Query 027973
Match_columns 216
No_of_seqs 198 out of 1653
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 04:20:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027973.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027973hhsearch_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 3.3E-33 7.1E-38 209.4 10.9 121 20-157 1-121 (121)
2 cd04713 BAH_plant_3 BAH, or Br 100.0 8.8E-32 1.9E-36 207.7 13.4 129 2-134 2-134 (146)
3 cd04716 BAH_plantDCM_I BAH, or 100.0 2.8E-31 6E-36 198.2 12.0 113 20-134 1-118 (122)
4 cd04717 BAH_polybromo BAH, or 100.0 1.4E-30 3.1E-35 195.3 11.1 115 20-135 1-118 (121)
5 cd04710 BAH_fungalPHD BAH, or 100.0 5.8E-29 1.3E-33 188.9 12.0 116 17-134 6-134 (135)
6 smart00439 BAH Bromo adjacent 100.0 7.5E-29 1.6E-33 184.9 12.4 113 22-135 1-118 (120)
7 cd04709 BAH_MTA BAH, or Bromo 100.0 5.4E-29 1.2E-33 194.4 12.0 116 21-138 2-141 (164)
8 cd04370 BAH BAH, or Bromo Adja 100.0 4.1E-29 9E-34 186.6 10.7 115 20-135 1-121 (123)
9 PF01426 BAH: BAH domain; Int 100.0 3.9E-29 8.6E-34 186.3 10.1 113 21-135 1-117 (119)
10 cd04721 BAH_plant_1 BAH, or Br 99.9 1.3E-27 2.8E-32 180.7 10.4 108 20-130 5-118 (130)
11 cd04760 BAH_Dnmt1_I BAH, or Br 99.9 1E-26 2.2E-31 172.8 11.0 112 20-134 1-124 (124)
12 cd04715 BAH_Orc1p_like BAH, or 99.9 3.2E-26 6.9E-31 178.3 11.8 104 4-112 13-125 (159)
13 cd04708 BAH_plantDCM_II BAH, o 99.9 1.1E-25 2.4E-30 179.9 11.6 118 15-134 2-143 (202)
14 cd04712 BAH_DCM_I BAH, or Brom 99.9 4.4E-25 9.6E-30 166.9 12.9 110 21-135 4-127 (130)
15 cd04718 BAH_plant_2 BAH, or Br 99.9 3.6E-27 7.8E-32 179.0 0.9 96 37-134 50-145 (148)
16 KOG1886 BAH domain proteins [T 99.9 8E-25 1.7E-29 192.2 11.4 180 4-189 33-217 (464)
17 cd04720 BAH_Orc1p_Yeast BAH, o 99.9 3.2E-24 7E-29 170.6 13.0 116 19-135 49-176 (179)
18 cd04711 BAH_Dnmt1_II BAH, or B 99.9 1.6E-23 3.5E-28 156.3 8.7 110 26-135 13-134 (137)
19 cd04719 BAH_Orc1p_animal BAH, 99.9 1.8E-23 3.9E-28 156.9 8.7 110 21-131 2-123 (128)
20 KOG1827 Chromatin remodeling c 99.5 5.6E-15 1.2E-19 134.9 6.1 126 14-142 184-312 (629)
21 KOG1973 Chromatin remodeling p 99.0 8.6E-11 1.9E-15 99.7 2.6 53 136-193 216-271 (274)
22 KOG3554 Histone deacetylase co 99.0 2.3E-11 4.9E-16 106.8 -2.1 117 22-140 5-167 (693)
23 PF00628 PHD: PHD-finger; Int 99.0 8.6E-11 1.9E-15 74.5 0.4 48 141-189 1-50 (51)
24 COG5034 TNG2 Chromatin remodel 98.9 8.9E-10 1.9E-14 90.2 2.9 49 137-190 219-270 (271)
25 smart00249 PHD PHD zinc finger 98.8 5.1E-09 1.1E-13 64.4 2.9 44 143-187 4-47 (47)
26 KOG1632 Uncharacterized PHD Zn 98.5 5.1E-08 1.1E-12 85.2 2.7 111 81-192 3-115 (345)
27 KOG4323 Polycomb-like PHD Zn-f 98.0 2.5E-06 5.4E-11 76.3 2.0 55 137-192 169-226 (464)
28 KOG2752 Uncharacterized conser 97.2 0.0002 4.3E-09 60.8 1.8 39 133-171 122-166 (345)
29 KOG0955 PHD finger protein BR1 97.0 0.0019 4.1E-08 63.5 7.0 55 137-194 218-273 (1051)
30 PF13831 PHD_2: PHD-finger; PD 96.6 0.0003 6.5E-09 41.1 -1.1 35 152-188 2-36 (36)
31 KOG1244 Predicted transcriptio 95.8 0.0033 7.2E-08 52.6 0.9 51 139-191 281-332 (336)
32 KOG1512 PHD Zn-finger protein 95.5 0.0039 8.4E-08 52.6 0.2 45 143-191 319-364 (381)
33 KOG0954 PHD finger protein [Ge 95.5 0.0069 1.5E-07 57.0 1.6 51 138-191 270-322 (893)
34 KOG0825 PHD Zn-finger protein 95.3 0.01 2.2E-07 56.3 2.0 51 139-191 215-267 (1134)
35 KOG1844 PHD Zn-finger proteins 95.2 0.011 2.3E-07 54.5 1.9 55 136-192 83-137 (508)
36 KOG0957 PHD finger protein [Ge 94.7 0.029 6.2E-07 50.9 3.3 56 137-193 542-601 (707)
37 KOG4299 PHD Zn-finger protein 93.7 0.032 7E-07 51.7 1.5 50 141-192 255-307 (613)
38 cd04718 BAH_plant_2 BAH, or Br 93.2 0.061 1.3E-06 41.4 2.2 28 164-192 2-29 (148)
39 KOG1632 Uncharacterized PHD Zn 93.2 0.0064 1.4E-07 53.4 -3.7 54 136-189 236-294 (345)
40 KOG0957 PHD finger protein [Ge 91.6 0.16 3.5E-06 46.2 3.1 57 135-191 116-180 (707)
41 PF07227 DUF1423: Protein of u 91.4 0.16 3.6E-06 45.6 2.9 52 141-192 131-194 (446)
42 KOG1512 PHD Zn-finger protein 89.8 0.12 2.6E-06 43.7 0.6 36 152-187 277-314 (381)
43 COG5076 Transcription factor i 89.3 0.055 1.2E-06 48.0 -1.9 94 14-110 270-363 (371)
44 PF09926 DUF2158: Uncharacteri 88.9 0.74 1.6E-05 29.2 3.6 39 23-66 1-39 (53)
45 KOG0956 PHD finger protein AF1 88.5 0.3 6.6E-06 46.1 2.2 52 138-192 5-59 (900)
46 KOG0383 Predicted helicase [Ge 87.8 0.23 5E-06 47.4 1.0 46 139-189 48-93 (696)
47 cd05834 HDGF_related The PWWP 87.7 1 2.2E-05 31.2 4.0 42 22-66 2-43 (83)
48 cd05835 Dnmt3b_related The PWW 86.8 0.94 2E-05 31.6 3.5 42 23-66 1-44 (87)
49 PF11302 DUF3104: Protein of u 86.6 2.6 5.6E-05 28.6 5.3 33 22-54 5-42 (75)
50 KOG1245 Chromatin remodeling c 86.4 0.11 2.4E-06 53.3 -2.0 53 138-192 1107-1160(1404)
51 PF07496 zf-CW: CW-type Zinc F 85.5 0.3 6.6E-06 30.4 0.4 33 153-186 2-34 (50)
52 PF10781 DSRB: Dextransucrase 85.4 5.7 0.00012 25.4 6.0 44 24-70 2-52 (62)
53 PRK10708 hypothetical protein; 85.3 5 0.00011 25.6 5.8 44 24-70 2-52 (62)
54 cd06080 MUM1_like Mutated mela 85.2 1.7 3.8E-05 29.9 4.1 39 23-67 1-39 (80)
55 KOG2626 Histone H3 (Lys4) meth 84.9 0.78 1.7E-05 42.1 2.8 57 136-192 17-78 (544)
56 PF14446 Prok-RING_1: Prokaryo 83.7 0.64 1.4E-05 29.5 1.3 27 143-169 10-36 (54)
57 KOG4628 Predicted E3 ubiquitin 79.7 2.2 4.9E-05 37.5 3.6 48 140-192 231-278 (348)
58 PF13922 PHD_3: PHD domain of 79.4 0.28 6.1E-06 32.2 -1.5 32 137-173 31-62 (69)
59 PF11717 Tudor-knot: RNA bindi 79.1 5 0.00011 25.3 4.3 28 23-52 1-28 (55)
60 cd05162 PWWP The PWWP domain, 78.8 3.4 7.3E-05 28.5 3.7 41 23-65 1-46 (87)
61 PTZ00112 origin recognition co 77.6 5.1 0.00011 39.9 5.6 118 9-128 441-602 (1164)
62 PF08940 DUF1918: Domain of un 76.3 4.9 0.00011 25.9 3.5 40 23-64 3-42 (58)
63 smart00293 PWWP domain with co 76.0 5 0.00011 26.0 3.7 41 23-65 1-47 (63)
64 PF07154 DUF1392: Protein of u 75.7 8.7 0.00019 29.4 5.3 50 7-68 74-123 (150)
65 COG5415 Predicted integral mem 75.7 2.4 5.1E-05 34.5 2.4 33 155-192 193-225 (251)
66 cd03703 aeIF5B_II aeIF5B_II: T 75.0 9.2 0.0002 28.0 5.2 47 3-54 9-55 (110)
67 PF00467 KOW: KOW motif; Inte 74.0 8.9 0.00019 21.2 3.9 26 25-52 1-26 (32)
68 PF02081 TrpBP: Tryptophan RNA 73.9 9.6 0.00021 25.5 4.5 47 59-105 19-65 (75)
69 PF13832 zf-HC5HC2H_2: PHD-zin 73.9 1.2 2.6E-05 32.1 0.4 29 140-171 57-87 (110)
70 PF13341 RAG2_PHD: RAG2 PHD do 73.6 2.1 4.5E-05 28.6 1.3 34 153-186 29-67 (78)
71 PF09871 DUF2098: Uncharacteri 73.2 9.9 0.00021 26.9 4.8 42 22-70 2-46 (91)
72 PF10383 Clr2: Transcription-s 72.6 24 0.00052 26.8 7.2 54 10-65 2-71 (139)
73 PRK13251 transcription attenua 72.6 13 0.00028 24.9 4.8 47 59-105 19-65 (75)
74 cd05840 SPBC215_ISWI_like The 71.4 4.9 0.00011 28.4 3.0 40 23-65 1-49 (93)
75 COG5475 Uncharacterized small 71.1 20 0.00044 22.8 5.3 50 21-84 3-52 (60)
76 PF00855 PWWP: PWWP domain; I 70.2 4 8.8E-05 27.7 2.3 42 23-66 1-44 (86)
77 PF15057 DUF4537: Domain of un 69.7 8.9 0.00019 28.6 4.2 44 22-65 55-98 (124)
78 KOG4443 Putative transcription 68.7 1.7 3.7E-05 41.0 0.2 41 151-191 32-72 (694)
79 smart00739 KOW KOW (Kyprides, 68.4 11 0.00025 19.5 3.4 26 23-50 2-27 (28)
80 COG4014 Uncharacterized protei 68.0 14 0.00031 25.9 4.5 40 24-69 10-52 (97)
81 COG5141 PHD zinc finger-contai 66.5 2.6 5.6E-05 38.6 0.8 49 139-190 193-243 (669)
82 COG3257 GlxB Uncharacterized p 62.6 20 0.00043 29.6 5.2 61 15-91 97-157 (264)
83 KOG4443 Putative transcription 60.6 2.1 4.5E-05 40.5 -0.9 46 143-188 150-200 (694)
84 PF04810 zf-Sec23_Sec24: Sec23 58.9 4.8 0.0001 23.7 0.8 34 154-192 2-35 (40)
85 PF13639 zf-RING_2: Ring finge 57.8 1.2 2.6E-05 26.6 -2.0 40 143-188 5-44 (44)
86 cd05836 N_Pac_NP60 The PWWP do 56.8 13 0.00029 25.7 2.9 42 23-66 1-45 (86)
87 COG1370 Prefoldin, molecular c 56.7 9.4 0.0002 29.5 2.2 39 5-45 94-132 (155)
88 KOG1473 Nucleosome remodeling 56.2 3 6.5E-05 41.8 -0.6 55 137-191 1121-1175(1414)
89 PF13913 zf-C2HC_2: zinc-finge 53.6 5.1 0.00011 21.0 0.3 13 154-166 2-14 (25)
90 KOG1568 Mitochondrial inner me 53.4 68 0.0015 25.3 6.5 88 8-105 56-148 (174)
91 PRK12281 rplX 50S ribosomal pr 53.2 31 0.00067 23.4 4.2 30 22-53 6-35 (76)
92 PF13901 DUF4206: Domain of un 52.5 7.4 0.00016 31.5 1.2 30 153-192 171-200 (202)
93 CHL00141 rpl24 ribosomal prote 52.1 32 0.00068 23.8 4.1 37 22-62 8-44 (83)
94 cd00350 rubredoxin_like Rubred 51.9 11 0.00025 21.0 1.6 24 156-190 3-26 (33)
95 PF15446 zf-PHD-like: PHD/FYVE 51.7 9.1 0.0002 30.1 1.5 22 151-172 14-35 (175)
96 PF03144 GTP_EFTU_D2: Elongati 50.6 37 0.00081 22.0 4.3 31 22-52 12-42 (74)
97 PRK00004 rplX 50S ribosomal pr 50.0 39 0.00085 24.4 4.5 36 22-61 4-39 (105)
98 cd03701 IF2_IF5B_II IF2_IF5B_I 49.6 51 0.0011 23.1 5.0 41 3-52 9-49 (95)
99 cd05837 MSH6_like The PWWP dom 49.3 23 0.00049 25.8 3.2 44 22-67 2-53 (110)
100 PF07649 C1_3: C1-like domain; 48.7 2.8 6.1E-05 22.9 -1.3 18 152-169 13-30 (30)
101 cd00730 rubredoxin Rubredoxin; 47.5 15 0.00032 22.9 1.7 36 156-191 3-44 (50)
102 PF09378 HAS-barrel: HAS barre 47.1 33 0.00072 23.3 3.7 36 13-51 14-49 (91)
103 cd03702 IF2_mtIF2_II This fami 46.9 51 0.0011 23.3 4.7 41 3-52 9-49 (95)
104 PF11132 SplA: Transcriptional 45.8 17 0.00037 24.5 1.9 25 22-47 5-29 (75)
105 KOG2752 Uncharacterized conser 43.5 24 0.00051 30.7 2.9 55 136-193 50-104 (345)
106 TIGR01079 rplX_bact ribosomal 41.8 52 0.0011 23.7 4.1 36 22-61 3-38 (104)
107 smart00743 Agenet Tudor-like d 41.7 40 0.00087 21.2 3.2 28 22-50 2-29 (61)
108 PRK01191 rpl24p 50S ribosomal 41.0 71 0.0015 23.8 4.7 39 21-63 44-82 (120)
109 smart00064 FYVE Protein presen 41.0 16 0.00035 23.7 1.2 52 139-190 10-65 (68)
110 PF10497 zf-4CXXC_R1: Zinc-fin 41.0 21 0.00045 25.8 1.9 32 158-189 31-69 (105)
111 TIGR00270 conserved hypothetic 40.8 13 0.00028 28.9 0.8 34 156-193 2-35 (154)
112 KOG1740 Predicted mitochondria 38.2 20 0.00043 25.7 1.4 30 9-38 36-65 (107)
113 PF13717 zinc_ribbon_4: zinc-r 37.9 23 0.00049 20.3 1.4 13 152-164 23-35 (36)
114 KOG2133 Transcriptional corepr 37.2 27 0.00058 34.9 2.5 112 21-133 144-280 (1229)
115 PF00667 FAD_binding_1: FAD bi 36.8 48 0.001 26.8 3.7 24 13-36 32-55 (219)
116 KOG4299 PHD Zn-finger protein 36.7 32 0.00069 32.5 2.8 41 152-192 57-97 (613)
117 smart00652 eIF1a eukaryotic tr 36.7 67 0.0014 22.1 3.8 29 20-50 41-69 (83)
118 PF05502 Dynactin_p62: Dynacti 36.6 23 0.0005 32.7 1.9 11 182-192 53-63 (483)
119 cd04466 S1_YloQ_GTPase S1_YloQ 36.6 60 0.0013 20.6 3.5 25 22-50 37-61 (68)
120 PF10377 ATG11: Autophagy-rela 36.4 64 0.0014 24.2 4.0 14 22-35 42-55 (129)
121 cd05793 S1_IF1A S1_IF1A: Trans 36.3 63 0.0014 21.9 3.6 28 21-50 37-64 (77)
122 PF03107 C1_2: C1 domain; Int 36.2 38 0.00082 18.4 2.1 26 143-169 5-30 (30)
123 cd06530 S26_SPase_I The S26 Ty 36.1 74 0.0016 21.2 4.1 25 23-47 32-56 (85)
124 PF12503 CMV_1a_C: Cucumber mo 36.1 29 0.00063 23.9 1.9 29 59-89 36-71 (85)
125 PF00301 Rubredoxin: Rubredoxi 35.0 53 0.0012 20.1 2.8 36 155-190 2-43 (47)
126 KOG1829 Uncharacterized conser 34.9 6.4 0.00014 37.0 -2.0 37 153-197 530-566 (580)
127 PTZ00194 60S ribosomal protein 34.5 1.2E+02 0.0026 23.3 5.2 41 21-65 45-85 (143)
128 PF01176 eIF-1a: Translation i 34.4 54 0.0012 21.3 2.9 25 21-47 40-64 (65)
129 COG1188 Ribosome-associated he 33.7 78 0.0017 22.8 3.8 44 5-52 32-75 (100)
130 PRK05610 rpsQ 30S ribosomal pr 33.6 1.6E+02 0.0035 20.3 5.4 27 12-38 43-69 (84)
131 cd04456 S1_IF1A_like S1_IF1A_l 32.6 68 0.0015 21.8 3.3 29 21-50 37-65 (78)
132 PF11926 DUF3444: Domain of un 32.3 1.2E+02 0.0027 24.9 5.3 45 21-68 26-70 (217)
133 COG0250 NusG Transcription ant 31.3 1.2E+02 0.0025 24.2 4.9 45 21-69 122-166 (178)
134 CHL00174 accD acetyl-CoA carbo 30.1 25 0.00055 30.3 1.0 34 150-191 34-67 (296)
135 CHL00142 rps17 ribosomal prote 29.8 1.9E+02 0.0042 20.0 5.8 28 11-38 39-66 (84)
136 cd06541 ASCH ASC-1 homology or 29.4 1.3E+02 0.0028 21.4 4.5 28 21-50 29-56 (105)
137 PF10844 DUF2577: Protein of u 29.2 54 0.0012 23.3 2.5 20 22-41 76-95 (100)
138 COG4101 Predicted mannose-6-ph 29.1 1.2E+02 0.0027 22.6 4.3 40 22-63 91-136 (142)
139 PF07883 Cupin_2: Cupin domain 29.0 43 0.00093 21.2 1.8 20 16-35 34-53 (71)
140 TIGR00515 accD acetyl-CoA carb 28.8 29 0.00062 29.8 1.1 36 149-192 21-56 (285)
141 cd03698 eRF3_II_like eRF3_II_l 28.7 1.4E+02 0.0029 20.0 4.4 24 22-50 26-49 (83)
142 PF11793 FANCL_C: FANCL C-term 28.1 23 0.00049 23.5 0.3 40 153-192 19-66 (70)
143 PF09416 UPF1_Zn_bind: RNA hel 28.0 24 0.00053 27.3 0.5 17 152-168 12-28 (152)
144 COG0662 {ManC} Mannose-6-phosp 27.9 48 0.001 24.4 2.1 22 15-36 71-92 (127)
145 PF04322 DUF473: Protein of un 27.9 95 0.0021 23.0 3.6 29 22-50 38-71 (119)
146 TIGR01080 rplX_A_E ribosomal p 27.5 1.9E+02 0.004 21.3 5.1 42 21-66 40-81 (114)
147 PF13771 zf-HC5HC2H: PHD-like 27.4 39 0.00084 23.0 1.4 28 142-172 40-69 (90)
148 TIGR02227 sigpep_I_bact signal 27.3 1.5E+02 0.0032 22.8 4.9 28 22-49 51-78 (163)
149 cd06555 ASCH_PF0470_like ASC-1 27.2 1.7E+02 0.0038 21.2 4.8 28 22-50 31-58 (109)
150 COG1917 Uncharacterized conser 27.1 66 0.0014 23.5 2.8 21 15-35 78-98 (131)
151 PF00649 Copper-fist: Copper f 27.0 38 0.00083 20.0 1.1 14 179-192 6-19 (40)
152 PRK05654 acetyl-CoA carboxylas 26.7 32 0.0007 29.6 1.1 36 149-192 22-57 (292)
153 PF14353 CpXC: CpXC protein 26.6 45 0.00099 24.5 1.8 38 155-192 2-49 (128)
154 TIGR01956 NusG_myco NusG famil 26.5 1.5E+02 0.0032 25.1 4.9 43 22-68 205-247 (258)
155 PF09963 DUF2197: Uncharacteri 26.4 22 0.00048 22.7 0.0 38 155-192 3-42 (56)
156 cd05838 WHSC1_related The PWWP 25.7 94 0.002 21.8 3.2 24 24-49 2-25 (95)
157 KOG2041 WD40 repeat protein [G 25.5 52 0.0011 32.1 2.2 50 136-189 1114-1164(1189)
158 KOG3799 Rab3 effector RIM1 and 25.3 33 0.0007 26.1 0.7 53 139-192 66-118 (169)
159 PRK04012 translation initiatio 25.3 1.2E+02 0.0026 21.7 3.7 28 21-50 58-85 (100)
160 COG5047 SEC23 Vesicle coat com 25.3 47 0.001 31.4 1.9 35 153-192 52-87 (755)
161 PF07494 Reg_prop: Two compone 24.9 99 0.0021 15.7 2.4 15 44-59 6-20 (24)
162 PF01079 Hint: Hint module; I 24.9 86 0.0019 25.7 3.2 28 22-50 105-132 (217)
163 PF02311 AraC_binding: AraC-li 24.6 1.3E+02 0.0028 21.1 3.9 21 15-35 37-57 (136)
164 PF09345 DUF1987: Domain of un 24.4 55 0.0012 23.4 1.8 16 56-71 76-91 (99)
165 PF04085 MreC: rod shape-deter 24.4 2.9E+02 0.0063 21.0 6.0 45 20-64 91-137 (152)
166 TIGR03214 ura-cupin putative a 23.9 75 0.0016 26.7 2.8 20 16-35 95-114 (260)
167 cd05841 BS69_related The PWWP 23.8 1.8E+02 0.0038 20.1 4.1 39 23-69 7-45 (83)
168 PF12961 DUF3850: Domain of Un 23.7 1.9E+02 0.0042 19.4 4.2 38 13-50 19-59 (72)
169 COG0198 RplX Ribosomal protein 23.7 1.3E+02 0.0027 21.8 3.5 30 21-52 3-32 (104)
170 PF00366 Ribosomal_S17: Riboso 23.6 88 0.0019 20.7 2.5 26 10-35 31-56 (69)
171 PF01363 FYVE: FYVE zinc finge 23.4 53 0.0012 21.2 1.5 57 134-190 4-66 (69)
172 TIGR00218 manA mannose-6-phosp 22.4 1.6E+02 0.0034 25.3 4.5 33 21-54 153-185 (302)
173 PRK03187 tgl transglutaminase; 22.3 73 0.0016 27.1 2.3 14 22-35 165-178 (272)
174 PF08921 DUF1904: Domain of un 22.0 32 0.00068 25.1 0.1 16 56-71 55-70 (108)
175 KOG3896 Dynactin, subunit p62 21.7 1E+02 0.0022 27.3 3.1 8 163-170 46-53 (449)
176 COG0777 AccD Acetyl-CoA carbox 21.7 51 0.0011 28.2 1.3 34 151-192 25-58 (294)
177 PF06940 DUF1287: Domain of un 21.3 1.7E+02 0.0037 23.0 4.0 38 14-54 98-135 (164)
178 KOG0956 PHD finger protein AF1 21.3 52 0.0011 31.8 1.4 52 138-189 116-179 (900)
179 KOG3896 Dynactin, subunit p62 21.2 89 0.0019 27.6 2.7 48 137-191 8-55 (449)
180 TIGR00922 nusG transcription t 20.7 2.3E+02 0.005 21.8 4.9 45 22-70 119-163 (172)
181 COG0186 RpsQ Ribosomal protein 20.6 3.1E+02 0.0067 19.2 5.3 39 11-49 44-82 (87)
182 TIGR03635 S17_bact 30S ribosom 20.2 1.6E+02 0.0034 19.7 3.2 25 12-36 38-62 (71)
183 PRK08559 nusG transcription an 20.1 2.3E+02 0.0049 21.7 4.6 42 22-69 94-135 (153)
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=3.3e-33 Score=209.39 Aligned_cols=121 Identities=45% Similarity=0.824 Sum_probs=108.5
Q ss_pred CcEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCCCCCCcccccCCCeEEEeCcccccccccEee
Q 027973 20 SKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQSADTIEG 99 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~~~~~~~~~~~~ELf~s~~~d~~~~~~I~g 99 (216)
|++|++||+|||.+++.+.++|||+|++||++.+| .++|+|+|||||+||.+++++.++++|||+|++.|++|+++|.|
T Consensus 1 ~~~~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~~g-~~~~~v~WfyrPeEt~~~~~~~~~~~EvF~S~~~d~~~~~~I~g 79 (121)
T cd04714 1 KEIIRVGDCVLFKSPGRPSLPYVARIESLWEDPEG-NMVVRVKWYYRPEETKGGRKPNHGEKELFASDHQDENSVQTIEH 79 (121)
T ss_pred CCEEEcCCEEEEeCCCCCCCCEEEEEEEEEEcCCC-CEEEEEEEEEcHHHccCcccccCCCCceEecCCcccccHHHhCc
Confidence 45999999999999886678999999999998887 89999999999999999988889999999999999999999999
Q ss_pred eeEEeeccccccccCCCCCceEEeeeecCCCCCCCCCCceeEEEecCCCCCCCceEEC
Q 027973 100 KCTVHSFKSYTKLDAVGNDDFFCRFEYNSSSGAFNPDRVAVYCKCEMPYNPDDLMVQC 157 (216)
Q Consensus 100 kc~V~~~~~~~~~~~~~~~~ff~r~~yd~~~~~f~p~~~~~~C~C~~~~~~~~~~i~C 157 (216)
||.|+++++|.++....+ .+..+..+|+|..+||++..||+|
T Consensus 80 kc~V~~~~ey~~~~~~~~----------------~~~~~~d~~~Ce~~yn~~~~~~~c 121 (121)
T cd04714 80 KCYVLTFAEYERLARVKK----------------KPQDGVDFYYCAGTYNPDTGMLKC 121 (121)
T ss_pred ccEEEehhHheecccccC----------------CCCcCCCEEEEeccCCCCcCcccC
Confidence 999999999998765322 344677889999999999999998
No 2
>cd04713 BAH_plant_3 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.98 E-value=8.8e-32 Score=207.65 Aligned_cols=129 Identities=26% Similarity=0.449 Sum_probs=114.5
Q ss_pred CCCCCCceeeeeEEEecCCcEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCCCCCCc---cccc
Q 027973 2 AKPKAPRRTLESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGR---RQFH 78 (216)
Q Consensus 2 ~~~~~~~~~y~~~~v~g~~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~~~~~---~~~~ 78 (216)
.|+++++.+|.++.++|. +|++||+|||.+++. .++|||+|++||++.++ .++|+|+|||||+||.... ....
