Query 027964
Match_columns 216
No_of_seqs 196 out of 1746
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 04:11:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027964.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027964hhsearch_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 4.8E-32 1E-36 202.3 11.1 121 20-156 1-121 (121)
2 cd04713 BAH_plant_3 BAH, or Br 100.0 1.2E-30 2.6E-35 200.5 12.9 129 2-133 2-134 (146)
3 cd04716 BAH_plantDCM_I BAH, or 100.0 1.4E-30 3.1E-35 193.6 11.9 113 20-133 1-118 (122)
4 cd04717 BAH_polybromo BAH, or 100.0 5.5E-29 1.2E-33 186.1 10.9 115 20-134 1-118 (121)
5 cd04370 BAH BAH, or Bromo Adja 100.0 4.3E-28 9.4E-33 180.6 10.5 115 20-134 1-121 (123)
6 smart00439 BAH Bromo adjacent 100.0 8.6E-28 1.9E-32 178.7 11.9 113 22-134 1-118 (120)
7 PF01426 BAH: BAH domain; Int 100.0 5.5E-28 1.2E-32 179.5 10.7 112 21-134 1-117 (119)
8 cd04710 BAH_fungalPHD BAH, or 99.9 1.8E-27 3.9E-32 180.0 12.3 116 16-133 5-134 (135)
9 cd04709 BAH_MTA BAH, or Bromo 99.9 1.3E-27 2.8E-32 185.9 11.5 115 21-136 2-140 (164)
10 cd04721 BAH_plant_1 BAH, or Br 99.9 3.2E-27 6.9E-32 177.9 9.9 108 19-128 4-117 (130)
11 cd04715 BAH_Orc1p_like BAH, or 99.9 8.3E-26 1.8E-30 175.2 11.6 107 3-113 12-127 (159)
12 cd04760 BAH_Dnmt1_I BAH, or Br 99.9 3.6E-25 7.8E-30 163.8 10.3 112 20-133 1-124 (124)
13 cd04708 BAH_plantDCM_II BAH, o 99.9 1.6E-24 3.4E-29 172.5 12.2 115 20-134 5-144 (202)
14 cd04712 BAH_DCM_I BAH, or Brom 99.9 2.8E-24 6E-29 161.9 12.9 110 20-134 3-127 (130)
15 KOG1886 BAH domain proteins [T 99.9 1.9E-24 4E-29 189.1 11.5 181 5-190 34-219 (464)
16 cd04718 BAH_plant_2 BAH, or Br 99.9 4.4E-26 9.6E-31 172.3 0.5 96 37-133 50-145 (148)
17 cd04720 BAH_Orc1p_Yeast BAH, o 99.9 7.1E-24 1.5E-28 168.0 12.8 116 19-135 49-177 (179)
18 cd04719 BAH_Orc1p_animal BAH, 99.9 2.1E-22 4.6E-27 150.5 8.7 109 21-130 2-123 (128)
19 cd04711 BAH_Dnmt1_II BAH, or B 99.9 9.9E-22 2.1E-26 146.1 8.0 108 27-134 14-134 (137)
20 KOG1827 Chromatin remodeling c 99.4 1.6E-13 3.5E-18 124.9 6.7 123 20-142 188-313 (629)
21 PF00628 PHD: PHD-finger; Int 99.1 2.6E-11 5.6E-16 76.6 0.9 48 140-188 1-50 (51)
22 KOG1973 Chromatin remodeling p 99.0 1.1E-10 2.3E-15 98.8 2.2 52 136-192 217-271 (274)
23 COG5034 TNG2 Chromatin remodel 98.9 4.6E-10 9.9E-15 91.5 2.6 49 136-189 219-270 (271)
24 KOG3554 Histone deacetylase co 98.9 7.9E-11 1.7E-15 103.0 -2.3 115 22-137 5-165 (693)
25 smart00249 PHD PHD zinc finger 98.9 1.5E-09 3.3E-14 66.6 2.9 44 142-186 4-47 (47)
26 KOG1632 Uncharacterized PHD Zn 98.6 2.2E-08 4.8E-13 87.1 2.2 113 80-193 3-117 (345)
27 KOG4323 Polycomb-like PHD Zn-f 98.1 1.2E-06 2.5E-11 78.1 2.2 55 136-191 169-226 (464)
28 KOG2752 Uncharacterized conser 97.4 9E-05 2E-09 62.6 2.0 40 132-171 122-167 (345)
29 KOG0825 PHD Zn-finger protein 96.9 0.00051 1.1E-08 64.5 2.4 55 137-193 214-270 (1134)
30 KOG0955 PHD finger protein BR1 96.9 0.0023 5E-08 62.8 6.5 54 137-193 219-273 (1051)
31 KOG1244 Predicted transcriptio 96.8 0.00042 9.2E-09 57.5 1.0 51 139-191 282-333 (336)
32 PF13831 PHD_2: PHD-finger; PD 96.6 0.00031 6.7E-09 40.8 -0.8 35 151-187 2-36 (36)
33 KOG0957 PHD finger protein [Ge 96.4 0.0024 5.3E-08 57.3 3.0 53 137-190 543-599 (707)
34 KOG1512 PHD Zn-finger protein 96.3 0.00096 2.1E-08 55.9 -0.2 44 142-189 319-363 (381)
35 KOG1844 PHD Zn-finger proteins 96.2 0.0023 5E-08 58.7 1.7 55 136-192 84-138 (508)
36 KOG4299 PHD Zn-finger protein 95.7 0.0031 6.7E-08 58.0 0.4 53 140-193 255-309 (613)
37 KOG0954 PHD finger protein [Ge 95.7 0.0084 1.8E-07 56.2 3.1 54 137-193 270-325 (893)
38 KOG1632 Uncharacterized PHD Zn 95.7 0.00081 1.8E-08 58.8 -3.4 58 136-193 237-300 (345)
39 cd04718 BAH_plant_2 BAH, or Br 93.8 0.043 9.3E-07 42.0 2.1 33 163-196 2-34 (148)
40 KOG0383 Predicted helicase [Ge 92.7 0.071 1.5E-06 50.6 2.2 46 141-191 51-96 (696)
41 KOG1512 PHD Zn-finger protein 92.4 0.046 1E-06 46.0 0.5 37 151-187 277-315 (381)
42 PF07227 DUF1423: Protein of u 91.9 0.14 3.1E-06 45.8 3.0 52 141-192 132-195 (446)
43 PF07496 zf-CW: CW-type Zinc F 90.9 0.079 1.7E-06 33.0 0.3 33 152-185 2-34 (50)
44 KOG2626 Histone H3 (Lys4) meth 90.4 0.24 5.2E-06 45.2 3.0 55 135-189 17-76 (544)
45 KOG1245 Chromatin remodeling c 90.2 0.05 1.1E-06 55.5 -1.6 54 136-191 1106-1160(1404)
46 PF09926 DUF2158: Uncharacteri 90.1 0.62 1.3E-05 29.4 3.8 41 23-67 1-41 (53)
47 PF14446 Prok-RING_1: Prokaryo 89.8 0.22 4.7E-06 31.5 1.5 30 139-168 6-36 (54)
48 KOG0957 PHD finger protein [Ge 88.5 0.35 7.6E-06 43.9 2.5 54 136-189 118-179 (707)
49 KOG4443 Putative transcription 88.2 0.081 1.7E-06 49.3 -1.6 50 139-188 146-201 (694)
50 PF11302 DUF3104: Protein of u 87.5 1.9 4.2E-05 29.1 5.1 30 22-51 5-39 (75)
51 cd05834 HDGF_related The PWWP 86.2 1.5 3.2E-05 30.3 4.1 43 22-66 2-44 (83)
52 COG5415 Predicted integral mem 86.2 0.57 1.2E-05 37.9 2.3 53 154-211 193-250 (251)
53 cd05835 Dnmt3b_related The PWW 84.5 1.5 3.2E-05 30.5 3.5 41 23-65 1-44 (87)
54 PF13832 zf-HC5HC2H_2: PHD-zin 84.0 0.43 9.4E-06 34.4 0.7 31 137-170 54-87 (110)
55 cd06080 MUM1_like Mutated mela 83.8 2.2 4.7E-05 29.3 4.0 39 23-66 1-39 (80)
56 PF15446 zf-PHD-like: PHD/FYVE 83.6 1.1 2.4E-05 35.1 2.7 46 150-195 14-66 (175)
57 PF08940 DUF1918: Domain of un 83.1 1.9 4.1E-05 27.6 3.2 39 24-63 4-42 (58)
58 KOG0956 PHD finger protein AF1 81.8 0.76 1.6E-05 43.4 1.5 52 138-192 6-60 (900)
59 COG5076 Transcription factor i 81.6 0.29 6.3E-06 43.3 -1.3 88 20-107 274-361 (371)
60 PF11717 Tudor-knot: RNA bindi 81.4 4.7 0.0001 25.3 4.7 36 23-61 1-36 (55)
61 COG5141 PHD zinc finger-contai 81.2 0.6 1.3E-05 42.4 0.6 46 140-188 195-242 (669)
62 COG4014 Uncharacterized protei 80.1 6.2 0.00013 27.5 5.1 39 24-68 10-52 (97)
63 PF13639 zf-RING_2: Ring finge 80.0 0.15 3.3E-06 30.4 -2.5 40 142-187 5-44 (44)
64 cd05162 PWWP The PWWP domain, 79.1 3.5 7.6E-05 28.3 3.9 40 23-64 1-46 (87)
65 PF13341 RAG2_PHD: RAG2 PHD do 78.2 1.5 3.2E-05 29.1 1.6 34 152-185 29-67 (78)
66 PF00467 KOW: KOW motif; Inte 76.7 6.4 0.00014 21.7 3.8 26 25-52 1-26 (32)
67 PF09871 DUF2098: Uncharacteri 76.6 6.9 0.00015 27.5 4.7 43 22-70 2-47 (91)
68 smart00293 PWWP domain with co 76.2 5 0.00011 25.9 3.7 40 23-64 1-47 (63)
69 KOG4628 Predicted E3 ubiquitin 75.6 4.6 0.0001 35.4 4.4 50 139-193 231-280 (348)
70 PF10781 DSRB: Dextransucrase 75.5 15 0.00033 23.3 5.5 44 24-69 2-52 (62)
71 PRK10708 hypothetical protein; 74.5 17 0.00037 23.1 5.5 43 24-68 2-51 (62)
72 PF07154 DUF1392: Protein of u 74.1 10 0.00023 28.8 5.3 50 7-67 74-123 (150)
73 cd05840 SPBC215_ISWI_like The 73.7 4.3 9.3E-05 28.6 3.1 40 23-64 1-49 (93)
74 PF07649 C1_3: C1-like domain; 72.9 0.88 1.9E-05 24.9 -0.5 26 142-168 5-30 (30)
75 COG1370 Prefoldin, molecular c 71.7 3.2 6.9E-05 31.9 2.1 39 5-45 94-132 (155)
76 PF02081 TrpBP: Tryptophan RNA 71.1 16 0.00035 24.3 5.1 47 58-104 19-65 (75)
77 PF10383 Clr2: Transcription-s 70.9 26 0.00057 26.5 7.1 51 10-62 2-69 (139)
78 PRK13251 transcription attenua 70.6 20 0.00043 23.9 5.4 47 58-104 19-65 (75)
79 PF13922 PHD_3: PHD domain of 69.1 0.84 1.8E-05 29.9 -1.2 32 136-172 31-62 (69)
80 PF00855 PWWP: PWWP domain; I 68.9 3.8 8.2E-05 27.8 1.9 40 23-64 1-43 (86)
81 cd03703 aeIF5B_II aeIF5B_II: T 66.6 17 0.00036 26.6 4.9 45 3-52 9-53 (110)
82 PRK12281 rplX 50S ribosomal pr 66.5 13 0.00029 25.1 4.2 35 22-59 6-40 (76)
83 smart00739 KOW KOW (Kyprides, 65.7 13 0.00027 19.3 3.3 26 23-50 2-27 (28)
84 PF10497 zf-4CXXC_R1: Zinc-fin 65.7 5.6 0.00012 28.7 2.3 31 158-188 35-69 (105)
85 KOG1568 Mitochondrial inner me 65.7 21 0.00046 27.9 5.6 67 21-103 67-147 (174)
86 PF13771 zf-HC5HC2H: PHD-like 64.1 3.6 7.8E-05 28.3 1.1 31 138-171 36-69 (90)
87 KOG4443 Putative transcription 63.2 2.5 5.4E-05 39.8 0.1 41 150-190 32-72 (694)
88 CHL00141 rpl24 ribosomal prote 62.9 16 0.00035 25.1 4.1 36 22-60 8-43 (83)
89 PF04810 zf-Sec23_Sec24: Sec23 61.8 3.8 8.2E-05 24.0 0.7 35 153-192 2-36 (40)
90 PF15057 DUF4537: Domain of un 60.3 16 0.00035 27.1 4.0 40 22-61 55-95 (124)
91 KOG1473 Nucleosome remodeling 59.4 3.1 6.8E-05 41.6 0.1 52 141-192 1126-1177(1414)
92 TIGR00270 conserved hypothetic 59.3 5 0.00011 31.1 1.2 34 155-192 2-35 (154)
93 PRK00004 rplX 50S ribosomal pr 58.5 20 0.00043 25.9 4.1 36 22-60 4-39 (105)
94 PF00130 C1_1: Phorbol esters/ 58.3 8.5 0.00018 23.5 1.9 35 137-171 10-46 (53)
95 PF13901 DUF4206: Domain of un 57.4 5.7 0.00012 32.1 1.3 31 152-192 171-201 (202)
96 cd03701 IF2_IF5B_II IF2_IF5B_I 55.0 38 0.00083 23.7 5.1 41 3-52 9-49 (95)
97 cd03702 IF2_mtIF2_II This fami 54.8 34 0.00073 24.1 4.7 42 3-53 9-50 (95)
98 PRK08359 transcription factor; 54.7 5.7 0.00012 31.5 0.8 35 155-192 8-42 (176)
99 smart00064 FYVE Protein presen 54.6 9.4 0.0002 24.7 1.7 56 134-189 6-65 (68)
100 TIGR02227 sigpep_I_bact signal 53.2 51 0.0011 25.4 6.0 28 22-49 51-78 (163)
101 cd00350 rubredoxin_like Rubred 53.0 10 0.00023 21.1 1.5 25 155-190 3-27 (33)
102 cd00730 rubredoxin Rubredoxin; 52.9 9.9 0.00021 23.6 1.5 36 155-190 3-44 (50)
103 TIGR01079 rplX_bact ribosomal 52.8 27 0.00058 25.2 4.0 35 22-59 3-37 (104)
104 PF13913 zf-C2HC_2: zinc-finge 52.8 5.1 0.00011 20.9 0.2 13 153-165 2-14 (25)
105 PRK01191 rpl24p 50S ribosomal 52.1 36 0.00079 25.2 4.6 41 21-64 44-84 (120)
106 PF02318 FYVE_2: FYVE-type zin 52.0 4.4 9.5E-05 29.7 -0.2 53 138-194 54-108 (118)
107 PTZ00112 origin recognition co 51.8 29 0.00063 34.8 5.2 95 9-105 441-577 (1164)
108 KOG1941 Acetylcholine receptor 51.7 2 4.4E-05 38.0 -2.3 68 136-208 363-432 (518)
109 COG5475 Uncharacterized small 51.3 62 0.0013 20.6 4.9 37 22-67 4-40 (60)
110 PF00301 Rubredoxin: Rubredoxi 51.0 22 0.00047 21.7 2.8 37 154-190 2-44 (47)
111 PF11926 DUF3444: Domain of un 49.7 39 0.00084 27.7 4.9 56 10-67 15-70 (217)
112 cd05836 N_Pac_NP60 The PWWP do 49.2 27 0.00058 24.1 3.4 42 23-66 1-46 (86)
113 cd06541 ASCH ASC-1 homology or 49.1 36 0.00079 24.2 4.3 43 6-50 14-56 (105)
114 PTZ00194 60S ribosomal protein 48.9 42 0.0009 25.7 4.6 42 21-65 45-86 (143)
115 cd05837 MSH6_like The PWWP dom 48.7 24 0.00052 25.5 3.2 43 22-66 2-53 (110)
116 PF03107 C1_2: C1 domain; Int 48.3 17 0.00037 19.7 1.9 26 142-168 5-30 (30)
117 KOG2752 Uncharacterized conser 47.4 15 0.00033 31.7 2.3 56 135-193 50-105 (345)
118 cd06555 ASCH_PF0470_like ASC-1 47.1 48 0.001 24.1 4.6 44 6-50 15-58 (109)
119 PF09465 LBR_tudor: Lamin-B re 46.8 23 0.00051 22.4 2.5 30 22-52 5-34 (55)
120 KOG1740 Predicted mitochondria 45.9 16 0.00035 26.1 1.8 29 9-37 36-64 (107)
121 KOG2846 Predicted membrane pro 45.9 21 0.00046 31.0 3.0 51 154-209 221-276 (328)
122 PF03144 GTP_EFTU_D2: Elongati 45.3 55 0.0012 21.1 4.4 30 22-51 12-41 (74)
123 PF13717 zinc_ribbon_4: zinc-r 44.3 17 0.00036 20.8 1.5 13 150-162 22-34 (36)
124 smart00743 Agenet Tudor-like d 43.9 31 0.00067 21.6 2.9 28 22-50 2-29 (61)
125 COG0198 RplX Ribosomal protein 43.4 50 0.0011 23.8 4.1 37 22-63 4-40 (104)
126 PF11793 FANCL_C: FANCL C-term 43.2 10 0.00022 25.1 0.5 42 152-193 19-68 (70)
127 smart00109 C1 Protein kinase C 42.8 9.2 0.0002 22.5 0.3 33 138-170 11-44 (49)
128 KOG3799 Rab3 effector RIM1 and 42.1 10 0.00023 28.6 0.5 51 142-193 70-120 (169)
129 PF05502 Dynactin_p62: Dynacti 41.7 18 0.00038 33.3 2.0 33 161-193 26-65 (483)
130 TIGR01080 rplX_A_E ribosomal p 40.6 69 0.0015 23.5 4.6 42 21-65 40-81 (114)
131 PF07494 Reg_prop: Two compone 39.5 44 0.00095 16.9 2.5 15 44-58 6-20 (24)
132 PF05207 zf-CSL: CSL zinc fing 39.2 11 0.00024 23.7 0.2 25 140-164 20-51 (55)
133 PF09378 HAS-barrel: HAS barre 38.9 43 0.00094 22.6 3.3 37 12-51 13-49 (91)
134 PF06940 DUF1287: Domain of un 38.4 41 0.0009 26.2 3.3 43 13-58 97-139 (164)
135 PF12678 zf-rbx1: RING-H2 zinc 38.3 5.8 0.00012 26.5 -1.3 31 152-187 43-73 (73)
136 KOG2133 Transcriptional corepr 37.5 22 0.00048 35.3 2.0 113 20-133 143-281 (1229)
137 KOG1829 Uncharacterized conser 36.7 7 0.00015 36.7 -1.4 34 152-193 530-563 (580)
138 smart00652 eIF1a eukaryotic tr 36.3 64 0.0014 22.1 3.7 28 21-50 42-69 (83)
139 cd06530 S26_SPase_I The S26 Ty 36.3 74 0.0016 21.1 4.1 25 23-47 32-56 (85)
140 COG0250 NusG Transcription ant 36.2 82 0.0018 24.9 4.8 46 21-69 122-167 (178)
141 COG1096 Predicted RNA-binding 36.0 1.5E+02 0.0032 23.8 6.1 19 142-160 154-172 (188)
142 CHL00142 rps17 ribosomal prote 35.8 1.3E+02 0.0028 20.8 5.1 28 12-39 40-67 (84)
143 PF12503 CMV_1a_C: Cucumber mo 35.6 1.2E+02 0.0027 20.8 4.8 42 45-88 20-71 (85)
144 PRK05610 rpsQ 30S ribosomal pr 34.4 1.3E+02 0.0028 20.7 5.0 26 13-38 44-69 (84)
145 cd05793 S1_IF1A S1_IF1A: Trans 34.2 66 0.0014 21.7 3.4 28 21-50 37-64 (77)
146 PF00667 FAD_binding_1: FAD bi 33.9 51 0.0011 26.6 3.4 22 14-35 33-54 (219)
147 PF11132 SplA: Transcriptional 33.8 30 0.00065 23.2 1.6 25 22-47 5-29 (75)
148 PF10844 DUF2577: Protein of u 33.7 31 0.00068 24.4 1.9 21 22-42 76-96 (100)
149 PF10367 Vps39_2: Vacuolar sor 33.2 37 0.00081 23.6 2.2 29 139-169 79-108 (109)
150 cd04456 S1_IF1A_like S1_IF1A_l 33.0 60 0.0013 22.0 3.1 29 21-50 37-65 (78)
151 KOG3896 Dynactin, subunit p62 32.8 50 0.0011 29.0 3.2 25 162-187 46-71 (449)
152 PF07754 DUF1610: Domain of un 32.7 30 0.00065 18.0 1.2 11 177-187 13-23 (24)
153 CHL00174 accD acetyl-CoA carbo 32.0 23 0.0005 30.4 1.1 37 149-193 34-70 (296)
