTDLYYRPDYLE 47 (91)
T ss_pred cceeCCEEEECCCC-----eEEEEEEE-EEeCCCeEEEEccCCceeecceeE
Confidence 57888887655443 58999999 44577788877 7788888654
No 54
>COG1370 Prefoldin, molecular chaperone implicated in de novo protein folding, alpha subunit [Posttranslational modification, protein turnover, chaperones]
Probab=66.72 E-value=4.7 Score=29.41 Aligned_cols=40 Identities=30% Similarity=0.407 Sum_probs=32.6
Q ss_pred CCCcceeeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEc
Q 031197 5 KPGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVE 46 (164)
Q Consensus 5 ~~~~~~Y~s~~i~g~~~~~~vGD~V~v~~~~~~~~~~ig~I~ 46 (164)
++||..+-.|.+.. +..+++||-|+|-+++ +.-.-+|+..
T Consensus 94 r~Gk~VFaKfVi~~-D~~iR~~dEvlVVne~-d~LlAvGra~ 133 (155)
T COG1370 94 RKGKSVFAKFVIDV-DEEIRAGDEVLVVNED-DELLAVGRAL 133 (155)
T ss_pred Hhccchhhhheecc-CcccCCCCeEEEECCC-CcEEEeeeEe
Confidence 57899999999997 4899999999999988 4555666643
No 55
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=64.44 E-value=37 Score=25.27 Aligned_cols=76 Identities=22% Similarity=0.289 Sum_probs=46.3
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeecccc---cCcc-cc-cCCCceeEEeCCeeeeccce
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEES---IGGR-RQ-FHGAKELFLSDHYDVQSAHT 95 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~e~---~~~~-~~-~~~~~Elf~s~~~d~i~~~~ 95 (164)
..+..||.|.+.+....++.+|-||..+--+ .+.. .-++++. |.|. +- .-...+=+=|+.+--++...
T Consensus 67 ~~~~rGDiVvl~sP~~p~~~~iKRv~alegd----~~~t---~~~k~~~v~vpkghcWVegDn~~hs~DSntFGPVS~gl 139 (174)
T KOG1568|consen 67 RKVSRGDIVVLKSPNDPDKVIIKRVAALEGD----IMVT---EDEKEEPVVVPKGHCWVEGDNQKHSYDSNTFGPVSTGL 139 (174)
T ss_pred ceeccCCEEEEeCCCChhheeeeeeeccccc----Eecc---CCCCCCceecCCCcEEEecCCcccccccCccCCcchhh
Confidence 4678999999988765688999999887532 2221 2223332 1110 00 01234445566667789999
Q ss_pred EEEeeEEE
Q 031197 96 IEGKCTVH 103 (164)
Q Consensus 96 I~gkc~V~ 103 (164)
|.|++.-.
T Consensus 140 i~grai~i 147 (174)
T KOG1568|consen 140 IVGRAIYI 147 (174)
T ss_pred eeeeEEEE
Confidence 99998543
No 56
>PTZ00112 origin recognition complex 1 protein; Provisional
Probab=63.33 E-value=15 Score=34.83 Aligned_cols=116 Identities=22% Similarity=0.311 Sum_probs=72.0
Q ss_pred ceeeeEEEcCCCeEEccCCEEEEccCCCC-------------------C---CCeEEEEcEEeeccC-CcEEEEEEEeee
Q 031197 9 KDLDSYNIKGTNKVVRPGDCVLMRPADSD-------------------K---PPYVARVEKIEADHR-NNVKVRVRWYYR 65 (164)
Q Consensus 9 ~~Y~s~~i~g~~~~~~vGD~V~v~~~~~~-------------------~---~~~ig~I~~i~~~~~-g~~~v~v~Wfyr 65 (164)
.-|+|..|++ +.|.+||.|+|.-+... . ..--|+|.+|+.... ..+.+.|..||-
T Consensus 441 ~iye~~~in~--~~ys~g~dv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~kg~is~fy~~~~~~~~~~e~c~y~d 518 (1164)
T PTZ00112 441 VIYESIQIND--VEYSIGDDVLIFCTGNGNTYNGKSGTKKNQNNKNIKENIYQLRKGKISSFYKNTNSNQVEAEVCIYYD 518 (1164)
T ss_pred eEEEEEEEcc--eeeccCCcEEEEEcCCCCccccccCccccccccchhhhhheecccccchhhhcCCCceeeEEEEEEEc
Confidence 3589999996 59999999999754311 1 223589999998764 468999999999
Q ss_pred cccccC---------cccccCCCceeEEeCC-----------eeeeccceEEEeeEEEeeec-cccc--CCCCcceEEEe
Q 031197 66 PEESIG---------GRRQFHGAKELFLSDH-----------YDVQSAHTIEGKCTVHTFKN-YTKL--ENVGAEDYFCR 122 (164)
Q Consensus 66 p~e~~~---------~~~~~~~~~Elf~s~~-----------~d~i~~~~I~gkc~V~~~~~-~~~~--~~~~~~~f~cr 122 (164)
..|-+- .|+ .-..-|+|+-+. +-...+.-|..|..|..-.+ |..- ...|.+-|.|-
T Consensus 519 ~~d~~~i~~~~~~~~~rr-~~~~f~~~~d~~~~~~~llgni~f~~~~~~~i~kki~~~ne~~~~~~d~~~~~g~~kflc~ 597 (1164)
T PTZ00112 519 QHDAQYIKELEEKQKSRR-CKADFEVFLDDDTKNFYLLGNIHFKILDAKMILKKIYVYNEKELYDEDKTAKQGKDKFLCT 597 (1164)
T ss_pred cccHHHHHHHHHHHHhhh-hhhhhhHhcccccceeEEecceeEEEechHhhhhhheeecchhhcccchhhhcccchhhhh
Confidence 887531 111 123455555543 34556667777777765432 2110 11356667775
Q ss_pred eeeec
Q 031197 123 FEYKA 127 (164)
Q Consensus 123 ~~yd~ 127 (164)
+..-.
T Consensus 598 ~~~k~ 602 (1164)
T PTZ00112 598 HYLKE 602 (1164)
T ss_pred Hhhhc
Confidence 54433
No 57
>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=63.26 E-value=3.6 Score=25.83 Aligned_cols=11 Identities=55% Similarity=1.310 Sum_probs=7.0
Q ss_pred ceEeCcccccc
Q 031197 152 LMVQCEGCKDW 162 (164)
Q Consensus 152 ~~~~C~~C~~w 162 (164)
-+++|++|++|
T Consensus 28 Viv~C~gC~~~ 38 (66)
T PF05180_consen 28 VIVQCPGCKNR 38 (66)
T ss_dssp EEEE-TTS--E
T ss_pred EEEECCCCcce
Confidence 68999999876
No 58
>PF04322 DUF473: Protein of unknown function (DUF473); InterPro: IPR007417 This is a family of uncharacterised archaeal proteins.
Probab=61.04 E-value=22 Score=24.92 Aligned_cols=43 Identities=26% Similarity=0.471 Sum_probs=30.5
Q ss_pred cceeeeEEEcCCC-----eEEccCCEEEEccCCC-----CCCCeEEEEcEEee
Q 031197 8 KKDLDSYNIKGTN-----KVVRPGDCVLMRPADS-----DKPPYVARVEKIEA 50 (164)
Q Consensus 8 ~~~Y~s~~i~g~~-----~~~~vGD~V~v~~~~~-----~~~~~ig~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 4567788777632 4569999999988662 35667888887753
No 59
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=60.29 E-value=19 Score=25.32 Aligned_cols=40 Identities=20% Similarity=0.059 Sum_probs=26.9
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEcEEeecc-CCcEEEEEE
Q 031197 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADH-RNNVKVRVR 61 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~-~g~~~v~v~ 61 (164)
.+++||.|+...+.....+.-|+|+...+.. .....+.|+
T Consensus 55 ~L~~GD~VLA~~~~~~~~Y~Pg~V~~~~~~~~~~~~~~~V~ 95 (124)
T PF15057_consen 55 SLQVGDKVLAPWEPDDCRYGPGTVIAGPERRASEDKEYTVR 95 (124)
T ss_pred cCCCCCEEEEecCcCCCEEeCEEEEECccccccCCceEEEE
Confidence 6899999999966533344459999876554 233555555
No 60
>COG4014 Uncharacterized protein conserved in archaea [Function unknown]
Probab=60.18 E-value=23 Score=23.50 Aligned_cols=41 Identities=27% Similarity=0.409 Sum_probs=30.0
Q ss_pred EccCCEE-EEccCCCCCCCeEEEEcEEeeccCCcEEEEEE---Eeeecccc
Q 031197 23 VRPGDCV-LMRPADSDKPPYVARVEKIEADHRNNVKVRVR---WYYRPEES 69 (164)
Q Consensus 23 ~~vGD~V-~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~---Wfyrp~e~ 69 (164)
..|||.| ||.++ .+|+|..|.++.+|+.|+..- -+||+.=+
T Consensus 9 ~~VG~avrYvnTg------TvgrV~dIkkdEdG~~WV~LdstdLwYre~~l 53 (97)
T COG4014 9 DKVGDAVRYVNTG------TVGRVVDIKKDEDGDIWVVLDSTDLWYREHYL 53 (97)
T ss_pred hhhcceEEEeecC------ceeeEEEEEeecCCceEEEEecCCceecccce
Confidence 3478875 45444 389999999999999998874 36676633
No 61
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=60.06 E-value=3.3 Score=20.64 Aligned_cols=12 Identities=25% Similarity=0.482 Sum_probs=9.7
Q ss_pred ceEeCccccccc
Q 031197 152 LMVQCEGCKDWI 163 (164)
Q Consensus 152 ~~~~C~~C~~w~ 163 (164)
++++|+.|++.|
T Consensus 1 ~l~~C~~CgR~F 12 (25)
T PF13913_consen 1 ELVPCPICGRKF 12 (25)
T ss_pred CCCcCCCCCCEE
Confidence 367899999876
No 62
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=60.01 E-value=36 Score=22.20 Aligned_cols=30 Identities=23% Similarity=0.212 Sum_probs=25.3
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeecc
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADH 52 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~ 52 (164)
..++.||.|.|.++. +.=-+|+|.++....
T Consensus 7 ~~I~~GD~V~Vi~G~--dKGK~G~V~~V~~~~ 36 (83)
T CHL00141 7 MHVKIGDTVKIISGS--DKGKIGEVLKIIKKS 36 (83)
T ss_pred CcccCCCEEEEeEcC--CCCcEEEEEEEEcCC
Confidence 478999999999986 667789999998753
No 63
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=59.21 E-value=19 Score=23.11 Aligned_cols=30 Identities=20% Similarity=0.217 Sum_probs=25.4
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeecc
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADH 52 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~ 52 (164)
..++.||.|.|.++. +.=-+|+|.++....