T Consensus 2 ~~~~~~~~~y~s~~~dg~--~y~vgD~Vlv~~~~~-~~pyI~~I~~i~~~~~~-~~~v~V~WFyRpeEi~~~~~~~~~~~ 77 (146)
T cd04713 2 GKGKKKKCHYTSFEKDGN--KYRLEDCVLLVPEDD-QKPYIAIIKDIYKQEEG-SLKLEVQWLYRPEEIEKKKGGNWKAE 77 (146)
T ss_pred CCCccceeeeeeEEECCE--EEECCCEEEEeCCCC-CCCEEEEEEEEEEcCCC-CEEEEEEeeECHHHhccccccccccC
Confidence 378899999999999987 999999999999875 78999999999998877 8999999999999997542 2234
Q ss_pred CCCeEEEeCcccccccccEeeeeEEeeccccccccCC-CCCceEEeeeecCCCCCCC
Q 027973 79 GSKEVFLSDHHDIQSADTIEGKCTVHSFKSYTKLDAV-GNDDFFCRFEYNSSSGAFN 134 (216)
Q Consensus 79 ~~~ELf~s~~~d~~~~~~I~gkc~V~~~~~~~~~~~~-~~~~ff~r~~yd~~~~~f~ 134 (216)
+++|||+|+|.|.+|+++|.|||.|+..+++.+++.. ..++||||..||...++|.
T Consensus 78 ~~~ElF~S~~~d~~~~~~I~gkc~V~~~~~~~~~~~~~~~~~F~cr~~yD~~~~~~~ 134 (146)
T cd04713 78 DPRELFYSFHRDEVPAESVLHPCKVAFVPKGKQIPLRKGHSGFIVRRVYDNVNKKLW 134 (146)
T ss_pred CCCeEEEeCCCCcCCHHHCcceeEEEECCccccCCccCCCCeEEEEEEEcCCCCcEe
Confidence 6899999999999999999999999999988877664 5679999999999988776
No 3
>cd04716 BAH_plantDCM_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.97 E-value=2.8e-31 Score=198.22 Aligned_cols=113 Identities=20% Similarity=0.369 Sum_probs=103.1
Q ss_pred CcEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCCCCCCc-ccccCCCeEEEeCcccccccccEe
Q 027973 20 SKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGR-RQFHGSKEVFLSDHHDIQSADTIE 98 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~~~~~-~~~~~~~ELf~s~~~d~~~~~~I~ 98 (216)
|++|++||+|||.+++. .++|||||++||++.+| ..+++|+|||||+||..++ ...++++|||+|+|.|.+|+++|+
T Consensus 1 g~~~~lgD~V~v~~~~~-~~~yi~rI~~i~e~~~g-~~~~~v~WyyRpeet~~~r~~~~~~~rEvFlS~~~D~~pl~~I~ 78 (122)
T cd04716 1 GITYNLGDDAYVQGGEG-EEPFICKITEFFEGTDG-KTYFTAQWFYRAEDTVIERQATNHDKKRVFYSEIKNDNPLDCLI 78 (122)
T ss_pred CcEEEcCCEEEEECCCC-CCCEEEEEEEEEEcCCC-ceEEEEEEEEcHHHhccccccccCCCceEEEecccCccchhhee
Confidence 45899999999999974 89999999999999888 7899999999999999886 567889999999999999999999
Q ss_pred eeeEEeeccccccc----cCCCCCceEEeeeecCCCCCCC
Q 027973 99 GKCTVHSFKSYTKL----DAVGNDDFFCRFEYNSSSGAFN 134 (216)
Q Consensus 99 gkc~V~~~~~~~~~----~~~~~~~ff~r~~yd~~~~~f~ 134 (216)
|||+|++++++..+ ...+.++|||+..|+....+|.
T Consensus 79 ~Kc~V~~~~~~~~~~~~~~~~~~~df~c~~~Y~~~~~tF~ 118 (122)
T cd04716 79 SKVKILQVPPNVGTKRKKPNSEKCDYYYDMEYCVPYSTFQ 118 (122)
T ss_pred eeeEEEEeCCCCCcccccccCCCceEEEeeEeccchhheE
Confidence 99999999888876 4467889999999999988886
No 4
>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.97 E-value=1.4e-30 Score=195.31 Aligned_cols=115 Identities=30% Similarity=0.501 Sum_probs=104.6
Q ss_pred CcEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCCCCCCcccccCCCeEEEeCcccccccccEee
Q 027973 20 SKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQSADTIEG 99 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~~~~~~~~~~~~ELf~s~~~d~~~~~~I~g 99 (216)
|..|++||+|||.+++.+.+++||+|.+||++.+| ..+|+|+|||||+||.++....+.++|||+|++.|++|+++|.|
T Consensus 1 g~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g-~~~~~~~Wf~rP~et~~~~~~~~~~~Evfls~~~d~~~~~~I~~ 79 (121)
T cd04717 1 GLQYRVGDCVYVANPEDPSKPIIFRIERLWKDEDG-EKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVG 79 (121)
T ss_pred CCEEECCCEEEEeCCCCCCCCEEEEEeEEEECCCC-CEEEEEEEEeChHHccCCCccccccCceEEcCccccccHHHhcC
Confidence 45899999999999886678999999999999887 89999999999999988877778999999999999999999999
Q ss_pred eeEEeeccccccccCC---CCCceEEeeeecCCCCCCCC
Q 027973 100 KCTVHSFKSYTKLDAV---GNDDFFCRFEYNSSSGAFNP 135 (216)
Q Consensus 100 kc~V~~~~~~~~~~~~---~~~~ff~r~~yd~~~~~f~p 135 (216)
||.|++.++|.+..+. ..++||||+.||...+.|.+
T Consensus 80 kc~Vl~~~~y~~~~p~~~~~~dvy~ce~~y~~~~~~~~~ 118 (121)
T cd04717 80 KCAVMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKK 118 (121)
T ss_pred eeEEEehHHHhcCCCCCCCCCCEEEEeEEECcccccEec
Confidence 9999999999987753 45789999999999988864
No 5
>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=5.8e-29 Score=188.95 Aligned_cols=116 Identities=22% Similarity=0.429 Sum_probs=100.3
Q ss_pred ecCCcEEccCCEEEEecCCCCCCCeEEEEEEEEecCC-----------CCeEEEEEEEEeecCCCCCCcccccCCCeEEE
Q 027973 17 KSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDAR-----------GANVKVHVRWYYRPEESIGGRRQFHGSKEVFL 85 (216)
Q Consensus 17 ~g~~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~-----------~~~~~v~v~WfyRp~d~~~~~~~~~~~~ELf~ 85 (216)
..+|.+|++||+|||.++++++|++||||++|+...+ .+.++|+|+|||||+||.... .++.+|||+
T Consensus 6 ~~~g~~~~vgD~Vyv~~~~~~ePyyIgrI~e~~~~~~~~~~~~~~~~~~~~~~vrV~wfYRp~Di~~~~--~~d~relf~ 83 (135)
T cd04710 6 LKNGELLKVNDHIYMSSEPPGEPYYIGRIMEFVPKHEFPSGIHARVFPASYFQVRLNWYYRPRDISRRV--VADSRLLYA 83 (135)
T ss_pred ccCCeEEeCCCEEEEecCCCCCCCEEEEEEEEEecCCCCccccccccCCCcEEEEEEEEeCHHHcCCcc--cCCceEEEE
Confidence 3455799999999999999889999999999998542 224799999999999985444 578999999
Q ss_pred eCcccccccccEeeeeEEeeccccccccC--CCCCceEEeeeecCCCCCCC
Q 027973 86 SDHHDIQSADTIEGKCTVHSFKSYTKLDA--VGNDDFFCRFEYNSSSGAFN 134 (216)
Q Consensus 86 s~~~d~~~~~~I~gkc~V~~~~~~~~~~~--~~~~~ff~r~~yd~~~~~f~ 134 (216)
|+|.|++|+++|+|||+|.+.+++.++.. ..+++|||...||+.+++|.
T Consensus 84 S~h~d~~p~~si~gKC~V~~~~di~~l~~~~~~~~~Fyf~~lyD~~~~r~~ 134 (135)
T cd04710 84 SMHSDICPIGSVRGKCTVRHRDQIPDLEEYKKRPNHFYFDQLFDRYILRYY 134 (135)
T ss_pred EeeEeeechHHEEeEEEEEEecccchhhhhccCCCEEEEEeeeCcchhhcc
Confidence 99999999999999999999998877654 35789999999999998874
No 6
>smart00439 BAH Bromo adjacent homology domain.
Probab=99.96 E-value=7.5e-29 Score=184.95 Aligned_cols=113 Identities=39% Similarity=0.700 Sum_probs=102.7
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCe-EEEEEEEEeecCCCCCCcccccCCCeEEEeCcccccccccEeee
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGAN-VKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQSADTIEGK 100 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~-~~v~v~WfyRp~d~~~~~~~~~~~~ELf~s~~~d~~~~~~I~gk 100 (216)
+|++||+|||.+++...+++||+|.+||++.++ . ++++|+|||||+||+++....+++||||+|++.+++++++|.||
T Consensus 1 ~~~vgd~V~v~~~~~~~~~~i~~I~~i~~~~~~-~~~~~~v~Wf~rp~e~~~~~~~~~~~~Elf~s~~~~~i~~~~I~~k 79 (120)
T smart00439 1 TIRVGDFVLVEPDDADEPYYIGRIEEIFETKKN-SEKMVRVRWFYRPEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGK 79 (120)
T ss_pred CcccCCEEEEeCCCCCCCCEEEEEEEEEECCCC-CEEEEEEEEEEChhhccccccccCCCcceEEEccCccCChHHeeeE
Confidence 478999999999986678999999999999888 6 89999999999999998877788999999999999999999999
Q ss_pred eEEeeccccccccCC----CCCceEEeeeecCCCCCCCC
Q 027973 101 CTVHSFKSYTKLDAV----GNDDFFCRFEYNSSSGAFNP 135 (216)
Q Consensus 101 c~V~~~~~~~~~~~~----~~~~ff~r~~yd~~~~~f~p 135 (216)
|.|++.+++.+.... ..+.||||+.||..+++|.+
T Consensus 80 c~V~~~~~~~~~~~~~~~~~~~~f~cr~~yd~~~~~f~~ 118 (120)
T smart00439 80 CNVLSKSDYPGLRPEGKIGEPDVFFCESLYDPEKGAFKK 118 (120)
T ss_pred EEEEEcchhcccccccCCCCCCeEEEEEEEccccCcccC
Confidence 999999999876553 46899999999999998874
No 7
>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=99.96 E-value=5.4e-29 Score=194.40 Aligned_cols=116 Identities=28% Similarity=0.490 Sum_probs=101.9
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCCCCCCc----------------------cccc
Q 027973 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGR----------------------RQFH 78 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~~~~~----------------------~~~~ 78 (216)
.+|++||+|||.++ ++.|++||||++|+++.++ .++++|+|||||+||+... +..+
T Consensus 2 ~~yrvGD~Vy~~~~-~~~Py~I~rI~e~~~~~~~-~~~vkV~wfYRp~DI~~~~~~l~~~~r~~~~~~~~~~~~~~~~~~ 79 (164)
T cd04709 2 NMYRVGDYVYFESS-PNNPYLIRRIEELNKTARG-HVEAKVVCYYRRRDIPDSLYQLADQHRRELEEKSDDLTPKQRHQL 79 (164)
T ss_pred cEEecCCEEEEECC-CCCCCEEEEEEEEEeCCCC-CEEEEEEEEEChhHccchhhhhcccccccccccccccchhhhhcc
Confidence 48999999999998 4568899999999999888 8999999999999986421 2235
Q ss_pred CCCeEEEeCcccccccccEeeeeEEeeccccccccCC--CCCceEEeeeecCCCCCCCCCCc
Q 027973 79 GSKEVFLSDHHDIQSADTIEGKCTVHSFKSYTKLDAV--GNDDFFCRFEYNSSSGAFNPDRV 138 (216)
Q Consensus 79 ~~~ELf~s~~~d~~~~~~I~gkc~V~~~~~~~~~~~~--~~~~ff~r~~yd~~~~~f~p~~~ 138 (216)
+.+|||+|+|.|.+|+++|+|||.|++++++.++... .+++|||+..||+.+++|..++.
T Consensus 80 ~~rELF~S~~~d~~p~~~IrGKC~V~~~~d~~~l~~~~~~~d~Ff~~~~YDP~~k~l~~~~g 141 (164)
T cd04709 80 RHRELFLSRQVETLPATHIRGKCSVTLLNDTESARSYLAREDTFFYSLVYDPEQKTLLADQG 141 (164)
T ss_pred CcceeEEecccccccHHHeeeeEEEEEehhhhhhhhccCCCCEEEEEEEECCCCCeecccce
Confidence 7999999999999999999999999999999888653 57899999999999999987543
No 8
>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=99.96 E-value=4.1e-29 Score=186.60 Aligned_cols=115 Identities=39% Similarity=0.772 Sum_probs=103.8
Q ss_pred CcEEccCCEEEEecCCC--CCCCeEEEEEEEEecCCCCeEEEEEEEEeecCCCCCCcccccCCCeEEEeCcccccccccE
Q 027973 20 SKTIKPGDCVLMRPSEP--SKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQSADTI 97 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~~--~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~~~~~~~~~~~~ELf~s~~~d~~~~~~I 97 (216)
|.+|++||+|||.+++. ++++|||+|.+||++.++ .++++|+|||||+||+.+....+++||||+|++.+++|+++|
T Consensus 1 g~~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~~~~~-~~~~~v~wf~rp~e~~~~~~~~~~~~Elf~s~~~~~i~v~~I 79 (123)
T cd04370 1 GITYEVGDSVYVEPDDSIKSDPPYIARIEELWEDTNG-SKQVKVRWFYRPEETPKGLSPFALRRELFLSDHLDEIPVESI 79 (123)
T ss_pred CCEEecCCEEEEecCCcCCCCCCEEEEEeeeeECCCC-CEEEEEEEEEchhHhccccccccccceeEEecCccccCHHHh
Confidence 45899999999999885 478999999999999888 899999999999999998777789999999999999999999
Q ss_pred eeeeEEeecccccccc----CCCCCceEEeeeecCCCCCCCC
Q 027973 98 EGKCTVHSFKSYTKLD----AVGNDDFFCRFEYNSSSGAFNP 135 (216)
Q Consensus 98 ~gkc~V~~~~~~~~~~----~~~~~~ff~r~~yd~~~~~f~p 135 (216)
.|+|.|++.+++.+.. ....++||||+.||..+++|.+
T Consensus 80 ~gkc~V~~~~~~~~~~~~~~~~~~~~f~~r~~yd~~~~~fk~ 121 (123)
T cd04370 80 IGKCKVLFVSEFEGLKQRPNKIDTDDFFCRLAYDPTTKEFKA 121 (123)
T ss_pred ccccEEEechHhhccccccccCCCCeEEEEEEECcCcceEEe
Confidence 9999999999988663 2456799999999999888764
No 9
>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=99.96 E-value=3.9e-29 Score=186.29 Aligned_cols=113 Identities=39% Similarity=0.764 Sum_probs=100.7
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCC-eEEEEEEEEeecCCCCCCcccccCCCeEEEeCcccccccccEee
Q 027973 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGA-NVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQSADTIEG 99 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~-~~~v~v~WfyRp~d~~~~~~~~~~~~ELf~s~~~d~~~~~~I~g 99 (216)
++|++||+|||.+++++.+++||+|++||++.+++ .++++|+|||||+||.. .....++|||+|++++.+|+++|+|
T Consensus 1 ~~~~vGD~V~v~~~~~~~~~~v~~I~~i~~~~~~~~~~~~~v~Wf~rp~d~~~--~~~~~~~Elf~s~~~~~~~~~~I~g 78 (119)
T PF01426_consen 1 VTYKVGDFVYVKPDDPPEPPYVARIEEIWEDKDGNKEKMVKVRWFYRPEDTSL--GKTFSPRELFLSDHCDDIPVESIRG 78 (119)
T ss_dssp EEEETTSEEEEECTSTTSEEEEEEEEEEEEETTTSEEEEEEEEEEEEGGGSTT--GGHSCTTEEEEEEEEEEEEGGGEEE
T ss_pred CEEeCCCEEEEeCCCCCCCCEEEEEEEEEcCCCCCEEEEEEEEEeECcccccc--cccCCCCEEEEECcEeEEehhhEEe
Confidence 37999999999999977899999999999998884 59999999999999932 3335679999999999999999999
Q ss_pred eeEEeeccccccccCC---CCCceEEeeeecCCCCCCCC
Q 027973 100 KCTVHSFKSYTKLDAV---GNDDFFCRFEYNSSSGAFNP 135 (216)
Q Consensus 100 kc~V~~~~~~~~~~~~---~~~~ff~r~~yd~~~~~f~p 135 (216)
||.|++.+++.+.... .+++||||+.||..+++|.+
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 9999999998877653 67899999999999999874
No 10
>cd04721 BAH_plant_1 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.95 E-value=1.3e-27 Score=180.74 Aligned_cols=108 Identities=29% Similarity=0.455 Sum_probs=96.9
Q ss_pred CcEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCCCCCCcccc-cCCCeEEEeCcccccccccEe
Q 027973 20 SKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQF-HGSKEVFLSDHHDIQSADTIE 98 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~~~~~~~~-~~~~ELf~s~~~d~~~~~~I~ 98 (216)
|.++++||+|||.+++ +++|||+|++||++.+| .++++|+||+||+|+.++..+. +.++|||+|++.+.+|+++|.
T Consensus 5 ~~~i~vGD~V~v~~~~--~~~~va~Ie~i~ed~~g-~~~v~v~WF~~p~E~~~~~~~~~~~~~EvFlS~~~d~i~~~~I~ 81 (130)
T cd04721 5 GVTISVHDFVYVLSEE--EDRYVAYIEDLYEDKKG-SKMVKVRWFHTTDEVGAALSPDSVNPREIFLSPNLQVISVECID 81 (130)
T ss_pred CEEEECCCEEEEeCCC--CCcEEEEEEEEEEcCCC-CEEEEEEEecCHHHhccccCCCCCCCCeEEEcCCccccchHHee
Confidence 4589999999999987 67899999999999888 8999999999999999876555 889999999999999999999
Q ss_pred eeeEEeeccccccccCCC-----CCceEEeeeecCCC
Q 027973 99 GKCTVHSFKSYTKLDAVG-----NDDFFCRFEYNSSS 130 (216)
Q Consensus 99 gkc~V~~~~~~~~~~~~~-----~~~ff~r~~yd~~~ 130 (216)
|||+|++.++|.++.... .++|+||..||...
T Consensus 82 gk~~Vls~~~y~k~~~~~~~~~~~~~f~C~~~~d~~~ 118 (130)
T cd04721 82 GLATVLTREHYEKFQSVPKNSSELQAYFCYRQIDNNK 118 (130)
T ss_pred eeeEECCHHHHhhhhccccCccccccEEEEEEecCCC
Confidence 999999999999876432 45899999999863
No 11
>cd04760 BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.94 E-value=1e-26 Score=172.76 Aligned_cols=112 Identities=25% Similarity=0.512 Sum_probs=97.7
Q ss_pred CcEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCCCCCCcccccCCCeEEEeCcccccccccEee
Q 027973 20 SKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQSADTIEG 99 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~~~~~~~~~~~~ELf~s~~~d~~~~~~I~g 99 (216)
|.+|.+||+|+|.++++..+++||+|++||++.++ .++++|+|||||+||.+++. ++++|||+|++++.+++++|.+
T Consensus 1 g~~i~vGD~V~v~~~~~~~p~~I~rV~~mfe~~~g-~k~~h~rWf~Rg~dTVlG~~--~~~kEvFlsd~c~d~~l~~I~~ 77 (124)
T cd04760 1 GEELEAGDCVSVKPDDPTKPLYIARVTYMWKDSIG-GKMFHAHWFCRGSDTVLGET--SDPLELFLVDECEDMALSSIHG 77 (124)
T ss_pred CCEEecCCEEEEecCCCCCCcEEEEEhhheecCCC-CcEEEEEEEEECCccccccc--CCCcEEEeecccCCcchHHhee
Confidence 35899999999999988889999999999999988 89999999999999999986 7899999999999999999999
Q ss_pred eeEEeecccc---cccc---------CCCCCceEEeeeecCCCCCCC
Q 027973 100 KCTVHSFKSY---TKLD---------AVGNDDFFCRFEYNSSSGAFN 134 (216)
Q Consensus 100 kc~V~~~~~~---~~~~---------~~~~~~ff~r~~yd~~~~~f~ 134 (216)
||+|.....- ..+. ..+..+|||+..||+...+|+
T Consensus 78 Kv~V~~~~p~~~w~~~~g~~~~~~~~~ddg~tffyq~~yd~~~arf~ 124 (124)
T cd04760 78 KVNVIYKAPSENWSMEGGMDEEDEIFEDDGKTFFYQKWYDPECARFE 124 (124)
T ss_pred eeEEEEeCCCcchhhhcCCCCccccccCCCCeEEEEEeeChhhhccC
Confidence 9999985432 2111 124468999999999988874
No 12
>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=99.94 E-value=3.2e-26 Score=178.25 Aligned_cols=104 Identities=27% Similarity=0.394 Sum_probs=90.4
Q ss_pred CCCCceeeeeEEEecCCcEEccCCEEEEecCCCCCCCeEEEEEEEEecCC--CCeEEEEEEEEeecCCCCCCcc--cccC
Q 027973 4 PKAPRRTLESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDAR--GANVKVHVRWYYRPEESIGGRR--QFHG 79 (216)
Q Consensus 4 ~~~~~~~y~~~~v~g~~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~--~~~~~v~v~WfyRp~d~~~~~~--~~~~ 79 (216)
.++++.+|.++.++|. +|++||+|||.+++ .++|||+|.+||++.+ + .++++|+|||||+||..... +.+.
T Consensus 13 ~~~~~~~Y~s~~~~g~--~y~lGD~Vlv~s~~--~~~yIgkI~~iwe~~~~~g-~~~~~v~WfyRp~E~~~~~~~~~~~~ 87 (159)
T cd04715 13 KKKDGQFYRSFTYDGV--EYRLYDDVYVHNGD--SEPYIGKIIKIYETAIDSG-KKKVKVIWFFRPSEIRMELKGEPKRH 87 (159)
T ss_pred ccCCceEEEEEEECCE--EEeCCCEEEEeCCC--CCCEEEEEEEEEEcCCcCC-ceEEEEEeeeCHHHhccccccCcccC
Confidence 4566779999999987 99999999999866 7999999999999764 5 89999999999999985432 3578
Q ss_pred CCeEEEeCcc-----cccccccEeeeeEEeeccccccc
Q 027973 80 SKEVFLSDHH-----DIQSADTIEGKCTVHSFKSYTKL 112 (216)
Q Consensus 80 ~~ELf~s~~~-----d~~~~~~I~gkc~V~~~~~~~~~ 112 (216)
+||||+|.|. +++|+++|.|||.|++.++|...
T Consensus 88 ~nEvFlS~~~d~~~~~~n~l~sI~gKC~Vl~~~ey~~~ 125 (159)
T cd04715 88 INEVFLACGRGEGLANINLLESIIGKCNVVCISEDFRN 125 (159)
T ss_pred CCcEEEecCcCccccccCcHHHccceeEEEEehHhhhC
Confidence 9999999986 66899999999999999998754
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=99.93 E-value=1.1e-25 Score=179.90 Aligned_cols=118 Identities=25% Similarity=0.453 Sum_probs=99.6
Q ss_pred EEecCCcEEccCCEEEEecCC-----------------CCCCCeEEEEEEEEecCCC-----CeEEEEEEEEeecCCCCC
Q 027973 15 TVKSISKTIKPGDCVLMRPSE-----------------PSKPSYVAKIERIESDARG-----ANVKVHVRWYYRPEESIG 72 (216)
Q Consensus 15 ~v~g~~~~~~vGD~V~v~~~~-----------------~~~~~~IarI~~i~~~~~~-----~~~~v~v~WfyRp~d~~~ 72 (216)
+++| ++|++||+|||.|+. ...+++||+|.+|+...++ ..+.|+|+|||||+||..