154 COG3257 GlxB Uncharacterized p 31.8 1.5E+02 0.0033 24.5 5.7 46 16-73 98-144 (264)
155 PF01176 eIF-1a: Translation i 31.6 55 0.0012 21.1 2.6 25 21-47 40-64 (65)
156 PF12961 DUF3850: Domain of Un 31.4 85 0.0018 21.0 3.5 37 13-49 19-58 (72)
157 cd05838 WHSC1_related The PWWP 31.1 68 0.0015 22.5 3.2 23 24-48 2-24 (95)
158 TIGR01956 NusG_myco NusG famil 30.8 1.1E+02 0.0023 25.8 4.8 44 22-68 205-248 (258)
159 KOG2041 WD40 repeat protein [G 30.5 47 0.001 32.2 2.9 51 135-189 1114-1165(1189)
160 PF01363 FYVE: FYVE zinc finge 30.3 33 0.00072 22.1 1.4 57 133-189 4-66 (69)
161 PF02559 CarD_CdnL_TRCF: CarD- 30.1 72 0.0016 22.1 3.2 24 23-52 2-25 (98)
162 COG2888 Predicted Zn-ribbon RN 30.0 50 0.0011 21.3 2.1 46 139-188 10-58 (61)
163 PF06689 zf-C4_ClpX: ClpX C4-t 29.9 23 0.00049 20.8 0.5 11 179-189 23-33 (41)
164 KOG1244 Predicted transcriptio 29.4 15 0.00033 31.0 -0.4 37 151-187 244-282 (336)
165 KOG2879 Predicted E3 ubiquitin 28.3 39 0.00084 28.7 1.8 49 137-191 238-287 (298)
166 cd04466 S1_YloQ_GTPase S1_YloQ 28.2 64 0.0014 20.4 2.5 25 22-50 37-61 (68)
167 PRK05654 acetyl-CoA carboxylas 27.9 31 0.00067 29.6 1.2 38 148-193 22-59 (292)
168 PF14085 DUF4265: Domain of un 27.4 1.2E+02 0.0025 22.1 4.0 40 22-67 25-64 (117)
169 PRK14872 rod shape-determining 27.2 4.3E+02 0.0094 23.2 8.1 38 20-57 258-297 (337)
170 PF09345 DUF1987: Domain of un 27.0 46 0.001 23.7 1.8 17 54-70 75-91 (99)
171 PF08921 DUF1904: Domain of un 27.0 26 0.00056 25.4 0.5 17 54-70 54-70 (108)
172 KOG0956 PHD finger protein AF1 27.0 72 0.0016 30.8 3.4 54 135-188 114-179 (900)
173 KOG2932 E3 ubiquitin ligase in 26.7 26 0.00057 30.3 0.5 30 140-172 92-122 (389)
174 TIGR00515 accD acetyl-CoA carb 26.2 39 0.00085 28.9 1.5 37 148-192 21-57 (285)
175 PF04322 DUF473: Protein of un 26.2 1.1E+02 0.0024 22.6 3.6 29 22-50 38-71 (119)
176 COG1773 Rubredoxin [Energy pro 25.5 57 0.0012 20.7 1.8 12 177-188 33-44 (55)
177 PF01079 Hint: Hint module; I 25.5 89 0.0019 25.6 3.4 28 22-50 105-132 (217)
178 PF12861 zf-Apc11: Anaphase-pr 25.4 24 0.00051 24.5 0.0 63 115-192 21-83 (85)
179 PF09416 UPF1_Zn_bind: RNA hel 25.3 30 0.00066 26.7 0.6 17 151-167 12-28 (152)
180 TIGR00922 nusG transcription t 25.2 1.6E+02 0.0036 22.5 4.8 45 22-69 119-163 (172)
181 PRK06424 transcription factor; 25.1 33 0.00072 26.2 0.8 32 156-191 3-34 (144)
182 PF04085 MreC: rod shape-deter 25.0 2.3E+02 0.005 21.5 5.5 45 20-64 91-138 (152)
183 PRK04012 translation initiatio 24.9 1.2E+02 0.0025 21.7 3.5 26 22-49 59-84 (100)
184 PF00366 Ribosomal_S17: Riboso 24.8 46 0.001 22.0 1.3 24 11-34 32-55 (69)
185 PRK04980 hypothetical protein; 24.1 1.2E+02 0.0025 21.9 3.4 37 14-50 22-59 (102)
186 COG0777 AccD Acetyl-CoA carbox 23.9 40 0.00087 28.7 1.1 37 149-193 24-60 (294)
187 PF13912 zf-C2H2_6: C2H2-type 23.6 38 0.00082 17.3 0.6 10 155-164 3-12 (27)
188 PF14353 CpXC: CpXC protein 22.9 63 0.0014 23.7 1.9 40 154-193 2-51 (128)
189 PF05180 zf-DNL: DNL zinc fing 22.8 27 0.00058 23.0 -0.1 18 146-163 22-39 (66)
190 PF08274 PhnA_Zn_Ribbon: PhnA 22.7 47 0.001 18.2 0.9 11 179-189 18-28 (30)
191 COG4127 Uncharacterized conser 22.7 53 0.0012 28.0 1.6 41 22-63 72-117 (318)
192 PRK13922 rod shape-determining 22.5 3.4E+02 0.0074 22.6 6.6 42 21-62 213-257 (276)
193 cd03694 GTPBP_II Domain II of 22.5 2.2E+02 0.0048 19.2 4.5 29 22-51 26-54 (87)
194 cd05841 BS69_related The PWWP 22.5 1.5E+02 0.0032 20.4 3.5 39 23-68 7-45 (83)
195 COG0186 RpsQ Ribosomal protein 22.5 2.5E+02 0.0054 19.5 4.6 27 13-39 46-72 (87)
196 KOG1708 Mitochondrial/chloropl 22.3 1.9E+02 0.004 23.6 4.5 71 20-92 70-149 (236)
197 TIGR03635 S17_bact 30S ribosom 22.3 1.1E+02 0.0023 20.4 2.7 23 13-35 39-61 (71)
198 PF06003 SMN: Survival motor n 22.0 1.3E+02 0.0029 25.3 3.9 30 21-51 67-96 (264)
199 TIGR01955 RfaH transcriptional 21.5 1.5E+02 0.0032 22.4 3.8 42 22-67 108-149 (159)
200 PF09986 DUF2225: Uncharacteri 21.5 48 0.001 26.9 1.1 41 153-193 5-61 (214)
201 smart00333 TUDOR Tudor domain. 21.2 1.9E+02 0.004 17.4 3.6 28 22-51 2-29 (57)
202 smart00451 ZnF_U1 U1-like zinc 21.1 43 0.00094 18.2 0.6 11 154-164 4-14 (35)
203 PF13719 zinc_ribbon_5: zinc-r 20.6 71 0.0015 18.1 1.4 31 154-189 3-34 (37)
204 cd00162 RING RING-finger (Real 20.4 17 0.00038 20.4 -1.3 30 156-189 15-44 (45)
205 smart00647 IBR In Between Ring 20.1 1.1E+02 0.0024 18.9 2.5 21 150-170 37-57 (64)
No 1
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.98 E-value=4.8e-32 Score=202.30 Aligned_cols=121 Identities=47% Similarity=0.857 Sum_probs=108.6
Q ss_pred CeEEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeecccccCCcccccCCCCeeeeeCccceeecceeeee
Q 027964 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGK 99 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~d~~~~~~~~~~~~ELF~s~~~d~~~~~~I~gk 99 (216)
|++|++||+|||.+++.+.++|||+|.+||++.+|.++|+|+|||||+||.+++...++++|||+|++.|++++.+|.||
T Consensus 1 ~~~~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~~g~~~~~v~WfyrPeEt~~~~~~~~~~~EvF~S~~~d~~~~~~I~gk 80 (121)
T cd04714 1 KEIIRVGDCVLFKSPGRPSLPYVARIESLWEDPEGNMVVRVKWYYRPEETKGGRKPNHGEKELFASDHQDENSVQTIEHK 80 (121)
T ss_pred CCEEEcCCEEEEeCCCCCCCCEEEEEEEEEEcCCCCEEEEEEEEEcHHHccCcccccCCCCceEecCCcccccHHHhCcc
Confidence 46999999999999875678999999999999889999999999999999999888899999999999999999999999
Q ss_pred eEEEeeeccccccCCCCcceEEeeeeecccCcccCCCCcceEEeCCCCCCCCceEeC
Q 027964 100 CTVHTFKNYTKLENVGAEDYFCRFEYKAATGGFTPDRVAVYCKCEMPYNPDDLMVQC 156 (216)
Q Consensus 100 c~V~~~~~~~~~~~~~~~~ffcr~~yd~~~~~f~p~~~~~~C~C~~~~~~~~~~i~C 156 (216)
|.|+++++|.++....+ .+......|+|..+||++..||||
T Consensus 81 c~V~~~~ey~~~~~~~~----------------~~~~~~d~~~Ce~~yn~~~~~~~c 121 (121)
T cd04714 81 CYVLTFAEYERLARVKK----------------KPQDGVDFYYCAGTYNPDTGMLKC 121 (121)
T ss_pred cEEEehhHheecccccC----------------CCCcCCCEEEEeccCCCCcCcccC
Confidence 99999999987654322 234577889999999999999998
No 2
>cd04713 BAH_plant_3 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.97 E-value=1.2e-30 Score=200.53 Aligned_cols=129 Identities=28% Similarity=0.462 Sum_probs=113.8
Q ss_pred CCCCCCCcceeeEEEcCCCeEEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeecccccCCcc---cccCC
Q 027964 2 AKTKPGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGR---RQFHG 78 (216)
Q Consensus 2 ~~~~~~~~~y~~~~v~~~~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~d~~~~~---~~~~~ 78 (216)
-|+++++++|.++.++| .+|++||+|||.+++. .++|||+|.+||+..++.++|+|+|||||+|+.... ...++
T Consensus 2 ~~~~~~~~~y~s~~~dg--~~y~vgD~Vlv~~~~~-~~pyI~~I~~i~~~~~~~~~v~V~WFyRpeEi~~~~~~~~~~~~ 78 (146)
T cd04713 2 GKGKKKKCHYTSFEKDG--NKYRLEDCVLLVPEDD-QKPYIAIIKDIYKQEEGSLKLEVQWLYRPEEIEKKKGGNWKAED 78 (146)
T ss_pred CCCccceeeeeeEEECC--EEEECCCEEEEeCCCC-CCCEEEEEEEEEEcCCCCEEEEEEeeECHHHhccccccccccCC
Confidence 37788999999999986 6999999999999874 899999999999988899999999999999997542 22346
Q ss_pred CCeeeeeCccceeecceeeeeeEEEeeeccccccCC-CCcceEEeeeeecccCccc
Q 027964 79 AKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLENV-GAEDYFCRFEYKAATGGFT 133 (216)
Q Consensus 79 ~~ELF~s~~~d~~~~~~I~gkc~V~~~~~~~~~~~~-~~~~ffcr~~yd~~~~~f~ 133 (216)
++|||+|++.|.+++++|.|||.|++.+++.+++.. ..++||||+.||...++|.
T Consensus 79 ~~ElF~S~~~d~~~~~~I~gkc~V~~~~~~~~~~~~~~~~~F~cr~~yD~~~~~~~ 134 (146)
T cd04713 79 PRELFYSFHRDEVPAESVLHPCKVAFVPKGKQIPLRKGHSGFIVRRVYDNVNKKLW 134 (146)
T ss_pred CCeEEEeCCCCcCCHHHCcceeEEEECCccccCCccCCCCeEEEEEEEcCCCCcEe
Confidence 899999999999999999999999999888877665 5678999999999988775
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=1.4e-30 Score=193.56 Aligned_cols=113 Identities=17% Similarity=0.342 Sum_probs=103.6
Q ss_pred CeEEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeecccccCCcc-cccCCCCeeeeeCccceeecceeee
Q 027964 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGR-RQFHGAKELFLSDHYDVQSAHTIEG 98 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~d~~~~~-~~~~~~~ELF~s~~~d~~~~~~I~g 98 (216)
|+.|++||+|||.+++ +.++|||||++||++.+|..+++|+|||||+||..++ ...++++|||+|++.|++|+++|.|
T Consensus 1 g~~~~lgD~V~v~~~~-~~~~yi~rI~~i~e~~~g~~~~~v~WyyRpeet~~~r~~~~~~~rEvFlS~~~D~~pl~~I~~ 79 (122)
T cd04716 1 GITYNLGDDAYVQGGE-GEEPFICKITEFFEGTDGKTYFTAQWFYRAEDTVIERQATNHDKKRVFYSEIKNDNPLDCLIS 79 (122)
T ss_pred CcEEEcCCEEEEECCC-CCCCEEEEEEEEEEcCCCceEEEEEEEEcHHHhccccccccCCCceEEEecccCccchhheee
Confidence 4689999999999997 4899999999999999999999999999999999886 5578899999999999999999999
Q ss_pred eeEEEeeeccccc----cCCCCcceEEeeeeecccCccc
Q 027964 99 KCTVHTFKNYTKL----ENVGAEDYFCRFEYKAATGGFT 133 (216)
Q Consensus 99 kc~V~~~~~~~~~----~~~~~~~ffcr~~yd~~~~~f~ 133 (216)
||+|++++++..+ ...+.++|||++.|+....+|.
T Consensus 80 Kc~V~~~~~~~~~~~~~~~~~~~df~c~~~Y~~~~~tF~ 118 (122)
T cd04716 80 KVKILQVPPNVGTKRKKPNSEKCDYYYDMEYCVPYSTFQ 118 (122)
T ss_pred eeEEEEeCCCCCcccccccCCCceEEEeeEeccchhheE
Confidence 9999999988766 4567889999999999988886
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=99.96 E-value=5.5e-29 Score=186.05 Aligned_cols=115 Identities=27% Similarity=0.491 Sum_probs=104.2
Q ss_pred CeEEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeecccccCCcccccCCCCeeeeeCccceeecceeeee
Q 027964 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGK 99 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~d~~~~~~~~~~~~ELF~s~~~d~~~~~~I~gk 99 (216)
|..|++||+|||.+++.++++|||+|.+||++.+|..+|+|+|||||+||.++....+.++|||+|++.|.+|+.+|.||
T Consensus 1 g~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~Wf~rP~et~~~~~~~~~~~Evfls~~~d~~~~~~I~~k 80 (121)
T cd04717 1 GLQYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGK 80 (121)
T ss_pred CCEEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEEEEEeChHHccCCCccccccCceEEcCccccccHHHhcCe
Confidence 46899999999999876688999999999999999999999999999999888777789999999999999999999999
Q ss_pred eEEEeeeccccccCC---CCcceEEeeeeecccCcccC
Q 027964 100 CTVHTFKNYTKLENV---GAEDYFCRFEYKAATGGFTP 134 (216)
Q Consensus 100 c~V~~~~~~~~~~~~---~~~~ffcr~~yd~~~~~f~p 134 (216)
|.|++.++|.+..+. ..+.|||++.||...+.|..
T Consensus 81 c~Vl~~~~y~~~~p~~~~~~dvy~ce~~y~~~~~~~~~ 118 (121)
T cd04717 81 CAVMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKK 118 (121)
T ss_pred eEEEehHHHhcCCCCCCCCCCEEEEeEEECcccccEec
Confidence 999999999877643 34679999999999888764
No 5
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=99.95 E-value=4.3e-28 Score=180.56 Aligned_cols=115 Identities=39% Similarity=0.772 Sum_probs=103.8
Q ss_pred CeEEccCCeEEEccCCC--CCCCeEEEEeEEEEcCCCCEEEEEEEeecccccCCcccccCCCCeeeeeCccceeecceee
Q 027964 20 NKVVRPGDCVLMRPADS--DKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIE 97 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~~--~~~~~I~~I~~i~~~~~g~~~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~ 80 (123)
T cd04370 1 GITYEVGDSVYVEPDDSIKSDPPYIARIEELWEDTNGSKQVKVRWFYRPEETPKGLSPFALRRELFLSDHLDEIPVESII 80 (123)
T ss_pred CCEEecCCEEEEecCCcCCCCCCEEEEEeeeeECCCCCEEEEEEEEEchhHhccccccccccceeEEecCccccCHHHhc
Confidence 46899999999999874 4789999999999999999999999999999999987778899999999999999999999
Q ss_pred eeeEEEeeecccccc----CCCCcceEEeeeeecccCcccC
Q 027964 98 GKCTVHTFKNYTKLE----NVGAEDYFCRFEYKAATGGFTP 134 (216)
Q Consensus 98 gkc~V~~~~~~~~~~----~~~~~~ffcr~~yd~~~~~f~p 134 (216)
|||.|++.+++.+.. ....+.||||+.||+.++.|.+
T Consensus 81 gkc~V~~~~~~~~~~~~~~~~~~~~f~~r~~yd~~~~~fk~ 121 (123)
T cd04370 81 GKCKVLFVSEFEGLKQRPNKIDTDDFFCRLAYDPTTKEFKA 121 (123)
T ss_pred cccEEEechHhhccccccccCCCCeEEEEEEECcCcceEEe
Confidence 999999999987653 2356789999999999888764
No 6
>smart00439 BAH Bromo adjacent homology domain.
Probab=99.95 E-value=8.6e-28 Score=178.67 Aligned_cols=113 Identities=38% Similarity=0.744 Sum_probs=102.6
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCC-EEEEEEEeecccccCCcccccCCCCeeeeeCccceeecceeeeee
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNN-VKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKC 100 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~-~~v~v~Wfyrp~d~~~~~~~~~~~~ELF~s~~~d~~~~~~I~gkc 100 (216)
+|++||+|||.+++.+.++|||+|.+||+..++. ++++|+|||||+||+.+....++++|||+|++.+++++++|.|||
T Consensus 1 ~~~vgd~V~v~~~~~~~~~~i~~I~~i~~~~~~~~~~~~v~Wf~rp~e~~~~~~~~~~~~Elf~s~~~~~i~~~~I~~kc 80 (120)
T smart00439 1 TIRVGDFVLVEPDDADEPYYIGRIEEIFETKKNSEKMVRVRWFYRPEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGKC 80 (120)
T ss_pred CcccCCEEEEeCCCCCCCCEEEEEEEEEECCCCCEEEEEEEEEEChhhccccccccCCCcceEEEccCccCChHHeeeEE
Confidence 4789999999999866799999999999999888 899999999999999987777899999999999999999999999
Q ss_pred EEEeeeccccccCC----CCcceEEeeeeecccCcccC
Q 027964 101 TVHTFKNYTKLENV----GAEDYFCRFEYKAATGGFTP 134 (216)
Q Consensus 101 ~V~~~~~~~~~~~~----~~~~ffcr~~yd~~~~~f~p 134 (216)
.|++.+++...... ..+.||||+.||..++.|.+
T Consensus 81 ~V~~~~~~~~~~~~~~~~~~~~f~cr~~yd~~~~~f~~ 118 (120)
T smart00439 81 NVLSKSDYPGLRPEGKIGEPDVFFCESLYDPEKGAFKK 118 (120)
T ss_pred EEEEcchhcccccccCCCCCCeEEEEEEEccccCcccC
Confidence 99999999766543 35789999999999998864
No 7
>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation. The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation [].; GO: 0003677 DNA binding; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 3SWR_A 3PTA_A 1M4Z_A 1ZBX_A ....