T Consensus 5 ~~I~kGD~V~Vi~G~--dKGK~G~V~~V~~~~ 34 (76)
T PRK12281 5 LKVKKGDMVKVIAGD--DKGKTGKVLAVLPKK 34 (76)
T ss_pred ccccCCCEEEEeEcC--CCCcEEEEEEEEcCC
Confidence 468999999999986 677889999998753
No 64
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=58.24 E-value=6.9 Score=26.45 Aligned_cols=28 Identities=21% Similarity=0.609 Sum_probs=20.4
Q ss_pred CCCcceee-eecCCCCCCCceEeCcc--cccccC
Q 031197 134 PDRVAVYC-KCEMPYNPDDLMVQCEG--CKDWIY 164 (164)
Q Consensus 134 p~~~~~~C-~C~~p~~pd~~~~~C~~--C~~w~h 164 (164)
++.+...| +|.+. ....++|.. |.++||
T Consensus 51 ~~~~~~~C~iC~~~---~G~~i~C~~~~C~~~fH 81 (110)
T PF13832_consen 51 PSRFKLKCSICGKS---GGACIKCSHPGCSTAFH 81 (110)
T ss_pred chhcCCcCcCCCCC---CceeEEcCCCCCCcCCC
Confidence 33444555 78776 567999975 999999
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=57.10 E-value=17 Score=23.78 Aligned_cols=42 Identities=21% Similarity=0.265 Sum_probs=30.0
Q ss_pred EccCCEEEEccCCCCCCCeEEEEcEEeecc----CCcEEEEEEEeeec
Q 031197 23 VRPGDCVLMRPADSDKPPYVARVEKIEADH----RNNVKVRVRWYYRP 66 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~----~g~~~v~v~Wfyrp 66 (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 4789999999886 789999998854331 11245777777644
No 66
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=56.95 E-value=9 Score=24.44 Aligned_cols=24 Identities=21% Similarity=0.526 Sum_probs=19.1
Q ss_pred eeEEEcCCCeEEccCCEEEEccCC
Q 031197 12 DSYNIKGTNKVVRPGDCVLMRPAD 35 (164)
Q Consensus 12 ~s~~i~g~~~~~~vGD~V~v~~~~ 35 (164)
+.|+++.++..|++||.+.+.-=+
T Consensus 18 KtfEiRkNDRdf~VGD~L~L~E~~ 41 (72)
T PF12961_consen 18 KTFEIRKNDRDFQVGDILVLREWD 41 (72)
T ss_pred ceEEEEecCCCCCCCCEEEEEEec
Confidence 467788888899999999887543
No 67
>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=56.20 E-value=26 Score=23.59 Aligned_cols=43 Identities=21% Similarity=0.431 Sum_probs=29.2
Q ss_pred CCcceeeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEcEEee
Q 031197 6 PGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (164)
Q Consensus 6 ~~~~~Y~s~~i~g~~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~ 50 (164)
+|+|..+.-........+++||.+.|..++ .+..+.+|.++..
T Consensus 14 ~G~Ktat~r~~~~~~~~~k~Gd~~i~~~~~--~~~~~i~v~~V~~ 56 (105)
T cd06541 14 SGRKTIEIRSLDIYEQLPKAGDYLIILDGQ--QPLAIAEVVKVEI 56 (105)
T ss_pred CCCCEEEEEcchhcccCCCCCCEEEEecCC--CcEEEEEEEEEEE
Confidence 456655544332222478999999998876 5667888888764
No 68
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=52.20 E-value=26 Score=23.90 Aligned_cols=30 Identities=17% Similarity=0.252 Sum_probs=25.5
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeecc
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADH 52 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~ 52 (164)
..++.||.|.|.++. +.=-+|+|.++....
T Consensus 3 ~~i~kGD~V~Vi~G~--dKGk~G~V~~V~~~~ 32 (105)
T PRK00004 3 MKIKKGDTVIVIAGK--DKGKRGKVLKVLPKK 32 (105)
T ss_pred CcccCCCEEEEeEcC--CCCcEEEEEEEEcCC
Confidence 368999999999987 677889999998653
No 69
>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=52.01 E-value=18 Score=23.20 Aligned_cols=36 Identities=22% Similarity=0.334 Sum_probs=23.8
Q ss_pred eEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEcEEeec
Q 031197 13 SYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEAD 51 (164)
Q Consensus 13 s~~i~g~~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~ 51 (164)
.|.++.. ...++|++|.+..++ +...+|+|.++...
T Consensus 14 ~f~~~~~-~~v~~GeyV~i~~~~--~~~vlG~V~~i~~~ 49 (91)
T PF09378_consen 14 EFIVEPS-KDVRVGEYVVIEYDD--GEKVLGMVTSISRG 49 (91)
T ss_dssp EEEEEE--TT-BTTEEEEES------TTEEEEEEEEES-
T ss_pred EEEEeCC-CCCCcCeEEEEEEec--hhhhhhhhheeEEc
Confidence 4445542 378999999999884 67899999999873
No 70
>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=51.34 E-value=5.5 Score=23.90 Aligned_cols=13 Identities=46% Similarity=1.370 Sum_probs=10.1
Q ss_pred CceEeCccccccc
Q 031197 151 DLMVQCEGCKDWI 163 (164)
Q Consensus 151 ~~~~~C~~C~~w~ 163 (164)
..+++|++|..|+
T Consensus 38 ~~iv~C~sCSL~I 50 (55)
T PF05207_consen 38 EVIVQCDSCSLWI 50 (55)
T ss_dssp --EEEETTTTEEE
T ss_pred CEEEECCCCccEE
Confidence 4789999999986
No 71
>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=50.86 E-value=22 Score=24.30 Aligned_cols=43 Identities=16% Similarity=0.126 Sum_probs=31.8
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEcEEeec---------cCCcEEEEEEEeeec
Q 031197 22 VVRPGDCVLMRPADSDKPPYVARVEKIEAD---------HRNNVKVRVRWYYRP 66 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~---------~~g~~~v~v~Wfyrp 66 (164)
+|.+||.|..+-.+ -+.|-|.|.+--.. ......+.|++|-..
T Consensus 2 ~~~~GdlVWaK~~g--~PwWPa~V~~~~~~~~~~~~~~~~~~~~~~~V~FFG~~ 53 (110)
T cd05837 2 KYQVGDLVWAKVSG--YPWWPCMVCSDPLLGTYTKTKRNKRKPRQYHVQFFGDN 53 (110)
T ss_pred CCCCCCEEEEeCCC--CCCCCEEEecccccchhhhhhhccCCCCeEEEEEcCCC
Confidence 58899999999887 68999999853211 123467889988754
No 72
>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=50.60 E-value=16 Score=23.84 Aligned_cols=30 Identities=30% Similarity=0.404 Sum_probs=20.1
Q ss_pred EEEEEEeeeccccc---------CcccccCCCceeEEeCCeee
Q 031197 57 KVRVRWYYRPEESI---------GGRRQFHGAKELFLSDHYDV 90 (164)
Q Consensus 57 ~v~v~Wfyrp~e~~---------~~~~~~~~~~Elf~s~~~d~ 90 (164)
+..++|+| |+++. +|.+ .++|||+-+..-+
T Consensus 35 f~~GrWm~-P~~~~Y~VGyNe~GLGpK---~~~ElyiVnk~Cv 73 (85)
T PF12503_consen 35 FPNGRWMY-PEGYEYMVGYNESGLGPK---FDGELYIVNKDCV 73 (85)
T ss_pred ecCCceec-CCCeEEEeeecCCCCCcC---cCCeEEEEcCcEE
Confidence 34578999 88764 2233 4899999876543
No 73
>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=50.57 E-value=29 Score=21.22 Aligned_cols=30 Identities=23% Similarity=0.299 Sum_probs=22.4
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEcEEeec
Q 031197 22 VVRPGDCVLMRPADSDKPPYVARVEKIEAD 51 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ig~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 899999999977321234578888888864
No 74
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=49.25 E-value=10 Score=22.56 Aligned_cols=13 Identities=31% Similarity=0.710 Sum_probs=10.8
Q ss_pred CceEeCccccccc
Q 031197 151 DLMVQCEGCKDWI 163 (164)
Q Consensus 151 ~~~~~C~~C~~w~ 163 (164)
..++.||+|++++
T Consensus 44 ~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 44 DEIVFCPNCGRIL 56 (56)
T ss_pred CCeEECcCCCccC
Confidence 4789999999875
No 75
>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=48.78 E-value=48 Score=22.82 Aligned_cols=28 Identities=21% Similarity=0.381 Sum_probs=20.9
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEcEEee
Q 031197 22 VVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ig~I~~i~~ 50 (164)
.+++||.+.+..-+ ......++|..|..
T Consensus 31 ~ikvGD~I~f~~~~-~~~~l~v~V~~i~~ 58 (109)
T cd06555 31 QIKVGDKILFNDLD-TGQQLLVKVVDIRK 58 (109)
T ss_pred cCCCCCEEEEEEcC-CCcEEEEEEEEEEe
Confidence 69999999997755 24567777777754
No 76
>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=48.43 E-value=32 Score=23.44 Aligned_cols=29 Identities=17% Similarity=0.211 Sum_probs=24.9
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEcEEeecc
Q 031197 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADH 52 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ig~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 57899999999987 777899999998653
No 77
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=48.23 E-value=12 Score=32.42 Aligned_cols=30 Identities=30% Similarity=0.758 Sum_probs=25.2
Q ss_pred CCcceeeeecCCCCCCCceEeCcccccccC
Q 031197 135 DRVAVYCKCEMPYNPDDLMVQCEGCKDWIY 164 (164)
Q Consensus 135 ~~~~~~C~C~~p~~pd~~~~~C~~C~~w~h 164 (164)
......|.|..-..++..++||+.|.+|=|
T Consensus 83 ~~~~~~c~c~~~~~~~g~~i~c~~c~~Wqh 112 (508)
T KOG1844|consen 83 AREISRCDCGLEDDMEGLMIQCDWCGRWQH 112 (508)
T ss_pred cCcccccccccccCCCceeeCCcccCcccC
Confidence 356678999877666889999999999977
No 78
>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=48.16 E-value=47 Score=22.16 Aligned_cols=40 Identities=10% Similarity=0.264 Sum_probs=29.6
Q ss_pred CCCCcceeeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEcEEeecc
Q 031197 4 TKPGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADH 52 (164)
Q Consensus 4 ~~~~~~~Y~s~~i~g~~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~ 52 (164)
--+|+-..-...+... ++++||++..-... |||..|+.+.
T Consensus 10 ~~~g~G~vatviV~~G--tL~~Gd~iv~G~~~-------gkVr~l~d~~ 49 (95)
T cd03702 10 LDKGRGPVATVLVQNG--TLKVGDVLVAGTTY-------GKVRAMFDEN 49 (95)
T ss_pred ecCCCCccEEEEEEcC--eEeCCCEEEEcccc-------cEEEEEECCC
Confidence 3466667777777654 99999999876543 5999998764
No 79
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=47.49 E-value=27 Score=20.72 Aligned_cols=28 Identities=21% Similarity=0.223 Sum_probs=22.7
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEcEEee
Q 031197 22 VVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ig~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 46677899999865
No 80
>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=47.06 E-value=25 Score=17.01 Aligned_cols=15 Identities=20% Similarity=0.266 Sum_probs=11.0
Q ss_pred EEcEEeeccCCcEEE
Q 031197 44 RVEKIEADHRNNVKV 58 (164)
Q Consensus 44 ~I~~i~~~~~g~~~v 58 (164)
.|..|.+|.+|.+|+
T Consensus 6 ~I~~i~~D~~G~lWi 20 (24)
T PF07494_consen 6 NIYSIYEDSDGNLWI 20 (24)
T ss_dssp CEEEEEE-TTSCEEE
T ss_pred eEEEEEEcCCcCEEE
Confidence 367888888888876
No 81
>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=46.71 E-value=60 Score=21.48 Aligned_cols=40 Identities=8% Similarity=0.291 Sum_probs=29.8
Q ss_pred CCCCcceeeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEcEEeecc
Q 031197 4 TKPGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADH 52 (164)
Q Consensus 4 ~~~~~~~Y~s~~i~g~~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~ 52 (164)
-.+|+-..-...+... ++++||++.+-... |+|..|+.+.