T Consensus 2 ~~~G--v~Y~vgD~VYv~p~~f~~~~~~~~~~~~G~N~~~~p~~I~qI~ei~~~k~~~~~~~~~~~vrVrwFYRPEdt~~ 79 (202)
T cd04708 2 VYDG--VTYSVGDFLYVSPDAFAEEERERATFKAGRNVGLKAFVVCQVLEIVVEKESKQADVASTQVKVRRFYRPEDVSP 79 (202)
T ss_pred cCCC--EEEecCCeEEECcccccccccccccccccccCCCCCcEEEEEEEEEecccCCCCCCcceEEEEEEEechhhcCc
Confidence 3455 599999999999991 1258999999999975433 268999999999999855
Q ss_pred CcccccCCCeEEEeCcccccccccEeeeeEEeeccccccccC--CCCCceEEeeeecCCCCCCC
Q 027973 73 GRRQFHGSKEVFLSDHHDIQSADTIEGKCTVHSFKSYTKLDA--VGNDDFFCRFEYNSSSGAFN 134 (216)
Q Consensus 73 ~~~~~~~~~ELf~s~~~d~~~~~~I~gkc~V~~~~~~~~~~~--~~~~~ff~r~~yd~~~~~f~ 134 (216)
......+.+|||+|++.+++|+++|.|||+|....++.++.. ..++.|||+..||+.++.|+
T Consensus 80 ~~~y~sd~rely~Sde~~~~~~~~I~GKC~V~~~~d~~~~~~~~~~~~~Ffc~~~Yd~~tg~f~ 143 (202)
T cd04708 80 EKAYASDIREVYYSEDTLTVPVEAVEGKCEVRKKSDLPDSDAPVIFEHVFFCELLYDPAKGSLK 143 (202)
T ss_pred ccceecCceeEEEeccceeechhHcceEEEEEecCcchhhhccccCCCceEEEEEEcCCCCccC
Confidence 333345899999999999999999999999999999877655 56889999999999999998
No 14
>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=99.93 E-value=4.4e-25 Score=166.93 Aligned_cols=110 Identities=24% Similarity=0.333 Sum_probs=92.1
Q ss_pred cEEccCCEEEEecCCCC----------CCCeEEEEEEEEecCCCCeEEEEEEEEeecCCCCCCcccccCCCeEEEeCccc
Q 027973 21 KTIKPGDCVLMRPSEPS----------KPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHD 90 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~----------~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~~~~~~~~~~~~ELf~s~~~d 90 (216)
..|++||+|+|.+++++ .+++|++|+.||++.+| .++|+|+|||||+||.++. .++++|||||+|++
T Consensus 4 ~~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~~~g-~~~~h~~W~yrp~eTv~g~--~~~~~ElFLSd~c~ 80 (130)
T cd04712 4 LTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKGSDG-SKMFHGRWLYRGCDTVLGN--YANERELFLTNECT 80 (130)
T ss_pred CEEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeecCCC-ceEEEEEEEEcchhccccc--cCCCceEEEecccc
Confidence 48999999999999875 38899999999999988 8999999999999999988 68999999999999
Q ss_pred ccccc----cEeeeeEEeeccccccccCCCCCceEEeeeecCCCCCCCC
Q 027973 91 IQSAD----TIEGKCTVHSFKSYTKLDAVGNDDFFCRFEYNSSSGAFNP 135 (216)
Q Consensus 91 ~~~~~----~I~gkc~V~~~~~~~~~~~~~~~~ff~r~~yd~~~~~f~p 135 (216)
.++++ .|.+||.|........ ...++.|||+..|+++++.|+.
T Consensus 81 ~~~~~~~~~~I~~k~~V~~~~~~~~--~~~~~~F~r~syy~~e~~~F~~ 127 (130)
T cd04712 81 CLELDLLSTEIKGVHKVDWSGTPWG--KGLPEFFVRQSYYWPERGAFTS 127 (130)
T ss_pred ccccccccceeEEEEEEEEecCcCC--cCCCCEEEEEEEECccCCceEc
Confidence 99999 9999999997655432 1133444455555558888873
No 15
>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=99.93 E-value=3.6e-27 Score=179.02 Aligned_cols=96 Identities=27% Similarity=0.533 Sum_probs=91.7
Q ss_pred CCCCeEEEEEEEEecCCCCeEEEEEEEEeecCCCCCCcccccCCCeEEEeCcccccccccEeeeeEEeeccccccccCCC
Q 027973 37 SKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQSADTIEGKCTVHSFKSYTKLDAVG 116 (216)
Q Consensus 37 ~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~~~~~~~~~~~~ELf~s~~~d~~~~~~I~gkc~V~~~~~~~~~~~~~ 116 (216)
++.+|||||++||++. | ..+++|+|||||+||.+|+++.+..+|||+|++.|.+++++|.|||.|+.+++|.+++..+
T Consensus 50 ~~~~~vArIekiW~~~-G-~~~~~grWy~rPEET~~gr~~~~~~kEvFlS~~~d~~~~~~I~gkC~V~~~keY~k~e~~g 127 (148)
T cd04718 50 SGDLWLARIEKLWEEN-G-TYWYAARWYTLPEETHMGRQPHNLRRELYLTNDFADIEMECILRHCSVKCPKEFRDASNDG 127 (148)
T ss_pred cCchHHHHHHHHHhcc-C-ceEEEEEEEeCchhccCccccccccceeeeccccccccHHHHhcccEEcCHHHcccccCCC
Confidence 4688999999999976 6 8999999999999999999999999999999999999999999999999999999998889
Q ss_pred CCceEEeeeecCCCCCCC
Q 027973 117 NDDFFCRFEYNSSSGAFN 134 (216)
Q Consensus 117 ~~~ff~r~~yd~~~~~f~ 134 (216)
.|+|||++.||..+++|.
T Consensus 128 ~Dvy~Ce~~Yd~~~~~Fk 145 (148)
T cd04718 128 DDVFLCEYEYDVHWQSFK 145 (148)
T ss_pred CceEEEEEEEhhhcCcee
Confidence 999999999999999986
No 16
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=99.92 E-value=8e-25 Score=192.15 Aligned_cols=180 Identities=30% Similarity=0.438 Sum_probs=159.7
Q ss_pred CCCCceeeeeEEEecCCcEEcc-CCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCCCCCCc---ccccC
Q 027973 4 PKAPRRTLESYTVKSISKTIKP-GDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGR---RQFHG 79 (216)
Q Consensus 4 ~~~~~~~y~~~~v~g~~~~~~v-GD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~~~~~---~~~~~ 79 (216)
+...+.||+.+.+++. .+.. ||.|.+.+++++.++|||+|.+|+.+..++.+.++|+|||||+|+..+. .....
T Consensus 33 ~~~k~~h~~t~~~~~g--~~~~~~d~vllvped~~~pPyvaii~~i~a~~~g~~~k~ev~W~YrPee~~~~~~~~~~a~~ 110 (464)
T KOG1886|consen 33 GGVKSLHFETFIYRGG--RYINYGDSVLLVPEDPGKPPYVAIIEDIYAQERGGNVKVEVQWFYRPEESEGGGSGKWGAKQ 110 (464)
T ss_pred cccccccccceeeccC--cccccCcceeecCCCCCCCCeeEEEeeeeccccCCCcceecccccCCCccCCCCCCCcccCC
Confidence 4556889999999987 6666 9999999999999999999999999988668999999999999998764 33456
Q ss_pred CCeEEEeCcccccccccEeeeeEEeeccccccccC-CCCCceEEeeeecCCCCCCCCCCceeEEEecCCCCCCCceEECC
Q 027973 80 SKEVFLSDHHDIQSADTIEGKCTVHSFKSYTKLDA-VGNDDFFCRFEYNSSSGAFNPDRVAVYCKCEMPYNPDDLMVQCE 158 (216)
Q Consensus 80 ~~ELf~s~~~d~~~~~~I~gkc~V~~~~~~~~~~~-~~~~~ff~r~~yd~~~~~f~p~~~~~~C~C~~~~~~~~~~i~C~ 158 (216)
++|||+|.|.|.+++++|.++|.|.++..+.++.. ..-+.|+||..||.-++.|.+.....||.|.+.+++...+.+|.
T Consensus 111 ~relF~SfH~De~~A~ti~~rC~V~fvp~~kqlp~~~~~~~f~~r~vYd~~~~~~~~~~~~~~~~~~k~e~d~~~~kt~~ 190 (464)
T KOG1886|consen 111 PRELFLSFHEDEAFAETILHRCKVHFVPAYKQLPNRVGHESFICRRVYDAVTSKLRKLRDGDFGDGQKLEIDMLVPKTGP 190 (464)
T ss_pred CccccccccccchhhhhhcccceeeeccccccccccCCCCCcccccccccccccccCccccchhcccccCCccchhhhcc
Confidence 68999999999999999999999999999999876 67789999999999999999989999999999999889999999
Q ss_pred CCCceecCCCCCCChhhhcCCCcEEeccccc
Q 027973 159 GCSDWFHPNCINMTAEEAKRLDHFFCESCST 189 (216)
Q Consensus 159 ~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~ 189 (216)
.|+.|+|..|+..+.. .....|..|..
T Consensus 191 ~~~~~~~p~~~~t~~~----~~~~~~~~~s~ 217 (464)
T KOG1886|consen 191 RRGTLPDPKKVQTLNA----AASKRSQQKSE 217 (464)
T ss_pred cCCCCCCccccccccc----cccceeccccc
Confidence 9999999999987752 25677777743
No 17
>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=99.92 E-value=3.2e-24 Score=170.59 Aligned_cols=116 Identities=22% Similarity=0.327 Sum_probs=101.4
Q ss_pred CCcEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCCCCCCcc--c-------ccCCCeEEEeCcc
Q 027973 19 ISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRR--Q-------FHGSKEVFLSDHH 89 (216)
Q Consensus 19 ~~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~~~~~~--~-------~~~~~ELf~s~~~ 89 (216)
+|++|++||+|+|.+++. .++|||.|.+|+.+..++.+.+.|+|||||.|+..++. + ...+||||+|.|.
T Consensus 49 d~~~~~vGD~Vlik~~~~-~~~~V~iI~ei~~~~~~~~v~i~v~Wy~r~~Ei~~~~~~~~~~~~~~~~~~~nElflT~~~ 127 (179)
T cd04720 49 DGLELSVGDTILVKDDVA-NSPSVYLIHEIRLNTLNNEVELWVMWFLRWFEINPARYYKQFDPEFRSESNKNELYLTAEL 127 (179)
T ss_pred CCeEEeCCCEEEEeCCCC-CCCEEEEEEEEEeCCCCCEEEEEEEEcCCHHHcccccccccccchhcccCCCceEEEeccc
Confidence 568999999999999875 78999999999998764478999999999999976542 2 2337999999999
Q ss_pred cccccccEeeeeEEeeccccccccCC---CCCceEEeeeecCCCCCCCC
Q 027973 90 DIQSADTIEGKCTVHSFKSYTKLDAV---GNDDFFCRFEYNSSSGAFNP 135 (216)
Q Consensus 90 d~~~~~~I~gkc~V~~~~~~~~~~~~---~~~~ff~r~~yd~~~~~f~p 135 (216)
|.+++.+|+++|+|++.++|.++... ...+||||++||+.++.|.+
T Consensus 128 d~i~l~~Ii~k~~Vls~~ef~~~~~~~~~~~~~F~cR~~~d~~~~~F~~ 176 (179)
T cd04720 128 SEIKLKDIIDKANVLSESEFNDLSTDDKNGERTFFCRYACEPDGEEFVW 176 (179)
T ss_pred ceEEhhheeeeEEEecHHHhhhhcccccCCCceEEEEEEEeCCCCeEcc
Confidence 99999999999999999999987654 56799999999999998886
No 18
>cd04711 BAH_Dnmt1_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.90 E-value=1.6e-23 Score=156.34 Aligned_cols=110 Identities=21% Similarity=0.436 Sum_probs=88.6
Q ss_pred CCEEEEecCCCCCCCeEEEEEEEEecCCCC------eEEEEEEEEeecCCCCCCccc-c-cCCCeEEEeCcccccccccE
Q 027973 26 GDCVLMRPSEPSKPSYVAKIERIESDARGA------NVKVHVRWYYRPEESIGGRRQ-F-HGSKEVFLSDHHDIQSADTI 97 (216)
Q Consensus 26 GD~V~v~~~~~~~~~~IarI~~i~~~~~~~------~~~v~v~WfyRp~d~~~~~~~-~-~~~~ELf~s~~~d~~~~~~I 97 (216)
+|.|-=.+-|.+.|++||||++|...+++. .++|+|+|||||+||..+... + .+-+|||+|+|.+++|+++|
T Consensus 13 ~~~~~~~~~d~~ePy~VgrI~eI~~~k~~~~k~~~~~ikvrV~~fYRPEdi~~g~~~ayhsDirevy~Sd~~~~~~~~~I 92 (137)
T cd04711 13 SDYIKGSNLDAPEPFRIGRIKEIFCAKRSNGKPNESDIKLRINKFYRPENTHKGFKATYHADINMLYWSDEEATVDFSAV 92 (137)
T ss_pred ccccccccCCCCCCcEEEEEEEEecCCCCCCCCCccceEEEEEEEecccccccccccccccceeeEEeecceeecChhhc
Confidence 444444455667899999999999876543 578999999999999987643 3 44499999999999999999
Q ss_pred eeeeEEeecccccc-c---cCCCCCceEEeeeecCCCCCCCC
Q 027973 98 EGKCTVHSFKSYTK-L---DAVGNDDFFCRFEYNSSSGAFNP 135 (216)
Q Consensus 98 ~gkc~V~~~~~~~~-~---~~~~~~~ff~r~~yd~~~~~f~p 135 (216)
.|||.|.+..+..+ + ...+++.|||+.+||.+++.|+.
T Consensus 93 ~GKC~V~~~~di~~s~~~y~~~gpd~Fyf~~~Y~a~t~~F~d 134 (137)
T cd04711 93 QGRCTVEYGEDLPESVQEYSGGGPDRFYFLEAYNAKTKSFED 134 (137)
T ss_pred cceEEEEeccccchhHHHHhcCCCcceEEhhhhccccCcccC
Confidence 99999997555432 2 22468999999999999999984
No 19
>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=99.89 E-value=1.8e-23 Score=156.93 Aligned_cols=110 Identities=25% Similarity=0.359 Sum_probs=92.9
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEEEEEecCCC--CeEEEEEEEEeecCCCCCCc----ccccCCCeEEEeCccc---c
Q 027973 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDARG--ANVKVHVRWYYRPEESIGGR----RQFHGSKEVFLSDHHD---I 91 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~--~~~~v~v~WfyRp~d~~~~~----~~~~~~~ELf~s~~~d---~ 91 (216)
.+|++||+|+|.++++ +++|||+|++|+++.++ ....++|||||||+|++... ....+++|||+|++.+ .
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 4899999999999996 77899999999998754 25799999999999997421 1236899999999874 8
Q ss_pred cccccEeeeeEEeeccccccccCC---CCCceEEeeeecCCCC
Q 027973 92 QSADTIEGKCTVHSFKSYTKLDAV---GNDDFFCRFEYNSSSG 131 (216)
Q Consensus 92 ~~~~~I~gkc~V~~~~~~~~~~~~---~~~~ff~r~~yd~~~~ 131 (216)
+++++|.|+|.|+.+++|.++... ....||.|..++.+..
T Consensus 81 i~~etI~gkc~V~~~~~y~~l~~~~~~~~~~~F~r~~~~~k~~ 123 (128)
T cd04719 81 IDAETIIGKVRVEPVEPKTDLPETKKKTGGPLFVKRYWDTKTF 123 (128)
T ss_pred EeHHHcccEEEEEEcCCccchhhhccccCceEEEEEEeccccc
Confidence 999999999999999999887732 4568999999998754
No 20
>KOG1827 consensus Chromatin remodeling complex RSC, subunit RSC1/Polybromo and related proteins [Chromatin structure and dynamics; Transcription]
Probab=99.55 E-value=5.6e-15 Score=134.87 Aligned_cols=126 Identities=26% Similarity=0.332 Sum_probs=111.8
Q ss_pred EEEecCCcEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCCCCCCcccccCCCeEEEeCcccccc
Q 027973 14 YTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQS 93 (216)
Q Consensus 14 ~~v~g~~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~~~~~~~~~~~~ELf~s~~~d~~~ 93 (216)
+.++|. .|.+||.|||...++...+.|++|..+|++.+| +.|+.+.|||||++|.+...+.+..+|+|.|.....++
T Consensus 184 ~~i~~~--~~~~gd~vlv~~~~d~~~p~v~~Ier~w~~~dg-~k~~~~~w~~rP~~T~H~a~r~F~k~Evfkt~~~~~~~ 260 (629)
T KOG1827|consen 184 VEIDGT--KYIVGDYVLVQNPADNLKPIVAQIERLWKLPDG-EKWPQGCWIYRPEETVHRADRKFYKQEVFKTSLYRDDL 260 (629)
T ss_pred ccccCc--ccccCceeeecCcccccCCceeeecccccCccc-ccccceeEeeCCccCccccccchhcccceecccccccH
Confidence 345554 999999999999987789999999999999999 99999999999999999877778899999999999999
Q ss_pred cccEeeeeEEeeccccccccC---CCCCceEEeeeecCCCCCCCCCCceeEE
Q 027973 94 ADTIEGKCTVHSFKSYTKLDA---VGNDDFFCRFEYNSSSGAFNPDRVAVYC 142 (216)
Q Consensus 94 ~~~I~gkc~V~~~~~~~~~~~---~~~~~ff~r~~yd~~~~~f~p~~~~~~C 142 (216)
++.|+|+|.|+.+.+|....+ .+.+.|.|.+.|+.+.+.|...+...-|
T Consensus 261 ~q~l~g~c~v~~~~~yi~~~p~~ls~~dv~lcesRyn~~~K~f~kirsw~~~ 312 (629)
T KOG1827|consen 261 VQRLLGKCYVMKPTEYISGDPENLSEEDVFLCESRYNEQLKKFNKIRSWKAF 312 (629)
T ss_pred HHHhhcceEEeehhHhhhcCcccccccceeeEEeeeccchhhhccccCchhc
Confidence 999999999999999987765 3678999999999999988865444433
No 21
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=99.04 E-value=8.6e-11 Score=99.69 Aligned_cols=53 Identities=26% Similarity=0.861 Sum_probs=44.3
Q ss_pred CCceeEEEecCCCCCCCceEECCC--CC-ceecCCCCCCChhhhcCCCcEEeccccccccc
Q 027973 136 DRVAVYCKCEMPYNPDDLMVQCEG--CS-DWFHPNCINMTAEEAKRLDHFFCESCSTEGQK 193 (216)
Q Consensus 136 ~~~~~~C~C~~~~~~~~~~i~C~~--C~-~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 193 (216)
....+||+|.+.. ...||+||. |. .|||+.||||+..|. +.|+|+.|...+..
T Consensus 216 ~~e~~yC~Cnqvs--yg~Mi~CDn~~C~~eWFH~~CVGL~~~Pk---gkWyC~~C~~~~~~ 271 (274)
T KOG1973|consen 216 PDEPTYCICNQVS--YGKMIGCDNPGCPIEWFHFTCVGLKTKPK---GKWYCPRCKAENKK 271 (274)
T ss_pred CCCCEEEEecccc--cccccccCCCCCCcceEEEeccccccCCC---Ccccchhhhhhhhc
Confidence 3579999999554 569999996 98 999999999996655 56999999877654
No 22
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=99.01 E-value=2.3e-11 Score=106.78 Aligned_cols=117 Identities=26% Similarity=0.463 Sum_probs=96.3
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCCCCCC--------cc------------------
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGG--------RR------------------ 75 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~~~~--------~~------------------ 75 (216)
.|++||+||+..... .|+.|-||+++.++.+| .+-.+|.-|||..|+... .+
T Consensus 5 ~y~vgd~vYf~~sss-~PYliRrIEELnKTa~G-nVeAkvVc~~RRRDIs~~L~~lAD~~ar~~~~y~a~~~a~~~~e~e 82 (693)
T KOG3554|consen 5 MYRVGDYVYFENSSS-NPYLIRRIEELNKTANG-NVEAKVVCYLRRRDISSHLLKLADKHARRFDNYAAPEAAPEATEAE 82 (693)
T ss_pred cceecceEEEecCCC-ChHHHHHHHHHhccccC-CcceEEEEEEEccchHHHHHHHHHHHhhhcccccCcccCcccchhh
Confidence 789999999999874 58889999999999999 899999999999986411 00
Q ss_pred ------------------cccCCCeEEEeCcccccccccEeeeeEEeeccccccccC--CCCCceEEeeeecCCCCCCCC
Q 027973 76 ------------------QFHGSKEVFLSDHHDIQSADTIEGKCTVHSFKSYTKLDA--VGNDDFFCRFEYNSSSGAFNP 135 (216)
Q Consensus 76 ------------------~~~~~~ELf~s~~~d~~~~~~I~gkc~V~~~~~~~~~~~--~~~~~ff~r~~yd~~~~~f~p 135 (216)
...-.+|||+|-..+..|+..|+|||.|..+.+-+.+.. ..+++||+-..||+..+++..
T Consensus 83 ~EEe~e~p~~vdlt~~qrhqLrhrElFlsRQ~EsLPAthIRGKCsV~LLnete~~~~YL~~eDtFfySLVyDP~~kTLLA 162 (693)
T KOG3554|consen 83 IEEESECPAPVDLTEKQRHQLRHRELFLSRQSESLPATHIRGKCSVTLLNETESLQSYLEKEDTFFYSLVYDPNQKTLLA 162 (693)
T ss_pred hhhhccCCCcCCCCHHHHHHHHHHHHHHhhhhccCchhhhccceeEEEecChHHHHhhccccceeEEEeeeccchhhhhc
Confidence 001127999999999999999999999999888766554 367899999999999998887
Q ss_pred CCcee
Q 027973 136 DRVAV 140 (216)
Q Consensus 136 ~~~~~ 140 (216)
++...
T Consensus 163 DkGeI 167 (693)
T KOG3554|consen 163 DKGEI 167 (693)
T ss_pred cCcce
Confidence 55433
No 23
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=98.99 E-value=8.6e-11 Score=74.47 Aligned_cols=48 Identities=27% Similarity=0.927 Sum_probs=38.2
Q ss_pred EE-EecCCCCCCCceEECCCCCceecCCCCCCChhhhcC-CCcEEeccccc
Q 027973 141 YC-KCEMPYNPDDLMVQCEGCSDWFHPNCINMTAEEAKR-LDHFFCESCST 189 (216)
Q Consensus 141 ~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~-~~~~~C~~C~~ 189 (216)
+| +|++ .++++.||+|+.|+.|||..|++++...... ...|+|+.|..
T Consensus 1 ~C~vC~~-~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQ-SDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTS-SCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCC-cCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 46 7888 4567899999999999999999998653322 14899999975
No 24
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=98.89 E-value=8.9e-10 Score=90.21 Aligned_cols=49 Identities=29% Similarity=0.907 Sum_probs=41.3
Q ss_pred CceeEEEecCCCCCCCceEECC--CC-CceecCCCCCCChhhhcCCCcEEecccccc
Q 027973 137 RVAVYCKCEMPYNPDDLMVQCE--GC-SDWFHPNCINMTAEEAKRLDHFFCESCSTE 190 (216)
Q Consensus 137 ~~~~~C~C~~~~~~~~~~i~C~--~C-~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~ 190 (216)
-..+||.|.++. .+.||.|| .| ..|||+.|||+...| + ..|+|+.|...
T Consensus 219 ~e~lYCfCqqvS--yGqMVaCDn~nCkrEWFH~~CVGLk~pP-K--G~WYC~eCk~~ 270 (271)
T COG5034 219 GEELYCFCQQVS--YGQMVACDNANCKREWFHLECVGLKEPP-K--GKWYCPECKKA 270 (271)
T ss_pred CceeEEEecccc--cccceecCCCCCchhheeccccccCCCC-C--CcEeCHHhHhc
Confidence 468999999987 45999998 89 799999999998543 3 78999999753
No 25
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=98.51 E-value=5.1e-08 Score=85.16 Aligned_cols=111 Identities=23% Similarity=0.414 Sum_probs=90.8
Q ss_pred CeEEEeCcccccccccEeeeeEEeeccccccccCCCCCceEEeeeecCCCCCCCCCCceeEEEecCCCCCCCceEECCCC
Q 027973 81 KEVFLSDHHDIQSADTIEGKCTVHSFKSYTKLDAVGNDDFFCRFEYNSSSGAFNPDRVAVYCKCEMPYNPDDLMVQCEGC 160 (216)
Q Consensus 81 ~ELf~s~~~d~~~~~~I~gkc~V~~~~~~~~~~~~~~~~ff~r~~yd~~~~~f~p~~~~~~C~C~~~~~~~~~~i~C~~C 160 (216)
.+.+++.+..--....+.+++.......+... .....+.+....+....+.+.+.....+|.|..+.+++.+|++|+.|
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~k~~~~~~~~a~~~~~~~~~~~~~p~~~~~~cd~C 81 (345)
T KOG1632|consen 3 KIPKTSKTFSKTESDRRAPIAQKTTKPPKEPV-PIERPVPDVFRGRKGRRGGLLKALTQRYCKCYKPCDPDDLMEQCDLC 81 (345)
T ss_pred CcccccceecccccccccccccccccCCcCCC-CCCCCCcccccccccccccccHhhhhchhhcccccCchhhhhccccc
Confidence 34556666666667777777777766665544 44566777888888888888887788899999999998899999999
Q ss_pred CceecCCC--CCCChhhhcCCCcEEecccccccc
Q 027973 161 SDWFHPNC--INMTAEEAKRLDHFFCESCSTEGQ 192 (216)
Q Consensus 161 ~~w~H~~C--v~~~~~~~~~~~~~~C~~C~~~~~ 192 (216)
..|||..| |+++..+...++.|+|..|.....
T Consensus 82 ~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~~ 115 (345)
T KOG1632|consen 82 EDWYHGECWEVGTAEKEAPKEDPKVCDECKEAQD 115 (345)
T ss_pred cccccccccccCchhhcCCccccccccccchhhh
Confidence 99999999 999998888889999999987775
No 27
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=98.00 E-value=2.5e-06 Score=76.29 Aligned_cols=55 Identities=25% Similarity=0.715 Sum_probs=42.0
Q ss_pred CceeEEEecCCCCCCCceEECCCCCceecCCCCCCChhh--h-cCCCcEEecccccccc
Q 027973 137 RVAVYCKCEMPYNPDDLMVQCEGCSDWFHPNCINMTAEE--A-KRLDHFFCESCSTEGQ 192 (216)
Q Consensus 137 ~~~~~C~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~--~-~~~~~~~C~~C~~~~~ 192 (216)
.+--||.|.++...+ .|+||+.|..|||..|......+ + +....|+|..|.....
T Consensus 169 ~qc~vC~~g~~~~~N-rmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~ 226 (464)
T KOG4323|consen 169 LQCSVCYCGGPGAGN-RMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPK 226 (464)
T ss_pred ceeeeeecCCcCccc-eeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccchh
Confidence 446677777776555 99999999999999999865322 2 2236899999988776
No 28
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=97.15 E-value=0.0002 Score=60.82 Aligned_cols=39 Identities=38% Similarity=1.077 Sum_probs=32.1
Q ss_pred CCCCCceeEEEecCCCCC-----CCceEECCCCCceec-CCCCCC
Q 027973 133 FNPDRVAVYCKCEMPYNP-----DDLMVQCEGCSDWFH-PNCINM 171 (216)
Q Consensus 133 f~p~~~~~~C~C~~~~~~-----~~~~i~C~~C~~w~H-~~Cv~~ 171 (216)
+..+...+||.|..+|++ +..|+||..|++||| -.|...
T Consensus 122 YNhNfqG~~C~Cd~~Ypdp~~~~e~~m~QC~iCEDWFHce~c~~~ 166 (345)
T KOG2752|consen 122 YNHNFQGLFCKCDTPYPDPVRTEEGEMLQCVICEDWFHCEGCMQA 166 (345)
T ss_pred hhhhhcceeEEecCCCCCccccccceeeeEEeccchhcccccCcc
Confidence 334678999999999975 359999999999999 677753
No 29
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=96.98 E-value=0.0019 Score=63.54 Aligned_cols=55 Identities=24% Similarity=0.551 Sum_probs=43.5
Q ss_pred CceeEEEecCCCC-CCCceEECCCCCceecCCCCCCChhhhcCCCcEEecccccccccc
Q 027973 137 RVAVYCKCEMPYN-PDDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEGQKK 194 (216)
Q Consensus 137 ~~~~~C~C~~~~~-~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~ 194 (216)
....+|+|..... +.+..++||.|+.-+|.+|.|+...+- ..|.|-.|..+..+.