Probab=99.95 E-value=5.5e-28 Score=179.54 Aligned_cols=112 Identities=38% Similarity=0.779 Sum_probs=100.1
Q ss_pred eEEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCC--EEEEEEEeecccccCCcccccCCCCeeeeeCccceeecceeee
Q 027964 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNN--VKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEG 98 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~--~~v~v~Wfyrp~d~~~~~~~~~~~~ELF~s~~~d~~~~~~I~g 98 (216)
++|++||+|||.+++.+.++|||+|++||++.++. ++++|+|||||+||..+ ....++|||+|++++.+|+++|.|
T Consensus 1 ~~~~vGD~V~v~~~~~~~~~~v~~I~~i~~~~~~~~~~~~~v~Wf~rp~d~~~~--~~~~~~Elf~s~~~~~~~~~~I~g 78 (119)
T PF01426_consen 1 VTYKVGDFVYVKPDDPPEPPYVARIEEIWEDKDGNKEKMVKVRWFYRPEDTSLG--KTFSPRELFLSDHCDDIPVESIRG 78 (119)
T ss_dssp EEEETTSEEEEECTSTTSEEEEEEEEEEEEETTTSEEEEEEEEEEEEGGGSTTG--GHSCTTEEEEEEEEEEEEGGGEEE
T ss_pred CEEeCCCEEEEeCCCCCCCCEEEEEEEEEcCCCCCEEEEEEEEEeECccccccc--ccCCCCEEEEECcEeEEehhhEEe
Confidence 48999999999999878999999999999998887 99999999999999333 335669999999999999999999
Q ss_pred eeEEEeeeccccccCC---CCcceEEeeeeecccCcccC
Q 027964 99 KCTVHTFKNYTKLENV---GAEDYFCRFEYKAATGGFTP 134 (216)
Q Consensus 99 kc~V~~~~~~~~~~~~---~~~~ffcr~~yd~~~~~f~p 134 (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 9999999998776643 57889999999999999875
No 8
>cd04710 BAH_fungalPHD BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.95 E-value=1.8e-27 Score=180.04 Aligned_cols=116 Identities=21% Similarity=0.444 Sum_probs=100.5
Q ss_pred EcCCCeEEccCCeEEEccCCCCCCCeEEEEeEEEEcCC------------CCEEEEEEEeecccccCCcccccCCCCeee
Q 027964 16 IKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHR------------NNVKVRVRWYYRPEESIGGRRQFHGAKELF 83 (216)
Q Consensus 16 v~~~~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~------------g~~~v~v~Wfyrp~d~~~~~~~~~~~~ELF 83 (216)
+..+|..|++||+|||.+++++.|+|||||++|+...+ +.+.|+|+|||||+|+.... .++.+|||
T Consensus 5 ~~~~g~~~~vgD~Vyv~~~~~~ePyyIgrI~e~~~~~~~~~~~~~~~~~~~~~~vrV~wfYRp~Di~~~~--~~d~relf 82 (135)
T cd04710 5 VLKNGELLKVNDHIYMSSEPPGEPYYIGRIMEFVPKHEFPSGIHARVFPASYFQVRLNWYYRPRDISRRV--VADSRLLY 82 (135)
T ss_pred EccCCeEEeCCCEEEEecCCCCCCCEEEEEEEEEecCCCCccccccccCCCcEEEEEEEEeCHHHcCCcc--cCCceEEE
Confidence 34457899999999999998889999999999998542 23789999999999985444 57999999
Q ss_pred eeCccceeecceeeeeeEEEeeeccccccCC--CCcceEEeeeeecccCccc
Q 027964 84 LSDHYDVQSAHTIEGKCTVHTFKNYTKLENV--GAEDYFCRFEYKAATGGFT 133 (216)
Q Consensus 84 ~s~~~d~~~~~~I~gkc~V~~~~~~~~~~~~--~~~~ffcr~~yd~~~~~f~ 133 (216)
+|+|.|++|+++|+|||+|.+.+++..+... .++.|||.+.||+.+.+|.
T Consensus 83 ~S~h~d~~p~~si~gKC~V~~~~di~~l~~~~~~~~~Fyf~~lyD~~~~r~~ 134 (135)
T cd04710 83 ASMHSDICPIGSVRGKCTVRHRDQIPDLEEYKKRPNHFYFDQLFDRYILRYY 134 (135)
T ss_pred EEeeEeeechHHEEeEEEEEEecccchhhhhccCCCEEEEEeeeCcchhhcc
Confidence 9999999999999999999999988766543 5788999999999998875
No 9
>cd04709 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.95 E-value=1.3e-27 Score=185.88 Aligned_cols=115 Identities=24% Similarity=0.467 Sum_probs=101.3
Q ss_pred eEEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeecccccCCcc----------------------cccCC
Q 027964 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGR----------------------RQFHG 78 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~d~~~~~----------------------~~~~~ 78 (216)
..|++||+|||.++. +.+++||+|++|+.+.+|.++++|+|||||+|++... ....+
T Consensus 2 ~~yrvGD~Vy~~~~~-~~Py~I~rI~e~~~~~~~~~~vkV~wfYRp~DI~~~~~~l~~~~r~~~~~~~~~~~~~~~~~~~ 80 (164)
T cd04709 2 NMYRVGDYVYFESSP-NNPYLIRRIEELNKTARGHVEAKVVCYYRRRDIPDSLYQLADQHRRELEEKSDDLTPKQRHQLR 80 (164)
T ss_pred cEEecCCEEEEECCC-CCCCEEEEEEEEEeCCCCCEEEEEEEEEChhHccchhhhhcccccccccccccccchhhhhccC
Confidence 489999999999984 5689999999999999999999999999999986421 12357
Q ss_pred CCeeeeeCccceeecceeeeeeEEEeeeccccccCC--CCcceEEeeeeecccCcccCCC
Q 027964 79 AKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLENV--GAEDYFCRFEYKAATGGFTPDR 136 (216)
Q Consensus 79 ~~ELF~s~~~d~~~~~~I~gkc~V~~~~~~~~~~~~--~~~~ffcr~~yd~~~~~f~p~~ 136 (216)
.+|||+|++.|.+|+.+|+|||.|++++++..+... .++.|||+..||+.+++|..++
T Consensus 81 ~rELF~S~~~d~~p~~~IrGKC~V~~~~d~~~l~~~~~~~d~Ff~~~~YDP~~k~l~~~~ 140 (164)
T cd04709 81 HRELFLSRQVETLPATHIRGKCSVTLLNDTESARSYLAREDTFFYSLVYDPEQKTLLADQ 140 (164)
T ss_pred cceeEEecccccccHHHeeeeEEEEEehhhhhhhhccCCCCEEEEEEEECCCCCeecccc
Confidence 999999999999999999999999999999887654 5688999999999999998754
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=99.94 E-value=3.2e-27 Score=177.93 Aligned_cols=108 Identities=27% Similarity=0.441 Sum_probs=97.2
Q ss_pred CCeEEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeecccccCCccccc-CCCCeeeeeCccceeecceee
Q 027964 19 TNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQF-HGAKELFLSDHYDVQSAHTIE 97 (216)
Q Consensus 19 ~~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~d~~~~~~~~-~~~~ELF~s~~~d~~~~~~I~ 97 (216)
+|.++++||+|||.+++ +++|||+|++||++.+|.++++|+||+||+|+.++..+. +.++|||+|++.|.+++++|.
T Consensus 4 ~~~~i~vGD~V~v~~~~--~~~~va~Ie~i~ed~~g~~~v~v~WF~~p~E~~~~~~~~~~~~~EvFlS~~~d~i~~~~I~ 81 (130)
T cd04721 4 NGVTISVHDFVYVLSEE--EDRYVAYIEDLYEDKKGSKMVKVRWFHTTDEVGAALSPDSVNPREIFLSPNLQVISVECID 81 (130)
T ss_pred CCEEEECCCEEEEeCCC--CCcEEEEEEEEEEcCCCCEEEEEEEecCHHHhccccCCCCCCCCeEEEcCCccccchHHee
Confidence 35799999999999887 788999999999999999999999999999999876555 899999999999999999999
Q ss_pred eeeEEEeeeccccccCCC-----CcceEEeeeeecc
Q 027964 98 GKCTVHTFKNYTKLENVG-----AEDYFCRFEYKAA 128 (216)
Q Consensus 98 gkc~V~~~~~~~~~~~~~-----~~~ffcr~~yd~~ 128 (216)
|||.|++.++|.++.... .++||||+.||..
T Consensus 82 gk~~Vls~~~y~k~~~~~~~~~~~~~f~C~~~~d~~ 117 (130)
T cd04721 82 GLATVLTREHYEKFQSVPKNSSELQAYFCYRQIDNN 117 (130)
T ss_pred eeeEECCHHHHhhhhccccCccccccEEEEEEecCC
Confidence 999999999998765432 4589999999876
No 11
>cd04715 BAH_Orc1p_like BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins. Orc1 is part of the Yeast Sir1-origin recognition complex, the Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.93 E-value=8.3e-26 Score=175.21 Aligned_cols=107 Identities=24% Similarity=0.357 Sum_probs=92.4
Q ss_pred CCCCCCcceeeEEEcCCCeEEccCCeEEEccCCCCCCCeEEEEeEEEEcCC--CCEEEEEEEeecccccCCccc--ccCC
Q 027964 3 KTKPGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHR--NNVKVRVRWYYRPEESIGGRR--QFHG 78 (216)
Q Consensus 3 ~~~~~~~~y~~~~v~~~~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~--g~~~v~v~Wfyrp~d~~~~~~--~~~~ 78 (216)
.+++++++|.++.++| ++|++||+|||.+++ .++|||+|.+||+..+ |.++++|+|||||+||..... +.+.
T Consensus 12 ~~~~~~~~Y~s~~~~g--~~y~lGD~Vlv~s~~--~~~yIgkI~~iwe~~~~~g~~~~~v~WfyRp~E~~~~~~~~~~~~ 87 (159)
T cd04715 12 GKKKDGQFYRSFTYDG--VEYRLYDDVYVHNGD--SEPYIGKIIKIYETAIDSGKKKVKVIWFFRPSEIRMELKGEPKRH 87 (159)
T ss_pred cccCCceEEEEEEECC--EEEeCCCEEEEeCCC--CCCEEEEEEEEEEcCCcCCceEEEEEeeeCHHHhccccccCcccC
Confidence 3567888999999986 699999999999866 8999999999999765 889999999999999986432 3578
Q ss_pred CCeeeeeCcc-----ceeecceeeeeeEEEeeeccccccC
Q 027964 79 AKELFLSDHY-----DVQSAHTIEGKCTVHTFKNYTKLEN 113 (216)
Q Consensus 79 ~~ELF~s~~~-----d~~~~~~I~gkc~V~~~~~~~~~~~ 113 (216)
++|||+|.|. +++|+++|.|||.|+++++|....+
T Consensus 88 ~nEvFlS~~~d~~~~~~n~l~sI~gKC~Vl~~~ey~~~~~ 127 (159)
T cd04715 88 INEVFLACGRGEGLANINLLESIIGKCNVVCISEDFRNPQ 127 (159)
T ss_pred CCcEEEecCcCccccccCcHHHccceeEEEEehHhhhCCC
Confidence 9999999986 5589999999999999999975443
No 12
>cd04760 BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.92 E-value=3.6e-25 Score=163.77 Aligned_cols=112 Identities=25% Similarity=0.426 Sum_probs=97.3
Q ss_pred CeEEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeecccccCCcccccCCCCeeeeeCccceeecceeeee
Q 027964 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGK 99 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~d~~~~~~~~~~~~ELF~s~~~d~~~~~~I~gk 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~~K 78 (124)
T cd04760 1 GEELEAGDCVSVKPDDPTKPLYIARVTYMWKDSIGGKMFHAHWFCRGSDTVLGET--SDPLELFLVDECEDMALSSIHGK 78 (124)
T ss_pred CCEEecCCEEEEecCCCCCCcEEEEEhhheecCCCCcEEEEEEEEECCccccccc--CCCcEEEeecccCCcchHHheee
Confidence 4689999999999988789999999999999999999999999999999999986 88999999999999999999999
Q ss_pred eEEEeeeccc--------cc----cCCCCcceEEeeeeecccCccc
Q 027964 100 CTVHTFKNYT--------KL----ENVGAEDYFCRFEYKAATGGFT 133 (216)
Q Consensus 100 c~V~~~~~~~--------~~----~~~~~~~ffcr~~yd~~~~~f~ 133 (216)
|.|.....-. +. .....++|||+.-||+...+|.
T Consensus 79 v~V~~~~p~~~w~~~~g~~~~~~~~~ddg~tffyq~~yd~~~arf~ 124 (124)
T cd04760 79 VNVIYKAPSENWSMEGGMDEEDEIFEDDGKTFFYQKWYDPECARFE 124 (124)
T ss_pred eEEEEeCCCcchhhhcCCCCccccccCCCCeEEEEEeeChhhhccC
Confidence 9999855431 11 1123467999999999888773
No 13
>cd04708 BAH_plantDCM_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.92 E-value=1.6e-24 Score=172.54 Aligned_cols=115 Identities=23% Similarity=0.427 Sum_probs=98.6
Q ss_pred CeEEccCCeEEEccCC-----------------CCCCCeEEEEeEEEEcCCC------CEEEEEEEeecccccCCccccc
Q 027964 20 NKVVRPGDCVLMRPAD-----------------SDKPPYVARVEKIEADHRN------NVKVRVRWYYRPEESIGGRRQF 76 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~-----------------~~~~~~I~~I~~i~~~~~g------~~~v~v~Wfyrp~d~~~~~~~~ 76 (216)
|++|++||+|||.++. ...++.||+|.+|+..+++ .++|+|+|||||+||.......
T Consensus 5 Gv~Y~vgD~VYv~p~~f~~~~~~~~~~~~G~N~~~~p~~I~qI~ei~~~k~~~~~~~~~~~vrVrwFYRPEdt~~~~~y~ 84 (202)
T cd04708 5 GVTYSVGDFLYVSPDAFAEEERERATFKAGRNVGLKAFVVCQVLEIVVEKESKQADVASTQVKVRRFYRPEDVSPEKAYA 84 (202)
T ss_pred CEEEecCCeEEECcccccccccccccccccccCCCCCcEEEEEEEEEecccCCCCCCcceEEEEEEEechhhcCccccee
Confidence 5799999999999981 1358999999999986544 5899999999999986533334
Q ss_pred CCCCeeeeeCccceeecceeeeeeEEEeeeccccccC--CCCcceEEeeeeecccCcccC
Q 027964 77 HGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLEN--VGAEDYFCRFEYKAATGGFTP 134 (216)
Q Consensus 77 ~~~~ELF~s~~~d~~~~~~I~gkc~V~~~~~~~~~~~--~~~~~ffcr~~yd~~~~~f~p 134 (216)
.+.+|||+|++.+++++.+|.|||+|....++..+.. ...+.|||+..||+.++.|..
T Consensus 85 sd~rely~Sde~~~~~~~~I~GKC~V~~~~d~~~~~~~~~~~~~Ffc~~~Yd~~tg~f~~ 144 (202)
T cd04708 85 SDIREVYYSEDTLTVPVEAVEGKCEVRKKSDLPDSDAPVIFEHVFFCELLYDPAKGSLKQ 144 (202)
T ss_pred cCceeEEEeccceeechhHcceEEEEEecCcchhhhccccCCCceEEEEEEcCCCCccCC
Confidence 5999999999999999999999999999988876554 467889999999999999983
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=99.92 E-value=2.8e-24 Score=161.93 Aligned_cols=110 Identities=26% Similarity=0.421 Sum_probs=93.2
Q ss_pred CeEEccCCeEEEccCCCC----------CCCeEEEEeEEEEcCCCCEEEEEEEeecccccCCcccccCCCCeeeeeCccc
Q 027964 20 NKVVRPGDCVLMRPADSD----------KPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYD 89 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~----------~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~d~~~~~~~~~~~~ELF~s~~~d 89 (216)
|..|++||+|+|.+++++ .+++|++|+.|+++.+|.++|+++|||||+||.+++ +++++|||||++++
T Consensus 3 ~~~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~~~g~~~~h~~W~yrp~eTv~g~--~~~~~ElFLSd~c~ 80 (130)
T cd04712 3 GLTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKGSDGSKMFHGRWLYRGCDTVLGN--YANERELFLTNECT 80 (130)
T ss_pred CCEEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeecCCCceEEEEEEEEcchhccccc--cCCCceEEEecccc
Confidence 468999999999998865 388999999999999999999999999999999998 68999999999999
Q ss_pred eeecc----eeeeeeEEEeeeccccccCCCCcceEEeeeee-cccCcccC
Q 027964 90 VQSAH----TIEGKCTVHTFKNYTKLENVGAEDYFCRFEYK-AATGGFTP 134 (216)
Q Consensus 90 ~~~~~----~I~gkc~V~~~~~~~~~~~~~~~~ffcr~~yd-~~~~~f~p 134 (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 9999999997665432 3344555555554 48888863
No 15
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=99.91 E-value=1.9e-24 Score=189.09 Aligned_cols=181 Identities=32% Similarity=0.429 Sum_probs=158.2
Q ss_pred CCCCcceeeEEEcCCCeEEccCCeEEEccCCCCCCCeEEEEeEEEEcCC-CCEEEEEEEeecccccCCccc---ccCCCC
Q 027964 5 KPGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHR-NNVKVRVRWYYRPEESIGGRR---QFHGAK 80 (216)
Q Consensus 5 ~~~~~~y~~~~v~~~~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~-g~~~v~v~Wfyrp~d~~~~~~---~~~~~~ 80 (216)
...+.||+++..+++ ..+..||.|++.+++++.++|||+|..|+.... +.+.++|+|||||+|+..+.. ....++
T Consensus 34 ~~k~~h~~t~~~~~g-~~~~~~d~vllvped~~~pPyvaii~~i~a~~~g~~~k~ev~W~YrPee~~~~~~~~~~a~~~r 112 (464)
T KOG1886|consen 34 GVKSLHFETFIYRGG-RYINYGDSVLLVPEDPGKPPYVAIIEDIYAQERGGNVKVEVQWFYRPEESEGGGSGKWGAKQPR 112 (464)
T ss_pred ccccccccceeeccC-cccccCcceeecCCCCCCCCeeEEEeeeeccccCCCcceecccccCCCccCCCCCCCcccCCCc
Confidence 445789999988874 344449999999999999999999999999876 589999999999999987643 345678
Q ss_pred eeeeeCccceeecceeeeeeEEEeeeccccccC-CCCcceEEeeeeecccCcccCCCCcceEEeCCCCCCCCceEeCccc
Q 027964 81 ELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLEN-VGAEDYFCRFEYKAATGGFTPDRVAVYCKCEMPYNPDDLMVQCEGC 159 (216)
Q Consensus 81 ELF~s~~~d~~~~~~I~gkc~V~~~~~~~~~~~-~~~~~ffcr~~yd~~~~~f~p~~~~~~C~C~~~~~~~~~~i~C~~C 159 (216)
|||+|.|.|.+++++|.++|.|.++..+.++.. .+.+.|+||..||..++.+.......+|.|++.+++...|.+|..|
T Consensus 113 elF~SfH~De~~A~ti~~rC~V~fvp~~kqlp~~~~~~~f~~r~vYd~~~~~~~~~~~~~~~~~~k~e~d~~~~kt~~~~ 192 (464)
T KOG1886|consen 113 ELFLSFHEDEAFAETILHRCKVHFVPAYKQLPNRVGHESFICRRVYDAVTSKLRKLRDGDFGDGQKLEIDMLVPKTGPRR 192 (464)
T ss_pred cccccccccchhhhhhcccceeeeccccccccccCCCCCcccccccccccccccCccccchhcccccCCccchhhhcccC
Confidence 999999999999999999999999999998876 6788999999999999999988899999999999999999999999
Q ss_pred cceecCcCCCCChhhhcCCCeEEcccccccc
Q 027964 160 KDWFHPSCMGMTIEEAKKLDHFLCSDCSSDV 190 (216)
Q Consensus 160 ~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~ 190 (216)
+.|+|..|++.... .....|..|....
T Consensus 193 ~~~~~p~~~~t~~~----~~~~~~~~~s~~~ 219 (464)
T KOG1886|consen 193 GTLPDPKKVQTLNA----AASKRSQQKSEIS 219 (464)
T ss_pred CCCCCccccccccc----cccceeccccccc
Confidence 99999999998772 3567888885544
No 16
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.91 E-value=4.4e-26 Score=172.31 Aligned_cols=96 Identities=26% Similarity=0.516 Sum_probs=92.0
Q ss_pred CCCCeEEEEeEEEEcCCCCEEEEEEEeecccccCCcccccCCCCeeeeeCccceeecceeeeeeEEEeeeccccccCCCC
Q 027964 37 DKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLENVGA 116 (216)
Q Consensus 37 ~~~~~I~~I~~i~~~~~g~~~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~ 128 (148)
T cd04718 50 SGDLWLARIEKLWEEN-GTYWYAARWYTLPEETHMGRQPHNLRRELYLTNDFADIEMECILRHCSVKCPKEFRDASNDGD 128 (148)
T ss_pred cCchHHHHHHHHHhcc-CceEEEEEEEeCchhccCccccccccceeeeccccccccHHHHhcccEEcCHHHcccccCCCC
Confidence 4689999999999976 999999999999999999999999999999999999999999999999999999999888899
Q ss_pred cceEEeeeeecccCccc
Q 027964 117 EDYFCRFEYKAATGGFT 133 (216)
Q Consensus 117 ~~ffcr~~yd~~~~~f~ 133 (216)
++|||++.||..++.|.
T Consensus 129 Dvy~Ce~~Yd~~~~~Fk 145 (148)
T cd04718 129 DVFLCEYEYDVHWQSFK 145 (148)
T ss_pred ceEEEEEEEhhhcCcee
Confidence 99999999999999885
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=99.91 E-value=7.1e-24 Score=167.97 Aligned_cols=116 Identities=22% Similarity=0.347 Sum_probs=101.3
Q ss_pred CCeEEccCCeEEEccCCCCCCCeEEEEeEEEEcCC-CCEEEEEEEeecccccCCccc--c-------cCCCCeeeeeCcc
Q 027964 19 TNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHR-NNVKVRVRWYYRPEESIGGRR--Q-------FHGAKELFLSDHY 88 (216)
Q Consensus 19 ~~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~-g~~~v~v~Wfyrp~d~~~~~~--~-------~~~~~ELF~s~~~ 88 (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 579999999999999874 8999999999998765 558999999999999976542 2 2337999999999
Q ss_pred ceeecceeeeeeEEEeeeccccccCC---CCcceEEeeeeecccCcccCC
Q 027964 89 DVQSAHTIEGKCTVHTFKNYTKLENV---GAEDYFCRFEYKAATGGFTPD 135 (216)
Q Consensus 89 d~~~~~~I~gkc~V~~~~~~~~~~~~---~~~~ffcr~~yd~~~~~f~p~ 135 (216)
|.+++.+|++||.|++.++|..+... ...+||||++||+.++.|.+.