T Consensus 10 ~~~g~G~vatviV~~G--tL~~Gd~iv~G~~~-------GkVr~~~d~~ 49 (95)
T cd03701 10 LDKGRGPVATVIVQNG--TLKKGDVIVAGGTY-------GKIRTMVDEN 49 (95)
T ss_pred ecCCCCeeEEEEEEcC--eEecCCEEEECCcc-------ceEEEEECCC
Confidence 3466777777777755 99999999876553 7888888753
No 82
>COG3257 GlxB Uncharacterized protein, possibly involved in glyoxylate utilization [General function prediction only]
Probab=45.66 E-value=78 Score=24.84 Aligned_cols=46 Identities=15% Similarity=0.467 Sum_probs=28.5
Q ss_pred EcCCCeEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeecccccCc
Q 031197 16 IKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGG 72 (164)
Q Consensus 16 i~g~~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~ 72 (164)
+.|....++.|+++|+.++.. | .+.. ...--.++.|+-++-+...|
T Consensus 98 ~~G~th~l~eggyaylPpgs~----~-----~~~N--~~~~~~rfhw~rk~Y~~VdG 143 (264)
T COG3257 98 AEGKTHALREGGYAYLPPGSG----W-----TLRN--AQKEDSRFHWIRKRYQPVEG 143 (264)
T ss_pred EcCeEEEeccCCeEEeCCCCc----c-----eEee--ccCCceEEEEEeecceeecC
Confidence 344445678888888888751 1 1111 12234788899888887665
No 83
>PF08921 DUF1904: Domain of unknown function (DUF1904); InterPro: IPR015017 This entry represents a family of hypothetical bacterial proteins. ; PDB: 1U9D_B.
Probab=45.30 E-value=10 Score=26.12 Aligned_cols=18 Identities=28% Similarity=0.390 Sum_probs=10.8
Q ss_pred CcEEEEEEEeeecccccC
Q 031197 54 NNVKVRVRWYYRPEESIG 71 (164)
Q Consensus 54 g~~~v~v~Wfyrp~e~~~ 71 (164)
+.++|.|.||-|+.|+..
T Consensus 54 ~~pfVEV~WF~R~qe~qd 71 (108)
T PF08921_consen 54 GYPFVEVLWFDRGQEVQD 71 (108)
T ss_dssp ---EEEEEES---HHHHH
T ss_pred cceeEEEEEecCCHHHHH
Confidence 446899999999999874
No 84
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=44.67 E-value=39 Score=22.00 Aligned_cols=30 Identities=27% Similarity=0.232 Sum_probs=21.1
Q ss_pred CeEEccCCEEEEccCCCCCCCeEEEEcEEeec
Q 031197 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEAD 51 (164)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~ 51 (164)
..-++.||+|.|...+ ...--|.|+..+..
T Consensus 41 ~iwI~~GD~VlVe~~~--~~~~kg~Iv~r~~~ 70 (83)
T smart00652 41 KVWIRRGDIVLVDPWD--FQDVKADIIYKYTK 70 (83)
T ss_pred cEEEcCCCEEEEEecC--CCCCEEEEEEEeCH
Confidence 3678999999998765 23567777766543
No 85
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=43.82 E-value=11 Score=31.37 Aligned_cols=23 Identities=22% Similarity=0.819 Sum_probs=15.4
Q ss_pred eeeecCC-CCCCCceEeCcccccc
Q 031197 140 YCKCEMP-YNPDDLMVQCEGCKDW 162 (164)
Q Consensus 140 ~C~C~~p-~~pd~~~~~C~~C~~w 162 (164)
.-.|+.= +.--.++-+||+|++|
T Consensus 354 ~YRC~~CGF~a~~l~W~CPsC~~W 377 (389)
T COG2956 354 RYRCQNCGFTAHTLYWHCPSCRAW 377 (389)
T ss_pred CceecccCCcceeeeeeCCCcccc
Confidence 3445432 2234589999999999
No 86
>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=43.53 E-value=19 Score=22.98 Aligned_cols=25 Identities=20% Similarity=0.262 Sum_probs=19.3
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEcE
Q 031197 22 VVRPGDCVLMRPADSDKPPYVARVEK 47 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ig~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 789999999987764 4566777764
No 87
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=43.38 E-value=13 Score=35.58 Aligned_cols=31 Identities=32% Similarity=0.756 Sum_probs=25.9
Q ss_pred CCCcceeeeecCCCCCCCceEeCcccccccC
Q 031197 134 PDRVAVYCKCEMPYNPDDLMVQCEGCKDWIY 164 (164)
Q Consensus 134 p~~~~~~C~C~~p~~pd~~~~~C~~C~~w~h 164 (164)
|...+..-+|..|+||-..++.|-.|-.|+|
T Consensus 1119 p~~~p~~~i~~~p~~pg~~~i~~~~~~~~~~ 1149 (1414)
T KOG1473|consen 1119 PTLSPVCFICTLPYNPGLTYIHCTVCMTWGH 1149 (1414)
T ss_pred CCCCccccceeeccCCCCCcceEEEeeccCc
Confidence 3344444499999999999999999999998
No 88
>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=42.82 E-value=47 Score=21.37 Aligned_cols=30 Identities=13% Similarity=0.272 Sum_probs=20.9
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeec
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEAD 51 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~ 51 (164)
.-++.||+|+|...+ .+..--|.|...+..
T Consensus 37 iwI~~GD~VlV~~~~-~~~~~kg~Iv~r~~~ 66 (78)
T cd04456 37 IWIKRGDFLIVDPIE-EGEDVKADIIFVYCK 66 (78)
T ss_pred EEEcCCCEEEEEecc-cCCCceEEEEEEeCH
Confidence 678999999998765 224566666666543
No 89
>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=42.71 E-value=41 Score=21.53 Aligned_cols=29 Identities=24% Similarity=0.159 Sum_probs=20.8
Q ss_pred CeEEccCCEEEEccCCCCCCCeEEEEcEEee
Q 031197 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (164)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~ 50 (164)
...++.||.|.|...+ -..--|+|...+.
T Consensus 36 ~iwI~~GD~V~Ve~~~--~d~~kg~Iv~r~~ 64 (77)
T cd05793 36 RVWINEGDIVLVAPWD--FQDDKADIIYKYT 64 (77)
T ss_pred cEEEcCCCEEEEEecc--ccCCEEEEEEEcC
Confidence 3678999999998765 3456677766554
No 90
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=42.16 E-value=52 Score=23.13 Aligned_cols=29 Identities=24% Similarity=0.241 Sum_probs=24.6
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeec
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEAD 51 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~ 51 (164)
..++.||.|.|.++. +.--.|+|.++...
T Consensus 44 ~~IkkGD~V~VisG~--~KGk~GkV~~V~~~ 72 (120)
T PRK01191 44 LPVRKGDTVKVMRGD--FKGEEGKVVEVDLK 72 (120)
T ss_pred ceEeCCCEEEEeecC--CCCceEEEEEEEcC
Confidence 579999999999997 55667999999765
No 91
>PF00667 FAD_binding_1: FAD binding domain; InterPro: IPR003097 This domain is found in sulphite reductase, NADPH cytochrome P450 reductase, nitric oxide synthase and methionine synthase reductase. Flavoprotein pyridine nucleotide cytochrome reductases [] (FPNCR) catalyse the interchange of reducing equivalents between one-electron carriers and the two-electron-carrying nicotinamide dinucleotides. The enzymes include ferredoxin:NADP+reductases (FNR) [], plant and fungal NAD(P)H:nitrate reductases [, ], NADH:cytochrome b5 reductases [], NADPH:P450 reductases [], NADPH:sulphite reductases [], nitric oxide synthases [], phthalate dioxygenase reductase [], and various other flavoproteins.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3QFR_B 3FJO_A 3QFC_B 3QE2_B 3QFS_A 3QFT_A 2B5O_B 2QTZ_A 2QTL_A 2BPO_B ....