T Consensus 218 ~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~ipe---g~WlCr~Cl~s~~~~ 273 (1051)
T KOG0955|consen 218 EDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPFIPE---GQWLCRRCLQSPQRP 273 (1051)
T ss_pred CCccceeecccccCCCceEEEcCCCcchhhhhccCCCCCCC---CcEeehhhccCcCcc
Confidence 3467889988764 347999999999999999999765433 679999998876643
No 30
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=96.59 E-value=0.0003 Score=41.08 Aligned_cols=35 Identities=20% Similarity=0.725 Sum_probs=19.9
Q ss_pred CceEECCCCCceecCCCCCCChhhhcCCCcEEecccc
Q 027973 152 DLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCS 188 (216)
Q Consensus 152 ~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~ 188 (216)
+.|++|+.|....|..|=|+...+.. +.|+|..|.
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~~~~~~--~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVSEVPDG--DDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-SS--SS-------HHH-
T ss_pred CceEEeCCCCCcCChhhCCcccCCCC--CcEECCcCC
Confidence 47999999999999999999876543 459998884
No 31
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=95.82 E-value=0.0033 Score=52.59 Aligned_cols=51 Identities=27% Similarity=0.652 Sum_probs=39.3
Q ss_pred eeEE-EecCCCCCCCceEECCCCCceecCCCCCCChhhhcCCCcEEeccccccc
Q 027973 139 AVYC-KCEMPYNPDDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEG 191 (216)
Q Consensus 139 ~~~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~ 191 (216)
-+|| +|+...| ++-..+|+.|+.=|||-|+.++..++.. ..|.|-.|....
T Consensus 281 ck~csicgtsen-ddqllfcddcdrgyhmyclsppm~eppe-gswsc~KOG~~~ 332 (336)
T KOG1244|consen 281 CKYCSICGTSEN-DDQLLFCDDCDRGYHMYCLSPPMVEPPE-GSWSCHLCLEEL 332 (336)
T ss_pred cceeccccCcCC-CceeEeecccCCceeeEecCCCcCCCCC-CchhHHHHHHHH
Confidence 3556 5666555 6788999999999999999987655544 789999997644
No 32
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.51 E-value=0.0039 Score=52.56 Aligned_cols=45 Identities=18% Similarity=0.488 Sum_probs=36.1
Q ss_pred EecCCCCCCCceEECCCCCceecCCCCCCChhhhcCCCcEEec-cccccc
Q 027973 143 KCEMPYNPDDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCE-SCSTEG 191 (216)
Q Consensus 143 ~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~-~C~~~~ 191 (216)
+|.+|.- .++|++||.|+.=||.-|||+...|. ..|+|. .|....
T Consensus 319 IC~~P~~-E~E~~FCD~CDRG~HT~CVGL~~lP~---G~WICD~~C~~~~ 364 (381)
T KOG1512|consen 319 ICLGPVI-ESEHLFCDVCDRGPHTLCVGLQDLPR---GEWICDMRCREAT 364 (381)
T ss_pred ccCCccc-chheeccccccCCCCccccccccccC---ccchhhhHHHHhc
Confidence 6777764 46899999999999999999987655 679998 565443
No 33
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=95.46 E-value=0.0069 Score=57.01 Aligned_cols=51 Identities=24% Similarity=0.592 Sum_probs=41.2
Q ss_pred ceeEE-EecCCCC-CCCceEECCCCCceecCCCCCCChhhhcCCCcEEeccccccc
Q 027973 138 VAVYC-KCEMPYN-PDDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEG 191 (216)
Q Consensus 138 ~~~~C-~C~~~~~-~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~ 191 (216)
+...| +|+.+.. ....||+|+.|..-.|..|-|+.+.+. ..|.|..|....
T Consensus 270 edviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIle~p~---gpWlCr~Calg~ 322 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGILEVPE---GPWLCRTCALGI 322 (893)
T ss_pred ccceeceecCCCccccceeEEeccchhHHHHhhhceeecCC---CCeeehhccccC
Confidence 45566 8888864 346999999999999999999987655 679999997553
No 34
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.26 E-value=0.01 Score=56.33 Aligned_cols=51 Identities=25% Similarity=0.841 Sum_probs=36.2
Q ss_pred eeEE-EecCCCCCCCceEECCCCCce-ecCCCCCCChhhhcCCCcEEeccccccc
Q 027973 139 AVYC-KCEMPYNPDDLMVQCEGCSDW-FHPNCINMTAEEAKRLDHFFCESCSTEG 191 (216)
Q Consensus 139 ~~~C-~C~~~~~~~~~~i~C~~C~~w-~H~~Cv~~~~~~~~~~~~~~C~~C~~~~ 191 (216)
..-| +|..+ ++.+.|+-|++|..- ||+.|+.+..-+.. +..|+|+.|....
T Consensus 215 ~~~C~IC~~~-DpEdVLLLCDsCN~~~YH~YCLDPdl~eiP-~~eWYC~NC~dL~ 267 (1134)
T KOG0825|consen 215 EVKCDICTVH-DPEDVLLLCDSCNKVYYHVYCLDPDLSESP-VNEWYCTNCSLLE 267 (1134)
T ss_pred cccceeeccC-ChHHhheeecccccceeeccccCccccccc-ccceecCcchhhh
Confidence 3344 45444 456799999999776 99999997642222 2679999997644
No 35
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=95.16 E-value=0.011 Score=54.51 Aligned_cols=55 Identities=27% Similarity=0.710 Sum_probs=45.0
Q ss_pred CCceeEEEecCCCCCCCceEECCCCCceecCCCCCCChhhhcCCCcEEecccccccc
Q 027973 136 DRVAVYCKCEMPYNPDDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEGQ 192 (216)
Q Consensus 136 ~~~~~~C~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 192 (216)
......|+|+.-...+.+||||+.|..|-|.-|+|...... ++.|.|..|....-
T Consensus 83 ~~~~~~c~c~~~~~~~g~~i~c~~c~~Wqh~~C~g~~~~~~--p~~y~c~~c~~~~~ 137 (508)
T KOG1844|consen 83 AREISRCDCGLEDDMEGLMIQCDWCGRWQHKICCGSFKSTK--PDKYVCEICTPRNK 137 (508)
T ss_pred cCcccccccccccCCCceeeCCcccCcccCceeeeecCCCC--chhceeeeeccccc
Confidence 35778899998876578999999999999999999875433 47899999976543
No 36
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=94.73 E-value=0.029 Score=50.87 Aligned_cols=56 Identities=20% Similarity=0.500 Sum_probs=38.2
Q ss_pred CceeEE-EecCCCCCCCceEECCCCCceecCCCCCCCh--hhhcC-CCcEEeccccccccc
Q 027973 137 RVAVYC-KCEMPYNPDDLMVQCEGCSDWFHPNCINMTA--EEAKR-LDHFFCESCSTEGQK 193 (216)
Q Consensus 137 ~~~~~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~--~~~~~-~~~~~C~~C~~~~~~ 193 (216)
.-...| +|.+.. .....++||.|..-||..|+.++- .|-+. -..|.|..|.+.-..
T Consensus 542 a~~ysCgiCkks~-dQHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECdk~esS 601 (707)
T KOG0957|consen 542 AMNYSCGICKKST-DQHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECDKNESS 601 (707)
T ss_pred ccceeeeeeccch-hhHHHhhcchhhceeeccccCCccccCcccccCcceeecccccccCc
Confidence 344556 666654 345889999999999999998642 22221 267999999544433
No 37
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=93.67 E-value=0.032 Score=51.71 Aligned_cols=50 Identities=24% Similarity=0.702 Sum_probs=36.2
Q ss_pred EE-EecCCCCCCCceEECCCCCceecCCCCCCC--hhhhcCCCcEEecccccccc
Q 027973 141 YC-KCEMPYNPDDLMVQCEGCSDWFHPNCINMT--AEEAKRLDHFFCESCSTEGQ 192 (216)
Q Consensus 141 ~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~--~~~~~~~~~~~C~~C~~~~~ 192 (216)
|| .|.+...- ...|+||.|..-||+.|+.++ .+.+. ...|+|+.|.-..-
T Consensus 255 fCsaCn~~~~F-~~~i~CD~Cp~sFH~~CLePPl~~eniP-~g~W~C~ec~~k~~ 307 (613)
T KOG4299|consen 255 FCSACNGSGLF-NDIICCDGCPRSFHQTCLEPPLEPENIP-PGSWFCPECKIKSV 307 (613)
T ss_pred HHHHhCCcccc-ccceeecCCchHHHHhhcCCCCCcccCC-CCccccCCCeeeee
Confidence 66 56665432 457999999999999999876 22222 26899999976554
No 38
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=93.23 E-value=0.061 Score=41.38 Aligned_cols=28 Identities=25% Similarity=0.624 Sum_probs=21.7
Q ss_pred ecCCCCCCChhhhcCCCcEEecccccccc
Q 027973 164 FHPNCINMTAEEAKRLDHFFCESCSTEGQ 192 (216)
Q Consensus 164 ~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 192 (216)
||+.|+.++-..... ..|+|+.|.....
T Consensus 2 ~H~~CL~Ppl~~~P~-g~W~Cp~C~~~~~ 29 (148)
T cd04718 2 FHLCCLRPPLKEVPE-GDWICPFCEVEKS 29 (148)
T ss_pred cccccCCCCCCCCCC-CCcCCCCCcCCCC
Confidence 899999877544444 5799999987655
No 39
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=93.19 E-value=0.0064 Score=53.40 Aligned_cols=54 Identities=19% Similarity=0.558 Sum_probs=41.5
Q ss_pred CCceeEEEecCCC-CCCCceEECCCCCceecCCCCCCChhhhcCCCc----EEeccccc
Q 027973 136 DRVAVYCKCEMPY-NPDDLMVQCEGCSDWFHPNCINMTAEEAKRLDH----FFCESCST 189 (216)
Q Consensus 136 ~~~~~~C~C~~~~-~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~----~~C~~C~~ 189 (216)
+.....|.+.+.. -...++|.|+.|..|||..||.+.+.....+.. |.|+.|..
T Consensus 236 ~~~~~~~~~cg~~~~~~~~~~~~~~~e~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~ 294 (345)
T KOG1632|consen 236 DYSKLICDPCGLSDANKKFEICCDLCESWFHGDCVQIFEARKRLNEIRNEVYKCPHCTV 294 (345)
T ss_pred ccccccccccCcchHHHHHHHHHHHHHHHhcccccccccchhhhhhhhccceecCceee
Confidence 3455677655543 233789999999999999999998776665566 99999976
No 40
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=91.65 E-value=0.16 Score=46.20 Aligned_cols=57 Identities=21% Similarity=0.563 Sum_probs=41.2
Q ss_pred CCCceeEEEecCCCC-CCCceEECCCCCceecCCCCCCChhhh-----c--CCCcEEeccccccc
Q 027973 135 PDRVAVYCKCEMPYN-PDDLMVQCEGCSDWFHPNCINMTAEEA-----K--RLDHFFCESCSTEG 191 (216)
Q Consensus 135 p~~~~~~C~C~~~~~-~~~~~i~C~~C~~w~H~~Cv~~~~~~~-----~--~~~~~~C~~C~~~~ 191 (216)
|..+..+|+|-..-. .-+..|||+.|+.-.|..|-|...... . ....|||..|.-..
T Consensus 116 pkk~~iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~Gv 180 (707)
T KOG0957|consen 116 PKKAVICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYGV 180 (707)
T ss_pred cccceEEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHhcCC
Confidence 345678999976553 336899999999999999999762111 0 12579999996543
No 41
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=91.41 E-value=0.16 Score=45.60 Aligned_cols=52 Identities=19% Similarity=0.526 Sum_probs=34.6
Q ss_pred EEEecCCCC--CCCceEECCCCCceecCCCCCCCh----hhhc------CCCcEEecccccccc
Q 027973 141 YCKCEMPYN--PDDLMVQCEGCSDWFHPNCINMTA----EEAK------RLDHFFCESCSTEGQ 192 (216)
Q Consensus 141 ~C~C~~~~~--~~~~~i~C~~C~~w~H~~Cv~~~~----~~~~------~~~~~~C~~C~~~~~ 192 (216)
.|+|.+-.+ ++-.||.|+.|+.|-|.+|.--.. .+.. ..-.|.|..|.....
T Consensus 131 C~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~se 194 (446)
T PF07227_consen 131 CCICSKFDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTSE 194 (446)
T ss_pred ccccCCcccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChhh
Confidence 457766432 234899999999999999973211 1111 114799999987765
No 42
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=89.83 E-value=0.12 Score=43.74 Aligned_cols=36 Identities=28% Similarity=0.670 Sum_probs=28.3
Q ss_pred CceEECCCCCceecCCCCCCChhhhcC--CCcEEeccc
Q 027973 152 DLMVQCEGCSDWFHPNCINMTAEEAKR--LDHFFCESC 187 (216)
Q Consensus 152 ~~~i~C~~C~~w~H~~Cv~~~~~~~~~--~~~~~C~~C 187 (216)
+.||.|..|..-+|+.||.++++.+.. ...|.|..|
T Consensus 277 ~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C 314 (381)
T KOG1512|consen 277 NSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSC 314 (381)
T ss_pred ccceeecccccCCCCcchhcCHHHHhHHhhcchhhccc
Confidence 589999999999999999998765432 256766665
No 43
>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]
Probab=89.32 E-value=0.055 Score=47.97 Aligned_cols=94 Identities=15% Similarity=0.034 Sum_probs=79.1
Q ss_pred EEEecCCcEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCCCCCCcccccCCCeEEEeCcccccc
Q 027973 14 YTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQS 93 (216)
Q Consensus 14 ~~v~g~~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~~~~~~~~~~~~ELf~s~~~d~~~ 93 (216)
+.+.+. ...+|+.+.+.+......+.++.+...|.+..+ ..+.-+.|||+|.++.......+..+++......+.+.
T Consensus 270 ~~i~~~--~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 346 (371)
T COG5076 270 VLITNS--QAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLST-KELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTDYY 346 (371)
T ss_pred hccccc--ccccccccccccCCcccccchhhhhhccccccc-chhhhhcccCCCccccccccchhhhcccccchhhhhhh
Confidence 344444 789999999999888889999999999998888 67779999999998877776677889999999999999
Q ss_pred cccEeeeeEEeeccccc
Q 027973 94 ADTIEGKCTVHSFKSYT 110 (216)
Q Consensus 94 ~~~I~gkc~V~~~~~~~ 110 (216)
.....+.|.|...-.+.
T Consensus 347 ~~~~~~~~~~~~~~~~~ 363 (371)
T COG5076 347 KNANVLEDFVIKKTRLI 363 (371)
T ss_pred hhccchhhhHhhhhhhh
Confidence 99999999887654433
No 44
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=88.92 E-value=0.74 Score=29.17 Aligned_cols=39 Identities=21% Similarity=0.359 Sum_probs=27.4
Q ss_pred EccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEee
Q 027973 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYR 66 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyR 66 (216)
|++||.|.+.++.| ...|..|..- .... .-++..+||--
T Consensus 1 f~~GDvV~LKSGGp--~MTV~~v~~~--~~~~-~~~v~C~WFd~ 39 (53)
T PF09926_consen 1 FKIGDVVQLKSGGP--RMTVTEVGPN--AGAS-GGWVECQWFDG 39 (53)
T ss_pred CCCCCEEEEccCCC--CeEEEEcccc--ccCC-CCeEEEEeCCC
Confidence 57899999999984 4566655443 1122 46899999975
No 45
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=88.51 E-value=0.3 Score=46.08 Aligned_cols=52 Identities=23% Similarity=0.618 Sum_probs=41.0
Q ss_pred ceeEEEecCCC-CCCCceEECC--CCCceecCCCCCCChhhhcCCCcEEecccccccc
Q 027973 138 VAVYCKCEMPY-NPDDLMVQCE--GCSDWFHPNCINMTAEEAKRLDHFFCESCSTEGQ 192 (216)
Q Consensus 138 ~~~~C~C~~~~-~~~~~~i~C~--~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 192 (216)
..-+|+|.+-- .++...|-|| .|..-.|-.|-||-+.+. ..|||..|....+
T Consensus 5 VGGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVPt---GpWfCrKCesqer 59 (900)
T KOG0956|consen 5 VGGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVPT---GPWFCRKCESQER 59 (900)
T ss_pred ccceeeecCcCCCccCceeeecCCCceeeeehhcceeEecCC---Cchhhhhhhhhhh
Confidence 35689997643 3467899998 999999999999977665 5699999965544
No 46
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=87.80 E-value=0.23 Score=47.37 Aligned_cols=46 Identities=20% Similarity=0.525 Sum_probs=34.6
Q ss_pred eeEEEecCCCCCCCceEECCCCCceecCCCCCCChhhhcCCCcEEeccccc
Q 027973 139 AVYCKCEMPYNPDDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCST 189 (216)
Q Consensus 139 ~~~C~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~ 189 (216)
...|+|... ...+.|+.|-.|||..|.+.+-.+..... |+|+.|.-
T Consensus 48 e~c~ic~~~----g~~l~c~tC~~s~h~~cl~~pl~~~p~~~-~~c~Rc~~ 93 (696)
T KOG0383|consen 48 EACRICADG----GELLWCDTCPASFHASCLGPPLTPQPNGE-FICPRCFC 93 (696)
T ss_pred hhhhhhcCC----CcEEEeccccHHHHHHccCCCCCcCCccc-eeeeeecc
Confidence 444566653 46788999999999999997765555545 99999943
No 47
>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=87.65 E-value=1 Score=31.23 Aligned_cols=42 Identities=21% Similarity=0.308 Sum_probs=34.1
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEee
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYR 66 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyR 66 (216)
.+++||.|...-.. -|+|-|+|.+.-..... ...+.|+||-.
T Consensus 2 ~f~~GdlVwaK~kG--yp~WPa~I~~~~~~~~~-~~~~~V~FfGt 43 (83)
T cd05834 2 QFKAGDLVFAKVKG--YPAWPARVDEPEDWKPP-GKKYPVYFFGT 43 (83)
T ss_pred CCCCCCEEEEecCC--CCCCCEEEecccccCCC-CCEEEEEEeCC
Confidence 47899999999866 79999999999775333 46689999985
No 48
>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=86.82 E-value=0.94 Score=31.60 Aligned_cols=42 Identities=17% Similarity=0.237 Sum_probs=32.3
Q ss_pred EccCCEEEEecCCCCCCCeEEEEEEEEecCC--CCeEEEEEEEEee
Q 027973 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDAR--GANVKVHVRWYYR 66 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~--~~~~~v~v~WfyR 66 (216)
|.+||.|...-.. -+.|-|+|.+...+.. ...-.+.|.||=.
T Consensus 1 f~vGDlVWaK~kg--~pwWP~~V~~~~~~~~~~~~~~~~~V~fFGs 44 (87)
T cd05835 1 FNVGDLVWGKIKG--FPWWPGRVVSITVTSKRPPVVGMRWVTWFGS 44 (87)
T ss_pred CCCCCEEEEecCC--CCCCCeEEechhhcccccCCCCeEEEEEeCC
Confidence 4689999999976 7899999999876542 1135688999863
No 49
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=86.56 E-value=2.6 Score=28.62 Aligned_cols=33 Identities=27% Similarity=0.557 Sum_probs=26.3
Q ss_pred EEccCCEEEEecCC-----CCCCCeEEEEEEEEecCCC
Q 027973 22 TIKPGDCVLMRPSE-----PSKPSYVAKIERIESDARG 54 (216)
Q Consensus 22 ~~~vGD~V~v~~~~-----~~~~~~IarI~~i~~~~~~ 54 (216)
.++.||+|.|..+. .+...|+|.|+......++
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ggaR~ 42 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGARD 42 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEeccccC
Confidence 46899999999977 2457899999999875433
No 50
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=86.43 E-value=0.11 Score=53.31 Aligned_cols=53 Identities=26% Similarity=0.631 Sum_probs=39.3
Q ss_pred ceeEE-EecCCCCCCCceEECCCCCceecCCCCCCChhhhcCCCcEEecccccccc
Q 027973 138 VAVYC-KCEMPYNPDDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEGQ 192 (216)
Q Consensus 138 ~~~~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 192 (216)
....| +|+... ....|+-|+.|..|||+-|+.+...... +..|.|+.|....+
T Consensus 1107 ~~~~c~~cr~k~-~~~~m~lc~~c~~~~h~~C~rp~~~~~~-~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1107 VNALCKVCRRKK-QDEKMLLCDECLSGFHLFCLRPALSSVP-PGDWMCPSCRKEHR 1160 (1404)
T ss_pred chhhhhhhhhcc-cchhhhhhHhhhhhHHHHhhhhhhccCC-cCCccCCccchhhh
Confidence 34455 565543 3569999999999999999987654332 25699999988774
No 51
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=85.51 E-value=0.3 Score=30.44 Aligned_cols=33 Identities=21% Similarity=0.557 Sum_probs=15.7
Q ss_pred ceEECCCCCceecCCCCCCChhhhcCCCcEEecc
Q 027973 153 LMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCES 186 (216)
Q Consensus 153 ~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~ 186 (216)
..|||+.|.+|=... .++.......++.|+|..
T Consensus 2 ~WVQCd~C~KWR~lp-~~~~~~~~~~~d~W~C~~ 34 (50)
T PF07496_consen 2 YWVQCDSCLKWRRLP-EEVDPIREELPDPWYCSM 34 (50)
T ss_dssp EEEE-TTT--EEEE--CCHHCTSCCSSTT--GGG
T ss_pred eEEECCCCCceeeCC-hhhCcccccCCCeEEcCC
Confidence 579999999998875 222111112235899976
No 52
>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=85.42 E-value=5.7 Score=25.36 Aligned_cols=44 Identities=20% Similarity=0.360 Sum_probs=33.3
Q ss_pred ccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEE-------EEEEEeecCCC
Q 027973 24 KPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKV-------HVRWYYRPEES 70 (216)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v-------~v~WfyRp~d~ 70 (216)
+++|.|.|..+. .+-.-|.|..+.+-..| -+++ .+.||+.-.+-
T Consensus 2 kvnD~VtVKTDG--~~rR~G~ilavE~F~EG-~MYLvaL~dYP~GiWFFNE~~~ 52 (62)
T PF10781_consen 2 KVNDRVTVKTDG--GPRREGVILAVEPFNEG-TMYLVALEDYPAGIWFFNEKDS 52 (62)
T ss_pred ccccEEEEecCC--cccccceEEEEeeccCc-EEEEEEcCcCCcceEEEecCCC
Confidence 689999999988 67788999998886666 4443 35788775543
No 53
>PRK10708 hypothetical protein; Provisional
Probab=85.29 E-value=5 Score=25.60 Aligned_cols=44 Identities=16% Similarity=0.302 Sum_probs=33.4
Q ss_pred ccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEE-------EEEEEeecCCC
Q 027973 24 KPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKV-------HVRWYYRPEES 70 (216)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v-------~v~WfyRp~d~ 70 (216)
+++|.|.|..+. .+-..|.|..+..-..| -+++ .+.||+.-.+-
T Consensus 2 kvnD~VtVKTDG--~~rR~G~iLavE~F~EG-~MyLvaL~dYP~GiWFFNE~~~ 52 (62)
T PRK10708 2 KVNDRVTVKTDG--GPRRPGVVLAVEEFSEG-TMYLVSLEDYPLGIWFFNEAGH 52 (62)
T ss_pred ccccEEEEecCC--CccccceEEEEeeccCc-EEEEEEcCcCCCceEEEeccCC
Confidence 689999999988 67889999999886666 4443 45788775443
No 54
>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=85.20 E-value=1.7 Score=29.90 Aligned_cols=39 Identities=21% Similarity=0.224 Sum_probs=31.0
Q ss_pred EccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeec
Q 027973 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRP 67 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp 67 (216)
|.+||.|.-.-.. -|+|.|+|.++... ...+.|.||=-.
T Consensus 1 f~~gdlVWaK~~g--~P~WPa~I~~~~~~----~~k~~V~FfG~~ 39 (80)
T cd06080 1 FEKNDLVWAKIQG--YPWWPAVIKSISRK----KQKARVNFIGDN 39 (80)
T ss_pred CCCCCEEEEeCCC--CCCCCEEEeeecCC----CCEEEEEEeCCC
Confidence 4689999998876 68999999998653 356888888665
No 55
>KOG2626 consensus Histone H3 (Lys4) methyltransferase complex, subunit CPS60/ASH2/BRE2 [Chromatin structure and dynamics; Transcription]
Probab=84.94 E-value=0.78 Score=42.13 Aligned_cols=57 Identities=26% Similarity=0.550 Sum_probs=42.8
Q ss_pred CCceeEEEecCCCCCCCceEECCCCCceecCCCCCCChh-----hhcCCCcEEecccccccc
Q 027973 136 DRVAVYCKCEMPYNPDDLMVQCEGCSDWFHPNCINMTAE-----EAKRLDHFFCESCSTEGQ 192 (216)
Q Consensus 136 ~~~~~~C~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~-----~~~~~~~~~C~~C~~~~~ 192 (216)
.....+|.|+...+....-+||..|.+|+|..|.-.... +...-+.|.|..|.....
T Consensus 17 ~~~~~~~y~e~~r~l~~~elqcs~clk~~~~~~~~~~~~~~s~~pf~t~y~fvc~~c~~~~~ 78 (544)
T KOG2626|consen 17 MKQATVCYCEGERNLGIVELQCSTCLKWFHLPTLEAFHLIKSSLPFMTSYEFVCKECTPSGR 78 (544)
T ss_pred ccCccccccccccccCceeeEeeecccccccccccccccccccCCcccceeEEeccccCcch
Confidence 357889999999998889999999999999866543321 111126889999987743
No 56
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=83.72 E-value=0.64 Score=29.50 Aligned_cols=27 Identities=26% Similarity=0.695 Sum_probs=24.0
Q ss_pred EecCCCCCCCceEECCCCCceecCCCC
Q 027973 143 KCEMPYNPDDLMVQCEGCSDWFHPNCI 169 (216)
Q Consensus 143 ~C~~~~~~~~~~i~C~~C~~w~H~~Cv 169 (216)
+|+.+..+.+..|.|..|+.=||.+|-
T Consensus 10 ~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 10 VCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred hhCCcccCCCCEEECCCCCCcccHHHH
Confidence 677777778899999999999999997
No 57
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=79.70 E-value=2.2 Score=37.45 Aligned_cols=48 Identities=27% Similarity=0.511 Sum_probs=35.4
Q ss_pred eEEEecCCCCCCCceEECCCCCceecCCCCCCChhhhcCCCcEEecccccccc
Q 027973 140 VYCKCEMPYNPDDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEGQ 192 (216)
Q Consensus 140 ~~C~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 192 (216)
.++||-..|..++.... --|+.-||..||..=-.+ ..=+||.|.+..+
T Consensus 231 ~CaIClEdY~~GdklRi-LPC~H~FH~~CIDpWL~~----~r~~CPvCK~di~ 278 (348)
T KOG4628|consen 231 TCAICLEDYEKGDKLRI-LPCSHKFHVNCIDPWLTQ----TRTFCPVCKRDIR 278 (348)
T ss_pred eEEEeecccccCCeeeE-ecCCCchhhccchhhHhh----cCccCCCCCCcCC
Confidence 78899999987665544 789999999999632111 2247999988665
No 58
>PF13922 PHD_3: PHD domain of transcriptional enhancer, Asx
Probab=79.41 E-value=0.28 Score=32.21 Aligned_cols=32 Identities=28% Similarity=0.877 Sum_probs=25.2
Q ss_pred CceeEEEecCCCCCCCceEECCCCCceecCCCCCCCh
Q 027973 137 RVAVYCKCEMPYNPDDLMVQCEGCSDWFHPNCINMTA 173 (216)
Q Consensus 137 ~~~~~C~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~ 173 (216)
....-|.|+- .-||.|..|+-.-|.+|||.+.