T Consensus 128 d~i~l~~Ii~k~~Vls~~ef~~~~~~~~~~~~~F~cR~~~d~~~~~F~~~ 177 (179)
T cd04720 128 SEIKLKDIIDKANVLSESEFNDLSTDDKNGERTFFCRYACEPDGEEFVWI 177 (179)
T ss_pred ceEEhhheeeeEEEecHHHhhhhcccccCCCceEEEEEEEeCCCCeEccc
Confidence 99999999999999999999877644 568899999999999999863
No 18
>cd04719 BAH_Orc1p_animal BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces cerevisiae Orc1p. Orc1 is part of the Yeast Sir1-origin recognition complex. The Orc1p BAH doman functions in epigenetic silencing. In vertebrates, a similar ORC protein complex exists, which has been shown essential for DNA replication in Xenopus laevis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.88 E-value=2.1e-22 Score=150.48 Aligned_cols=109 Identities=25% Similarity=0.347 Sum_probs=91.6
Q ss_pred eEEccCCeEEEccCCCCCCCeEEEEeEEEEcCCC---CEEEEEEEeecccccCCcc----cccCCCCeeeeeCccc---e
Q 027964 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRN---NVKVRVRWYYRPEESIGGR----RQFHGAKELFLSDHYD---V 90 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g---~~~v~v~Wfyrp~d~~~~~----~~~~~~~ELF~s~~~d---~ 90 (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 4899999999999985 78899999999998765 5799999999999997421 1236899999999874 7
Q ss_pred eecceeeeeeEEEeeeccccccCC---CCcceEEeeeeecccC
Q 027964 91 QSAHTIEGKCTVHTFKNYTKLENV---GAEDYFCRFEYKAATG 130 (216)
Q Consensus 91 ~~~~~I~gkc~V~~~~~~~~~~~~---~~~~ffcr~~yd~~~~ 130 (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 3567999998887654
No 19
>cd04711 BAH_Dnmt1_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.86 E-value=9.9e-22 Score=146.11 Aligned_cols=108 Identities=24% Similarity=0.482 Sum_probs=86.4
Q ss_pred CeEEEccCCCCCCCeEEEEeEEEEcCCC-------CEEEEEEEeecccccCCcccc-cCC-CCeeeeeCccceeecceee
Q 027964 27 DCVLMRPADSDKPPYVARVEKIEADHRN-------NVKVRVRWYYRPEESIGGRRQ-FHG-AKELFLSDHYDVQSAHTIE 97 (216)
Q Consensus 27 D~V~v~~~~~~~~~~I~~I~~i~~~~~g-------~~~v~v~Wfyrp~d~~~~~~~-~~~-~~ELF~s~~~d~~~~~~I~ 97 (216)
|.|-=.+-+.+.|++||||++|...+++ .++|+|+|||||+|+..++.. ++. -+|||+|+|.+++++.+|.
T Consensus 14 ~~~~~~~~d~~ePy~VgrI~eI~~~k~~~~k~~~~~ikvrV~~fYRPEdi~~g~~~ayhsDirevy~Sd~~~~~~~~~I~ 93 (137)
T cd04711 14 DYIKGSNLDAPEPFRIGRIKEIFCAKRSNGKPNESDIKLRINKFYRPENTHKGFKATYHADINMLYWSDEEATVDFSAVQ 93 (137)
T ss_pred cccccccCCCCCCcEEEEEEEEecCCCCCCCCCccceEEEEEEEecccccccccccccccceeeEEeecceeecChhhcc
Confidence 3333344456789999999999986533 378999999999999987544 444 4999999999999999999
Q ss_pred eeeEEEeeecccc-c---cCCCCcceEEeeeeecccCcccC
Q 027964 98 GKCTVHTFKNYTK-L---ENVGAEDYFCRFEYKAATGGFTP 134 (216)
Q Consensus 98 gkc~V~~~~~~~~-~---~~~~~~~ffcr~~yd~~~~~f~p 134 (216)
|||+|.+..+..+ + ...+++.|||+..||..++.|..
T Consensus 94 GKC~V~~~~di~~s~~~y~~~gpd~Fyf~~~Y~a~t~~F~d 134 (137)
T cd04711 94 GRCTVEYGEDLPESVQEYSGGGPDRFYFLEAYNAKTKSFED 134 (137)
T ss_pred ceEEEEeccccchhHHHHhcCCCcceEEhhhhccccCcccC
Confidence 9999997555431 2 23568999999999999999984
No 20
>KOG1827 consensus Chromatin remodeling complex RSC, subunit RSC1/Polybromo and related proteins [Chromatin structure and dynamics; Transcription]
Probab=99.43 E-value=1.6e-13 Score=124.89 Aligned_cols=123 Identities=21% Similarity=0.303 Sum_probs=109.4
Q ss_pred CeEEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeecccccCCcccccCCCCeeeeeCccceeecceeeee
Q 027964 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGK 99 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~d~~~~~~~~~~~~ELF~s~~~d~~~~~~I~gk 99 (216)
|..|.+||.|||...+....+.|++|.++|...+|..|+.+.|||||.+|.+...+-+.++|+|.+......++..|+|+
T Consensus 188 ~~~~~~gd~vlv~~~~d~~~p~v~~Ier~w~~~dg~k~~~~~w~~rP~~T~H~a~r~F~k~Evfkt~~~~~~~~q~l~g~ 267 (629)
T KOG1827|consen 188 GTKYIVGDYVLVQNPADNLKPIVAQIERLWKLPDGEKWPQGCWIYRPEETVHRADRKFYKQEVFKTSLYRDDLVQRLLGK 267 (629)
T ss_pred CcccccCceeeecCcccccCCceeeecccccCcccccccceeEeeCCccCccccccchhcccceecccccccHHHHhhcc
Confidence 56999999999999886689999999999999999999999999999999988766689999999999999999999999
Q ss_pred eEEEeeeccccccCC---CCcceEEeeeeecccCcccCCCCcceEE
Q 027964 100 CTVHTFKNYTKLENV---GAEDYFCRFEYKAATGGFTPDRVAVYCK 142 (216)
Q Consensus 100 c~V~~~~~~~~~~~~---~~~~ffcr~~yd~~~~~f~p~~~~~~C~ 142 (216)
|.|+++.+|....+. ..+.|.|.+.|+...+.|..-+....|.
T Consensus 268 c~v~~~~~yi~~~p~~ls~~dv~lcesRyn~~~K~f~kirsw~~~~ 313 (629)
T KOG1827|consen 268 CYVMKPTEYISGDPENLSEEDVFLCESRYNEQLKKFNKIRSWKAFL 313 (629)
T ss_pred eEEeehhHhhhcCcccccccceeeEEeeeccchhhhccccCchhcC
Confidence 999999999876542 4577999999999999888755555443
No 21
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=99.08 E-value=2.6e-11 Score=76.59 Aligned_cols=48 Identities=29% Similarity=0.918 Sum_probs=39.1
Q ss_pred eE-EeCCCCCCCCceEeCccccceecCcCCCCChhhhcCC-CeEEcccccc
Q 027964 140 YC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKL-DHFLCSDCSS 188 (216)
Q Consensus 140 ~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~-~~~~C~~C~~ 188 (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 8888 45688999999999999999999997644332 3899999975
No 22
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=99.02 E-value=1.1e-10 Score=98.78 Aligned_cols=52 Identities=25% Similarity=0.843 Sum_probs=44.3
Q ss_pred CCcceEEeCCCCCCCCceEeCcc--cc-ceecCcCCCCChhhhcCCCeEEcccccccccc
Q 027964 136 RVAVYCKCEMPYNPDDLMVQCEG--CK-DWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (216)
Q Consensus 136 ~~~~~C~C~~~~~~~~~~i~C~~--C~-~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (216)
..+.||+|.+. ..+.||.||. |. +|||+.|||+...+. ++|+|+.|......
T Consensus 217 ~e~~yC~Cnqv--syg~Mi~CDn~~C~~eWFH~~CVGL~~~Pk---gkWyC~~C~~~~~~ 271 (274)
T KOG1973|consen 217 DEPTYCICNQV--SYGKMIGCDNPGCPIEWFHFTCVGLKTKPK---GKWYCPRCKAENKK 271 (274)
T ss_pred CCCEEEEeccc--ccccccccCCCCCCcceEEEeccccccCCC---Ccccchhhhhhhhc
Confidence 57899999954 6889999996 98 999999999996654 57999999987653
No 23
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=98.93 E-value=4.6e-10 Score=91.49 Aligned_cols=49 Identities=29% Similarity=0.913 Sum_probs=41.6
Q ss_pred CCcceEEeCCCCCCCCceEeCc--cc-cceecCcCCCCChhhhcCCCeEEccccccc
Q 027964 136 RVAVYCKCEMPYNPDDLMVQCE--GC-KDWFHPSCMGMTIEEAKKLDHFLCSDCSSD 189 (216)
Q Consensus 136 ~~~~~C~C~~~~~~~~~~i~C~--~C-~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~ 189 (216)
...+||.|+++ ..+.||.|| .| .+|||+.|||+...+- .+|+|+.|...
T Consensus 219 ~e~lYCfCqqv--SyGqMVaCDn~nCkrEWFH~~CVGLk~pPK---G~WYC~eCk~~ 270 (271)
T COG5034 219 GEELYCFCQQV--SYGQMVACDNANCKREWFHLECVGLKEPPK---GKWYCPECKKA 270 (271)
T ss_pred CceeEEEeccc--ccccceecCCCCCchhheeccccccCCCCC---CcEeCHHhHhc
Confidence 47899999998 588999999 69 5999999999976442 58999999753
No 24
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=98.92 E-value=7.9e-11 Score=102.98 Aligned_cols=115 Identities=24% Similarity=0.426 Sum_probs=95.1
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeecccccCCc---------c-------------------
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGG---------R------------------- 73 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~d~~~~---------~------------------- 73 (216)
.|+|||+||+.... ..+|.|-||+++....+|.+..+|--|||..|+... +
T Consensus 5 ~y~vgd~vYf~~ss-s~PYliRrIEELnKTa~GnVeAkvVc~~RRRDIs~~L~~lAD~~ar~~~~y~a~~~a~~~~e~e~ 83 (693)
T KOG3554|consen 5 MYRVGDYVYFENSS-SNPYLIRRIEELNKTANGNVEAKVVCYLRRRDISSHLLKLADKHARRFDNYAAPEAAPEATEAEI 83 (693)
T ss_pred cceecceEEEecCC-CChHHHHHHHHHhccccCCcceEEEEEEEccchHHHHHHHHHHHhhhcccccCcccCcccchhhh
Confidence 79999999999987 469999999999999999999999999999986311 0
Q ss_pred -----cc-----------cCCCCeeeeeCccceeecceeeeeeEEEeeeccccccC--CCCcceEEeeeeecccCcccCC
Q 027964 74 -----RQ-----------FHGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLEN--VGAEDYFCRFEYKAATGGFTPD 135 (216)
Q Consensus 74 -----~~-----------~~~~~ELF~s~~~d~~~~~~I~gkc~V~~~~~~~~~~~--~~~~~ffcr~~yd~~~~~f~p~ 135 (216)
.+ ..-.+|||+|...+..|+..|+|||.|.-+.+-+.+.+ ..+++||+...||+..+.+..+
T Consensus 84 EEe~e~p~~vdlt~~qrhqLrhrElFlsRQ~EsLPAthIRGKCsV~LLnete~~~~YL~~eDtFfySLVyDP~~kTLLAD 163 (693)
T KOG3554|consen 84 EEESECPAPVDLTEKQRHQLRHRELFLSRQSESLPATHIRGKCSVTLLNETESLQSYLEKEDTFFYSLVYDPNQKTLLAD 163 (693)
T ss_pred hhhccCCCcCCCCHHHHHHHHHHHHHHhhhhccCchhhhccceeEEEecChHHHHhhccccceeEEEeeeccchhhhhcc
Confidence 00 01246999999999999999999999999888766554 3567899999999998887765
Q ss_pred CC
Q 027964 136 RV 137 (216)
Q Consensus 136 ~~ 137 (216)
+.
T Consensus 164 kG 165 (693)
T KOG3554|consen 164 KG 165 (693)
T ss_pred Cc
Confidence 44
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=98.58 E-value=2.2e-08 Score=87.08 Aligned_cols=113 Identities=27% Similarity=0.455 Sum_probs=90.5
Q ss_pred CeeeeeCccceeecceeeeeeEEEeeeccccccCCCCcceEEeeeeecccCcccCCCCcceEEeCCCCCCCCceEeCccc
Q 027964 80 KELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLENVGAEDYFCRFEYKAATGGFTPDRVAVYCKCEMPYNPDDLMVQCEGC 159 (216)
Q Consensus 80 ~ELF~s~~~d~~~~~~I~gkc~V~~~~~~~~~~~~~~~~ffcr~~yd~~~~~f~p~~~~~~C~C~~~~~~~~~~i~C~~C 159 (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 34555666666666777777777666655544 44556677777888888888887888899999999999999999999
Q ss_pred cceecCcC--CCCChhhhcCCCeEEccccccccccc
Q 027964 160 KDWFHPSC--MGMTIEEAKKLDHFLCSDCSSDVDAK 193 (216)
Q Consensus 160 ~~w~H~~C--v~~~~~~~~~~~~~~C~~C~~~~~~~ 193 (216)
..|||+.| |+++..+...++.|+|..|......-
T Consensus 82 ~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~~~~ 117 (345)
T KOG1632|consen 82 EDWYHGECWEVGTAEKEAPKEDPKVCDECKEAQDGM 117 (345)
T ss_pred cccccccccccCchhhcCCccccccccccchhhhhh
Confidence 99999999 99999998888999999999876544
No 27
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=98.12 E-value=1.2e-06 Score=78.07 Aligned_cols=55 Identities=25% Similarity=0.677 Sum_probs=42.5
Q ss_pred CCcceEEeCCCCCCCCceEeCccccceecCcCCCCChh--hh-cCCCeEEccccccccc
Q 027964 136 RVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIE--EA-KKLDHFLCSDCSSDVD 191 (216)
Q Consensus 136 ~~~~~C~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~--~~-~~~~~~~C~~C~~~~~ 191 (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 346678888887666 9999999999999999986543 22 3345999999997644
No 28
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=97.37 E-value=9e-05 Score=62.61 Aligned_cols=40 Identities=38% Similarity=1.033 Sum_probs=33.1
Q ss_pred ccCCCCcceEEeCCCCCC-----CCceEeCccccceec-CcCCCCC
Q 027964 132 FTPDRVAVYCKCEMPYNP-----DDLMVQCEGCKDWFH-PSCMGMT 171 (216)
Q Consensus 132 f~p~~~~~~C~C~~~~~~-----~~~~i~C~~C~~w~H-~~Cv~~~ 171 (216)
+..+....+|.|..+|++ ++.|+||-.|++||| -.|+...
T Consensus 122 YNhNfqG~~C~Cd~~Ypdp~~~~e~~m~QC~iCEDWFHce~c~~~~ 167 (345)
T KOG2752|consen 122 YNHNFQGLFCKCDTPYPDPVRTEEGEMLQCVICEDWFHCEGCMQAK 167 (345)
T ss_pred hhhhhcceeEEecCCCCCccccccceeeeEEeccchhcccccCccc
Confidence 345678999999999975 469999999999999 7777543
No 29
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.92 E-value=0.00051 Score=64.46 Aligned_cols=55 Identities=24% Similarity=0.703 Sum_probs=41.3
Q ss_pred CcceE-EeCCCCCCCCceEeCccccce-ecCcCCCCChhhhcCCCeEEccccccccccc
Q 027964 137 VAVYC-KCEMPYNPDDLMVQCEGCKDW-FHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 193 (216)
Q Consensus 137 ~~~~C-~C~~~~~~~~~~i~C~~C~~w-~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~ 193 (216)
....| +|..+. +.+.|+.||.|+.- ||+-||.++.-+. -+..|+|.+|....-+.
T Consensus 214 E~~~C~IC~~~D-pEdVLLLCDsCN~~~YH~YCLDPdl~ei-P~~eWYC~NC~dL~~~e 270 (1134)
T KOG0825|consen 214 EEVKCDICTVHD-PEDVLLLCDSCNKVYYHVYCLDPDLSES-PVNEWYCTNCSLLEITE 270 (1134)
T ss_pred ccccceeeccCC-hHHhheeecccccceeeccccCcccccc-cccceecCcchhhhhhh
Confidence 34456 787765 57899999999766 9999999976433 23689999998765443
No 30
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=96.87 E-value=0.0023 Score=62.76 Aligned_cols=54 Identities=26% Similarity=0.598 Sum_probs=41.8
Q ss_pred CcceEEeCCCCCC-CCceEeCccccceecCcCCCCChhhhcCCCeEEccccccccccc
Q 027964 137 VAVYCKCEMPYNP-DDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 193 (216)
Q Consensus 137 ~~~~C~C~~~~~~-~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~ 193 (216)
....|+|...... ....|+||+|+.-+|..|.|++.-+. ..|.|..|.......
T Consensus 219 D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~ipe---g~WlCr~Cl~s~~~~ 273 (1051)
T KOG0955|consen 219 DAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPFIPE---GQWLCRRCLQSPQRP 273 (1051)
T ss_pred CccceeecccccCCCceEEEcCCCcchhhhhccCCCCCCC---CcEeehhhccCcCcc
Confidence 4556799886643 36889999999999999999654321 489999999876654
No 31
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=96.82 E-value=0.00042 Score=57.54 Aligned_cols=51 Identities=25% Similarity=0.696 Sum_probs=41.6
Q ss_pred ceE-EeCCCCCCCCceEeCccccceecCcCCCCChhhhcCCCeEEccccccccc
Q 027964 139 VYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 191 (216)
Q Consensus 139 ~~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 191 (216)
++| +|+...| |..+++||.|+.=||+-|+.++..++.. ..|.|-.|.....
T Consensus 282 k~csicgtsen-ddqllfcddcdrgyhmyclsppm~eppe-gswsc~KOG~~~~ 333 (336)
T KOG1244|consen 282 KYCSICGTSEN-DDQLLFCDDCDRGYHMYCLSPPMVEPPE-GSWSCHLCLEELK 333 (336)
T ss_pred ceeccccCcCC-CceeEeecccCCceeeEecCCCcCCCCC-CchhHHHHHHHHh
Confidence 466 8888876 5678999999999999999998766533 4899999987644
No 32
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=96.65 E-value=0.00031 Score=40.82 Aligned_cols=35 Identities=29% Similarity=0.740 Sum_probs=19.8
Q ss_pred CceEeCccccceecCcCCCCChhhhcCCCeEEccccc
Q 027964 151 DLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCS 187 (216)
Q Consensus 151 ~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~ 187 (216)
..|++|+.|....|.+|=|+...+. .+.|+|..|.
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~~~~~--~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVSEVPD--GDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-SS--S--S-----HHH-
T ss_pred CceEEeCCCCCcCChhhCCcccCCC--CCcEECCcCC
Confidence 4789999999999999999987653 2359999884
No 33
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=96.41 E-value=0.0024 Score=57.30 Aligned_cols=53 Identities=23% Similarity=0.622 Sum_probs=38.6
Q ss_pred CcceE-EeCCCCCCCCceEeCccccceecCcCCCCChhhhcC---CCeEEcccccccc
Q 027964 137 VAVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKK---LDHFLCSDCSSDV 190 (216)
Q Consensus 137 ~~~~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~---~~~~~C~~C~~~~ 190 (216)
....| +|...-+ ..+.++||.|..-||..|+..+...... -.-|.|..|-+..
T Consensus 543 ~~ysCgiCkks~d-QHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECdk~e 599 (707)
T KOG0957|consen 543 MNYSCGICKKSTD-QHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECDKNE 599 (707)
T ss_pred cceeeeeeccchh-hHHHhhcchhhceeeccccCCccccCcccccCcceeeccccccc
Confidence 34457 8887642 4577999999999999999988654322 1369999994433
No 34
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.30 E-value=0.00096 Score=55.87 Aligned_cols=44 Identities=20% Similarity=0.520 Sum_probs=36.1
Q ss_pred EeCCCCCCCCceEeCccccceecCcCCCCChhhhcCCCeEEcc-ccccc
Q 027964 142 KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCS-DCSSD 189 (216)
Q Consensus 142 ~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~-~C~~~ 189 (216)
+|++|.. .++|++||.|+.=||.-|||+...+. ..|+|. .|...