Probab=41.67 E-value=37 Score=25.87 Aligned_cols=25 Identities=16% Similarity=0.319 Sum_probs=14.5
Q ss_pred eeeEEEcCCCeEEccCCEEEEccCC
Q 031197 11 LDSYNIKGTNKVVRPGDCVLMRPAD 35 (164)
Q Consensus 11 Y~s~~i~g~~~~~~vGD~V~v~~~~ 35 (164)
.=.+.+.+.+..|++||.+.|.+.+
T Consensus 30 hieldl~~~~l~Y~pGD~l~V~P~N 54 (219)
T PF00667_consen 30 HIELDLSDSGLSYQPGDHLGVYPPN 54 (219)
T ss_dssp EEEEE-TTSTG---TT-EEEEE-SS
T ss_pred EEEEEeCCCCCcccCCCEEEEEccC
Confidence 3344556668999999999999998
No 92
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=39.95 E-value=12 Score=30.35 Aligned_cols=24 Identities=21% Similarity=0.423 Sum_probs=19.2
Q ss_pred ee-eecCCCCCCCceEeCcccccccC
Q 031197 140 YC-KCEMPYNPDDLMVQCEGCKDWIY 164 (164)
Q Consensus 140 ~C-~C~~p~~pd~~~~~C~~C~~w~h 164 (164)
+| +|.+|.. +..++.||-|.+=||
T Consensus 316 lC~IC~~P~~-E~E~~FCD~CDRG~H 340 (381)
T KOG1512|consen 316 LCRICLGPVI-ESEHLFCDVCDRGPH 340 (381)
T ss_pred hhhccCCccc-chheeccccccCCCC
Confidence 44 7888855 457899999999888
No 93
>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=39.75 E-value=30 Score=25.62 Aligned_cols=41 Identities=17% Similarity=0.127 Sum_probs=29.5
Q ss_pred EEEcCCCeEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEE
Q 031197 14 YNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVK 57 (164)
Q Consensus 14 ~~i~g~~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~ 57 (164)
.++......++.||.|...-++ ..+.||.|..-... +|..+
T Consensus 98 L~~~~~~~~~q~GDIVtw~l~~--~~~HIgIVSd~r~~-~G~p~ 138 (164)
T PF06940_consen 98 LTTDINPEDWQPGDIVTWRLPG--GLPHIGIVSDRRSK-DGVPL 138 (164)
T ss_pred ccCCCChhhcCCCCEEEEeCCC--CCCeEEEEeCCcCC-CCCEE
Confidence 3344444689999999998776 68999999887543 45433
No 94
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=38.44 E-value=18 Score=19.68 Aligned_cols=11 Identities=18% Similarity=0.890 Sum_probs=7.1
Q ss_pred eEeCccccccc
Q 031197 153 MVQCEGCKDWI 163 (164)
Q Consensus 153 ~~~C~~C~~w~ 163 (164)
.|+|++|+.-|
T Consensus 2 ~i~CP~C~~~f 12 (37)
T PF13719_consen 2 IITCPNCQTRF 12 (37)
T ss_pred EEECCCCCceE
Confidence 36777777544
No 95
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=37.29 E-value=11 Score=22.89 Aligned_cols=23 Identities=22% Similarity=0.525 Sum_probs=16.6
Q ss_pred eeecCCCCCCC---ceEeCccccccc
Q 031197 141 CKCEMPYNPDD---LMVQCEGCKDWI 163 (164)
Q Consensus 141 C~C~~p~~pd~---~~~~C~~C~~w~ 163 (164)
=+|.+.+-|-+ .+.-|+.|++.|
T Consensus 29 ALCGk~wvp~rdp~~~PVCP~Ck~iy 54 (58)
T PF11238_consen 29 ALCGKVWVPTRDPKPFPVCPECKEIY 54 (58)
T ss_pred eeeCceeCCCCCCCCCCCCcCHHHHH
Confidence 35776666543 588999999876
No 96
>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=37.04 E-value=42 Score=20.13 Aligned_cols=25 Identities=32% Similarity=0.388 Sum_probs=15.7
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEcEEee
Q 031197 22 VVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ig~I~~i~~ 50 (164)
...+||.|.+...+ ++. +.|.++.+
T Consensus 37 ~~~VGD~V~~~~~~-~~~---~~I~~vl~ 61 (68)
T cd04466 37 PPAVGDRVEFEPED-DGE---GVIEEILP 61 (68)
T ss_pred CCCCCcEEEEEECC-CCc---EEEEEEec
Confidence 46899999997543 122 45655553
No 97
>COG1935 Uncharacterized conserved protein [Function unknown]
Probab=36.85 E-value=66 Score=22.50 Aligned_cols=42 Identities=17% Similarity=0.396 Sum_probs=28.1
Q ss_pred cceeeeEEEcCCC-----eEEccCCEEEEccCCC-----CCCCeEEEEcEEe
Q 031197 8 KKDLDSYNIKGTN-----KVVRPGDCVLMRPADS-----DKPPYVARVEKIE 49 (164)
Q Consensus 8 ~~~Y~s~~i~g~~-----~~~~vGD~V~v~~~~~-----~~~~~ig~I~~i~ 49 (164)
+..|+.++++... ..++.||+|++.+... ...=.||+|.++-
T Consensus 19 ~~~~rTieiRsa~N~~tv~rl~~GDlVFlT~~~~~Dl~~GtsGiiAkV~~ve 70 (122)
T COG1935 19 RNPIRTIEIRSARNLLTVLRLHEGDLVFLTSTSLEDLTKGTSGIIAKVRRVE 70 (122)
T ss_pred hCCceEEEEEcccchHHhhcCCCCCEEEEehhHhhHhhcCcceeEEEEEEEE
Confidence 3567778776522 5679999999988642 2344677777664
No 98
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=36.70 E-value=86 Score=22.73 Aligned_cols=37 Identities=14% Similarity=0.141 Sum_probs=27.0
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEE
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRV 60 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v 60 (164)
..|+.||.|.|.++. +.=-.|+|.++... ++.+.|..
T Consensus 45 ~~IkkGD~V~Vi~Gk--~KGk~GkV~~V~~k-~~~ViVEg 81 (143)
T PTZ00194 45 MPVRKDDEVMVVRGH--HKGREGKVTAVYRK-KWVIHIEK 81 (143)
T ss_pred ceeecCCEEEEecCC--CCCCceEEEEEEcC-CCEEEEeC
Confidence 579999999999997 45556999999764 23344433
No 99
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=36.62 E-value=14 Score=20.05 Aligned_cols=13 Identities=15% Similarity=0.539 Sum_probs=8.2
Q ss_pred ceEeCcccccccC
Q 031197 152 LMVQCEGCKDWIY 164 (164)
Q Consensus 152 ~~~~C~~C~~w~h 164 (164)
.+++|++|+-..|
T Consensus 3 ~ll~C~~C~v~VH 15 (36)
T PF13831_consen 3 PLLFCDNCNVAVH 15 (36)
T ss_dssp EEEE-SSS--EEE
T ss_pred ceEEeCCCCCcCC
Confidence 5899999987766
No 100
>COG0662 {ManC} Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=36.50 E-value=22 Score=24.76 Aligned_cols=23 Identities=26% Similarity=0.459 Sum_probs=17.3
Q ss_pred EEcCCCeEEccCCEEEEccCCCC
Q 031197 15 NIKGTNKVVRPGDCVLMRPADSD 37 (164)
Q Consensus 15 ~i~g~~~~~~vGD~V~v~~~~~~ 37 (164)
.+++..+.++.||+++|.++.++
T Consensus 71 ~~~~~~~~v~~gd~~~iP~g~~H 93 (127)
T COG0662 71 TIGGEEVEVKAGDSVYIPAGTPH 93 (127)
T ss_pred EECCEEEEecCCCEEEECCCCcE
Confidence 34444577899999999988753
No 101
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=36.00 E-value=20 Score=27.16 Aligned_cols=22 Identities=23% Similarity=0.720 Sum_probs=18.9
Q ss_pred eeeecCCCCCCCceEeCccccc
Q 031197 140 YCKCEMPYNPDDLMVQCEGCKD 161 (164)
Q Consensus 140 ~C~C~~p~~pd~~~~~C~~C~~ 161 (164)
.-.|..+.-++..++.|+.|+.
T Consensus 152 CsrC~~~L~~~~~~l~Cp~Cg~ 173 (188)
T COG1096 152 CSRCRAPLVKKGNMLKCPNCGN 173 (188)
T ss_pred ccCCCcceEEcCcEEECCCCCC
Confidence 3478999999999999999975
No 102
>KOG1740 consensus Predicted mitochondrial/chloroplast ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=35.98 E-value=29 Score=23.61 Aligned_cols=30 Identities=20% Similarity=0.256 Sum_probs=24.3
Q ss_pred cceeeeEEEcCCCeEEccCCEEEEccCCCC
Q 031197 8 KKDLDSYNIKGTNKVVRPGDCVLMRPADSD 37 (164)
Q Consensus 8 ~~~Y~s~~i~g~~~~~~vGD~V~v~~~~~~ 37 (164)
-+++..|-.+.++...++||.|-+.+..|-
T Consensus 35 v~~~~kymahD~~n~cnvGD~VrlepsRPl 64 (107)
T KOG1740|consen 35 VKRTSKYMAHDDKNQCNVGDRVRLEPSRPL 64 (107)
T ss_pred HHHhhheeecCccccccccceEEeccCCcc
Confidence 356777888887788999999999987753
No 103
>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=35.75 E-value=34 Score=20.99 Aligned_cols=24 Identities=25% Similarity=0.383 Sum_probs=15.8
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEc
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVE 46 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~ 46 (164)
..++.||+|.|...+ ...--|+|.
T Consensus 40 iwI~~GD~V~V~~~~--~d~~kG~Ii 63 (65)
T PF01176_consen 40 IWIKRGDFVLVEPSP--YDKVKGRII 63 (65)
T ss_dssp C---TTEEEEEEEST--TCTTEEEEE
T ss_pred EecCCCCEEEEEecc--cCCCeEEEE
Confidence 568999999999765 336677765
No 104
>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=34.90 E-value=21 Score=22.10 Aligned_cols=16 Identities=13% Similarity=0.146 Sum_probs=13.2
Q ss_pred CCCCceEeCccccccc
Q 031197 148 NPDDLMVQCEGCKDWI 163 (164)
Q Consensus 148 ~pd~~~~~C~~C~~w~ 163 (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 4556889999999998
No 105
>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=34.79 E-value=44 Score=25.84 Aligned_cols=28 Identities=32% Similarity=0.487 Sum_probs=16.9
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEcEEee
Q 031197 22 VVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ig~I~~i~~ 50 (164)
.+++||+|++...+ .......+|.++..
T Consensus 105 ~V~~Gd~v~~~~~~-~~~~~~~~V~~v~~ 132 (217)
T PF01079_consen 105 DVRVGDCVLVSDEG-GGKLRPSRVVRVST 132 (217)
T ss_dssp G--TT-EEEEE-TT-T--EEEEEEEEEEE
T ss_pred hCCCCCEEEEEEcC-CCcEEEEEEEEEEE
Confidence 68999999994444 36777888888865
No 106
>KOG2133 consensus Transcriptional corepressor Atrophin-1/DRPLA [General function prediction only]
Probab=34.35 E-value=26 Score=33.12 Aligned_cols=112 Identities=17% Similarity=0.199 Sum_probs=79.9
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeeccC-CcEEEEEEEeeeccccc-Cc----------cc-------ccCCCce
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHR-NNVKVRVRWYYRPEESI-GG----------RR-------QFHGAKE 81 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~-g~~~v~v~Wfyrp~e~~-~~----------~~-------~~~~~~E 81 (164)
..|.++|.|.+....+ .++.|+.|-.+-..++ ....++...+.|+++++ .+ +. +-...+|
T Consensus 144 ~~y~~~~~l~~~v~~~-~p~lia~~~~~~~~Kr~~~~~~k~s~~~r~~d~Pet~y~~~m~pe~Ar~e~~P~~~pq~~sq~ 222 (1229)
T KOG2133|consen 144 TLYDLRDSLFVEVSQP-EPYLIAAICGFKYTKRDDRQVVKLSFYFRADDIPETGYLNLMKPERARLEINPHLCPQPLSQE 222 (1229)
T ss_pred hhhhhhhhhhhhhccC-CccccccccCccccccccccccccccccccccCcccccccccCchhhhhccCCccCCCcchhh
Confidence 4789999999988874 6777888777766554 45677888899999988 22 00 1135789
Q ss_pred eEEeCCe-eeeccceEEEeeEEEeeecccccCC------CCcceEEEeeeeecccceec
Q 031197 82 LFLSDHY-DVQSAHTIEGKCTVHTFKNYTKLEN------VGAEDYFCRFEYKAATGGFT 133 (164)
Q Consensus 82 lf~s~~~-d~i~~~~I~gkc~V~~~~~~~~~~~------~~~~~f~cr~~yd~~~~~f~ 133 (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 9998877 5688999999999986666543321 23567777788888765544
No 107
>PRK04980 hypothetical protein; Provisional
Probab=33.86 E-value=95 Score=21.15 Aligned_cols=36 Identities=17% Similarity=0.313 Sum_probs=20.7
Q ss_pred EEEcC-CCeEEccCCEEEEccCCCCCCCeEEEEcEEe
Q 031197 14 YNIKG-TNKVVRPGDCVLMRPADSDKPPYVARVEKIE 49 (164)
Q Consensus 14 ~~i~g-~~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~ 49 (164)
.+++. ....+++||.|.|...+.+.+....+|.++.