T Consensus 31 ~~~~~C~C~L-----kAMi~Cq~CGAFCHDDCIgpsk 62 (69)
T PF13922_consen 31 STSNKCACSL-----KAMIMCQGCGAFCHDDCIGPSK 62 (69)
T ss_pred ccccccccch-----HHHHHHhhccchhccccccHHH
Confidence 3455676664 3799999999999999999663
No 59
>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=79.13 E-value=5 Score=25.30 Aligned_cols=28 Identities=29% Similarity=0.339 Sum_probs=22.2
Q ss_pred EccCCEEEEecCCCCCCCeEEEEEEEEecC
Q 027973 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDA 52 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~IarI~~i~~~~ 52 (216)
+.+|+.|++.-.+ ...+-|+|+++....
T Consensus 1 ~~vG~~v~~~~~~--~~~y~A~I~~~r~~~ 28 (55)
T PF11717_consen 1 FEVGEKVLCKYKD--GQWYEAKILDIREKN 28 (55)
T ss_dssp --TTEEEEEEETT--TEEEEEEEEEEEECT
T ss_pred CCcCCEEEEEECC--CcEEEEEEEEEEecC
Confidence 4689999999943 579999999999943
No 60
>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=78.80 E-value=3.4 Score=28.49 Aligned_cols=41 Identities=24% Similarity=0.344 Sum_probs=31.3
Q ss_pred EccCCEEEEecCCCCCCCeEEEEEEEEecCC-----CCeEEEEEEEEe
Q 027973 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDAR-----GANVKVHVRWYY 65 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~-----~~~~~v~v~Wfy 65 (216)
|++||.|...-.. -+.|-|+|.+...... .....+.|++|-
T Consensus 1 f~~GdlVwaK~~g--~pwWPa~V~~~~~~~~~~~~~~~~~~~~V~Ffg 46 (87)
T cd05162 1 FRPGDLVWAKMKG--YPWWPALVVDPPKDSKKAKKKAKEGKVLVLFFG 46 (87)
T ss_pred CCCCCEEEEeCCC--CCCCCEEEccccccchhhhccCCCCEEEEEEeC
Confidence 5789999999986 6899999999987532 113467777775
No 61
>PTZ00112 origin recognition complex 1 protein; Provisional
Probab=77.57 E-value=5.1 Score=39.93 Aligned_cols=118 Identities=24% Similarity=0.292 Sum_probs=73.6
Q ss_pred eeeeeEEEecCCcEEccCCEEEEecCCCCC----------------------CCeEEEEEEEEecCCCCeEEEEEEEEee
Q 027973 9 RTLESYTVKSISKTIKPGDCVLMRPSEPSK----------------------PSYVAKIERIESDARGANVKVHVRWYYR 66 (216)
Q Consensus 9 ~~y~~~~v~g~~~~~~vGD~V~v~~~~~~~----------------------~~~IarI~~i~~~~~~~~~~v~v~WfyR 66 (216)
..|+++.++++ .|.+||.|+|..+.... ..-=|+|.+|+.......+.+.|..||-
T Consensus 441 ~iye~~~in~~--~ys~g~dv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~kg~is~fy~~~~~~~~~~e~c~y~d 518 (1164)
T PTZ00112 441 VIYESIQINDV--EYSIGDDVLIFCTGNGNTYNGKSGTKKNQNNKNIKENIYQLRKGKISSFYKNTNSNQVEAEVCIYYD 518 (1164)
T ss_pred eEEEEEEEcce--eeccCCcEEEEEcCCCCccccccCccccccccchhhhhheecccccchhhhcCCCceeeEEEEEEEc
Confidence 57999999887 99999999999865321 1235889999987666579999999999
Q ss_pred cCCCC--------CCcccccCCCeEEEeCc-----------ccccccccEeeeeEEeeccccccc---cCCCCCceEEee
Q 027973 67 PEESI--------GGRRQFHGSKEVFLSDH-----------HDIQSADTIEGKCTVHSFKSYTKL---DAVGNDDFFCRF 124 (216)
Q Consensus 67 p~d~~--------~~~~~~~~~~ELf~s~~-----------~d~~~~~~I~gkc~V~~~~~~~~~---~~~~~~~ff~r~ 124 (216)
..|.+ ...++.-..-|+|+-+. +-++.+.-|..|+.|....+-..- ...+.+-|.|-+
T Consensus 519 ~~d~~~i~~~~~~~~~rr~~~~f~~~~d~~~~~~~llgni~f~~~~~~~i~kki~~~ne~~~~~~d~~~~~g~~kflc~~ 598 (1164)
T PTZ00112 519 QHDAQYIKELEEKQKSRRCKADFEVFLDDDTKNFYLLGNIHFKILDAKMILKKIYVYNEKELYDEDKTAKQGKDKFLCTH 598 (1164)
T ss_pred cccHHHHHHHHHHHHhhhhhhhhhHhcccccceeEEecceeEEEechHhhhhhheeecchhhcccchhhhcccchhhhhH
Confidence 88753 00111223345555433 344555566777777653321111 112455666655
Q ss_pred eecC
Q 027973 125 EYNS 128 (216)
Q Consensus 125 ~yd~ 128 (216)
....
T Consensus 599 ~~k~ 602 (1164)
T PTZ00112 599 YLKE 602 (1164)
T ss_pred hhhc
Confidence 4433
No 62
>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=76.34 E-value=4.9 Score=25.88 Aligned_cols=40 Identities=20% Similarity=0.373 Sum_probs=25.9
Q ss_pred EccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEE
Q 027973 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWY 64 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~Wf 64 (216)
-++||.+.|...-...+...|.|+++.. .+| ..-..|+|-
T Consensus 3 A~vGD~lvv~g~~vg~~~r~GeIveV~g-~dG-~PPY~VRw~ 42 (58)
T PF08940_consen 3 ASVGDRLVVHGRTVGQPDRHGEIVEVRG-PDG-SPPYLVRWD 42 (58)
T ss_dssp --TTEEEEES-TTTS--EEEEEEEE-S--SSS--S-EEEEET
T ss_pred CCCCCEEEEcCCcCCCCCcEeEEEEEEC-CCC-CCCEEEEec
Confidence 3689999999988778999999999998 444 466778884
No 63
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=75.96 E-value=5 Score=26.00 Aligned_cols=41 Identities=20% Similarity=0.194 Sum_probs=30.3
Q ss_pred EccCCEEEEecCCCCCCCeEEEEEEEEecCC------CCeEEEEEEEEe
Q 027973 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDAR------GANVKVHVRWYY 65 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~------~~~~~v~v~Wfy 65 (216)
|++||.|...-.. -+.|-|+|+.-..... .....+.|++|-
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 6899999999876421 113466777664
No 64
>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=75.70 E-value=8.7 Score=29.36 Aligned_cols=50 Identities=26% Similarity=0.290 Sum_probs=33.8
Q ss_pred CceeeeeEEEecCCcEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecC
Q 027973 7 PRRTLESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPE 68 (216)
Q Consensus 7 ~~~~y~~~~v~g~~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~ 68 (216)
|...+++.++... .+++||.|.+...+ +.+-.-.|..|.- +.-.|||-=+
T Consensus 74 ~tg~~q~~tv~kp--~F~LGd~V~~~f~~--~~pkqRlIlGv~l--------v~~~W~Y~VE 123 (150)
T PF07154_consen 74 GTGQLQSLTVQKP--AFRLGDRVEFRFYS--DGPKQRLILGVFL--------VNNSWFYAVE 123 (150)
T ss_pred ecCccceeeccCC--ceecCCEEEEEecC--CCCceEEEEEEEE--------ecCceEEEEE
Confidence 3445666677666 78999999998854 3456666666665 5556888643
No 65
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=75.70 E-value=2.4 Score=34.54 Aligned_cols=33 Identities=18% Similarity=0.591 Sum_probs=24.4
Q ss_pred EECCCCCceecCCCCCCChhhhcCCCcEEecccccccc
Q 027973 155 VQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEGQ 192 (216)
Q Consensus 155 i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 192 (216)
+.|..|.. |-.|+.+.+.+. +.|+|+.|...++
T Consensus 193 lIC~~C~h--hngl~~~~ek~~---~efiC~~Cn~~n~ 225 (251)
T COG5415 193 LICPQCHH--HNGLYRLAEKPI---IEFICPHCNHKND 225 (251)
T ss_pred hccccccc--cccccccccccc---hheecccchhhcC
Confidence 56777753 678888776554 5799999988775
No 66
>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=74.97 E-value=9.2 Score=28.01 Aligned_cols=47 Identities=15% Similarity=0.101 Sum_probs=36.8
Q ss_pred CCCCCceeeeeEEEecCCcEEccCCEEEEecCCCCCCCeEEEEEEEEecCCC
Q 027973 3 KPKAPRRTLESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARG 54 (216)
Q Consensus 3 ~~~~~~~~y~~~~v~g~~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~ 54 (216)
|..+|+-....+.+-.. ++++||.|.+-..+ -|-+++|..|.....-
T Consensus 9 k~~~G~G~t~dvIl~~G--tL~~GD~Iv~g~~~---Gpi~tkVRaLl~~~~~ 55 (110)
T cd03703 9 KEEEGLGTTIDVILYDG--TLREGDTIVVCGLN---GPIVTKVRALLKPQPL 55 (110)
T ss_pred EEcCCCceEEEEEEECC--eEecCCEEEEccCC---CCceEEEeEecCCCCc
Confidence 44567777777766555 89999999998875 4789999999986654
No 67
>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=73.95 E-value=8.9 Score=21.23 Aligned_cols=26 Identities=23% Similarity=0.259 Sum_probs=22.2
Q ss_pred cCCEEEEecCCCCCCCeEEEEEEEEecC
Q 027973 25 PGDCVLMRPSEPSKPSYVAKIERIESDA 52 (216)
Q Consensus 25 vGD~V~v~~~~~~~~~~IarI~~i~~~~ 52 (216)
+||.|.|..+. ..-.+|+|.+|..+.
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 59999999987 567999999998754
No 68
>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=73.89 E-value=9.6 Score=25.49 Aligned_cols=47 Identities=21% Similarity=0.175 Sum_probs=36.9
Q ss_pred EEEEEEeecCCCCCCcccccCCCeEEEeCcccccccccEeeeeEEee
Q 027973 59 VHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQSADTIEGKCTVHS 105 (216)
Q Consensus 59 v~v~WfyRp~d~~~~~~~~~~~~ELf~s~~~d~~~~~~I~gkc~V~~ 105 (216)
|.|.=+-|..||.-....-.+..||.....++-.++-.|+|++.|+.
T Consensus 19 V~ViGlTRG~dtkfhHtEkLDkGEVmIaQFTehtsaiKiRGkA~I~t 65 (75)
T PF02081_consen 19 VTVIGLTRGTDTKFHHTEKLDKGEVMIAQFTEHTSAIKIRGKAEILT 65 (75)
T ss_dssp EEEEEEESSSSSSEEEEEEE-TT-EEEEE-BSSEEEEEEESSEEEEE
T ss_pred eEEEEEecCCcccchhhhccCCCcEEEEEeecceEEEEEeeeEEEEe
Confidence 77777888888864444447899999999999999999999999986
No 69
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=73.87 E-value=1.2 Score=32.12 Aligned_cols=29 Identities=28% Similarity=0.682 Sum_probs=22.8
Q ss_pred eEEEecCCCCCCCceEECCC--CCceecCCCCCC
Q 027973 140 VYCKCEMPYNPDDLMVQCEG--CSDWFHPNCINM 171 (216)
Q Consensus 140 ~~C~C~~~~~~~~~~i~C~~--C~~w~H~~Cv~~ 171 (216)
...+|+.. .+..|+|.. |..+||+.|...
T Consensus 57 ~C~iC~~~---~G~~i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 57 KCSICGKS---GGACIKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred cCcCCCCC---CceeEEcCCCCCCcCCCHHHHHH
Confidence 44477776 457999986 999999999854
No 70
>PF13341 RAG2_PHD: RAG2 PHD domain; PDB: 2JWO_A 2V86_B 2V85_B 2V87_A 2V83_C 2V89_A 2V88_A.
Probab=73.62 E-value=2.1 Score=28.57 Aligned_cols=34 Identities=21% Similarity=0.746 Sum_probs=19.1
Q ss_pred ceEECCC-CCceecCCCCCCChhhh----cCCCcEEecc
Q 027973 153 LMVQCEG-CSDWFHPNCINMTAEEA----KRLDHFFCES 186 (216)
Q Consensus 153 ~~i~C~~-C~~w~H~~Cv~~~~~~~----~~~~~~~C~~ 186 (216)
-||.|.. =+.|.|..|+.+++..+ +.-.+|+|..
T Consensus 29 AMI~cs~~~GHWvhaqCm~LsE~~L~~LSq~n~KYfC~d 67 (78)
T PF13341_consen 29 AMIFCSRGGGHWVHAQCMDLSETMLIQLSQENTKYFCND 67 (78)
T ss_dssp -EEEE-STT-EEEETGGGT--HHHHHHHHHSSS-B--TT
T ss_pred eEEEEeCCCceEeEeecccchHHHHHHHccCCceEEEhh
Confidence 7999974 48999999999986443 2236799875
No 71
>PF09871 DUF2098: Uncharacterized protein conserved in archaea (DUF2098); InterPro: IPR019209 This family of proteins have no known function.
Probab=73.22 E-value=9.9 Score=26.86 Aligned_cols=42 Identities=31% Similarity=0.428 Sum_probs=31.6
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEE---EEEeecCCC
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHV---RWYYRPEES 70 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v---~WfyRp~d~ 70 (216)
.|.+|++|--.... .+|+|.+|.. .++ ..|+.+ .-||||.-+
T Consensus 2 ~I~vGs~VRY~~TG-----T~G~V~diK~-ed~-~~wv~LD~t~L~Yr~~~L 46 (91)
T PF09871_consen 2 PIKVGSYVRYINTG-----TVGKVVDIKE-EDG-ETWVLLDSTDLYYRPDYL 46 (91)
T ss_pred cceeCCEEEECCCC-----eEEEEEEEEE-eCC-CeEEEEccCCceeeccee
Confidence 47889999777665 7999999954 455 578777 677887654
No 72
>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=72.61 E-value=24 Score=26.82 Aligned_cols=54 Identities=19% Similarity=0.203 Sum_probs=35.7
Q ss_pred eeeeEEEecCCcEEccCCEEEEecCC----------CCCCCeEEEEEEEEecCCCC------eEEEEEEEEe
Q 027973 10 TLESYTVKSISKTIKPGDCVLMRPSE----------PSKPSYVAKIERIESDARGA------NVKVHVRWYY 65 (216)
Q Consensus 10 ~y~~~~v~g~~~~~~vGD~V~v~~~~----------~~~~~~IarI~~i~~~~~~~------~~~v~v~Wfy 65 (216)
||+.+.+..+ .|.+||.|-|.+.. .+...-|-.|.+|....... .+.|++.-|-
T Consensus 2 ~y~GiflGAE--~I~vGD~VRl~~~~~~~~~~~~~~~~~~tdvMvI~~I~~~~~~~~~~~~~~v~~~G~lY~ 71 (139)
T PF10383_consen 2 YYRGIFLGAE--MIWVGDAVRLKPLNASPSPNQSDGNPDVTDVMVIDEIQLRLINCDPDSPSTVRFRGDLYT 71 (139)
T ss_pred eECeEEEeeE--EEEeCCEEEECccCCCcccccccCCCCceeEEEEeEEEEecccCCCCCCceEEEEeEece
Confidence 6777777654 99999999995532 12345677888887643221 4677776554
No 73
>PRK13251 transcription attenuation protein MtrB; Provisional
Probab=72.61 E-value=13 Score=24.87 Aligned_cols=47 Identities=21% Similarity=0.217 Sum_probs=38.9
Q ss_pred EEEEEEeecCCCCCCcccccCCCeEEEeCcccccccccEeeeeEEee
Q 027973 59 VHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDIQSADTIEGKCTVHS 105 (216)
Q Consensus 59 v~v~WfyRp~d~~~~~~~~~~~~ELf~s~~~d~~~~~~I~gkc~V~~ 105 (216)
|.|.=+-|..|+.-....-.+..||.....++-.++-.|+|++.|+.
T Consensus 19 V~vIgltrg~dtkfhhtEkLDkGEVmiaqftehtsaiKirGkA~I~t 65 (75)
T PRK13251 19 VNVIGLTRGKDTKFHHTEKLDKGEVMIAQFTEHTSAIKIRGKAEIQT 65 (75)
T ss_pred eEEEEEecCCCccchhhhhcCCCcEEEEEeecceeEEEEeceEEEEe
Confidence 77777888888854433347899999999999999999999999986
No 74
>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=71.41 E-value=4.9 Score=28.43 Aligned_cols=40 Identities=23% Similarity=0.344 Sum_probs=29.1
Q ss_pred EccCCEEEEecCCCCCCCeEEEEEEEEe---------cCCCCeEEEEEEEEe
Q 027973 23 IKPGDCVLMRPSEPSKPSYVAKIERIES---------DARGANVKVHVRWYY 65 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~IarI~~i~~---------~~~~~~~~v~v~Wfy 65 (216)
|++||.|...-.. -|+|-|+|+.-.. .... ...+.|++|-
T Consensus 1 f~~GDlVwaK~~G--yPwWPA~V~~~~~~p~~~l~~~~~~~-~~~~~V~FFg 49 (93)
T cd05840 1 FQPGDRVLAKVKG--FPAWPAIVVPEEMLPDSVLKGKKKKN-KRTYPVMFFP 49 (93)
T ss_pred CCCCCEEEEeCCC--CCCCCEEECChHHCCHHHHhcccCCC-CCeEEEEEeC
Confidence 5789999999987 7999999987321 1122 4668888883
No 75
>COG5475 Uncharacterized small protein [Function unknown]
Probab=71.14 E-value=20 Score=22.84 Aligned_cols=50 Identities=18% Similarity=0.270 Sum_probs=31.2
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCCCCCCcccccCCCeEE
Q 027973 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVF 84 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~~~~~~~~~~~~ELf 84 (216)
..+.+||.|.|.++.|. . |++=.. . .-+++.+||-+-. .....++++||.
T Consensus 3 ~~FstgdvV~lKsGGP~--M----tvs~~s---s-~Gmy~C~Wf~g~g----~~~~~F~ed~Lv 52 (60)
T COG5475 3 MSFSTGDVVTLKSGGPR--M----TVSGYS---S-DGMYECRWFDGYG----VKREAFHEDELV 52 (60)
T ss_pred ceeecCcEEEeecCCce--E----EEeccc---c-CCeEEEEEecCCC----ccccccccccee
Confidence 37899999999998841 1 111111 1 2478999998854 223335666664
No 76
>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=70.23 E-value=4 Score=27.73 Aligned_cols=42 Identities=21% Similarity=0.389 Sum_probs=29.8
Q ss_pred EccCCEEEEecCCCCCCCeEEEEEEEEecC--CCCeEEEEEEEEee
Q 027973 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDA--RGANVKVHVRWYYR 66 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~IarI~~i~~~~--~~~~~~v~v~WfyR 66 (216)
|.+||.|.+.-.. -+.|-|+|....... ....-.+.|.||-.
T Consensus 1 f~~GdlVWaK~~g--~pwWPa~V~~~~~~~~~~~~~~~~~V~Ffg~ 44 (86)
T PF00855_consen 1 FRPGDLVWAKLKG--YPWWPARVCDPDEKSKKKRKDGHVLVRFFGD 44 (86)
T ss_dssp -STTEEEEEEETT--SEEEEEEEEECCHCTSCSSSSTEEEEEETTT
T ss_pred CCCCCEEEEEeCC--CCCCceEEeecccccccCCCCCEEEEEecCC
Confidence 5789999999976 689999999987532 11135567776653
No 77
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=69.65 E-value=8.9 Score=28.56 Aligned_cols=44 Identities=16% Similarity=0.111 Sum_probs=30.3
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEe
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYY 65 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~Wfy 65 (216)
.+++||.|+...+.....+..|.|+...+........+.|.-|-
T Consensus 55 ~L~~GD~VLA~~~~~~~~Y~Pg~V~~~~~~~~~~~~~~~V~f~n 98 (124)
T PF15057_consen 55 SLQVGDKVLAPWEPDDCRYGPGTVIAGPERRASEDKEYTVRFYN 98 (124)
T ss_pred cCCCCCEEEEecCcCCCEEeCEEEEECccccccCCceEEEEEEC
Confidence 78999999999766545555699998876553324555555443
No 78
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=68.65 E-value=1.7 Score=40.96 Aligned_cols=41 Identities=24% Similarity=0.580 Sum_probs=31.2
Q ss_pred CCceEECCCCCceecCCCCCCChhhhcCCCcEEeccccccc
Q 027973 151 DDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEG 191 (216)
Q Consensus 151 ~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~ 191 (216)
...|..|..|...||+.||.+-...+....-|.|+.|..-.
T Consensus 32 ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe 72 (694)
T KOG4443|consen 32 AGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCE 72 (694)
T ss_pred cCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeee
Confidence 45799999999999999998654444334558888886544
No 79
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=68.41 E-value=11 Score=19.52 Aligned_cols=26 Identities=19% Similarity=0.261 Sum_probs=20.8
Q ss_pred EccCCEEEEecCCCCCCCeEEEEEEEEe
Q 027973 23 IKPGDCVLMRPSEPSKPSYVAKIERIES 50 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~IarI~~i~~ 50 (216)
+.+||.|.|..+. ..-.+|.|.++..
T Consensus 2 ~~~G~~V~I~~G~--~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGP--FKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECC--CCCcEEEEEEEcC
Confidence 5789999999977 4567899988753
No 80
>COG4014 Uncharacterized protein conserved in archaea [Function unknown]
Probab=67.99 E-value=14 Score=25.85 Aligned_cols=40 Identities=28% Similarity=0.432 Sum_probs=30.2
Q ss_pred ccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEE---EEeecCC
Q 027973 24 KPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVR---WYYRPEE 69 (216)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~---WfyRp~d 69 (216)
.+||.|--...+ .+|+|.+|.++.+| .+|+.+- -+||+.=
T Consensus 10 ~VG~avrYvnTg-----TvgrV~dIkkdEdG-~~WV~LdstdLwYre~~ 52 (97)
T COG4014 10 KVGDAVRYVNTG-----TVGRVVDIKKDEDG-DIWVVLDSTDLWYREHY 52 (97)
T ss_pred hhcceEEEeecC-----ceeeEEEEEeecCC-ceEEEEecCCceecccc
Confidence 478877655544 68999999999999 8898873 4666653
No 81
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=66.54 E-value=2.6 Score=38.60 Aligned_cols=49 Identities=24% Similarity=0.640 Sum_probs=35.4
Q ss_pred eeEE-EecCCCCC-CCceEECCCCCceecCCCCCCChhhhcCCCcEEecccccc
Q 027973 139 AVYC-KCEMPYNP-DDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTE 190 (216)
Q Consensus 139 ~~~C-~C~~~~~~-~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~ 190 (216)
...| +|....+. .+-.|.|++|+.-.|-+|-|+.-.+. ..|+|-.|.-.
T Consensus 193 d~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~f~pe---G~WlCrkCi~~ 243 (669)
T COG5141 193 DDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPE---GFWLCRKCIYG 243 (669)
T ss_pred hhhhHhccccccCCcceEEEecCcchhhhhhcccceecCc---chhhhhhhccc
Confidence 3344 66666553 35789999999999999999875433 46888887643
No 82
>COG3257 GlxB Uncharacterized protein, possibly involved in glyoxylate utilization [General function prediction only]
Probab=62.57 E-value=20 Score=29.60 Aligned_cols=61 Identities=10% Similarity=0.274 Sum_probs=37.7
Q ss_pred EEecCCcEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCCCCCCcccccCCCeEEEeCcccc
Q 027973 15 TVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESIGGRRQFHGSKEVFLSDHHDI 91 (216)
Q Consensus 15 ~v~g~~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~~~~~~~~~~~~ELf~s~~~d~ 91 (216)
.+.|....++-|+++|+.++.. |.-.+.+.--.++.||-++-+...|.. .-|+|.+++.|+
T Consensus 97 ~~~G~th~l~eggyaylPpgs~------------~~~~N~~~~~~rfhw~rk~Y~~VdG~~----~P~~~~~Ne~ei 157 (264)
T COG3257 97 KAEGKTHALREGGYAYLPPGSG------------WTLRNAQKEDSRFHWIRKRYQPVEGVQ----APELVSGNESEI 157 (264)
T ss_pred EEcCeEEEeccCCeEEeCCCCc------------ceEeeccCCceEEEEEeecceeecCcc----CCcceecChhhC
Confidence 3445555678899999988751 111222234478889888877765532 446666666554
No 83
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=60.64 E-value=2.1 Score=40.45 Aligned_cols=46 Identities=26% Similarity=0.707 Sum_probs=32.6
Q ss_pred EecCCCC--CCCceEECCCCCceecCCCCCCChhhhcC--CC-cEEecccc
Q 027973 143 KCEMPYN--PDDLMVQCEGCSDWFHPNCINMTAEEAKR--LD-HFFCESCS 188 (216)
Q Consensus 143 ~C~~~~~--~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~--~~-~~~C~~C~ 188 (216)
+|...|- ....|++|..|..|.|..|.++..+.... .+ .|-|..|.