T Consensus 319 IC~~P~~-E~E~~FCD~CDRG~HT~CVGL~~lP~---G~WICD~~C~~~ 363 (381)
T KOG1512|consen 319 ICLGPVI-ESEHLFCDVCDRGPHTLCVGLQDLPR---GEWICDMRCREA 363 (381)
T ss_pred ccCCccc-chheeccccccCCCCccccccccccC---ccchhhhHHHHh
Confidence 8888874 67899999999999999999987553 589998 45544
No 35
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=96.19 E-value=0.0023 Score=58.70 Aligned_cols=55 Identities=27% Similarity=0.691 Sum_probs=45.9
Q ss_pred CCcceEEeCCCCCCCCceEeCccccceecCcCCCCChhhhcCCCeEEcccccccccc
Q 027964 136 RVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (216)
Q Consensus 136 ~~~~~C~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (216)
.....|.|+.-...+++||+|+.|..|-|..|+|...... ++.|.|..|....-.
T Consensus 84 ~~~~~c~c~~~~~~~g~~i~c~~c~~Wqh~~C~g~~~~~~--p~~y~c~~c~~~~~~ 138 (508)
T KOG1844|consen 84 REISRCDCGLEDDMEGLMIQCDWCGRWQHKICCGSFKSTK--PDKYVCEICTPRNKE 138 (508)
T ss_pred CcccccccccccCCCceeeCCcccCcccCceeeeecCCCC--chhceeeeecccccc
Confidence 4677899999876589999999999999999999876543 689999999876543
No 36
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.73 E-value=0.0031 Score=58.03 Aligned_cols=53 Identities=21% Similarity=0.620 Sum_probs=39.8
Q ss_pred eE-EeCCCCCCCCceEeCccccceecCcCCCCChhhhcC-CCeEEccccccccccc
Q 027964 140 YC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKK-LDHFLCSDCSSDVDAK 193 (216)
Q Consensus 140 ~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~-~~~~~C~~C~~~~~~~ 193 (216)
|| .|.+...- ...|+||+|..-||+.|+.+|.+.... .+.|+|+.|....-..
T Consensus 255 fCsaCn~~~~F-~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k~~in 309 (613)
T KOG4299|consen 255 FCSACNGSGLF-NDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKIKSVIN 309 (613)
T ss_pred HHHHhCCcccc-ccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCeeeeecc
Confidence 78 78776542 456999999999999999998443222 2589999998765544
No 37
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=95.71 E-value=0.0084 Score=56.23 Aligned_cols=54 Identities=26% Similarity=0.653 Sum_probs=43.8
Q ss_pred CcceE-EeCCCCCC-CCceEeCccccceecCcCCCCChhhhcCCCeEEccccccccccc
Q 027964 137 VAVYC-KCEMPYNP-DDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 193 (216)
Q Consensus 137 ~~~~C-~C~~~~~~-~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~ 193 (216)
....| +|+.|+.. ...||.||.|+.-.|..|-|+.+.+. ..|.|.-|.....++
T Consensus 270 edviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIle~p~---gpWlCr~Calg~~pp 325 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGILEVPE---GPWLCRTCALGIEPP 325 (893)
T ss_pred ccceeceecCCCccccceeEEeccchhHHHHhhhceeecCC---CCeeehhccccCCCC
Confidence 45678 99998653 35999999999999999999987543 579999998775554
No 38
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=95.69 E-value=0.00081 Score=58.77 Aligned_cols=58 Identities=19% Similarity=0.637 Sum_probs=44.6
Q ss_pred CCcceE-EeCCCCCCCCceEeCccccceecCcCCCCChhhhcCCCe----EEcccccc-ccccc
Q 027964 136 RVAVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDH----FLCSDCSS-DVDAK 193 (216)
Q Consensus 136 ~~~~~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~----~~C~~C~~-~~~~~ 193 (216)
.....| .|+..+..+.+||.|+.|..|||+.|+.+.......... |.|+.|.. ..+.+
T Consensus 237 ~~~~~~~~cg~~~~~~~~~~~~~~~e~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~~~~~k~ 300 (345)
T KOG1632|consen 237 YSKLICDPCGLSDANKKFEICCDLCESWFHGDCVQIFEARKRLNEIRNEVYKCPHCTVLKFEKK 300 (345)
T ss_pred cccccccccCcchHHHHHHHHHHHHHHHhcccccccccchhhhhhhhccceecCceeecccchh
Confidence 344566 566666556889999999999999999998877666666 99999998 44433
No 39
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=93.77 E-value=0.043 Score=42.04 Aligned_cols=33 Identities=18% Similarity=0.630 Sum_probs=25.5
Q ss_pred ecCcCCCCChhhhcCCCeEEcccccccccccccC
Q 027964 163 FHPSCMGMTIEEAKKLDHFLCSDCSSDVDAKRSL 196 (216)
Q Consensus 163 ~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~~~~ 196 (216)
||+.|+.++...... ..|+|+.|......+...
T Consensus 2 ~H~~CL~Ppl~~~P~-g~W~Cp~C~~~~~~~~~~ 34 (148)
T cd04718 2 FHLCCLRPPLKEVPE-GDWICPFCEVEKSGQSAM 34 (148)
T ss_pred cccccCCCCCCCCCC-CCcCCCCCcCCCCCCccc
Confidence 899999999876544 479999999876655343
No 40
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=92.73 E-value=0.071 Score=50.58 Aligned_cols=46 Identities=24% Similarity=0.642 Sum_probs=35.8
Q ss_pred EEeCCCCCCCCceEeCccccceecCcCCCCChhhhcCCCeEEccccccccc
Q 027964 141 CKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 191 (216)
Q Consensus 141 C~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 191 (216)
++|.. ++..+.|+.|..|||..|++.+..+....+ |+|..|.-..+
T Consensus 51 ~ic~~----~g~~l~c~tC~~s~h~~cl~~pl~~~p~~~-~~c~Rc~~p~~ 96 (696)
T KOG0383|consen 51 RICAD----GGELLWCDTCPASFHASCLGPPLTPQPNGE-FICPRCFCPKN 96 (696)
T ss_pred hhhcC----CCcEEEeccccHHHHHHccCCCCCcCCccc-eeeeeeccCCC
Confidence 37765 457788999999999999999876655555 99999954444
No 41
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=92.38 E-value=0.046 Score=46.03 Aligned_cols=37 Identities=27% Similarity=0.628 Sum_probs=30.4
Q ss_pred CceEeCccccceecCcCCCCChhhhcCC--CeEEccccc
Q 027964 151 DLMVQCEGCKDWFHPSCMGMTIEEAKKL--DHFLCSDCS 187 (216)
Q Consensus 151 ~~~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~ 315 (381)
T KOG1512|consen 277 NSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSCE 315 (381)
T ss_pred ccceeecccccCCCCcchhcCHHHHhHHhhcchhhcccH
Confidence 5899999999999999999998876554 367666664
No 42
>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=91.89 E-value=0.14 Score=45.82 Aligned_cols=52 Identities=19% Similarity=0.472 Sum_probs=34.6
Q ss_pred EEeCCCCCC--CCceEeCccccceecCcCCCCCh--------hhh--cCCCeEEcccccccccc
Q 027964 141 CKCEMPYNP--DDLMVQCEGCKDWFHPSCMGMTI--------EEA--KKLDHFLCSDCSSDVDA 192 (216)
Q Consensus 141 C~C~~~~~~--~~~~i~C~~C~~w~H~~Cv~~~~--------~~~--~~~~~~~C~~C~~~~~~ 192 (216)
|+|..-+.. .-.||.||.|+.|-|.+|.--.. ..+ ...-.|.|..|.+..++
T Consensus 132 ~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~seL 195 (446)
T PF07227_consen 132 CICSKFDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTSEL 195 (446)
T ss_pred cccCCcccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChhhH
Confidence 377663321 23899999999999999963221 111 01138999999987664
No 43
>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=90.91 E-value=0.079 Score=32.97 Aligned_cols=33 Identities=24% Similarity=0.485 Sum_probs=16.7
Q ss_pred ceEeCccccceecCcCCCCChhhhcCCCeEEccc
Q 027964 152 LMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSD 185 (216)
Q Consensus 152 ~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~ 185 (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 579999999998876 222221122346899986
No 44
>KOG2626 consensus Histone H3 (Lys4) methyltransferase complex, subunit CPS60/ASH2/BRE2 [Chromatin structure and dynamics; Transcription]
Probab=90.41 E-value=0.24 Score=45.16 Aligned_cols=55 Identities=25% Similarity=0.533 Sum_probs=42.5
Q ss_pred CCCcceEEeCCCCCCCCceEeCccccceecCcCCCCChhhh-----cCCCeEEccccccc
Q 027964 135 DRVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEA-----KKLDHFLCSDCSSD 189 (216)
Q Consensus 135 ~~~~~~C~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~-----~~~~~~~C~~C~~~ 189 (216)
.....+|.|+...+....-+||..|.+|||..|+-...... ..-+.|.|..|...
T Consensus 17 ~~~~~~~y~e~~r~l~~~elqcs~clk~~~~~~~~~~~~~~s~~pf~t~y~fvc~~c~~~ 76 (544)
T KOG2626|consen 17 MKQATVCYCEGERNLGIVELQCSTCLKWFHLPTLEAFHLIKSSLPFMTSYEFVCKECTPS 76 (544)
T ss_pred ccCccccccccccccCceeeEeeecccccccccccccccccccCCcccceeEEeccccCc
Confidence 35678999999998888999999999999987665443221 11258999999987
No 45
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=90.23 E-value=0.05 Score=55.53 Aligned_cols=54 Identities=22% Similarity=0.616 Sum_probs=42.1
Q ss_pred CCcceE-EeCCCCCCCCceEeCccccceecCcCCCCChhhhcCCCeEEccccccccc
Q 027964 136 RVAVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 191 (216)
Q Consensus 136 ~~~~~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 191 (216)
.....| +|.... ....|+.|+.|..|||+-|+.+..... .+..|.|+.|...++
T Consensus 1106 ~~~~~c~~cr~k~-~~~~m~lc~~c~~~~h~~C~rp~~~~~-~~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1106 AVNALCKVCRRKK-QDEKMLLCDECLSGFHLFCLRPALSSV-PPGDWMCPSCRKEHR 1160 (1404)
T ss_pred cchhhhhhhhhcc-cchhhhhhHhhhhhHHHHhhhhhhccC-CcCCccCCccchhhh
Confidence 345567 666643 457999999999999999999876554 335699999999885
No 46
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=90.07 E-value=0.62 Score=29.36 Aligned_cols=41 Identities=17% Similarity=0.235 Sum_probs=27.9
Q ss_pred EccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeeccc
Q 027964 23 VRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPE 67 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~ 67 (216)
+++||.|.+.++. ...-|..|..- .....-++..+||---.
T Consensus 1 f~~GDvV~LKSGG--p~MTV~~v~~~--~~~~~~~v~C~WFd~~~ 41 (53)
T PF09926_consen 1 FKIGDVVQLKSGG--PRMTVTEVGPN--AGASGGWVECQWFDGHG 41 (53)
T ss_pred CCCCCEEEEccCC--CCeEEEEcccc--ccCCCCeEEEEeCCCCC
Confidence 4789999999998 35555555433 12344789999996433
No 47
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=89.75 E-value=0.22 Score=31.50 Aligned_cols=30 Identities=27% Similarity=0.703 Sum_probs=26.1
Q ss_pred ceE-EeCCCCCCCCceEeCccccceecCcCC
Q 027964 139 VYC-KCEMPYNPDDLMVQCEGCKDWFHPSCM 168 (216)
Q Consensus 139 ~~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv 168 (216)
..| +|+.+..+++..|.|..|+.=||-.|-
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 346 789988778899999999999998886
No 48
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=88.47 E-value=0.35 Score=43.91 Aligned_cols=54 Identities=19% Similarity=0.518 Sum_probs=37.9
Q ss_pred CCcceEEeCCCCC-CCCceEeCccccceecCcCCCCChhh----hcC---CCeEEccccccc
Q 027964 136 RVAVYCKCEMPYN-PDDLMVQCEGCKDWFHPSCMGMTIEE----AKK---LDHFLCSDCSSD 189 (216)
Q Consensus 136 ~~~~~C~C~~~~~-~~~~~i~C~~C~~w~H~~Cv~~~~~~----~~~---~~~~~C~~C~~~ 189 (216)
++...|+|-.... .-++.||||.|+.-.|-.|-|+.... ... ...|+|..|.--
T Consensus 118 k~~iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~G 179 (707)
T KOG0957|consen 118 KAVICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYG 179 (707)
T ss_pred cceEEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHhcC
Confidence 4456789955442 23688999999999999999987321 111 257999988753
No 49
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=88.24 E-value=0.081 Score=49.28 Aligned_cols=50 Identities=32% Similarity=0.817 Sum_probs=36.2
Q ss_pred ceE-EeCCCCCCC--CceEeCccccceecCcCCCCChhhhc--CCC-eEEcccccc
Q 027964 139 VYC-KCEMPYNPD--DLMVQCEGCKDWFHPSCMGMTIEEAK--KLD-HFLCSDCSS 188 (216)
Q Consensus 139 ~~C-~C~~~~~~~--~~~i~C~~C~~w~H~~Cv~~~~~~~~--~~~-~~~C~~C~~ 188 (216)
.+| +|...|-.. ..|++|+.|..|-|..|.++..+... ..| .|.|+.|.-
T Consensus 146 ~~cPvc~~~Y~~~e~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~CR~ 201 (694)
T KOG4443|consen 146 SYCPVCLIVYQDSESLPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTCRG 201 (694)
T ss_pred ccCchHHHhhhhccchhhHHHHHhcccccCCCCccchHHHHHHhhhhhcccceeeh
Confidence 344 455555333 36799999999999999999876432 235 899999984
No 50
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=87.51 E-value=1.9 Score=29.08 Aligned_cols=30 Identities=30% Similarity=0.529 Sum_probs=24.9
Q ss_pred EEccCCeEEEccCC-----CCCCCeEEEEeEEEEc
Q 027964 22 VVRPGDCVLMRPAD-----SDKPPYVARVEKIEAD 51 (216)
Q Consensus 22 ~~~vGD~V~v~~~~-----~~~~~~I~~I~~i~~~ 51 (216)
.++.||+|.|..++ .+...|+|.|+.....
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~gg 39 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGG 39 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEecc
Confidence 46889999999976 3468999999998874
No 51
>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=86.25 E-value=1.5 Score=30.29 Aligned_cols=43 Identities=23% Similarity=0.299 Sum_probs=34.3
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeecc
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRP 66 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp 66 (216)
.+.+||.|.-.-.. -++|-|+|.+.-......-.+.|+||-..
T Consensus 2 ~f~~GdlVwaK~kG--yp~WPa~I~~~~~~~~~~~~~~V~FfGt~ 44 (83)
T cd05834 2 QFKAGDLVFAKVKG--YPAWPARVDEPEDWKPPGKKYPVYFFGTH 44 (83)
T ss_pred CCCCCCEEEEecCC--CCCCCEEEecccccCCCCCEEEEEEeCCC
Confidence 47899999999876 89999999998765344467889898753
No 52
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=86.23 E-value=0.57 Score=37.86 Aligned_cols=53 Identities=19% Similarity=0.406 Sum_probs=35.3
Q ss_pred EeCccccceecCcCCCCChhhhcCCCeEEccccccccccc-----ccCCCCCCCCCCCCCCCc
Q 027964 154 VQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK-----RSLNTFSVSPSVEAKVEP 211 (216)
Q Consensus 154 i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~-----~~~~~~~~~~~~~~~~~~ 211 (216)
+.|..|. .|..|+.+.+... +.|+|+.|...++.. .+...++++||-+.|-++
T Consensus 193 lIC~~C~--hhngl~~~~ek~~---~efiC~~Cn~~n~~~~~~~dsn~~~~p~~~s~~~k~~t 250 (251)
T COG5415 193 LICPQCH--HHNGLYRLAEKPI---IEFICPHCNHKNDEVKEREDSNEAKQPAQPSQSEKEKT 250 (251)
T ss_pred hcccccc--ccccccccccccc---hheecccchhhcCcccccccchhhcCCCCccccccccC
Confidence 5677774 3678888876543 589999999877433 455556666665555443
No 53
>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=84.47 E-value=1.5 Score=30.49 Aligned_cols=41 Identities=22% Similarity=0.199 Sum_probs=31.9
Q ss_pred EccCCeEEEccCCCCCCCeEEEEeEEEEcC---CCCEEEEEEEeec
Q 027964 23 VRPGDCVLMRPADSDKPPYVARVEKIEADH---RNNVKVRVRWYYR 65 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~---~g~~~v~v~Wfyr 65 (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 4689999999876 789999999986543 1235688889873
No 54
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=84.02 E-value=0.43 Score=34.41 Aligned_cols=31 Identities=26% Similarity=0.753 Sum_probs=24.4
Q ss_pred CcceE-EeCCCCCCCCceEeCcc--ccceecCcCCCC
Q 027964 137 VAVYC-KCEMPYNPDDLMVQCEG--CKDWFHPSCMGM 170 (216)
Q Consensus 137 ~~~~C-~C~~~~~~~~~~i~C~~--C~~w~H~~Cv~~ 170 (216)
....| +|+.. .+..|+|.. |..+||..|...
T Consensus 54 ~~~~C~iC~~~---~G~~i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 54 FKLKCSICGKS---GGACIKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred cCCcCcCCCCC---CceeEEcCCCCCCcCCCHHHHHH
Confidence 34445 88886 678999996 999999999744
No 55
>cd06080 MUM1_like Mutated melanoma-associated antigen 1 (MUM-1) is a melanoma-associated antigen (MAA). MUM-1 belongs to the mutated or aberrantly expressed type of MAAs, along with antigens such as CDK4, beta-catenin, gp100-in4, p15, and N-acetylglucosaminyltransferase V. It is highly expressed in several types of human cancers. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=83.75 E-value=2.2 Score=29.31 Aligned_cols=39 Identities=21% Similarity=0.223 Sum_probs=31.4
Q ss_pred EccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeecc
Q 027964 23 VRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRP 66 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp 66 (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 4689999988876 79999999998643 567888888766
No 56
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=83.58 E-value=1.1 Score=35.07 Aligned_cols=46 Identities=22% Similarity=0.535 Sum_probs=33.0
Q ss_pred CCceEeCccccceecCcCCCCChhh-------hcCCCeEEccccccccccccc
Q 027964 150 DDLMVQCEGCKDWFHPSCMGMTIEE-------AKKLDHFLCSDCSSDVDAKRS 195 (216)
Q Consensus 150 ~~~~i~C~~C~~w~H~~Cv~~~~~~-------~~~~~~~~C~~C~~~~~~~~~ 195 (216)
-+.||.|-+|..-||-.|+|..... .++.-.-.|..|......|+.
T Consensus 14 kG~Lv~CQGCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~~~kKD~ 66 (175)
T PF15446_consen 14 KGPLVYCQGCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGIAHKKDP 66 (175)
T ss_pred CCCeEEcCccChHHHhhhcCCccccceeeEEEcCCceEEechhhcChhhcccC
Confidence 4699999999999999999986433 112224578888876665543
No 57
>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=83.14 E-value=1.9 Score=27.62 Aligned_cols=39 Identities=15% Similarity=0.304 Sum_probs=26.9
Q ss_pred ccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEe
Q 027964 24 RPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWY 63 (216)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wf 63 (216)
++||.+.|.....+.+...|.|+++.. .+|..-..|+|-
T Consensus 4 ~vGD~lvv~g~~vg~~~r~GeIveV~g-~dG~PPY~VRw~ 42 (58)
T PF08940_consen 4 SVGDRLVVHGRTVGQPDRHGEIVEVRG-PDGSPPYLVRWD 42 (58)
T ss_dssp -TTEEEEES-TTTS--EEEEEEEE-S--SSS-S-EEEEET
T ss_pred CCCCEEEEcCCcCCCCCcEeEEEEEEC-CCCCCCEEEEec
Confidence 689999999987778999999999988 567677888884
No 58
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=81.82 E-value=0.76 Score=43.37 Aligned_cols=52 Identities=23% Similarity=0.613 Sum_probs=38.6
Q ss_pred cceEEeCCCCC-CCCceEeCc--cccceecCcCCCCChhhhcCCCeEEcccccccccc
Q 027964 138 AVYCKCEMPYN-PDDLMVQCE--GCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (216)
Q Consensus 138 ~~~C~C~~~~~-~~~~~i~C~--~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (216)
.-.|+|-.-.. ++..+|-|| .|..-.|..|-|+-.-+. ..|+|..|.....+
T Consensus 6 GGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVPt---GpWfCrKCesqera 60 (900)
T KOG0956|consen 6 GGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVPT---GPWFCRKCESQERA 60 (900)
T ss_pred cceeeecCcCCCccCceeeecCCCceeeeehhcceeEecCC---Cchhhhhhhhhhhh
Confidence 45789955322 356889999 699999999999865443 47999999875543
No 59
>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]
Probab=81.57 E-value=0.29 Score=43.28 Aligned_cols=88 Identities=15% Similarity=0.093 Sum_probs=73.7
Q ss_pred CeEEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeecccccCCcccccCCCCeeeeeCccceeecceeeee
Q 027964 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGK 99 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~d~~~~~~~~~~~~ELF~s~~~d~~~~~~I~gk 99 (216)
+....+|+.+.+.+......+.++.+...|.+.++..+.-+.|||+|..+.......+..+++......+........+.