T Consensus 22 iTiRd~se~~~~~G~~~~V~~~e~g~~~c~ieI~sV~ 58 (102)
T PRK04980 22 ITIRDESESHFKPGDVLRVGTFEDDRYFCTIEVLSVS 58 (102)
T ss_pred EEeeCCcccCCCCCCEEEEEECCCCcEEEEEEEEEEE
Confidence 44443 2346899999999643312344455555554
No 108
>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=33.62 E-value=40 Score=20.07 Aligned_cols=20 Identities=25% Similarity=0.677 Sum_probs=13.6
Q ss_pred EcCCCeEEccCCEEEEccCC
Q 031197 16 IKGTNKVVRPGDCVLMRPAD 35 (164)
Q Consensus 16 i~g~~~~~~vGD~V~v~~~~ 35 (164)
+++....++.||.+++.++.
T Consensus 34 ~~~~~~~l~~Gd~~~i~~~~ 53 (71)
T PF07883_consen 34 VDGERVELKPGDAIYIPPGV 53 (71)
T ss_dssp ETTEEEEEETTEEEEEETTS
T ss_pred EccEEeEccCCEEEEECCCC
Confidence 44444667788888887764
No 109
>PRK02935 hypothetical protein; Provisional
Probab=33.46 E-value=22 Score=24.44 Aligned_cols=10 Identities=30% Similarity=0.896 Sum_probs=8.5
Q ss_pred ceEeCccccc
Q 031197 152 LMVQCEGCKD 161 (164)
Q Consensus 152 ~~~~C~~C~~ 161 (164)
..++||+|+|
T Consensus 69 vqV~CP~C~K 78 (110)
T PRK02935 69 VQVICPSCEK 78 (110)
T ss_pred eeeECCCCCc
Confidence 5689999987
No 110
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=33.16 E-value=1.1e+02 Score=22.91 Aligned_cols=45 Identities=27% Similarity=0.465 Sum_probs=34.7
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeeccc
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEE 68 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~e 68 (164)
..+.+||.|-|.++. =..+.|+|.++..+ .+...+.+.-|-|+--
T Consensus 122 ~~~e~Gd~VrI~~Gp--Fa~f~g~V~evd~e-k~~~~v~v~ifgr~tP 166 (178)
T COG0250 122 VDFEPGDVVRIIDGP--FAGFKAKVEEVDEE-KGKLKVEVSIFGRPTP 166 (178)
T ss_pred ccCCCCCEEEEeccC--CCCccEEEEEEcCc-CcEEEEEEEEeCCceE
Confidence 578999999999986 56799999999765 3456677766666553
No 111
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=32.92 E-value=17 Score=20.02 Aligned_cols=10 Identities=30% Similarity=0.982 Sum_probs=4.3
Q ss_pred EeCccccccc
Q 031197 154 VQCEGCKDWI 163 (164)
Q Consensus 154 ~~C~~C~~w~ 163 (164)
.-|+-|+.|+
T Consensus 4 yyCdyC~~~~ 13 (38)
T PF06220_consen 4 YYCDYCKKYL 13 (38)
T ss_dssp -B-TTT--B-
T ss_pred eeccccccee
Confidence 4599999997
No 112
>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=32.87 E-value=72 Score=21.16 Aligned_cols=38 Identities=13% Similarity=-0.000 Sum_probs=26.4
Q ss_pred ccCCEEEEccCCCCCCCeEEEEcEEeecc-------CCcEEEEEEEe
Q 031197 24 RPGDCVLMRPADSDKPPYVARVEKIEADH-------RNNVKVRVRWY 63 (164)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~ig~I~~i~~~~-------~g~~~v~v~Wf 63 (164)
.+||.|..+-+. -+.|-|+|.+-.+.+ ...-.+-|++|
T Consensus 2 ~~GdlVWaK~~g--~pwWPa~V~~~~~~p~~~~~~~~~~~~~~V~Ff 46 (95)
T cd05838 2 LYGDIVWAKLGN--FRWWPAIICDPREVPPNIQVLRHCIGEFCVMFF 46 (95)
T ss_pred CcCCEEEEECCC--CCCCCeEEcChhhcChhHhhccCCCCeEEEEEe
Confidence 579999999886 789999998743211 12235677766
No 113
>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=32.53 E-value=18 Score=17.60 Aligned_cols=10 Identities=20% Similarity=0.787 Sum_probs=8.2
Q ss_pred EeCccccccc
Q 031197 154 VQCEGCKDWI 163 (164)
Q Consensus 154 ~~C~~C~~w~ 163 (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 5799998876
No 114
>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=32.43 E-value=9.6 Score=23.33 Aligned_cols=24 Identities=29% Similarity=0.679 Sum_probs=17.2
Q ss_pred ceee-eecCCCCCCCceEeC-ccccccc
Q 031197 138 AVYC-KCEMPYNPDDLMVQC-EGCKDWI 163 (164)
Q Consensus 138 ~~~C-~C~~p~~pd~~~~~C-~~C~~w~ 163 (164)
.+.| .|.+|..|| ...| +.|++-|
T Consensus 3 HkHC~~CG~~Ip~~--~~fCS~~C~~~~ 28 (59)
T PF09889_consen 3 HKHCPVCGKPIPPD--ESFCSPKCREEY 28 (59)
T ss_pred CCcCCcCCCcCCcc--hhhhCHHHHHHH
Confidence 4567 799998887 4568 5787644
No 115
>PRK03187 tgl transglutaminase; Provisional
Probab=31.90 E-value=42 Score=26.90 Aligned_cols=15 Identities=40% Similarity=0.802 Sum_probs=13.4
Q ss_pred eEEccCCEEEEccCC
Q 031197 21 KVVRPGDCVLMRPAD 35 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~ 35 (164)
..+-+||+||+++++
T Consensus 164 ~~~~PGD~vYFkNPd 178 (272)
T PRK03187 164 GDFLPGDCVYFKNPD 178 (272)
T ss_pred CCCCCCcEEEecCCC
Confidence 489999999999976
No 116
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=31.63 E-value=99 Score=21.15 Aligned_cols=30 Identities=20% Similarity=0.202 Sum_probs=24.4
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeecc
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADH 52 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~ 52 (164)
..++.||.|+|.++. +.=--|+|.++....
T Consensus 3 ~~IrkGD~V~Vi~Gk--dKGk~GkVl~v~~k~ 32 (104)
T COG0198 3 MKVKKGDTVKVIAGK--DKGKEGKVLKVLPKK 32 (104)
T ss_pred cceecCCEEEEEecC--CCCcceEEEEEecCe
Confidence 368899999999997 667788888887653
No 117
>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=31.59 E-value=1.3e+02 Score=20.91 Aligned_cols=29 Identities=28% Similarity=0.276 Sum_probs=24.5
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeec
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEAD 51 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~ 51 (164)
..++.||.|.|.++. +.=..|+|.++...
T Consensus 40 ~~IkkGD~V~Vi~Gk--~KGk~GkV~~V~~~ 68 (114)
T TIGR01080 40 LPVRKGDKVRIMRGD--FKGHEGKVSKVDLK 68 (114)
T ss_pred ceeecCCEEEEecCC--CCCCEEEEEEEEcC
Confidence 578999999999997 56678999999743
No 118
>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=31.51 E-value=1.1e+02 Score=23.84 Aligned_cols=46 Identities=22% Similarity=0.440 Sum_probs=36.0
Q ss_pred CeEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeecc
Q 031197 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPE 67 (164)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~ 67 (164)
...+++|+.=.+..+...-|-+.|+|.++... +.-.|++.|+-.-.
T Consensus 25 ~~~F~~gQIWAlYd~~D~mPR~Ya~I~kV~~~--~~Fkl~i~wLe~~~ 70 (217)
T PF11926_consen 25 EEKFQVGQIWALYDDDDGMPRYYARIKKVDSS--NPFKLHITWLEPCP 70 (217)
T ss_pred HHhCCCCCEEEEeeCCCCCeeeEEEEEEEecC--CCeEEEEEEccccC
Confidence 35789999988888754688999999999864 34689999986544
No 119
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=31.02 E-value=37 Score=18.31 Aligned_cols=16 Identities=25% Similarity=0.717 Sum_probs=11.7
Q ss_pred CCCceEeCcccccccC
Q 031197 149 PDDLMVQCEGCKDWIY 164 (164)
Q Consensus 149 pd~~~~~C~~C~~w~h 164 (164)
|....++|..|+.-|+
T Consensus 21 ~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 21 PKGRKVRCSKCGHVFF 36 (36)
T ss_pred CCCcEEECCCCCCEeC
Confidence 3347899999987654
No 120
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=30.51 E-value=70 Score=22.00 Aligned_cols=21 Identities=24% Similarity=0.669 Sum_probs=17.0
Q ss_pred EEcCCCeEEccCCEEEEccCC
Q 031197 15 NIKGTNKVVRPGDCVLMRPAD 35 (164)
Q Consensus 15 ~i~g~~~~~~vGD~V~v~~~~ 35 (164)
.+.|...+++.||++++.++.
T Consensus 78 ~~~g~~~~l~~Gd~i~ip~g~ 98 (131)
T COG1917 78 QLEGEKKELKAGDVIIIPPGV 98 (131)
T ss_pred EecCCceEecCCCEEEECCCC
Confidence 445666889999999999875
No 121
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=30.43 E-value=11 Score=23.87 Aligned_cols=21 Identities=24% Similarity=0.479 Sum_probs=12.1
Q ss_pred eecCCCCCCCceEeCcccccc
Q 031197 142 KCEMPYNPDDLMVQCEGCKDW 162 (164)
Q Consensus 142 ~C~~p~~pd~~~~~C~~C~~w 162 (164)
.|+++..+....+.|+.|++-
T Consensus 6 ~C~~~L~~~~~~~~C~~C~~~ 26 (70)
T PF07191_consen 6 KCQQELEWQGGHYHCEACQKD 26 (70)
T ss_dssp SS-SBEEEETTEEEETTT--E
T ss_pred CCCCccEEeCCEEECcccccc
Confidence 566666666667777777653
No 122
>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=29.33 E-value=1.3e+02 Score=24.05 Aligned_cols=45 Identities=18% Similarity=0.264 Sum_probs=35.6
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeeccc
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEE 68 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~e 68 (164)
..+.+||.|.|.++. -.-+.|.|.++..+ .+...|.+..|-|.--
T Consensus 204 ~~f~vGd~VrI~dGP--F~GfeG~I~eid~~-k~Rv~VlV~IfGR~Tp 248 (258)
T TIGR01956 204 SKFRVGNFVKIVDGP--FKGIVGKIKKIDQE-KKKAIVEVEILGKSVD 248 (258)
T ss_pred cCCCCCCEEEEEecC--CCCcEEEEEEEeCC-CCEEEEEEEecCCcEE
Confidence 347899999999997 67789999999753 4567888888877653
No 123
>COG3450 Predicted enzyme of the cupin superfamily [General function prediction only]
Probab=29.08 E-value=46 Score=23.22 Aligned_cols=16 Identities=25% Similarity=0.297 Sum_probs=13.2
Q ss_pred CeEEccCCEEEEccCC
Q 031197 20 NKVVRPGDCVLMRPAD 35 (164)
Q Consensus 20 ~~~~~vGD~V~v~~~~ 35 (164)
-.+|+.||.+++.++-
T Consensus 83 ~v~~~aGD~~~~~~G~ 98 (116)
T COG3450 83 PVEVRAGDSFVFPAGF 98 (116)
T ss_pred EEEEcCCCEEEECCCC
Confidence 3678999999998875
No 124
>COG4127 Uncharacterized conserved protein [Function unknown]
Probab=28.54 E-value=41 Score=27.29 Aligned_cols=41 Identities=17% Similarity=0.355 Sum_probs=30.2
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEcEEeeccC----C-cEEEEEEEe
Q 031197 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHR----N-NVKVRVRWY 63 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~----g-~~~v~v~Wf 63 (164)
+++.||-|.+.+.. ....+||+|.+=++-.. | ..-.+|.|.