T Consensus 150 vc~~~Y~~~e~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~CR 200 (694)
T KOG4443|consen 150 VCLIVYQDSESLPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTCR 200 (694)
T ss_pred hHHHhhhhccchhhHHHHHhcccccCCCCccchHHHHHHhhhhhcccceee
Confidence 3444442 23477999999999999999987543211 23 79999996
No 84
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=58.88 E-value=4.8 Score=23.69 Aligned_cols=34 Identities=24% Similarity=0.633 Sum_probs=17.7
Q ss_pred eEECCCCCceecCCCCCCChhhhcCCCcEEecccccccc
Q 027973 154 MVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEGQ 192 (216)
Q Consensus 154 ~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 192 (216)
.+.|..|+-...+-|.-.. ....|.|+.|...+.
T Consensus 2 p~rC~~C~aylNp~~~~~~-----~~~~w~C~~C~~~N~ 35 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDD-----GGKTWICNFCGTKNP 35 (40)
T ss_dssp S-B-TTT--BS-TTSEEET-----TTTEEEETTT--EEE
T ss_pred ccccCCCCCEECCcceEcC-----CCCEEECcCCCCcCC
Confidence 3677777776666665322 226799999987654
No 85
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=57.84 E-value=1.2 Score=26.56 Aligned_cols=40 Identities=23% Similarity=0.537 Sum_probs=25.1
Q ss_pred EecCCCCCCCceEECCCCCceecCCCCCCChhhhcCCCcEEecccc
Q 027973 143 KCEMPYNPDDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCS 188 (216)
Q Consensus 143 ~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~ 188 (216)
+|.....+++.++... |+..||.+|+..-.. ....||.|.
T Consensus 5 IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~-----~~~~CP~CR 44 (44)
T PF13639_consen 5 ICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLK-----RNNSCPVCR 44 (44)
T ss_dssp TTTCBHHTTSCEEEET-TSEEEEHHHHHHHHH-----HSSB-TTTH
T ss_pred CCChhhcCCCeEEEcc-CCCeeCHHHHHHHHH-----hCCcCCccC
Confidence 5555554455666666 999999999853211 124788884
No 86
>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=56.76 E-value=13 Score=25.70 Aligned_cols=42 Identities=21% Similarity=0.314 Sum_probs=29.0
Q ss_pred EccCCEEEEecCCCCCCCeEEEEEEEEecCC---CCeEEEEEEEEee
Q 027973 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDAR---GANVKVHVRWYYR 66 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~---~~~~~v~v~WfyR 66 (216)
+++||.|.-.-.. -|.|-|+|.+-..+.. .....+.|.||=.
T Consensus 1 f~~GDlVwaK~~g--~P~WPa~V~~~~~~~~~~~~~~~~~~V~FFG~ 45 (86)
T cd05836 1 LKLGDLVWAKMKG--FPPWPGRIVKPPKDLKKPRGKAKCFFVFFFGS 45 (86)
T ss_pred CCCCCEEEEeCCC--CCCCCEEEechhhhcccccCCCCeEEEEEeCC
Confidence 4789999999876 7999999998643311 1024466777654
No 87
>COG1370 Prefoldin, molecular chaperone implicated in de novo protein folding, alpha subunit [Posttranslational modification, protein turnover, chaperones]
Probab=56.69 E-value=9.4 Score=29.46 Aligned_cols=39 Identities=15% Similarity=0.295 Sum_probs=31.6
Q ss_pred CCCceeeeeEEEecCCcEEccCCEEEEecCCCCCCCeEEEE
Q 027973 5 KAPRRTLESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKI 45 (216)
Q Consensus 5 ~~~~~~y~~~~v~g~~~~~~vGD~V~v~~~~~~~~~~IarI 45 (216)
++|+..|.++.++.+ ..++.||-|+|-.++. ...-+|+.
T Consensus 94 r~Gk~VFaKfVi~~D-~~iR~~dEvlVVne~d-~LlAvGra 132 (155)
T COG1370 94 RKGKSVFAKFVIDVD-EEIRAGDEVLVVNEDD-ELLAVGRA 132 (155)
T ss_pred HhccchhhhheeccC-cccCCCCeEEEECCCC-cEEEeeeE
Confidence 678999999999987 6899999999999883 44455653
No 88
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=56.20 E-value=3 Score=41.84 Aligned_cols=55 Identities=24% Similarity=0.578 Sum_probs=41.9
Q ss_pred CceeEEEecCCCCCCCceEECCCCCceecCCCCCCChhhhcCCCcEEeccccccc
Q 027973 137 RVAVYCKCEMPYNPDDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEG 191 (216)
Q Consensus 137 ~~~~~C~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~ 191 (216)
..+.+=+|..|++|+...|-|..|..|+|..-|.+...+....-.+.|-.|.+-.
T Consensus 1121 ~~p~~~i~~~p~~pg~~~i~~~~~~~~~~~~~v~ln~s~~p~~~~~k~~~~~ri~ 1175 (1414)
T KOG1473|consen 1121 LSPVCFICTLPYNPGLTYIHCTVCMTWGHKEAVKLNSSPIPEVVGFKCCQCRRIR 1175 (1414)
T ss_pred CCccccceeeccCCCCCcceEEEeeccCcceeEecCCCcchHHhhhhHHhhhccC
Confidence 3445559999999999999999999999999998775443332456777776543
No 89
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=53.57 E-value=5.1 Score=21.03 Aligned_cols=13 Identities=38% Similarity=0.933 Sum_probs=9.6
Q ss_pred eEECCCCCceecC
Q 027973 154 MVQCEGCSDWFHP 166 (216)
Q Consensus 154 ~i~C~~C~~w~H~ 166 (216)
|++|..|+..|..
T Consensus 2 l~~C~~CgR~F~~ 14 (25)
T PF13913_consen 2 LVPCPICGRKFNP 14 (25)
T ss_pred CCcCCCCCCEECH
Confidence 6778888887754
No 90
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=53.39 E-value=68 Score=25.28 Aligned_cols=88 Identities=19% Similarity=0.271 Sum_probs=53.3
Q ss_pred ceeeeeEEEecCCcEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCCC---CCCc--ccccCCCe
Q 027973 8 RRTLESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEES---IGGR--RQFHGSKE 82 (216)
Q Consensus 8 ~~~y~~~~v~g~~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~---~~~~--~~~~~~~E 82 (216)
......+.++. ..+..||.|.+.++..++..+|-||..+.-+. +.. +-++++. +.|. ..--...+
T Consensus 56 ~Vll~k~~v~n--~~~~rGDiVvl~sP~~p~~~~iKRv~alegd~-----~~t---~~~k~~~v~vpkghcWVegDn~~h 125 (174)
T KOG1568|consen 56 TVLLRKWNVKN--RKVSRGDIVVLKSPNDPDKVIIKRVAALEGDI-----MVT---EDEKEEPVVVPKGHCWVEGDNQKH 125 (174)
T ss_pred EEEEEeecccc--ceeccCCEEEEeCCCChhheeeeeeecccccE-----ecc---CCCCCCceecCCCcEEEecCCccc
Confidence 34455555554 36789999999998877889999998875431 111 1222222 1111 00011234
Q ss_pred EEEeCcccccccccEeeeeEEee
Q 027973 83 VFLSDHHDIQSADTIEGKCTVHS 105 (216)
Q Consensus 83 Lf~s~~~d~~~~~~I~gkc~V~~ 105 (216)
=+=|+.+--++...|.|++.-..
T Consensus 126 s~DSntFGPVS~gli~grai~il 148 (174)
T KOG1568|consen 126 SYDSNTFGPVSTGLIVGRAIYIL 148 (174)
T ss_pred ccccCccCCcchhheeeeEEEEE
Confidence 45567777899999999986554
No 91
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=53.20 E-value=31 Score=23.42 Aligned_cols=30 Identities=17% Similarity=0.255 Sum_probs=25.4
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEEecCC
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDAR 53 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~ 53 (216)
.++.||-|.|.++. +.--+|+|.++.....
T Consensus 6 ~I~kGD~V~Vi~G~--dKGK~G~V~~V~~~~~ 35 (76)
T PRK12281 6 KVKKGDMVKVIAGD--DKGKTGKVLAVLPKKN 35 (76)
T ss_pred cccCCCEEEEeEcC--CCCcEEEEEEEEcCCC
Confidence 68999999999987 5678899999987543
No 92
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=52.45 E-value=7.4 Score=31.54 Aligned_cols=30 Identities=30% Similarity=0.799 Sum_probs=24.4
Q ss_pred ceEECCCCCceecCCCCCCChhhhcCCCcEEecccccccc
Q 027973 153 LMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEGQ 192 (216)
Q Consensus 153 ~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 192 (216)
.-++|+.|..-||..|... . .||.|.+...
T Consensus 171 ~~~~C~~C~~v~H~~C~~~-----~-----~CpkC~R~~~ 200 (202)
T PF13901_consen 171 TTVRCPKCKSVFHKSCFRK-----K-----SCPKCARRQK 200 (202)
T ss_pred CeeeCCcCccccchhhcCC-----C-----CCCCcHhHhc
Confidence 6689999999999999972 1 1999987654
No 93
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=52.08 E-value=32 Score=23.79 Aligned_cols=37 Identities=19% Similarity=0.239 Sum_probs=28.2
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEE
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVR 62 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~ 62 (216)
.++.||.|.|..+. +.--+|+|.++..... .+.+.+.
T Consensus 8 ~I~~GD~V~Vi~G~--dKGK~G~V~~V~~~~~--~V~Vegv 44 (83)
T CHL00141 8 HVKIGDTVKIISGS--DKGKIGEVLKIIKKSN--KVIVKGI 44 (83)
T ss_pred cccCCCEEEEeEcC--CCCcEEEEEEEEcCCC--EEEEcCc
Confidence 68999999999987 5668899999987543 3444443
No 94
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=51.90 E-value=11 Score=21.00 Aligned_cols=24 Identities=17% Similarity=0.551 Sum_probs=15.7
Q ss_pred ECCCCCceecCCCCCCChhhhcCCCcEEecccccc
Q 027973 156 QCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTE 190 (216)
Q Consensus 156 ~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~ 190 (216)
.|..|+..|.+.- ..|.||.|...
T Consensus 3 ~C~~CGy~y~~~~-----------~~~~CP~Cg~~ 26 (33)
T cd00350 3 VCPVCGYIYDGEE-----------APWVCPVCGAP 26 (33)
T ss_pred ECCCCCCEECCCc-----------CCCcCcCCCCc
Confidence 5777776554432 45899999653
No 95
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=51.72 E-value=9.1 Score=30.15 Aligned_cols=22 Identities=32% Similarity=0.845 Sum_probs=19.9
Q ss_pred CCceEECCCCCceecCCCCCCC
Q 027973 151 DDLMVQCEGCSDWFHPNCINMT 172 (216)
Q Consensus 151 ~~~~i~C~~C~~w~H~~Cv~~~ 172 (216)
-..||.|.+|..-||-.|+|..
T Consensus 14 kG~Lv~CQGCs~sYHk~CLG~R 35 (175)
T PF15446_consen 14 KGPLVYCQGCSSSYHKACLGPR 35 (175)
T ss_pred CCCeEEcCccChHHHhhhcCCc
Confidence 3599999999999999999975
No 96
>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=50.63 E-value=37 Score=21.99 Aligned_cols=31 Identities=35% Similarity=0.346 Sum_probs=23.6
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEEecC
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDA 52 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~ 52 (216)
+++.||.|++.+.+....+..++|.+|+...
T Consensus 12 ~l~~gd~v~~~~~~~~~~~~~~~I~~i~~~~ 42 (74)
T PF03144_consen 12 TLKKGDKVRVLPNGTGKKGQVVKIKSIFMFN 42 (74)
T ss_dssp EEETTEEEEEESTTTTEECEEEEEEEEEETT
T ss_pred EEcCCCEEEECccCCcceeeeeecccccccc
Confidence 8999999999883322345789999998753
No 97
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=50.03 E-value=39 Score=24.37 Aligned_cols=36 Identities=22% Similarity=0.292 Sum_probs=28.1
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEE
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHV 61 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v 61 (216)
.|+.||-|.|..+. +.--+|+|.++....+ .+.|.+
T Consensus 4 ~i~kGD~V~Vi~G~--dKGk~G~V~~V~~~~~--~V~Veg 39 (105)
T PRK00004 4 KIKKGDTVIVIAGK--DKGKRGKVLKVLPKKN--KVIVEG 39 (105)
T ss_pred cccCCCEEEEeEcC--CCCcEEEEEEEEcCCC--EEEEcC
Confidence 68999999999987 5678999999987543 344444
No 98
>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=49.56 E-value=51 Score=23.14 Aligned_cols=41 Identities=22% Similarity=0.316 Sum_probs=31.3
Q ss_pred CCCCCceeeeeEEEecCCcEEccCCEEEEecCCCCCCCeEEEEEEEEecC
Q 027973 3 KPKAPRRTLESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDA 52 (216)
Q Consensus 3 ~~~~~~~~y~~~~v~g~~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~ 52 (216)
+..+++.....+.+... ++++||++.+-.. -|+|..|+.+.
T Consensus 9 ~~~~g~G~vatviV~~G--tL~~Gd~iv~G~~-------~GkVr~~~d~~ 49 (95)
T cd03701 9 KLDKGRGPVATVIVQNG--TLKKGDVIVAGGT-------YGKIRTMVDEN 49 (95)
T ss_pred EecCCCCeeEEEEEEcC--eEecCCEEEECCc-------cceEEEEECCC
Confidence 45567777888877776 9999999987654 47888888754
No 99
>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=49.35 E-value=23 Score=25.75 Aligned_cols=44 Identities=16% Similarity=0.147 Sum_probs=31.5
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEEec--------CCCCeEEEEEEEEeec
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESD--------ARGANVKVHVRWYYRP 67 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~~~--------~~~~~~~v~v~WfyRp 67 (216)
+|.+||.|...-.. -|.|-|+|..--.. .......+.|++|--.
T Consensus 2 ~~~~GdlVWaK~~g--~PwWPa~V~~~~~~~~~~~~~~~~~~~~~~~V~FFG~~ 53 (110)
T cd05837 2 KYQVGDLVWAKVSG--YPWWPCMVCSDPLLGTYTKTKRNKRKPRQYHVQFFGDN 53 (110)
T ss_pred CCCCCCEEEEeCCC--CCCCCEEEecccccchhhhhhhccCCCCeEEEEEcCCC
Confidence 58899999999987 68999999963211 1111467888888754
No 100
>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=48.72 E-value=2.8 Score=22.90 Aligned_cols=18 Identities=22% Similarity=0.625 Sum_probs=7.4
Q ss_pred CceEECCCCCceecCCCC
Q 027973 152 DLMVQCEGCSDWFHPNCI 169 (216)
Q Consensus 152 ~~~i~C~~C~~w~H~~Cv 169 (216)
.....|..|+-..|..|+
T Consensus 13 ~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 13 GWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --EEE-TTT-----HHHH
T ss_pred CceEECccCCCccChhcC
Confidence 366778888888887763
No 101
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=47.45 E-value=15 Score=22.90 Aligned_cols=36 Identities=17% Similarity=0.427 Sum_probs=19.9
Q ss_pred ECCCCCceecCCCC----CCCh--hhhcCCCcEEeccccccc
Q 027973 156 QCEGCSDWFHPNCI----NMTA--EEAKRLDHFFCESCSTEG 191 (216)
Q Consensus 156 ~C~~C~~w~H~~Cv----~~~~--~~~~~~~~~~C~~C~~~~ 191 (216)
+|..|+--|...== ++.+ .-.+.++.|.||.|....
T Consensus 3 ~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a~K 44 (50)
T cd00730 3 ECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAGK 44 (50)
T ss_pred CCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCCcH
Confidence 57777766665321 1111 111234789999997543
No 102
>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=47.08 E-value=33 Score=23.28 Aligned_cols=36 Identities=14% Similarity=0.347 Sum_probs=23.6
Q ss_pred eEEEecCCcEEccCCEEEEecCCCCCCCeEEEEEEEEec
Q 027973 13 SYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESD 51 (216)
Q Consensus 13 ~~~v~g~~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~ 51 (216)
.|.+++. ...++||+|.+..++ ....+|+|.+|...
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 3445543 268999999999984 46799999999984
No 103
>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=46.87 E-value=51 Score=23.27 Aligned_cols=41 Identities=20% Similarity=0.277 Sum_probs=30.7
Q ss_pred CCCCCceeeeeEEEecCCcEEccCCEEEEecCCCCCCCeEEEEEEEEecC
Q 027973 3 KPKAPRRTLESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDA 52 (216)
Q Consensus 3 ~~~~~~~~y~~~~v~g~~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~ 52 (216)
+..+++.....+.+... ++++||++.+-.. .|||..|+.+.
T Consensus 9 ~~~~g~G~vatviV~~G--tL~~Gd~iv~G~~-------~gkVr~l~d~~ 49 (95)
T cd03702 9 KLDKGRGPVATVLVQNG--TLKVGDVLVAGTT-------YGKVRAMFDEN 49 (95)
T ss_pred EecCCCCccEEEEEEcC--eEeCCCEEEEccc-------ccEEEEEECCC
Confidence 34566677777777665 8999999987654 35999999864
No 104
>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=45.82 E-value=17 Score=24.50 Aligned_cols=25 Identities=28% Similarity=0.389 Sum_probs=19.8
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEE
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIER 47 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~ 47 (216)
.|+.||.|||.=.+| .-+-||-|.+
T Consensus 5 ~~~~GD~VyViYrNP-Ht~~VanIqe 29 (75)
T PF11132_consen 5 PYHAGDIVYVIYRNP-HTQDVANIQE 29 (75)
T ss_pred ccCCCCEEEEEEcCC-CCccccccch
Confidence 689999999998875 4567777765
No 105
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=43.50 E-value=24 Score=30.66 Aligned_cols=55 Identities=15% Similarity=0.210 Sum_probs=40.2
Q ss_pred CCceeEEEecCCCCCCCceEECCCCCceecCCCCCCChhhhcCCCcEEeccccccccc
Q 027973 136 DRVAVYCKCEMPYNPDDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEGQK 193 (216)
Q Consensus 136 ~~~~~~C~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 193 (216)
.....+|.|-.++...+.+..|-.|..|+|..-..+..- .+ -.|-|.=|..+.+.
T Consensus 50 ~~rQ~l~sClTC~P~~~~agvC~~C~~~CH~~H~lveL~-tK--R~FrCDCg~sk~g~ 104 (345)
T KOG2752|consen 50 KKRQALFSCLTCTPAPEMAGVCYACSLSCHDGHELVELY-TK--RNFRCDCGNSKFGR 104 (345)
T ss_pred ccccceeEeecccCChhhceeEEEeeeeecCCceeeecc-cc--CCcccccccccccc
Confidence 344567888888766669999999999999998875422 22 46888777666653
No 106
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=41.84 E-value=52 Score=23.73 Aligned_cols=36 Identities=22% Similarity=0.257 Sum_probs=27.8
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEE
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHV 61 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v 61 (216)
.++.||-|.|..+. +.--+|.|.++....+ .+.|..
T Consensus 3 ~ikkGD~V~Vi~G~--dKGK~G~V~~V~~~~~--~V~Veg 38 (104)
T TIGR01079 3 KIKKGDTVKVISGK--DKGKRGKVLKVLPKTN--KVIVEG 38 (104)
T ss_pred cccCCCEEEEeEcC--CCCcEEEEEEEEcCCC--EEEECC
Confidence 57899999999987 5678999999987543 344443
No 107
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=41.67 E-value=40 Score=21.18 Aligned_cols=28 Identities=21% Similarity=0.274 Sum_probs=22.9
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEEe
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIES 50 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~~ 50 (216)
.|++||.|.+...+ ....|-|+|+++-.
T Consensus 2 ~~~~G~~Ve~~~~~-~~~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKE-EDSWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECC-CCEEEEEEEEEECC
Confidence 47899999999855 25678899999876
No 108
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=41.04 E-value=71 Score=23.75 Aligned_cols=39 Identities=13% Similarity=0.118 Sum_probs=28.9
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEE
Q 027973 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRW 63 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~W 63 (216)
..|+.||-|.|.++. +.--.|+|.++....+ .+.|.+.=
T Consensus 44 ~~IkkGD~V~VisG~--~KGk~GkV~~V~~~~~--~V~VeGvn 82 (120)
T PRK01191 44 LPVRKGDTVKVMRGD--FKGEEGKVVEVDLKRG--RIYVEGVT 82 (120)
T ss_pred ceEeCCCEEEEeecC--CCCceEEEEEEEcCCC--EEEEeCcE
Confidence 478999999999998 4557799999977433 35554433
No 109
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=40.98 E-value=21 Score=25.83 Aligned_cols=32 Identities=22% Similarity=0.511 Sum_probs=21.5
Q ss_pred CCC---CceecCCCCCCC----hhhhcCCCcEEeccccc
Q 027973 158 EGC---SDWFHPNCINMT----AEEAKRLDHFFCESCST 189 (216)
Q Consensus 158 ~~C---~~w~H~~Cv~~~----~~~~~~~~~~~C~~C~~ 189 (216)
..| ..-|...|+... ..++.....|.||.|..
T Consensus 31 ~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 31 SSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred CCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 556 888999998532 22222336899999965
No 111
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=40.75 E-value=13 Score=28.88 Aligned_cols=34 Identities=21% Similarity=0.445 Sum_probs=19.1
Q ss_pred ECCCCCceecCCCCCCChhhhcCCCcEEeccccccccc
Q 027973 156 QCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEGQK 193 (216)
Q Consensus 156 ~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 193 (216)
+|+.|+.-..+....+.-+-+ .-.+|..|. +.++
T Consensus 2 ~CEiCG~~i~~~~~~v~iega---~l~vC~~C~-k~G~ 35 (154)
T TIGR00270 2 NCEICGRKIKGKGFKIVIEGS---EMTVCGECR-KFGK 35 (154)
T ss_pred ccccCCCccCCCCeEEEEcCe---EEehhhhHH-hcCC
Confidence 488887666554332221111 346899998 5554
No 112
>KOG1740 consensus Predicted mitochondrial/chloroplast ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=38.16 E-value=20 Score=25.73 Aligned_cols=30 Identities=23% Similarity=0.381 Sum_probs=24.5
Q ss_pred eeeeeEEEecCCcEEccCCEEEEecCCCCC
Q 027973 9 RTLESYTVKSISKTIKPGDCVLMRPSEPSK 38 (216)
Q Consensus 9 ~~y~~~~v~g~~~~~~vGD~V~v~~~~~~~ 38 (216)
..++.+.+++++...++||.|-|.+.-|-+
T Consensus 36 ~~~~kymahD~~n~cnvGD~VrlepsRPlS 65 (107)
T KOG1740|consen 36 KRTSKYMAHDDKNQCNVGDRVRLEPSRPLS 65 (107)
T ss_pred HHhhheeecCccccccccceEEeccCCccc
Confidence 456778888888889999999999987643
No 113
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=37.87 E-value=23 Score=20.29 Aligned_cols=13 Identities=31% Similarity=0.736 Sum_probs=8.0
Q ss_pred CceEECCCCCcee
Q 027973 152 DLMVQCEGCSDWF 164 (216)
Q Consensus 152 ~~~i~C~~C~~w~ 164 (216)
..+++|..|+.-|
T Consensus 23 g~~v~C~~C~~~f 35 (36)
T PF13717_consen 23 GRKVRCSKCGHVF 35 (36)
T ss_pred CcEEECCCCCCEe
Confidence 3567777775544
No 114
>KOG2133 consensus Transcriptional corepressor Atrophin-1/DRPLA [General function prediction only]
Probab=37.20 E-value=27 Score=34.87 Aligned_cols=112 Identities=21% Similarity=0.206 Sum_probs=77.5
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCCCC-CC---c--------------ccccCCCe
Q 027973 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEESI-GG---R--------------RQFHGSKE 82 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~~-~~---~--------------~~~~~~~E 82 (216)
..|.++|.|.+....+ .++.|+.|-.+-..++...+.++.-.+.|++|++ .+ . .+-...+|
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 3788999999998875 6778888777766664216778888899999987 22 0 00123478
Q ss_pred EEEeCcc-cccccccEeeeeEEeeccccccccC------CCCCceEEeeeecCCCCCC
Q 027973 83 VFLSDHH-DIQSADTIEGKCTVHSFKSYTKLDA------VGNDDFFCRFEYNSSSGAF 133 (216)
Q Consensus 83 Lf~s~~~-d~~~~~~I~gkc~V~~~~~~~~~~~------~~~~~ff~r~~yd~~~~~f 133 (216)
||.+... -.-|.++..|||.+....++.-... .+.++||..+.|..-++..
T Consensus 223 l~~s~l~~i~qppscp~gk~~~~~skd~~h~~~~n~p~~ld~~i~fk~agglpps~k~ 280 (1229)
T KOG2133|consen 223 LFNSELQGITQPPSCPRGKGIAEYSKDVRHGGNTNAPFSLDNDIFFKCAGGLPPSTKP 280 (1229)
T ss_pred hhcccccCCCCCCcCCCCCceEEeecccccCCccCCCCcccceeeeecccCCCCCCCC
Confidence 9988877 5588999999999986555543221 2446777778887654433
No 115
>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=36.84 E-value=48 Score=26.85 Aligned_cols=24 Identities=17% Similarity=0.340 Sum_probs=14.1
Q ss_pred eEEEecCCcEEccCCEEEEecCCC
Q 027973 13 SYTVKSISKTIKPGDCVLMRPSEP 36 (216)
Q Consensus 13 ~~~v~g~~~~~~vGD~V~v~~~~~ 36 (216)
.+.+.+.+..|++||.+.|.+.++
T Consensus 32 eldl~~~~l~Y~pGD~l~V~P~N~ 55 (219)
T PF00667_consen 32 ELDLSDSGLSYQPGDHLGVYPPND 55 (219)
T ss_dssp EEE-TTSTG---TT-EEEEE-SSE
T ss_pred EEEeCCCCCcccCCCEEEEEccCC
Confidence 334566689999999999999983
No 116
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=36.74 E-value=32 Score=32.53 Aligned_cols=41 Identities=17% Similarity=0.446 Sum_probs=31.6
Q ss_pred CceEECCCCCceecCCCCCCChhhhcCCCcEEecccccccc
Q 027973 152 DLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEGQ 192 (216)
Q Consensus 152 ~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 192 (216)
.....|+.|..-||..|.+....+...+..+.|..|....+
T Consensus 57 gn~~~~~~~~~s~h~~~~~~~~sp~~~~~~~~~~~~~~~~~ 97 (613)
T KOG4299|consen 57 GNLLCCDHCPASFHLECDKPPLSPDLKGSEINCSRCPKGRE 97 (613)
T ss_pred CCccccccCccccchhccCcccCcccccccccccCCCcccc
Confidence 35678999999999999998776665556777777766543
No 117
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=36.72 E-value=67 Score=22.12 Aligned_cols=29 Identities=28% Similarity=0.225 Sum_probs=20.8
Q ss_pred CcEEccCCEEEEecCCCCCCCeEEEEEEEEe
Q 027973 20 SKTIKPGDCVLMRPSEPSKPSYVAKIERIES 50 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~ 50 (216)
..-++.||+|.|.+.+- ..--|.|+....