T Consensus 274 ~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 (371)
T COG5076 274 NSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTDYYKNANVLE 353 (371)
T ss_pred ccccccccccccccCCcccccchhhhhhcccccccchhhhhcccCCCccccccccchhhhcccccchhhhhhhhhccchh
Confidence 34888999999999877789999999999999888888899999999987777666678888888888888888888888
Q ss_pred eEEEeeec
Q 027964 100 CTVHTFKN 107 (216)
Q Consensus 100 c~V~~~~~ 107 (216)
|.|...-.
T Consensus 354 ~~~~~~~~ 361 (371)
T COG5076 354 DFVIKKTR 361 (371)
T ss_pred hhHhhhhh
Confidence 77765433
No 60
>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=81.39 E-value=4.7 Score=25.30 Aligned_cols=36 Identities=22% Similarity=0.263 Sum_probs=25.9
Q ss_pred EccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEE
Q 027964 23 VRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVR 61 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~ 61 (216)
+.+|+.|++.-.+ +..+-|+|+++.. ..+.....|.
T Consensus 1 ~~vG~~v~~~~~~--~~~y~A~I~~~r~-~~~~~~YyVH 36 (55)
T PF11717_consen 1 FEVGEKVLCKYKD--GQWYEAKILDIRE-KNGEPEYYVH 36 (55)
T ss_dssp --TTEEEEEEETT--TEEEEEEEEEEEE-CTTCEEEEEE
T ss_pred CCcCCEEEEEECC--CcEEEEEEEEEEe-cCCCEEEEEE
Confidence 4689999999943 6899999999999 4444444443
No 61
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=81.23 E-value=0.6 Score=42.39 Aligned_cols=46 Identities=33% Similarity=0.824 Sum_probs=32.7
Q ss_pred eE-EeCCCCCCC-CceEeCccccceecCcCCCCChhhhcCCCeEEcccccc
Q 027964 140 YC-KCEMPYNPD-DLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSS 188 (216)
Q Consensus 140 ~C-~C~~~~~~~-~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~ 188 (216)
.| +|....+.+ ...|.||+|+--.|.+|-|+.--+. ..|.|..|.-
T Consensus 195 ~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~f~pe---G~WlCrkCi~ 242 (669)
T COG5141 195 ICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPE---GFWLCRKCIY 242 (669)
T ss_pred hhHhccccccCCcceEEEecCcchhhhhhcccceecCc---chhhhhhhcc
Confidence 45 777766543 5779999999999999999975331 2566655553
No 62
>COG4014 Uncharacterized protein conserved in archaea [Function unknown]
Probab=80.14 E-value=6.2 Score=27.48 Aligned_cols=39 Identities=28% Similarity=0.488 Sum_probs=29.7
Q ss_pred ccCCeE-EEccCCCCCCCeEEEEeEEEEcCCCCEEEEEE---Eeecccc
Q 027964 24 RPGDCV-LMRPADSDKPPYVARVEKIEADHRNNVKVRVR---WYYRPEE 68 (216)
Q Consensus 24 ~vGD~V-~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~---Wfyrp~d 68 (216)
.|||.| ||.++. +|+|.+|.++.+|.+||.+- .+||+.=
T Consensus 10 ~VG~avrYvnTgT------vgrV~dIkkdEdG~~WV~LdstdLwYre~~ 52 (97)
T COG4014 10 KVGDAVRYVNTGT------VGRVVDIKKDEDGDIWVVLDSTDLWYREHY 52 (97)
T ss_pred hhcceEEEeecCc------eeeEEEEEeecCCceEEEEecCCceecccc
Confidence 478766 555555 99999999999999999875 4566653
No 63
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=80.02 E-value=0.15 Score=30.44 Aligned_cols=40 Identities=23% Similarity=0.544 Sum_probs=27.5
Q ss_pred EeCCCCCCCCceEeCccccceecCcCCCCChhhhcCCCeEEccccc
Q 027964 142 KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCS 187 (216)
Q Consensus 142 ~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~ 187 (216)
+|.....++..++... |+..||.+|+..-... ...||.|+
T Consensus 5 IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~-----~~~CP~CR 44 (44)
T PF13639_consen 5 ICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKR-----NNSCPVCR 44 (44)
T ss_dssp TTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHH-----SSB-TTTH
T ss_pred CCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHh-----CCcCCccC
Confidence 6767666566677666 9999999998654432 23888874
No 64
>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=79.11 E-value=3.5 Score=28.30 Aligned_cols=40 Identities=30% Similarity=0.321 Sum_probs=30.8
Q ss_pred EccCCeEEEccCCCCCCCeEEEEeEEEEcC------CCCEEEEEEEee
Q 027964 23 VRPGDCVLMRPADSDKPPYVARVEKIEADH------RNNVKVRVRWYY 64 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~------~g~~~v~v~Wfy 64 (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 4789999999987 799999999988752 223467777775
No 65
>PF13341 RAG2_PHD: RAG2 PHD domain; PDB: 2JWO_A 2V86_B 2V85_B 2V87_A 2V83_C 2V89_A 2V88_A.
Probab=78.17 E-value=1.5 Score=29.08 Aligned_cols=34 Identities=24% Similarity=0.697 Sum_probs=18.9
Q ss_pred ceEeCcc-ccceecCcCCCCChhhh----cCCCeEEccc
Q 027964 152 LMVQCEG-CKDWFHPSCMGMTIEEA----KKLDHFLCSD 185 (216)
Q Consensus 152 ~~i~C~~-C~~w~H~~Cv~~~~~~~----~~~~~~~C~~ 185 (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 6899984 47999999999997643 2224788865
No 66
>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=76.72 E-value=6.4 Score=21.73 Aligned_cols=26 Identities=15% Similarity=0.233 Sum_probs=22.3
Q ss_pred cCCeEEEccCCCCCCCeEEEEeEEEEcC
Q 027964 25 PGDCVLMRPADSDKPPYVARVEKIEADH 52 (216)
Q Consensus 25 vGD~V~v~~~~~~~~~~I~~I~~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 677999999998754
No 67
>PF09871 DUF2098: Uncharacterized protein conserved in archaea (DUF2098); InterPro: IPR019209 This family of proteins have no known function.
Probab=76.64 E-value=6.9 Score=27.54 Aligned_cols=43 Identities=23% Similarity=0.328 Sum_probs=32.0
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEE---EEeecccccC
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRV---RWYYRPEESI 70 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v---~Wfyrp~d~~ 70 (216)
.|.+|++|--.+.. -+|+|.+|.. .++..|+.+ ..||||.-+.
T Consensus 2 ~I~vGs~VRY~~TG-----T~G~V~diK~-ed~~~wv~LD~t~L~Yr~~~Le 47 (91)
T PF09871_consen 2 PIKVGSYVRYINTG-----TVGKVVDIKE-EDGETWVLLDSTDLYYRPDYLE 47 (91)
T ss_pred cceeCCEEEECCCC-----eEEEEEEEEE-eCCCeEEEEccCCceeecceeE
Confidence 57889998665554 2999999955 567788888 4778887653
No 68
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=76.23 E-value=5 Score=25.90 Aligned_cols=40 Identities=23% Similarity=0.212 Sum_probs=29.8
Q ss_pred EccCCeEEEccCCCCCCCeEEEEeEEEEcC-------CCCEEEEEEEee
Q 027964 23 VRPGDCVLMRPADSDKPPYVARVEKIEADH-------RNNVKVRVRWYY 64 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~-------~g~~~v~v~Wfy 64 (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 789999998877542 223566676664
No 69
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=75.61 E-value=4.6 Score=35.39 Aligned_cols=50 Identities=20% Similarity=0.484 Sum_probs=36.2
Q ss_pred ceEEeCCCCCCCCceEeCccccceecCcCCCCChhhhcCCCeEEccccccccccc
Q 027964 139 VYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 193 (216)
Q Consensus 139 ~~C~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~ 193 (216)
..++|-..|..++.... --|+.-||..||..=..+. .-+||.|.......
T Consensus 231 ~CaIClEdY~~GdklRi-LPC~H~FH~~CIDpWL~~~----r~~CPvCK~di~~~ 280 (348)
T KOG4628|consen 231 TCAICLEDYEKGDKLRI-LPCSHKFHVNCIDPWLTQT----RTFCPVCKRDIRTD 280 (348)
T ss_pred eEEEeecccccCCeeeE-ecCCCchhhccchhhHhhc----CccCCCCCCcCCCC
Confidence 45599999976655433 6899999999998654432 23799999865544
No 70
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=75.45 E-value=15 Score=23.31 Aligned_cols=44 Identities=14% Similarity=0.299 Sum_probs=32.6
Q ss_pred ccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEE-------EEEeeccccc
Q 027964 24 RPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVR-------VRWYYRPEES 69 (216)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~-------v~Wfyrp~d~ 69 (216)
+++|.|+|..+. .+.--|.|..+..-..|.+++. +.||..-.+-
T Consensus 2 kvnD~VtVKTDG--~~rR~G~ilavE~F~EG~MYLvaL~dYP~GiWFFNE~~~ 52 (62)
T PF10781_consen 2 KVNDRVTVKTDG--GPRREGVILAVEPFNEGTMYLVALEDYPAGIWFFNEKDS 52 (62)
T ss_pred ccccEEEEecCC--cccccceEEEEeeccCcEEEEEEcCcCCcceEEEecCCC
Confidence 579999999987 6788899988888777765543 3477654443
No 71
>PRK10708 hypothetical protein; Provisional
Probab=74.50 E-value=17 Score=23.09 Aligned_cols=43 Identities=14% Similarity=0.243 Sum_probs=32.4
Q ss_pred ccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEE-------EEEeecccc
Q 027964 24 RPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVR-------VRWYYRPEE 68 (216)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~-------v~Wfyrp~d 68 (216)
+++|.|.|..+. .+.-.|.|..+..-..|.+++. +.||..-.+
T Consensus 2 kvnD~VtVKTDG--~~rR~G~iLavE~F~EG~MyLvaL~dYP~GiWFFNE~~ 51 (62)
T PRK10708 2 KVNDRVTVKTDG--GPRRPGVVLAVEEFSEGTMYLVSLEDYPLGIWFFNEAG 51 (62)
T ss_pred ccccEEEEecCC--CccccceEEEEeeccCcEEEEEEcCcCCCceEEEeccC
Confidence 579999999987 6788899999888777765543 347765443
No 72
>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=74.06 E-value=10 Score=28.83 Aligned_cols=50 Identities=26% Similarity=0.386 Sum_probs=33.9
Q ss_pred CCcceeeEEEcCCCeEEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeeccc
Q 027964 7 GKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPE 67 (216)
Q Consensus 7 ~~~~y~~~~v~~~~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~ 67 (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 4455666666654 88999999998854 3556667777766 4445888654
No 73
>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=73.66 E-value=4.3 Score=28.60 Aligned_cols=40 Identities=28% Similarity=0.382 Sum_probs=29.5
Q ss_pred EccCCeEEEccCCCCCCCeEEEEeEEE---------EcCCCCEEEEEEEee
Q 027964 23 VRPGDCVLMRPADSDKPPYVARVEKIE---------ADHRNNVKVRVRWYY 64 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~~I~~i~---------~~~~g~~~v~v~Wfy 64 (216)
|++||.|...-.. -+.|-|+|..=. ..+.....+.|++|-
T Consensus 1 f~~GDlVwaK~~G--yPwWPA~V~~~~~~p~~~l~~~~~~~~~~~~V~FFg 49 (93)
T cd05840 1 FQPGDRVLAKVKG--FPAWPAIVVPEEMLPDSVLKGKKKKNKRTYPVMFFP 49 (93)
T ss_pred CCCCCEEEEeCCC--CCCCCEEECChHHCCHHHHhcccCCCCCeEEEEEeC
Confidence 4789999999987 899999997622 112334678888874
No 74
>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=72.88 E-value=0.88 Score=24.86 Aligned_cols=26 Identities=23% Similarity=0.635 Sum_probs=10.4
Q ss_pred EeCCCCCCCCceEeCccccceecCcCC
Q 027964 142 KCEMPYNPDDLMVQCEGCKDWFHPSCM 168 (216)
Q Consensus 142 ~C~~~~~~~~~~i~C~~C~~w~H~~Cv 168 (216)
.|+.+... .....|..|+...|..|+
T Consensus 5 ~C~~~~~~-~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 5 ACGKPIDG-GWFYRCSECDFDLHEECA 30 (30)
T ss_dssp TTS----S---EEE-TTT-----HHHH
T ss_pred cCCCcCCC-CceEECccCCCccChhcC
Confidence 46665432 477889999999998884
No 75
>COG1370 Prefoldin, molecular chaperone implicated in de novo protein folding, alpha subunit [Posttranslational modification, protein turnover, chaperones]
Probab=71.69 E-value=3.2 Score=31.86 Aligned_cols=39 Identities=31% Similarity=0.422 Sum_probs=32.0
Q ss_pred CCCCcceeeEEEcCCCeEEccCCeEEEccCCCCCCCeEEEE
Q 027964 5 KPGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARV 45 (216)
Q Consensus 5 ~~~~~~y~~~~v~~~~~~~~vGD~V~v~~~~~~~~~~I~~I 45 (216)
++|+..|..|.+..+ +.++.||-|+|-.++ +...-+|+.
T Consensus 94 r~Gk~VFaKfVi~~D-~~iR~~dEvlVVne~-d~LlAvGra 132 (155)
T COG1370 94 RKGKSVFAKFVIDVD-EEIRAGDEVLVVNED-DELLAVGRA 132 (155)
T ss_pred HhccchhhhheeccC-cccCCCCeEEEECCC-CcEEEeeeE
Confidence 689999999999885 799999999999987 355555554
No 76
>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=71.06 E-value=16 Score=24.31 Aligned_cols=47 Identities=21% Similarity=0.169 Sum_probs=34.7
Q ss_pred EEEEEeecccccCCcccccCCCCeeeeeCccceeecceeeeeeEEEe
Q 027964 58 VRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHT 104 (216)
Q Consensus 58 v~v~Wfyrp~d~~~~~~~~~~~~ELF~s~~~d~~~~~~I~gkc~V~~ 104 (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 56666777788754433446899999999999999999999999986
No 77
>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=70.92 E-value=26 Score=26.49 Aligned_cols=51 Identities=20% Similarity=0.308 Sum_probs=34.7
Q ss_pred ceeeEEEcCCCeEEccCCeEEEccCC----------CCCCCeEEEEeEEEEcCCC-------CEEEEEEE
Q 027964 10 DLDSYNIKGTNKVVRPGDCVLMRPAD----------SDKPPYVARVEKIEADHRN-------NVKVRVRW 62 (216)
Q Consensus 10 ~y~~~~v~~~~~~~~vGD~V~v~~~~----------~~~~~~I~~I~~i~~~~~g-------~~~v~v~W 62 (216)
||+...+ | .|.|.+||.|-|.+.. .++.--|-.|.+|...... .+.|++.-
T Consensus 2 ~y~Gifl-G-AE~I~vGD~VRl~~~~~~~~~~~~~~~~~~tdvMvI~~I~~~~~~~~~~~~~~v~~~G~l 69 (139)
T PF10383_consen 2 YYRGIFL-G-AEMIWVGDAVRLKPLNASPSPNQSDGNPDVTDVMVIDEIQLRLINCDPDSPSTVRFRGDL 69 (139)
T ss_pred eECeEEE-e-eEEEEeCCEEEECccCCCcccccccCCCCceeEEEEeEEEEecccCCCCCCceEEEEeEe
Confidence 5666656 4 4899999999995432 2345678888888875332 36677654
No 78
>PRK13251 transcription attenuation protein MtrB; Provisional
Probab=70.60 E-value=20 Score=23.87 Aligned_cols=47 Identities=21% Similarity=0.204 Sum_probs=36.9
Q ss_pred EEEEEeecccccCCcccccCCCCeeeeeCccceeecceeeeeeEEEe
Q 027964 58 VRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHT 104 (216)
Q Consensus 58 v~v~Wfyrp~d~~~~~~~~~~~~ELF~s~~~d~~~~~~I~gkc~V~~ 104 (216)
|.|.=+-|..|+.--.....+..||.+...++-.++..|+|++.++.
T Consensus 19 V~vIgltrg~dtkfhhtEkLDkGEVmiaqftehtsaiKirGkA~I~t 65 (75)
T PRK13251 19 VNVIGLTRGKDTKFHHTEKLDKGEVMIAQFTEHTSAIKIRGKAEIQT 65 (75)
T ss_pred eEEEEEecCCCccchhhhhcCCCcEEEEEeecceeEEEEeceEEEEe
Confidence 55556677777754333346899999999999999999999999986
No 79
>PF13922 PHD_3: PHD domain of transcriptional enhancer, Asx
Probab=69.07 E-value=0.84 Score=29.86 Aligned_cols=32 Identities=28% Similarity=0.874 Sum_probs=26.2
Q ss_pred CCcceEEeCCCCCCCCceEeCccccceecCcCCCCCh
Q 027964 136 RVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTI 172 (216)
Q Consensus 136 ~~~~~C~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~ 172 (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 3455677755 3899999999999999999875
No 80
>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=68.95 E-value=3.8 Score=27.78 Aligned_cols=40 Identities=33% Similarity=0.462 Sum_probs=28.7
Q ss_pred EccCCeEEEccCCCCCCCeEEEEeEEEEc---CCCCEEEEEEEee
Q 027964 23 VRPGDCVLMRPADSDKPPYVARVEKIEAD---HRNNVKVRVRWYY 64 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~~I~~i~~~---~~g~~~v~v~Wfy 64 (216)
|.+||.|...-.+ -+.|-|+|...... ....-.+.|.||-
T Consensus 1 f~~GdlVWaK~~g--~pwWPa~V~~~~~~~~~~~~~~~~~V~Ffg 43 (86)
T PF00855_consen 1 FRPGDLVWAKLKG--YPWWPARVCDPDEKSKKKRKDGHVLVRFFG 43 (86)
T ss_dssp -STTEEEEEEETT--SEEEEEEEEECCHCTSCSSSSTEEEEEETT
T ss_pred CCCCCEEEEEeCC--CCCCceEEeecccccccCCCCCEEEEEecC
Confidence 5789999999876 78999999987643 1223556666654
No 81
>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=66.59 E-value=17 Score=26.55 Aligned_cols=45 Identities=18% Similarity=0.257 Sum_probs=33.2
Q ss_pred CCCCCCcceeeEEEcCCCeEEccCCeEEEccCCCCCCCeEEEEeEEEEcC
Q 027964 3 KTKPGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADH 52 (216)
Q Consensus 3 ~~~~~~~~y~~~~v~~~~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~ 52 (216)
|..+|.=.....++-.. ++++||.|.+-..+ -+-+++|..+..+.
T Consensus 9 k~~~G~G~t~dvIl~~G--tL~~GD~Iv~g~~~---Gpi~tkVRaLl~~~ 53 (110)
T cd03703 9 KEEEGLGTTIDVILYDG--TLREGDTIVVCGLN---GPIVTKVRALLKPQ 53 (110)
T ss_pred EEcCCCceEEEEEEECC--eEecCCEEEEccCC---CCceEEEeEecCCC
Confidence 44556666666666432 89999999998875 46699999998854
No 82
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=66.48 E-value=13 Score=25.10 Aligned_cols=35 Identities=23% Similarity=0.261 Sum_probs=27.2
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEE
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVR 59 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~ 59 (216)
.++.||.|.|..+. +.--+|+|.++....+ .+.++
T Consensus 6 ~I~kGD~V~Vi~G~--dKGK~G~V~~V~~~~~-~V~Ve 40 (76)
T PRK12281 6 KVKKGDMVKVIAGD--DKGKTGKVLAVLPKKN-RVIVE 40 (76)
T ss_pred cccCCCEEEEeEcC--CCCcEEEEEEEEcCCC-EEEEc
Confidence 58899999999986 6778999999988543 34443
No 83
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=65.75 E-value=13 Score=19.25 Aligned_cols=26 Identities=19% Similarity=0.221 Sum_probs=20.5
Q ss_pred EccCCeEEEccCCCCCCCeEEEEeEEEE
Q 027964 23 VRPGDCVLMRPADSDKPPYVARVEKIEA 50 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~~I~~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 4689999999976 5666899888753
No 84
>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=65.73 E-value=5.6 Score=28.70 Aligned_cols=31 Identities=26% Similarity=0.693 Sum_probs=20.5
Q ss_pred cccceecCcCCCCC----hhhhcCCCeEEcccccc
Q 027964 158 GCKDWFHPSCMGMT----IEEAKKLDHFLCSDCSS 188 (216)
Q Consensus 158 ~C~~w~H~~Cv~~~----~~~~~~~~~~~C~~C~~ 188 (216)
.|..-|...||-.. ..++.....|.||.|..