T Consensus 72 eI~KGDlvi~y~k~-~r~y~IGkVtsdYEy~p~~~~~i~hTrkVkWL 117 (318)
T COG4127 72 EIQKGDLVITYSKS-NRTYLIGKVTSDYEYHPEWLEGIGHTRKVKWL 117 (318)
T ss_pred HhccCcEEEeeccc-CceEEEEEecCCcccCccccccCchhhHhHHh
Confidence 58999999999877 58899999998765321 1 123567776
No 125
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=28.15 E-value=1.1e+02 Score=20.67 Aligned_cols=28 Identities=25% Similarity=0.223 Sum_probs=18.0
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEee
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~ 50 (164)
..++.||.|.|...+- + .--|.|...+.
T Consensus 58 IwI~~GD~VlVe~~~~-~-~~kg~Iv~r~~ 85 (100)
T PRK04012 58 MWIREGDVVIVAPWDF-Q-DEKADIIWRYT 85 (100)
T ss_pred EEecCCCEEEEEeccc-C-CCEEEEEEEcC
Confidence 5678888888876541 2 44566665543
No 126
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=27.88 E-value=1.8e+02 Score=19.02 Aligned_cols=29 Identities=17% Similarity=0.247 Sum_probs=20.8
Q ss_pred ceeeeEEEcCCCeEEccCCEEEEccCCCC
Q 031197 9 KDLDSYNIKGTNKVVRPGDCVLMRPADSD 37 (164)
Q Consensus 9 ~~Y~s~~i~g~~~~~~vGD~V~v~~~~~~ 37 (164)
+..+.|.++..+...++||.|.|....|-
T Consensus 37 ~r~kk~~aHDe~n~~~~GD~V~I~e~RPl 65 (84)
T CHL00142 37 TKTKKYLVHDEENECNIGDQVLIEETRPL 65 (84)
T ss_pred EeeEEEEEeCCCCCCCCCCEEEEEEcCCC
Confidence 34455666766667999999999876543
No 127
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=27.70 E-value=17 Score=19.75 Aligned_cols=10 Identities=20% Similarity=0.448 Sum_probs=8.0
Q ss_pred eCcccccccC
Q 031197 155 QCEGCKDWIY 164 (164)
Q Consensus 155 ~C~~C~~w~h 164 (164)
.|++|+.-||
T Consensus 3 ~C~~Cg~~Yh 12 (36)
T PF05191_consen 3 ICPKCGRIYH 12 (36)
T ss_dssp EETTTTEEEE
T ss_pred CcCCCCCccc
Confidence 5888888887
No 128
>PF11012 DUF2850: Protein of unknown function (DUF2850); InterPro: IPR021271 This family of proteins with unknown function appear to be restricted to Vibrionaceae.
Probab=27.50 E-value=84 Score=20.38 Aligned_cols=30 Identities=17% Similarity=0.232 Sum_probs=25.3
Q ss_pred CCCCcceeeeEEEcCCCeEEccCCEEEEcc
Q 031197 4 TKPGKKDLDSYNIKGTNKVVRPGDCVLMRP 33 (164)
Q Consensus 4 ~~~~~~~Y~s~~i~g~~~~~~vGD~V~v~~ 33 (164)
..+||--=.+|..+|...+|++|+-+++..
T Consensus 27 ~~ngrlV~T~F~fDG~~l~~~~G~~~~~y~ 56 (79)
T PF11012_consen 27 FRNGRLVATSFEFDGKTLEYRTGSGTYRYQ 56 (79)
T ss_pred EECCCEEeeEEEECCCEEEEEECCeEEEEE
Confidence 356788888999999989999999988765
No 129
>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=27.41 E-value=26 Score=15.94 Aligned_cols=9 Identities=33% Similarity=0.659 Sum_probs=5.0
Q ss_pred eCccccccc
Q 031197 155 QCEGCKDWI 163 (164)
Q Consensus 155 ~C~~C~~w~ 163 (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 688887754
No 130
>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=27.21 E-value=32 Score=23.88 Aligned_cols=11 Identities=27% Similarity=0.773 Sum_probs=9.1
Q ss_pred ceEeCcccccc
Q 031197 152 LMVQCEGCKDW 162 (164)
Q Consensus 152 ~~~~C~~C~~w 162 (164)
.+++||+|++.
T Consensus 68 v~V~CP~C~K~ 78 (114)
T PF11023_consen 68 VQVECPNCGKQ 78 (114)
T ss_pred eeeECCCCCCh
Confidence 67899999874
No 131
>cd06552 ASCH_yqfb_like ASC-1 homology domain, subfamily similar to Escherichia coli Yqfb. 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=27.16 E-value=1.1e+02 Score=20.04 Aligned_cols=28 Identities=21% Similarity=0.366 Sum_probs=21.0
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEee
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~ 50 (164)
..+++||.+++..+. ...-+++|.++..
T Consensus 27 ~~~~~Gd~~~~~~~~--~~~~~~~v~~V~~ 54 (100)
T cd06552 27 SHLKPGDVVEVHTGE--RIFGEAEITSVEE 54 (100)
T ss_pred cCCCCCCEEEEEECC--EEEEEEEEEEEEE
Confidence 358999999888775 5666777777754
No 132
>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=26.99 E-value=1e+02 Score=19.87 Aligned_cols=15 Identities=33% Similarity=0.658 Sum_probs=11.9
Q ss_pred eEEccCCEEEEccCC
Q 031197 21 KVVRPGDCVLMRPAD 35 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~ 35 (164)
.-++-||+|+|.+-+
T Consensus 37 iWIkrGd~VlV~p~~ 51 (78)
T cd05792 37 IWIKRGDFVLVEPIE 51 (78)
T ss_pred EEEEeCCEEEEEecc
Confidence 558999999997754
No 133
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=26.74 E-value=46 Score=22.44 Aligned_cols=16 Identities=38% Similarity=0.792 Sum_probs=13.2
Q ss_pred cEEEEEEEeeeccccc
Q 031197 55 NVKVRVRWYYRPEESI 70 (164)
Q Consensus 55 ~~~v~v~Wfyrp~e~~ 70 (164)
-..|+|.|||.++|..
T Consensus 76 g~~V~v~Wyyd~dD~~ 91 (99)
T PF09345_consen 76 GGKVTVNWYYDEDDED 91 (99)
T ss_pred CCcEEEEEEECCCCch
Confidence 3789999999988754
No 134
>CHL00010 infA translation initiation factor 1
Probab=26.65 E-value=1.5e+02 Score=18.89 Aligned_cols=12 Identities=33% Similarity=0.462 Sum_probs=7.6
Q ss_pred EEccCCEEEEcc
Q 031197 22 VVRPGDCVLMRP 33 (164)
Q Consensus 22 ~~~vGD~V~v~~ 33 (164)
.+.+||.|.|..
T Consensus 46 ~~~vGD~V~ve~ 57 (78)
T CHL00010 46 RILPGDRVKVEL 57 (78)
T ss_pred ccCCCCEEEEEE
Confidence 355677777764
No 135
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=26.43 E-value=74 Score=23.44 Aligned_cols=40 Identities=13% Similarity=0.110 Sum_probs=21.7
Q ss_pred EcCCCeEEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeec
Q 031197 16 IKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRP 66 (164)
Q Consensus 16 i~g~~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp 66 (164)
+++....+..||++++.++.++ -|.. .+...+++.|...|
T Consensus 143 ~~~~~~~l~~Gd~~~~~~~~~H----------~~~n-~~~~~~~~l~~~~p 182 (185)
T PRK09943 143 INGQDYHLVAGQSYAINTGIPH----------SFSN-TSAGICRIISAHTP 182 (185)
T ss_pred ECCEEEEecCCCEEEEcCCCCe----------eeeC-CCCCCeEEEEEeCC
Confidence 4444456677777777776521 1222 23344577776655
No 136
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=26.21 E-value=1.9e+02 Score=18.82 Aligned_cols=25 Identities=20% Similarity=0.345 Sum_probs=18.0
Q ss_pred eeEEEcCCCeEEccCCEEEEccCCC
Q 031197 12 DSYNIKGTNKVVRPGDCVLMRPADS 36 (164)
Q Consensus 12 ~s~~i~g~~~~~~vGD~V~v~~~~~ 36 (164)
+.|.++..+...++||.|.|....|
T Consensus 43 kk~~aHD~~n~~k~GD~V~I~e~rP 67 (84)
T PRK05610 43 KKYHAHDENNEAKIGDVVRIMETRP 67 (84)
T ss_pred eEEEEECCCCCCCCCCEEEEEEccc
Confidence 3455565556789999999987654
No 137
>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=26.09 E-value=1.6e+02 Score=19.29 Aligned_cols=21 Identities=33% Similarity=0.729 Sum_probs=12.4
Q ss_pred EEcCCCeEEccCCEEEEccCC
Q 031197 15 NIKGTNKVVRPGDCVLMRPAD 35 (164)
Q Consensus 15 ~i~g~~~~~~vGD~V~v~~~~ 35 (164)
.+++....++.||.+++.++.
T Consensus 37 ~~~~~~~~l~~g~~~li~p~~ 57 (136)
T PF02311_consen 37 HIDGQEYPLKPGDLFLIPPGQ 57 (136)
T ss_dssp EETTEEEEE-TT-EEEE-TTS
T ss_pred EECCEEEEEECCEEEEecCCc
Confidence 455555667888888888776
No 138
>COG2895 CysN GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]
Probab=25.25 E-value=90 Score=26.50 Aligned_cols=25 Identities=32% Similarity=0.493 Sum_probs=20.3
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEcEE
Q 031197 22 VVRPGDCVLMRPADSDKPPYVARVEKI 48 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ig~I~~i 48 (164)
.+++||.|.|.+++ ....|.+|..+
T Consensus 249 ~v~~Gd~vvvlPsG--~~s~V~~Ivt~ 273 (431)
T COG2895 249 SVKVGDEVVVLPSG--KTSRVKRIVTF 273 (431)
T ss_pred ceecCCeEEEccCC--CeeeEEEEecc
Confidence 89999999999987 55667777655
No 139
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=25.23 E-value=1.3e+02 Score=20.39 Aligned_cols=42 Identities=19% Similarity=0.347 Sum_probs=32.0
Q ss_pred CCcceeeeEEEcCCCeEEccCCEEEEccCCCCCCCeEEEEcEEeec
Q 031197 6 PGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEAD 51 (164)
Q Consensus 6 ~~~~~Y~s~~i~g~~~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~ 51 (164)
.||.++..-..+- ...+++||.+.|.-+. ..+..+|..+-..