T Consensus 41 ~iwI~~GD~VlVe~~~~--~~~kg~Iv~r~~ 69 (83)
T smart00652 41 KVWIRRGDIVLVDPWDF--QDVKADIIYKYT 69 (83)
T ss_pred cEEEcCCCEEEEEecCC--CCCEEEEEEEeC
Confidence 35689999999987652 356777777665
No 118
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=36.62 E-value=23 Score=32.71 Aligned_cols=11 Identities=27% Similarity=0.522 Sum_probs=6.3
Q ss_pred EEecccccccc
Q 027973 182 FFCESCSTEGQ 192 (216)
Q Consensus 182 ~~C~~C~~~~~ 192 (216)
|-||.|.-...
T Consensus 53 f~CP~C~~~L~ 63 (483)
T PF05502_consen 53 FDCPICFSPLS 63 (483)
T ss_pred ccCCCCCCcce
Confidence 56666654444
No 119
>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=36.59 E-value=60 Score=20.64 Aligned_cols=25 Identities=28% Similarity=0.298 Sum_probs=16.5
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEEe
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIES 50 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~~ 50 (216)
.+-+||.|.+...+. + -+.|.++.+
T Consensus 37 ~~~VGD~V~~~~~~~-~---~~~I~~vl~ 61 (68)
T cd04466 37 PPAVGDRVEFEPEDD-G---EGVIEEILP 61 (68)
T ss_pred CCCCCcEEEEEECCC-C---cEEEEEEec
Confidence 357999999976442 2 256666665
No 120
>PF10377 ATG11: Autophagy-related protein 11; InterPro: IPR019460 This family consists of proteins involved in telomere maintenance. In Schizosaccharomyces pombe (fission yeast) this protein is called Taf1 (taz1 interacting factor) and is part of the telomere cap complex. In Saccharomyces cerevisiae (baker's yeast) this protein is called ATG11 and is known to be involved in vacuolar targeting and peroxisome degradation [, ].
Probab=36.43 E-value=64 Score=24.18 Aligned_cols=14 Identities=36% Similarity=0.650 Sum_probs=11.1
Q ss_pred EEccCCEEEEecCC
Q 027973 22 TIKPGDCVLMRPSE 35 (216)
Q Consensus 22 ~~~vGD~V~v~~~~ 35 (216)
.+++||.|++.+..
T Consensus 42 ~f~~GDlvLflpt~ 55 (129)
T PF10377_consen 42 NFQVGDLVLFLPTR 55 (129)
T ss_pred cCCCCCEEEEEecC
Confidence 46888988888865
No 121
>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=36.33 E-value=63 Score=21.89 Aligned_cols=28 Identities=29% Similarity=0.196 Sum_probs=20.5
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEEEEEe
Q 027973 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIES 50 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~IarI~~i~~ 50 (216)
..+..||.|.|...+ ...-=|+|+..+.
T Consensus 37 iwI~~GD~V~Ve~~~--~d~~kg~Iv~r~~ 64 (77)
T cd05793 37 VWINEGDIVLVAPWD--FQDDKADIIYKYT 64 (77)
T ss_pred EEEcCCCEEEEEecc--ccCCEEEEEEEcC
Confidence 577899999998765 3456777776654
No 122
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=36.20 E-value=38 Score=18.35 Aligned_cols=26 Identities=19% Similarity=0.436 Sum_probs=16.8
Q ss_pred EecCCCCCCCceEECCCCCceecCCCC
Q 027973 143 KCEMPYNPDDLMVQCEGCSDWFHPNCI 169 (216)
Q Consensus 143 ~C~~~~~~~~~~i~C~~C~~w~H~~Cv 169 (216)
+|++.-++.. ...|..|.--.|..|+
T Consensus 5 ~C~~~~~~~~-~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 5 VCRRKIDGFY-FYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCcCCCE-eEEeCCCCCeEcCccC
Confidence 4555444322 7778888888888774
No 123
>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=36.11 E-value=74 Score=21.19 Aligned_cols=25 Identities=16% Similarity=0.308 Sum_probs=10.3
Q ss_pred EccCCEEEEecCCCCCCCeEEEEEE
Q 027973 23 IKPGDCVLMRPSEPSKPSYVAKIER 47 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~IarI~~ 47 (216)
++.||.|.+.........+|.||..
T Consensus 32 ~~~GDiv~~~~~~~~~~~~vkRv~~ 56 (85)
T cd06530 32 PKRGDVVVFKSPGDPGKPIIKRVIG 56 (85)
T ss_pred CCCCCEEEEeCCCCCCCEEEEEEEE
Confidence 3444444444433212344444444
No 124
>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=36.10 E-value=29 Score=23.93 Aligned_cols=29 Identities=24% Similarity=0.487 Sum_probs=18.6
Q ss_pred EEEEEEeecCCCC-------CCcccccCCCeEEEeCcc
Q 027973 59 VHVRWYYRPEESI-------GGRRQFHGSKEVFLSDHH 89 (216)
Q Consensus 59 v~v~WfyRp~d~~-------~~~~~~~~~~ELf~s~~~ 89 (216)
-.++|+| |.++. .|..+ ..++|||+.+..
T Consensus 36 ~~GrWm~-P~~~~Y~VGyNe~GLGp-K~~~ElyiVnk~ 71 (85)
T PF12503_consen 36 PNGRWMY-PEGYEYMVGYNESGLGP-KFDGELYIVNKD 71 (85)
T ss_pred cCCceec-CCCeEEEeeecCCCCCc-CcCCeEEEEcCc
Confidence 3468999 88763 11111 247999998864
No 125
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=35.02 E-value=53 Score=20.08 Aligned_cols=36 Identities=19% Similarity=0.447 Sum_probs=17.9
Q ss_pred EECCCCCceecCCCC----CCCh--hhhcCCCcEEecccccc
Q 027973 155 VQCEGCSDWFHPNCI----NMTA--EEAKRLDHFFCESCSTE 190 (216)
Q Consensus 155 i~C~~C~~w~H~~Cv----~~~~--~~~~~~~~~~C~~C~~~ 190 (216)
-+|..|+--|...=- ++.+ .-.+.++.|.||.|...
T Consensus 2 y~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred cCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence 367777776766432 1111 11122478999999754
No 126
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=34.89 E-value=6.4 Score=37.03 Aligned_cols=37 Identities=22% Similarity=0.584 Sum_probs=26.6
Q ss_pred ceEECCCCCceecCCCCCCChhhhcCCCcEEeccccccccccccC
Q 027973 153 LMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEGQKKLQN 197 (216)
Q Consensus 153 ~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~~~~ 197 (216)
.-..|+.|..+||-.|..-... .||.|.+-..++...
T Consensus 530 ~~~rC~~C~avfH~~C~~r~s~--------~CPrC~R~q~r~~~~ 566 (580)
T KOG1829|consen 530 NTRRCSTCLAVFHKKCLRRKSP--------CCPRCERRQKRAEQG 566 (580)
T ss_pred cceeHHHHHHHHHHHHHhccCC--------CCCchHHHHHHhhcc
Confidence 4477999999999999964321 199998766544333
No 127
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=34.48 E-value=1.2e+02 Score=23.30 Aligned_cols=41 Identities=7% Similarity=0.016 Sum_probs=29.5
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEe
Q 027973 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYY 65 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~Wfy 65 (216)
..|+.||.|.|.++.. .--.|+|.++.... + .+.|.+.=.-
T Consensus 45 ~~IkkGD~V~Vi~Gk~--KGk~GkV~~V~~k~-~-~ViVEgvn~~ 85 (143)
T PTZ00194 45 MPVRKDDEVMVVRGHH--KGREGKVTAVYRKK-W-VIHIEKITRE 85 (143)
T ss_pred ceeecCCEEEEecCCC--CCCceEEEEEEcCC-C-EEEEeCeEEE
Confidence 4789999999999984 45669999997633 3 4555554433
No 128
>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=34.36 E-value=54 Score=21.28 Aligned_cols=25 Identities=36% Similarity=0.349 Sum_probs=16.6
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEEE
Q 027973 21 KTIKPGDCVLMRPSEPSKPSYVAKIER 47 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~IarI~~ 47 (216)
..++.||+|.|...+- ..--|+|+.
T Consensus 40 iwI~~GD~V~V~~~~~--d~~kG~Ii~ 64 (65)
T PF01176_consen 40 IWIKRGDFVLVEPSPY--DKVKGRIIY 64 (65)
T ss_dssp C---TTEEEEEEESTT--CTTEEEEEE
T ss_pred EecCCCCEEEEEeccc--CCCeEEEEE
Confidence 4679999999998663 367777764
No 129
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=33.66 E-value=78 Score=22.75 Aligned_cols=44 Identities=18% Similarity=0.299 Sum_probs=34.3
Q ss_pred CCCceeeeeEEEecCCcEEccCCEEEEecCCCCCCCeEEEEEEEEecC
Q 027973 5 KAPRRTLESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDA 52 (216)
Q Consensus 5 ~~~~~~y~~~~v~g~~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~ 52 (216)
.+|+.+++.-.++.. ..+++||.+.|.-+. ..+..+|..+-...
T Consensus 32 ~~GrV~vNG~~aKpS-~~VK~GD~l~i~~~~---~~~~v~Vl~~~~~r 75 (100)
T COG1188 32 EGGRVKVNGQRAKPS-KEVKVGDILTIRFGN---KEFTVKVLALGEQR 75 (100)
T ss_pred HCCeEEECCEEcccc-cccCCCCEEEEEeCC---cEEEEEEEeccccc
Confidence 367888888877544 689999999999876 57888888887743
No 130
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=33.64 E-value=1.6e+02 Score=20.31 Aligned_cols=27 Identities=22% Similarity=0.359 Sum_probs=19.9
Q ss_pred eeEEEecCCcEEccCCEEEEecCCCCC
Q 027973 12 ESYTVKSISKTIKPGDCVLMRPSEPSK 38 (216)
Q Consensus 12 ~~~~v~g~~~~~~vGD~V~v~~~~~~~ 38 (216)
..+.+++.+...++||.|.|...-|-+
T Consensus 43 kk~~aHD~~n~~k~GD~V~I~e~rPlS 69 (84)
T PRK05610 43 KKYHAHDENNEAKIGDVVRIMETRPLS 69 (84)
T ss_pred eEEEEECCCCCCCCCCEEEEEEcccCC
Confidence 345566666678999999999876543
No 131
>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=32.58 E-value=68 Score=21.81 Aligned_cols=29 Identities=28% Similarity=0.273 Sum_probs=20.2
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEEEEEe
Q 027973 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIES 50 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~IarI~~i~~ 50 (216)
.-++.||+|.|.+.+- +..-=|.|+....
T Consensus 37 iwI~~GD~VlV~~~~~-~~~~kg~Iv~r~~ 65 (78)
T cd04456 37 IWIKRGDFLIVDPIEE-GEDVKADIIFVYC 65 (78)
T ss_pred EEEcCCCEEEEEeccc-CCCceEEEEEEeC
Confidence 5689999999987652 2355667766654
No 132
>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=32.35 E-value=1.2e+02 Score=24.88 Aligned_cols=45 Identities=20% Similarity=0.464 Sum_probs=36.7
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecC
Q 027973 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPE 68 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~ 68 (216)
..+++|+.=.+..+...-|-+-|+|.++... + ...|++.|+---.
T Consensus 26 ~~F~~gQIWAlYd~~D~mPR~Ya~I~kV~~~--~-~Fkl~i~wLe~~~ 70 (217)
T PF11926_consen 26 EKFQVGQIWALYDDDDGMPRYYARIKKVDSS--N-PFKLHITWLEPCP 70 (217)
T ss_pred HhCCCCCEEEEeeCCCCCeeeEEEEEEEecC--C-CeEEEEEEccccC
Confidence 4789999999998877789999999999884 2 4679999986543
No 133
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=31.29 E-value=1.2e+02 Score=24.15 Aligned_cols=45 Identities=29% Similarity=0.535 Sum_probs=35.0
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCC
Q 027973 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEE 69 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d 69 (216)
..+.+||.|-|.++. -..+.|+|+++-.++ + ...+.|.-|-|+--
T Consensus 122 ~~~e~Gd~VrI~~Gp--Fa~f~g~V~evd~ek-~-~~~v~v~ifgr~tP 166 (178)
T COG0250 122 VDFEPGDVVRIIDGP--FAGFKAKVEEVDEEK-G-KLKVEVSIFGRPTP 166 (178)
T ss_pred ccCCCCCEEEEeccC--CCCccEEEEEEcCcC-c-EEEEEEEEeCCceE
Confidence 478999999999987 566999999998854 3 46777777766543
No 134
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=30.11 E-value=25 Score=30.32 Aligned_cols=34 Identities=29% Similarity=0.425 Sum_probs=21.9
Q ss_pred CCCceEECCCCCceecCCCCCCChhhhcCCCcEEeccccccc
Q 027973 150 PDDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEG 191 (216)
Q Consensus 150 ~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~ 191 (216)
|+..++.|+.|+...+ ..+.+. ..++||.|..-.
T Consensus 34 p~~lw~kc~~C~~~~~-------~~~l~~-~~~vcp~c~~h~ 67 (296)
T CHL00174 34 YKHLWVQCENCYGLNY-------KKFLKS-KMNICEQCGYHL 67 (296)
T ss_pred CCCCeeECCCccchhh-------HHHHHH-cCCCCCCCCCCc
Confidence 4568999999976432 222322 458999996533
No 135
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=29.83 E-value=1.9e+02 Score=19.99 Aligned_cols=28 Identities=25% Similarity=0.388 Sum_probs=20.9
Q ss_pred eeeEEEecCCcEEccCCEEEEecCCCCC
Q 027973 11 LESYTVKSISKTIKPGDCVLMRPSEPSK 38 (216)
Q Consensus 11 y~~~~v~g~~~~~~vGD~V~v~~~~~~~ 38 (216)
...+.+++.+...++||.|.|..--|-+
T Consensus 39 ~kk~~aHDe~n~~~~GD~V~I~e~RPlS 66 (84)
T CHL00142 39 TKKYLVHDEENECNIGDQVLIEETRPLS 66 (84)
T ss_pred eEEEEEeCCCCCCCCCCEEEEEEcCCCC
Confidence 3455667776679999999999877644
No 136
>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=29.40 E-value=1.3e+02 Score=21.37 Aligned_cols=28 Identities=21% Similarity=0.459 Sum_probs=22.7
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEEEEEe
Q 027973 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIES 50 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~IarI~~i~~ 50 (216)
..+++||.+.|...+ .+.-+.+|.++..
T Consensus 29 ~~~k~Gd~~i~~~~~--~~~~~i~v~~V~~ 56 (105)
T cd06541 29 QLPKAGDYLIILDGQ--QPLAIAEVVKVEI 56 (105)
T ss_pred cCCCCCCEEEEecCC--CcEEEEEEEEEEE
Confidence 478999999998876 5667888888865
No 137
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=29.22 E-value=54 Score=23.31 Aligned_cols=20 Identities=25% Similarity=0.277 Sum_probs=14.9
Q ss_pred EEccCCEEEEecCCCCCCCe
Q 027973 22 TIKPGDCVLMRPSEPSKPSY 41 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~ 41 (216)
.+++||.|.+.+...++.++
T Consensus 76 ~Lk~GD~V~ll~~~~gQ~yi 95 (100)
T PF10844_consen 76 GLKVGDKVLLLRVQGGQKYI 95 (100)
T ss_pred CCcCCCEEEEEEecCCCEEE
Confidence 57999999999966444443
No 138
>COG4101 Predicted mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=29.05 E-value=1.2e+02 Score=22.59 Aligned_cols=40 Identities=23% Similarity=0.307 Sum_probs=23.2
Q ss_pred EEccCCEEEEecCCCC------CCCeEEEEEEEEecCCCCeEEEEEEE
Q 027973 22 TIKPGDCVLMRPSEPS------KPSYVAKIERIESDARGANVKVHVRW 63 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~------~~~~IarI~~i~~~~~~~~~~v~v~W 63 (216)
+...||+.||.+.-+. ..+..+.|..- |.+.++.-+.+.|
T Consensus 91 ~~~pGDf~YiPpgVPHqp~N~S~ep~s~vIaRs--Dp~~~Esv~~lpe 136 (142)
T COG4101 91 EVGPGDFFYIPPGVPHQPANLSTEPLSAVIARS--DPNPQESVQLLPE 136 (142)
T ss_pred EecCCCeEEcCCCCCCcccccCCCCeEEEEEcc--CCCCCcCcEEecc
Confidence 5688999999987652 34555555432 4444333333333
No 139
>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=29.04 E-value=43 Score=21.17 Aligned_cols=20 Identities=30% Similarity=0.597 Sum_probs=14.3
Q ss_pred EecCCcEEccCCEEEEecCC
Q 027973 16 VKSISKTIKPGDCVLMRPSE 35 (216)
Q Consensus 16 v~g~~~~~~vGD~V~v~~~~ 35 (216)
++|....++.||.+++.++.
T Consensus 34 ~~~~~~~l~~Gd~~~i~~~~ 53 (71)
T PF07883_consen 34 VDGERVELKPGDAIYIPPGV 53 (71)
T ss_dssp ETTEEEEEETTEEEEEETTS
T ss_pred EccEEeEccCCEEEEECCCC
Confidence 45555577888888888765
No 140
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=28.82 E-value=29 Score=29.78 Aligned_cols=36 Identities=19% Similarity=0.535 Sum_probs=23.0
Q ss_pred CCCCceEECCCCCceecCCCCCCChhhhcCCCcEEecccccccc
Q 027973 149 NPDDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEGQ 192 (216)
Q Consensus 149 ~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 192 (216)
-|+..++.|+.|+...+. .+.+. ..++||.|..-.+
T Consensus 21 ~~~~~~~~c~~c~~~~~~-------~~l~~-~~~vc~~c~~h~r 56 (285)
T TIGR00515 21 VPEGVWTKCPKCGQVLYT-------KELER-NLEVCPKCDHHMR 56 (285)
T ss_pred CCCCCeeECCCCcchhhH-------HHHHh-hCCCCCCCCCcCc
Confidence 356689999999774332 22322 4589999965443
No 141
>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=28.75 E-value=1.4e+02 Score=20.04 Aligned_cols=24 Identities=29% Similarity=0.499 Sum_probs=19.5
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEEe
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIES 50 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~~ 50 (216)
++++||.|++.|.+ ..++|.+|..
T Consensus 26 ~i~~Gd~v~i~P~~-----~~~~V~si~~ 49 (83)
T cd03698 26 SIQKGDTLLVMPSK-----ESVEVKSIYV 49 (83)
T ss_pred EEeCCCEEEEeCCC-----cEEEEEEEEE
Confidence 79999999999976 2478888765
No 142
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=28.10 E-value=23 Score=23.52 Aligned_cols=40 Identities=25% Similarity=0.287 Sum_probs=16.6
Q ss_pred ceEECC--CCCceecCCCCCCC--hhhh----cCCCcEEecccccccc
Q 027973 153 LMVQCE--GCSDWFHPNCINMT--AEEA----KRLDHFFCESCSTEGQ 192 (216)
Q Consensus 153 ~~i~C~--~C~~w~H~~Cv~~~--~~~~----~~~~~~~C~~C~~~~~ 192 (216)
.-+.|+ .|..-||..|+--- ..+. -.+-...||.|.....
T Consensus 19 p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 19 PDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp --B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 557887 99999999999521 1111 1123568999987655
No 143
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=28.00 E-value=24 Score=27.31 Aligned_cols=17 Identities=29% Similarity=0.919 Sum_probs=13.1
Q ss_pred CceEECCCCCceecCCC
Q 027973 152 DLMVQCEGCSDWFHPNC 168 (216)
Q Consensus 152 ~~~i~C~~C~~w~H~~C 168 (216)
.-.++|..|++||.-.=
T Consensus 12 ~~vv~C~~c~kWFCNg~ 28 (152)
T PF09416_consen 12 SCVVKCNTCNKWFCNGR 28 (152)
T ss_dssp CCEEEETTTTEEEES--
T ss_pred ccEeEcCCCCcEeecCC
Confidence 36799999999998644
No 144
>COG0662 {ManC} Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=27.94 E-value=48 Score=24.41 Aligned_cols=22 Identities=27% Similarity=0.483 Sum_probs=17.3
Q ss_pred EEecCCcEEccCCEEEEecCCC
Q 027973 15 TVKSISKTIKPGDCVLMRPSEP 36 (216)
Q Consensus 15 ~v~g~~~~~~vGD~V~v~~~~~ 36 (216)
.++|..+.++.||+|+|.++-+
T Consensus 71 ~~~~~~~~v~~gd~~~iP~g~~ 92 (127)
T COG0662 71 TIGGEEVEVKAGDSVYIPAGTP 92 (127)
T ss_pred EECCEEEEecCCCEEEECCCCc
Confidence 4555566889999999999874
No 145
>PF04322 DUF473: Protein of unknown function (DUF473); InterPro: IPR007417 This is a family of uncharacterised archaeal proteins.
Probab=27.90 E-value=95 Score=23.04 Aligned_cols=29 Identities=24% Similarity=0.529 Sum_probs=21.8
Q ss_pred EEccCCEEEEecCCC-----CCCCeEEEEEEEEe
Q 027973 22 TIKPGDCVLMRPSEP-----SKPSYVAKIERIES 50 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~-----~~~~~IarI~~i~~ 50 (216)
.+.+||+|++-+... +..-.||+|.++.-
T Consensus 38 ~~~~Gd~VFlT~~~~~Dl~~Gt~GiIa~V~~~~i 71 (119)
T PF04322_consen 38 SLDPGDRVFLTSVSLEDLTPGTEGIIAEVKKIEI 71 (119)
T ss_pred cCCCCCEEEEecCCHHHCCCCCCeEEEEEEEEEE
Confidence 458999999998763 34557888887754
No 146
>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=27.47 E-value=1.9e+02 Score=21.31 Aligned_cols=42 Identities=14% Similarity=0.138 Sum_probs=30.1
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEee
Q 027973 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYR 66 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyR 66 (216)
..|+.||-|.|..+. +.-..|+|.++... .+ .+.|.+.-...
T Consensus 40 ~~IkkGD~V~Vi~Gk--~KGk~GkV~~V~~~-~~-~V~Vegvn~~k 81 (114)
T TIGR01080 40 LPVRKGDKVRIMRGD--FKGHEGKVSKVDLK-RY-RIYVEGVTKEK 81 (114)
T ss_pred ceeecCCEEEEecCC--CCCCEEEEEEEEcC-CC-EEEEcCeEEEC
Confidence 478999999999998 45678999999843 33 45555444333
No 147
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=27.43 E-value=39 Score=23.04 Aligned_cols=28 Identities=29% Similarity=0.688 Sum_probs=21.6
Q ss_pred EEecCCCCCCCceEECC--CCCceecCCCCCCC
Q 027973 142 CKCEMPYNPDDLMVQCE--GCSDWFHPNCINMT 172 (216)
Q Consensus 142 C~C~~~~~~~~~~i~C~--~C~~w~H~~Cv~~~ 172 (216)
.+|+++ .+-.|+|. .|...||..|....
T Consensus 40 ~~C~~~---~Ga~i~C~~~~C~~~fH~~CA~~~ 69 (90)
T PF13771_consen 40 SICKKK---GGACIGCSHPGCSRSFHVPCARKA 69 (90)
T ss_pred cCCCCC---CCeEEEEeCCCCCcEEChHHHccC
Confidence 366665 34789996 79999999998654
No 148
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=27.29 E-value=1.5e+02 Score=22.79 Aligned_cols=28 Identities=25% Similarity=0.450 Sum_probs=19.6
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEE
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIE 49 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~ 49 (216)
.++.||.|.+..+......+|.||..+-
T Consensus 51 ~~~rGDiVvf~~~~~~~~~~iKRVig~p 78 (163)
T TIGR02227 51 DPKRGDIVVFKDPDDNKNIYVKRVIGLP 78 (163)
T ss_pred CCCCCcEEEEecCCCCCceeEEEEEecC
Confidence 4677888888765434567888888774
No 149
>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=27.21 E-value=1.7e+02 Score=21.25 Aligned_cols=28 Identities=25% Similarity=0.386 Sum_probs=20.6
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEEe
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIES 50 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~~ 50 (216)
.|++||.+.+..-+. .....++|.+|..
T Consensus 31 ~ikvGD~I~f~~~~~-~~~l~v~V~~i~~ 58 (109)
T cd06555 31 QIKVGDKILFNDLDT-GQQLLVKVVDIRK 58 (109)
T ss_pred cCCCCCEEEEEEcCC-CcEEEEEEEEEEe
Confidence 689999999987653 3456677777765
No 150
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=27.09 E-value=66 Score=23.52 Aligned_cols=21 Identities=24% Similarity=0.558 Sum_probs=17.5
Q ss_pred EEecCCcEEccCCEEEEecCC
Q 027973 15 TVKSISKTIKPGDCVLMRPSE 35 (216)
Q Consensus 15 ~v~g~~~~~~vGD~V~v~~~~ 35 (216)
+++|...+++.||+|++.++.
T Consensus 78 ~~~g~~~~l~~Gd~i~ip~g~ 98 (131)
T COG1917 78 QLEGEKKELKAGDVIIIPPGV 98 (131)
T ss_pred EecCCceEecCCCEEEECCCC
Confidence 456677789999999999976
No 151
>PF00649 Copper-fist: Copper fist DNA binding domain; InterPro: IPR001083 Some fungal transcription factors contain an N-terminal domain, the copper fist, which seems to be involved in copper-dependent DNA-binding [, ]. These proteins activate the transcription of the metallothionein gene in response to copper. Metallothionein maintains copper levels in yeast [, ]. The copper fist domain, which is similar in structure to metallothionein itself, undergoes a large conformational change on copper-binding that allows DNA-binding. The domain contains a conserved array of zinc-binding residues (Cys-X2-Cys-X8-Cys-X-His) and forms a three-stranded antiparallel beta-sheet with two short helical segments that project from one end of the beta-sheet []. Conserved residues form a basic patch that may be important for DNA binding. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0005507 copper ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1CO4_A.