T Consensus 35 ~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 35 GCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred cCcceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 33888999998432 23333335899998875
No 85
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=65.69 E-value=21 Score=27.93 Aligned_cols=67 Identities=21% Similarity=0.313 Sum_probs=44.2
Q ss_pred eEEccCCeEEEccCCCCCCCeEEEEeEEEEcC--------------CCCEEEEEEEeecccccCCcccccCCCCeeeeeC
Q 027964 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADH--------------RNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSD 86 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~--------------~g~~~v~v~Wfyrp~d~~~~~~~~~~~~ELF~s~ 86 (216)
-.+..||.|.+.++..+++.+|-||..+.-+. .|+.||++ -...+-+=|+
T Consensus 67 ~~~~rGDiVvl~sP~~p~~~~iKRv~alegd~~~t~~~k~~~v~vpkghcWVeg----------------Dn~~hs~DSn 130 (174)
T KOG1568|consen 67 RKVSRGDIVVLKSPNDPDKVIIKRVAALEGDIMVTEDEKEEPVVVPKGHCWVEG----------------DNQKHSYDSN 130 (174)
T ss_pred ceeccCCEEEEeCCCChhheeeeeeecccccEeccCCCCCCceecCCCcEEEec----------------CCcccccccC
Confidence 35778999999998878899999998765431 22233322 1123344455
Q ss_pred ccceeecceeeeeeEEE
Q 027964 87 HYDVQSAHTIEGKCTVH 103 (216)
Q Consensus 87 ~~d~~~~~~I~gkc~V~ 103 (216)
.+--++...|.|++.-.
T Consensus 131 tFGPVS~gli~grai~i 147 (174)
T KOG1568|consen 131 TFGPVSTGLIVGRAIYI 147 (174)
T ss_pred ccCCcchhheeeeEEEE
Confidence 56668899999988544
No 86
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=64.09 E-value=3.6 Score=28.27 Aligned_cols=31 Identities=26% Similarity=0.715 Sum_probs=24.0
Q ss_pred cceE-EeCCCCCCCCceEeCc--cccceecCcCCCCC
Q 027964 138 AVYC-KCEMPYNPDDLMVQCE--GCKDWFHPSCMGMT 171 (216)
Q Consensus 138 ~~~C-~C~~~~~~~~~~i~C~--~C~~w~H~~Cv~~~ 171 (216)
...| +|+++ .+-.|+|. .|...||..|....
T Consensus 36 ~~~C~~C~~~---~Ga~i~C~~~~C~~~fH~~CA~~~ 69 (90)
T PF13771_consen 36 KLKCSICKKK---GGACIGCSHPGCSRSFHVPCARKA 69 (90)
T ss_pred CCCCcCCCCC---CCeEEEEeCCCCCcEEChHHHccC
Confidence 3445 77765 46889998 69999999998664
No 87
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=63.24 E-value=2.5 Score=39.79 Aligned_cols=41 Identities=20% Similarity=0.497 Sum_probs=31.6
Q ss_pred CCceEeCccccceecCcCCCCChhhhcCCCeEEcccccccc
Q 027964 150 DDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDV 190 (216)
Q Consensus 150 ~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~ 190 (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 46899999999999999999755544444458888887644
No 88
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=62.91 E-value=16 Score=25.14 Aligned_cols=36 Identities=28% Similarity=0.270 Sum_probs=27.7
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEE
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRV 60 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v 60 (216)
.++.||.|.|..+. +.--+|+|.++.... +.+.+..
T Consensus 8 ~I~~GD~V~Vi~G~--dKGK~G~V~~V~~~~-~~V~Veg 43 (83)
T CHL00141 8 HVKIGDTVKIISGS--DKGKIGEVLKIIKKS-NKVIVKG 43 (83)
T ss_pred cccCCCEEEEeEcC--CCCcEEEEEEEEcCC-CEEEEcC
Confidence 68899999999986 677899999998754 3344443
No 89
>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=61.85 E-value=3.8 Score=24.02 Aligned_cols=35 Identities=20% Similarity=0.577 Sum_probs=17.4
Q ss_pred eEeCccccceecCcCCCCChhhhcCCCeEEcccccccccc
Q 027964 153 MVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (216)
Q Consensus 153 ~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (216)
.+.|..|+...-.-|.-.. ....|+|+.|...+..
T Consensus 2 p~rC~~C~aylNp~~~~~~-----~~~~w~C~~C~~~N~l 36 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDD-----GGKTWICNFCGTKNPL 36 (40)
T ss_dssp S-B-TTT--BS-TTSEEET-----TTTEEEETTT--EEE-
T ss_pred ccccCCCCCEECCcceEcC-----CCCEEECcCCCCcCCC
Confidence 3567777776655553332 2258999999987654
No 90
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=60.28 E-value=16 Score=27.08 Aligned_cols=40 Identities=20% Similarity=0.059 Sum_probs=27.4
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEcC-CCCEEEEEE
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADH-RNNVKVRVR 61 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~-~g~~~v~v~ 61 (216)
.+++||.|+...+.....+.-|+|+...+.. .....+.|.
T Consensus 55 ~L~~GD~VLA~~~~~~~~Y~Pg~V~~~~~~~~~~~~~~~V~ 95 (124)
T PF15057_consen 55 SLQVGDKVLAPWEPDDCRYGPGTVIAGPERRASEDKEYTVR 95 (124)
T ss_pred cCCCCCEEEEecCcCCCEEeCEEEEECccccccCCceEEEE
Confidence 7899999999987654556669999876543 222444454
No 91
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=59.39 E-value=3.1 Score=41.57 Aligned_cols=52 Identities=23% Similarity=0.595 Sum_probs=41.6
Q ss_pred EEeCCCCCCCCceEeCccccceecCcCCCCChhhhcCCCeEEcccccccccc
Q 027964 141 CKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (216)
Q Consensus 141 C~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (216)
=+|..|++|+..+|-|-.|..|+|..-+.+....-...-.+.|-.|.+.+.+
T Consensus 1126 ~i~~~p~~pg~~~i~~~~~~~~~~~~~v~ln~s~~p~~~~~k~~~~~ri~~P 1177 (1414)
T KOG1473|consen 1126 FICTLPYNPGLTYIHCTVCMTWGHKEAVKLNSSPIPEVVGFKCCQCRRIRSP 1177 (1414)
T ss_pred cceeeccCCCCCcceEEEeeccCcceeEecCCCcchHHhhhhHHhhhccCCC
Confidence 3999999999999999999999999999887543222236888888876653
No 92
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=59.30 E-value=5 Score=31.05 Aligned_cols=34 Identities=21% Similarity=0.531 Sum_probs=22.6
Q ss_pred eCccccceecCcCCCCChhhhcCCCeEEcccccccccc
Q 027964 155 QCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (216)
Q Consensus 155 ~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (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 388888766666555544444 357999999 5554
No 93
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=58.51 E-value=20 Score=25.86 Aligned_cols=36 Identities=22% Similarity=0.282 Sum_probs=28.0
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEE
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRV 60 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v 60 (216)
.++.||.|.|..+. +.--+|+|.++.... +.+.|+.
T Consensus 4 ~i~kGD~V~Vi~G~--dKGk~G~V~~V~~~~-~~V~Veg 39 (105)
T PRK00004 4 KIKKGDTVIVIAGK--DKGKRGKVLKVLPKK-NKVIVEG 39 (105)
T ss_pred cccCCCEEEEeEcC--CCCcEEEEEEEEcCC-CEEEEcC
Confidence 68899999999987 677899999998753 3344443
No 94
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=58.34 E-value=8.5 Score=23.55 Aligned_cols=35 Identities=20% Similarity=0.387 Sum_probs=24.2
Q ss_pred CcceE-EeCCCCC-CCCceEeCccccceecCcCCCCC
Q 027964 137 VAVYC-KCEMPYN-PDDLMVQCEGCKDWFHPSCMGMT 171 (216)
Q Consensus 137 ~~~~C-~C~~~~~-~~~~~i~C~~C~~w~H~~Cv~~~ 171 (216)
.+.+| +|+...- .......|..|+...|..|+..-
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~~ 46 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSKV 46 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCTS
T ss_pred CCCCCcccCcccCCCCCCeEEECCCCChHhhhhhhhc
Confidence 45566 7777652 24566899999999999998653
No 95
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=57.40 E-value=5.7 Score=32.08 Aligned_cols=31 Identities=32% Similarity=0.783 Sum_probs=25.3
Q ss_pred ceEeCccccceecCcCCCCChhhhcCCCeEEcccccccccc
Q 027964 152 LMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (216)
Q Consensus 152 ~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (216)
.-++|+.|..-||..|... . .||.|.+....
T Consensus 171 ~~~~C~~C~~v~H~~C~~~--~--------~CpkC~R~~~r 201 (202)
T PF13901_consen 171 TTVRCPKCKSVFHKSCFRK--K--------SCPKCARRQKR 201 (202)
T ss_pred CeeeCCcCccccchhhcCC--C--------CCCCcHhHhcc
Confidence 6689999999999999883 1 39999887553
No 96
>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=54.97 E-value=38 Score=23.72 Aligned_cols=41 Identities=10% Similarity=0.323 Sum_probs=29.8
Q ss_pred CCCCCCcceeeEEEcCCCeEEccCCeEEEccCCCCCCCeEEEEeEEEEcC
Q 027964 3 KTKPGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADH 52 (216)
Q Consensus 3 ~~~~~~~~y~~~~v~~~~~~~~vGD~V~v~~~~~~~~~~I~~I~~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 44566556666666543 9999999988766 48899988854
No 97
>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=54.78 E-value=34 Score=24.12 Aligned_cols=42 Identities=12% Similarity=0.283 Sum_probs=30.3
Q ss_pred CCCCCCcceeeEEEcCCCeEEccCCeEEEccCCCCCCCeEEEEeEEEEcCC
Q 027964 3 KTKPGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHR 53 (216)
Q Consensus 3 ~~~~~~~~y~~~~v~~~~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~ 53 (216)
+..+|.-.....+|... ++++||++.+-.. .|||..|+.+..
T Consensus 9 ~~~~g~G~vatviV~~G--tL~~Gd~iv~G~~-------~gkVr~l~d~~g 50 (95)
T cd03702 9 KLDKGRGPVATVLVQNG--TLKVGDVLVAGTT-------YGKVRAMFDENG 50 (95)
T ss_pred EecCCCCccEEEEEEcC--eEeCCCEEEEccc-------ccEEEEEECCCC
Confidence 44566556666767543 9999999988765 469999998643
No 98
>PRK08359 transcription factor; Validated
Probab=54.74 E-value=5.7 Score=31.48 Aligned_cols=35 Identities=23% Similarity=0.452 Sum_probs=23.5
Q ss_pred eCccccceecCcCCCCChhhhcCCCeEEcccccccccc
Q 027964 155 QCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (216)
Q Consensus 155 ~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (216)
+|+.|+.=..+....+..+.+ .-.+|..|..+.|.
T Consensus 8 ~CEiCG~~i~g~~~~v~ieGa---el~VC~~Ca~k~G~ 42 (176)
T PRK08359 8 YCEICGAEIRGPGHRIRIEGA---ELLVCDRCYEKYGR 42 (176)
T ss_pred eeecCCCccCCCCeEEEEcCe---EEehHHHHHHHhCC
Confidence 488887766666554444444 35799999966665
No 99
>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 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=53.20 E-value=51 Score=25.36 Aligned_cols=28 Identities=32% Similarity=0.488 Sum_probs=20.8
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEE
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIE 49 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~ 49 (216)
.++.||.|.+..+......+|.||..+-
T Consensus 51 ~~~rGDiVvf~~~~~~~~~~iKRVig~p 78 (163)
T TIGR02227 51 DPKRGDIVVFKDPDDNKNIYVKRVIGLP 78 (163)
T ss_pred CCCCCcEEEEecCCCCCceeEEEEEecC
Confidence 5678898888876544668888887764
No 101
>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=52.98 E-value=10 Score=21.06 Aligned_cols=25 Identities=16% Similarity=0.490 Sum_probs=16.2
Q ss_pred eCccccceecCcCCCCChhhhcCCCeEEcccccccc
Q 027964 155 QCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDV 190 (216)
Q Consensus 155 ~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~ 190 (216)
+|..|+..|.+.- +.|.||.|....
T Consensus 3 ~C~~CGy~y~~~~-----------~~~~CP~Cg~~~ 27 (33)
T cd00350 3 VCPVCGYIYDGEE-----------APWVCPVCGAPK 27 (33)
T ss_pred ECCCCCCEECCCc-----------CCCcCcCCCCcH
Confidence 5667766554432 468999997643
No 102
>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=52.92 E-value=9.9 Score=23.57 Aligned_cols=36 Identities=19% Similarity=0.499 Sum_probs=20.1
Q ss_pred eCccccceecCcCC----CCC--hhhhcCCCeEEcccccccc
Q 027964 155 QCEGCKDWFHPSCM----GMT--IEEAKKLDHFLCSDCSSDV 190 (216)
Q Consensus 155 ~C~~C~~w~H~~Cv----~~~--~~~~~~~~~~~C~~C~~~~ 190 (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 46677755554311 111 1122356789999998653
No 103
>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=52.78 E-value=27 Score=25.16 Aligned_cols=35 Identities=23% Similarity=0.267 Sum_probs=27.3
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEE
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVR 59 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~ 59 (216)
.++.||.|.|..+. +.--+|.|.+|.... +.+.|+
T Consensus 3 ~ikkGD~V~Vi~G~--dKGK~G~V~~V~~~~-~~V~Ve 37 (104)
T TIGR01079 3 KIKKGDTVKVISGK--DKGKRGKVLKVLPKT-NKVIVE 37 (104)
T ss_pred cccCCCEEEEeEcC--CCCcEEEEEEEEcCC-CEEEEC
Confidence 47889999999987 677899999998754 334443
No 104
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=52.78 E-value=5.1 Score=20.93 Aligned_cols=13 Identities=38% Similarity=0.894 Sum_probs=9.6
Q ss_pred eEeCccccceecC
Q 027964 153 MVQCEGCKDWFHP 165 (216)
Q Consensus 153 ~i~C~~C~~w~H~ 165 (216)
|++|..|+..|..
T Consensus 2 l~~C~~CgR~F~~ 14 (25)
T PF13913_consen 2 LVPCPICGRKFNP 14 (25)
T ss_pred CCcCCCCCCEECH
Confidence 6778888887753
No 105
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=52.09 E-value=36 Score=25.18 Aligned_cols=41 Identities=22% Similarity=0.157 Sum_probs=30.4
Q ss_pred eEEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEee
Q 027964 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYY 64 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfy 64 (216)
..|+.||.|.|.++. +.--.|+|.++... .+.+.|+..-.-
T Consensus 44 ~~IkkGD~V~VisG~--~KGk~GkV~~V~~~-~~~V~VeGvn~~ 84 (120)
T PRK01191 44 LPVRKGDTVKVMRGD--FKGEEGKVVEVDLK-RGRIYVEGVTVK 84 (120)
T ss_pred ceEeCCCEEEEeecC--CCCceEEEEEEEcC-CCEEEEeCcEEE
Confidence 479999999999997 56668999999774 344555554433
No 106
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=51.97 E-value=4.4 Score=29.73 Aligned_cols=53 Identities=21% Similarity=0.456 Sum_probs=36.3
Q ss_pred cceE-EeCCCCCC-CCceEeCccccceecCcCCCCChhhhcCCCeEEcccccccccccc
Q 027964 138 AVYC-KCEMPYNP-DDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAKR 194 (216)
Q Consensus 138 ~~~C-~C~~~~~~-~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~~ 194 (216)
...| .|+.+... +..-..|..|+..+...|-..... -..|+|..|.+....+.
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~~~----~~~WlC~vC~k~rel~~ 108 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYSKK----EPIWLCKVCQKQRELKK 108 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEETSS----SCCEEEHHHHHHHHHHH
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCcCCC----CCCEEChhhHHHHHHHH
Confidence 4467 67776532 223488999999999999877322 24799999998877653
No 107
>PTZ00112 origin recognition complex 1 protein; Provisional
Probab=51.85 E-value=29 Score=34.77 Aligned_cols=95 Identities=21% Similarity=0.219 Sum_probs=60.6
Q ss_pred cceeeEEEcCCCeEEccCCeEEEccCCCC--------------------C--CCeEEEEeEEEEcC-CCCEEEEEEEeec
Q 027964 9 KDLDSYNIKGTNKVVRPGDCVLMRPADSD--------------------K--PPYVARVEKIEADH-RNNVKVRVRWYYR 65 (216)
Q Consensus 9 ~~y~~~~v~~~~~~~~vGD~V~v~~~~~~--------------------~--~~~I~~I~~i~~~~-~g~~~v~v~Wfyr 65 (216)
--|.+..|++ +.|.+||.|+|..+... . ..-=|+|.+|+... ...+.++|..||-
T Consensus 441 ~iye~~~in~--~~ys~g~dv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~kg~is~fy~~~~~~~~~~e~c~y~d 518 (1164)
T PTZ00112 441 VIYESIQIND--VEYSIGDDVLIFCTGNGNTYNGKSGTKKNQNNKNIKENIYQLRKGKISSFYKNTNSNQVEAEVCIYYD 518 (1164)
T ss_pred eEEEEEEEcc--eeeccCCcEEEEEcCCCCccccccCccccccccchhhhhheecccccchhhhcCCCceeeEEEEEEEc
Confidence 3577888875 79999999999875421 0 12348899998865 4458999999998
Q ss_pred ccccCCc--------ccccCCCCeeeeeCc-----------cceeecceeeeeeEEEee
Q 027964 66 PEESIGG--------RRQFHGAKELFLSDH-----------YDVQSAHTIEGKCTVHTF 105 (216)
Q Consensus 66 p~d~~~~--------~~~~~~~~ELF~s~~-----------~d~~~~~~I~gkc~V~~~ 105 (216)
..|..-. .+..-..-|+|+-+. +-.+.+..|..|..|...
T Consensus 519 ~~d~~~i~~~~~~~~~rr~~~~f~~~~d~~~~~~~llgni~f~~~~~~~i~kki~~~ne 577 (1164)
T PTZ00112 519 QHDAQYIKELEEKQKSRRCKADFEVFLDDDTKNFYLLGNIHFKILDAKMILKKIYVYNE 577 (1164)
T ss_pred cccHHHHHHHHHHHHhhhhhhhhhHhcccccceeEEecceeEEEechHhhhhhheeecc
Confidence 8874310 111123446666544 333455566666666653
No 108
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=51.66 E-value=2 Score=38.02 Aligned_cols=68 Identities=24% Similarity=0.423 Sum_probs=43.7
Q ss_pred CCcceE-EeCCCCCCCCceEeCccccceecCcCCCCChhhhcCCCeEEccccccccc-ccccCCCCCCCCCCCCC
Q 027964 136 RVAVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD-AKRSLNTFSVSPSVEAK 208 (216)
Q Consensus 136 ~~~~~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~-~~~~~~~~~~~~~~~~~ 208 (216)
....|| .|++.+.--.+-.|--.|...||..|+..-.+. -..-.||.|.+-.. ++ +-++-++++.++.
T Consensus 363 e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~---n~~rsCP~CrklrSs~~--rpgfvgs~~Vese 432 (518)
T KOG1941|consen 363 ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN---NGTRSCPNCRKLRSSMK--RPGFVGSVPVESE 432 (518)
T ss_pred HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh---CCCCCCccHHHHHhhcc--CCCCcCCCccccc
Confidence 457789 899887555566777789999999998632211 13468999994322 12 2344455555543
No 109
>COG5475 Uncharacterized small protein [Function unknown]
Probab=51.26 E-value=62 Score=20.57 Aligned_cols=37 Identities=14% Similarity=0.210 Sum_probs=24.7
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeeccc
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPE 67 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~ 67 (216)
.+.+||.|.+..+.+ .-|++=.. ..-+++.+||-+..
T Consensus 4 ~FstgdvV~lKsGGP------~Mtvs~~s---s~Gmy~C~Wf~g~g 40 (60)
T COG5475 4 SFSTGDVVTLKSGGP------RMTVSGYS---SDGMYECRWFDGYG 40 (60)
T ss_pred eeecCcEEEeecCCc------eEEEeccc---cCCeEEEEEecCCC
Confidence 688999999999873 12222111 11578999997765
No 110
>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=51.02 E-value=22 Score=21.73 Aligned_cols=37 Identities=22% Similarity=0.467 Sum_probs=18.3
Q ss_pred EeCccccceecCcCC----CCC--hhhhcCCCeEEcccccccc
Q 027964 154 VQCEGCKDWFHPSCM----GMT--IEEAKKLDHFLCSDCSSDV 190 (216)
Q Consensus 154 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~K 44 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAPK 44 (47)
T ss_dssp EEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSBG
T ss_pred cCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCcc
Confidence 356677766654322 111 1123346789999998753
No 111
>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=49.68 E-value=39 Score=27.72 Aligned_cols=56 Identities=20% Similarity=0.425 Sum_probs=41.9
Q ss_pred ceeeEEEcCCCeEEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeeccc
Q 027964 10 DLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPE 67 (216)
Q Consensus 10 ~y~~~~v~~~~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~ 67 (216)
.|+-|.-+.....+.+|+.=.+..+...-|-+.|+|..|... +...|++.|+---.