T Consensus 33 ~GrV~vNG~~aKp-S~~VK~GD~l~i~~~~---~~~~v~Vl~~~~~ 74 (100)
T COG1188 33 GGRVKVNGQRAKP-SKEVKVGDILTIRFGN---KEFTVKVLALGEQ 74 (100)
T ss_pred CCeEEECCEEccc-ccccCCCCEEEEEeCC---cEEEEEEEecccc
Confidence 5777777776653 4689999999998885 6788888887654
No 140
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=25.13 E-value=40 Score=18.02 Aligned_cols=9 Identities=44% Similarity=1.058 Sum_probs=4.9
Q ss_pred EeCcccccc
Q 031197 154 VQCEGCKDW 162 (164)
Q Consensus 154 ~~C~~C~~w 162 (164)
+.|+.|+..
T Consensus 3 ~~CP~C~~~ 11 (38)
T TIGR02098 3 IQCPNCKTS 11 (38)
T ss_pred EECCCCCCE
Confidence 456666543
No 141
>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=25.00 E-value=1e+02 Score=19.24 Aligned_cols=25 Identities=24% Similarity=0.449 Sum_probs=11.6
Q ss_pred EccCCEEEEccCCCCCCCeEEEEcE
Q 031197 23 VRPGDCVLMRPADSDKPPYVARVEK 47 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~ig~I~~ 47 (164)
++.||.|.+...+.....++.||..
T Consensus 32 ~~~GDiv~~~~~~~~~~~~vkRv~~ 56 (85)
T cd06530 32 PKRGDVVVFKSPGDPGKPIIKRVIG 56 (85)
T ss_pred CCCCCEEEEeCCCCCCCEEEEEEEE
Confidence 4445555555443112445555544
No 142
>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=24.92 E-value=44 Score=20.93 Aligned_cols=17 Identities=12% Similarity=0.243 Sum_probs=12.6
Q ss_pred CCeEEccCCEEEEccCC
Q 031197 19 TNKVVRPGDCVLMRPAD 35 (164)
Q Consensus 19 ~~~~~~vGD~V~v~~~~ 35 (164)
...+++.||.+++..+-
T Consensus 44 ~~~~~~aGD~~~~p~G~ 60 (74)
T PF05899_consen 44 ETVTFKAGDAFFLPKGW 60 (74)
T ss_dssp EEEEEETTEEEEE-TTE
T ss_pred CEEEEcCCcEEEECCCC
Confidence 33778999999998774
No 143
>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=24.41 E-value=27 Score=17.46 Aligned_cols=10 Identities=40% Similarity=0.674 Sum_probs=7.2
Q ss_pred eEeCcccccc
Q 031197 153 MVQCEGCKDW 162 (164)
Q Consensus 153 ~~~C~~C~~w 162 (164)
++.||.|++-
T Consensus 1 ~v~CPiC~~~ 10 (26)
T smart00734 1 LVQCPVCFRE 10 (26)
T ss_pred CCcCCCCcCc
Confidence 4689998753
No 144
>COG4101 Predicted mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=24.02 E-value=1.3e+02 Score=21.38 Aligned_cols=28 Identities=25% Similarity=0.437 Sum_probs=19.9
Q ss_pred eEEccCCEEEEccCCC------CCCCeEEEEcEE
Q 031197 21 KVVRPGDCVLMRPADS------DKPPYVARVEKI 48 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~------~~~~~ig~I~~i 48 (164)
.+...||+.||.++-| ++.+..+.|.+-
T Consensus 90 a~~~pGDf~YiPpgVPHqp~N~S~ep~s~vIaRs 123 (142)
T COG4101 90 AEVGPGDFFYIPPGVPHQPANLSTEPLSAVIARS 123 (142)
T ss_pred EEecCCCeEEcCCCCCCcccccCCCCeEEEEEcc
Confidence 3678999999998764 345666666544
No 145
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=24.00 E-value=27 Score=27.56 Aligned_cols=15 Identities=33% Similarity=0.702 Sum_probs=12.3
Q ss_pred CCceEeCcccccccC
Q 031197 150 DDLMVQCEGCKDWIY 164 (164)
Q Consensus 150 d~~~~~C~~C~~w~h 164 (164)
...+++||.|+..++
T Consensus 218 ~d~iv~CP~CgRILy 232 (239)
T COG1579 218 KDEIVFCPYCGRILY 232 (239)
T ss_pred CCCCccCCccchHHH
Confidence 568999999998764
No 146
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=23.80 E-value=23 Score=19.09 Aligned_cols=11 Identities=27% Similarity=0.746 Sum_probs=6.7
Q ss_pred eEeCccccccc
Q 031197 153 MVQCEGCKDWI 163 (164)
Q Consensus 153 ~~~C~~C~~w~ 163 (164)
|..|+.|++++
T Consensus 1 m~FCp~C~nlL 11 (35)
T PF02150_consen 1 MRFCPECGNLL 11 (35)
T ss_dssp --BETTTTSBE
T ss_pred CeeCCCCCccc
Confidence 35688887765
No 147
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=23.73 E-value=37 Score=23.68 Aligned_cols=20 Identities=20% Similarity=0.581 Sum_probs=16.0
Q ss_pred eecCCCCCCCceEeCccccc
Q 031197 142 KCEMPYNPDDLMVQCEGCKD 161 (164)
Q Consensus 142 ~C~~p~~pd~~~~~C~~C~~ 161 (164)
.|+++..|+..-..||.|+.
T Consensus 75 ~C~~~~~~e~~~~~CP~C~s 94 (115)
T COG0375 75 DCGQEVELEELDYRCPKCGS 94 (115)
T ss_pred cCCCeecchhheeECCCCCC
Confidence 46788889987777999973
No 148
>PF00366 Ribosomal_S17: Ribosomal protein S17; InterPro: IPR000266 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 ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence [] has revealed that S17 has virtually no groups exposed on the ribosomal surface.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_Q 2VHP_Q 3BBN_Q 2QAL_Q 3OAR_Q 1VS5_Q 3KC4_Q 2AW7_Q 3E1C_J 2AVY_Q ....
Probab=23.64 E-value=47 Score=20.77 Aligned_cols=27 Identities=26% Similarity=0.384 Sum_probs=18.1
Q ss_pred cceeeeEEEcCCCeEEccCCEEEEccC
Q 031197 8 KKDLDSYNIKGTNKVVRPGDCVLMRPA 34 (164)
Q Consensus 8 ~~~Y~s~~i~g~~~~~~vGD~V~v~~~ 34 (164)
-+..+.|.++..+...++||.|.|...
T Consensus 29 ~~~~kk~~aHD~~~~~~vGD~V~I~e~ 55 (69)
T PF00366_consen 29 IKRTKKYMAHDENNICKVGDKVRIREC 55 (69)
T ss_dssp EEEEEEEEEE-TTSSSTTTSEEEEEEE
T ss_pred cCccccEEEeCCccCCCCCCEEEEEee
Confidence 344566667765556689999999654
No 149
>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=23.36 E-value=38 Score=16.61 Aligned_cols=9 Identities=22% Similarity=1.132 Sum_probs=6.9
Q ss_pred eCccccccc
Q 031197 155 QCEGCKDWI 163 (164)
Q Consensus 155 ~C~~C~~w~ 163 (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 488888876
No 150
>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=23.14 E-value=1.1e+02 Score=24.66 Aligned_cols=31 Identities=29% Similarity=0.285 Sum_probs=24.8
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeecc
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADH 52 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~ 52 (164)
+.+.+||.|.|...+ -....-+||.++-.+.
T Consensus 276 e~v~lGDtV~v~~~~-~~i~~~~RVi~~~~~~ 306 (317)
T TIGR01665 276 EPIGIGDTVRLKHTD-FNIKVYARVIKVEYSP 306 (317)
T ss_pred ccccCCCEEEEEcCC-CCceeEEEEEEEeccc
Confidence 479999999999987 3556669999987664
No 151
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=23.13 E-value=1.3e+02 Score=18.75 Aligned_cols=13 Identities=31% Similarity=0.378 Sum_probs=8.9
Q ss_pred eEEccCCEEEEcc
Q 031197 21 KVVRPGDCVLMRP 33 (164)
Q Consensus 21 ~~~~vGD~V~v~~ 33 (164)
..+.+||.|.|..
T Consensus 45 i~i~vGD~V~ve~ 57 (72)
T PRK00276 45 IRILPGDKVTVEL 57 (72)
T ss_pred cccCCCCEEEEEE
Confidence 3467788887774
No 152
>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=23.11 E-value=1.8e+02 Score=18.32 Aligned_cols=25 Identities=28% Similarity=0.537 Sum_probs=19.7
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEcEEeec
Q 031197 22 VVRPGDCVLMRPADSDKPPYVARVEKIEAD 51 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ig~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 89999999999875 2 4778777643
No 153
>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=22.74 E-value=2.2e+02 Score=20.62 Aligned_cols=45 Identities=18% Similarity=0.271 Sum_probs=34.3
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeecccc
Q 031197 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEES 69 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~e~ 69 (164)
.+++||.|.|.++. -.-+.|.|.++.. .++...+.+.+|-+...+
T Consensus 119 ~~~~G~~V~I~~Gp--f~G~~g~v~~~~~-~~~r~~V~v~~~g~~~~v 163 (172)
T TIGR00922 119 DFEVGEQVRVNDGP--FANFTGTVEEVDY-EKSKLKVSVSIFGRETPV 163 (172)
T ss_pred CCCCCCEEEEeecC--CCCcEEEEEEEcC-CCCEEEEEEEECCCceEE
Confidence 47899999999886 6678999999853 245678888888776544
No 154
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=22.72 E-value=78 Score=21.18 Aligned_cols=14 Identities=29% Similarity=0.382 Sum_probs=12.1
Q ss_pred EEccCCEEEEccCC
Q 031197 22 VVRPGDCVLMRPAD 35 (164)
Q Consensus 22 ~~~vGD~V~v~~~~ 35 (164)
.+++||.|++.+..
T Consensus 76 ~Lk~GD~V~ll~~~ 89 (100)
T PF10844_consen 76 GLKVGDKVLLLRVQ 89 (100)
T ss_pred CCcCCCEEEEEEec
Confidence 67999999999854
No 155
>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=22.60 E-value=42 Score=17.25 Aligned_cols=10 Identities=20% Similarity=0.454 Sum_probs=8.0
Q ss_pred EeCccccccc
Q 031197 154 VQCEGCKDWI 163 (164)
Q Consensus 154 ~~C~~C~~w~ 163 (164)
..|+-|++||
T Consensus 4 ~~C~~C~~~~ 13 (35)
T smart00451 4 FYCKLCNVTF 13 (35)
T ss_pred eEccccCCcc
Confidence 4689998887
No 156
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=22.52 E-value=1.4e+02 Score=18.76 Aligned_cols=25 Identities=20% Similarity=0.163 Sum_probs=15.8
Q ss_pred CeEEccCCEEEEccCCCCCCCeEEEEc
Q 031197 20 NKVVRPGDCVLMRPADSDKPPYVARVE 46 (164)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~ig~I~ 46 (164)
...+.+||.|.|...+ -.+-=|+|.