Probab=26.96 E-value=38 Score=20.03 Aligned_cols=14 Identities=29% Similarity=0.662 Sum_probs=12.2
Q ss_pred CCcEEecccccccc
Q 027973 179 LDHFFCESCSTEGQ 192 (216)
Q Consensus 179 ~~~~~C~~C~~~~~ 192 (216)
+.+|.|..|.+.++
T Consensus 6 g~KyAC~~CirGHR 19 (40)
T PF00649_consen 6 GEKYACESCIRGHR 19 (40)
T ss_dssp TEEEEETTTTTTSG
T ss_pred CeEEEhhhhhCccc
Confidence 46899999999887
No 152
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=26.66 E-value=32 Score=29.58 Aligned_cols=36 Identities=19% Similarity=0.517 Sum_probs=23.1
Q ss_pred CCCCceEECCCCCceecCCCCCCChhhhcCCCcEEecccccccc
Q 027973 149 NPDDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEGQ 192 (216)
Q Consensus 149 ~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 192 (216)
-|+..|+.|+.|+...+. .+.+. ..++||.|..-.+
T Consensus 22 ~~~~~~~~c~~c~~~~~~-------~~l~~-~~~vc~~c~~h~r 57 (292)
T PRK05654 22 VPEGLWTKCPSCGQVLYR-------KELEA-NLNVCPKCGHHMR 57 (292)
T ss_pred CCCCCeeECCCccchhhH-------HHHHh-cCCCCCCCCCCee
Confidence 356689999999774432 22322 4579999965443
No 153
>PF14353 CpXC: CpXC protein
Probab=26.64 E-value=45 Score=24.54 Aligned_cols=38 Identities=26% Similarity=0.518 Sum_probs=19.4
Q ss_pred EECCCCCceecC---CCCCCChhh-------hcCCCcEEecccccccc
Q 027973 155 VQCEGCSDWFHP---NCINMTAEE-------AKRLDHFFCESCSTEGQ 192 (216)
Q Consensus 155 i~C~~C~~w~H~---~Cv~~~~~~-------~~~~~~~~C~~C~~~~~ 192 (216)
|.|..|+.-|.. .-|+.+..+ ...+..+.||.|.....
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFR 49 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCcee
Confidence 456666655544 334433222 12245677777765543
No 154
>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=26.47 E-value=1.5e+02 Score=25.10 Aligned_cols=43 Identities=19% Similarity=0.271 Sum_probs=34.7
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecC
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPE 68 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~ 68 (216)
.|.+||.|.|..+. -.-+.|.|.++-.+ .+ .+.|.+.+|-|.-
T Consensus 205 ~f~vGd~VrI~dGP--F~GfeG~I~eid~~-k~-Rv~VlV~IfGR~T 247 (258)
T TIGR01956 205 KFRVGNFVKIVDGP--FKGIVGKIKKIDQE-KK-KAIVEVEILGKSV 247 (258)
T ss_pred CCCCCCEEEEEecC--CCCcEEEEEEEeCC-CC-EEEEEEEecCCcE
Confidence 47899999999987 45689999999763 34 6889999888754
No 155
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=26.44 E-value=22 Score=22.71 Aligned_cols=38 Identities=16% Similarity=0.379 Sum_probs=20.6
Q ss_pred EECCCCCceecCCCCCCChhhh--cCCCcEEecccccccc
Q 027973 155 VQCEGCSDWFHPNCINMTAEEA--KRLDHFFCESCSTEGQ 192 (216)
Q Consensus 155 i~C~~C~~w~H~~Cv~~~~~~~--~~~~~~~C~~C~~~~~ 192 (216)
|.|-.|++-+-.+=-.+....+ ..+..|.|..|.....
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~RI~ 42 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKERIR 42 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHHHh
Confidence 4566666544332222221111 1247899999987665
No 156
>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=25.69 E-value=94 Score=21.83 Aligned_cols=24 Identities=21% Similarity=0.034 Sum_probs=20.3
Q ss_pred ccCCEEEEecCCCCCCCeEEEEEEEE
Q 027973 24 KPGDCVLMRPSEPSKPSYVAKIERIE 49 (216)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~IarI~~i~ 49 (216)
.+||.|...-.. .++|-|+|.+-.
T Consensus 2 ~~GdlVWaK~~g--~pwWPa~V~~~~ 25 (95)
T cd05838 2 LYGDIVWAKLGN--FRWWPAIICDPR 25 (95)
T ss_pred CcCCEEEEECCC--CCCCCeEEcChh
Confidence 479999999887 789999998743
No 157
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=25.53 E-value=52 Score=32.12 Aligned_cols=50 Identities=26% Similarity=0.652 Sum_probs=32.9
Q ss_pred CCceeEE-EecCCCCCCCceEECCCCCceecCCCCCCChhhhcCCCcEEeccccc
Q 027973 136 DRVAVYC-KCEMPYNPDDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCST 189 (216)
Q Consensus 136 ~~~~~~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~ 189 (216)
....+-| +|+.+-+| ...+|..|+.-| +.||.......+. -.|.|+.|..
T Consensus 1114 ~~~~vdc~~cg~~i~~--~~~~c~ec~~kf-P~CiasG~pIt~~-~fWlC~~CkH 1164 (1189)
T KOG2041|consen 1114 NSAKVDCSVCGAKIDP--YDLQCSECQTKF-PVCIASGRPITDN-IFWLCPRCKH 1164 (1189)
T ss_pred CccceeeeecCCcCCc--cCCCChhhcCcC-ceeeccCCccccc-eEEEcccccc
Confidence 3455666 67766543 457899997655 6788655433333 5899999964
No 158
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.30 E-value=33 Score=26.09 Aligned_cols=53 Identities=17% Similarity=0.337 Sum_probs=35.7
Q ss_pred eeEEEecCCCCCCCceEECCCCCceecCCCCCCChhhhcCCCcEEecccccccc
Q 027973 139 AVYCKCEMPYNPDDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEGQ 192 (216)
Q Consensus 139 ~~~C~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 192 (216)
+.+-+|.+.--.|.---.|.-|..-|...|-|--.... +--.|+|..|.+..+
T Consensus 66 atC~IC~KTKFADG~GH~C~YCq~r~CARCGGrv~lrs-NKv~wvcnlc~k~q~ 118 (169)
T KOG3799|consen 66 ATCGICHKTKFADGCGHNCSYCQTRFCARCGGRVSLRS-NKVMWVCNLCRKQQE 118 (169)
T ss_pred cchhhhhhcccccccCcccchhhhhHHHhcCCeeeecc-CceEEeccCCcHHHH
Confidence 34447777655555556688888888888887432222 225799999987766
No 159
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=25.30 E-value=1.2e+02 Score=21.70 Aligned_cols=28 Identities=25% Similarity=0.215 Sum_probs=17.4
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEEEEEe
Q 027973 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIES 50 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~IarI~~i~~ 50 (216)
.-+..||.|.|...+- ..-=|+|+..+.
T Consensus 58 IwI~~GD~VlVe~~~~--~~~kg~Iv~r~~ 85 (100)
T PRK04012 58 MWIREGDVVIVAPWDF--QDEKADIIWRYT 85 (100)
T ss_pred EEecCCCEEEEEeccc--CCCEEEEEEEcC
Confidence 4567788888876552 244566666553
No 160
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=25.26 E-value=47 Score=31.42 Aligned_cols=35 Identities=20% Similarity=0.573 Sum_probs=26.3
Q ss_pred ceEECCC-CCceecCCCCCCChhhhcCCCcEEecccccccc
Q 027973 153 LMVQCEG-CSDWFHPNCINMTAEEAKRLDHFFCESCSTEGQ 192 (216)
Q Consensus 153 ~~i~C~~-C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 192 (216)
.-|.|.. |+-.+.+.|.--... ..|+|+.|...+.
T Consensus 52 epv~C~~pC~avlnpyC~id~r~-----~~W~CpfCnqrn~ 87 (755)
T COG5047 52 EPVKCTAPCKAVLNPYCHIDERN-----QSWICPFCNQRNT 87 (755)
T ss_pred CCceecccchhhcCcceeeccCC-----ceEecceecCCCC
Confidence 3467776 888999999854332 5799999988774
No 161
>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=24.94 E-value=99 Score=15.65 Aligned_cols=15 Identities=33% Similarity=0.461 Sum_probs=10.3
Q ss_pred EEEEEEecCCCCeEEE
Q 027973 44 KIERIESDARGANVKV 59 (216)
Q Consensus 44 rI~~i~~~~~~~~~~v 59 (216)
.|..|.+|++| .+|+
T Consensus 6 ~I~~i~~D~~G-~lWi 20 (24)
T PF07494_consen 6 NIYSIYEDSDG-NLWI 20 (24)
T ss_dssp CEEEEEE-TTS-CEEE
T ss_pred eEEEEEEcCCc-CEEE
Confidence 36788888888 6765
No 162
>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=24.85 E-value=86 Score=25.72 Aligned_cols=28 Identities=21% Similarity=0.498 Sum_probs=16.6
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEEe
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIES 50 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~~ 50 (216)
.+++||+|++...+ .......+|.+|..
T Consensus 105 ~V~~Gd~v~~~~~~-~~~~~~~~V~~v~~ 132 (217)
T PF01079_consen 105 DVRVGDCVLVSDEG-GGKLRPSRVVRVST 132 (217)
T ss_dssp G--TT-EEEEE-TT-T--EEEEEEEEEEE
T ss_pred hCCCCCEEEEEEcC-CCcEEEEEEEEEEE
Confidence 47999999994443 25677888888866
No 163
>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=24.65 E-value=1.3e+02 Score=21.11 Aligned_cols=21 Identities=29% Similarity=0.616 Sum_probs=11.1
Q ss_pred EEecCCcEEccCCEEEEecCC
Q 027973 15 TVKSISKTIKPGDCVLMRPSE 35 (216)
Q Consensus 15 ~v~g~~~~~~vGD~V~v~~~~ 35 (216)
.++|....++.||.+++.++.
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 344444566777777777765
No 164
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=24.42 E-value=55 Score=23.38 Aligned_cols=16 Identities=38% Similarity=0.790 Sum_probs=13.0
Q ss_pred eEEEEEEEEeecCCCC
Q 027973 56 NVKVHVRWYYRPEESI 71 (216)
Q Consensus 56 ~~~v~v~WfyRp~d~~ 71 (216)
...|+|.|||.++|..
T Consensus 76 g~~V~v~Wyyd~dD~~ 91 (99)
T PF09345_consen 76 GGKVTVNWYYDEDDED 91 (99)
T ss_pred CCcEEEEEEECCCCch
Confidence 3679999999988754
No 165
>PF04085 MreC: rod shape-determining protein MreC; InterPro: IPR007221 MreC (murein formation C) is involved in the rod shape determination in Escherichia coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped.; GO: 0008360 regulation of cell shape; PDB: 2J5U_B 2QF4_B 2QF5_A.
Probab=24.41 E-value=2.9e+02 Score=20.97 Aligned_cols=45 Identities=24% Similarity=0.214 Sum_probs=26.8
Q ss_pred CcEEccCCEEEEecCCC--CCCCeEEEEEEEEecCCCCeEEEEEEEE
Q 027973 20 SKTIKPGDCVLMRPSEP--SKPSYVAKIERIESDARGANVKVHVRWY 64 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~~--~~~~~IarI~~i~~~~~~~~~~v~v~Wf 64 (216)
+..++.||.|+-...+. +....||+|.++..+..+....+.+.=+
T Consensus 91 ~~~i~~GD~V~TSG~~~~fP~Gi~VG~V~~v~~~~~~~~~~~~v~p~ 137 (152)
T PF04085_consen 91 DADIKKGDIVVTSGLGGIFPPGIPVGTVSSVEPDKSGLFKEVYVKPA 137 (152)
T ss_dssp TS---TT-EEEEE-TTSSS-CCEEEEEEEEEECTTTCCCEEEEEEES
T ss_pred CCCCCCCCEEEECCCCCcCCCCCEEEEEEEEEeCCCCcEEEEEEEEC
Confidence 35789999998765442 2456899999999987763444554433
No 166
>TIGR03214 ura-cupin putative allantoin catabolism protein. This model represents a protein containing a tandem arrangement of cupin domains (N-terminal part of pfam07883 and C-terminal more distantly related to pfam00190). This protein is found in the vicinity of genes involved in the catabolism of allantoin, a breakdown product of urate and sometimes of urate iteslf. The distribution of pathway components in the genomes in which this family is observed suggests that the function is linked to the allantoate catabolism to glyoxylate pathway (GenProp0686) since it is sometimes found in genomes lacking any elements of the xanthine-to-allantoin pathways (e.g. in Enterococcus faecalis).
Probab=23.85 E-value=75 Score=26.68 Aligned_cols=20 Identities=10% Similarity=0.375 Sum_probs=14.8
Q ss_pred EecCCcEEccCCEEEEecCC
Q 027973 16 VKSISKTIKPGDCVLMRPSE 35 (216)
Q Consensus 16 v~g~~~~~~vGD~V~v~~~~ 35 (216)
++|....+..||++|+.++.
T Consensus 95 ~~g~~~~L~~Gd~~y~pa~~ 114 (260)
T TIGR03214 95 AEGETHELREGGYAYLPPGS 114 (260)
T ss_pred ECCEEEEECCCCEEEECCCC
Confidence 34444577889999998876
No 167
>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=23.82 E-value=1.8e+02 Score=20.10 Aligned_cols=39 Identities=26% Similarity=0.419 Sum_probs=28.6
Q ss_pred EccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCC
Q 027973 23 IKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEE 69 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d 69 (216)
...||.|.-.-.+ -++|-|+|++.- ...+.|++|-...|
T Consensus 7 ~~p~dLVwAK~kG--yp~WPAkV~~~~------~~~~~V~FFG~t~~ 45 (83)
T cd05841 7 RPPHELVWAKLKG--FPYWPAKVMRVE------DNQVDVRFFGGQHD 45 (83)
T ss_pred CCCCCEEEEeCCC--CCCCCEEEeecC------CCeEEEEEcCCCCC
Confidence 4689999988877 789999998642 13477888874333
No 168
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=23.68 E-value=1.9e+02 Score=19.42 Aligned_cols=38 Identities=16% Similarity=0.343 Sum_probs=23.9
Q ss_pred eEEEecCCcEEccCCEEEEecCCCC---CCCeEEEEEEEEe
Q 027973 13 SYTVKSISKTIKPGDCVLMRPSEPS---KPSYVAKIERIES 50 (216)
Q Consensus 13 ~~~v~g~~~~~~vGD~V~v~~~~~~---~~~~IarI~~i~~ 50 (216)
.|.+..++-.|++||.+.+..=++. .....++|..|-.
T Consensus 19 tfEiRkNDRdf~VGD~L~L~E~~~~~YTGr~~~~~Ityi~~ 59 (72)
T PF12961_consen 19 TFEIRKNDRDFQVGDILVLREWDNGEYTGREIEAEITYITD 59 (72)
T ss_pred eEEEEecCCCCCCCCEEEEEEecCCCccccEEEEEEEEEee
Confidence 3455555568999999999875532 2334566666643
No 169
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=23.67 E-value=1.3e+02 Score=21.83 Aligned_cols=30 Identities=17% Similarity=0.240 Sum_probs=24.3
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEEEEEecC
Q 027973 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDA 52 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~ 52 (216)
..++.||.|+|.++. +.---|+|.++....
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 368899999999998 556788888888743
No 170
>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=23.59 E-value=88 Score=20.68 Aligned_cols=26 Identities=23% Similarity=0.307 Sum_probs=18.1
Q ss_pred eeeeEEEecCCcEEccCCEEEEecCC
Q 027973 10 TLESYTVKSISKTIKPGDCVLMRPSE 35 (216)
Q Consensus 10 ~y~~~~v~g~~~~~~vGD~V~v~~~~ 35 (216)
....+.+++.+...++||.|.|..--
T Consensus 31 ~~kk~~aHD~~~~~~vGD~V~I~e~r 56 (69)
T PF00366_consen 31 RTKKYMAHDENNICKVGDKVRIRECR 56 (69)
T ss_dssp EEEEEEEE-TTSSSTTTSEEEEEEEE
T ss_pred ccccEEEeCCccCCCCCCEEEEEeee
Confidence 34566777766677899999997643
No 171
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=23.36 E-value=53 Score=21.18 Aligned_cols=57 Identities=19% Similarity=0.391 Sum_probs=27.5
Q ss_pred CCCCceeEE-EecCCCCCCCceEECCCCCceecCCCCCCChhh-----hcCCCcEEecccccc
Q 027973 134 NPDRVAVYC-KCEMPYNPDDLMVQCEGCSDWFHPNCINMTAEE-----AKRLDHFFCESCSTE 190 (216)
Q Consensus 134 ~p~~~~~~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~-----~~~~~~~~C~~C~~~ 190 (216)
.|+.....| +|....+-...-..|..|+..|...|....... ......-+|..|...
T Consensus 4 ~~d~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~~~~~~~~~~~~~~RvC~~C~~~ 66 (69)
T PF01363_consen 4 VPDSEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRIPLPTPSSGSGEPVRVCDSCYSK 66 (69)
T ss_dssp SSGGG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEEEET--GGTESEEEEE-HHHHHH
T ss_pred CCCCCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEEcccccccCCCCcCEECHHHHHH
Confidence 455556666 577777544556779999999999998743211 111135677777543
No 172
>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=22.37 E-value=1.6e+02 Score=25.26 Aligned_cols=33 Identities=15% Similarity=0.275 Sum_probs=26.5
Q ss_pred cEEccCCEEEEecCCCCCCCeEEEEEEEEecCCC
Q 027973 21 KTIKPGDCVLMRPSEPSKPSYVAKIERIESDARG 54 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~ 54 (216)
..++.||+|||.++-... +-=+.|.+|.+.++.
T Consensus 153 v~v~~Gd~i~ipaGt~HA-~~g~~~~Eiq~~SD~ 185 (302)
T TIGR00218 153 IKLKPGDFFYVPSGTPHA-YKGGLVLEVMQNSDN 185 (302)
T ss_pred cccCCCCEEEeCCCCccc-ccCceEEEEEcCCCc
Confidence 367999999999998755 555689999986665
No 173
>PRK03187 tgl transglutaminase; Provisional
Probab=22.31 E-value=73 Score=27.06 Aligned_cols=14 Identities=36% Similarity=0.933 Sum_probs=12.9
Q ss_pred EEccCCEEEEecCC
Q 027973 22 TIKPGDCVLMRPSE 35 (216)
Q Consensus 22 ~~~vGD~V~v~~~~ 35 (216)
.+-+||+||+.++|
T Consensus 165 ~~~PGD~vYFkNPd 178 (272)
T PRK03187 165 DFLPGDCVYFKNPD 178 (272)
T ss_pred CCCCCcEEEecCCC
Confidence 78999999999977
No 174
>PF08921 DUF1904: Domain of unknown function (DUF1904); InterPro: IPR015017 This entry represents a family of hypothetical bacterial proteins. ; PDB: 1U9D_B.
Probab=22.01 E-value=32 Score=25.06 Aligned_cols=16 Identities=31% Similarity=0.428 Sum_probs=9.9
Q ss_pred eEEEEEEEEeecCCCC
Q 027973 56 NVKVHVRWYYRPEESI 71 (216)
Q Consensus 56 ~~~v~v~WfyRp~d~~ 71 (216)
-.+|.|.||-|+.|+.
T Consensus 55 ~pfVEV~WF~R~qe~q 70 (108)
T PF08921_consen 55 YPFVEVLWFDRGQEVQ 70 (108)
T ss_dssp --EEEEEES---HHHH
T ss_pred ceeEEEEEecCCHHHH
Confidence 4689999999999875
No 175
>KOG3896 consensus Dynactin, subunit p62 [Cell motility]
Probab=21.75 E-value=1e+02 Score=27.27 Aligned_cols=8 Identities=38% Similarity=1.165 Sum_probs=3.7
Q ss_pred eecCCCCC
Q 027973 163 WFHPNCIN 170 (216)
Q Consensus 163 w~H~~Cv~ 170 (216)
.|++.|+.
T Consensus 46 hfCp~CLE 53 (449)
T KOG3896|consen 46 HFCPRCLE 53 (449)
T ss_pred ccchhhcc
Confidence 34445544
No 176
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=21.72 E-value=51 Score=28.20 Aligned_cols=34 Identities=15% Similarity=0.462 Sum_probs=23.1
Q ss_pred CCceEECCCCCceecCCCCCCChhhhcCCCcEEecccccccc
Q 027973 151 DDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEGQ 192 (216)
Q Consensus 151 ~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 192 (216)
++.|+.|..|+...|..= +.. +.++||.|..-.+
T Consensus 25 e~lw~KCp~c~~~~y~~e-------L~~-n~~vcp~c~~h~r 58 (294)
T COG0777 25 EGLWTKCPSCGEMLYRKE-------LES-NLKVCPKCGHHMR 58 (294)
T ss_pred CCceeECCCccceeeHHH-------HHh-hhhcccccCcccc
Confidence 679999999976544322 221 5689999965544
No 177
>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=21.29 E-value=1.7e+02 Score=22.97 Aligned_cols=38 Identities=21% Similarity=0.230 Sum_probs=27.4
Q ss_pred EEEecCCcEEccCCEEEEecCCCCCCCeEEEEEEEEecCCC
Q 027973 14 YTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIESDARG 54 (216)
Q Consensus 14 ~~v~g~~~~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~ 54 (216)
+.+......++.||.|...-+. ..+.||.|.+-.. .+|
T Consensus 98 L~~~~~~~~~q~GDIVtw~l~~--~~~HIgIVSd~r~-~~G 135 (164)
T PF06940_consen 98 LTTDINPEDWQPGDIVTWRLPG--GLPHIGIVSDRRS-KDG 135 (164)
T ss_pred ccCCCChhhcCCCCEEEEeCCC--CCCeEEEEeCCcC-CCC
Confidence 3334444589999999998665 5789999988765 344
No 178
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=21.28 E-value=52 Score=31.75 Aligned_cols=52 Identities=25% Similarity=0.597 Sum_probs=31.1
Q ss_pred ceeEE-EecCCCCCC----CceEECC--CCCceecCCCCCCCh---hhh--cCCCcEEeccccc
Q 027973 138 VAVYC-KCEMPYNPD----DLMVQCE--GCSDWFHPNCINMTA---EEA--KRLDHFFCESCST 189 (216)
Q Consensus 138 ~~~~C-~C~~~~~~~----~~~i~C~--~C~~w~H~~Cv~~~~---~~~--~~~~~~~C~~C~~ 189 (216)
..+.| ||.....+. .-..+|. .|+.-||..|....- ++. .....-||-.|..
T Consensus 116 fnKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~ 179 (900)
T KOG0956|consen 116 FNKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKY 179 (900)
T ss_pred hcceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccccccccceechhHHH
Confidence 34455 776553332 2446775 999999999985331 111 1114568999954
No 179
>KOG3896 consensus Dynactin, subunit p62 [Cell motility]
Probab=21.16 E-value=89 Score=27.58 Aligned_cols=48 Identities=27% Similarity=0.620 Sum_probs=26.7
Q ss_pred CceeEEEecCCCCCCCceEECCCCCceecCCCCCCChhhhcCCCcEEeccccccc
Q 027973 137 RVAVYCKCEMPYNPDDLMVQCEGCSDWFHPNCINMTAEEAKRLDHFFCESCSTEG 191 (216)
Q Consensus 137 ~~~~~C~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~ 191 (216)
+..--|.|+. .+|-...++|.-|-+.-...||--. . +.-+|+.|....
T Consensus 8 rvkY~c~cg~-~~pl~~L~FCRyC~klrc~~Cv~hE---v---dshfCp~CLEn~ 55 (449)
T KOG3896|consen 8 RVKYECTCGK-FRPLPDLVFCRYCFKLRCDDCVLHE---V---DSHFCPRCLENS 55 (449)
T ss_pred ceeEEeeccc-cccccceeeeecccccccccccccc---c---ccccchhhccCC
Confidence 3344566663 3444566777777777777776321 1 345566665444
No 180
>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=20.70 E-value=2.3e+02 Score=21.75 Aligned_cols=45 Identities=16% Similarity=0.308 Sum_probs=34.4
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCCC
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEES 70 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d~ 70 (216)
.+..||.|.|..+. -.-+.|.|.++.. .++ ...|.+.+|-+...+
T Consensus 119 ~~~~G~~V~I~~Gp--f~G~~g~v~~~~~-~~~-r~~V~v~~~g~~~~v 163 (172)
T TIGR00922 119 DFEVGEQVRVNDGP--FANFTGTVEEVDY-EKS-KLKVSVSIFGRETPV 163 (172)
T ss_pred CCCCCCEEEEeecC--CCCcEEEEEEEcC-CCC-EEEEEEEECCCceEE
Confidence 47899999999876 4568999999754 334 688999888876544
No 181
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=20.64 E-value=3.1e+02 Score=19.17 Aligned_cols=39 Identities=18% Similarity=0.202 Sum_probs=24.0
Q ss_pred eeeEEEecCCcEEccCCEEEEecCCCCCCCeEEEEEEEE
Q 027973 11 LESYTVKSISKTIKPGDCVLMRPSEPSKPSYVAKIERIE 49 (216)
Q Consensus 11 y~~~~v~g~~~~~~vGD~V~v~~~~~~~~~~IarI~~i~ 49 (216)
...+.++++...+++||.|.|..--|.+.--=-+|.++.
T Consensus 44 ~kK~~aHde~~~~k~GD~V~I~EtRPLSKtK~~~vv~i~ 82 (87)
T COG0186 44 SKKYHAHDECNEAKVGDIVRIAETRPLSKTKRFVVVEIV 82 (87)
T ss_pred EeeeEeecccccCCCCCEEEEEEccccCCcceEEEEEEe
Confidence 344555666667899999999887654433223344443
No 182
>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=20.18 E-value=1.6e+02 Score=19.67 Aligned_cols=25 Identities=24% Similarity=0.412 Sum_probs=18.2
Q ss_pred eeEEEecCCcEEccCCEEEEecCCC
Q 027973 12 ESYTVKSISKTIKPGDCVLMRPSEP 36 (216)
Q Consensus 12 ~~~~v~g~~~~~~vGD~V~v~~~~~ 36 (216)
..+.+++.....++||.|.|..--|
T Consensus 38 kk~~aHD~~~~~k~GD~V~I~ecrP 62 (71)
T TIGR03635 38 KKYHAHDENNECKVGDVVRIIETRP 62 (71)
T ss_pred EEEEEECCCCCCCCCCEEEEEEcCC
Confidence 3455666656789999999987654
No 183
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=20.09 E-value=2.3e+02 Score=21.67 Aligned_cols=42 Identities=21% Similarity=0.219 Sum_probs=31.4
Q ss_pred EEccCCEEEEecCCCCCCCeEEEEEEEEecCCCCeEEEEEEEEeecCC
Q 027973 22 TIKPGDCVLMRPSEPSKPSYVAKIERIESDARGANVKVHVRWYYRPEE 69 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~IarI~~i~~~~~~~~~~v~v~WfyRp~d 69 (216)
.+.+||.|.|..+. -.-+.|+|.++... +. . +.+..+-+.-.
T Consensus 94 ~~~~G~~V~I~~Gp--f~g~~g~V~~vd~~-k~--~-v~v~ll~~~~~ 135 (153)
T PRK08559 94 GIKEGDIVELIAGP--FKGEKARVVRVDES-KE--E-VTVELLEAAVP 135 (153)
T ss_pred CCCCCCEEEEeccC--CCCceEEEEEEcCC-CC--E-EEEEEECCcce
Confidence 48999999999987 45689999999774 22 2 67777666544
Done!