T Consensus 42 rI~I~~GD~V~Ve~sp--yd~tkgrIi 66 (68)
T TIGR00008 42 YIRILPGDKVKVELSP--YDLTRGRIT 66 (68)
T ss_pred cEEECCCCEEEEEECc--ccCCcEeEE
Confidence 3567888888887664 224445553
No 157
>PRK04151 IMP cyclohydrolase; Provisional
Probab=22.18 E-value=1.9e+02 Score=22.16 Aligned_cols=42 Identities=29% Similarity=0.596 Sum_probs=29.0
Q ss_pred CCCCCCCcceeeeEEEcCCC----eEEccCCEEEEccCCC---CCCCeEE
Q 031197 1 MAKTKPGKKDLDSYNIKGTN----KVVRPGDCVLMRPADS---DKPPYVA 43 (164)
Q Consensus 1 ~~~~~~~~~~Y~s~~i~g~~----~~~~vGD~V~v~~~~~---~~~~~ig 43 (164)
.|||..|++ +..+.|.|.. ..+..++-|.+.+-++ .+++||.
T Consensus 9 vG~s~dG~~-~~aY~V~sRSfpnR~~v~~~~~i~~~p~d~~~l~dnpyI~ 57 (197)
T PRK04151 9 VGKTEEGKP-FAAYRVSSRSFPNRRAVVRDNTVAIVPKDDAEETKNPYIS 57 (197)
T ss_pred EccCCCCCe-EEEEEEecCCCCCceeEEeCCeeEEeeCChhhccCCCceE
Confidence 489999998 4777777632 4556778888887654 3566654
No 158
>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=22.06 E-value=11 Score=25.95 Aligned_cols=25 Identities=24% Similarity=0.731 Sum_probs=18.2
Q ss_pred ceee-eecCCCCCCCceEeCcccccc
Q 031197 138 AVYC-KCEMPYNPDDLMVQCEGCKDW 162 (164)
Q Consensus 138 ~~~C-~C~~p~~pd~~~~~C~~C~~w 162 (164)
.-.| .|...+.|+.....||.|+..
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PF01155_consen 70 RARCRDCGHEFEPDEFDFSCPRCGSP 95 (113)
T ss_dssp EEEETTTS-EEECHHCCHH-SSSSSS
T ss_pred cEECCCCCCEEecCCCCCCCcCCcCC
Confidence 4467 788888888888889999864
No 159
>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=22.04 E-value=36 Score=23.51 Aligned_cols=25 Identities=20% Similarity=0.591 Sum_probs=19.1
Q ss_pred ceee-eecCCCCCCCceEeCcccccc
Q 031197 138 AVYC-KCEMPYNPDDLMVQCEGCKDW 162 (164)
Q Consensus 138 ~~~C-~C~~p~~pd~~~~~C~~C~~w 162 (164)
.-.| .|...+.++.....||.|+..
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (115)
T TIGR00100 70 ECECEDCSEEVSPEIDLYRCPKCHGI 95 (115)
T ss_pred EEEcccCCCEEecCCcCccCcCCcCC
Confidence 3466 688888888777889999854
No 160
>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=22.02 E-value=1.7e+02 Score=19.02 Aligned_cols=35 Identities=26% Similarity=0.414 Sum_probs=27.6
Q ss_pred EccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEee
Q 031197 23 VRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYY 64 (164)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfy 64 (164)
...||.|.-+-.+ -++|-|+|.+.- ...+.|++|-
T Consensus 7 ~~p~dLVwAK~kG--yp~WPAkV~~~~-----~~~~~V~FFG 41 (83)
T cd05841 7 RPPHELVWAKLKG--FPYWPAKVMRVE-----DNQVDVRFFG 41 (83)
T ss_pred CCCCCEEEEeCCC--CCCCCEEEeecC-----CCeEEEEEcC
Confidence 4689999998876 789999998742 2468888887
No 161
>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=22.02 E-value=2.9e+02 Score=19.76 Aligned_cols=20 Identities=35% Similarity=0.424 Sum_probs=9.6
Q ss_pred EEcCCCeEEccCCEEEEccCC
Q 031197 15 NIKGTNKVVRPGDCVLMRPAD 35 (164)
Q Consensus 15 ~i~g~~~~~~vGD~V~v~~~~ 35 (164)
.+.|. +.+.+|+-++....+
T Consensus 29 vlQG~-K~~~~g~~~~~Y~~g 48 (155)
T PF06719_consen 29 VLQGS-KRVHLGDQVFEYDAG 48 (155)
T ss_pred EEeee-EEEEECCceEEecCC
Confidence 44442 455555555554443
No 162
>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=21.84 E-value=1.5e+02 Score=23.80 Aligned_cols=32 Identities=13% Similarity=0.159 Sum_probs=25.2
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEeeccC
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHR 53 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~ 53 (164)
+.++.||+++|.++.++. .-=+.|.+|-+..+
T Consensus 153 v~v~~Gd~i~ipaGt~HA-~~g~~~~Eiq~~SD 184 (302)
T TIGR00218 153 IKLKPGDFFYVPSGTPHA-YKGGLVLEVMQNSD 184 (302)
T ss_pred cccCCCCEEEeCCCCccc-ccCceEEEEEcCCC
Confidence 578999999999998766 45567788877644
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=21.65 E-value=61 Score=17.32 Aligned_cols=10 Identities=30% Similarity=0.803 Sum_probs=6.8
Q ss_pred ceEeCccccc
Q 031197 152 LMVQCEGCKD 161 (164)
Q Consensus 152 ~~~~C~~C~~ 161 (164)
.++.|++|++
T Consensus 3 ~~~~C~nC~R 12 (33)
T PF08209_consen 3 PYVECPNCGR 12 (33)
T ss_dssp -EEE-TTTSS
T ss_pred CeEECCCCcC
Confidence 5789999986
No 164
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=21.13 E-value=1.7e+02 Score=21.54 Aligned_cols=14 Identities=21% Similarity=0.294 Sum_probs=8.1
Q ss_pred eEEccCCEEEEccC
Q 031197 21 KVVRPGDCVLMRPA 34 (164)
Q Consensus 21 ~~~~vGD~V~v~~~ 34 (164)
+.+..||.|+|...
T Consensus 69 IWI~~GD~VlVel~ 82 (155)
T PTZ00329 69 VWINIGDIILVSLR 82 (155)
T ss_pred EEecCCCEEEEecc
Confidence 44566666666543
No 165
>PLN00208 translation initiation factor (eIF); Provisional
Probab=21.00 E-value=1.7e+02 Score=21.26 Aligned_cols=16 Identities=31% Similarity=0.264 Sum_probs=8.9
Q ss_pred EEEEEEEeeecccccC
Q 031197 56 VKVRVRWYYRPEESIG 71 (164)
Q Consensus 56 ~~v~v~Wfyrp~e~~~ 71 (164)
....+.|=|.++++..
T Consensus 87 ~KgdIv~ry~~dqvr~ 102 (145)
T PLN00208 87 DKADVILKYMPDEARL 102 (145)
T ss_pred CEEEEEEEcCHHHHHH
Confidence 3455556666666553
No 166
>PRK15457 ethanolamine utilization protein EutQ; Provisional
Probab=20.95 E-value=1e+02 Score=24.27 Aligned_cols=22 Identities=14% Similarity=0.409 Sum_probs=17.3
Q ss_pred EEEcCCCeEEccCCEEEEccCC
Q 031197 14 YNIKGTNKVVRPGDCVLMRPAD 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 4566666778999999998886
No 167
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=20.78 E-value=1.4e+02 Score=18.75 Aligned_cols=25 Identities=20% Similarity=0.345 Sum_probs=17.1
Q ss_pred eeEEEcCCCeEEccCCEEEEccCCC
Q 031197 12 DSYNIKGTNKVVRPGDCVLMRPADS 36 (164)
Q Consensus 12 ~s~~i~g~~~~~~vGD~V~v~~~~~ 36 (164)
+.+.++......++||.|.|..--|
T Consensus 38 kk~~aHD~~~~~k~GD~V~I~ecrP 62 (71)
T TIGR03635 38 KKYHAHDENNECKVGDVVRIIETRP 62 (71)
T ss_pred EEEEEECCCCCCCCCCEEEEEEcCC
Confidence 3445555555789999999976543
No 168
>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=20.52 E-value=63 Score=20.72 Aligned_cols=14 Identities=36% Similarity=0.406 Sum_probs=11.6
Q ss_pred EEccCCEEEEccCC
Q 031197 22 VVRPGDCVLMRPAD 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 47999999998763
No 169
>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=20.40 E-value=2.9e+02 Score=19.42 Aligned_cols=43 Identities=14% Similarity=0.169 Sum_probs=31.0
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeecccc
Q 031197 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEES 69 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~e~ 69 (164)
.++.||.|.|.++. -.-+.|+|.++... +. .+.+...-+.-.|
T Consensus 86 ~~~~Gd~V~I~~GP--f~G~~g~v~~~d~~-k~--~v~v~l~~~~~~~ 128 (145)
T TIGR00405 86 SIKKGDIVEIISGP--FKGERAKVIRVDES-KE--EVTLELIEAAVPI 128 (145)
T ss_pred ccCCCCEEEEeecC--CCCCeEEEEEEcCC-CC--EEEEEEEEcCccc
Confidence 48899999999986 67788999998652 22 5666665555443
No 170
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=20.34 E-value=1.6e+02 Score=19.84 Aligned_cols=29 Identities=17% Similarity=0.190 Sum_probs=16.1
Q ss_pred eEEccCCEEEEccCCCCCCCeEEEEcEEee
Q 031197 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (164)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~ig~I~~i~~ 50 (164)
..++.||+|+|.+-+. +..--|.|...+.
T Consensus 56 iwI~~GD~VlVsp~d~-~~~~kg~Iv~r~~ 84 (99)
T TIGR00523 56 IWIREGDVVIVKPWEF-QGDDKCDIVWRYT 84 (99)
T ss_pred EEecCCCEEEEEEccC-CCCccEEEEEEcC
Confidence 5678888888854331 2122355555443
No 171
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=20.19 E-value=1.8e+02 Score=20.71 Aligned_cols=42 Identities=10% Similarity=0.001 Sum_probs=31.3
Q ss_pred EEccCCEEEEccCCCCCCCeEEEEcEEeeccCCcEEEEEEEeeecc
Q 031197 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPE 67 (164)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ig~I~~i~~~~~g~~~v~v~Wfyrp~ 67 (164)
.+..||.|.|.++. -.-+.|.|.++. ..+...+.+..|-|..
T Consensus 108 ~~~~G~~V~V~~GP--f~g~~g~v~~~~--~~~r~~v~l~~~gr~~ 149 (159)
T TIGR01955 108 LPYKGDKVRITDGA--FAGFEAIFLEPD--GEKRSMLLLNMIGKQI 149 (159)
T ss_pred CCCCCCEEEEeccC--CCCcEEEEEEEC--CCceEEEEEhhhCCce
Confidence 47899999999986 677889999985 2345667766665553
Done!