T Consensus 15 dF~dF~~~R~~~~F~~gQIWAlYd~~D~mPR~Ya~I~kV~~~--~~Fkl~i~wLe~~~ 70 (217)
T PF11926_consen 15 DFYDFDKDRSEEKFQVGQIWALYDDDDGMPRYYARIKKVDSS--NPFKLHITWLEPCP 70 (217)
T ss_pred ccccccCCchHHhCCCCCEEEEeeCCCCCeeeEEEEEEEecC--CCeEEEEEEccccC
Confidence 344554444456889999999998766789999999999874 34689999975544
No 112
>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=49.22 E-value=27 Score=24.09 Aligned_cols=42 Identities=21% Similarity=0.265 Sum_probs=29.1
Q ss_pred EccCCeEEEccCCCCCCCeEEEEeEEEEcC----CCCEEEEEEEeecc
Q 027964 23 VRPGDCVLMRPADSDKPPYVARVEKIEADH----RNNVKVRVRWYYRP 66 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~----~g~~~v~v~Wfyrp 66 (216)
+++||.|.-.-.. -+.|-|+|.+-..+. ...-.+.|.||-.+
T Consensus 1 f~~GDlVwaK~~g--~P~WPa~V~~~~~~~~~~~~~~~~~~V~FFG~~ 46 (86)
T cd05836 1 LKLGDLVWAKMKG--FPPWPGRIVKPPKDLKKPRGKAKCFFVFFFGSE 46 (86)
T ss_pred CCCCCEEEEeCCC--CCCCCEEEechhhhcccccCCCCeEEEEEeCCC
Confidence 4689999999886 899999998754321 11245667776644
No 113
>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=49.10 E-value=36 Score=24.20 Aligned_cols=43 Identities=21% Similarity=0.431 Sum_probs=29.3
Q ss_pred CCCcceeeEEEcCCCeEEccCCeEEEccCCCCCCCeEEEEeEEEE
Q 027964 6 PGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (216)
Q Consensus 6 ~~~~~y~~~~v~~~~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~ 50 (216)
+|+|.-..-........+++||.+.|...+ .+.-+.+|.++..
T Consensus 14 ~G~Ktat~r~~~~~~~~~k~Gd~~i~~~~~--~~~~~i~v~~V~~ 56 (105)
T cd06541 14 SGRKTIEIRSLDIYEQLPKAGDYLIILDGQ--QPLAIAEVVKVEI 56 (105)
T ss_pred CCCCEEEEEcchhcccCCCCCCEEEEecCC--CcEEEEEEEEEEE
Confidence 455555544333223578999999998876 6667888888765
No 114
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=48.94 E-value=42 Score=25.67 Aligned_cols=42 Identities=12% Similarity=0.063 Sum_probs=30.9
Q ss_pred eEEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeec
Q 027964 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYR 65 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyr 65 (216)
..|+.||.|.|.++. +.--.|+|.++... ++.+.|...-.-.
T Consensus 45 ~~IkkGD~V~Vi~Gk--~KGk~GkV~~V~~k-~~~ViVEgvn~~K 86 (143)
T PTZ00194 45 MPVRKDDEVMVVRGH--HKGREGKVTAVYRK-KWVIHIEKITREK 86 (143)
T ss_pred ceeecCCEEEEecCC--CCCCceEEEEEEcC-CCEEEEeCeEEEe
Confidence 479999999999997 45567999999773 4456665544433
No 115
>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=48.66 E-value=24 Score=25.53 Aligned_cols=43 Identities=16% Similarity=0.174 Sum_probs=31.5
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEE---------cCCCCEEEEEEEeecc
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEA---------DHRNNVKVRVRWYYRP 66 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~---------~~~g~~~v~v~Wfyrp 66 (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 58899999999886 7999999985211 1223367888888754
No 116
>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=48.32 E-value=17 Score=19.66 Aligned_cols=26 Identities=19% Similarity=0.393 Sum_probs=18.1
Q ss_pred EeCCCCCCCCceEeCccccceecCcCC
Q 027964 142 KCEMPYNPDDLMVQCEGCKDWFHPSCM 168 (216)
Q Consensus 142 ~C~~~~~~~~~~i~C~~C~~w~H~~Cv 168 (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 4655543333 7888988888888884
No 117
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=47.40 E-value=15 Score=31.69 Aligned_cols=56 Identities=13% Similarity=0.163 Sum_probs=41.5
Q ss_pred CCCcceEEeCCCCCCCCceEeCccccceecCcCCCCChhhhcCCCeEEccccccccccc
Q 027964 135 DRVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 193 (216)
Q Consensus 135 ~~~~~~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~~ 105 (345)
T KOG2752|consen 50 KKRQALFSCLTCTPAPEMAGVCYACSLSCHDGHELVELYTK---RNFRCDCGNSKFGRC 105 (345)
T ss_pred ccccceeEeecccCChhhceeEEEeeeeecCCceeeecccc---CCccccccccccccc
Confidence 34566788877776666899999999999998877643221 368898888777655
No 118
>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=47.06 E-value=48 Score=24.05 Aligned_cols=44 Identities=20% Similarity=0.339 Sum_probs=27.6
Q ss_pred CCCcceeeEEEcCCCeEEccCCeEEEccCCCCCCCeEEEEeEEEE
Q 027964 6 PGKKDLDSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (216)
Q Consensus 6 ~~~~~y~~~~v~~~~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~ 50 (216)
+|+|.+---.-+.+-..|++||.+.+..-+. ......+|..|..
T Consensus 15 ~G~KtiEiRlnD~kr~~ikvGD~I~f~~~~~-~~~l~v~V~~i~~ 58 (109)
T cd06555 15 SGKKTIEIRLNDEKRQQIKVGDKILFNDLDT-GQQLLVKVVDIRK 58 (109)
T ss_pred cCCCEEEEEecccchhcCCCCCEEEEEEcCC-CcEEEEEEEEEEe
Confidence 5666655443333223699999999987652 4456667776655
No 119
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=46.76 E-value=23 Score=22.41 Aligned_cols=30 Identities=17% Similarity=0.233 Sum_probs=21.5
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEcC
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADH 52 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~ 52 (216)
.+..|+.|.+..++ +..+|-|+|.++-...
T Consensus 5 k~~~Ge~V~~rWP~-s~lYYe~kV~~~d~~~ 34 (55)
T PF09465_consen 5 KFAIGEVVMVRWPG-SSLYYEGKVLSYDSKS 34 (55)
T ss_dssp SS-SS-EEEEE-TT-TS-EEEEEEEEEETTT
T ss_pred cccCCCEEEEECCC-CCcEEEEEEEEecccC
Confidence 46789999999998 5788899999987643
No 120
>KOG1740 consensus Predicted mitochondrial/chloroplast ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=45.89 E-value=16 Score=26.10 Aligned_cols=29 Identities=21% Similarity=0.284 Sum_probs=24.1
Q ss_pred cceeeEEEcCCCeEEccCCeEEEccCCCC
Q 027964 9 KDLDSYNIKGTNKVVRPGDCVLMRPADSD 37 (216)
Q Consensus 9 ~~y~~~~v~~~~~~~~vGD~V~v~~~~~~ 37 (216)
+++..|-+++++...++||.|-+.+.-+.
T Consensus 36 ~~~~kymahD~~n~cnvGD~VrlepsRPl 64 (107)
T KOG1740|consen 36 KRTSKYMAHDDKNQCNVGDRVRLEPSRPL 64 (107)
T ss_pred HHhhheeecCccccccccceEEeccCCcc
Confidence 45667888888889999999999997643
No 121
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=45.85 E-value=21 Score=30.98 Aligned_cols=51 Identities=27% Similarity=0.440 Sum_probs=30.8
Q ss_pred EeCccccceecCcCCCCChhhhcCCCeEEccccccccccccc-----CCCCCCCCCCCCCC
Q 027964 154 VQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAKRS-----LNTFSVSPSVEAKV 209 (216)
Q Consensus 154 i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~~~-----~~~~~~~~~~~~~~ 209 (216)
+.|..|.. |-.|+.. ++. ..-.|+|+.|..-++.+.. ...+.+.|++++|.
T Consensus 221 LIC~~C~~--HNGla~~--ee~-~yi~F~C~~Cn~LN~~~k~~e~s~~~~~~a~ps~s~k~ 276 (328)
T KOG2846|consen 221 LICSQCHH--HNGLARK--EEY-EYITFRCPHCNALNPAKKSPENSLEAPQPAPPSSSSKP 276 (328)
T ss_pred hcchhhcc--ccCcCCh--hhc-CceEEECccccccCCCcCCcccccccCCCCCcccccCC
Confidence 55666653 6666655 222 2248999999998887744 33444445554443
No 122
>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=45.33 E-value=55 Score=21.08 Aligned_cols=30 Identities=23% Similarity=0.299 Sum_probs=23.0
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEc
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEAD 51 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~ 51 (216)
++++||.|++.+.+.+..+..++|.+|+..
T Consensus 12 ~l~~gd~v~~~~~~~~~~~~~~~I~~i~~~ 41 (74)
T PF03144_consen 12 TLKKGDKVRVLPNGTGKKGQVVKIKSIFMF 41 (74)
T ss_dssp EEETTEEEEEESTTTTEECEEEEEEEEEET
T ss_pred EEcCCCEEEECccCCcceeeeeeccccccc
Confidence 899999999977322244578999998875
No 123
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=44.33 E-value=17 Score=20.77 Aligned_cols=13 Identities=23% Similarity=0.532 Sum_probs=7.7
Q ss_pred CCceEeCccccce
Q 027964 150 DDLMVQCEGCKDW 162 (216)
Q Consensus 150 ~~~~i~C~~C~~w 162 (216)
.+.+++|..|+.-
T Consensus 22 ~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 22 KGRKVRCSKCGHV 34 (36)
T ss_pred CCcEEECCCCCCE
Confidence 4456777777543
No 124
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=43.90 E-value=31 Score=21.63 Aligned_cols=28 Identities=21% Similarity=0.223 Sum_probs=23.1
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEE
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~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 47899999999865 46788899998865
No 125
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=43.38 E-value=50 Score=23.82 Aligned_cols=37 Identities=22% Similarity=0.136 Sum_probs=28.8
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEe
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWY 63 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wf 63 (216)
.++.||.|+|.++. +.---|+|.++.... +.|++--.
T Consensus 4 ~IrkGD~V~Vi~Gk--dKGk~GkVl~v~~k~---V~VEGvnv 40 (104)
T COG0198 4 KVKKGDTVKVIAGK--DKGKEGKVLKVLPKK---VVVEGVNV 40 (104)
T ss_pred ceecCCEEEEEecC--CCCcceEEEEEecCe---EEEECcEE
Confidence 67899999999997 677789999988754 55555433
No 126
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=43.21 E-value=10 Score=25.15 Aligned_cols=42 Identities=26% Similarity=0.341 Sum_probs=17.8
Q ss_pred ceEeCc--cccceecCcCCCCChh--hhc----CCCeEEccccccccccc
Q 027964 152 LMVQCE--GCKDWFHPSCMGMTIE--EAK----KLDHFLCSDCSSDVDAK 193 (216)
Q Consensus 152 ~~i~C~--~C~~w~H~~Cv~~~~~--~~~----~~~~~~C~~C~~~~~~~ 193 (216)
.-+.|+ .|..-||..|+-.--. +.. .+-...||.|......+
T Consensus 19 p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~ 68 (70)
T PF11793_consen 19 PDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS 68 (70)
T ss_dssp --B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred CceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence 457798 8999999999943211 111 12357899999876543
No 127
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=42.83 E-value=9.2 Score=22.55 Aligned_cols=33 Identities=21% Similarity=0.370 Sum_probs=22.7
Q ss_pred cceE-EeCCCCCCCCceEeCccccceecCcCCCC
Q 027964 138 AVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGM 170 (216)
Q Consensus 138 ~~~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~ 170 (216)
+.+| +|+...-.......|..|+.-.|..|+..
T Consensus 11 ~~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~~ 44 (49)
T smart00109 11 PTKCCVCRKSIWGSFQGLRCSWCKVKCHKKCAEK 44 (49)
T ss_pred CCCccccccccCcCCCCcCCCCCCchHHHHHHhh
Confidence 4456 67665432113678999999999999754
No 128
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=42.15 E-value=10 Score=28.56 Aligned_cols=51 Identities=20% Similarity=0.400 Sum_probs=36.0
Q ss_pred EeCCCCCCCCceEeCccccceecCcCCCCChhhhcCCCeEEccccccccccc
Q 027964 142 KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 193 (216)
Q Consensus 142 ~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~ 193 (216)
+|...--.|+---.|.-|+.-|...|-|--...... ..|+|..|.....+-
T Consensus 70 IC~KTKFADG~GH~C~YCq~r~CARCGGrv~lrsNK-v~wvcnlc~k~q~il 120 (169)
T KOG3799|consen 70 ICHKTKFADGCGHNCSYCQTRFCARCGGRVSLRSNK-VMWVCNLCRKQQEIL 120 (169)
T ss_pred hhhhcccccccCcccchhhhhHHHhcCCeeeeccCc-eEEeccCCcHHHHHH
Confidence 777765556655678889999999998754433322 479999999866543
No 129
>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=41.74 E-value=18 Score=33.34 Aligned_cols=33 Identities=24% Similarity=0.607 Sum_probs=17.5
Q ss_pred ceecCcCCC-CChhhhcC-----C-CeEEccccccccccc
Q 027964 161 DWFHPSCMG-MTIEEAKK-----L-DHFLCSDCSSDVDAK 193 (216)
Q Consensus 161 ~w~H~~Cv~-~~~~~~~~-----~-~~~~C~~C~~~~~~~ 193 (216)
-||++.|+- ++..++.. . .=|.||.|.......
T Consensus 26 ~~yCp~CL~~~p~~e~~~~~nrC~r~Cf~CP~C~~~L~~~ 65 (483)
T PF05502_consen 26 SYYCPNCLFEVPSSEARSEKNRCSRNCFDCPICFSPLSVR 65 (483)
T ss_pred eeECccccccCChhhheeccceeccccccCCCCCCcceeE
Confidence 477777773 44333311 0 127777787654433
No 130
>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=40.64 E-value=69 Score=23.49 Aligned_cols=42 Identities=24% Similarity=0.173 Sum_probs=31.3
Q ss_pred eEEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeec
Q 027964 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYR 65 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyr 65 (216)
..++.||.|.|..+. +.-..|+|.+|.. ..+.+.|+..-...
T Consensus 40 ~~IkkGD~V~Vi~Gk--~KGk~GkV~~V~~-~~~~V~Vegvn~~k 81 (114)
T TIGR01080 40 LPVRKGDKVRIMRGD--FKGHEGKVSKVDL-KRYRIYVEGVTKEK 81 (114)
T ss_pred ceeecCCEEEEecCC--CCCCEEEEEEEEc-CCCEEEEcCeEEEC
Confidence 478999999999997 5677899999984 34456665544444
No 131
>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=39.51 E-value=44 Score=16.94 Aligned_cols=15 Identities=20% Similarity=0.266 Sum_probs=10.8
Q ss_pred EEeEEEEcCCCCEEE
Q 027964 44 RVEKIEADHRNNVKV 58 (216)
Q Consensus 44 ~I~~i~~~~~g~~~v 58 (216)
.|..|.++++|.+||
T Consensus 6 ~I~~i~~D~~G~lWi 20 (24)
T PF07494_consen 6 NIYSIYEDSDGNLWI 20 (24)
T ss_dssp CEEEEEE-TTSCEEE
T ss_pred eEEEEEEcCCcCEEE
Confidence 367888888888776
No 132
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=39.24 E-value=11 Score=23.74 Aligned_cols=25 Identities=28% Similarity=0.992 Sum_probs=16.1
Q ss_pred eEEeCCCCC-------CCCceEeCccccceec
Q 027964 140 YCKCEMPYN-------PDDLMVQCEGCKDWFH 164 (216)
Q Consensus 140 ~C~C~~~~~-------~~~~~i~C~~C~~w~H 164 (216)
.|.|+..+. .....++|++|.-|.+
T Consensus 20 ~CRCG~~f~i~e~~l~~~~~iv~C~sCSL~I~ 51 (55)
T PF05207_consen 20 PCRCGGEFEISEEDLEEGEVIVQCDSCSLWIR 51 (55)
T ss_dssp EETTSSEEEEEHHHHHCT--EEEETTTTEEEE
T ss_pred cCCCCCEEEEcchhccCcCEEEECCCCccEEE
Confidence 477776551 1357799999998865
No 133
>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=38.95 E-value=43 Score=22.61 Aligned_cols=37 Identities=22% Similarity=0.284 Sum_probs=24.8
Q ss_pred eeEEEcCCCeEEccCCeEEEccCCCCCCCeEEEEeEEEEc
Q 027964 12 DSYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEAD 51 (216)
Q Consensus 12 ~~~~v~~~~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~ 51 (216)
..|.++.. ...++||+|.+...+ ...-+|+|.++...
T Consensus 13 ~~f~~~~~-~~v~~GeyV~i~~~~--~~~vlG~V~~i~~~ 49 (91)
T PF09378_consen 13 FEFIVEPS-KDVRVGEYVVIEYDD--GEKVLGMVTSISRG 49 (91)
T ss_dssp TEEEEEE--TT-BTTEEEEES------TTEEEEEEEEES-
T ss_pred EEEEEeCC-CCCCcCeEEEEEEec--hhhhhhhhheeEEc
Confidence 35556542 378999999999984 57899999999884
No 134
>PF06940 DUF1287: Domain of unknown function (DUF1287); InterPro: IPR009706 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=38.41 E-value=41 Score=26.21 Aligned_cols=43 Identities=21% Similarity=0.165 Sum_probs=30.7
Q ss_pred eEEEcCCCeEEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEE
Q 027964 13 SYNIKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKV 58 (216)
Q Consensus 13 ~~~v~~~~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v 58 (216)
+..+..+...++.||.|...-++ ..++||.|..-.. .+|..++
T Consensus 97 ~L~~~~~~~~~q~GDIVtw~l~~--~~~HIgIVSd~r~-~~G~p~v 139 (164)
T PF06940_consen 97 SLTTDINPEDWQPGDIVTWRLPG--GLPHIGIVSDRRS-KDGVPLV 139 (164)
T ss_pred eccCCCChhhcCCCCEEEEeCCC--CCCeEEEEeCCcC-CCCCEEE
Confidence 34444445689999999998765 6899999988765 3554443
No 135
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=38.29 E-value=5.8 Score=26.49 Aligned_cols=31 Identities=19% Similarity=0.473 Sum_probs=18.5
Q ss_pred ceEeCccccceecCcCCCCChhhhcCCCeEEccccc
Q 027964 152 LMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCS 187 (216)
Q Consensus 152 ~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~ 187 (216)
..+.=..|+..||..|+..=... .-.||.|+
T Consensus 43 ~~i~~~~C~H~FH~~Ci~~Wl~~-----~~~CP~CR 73 (73)
T PF12678_consen 43 CPIVWGPCGHIFHFHCISQWLKQ-----NNTCPLCR 73 (73)
T ss_dssp S-EEEETTSEEEEHHHHHHHHTT-----SSB-TTSS
T ss_pred cceEecccCCCEEHHHHHHHHhc-----CCcCCCCC
Confidence 33444569999999999532221 12888884
No 136
>KOG2133 consensus Transcriptional corepressor Atrophin-1/DRPLA [General function prediction only]
Probab=37.51 E-value=22 Score=35.26 Aligned_cols=113 Identities=15% Similarity=0.191 Sum_probs=77.7
Q ss_pred CeEEccCCeEEEccCCCCCCCeEEEEeEEEEcCC-CCEEEEEEEeecccccC-Cc---c--------------cccCCCC
Q 027964 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEADHR-NNVKVRVRWYYRPEESI-GG---R--------------RQFHGAK 80 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~-g~~~v~v~Wfyrp~d~~-~~---~--------------~~~~~~~ 80 (216)
+..|.++|.|.+....+ .++.|+.|-.+...++ ..+.++...+.|++|++ .+ . .+-...+
T Consensus 143 e~~y~~~~~l~~~v~~~-~p~lia~~~~~~~~Kr~~~~~~k~s~~~r~~d~Pet~y~~~m~pe~Ar~e~~P~~~pq~~sq 221 (1229)
T KOG2133|consen 143 ETLYDLRDSLFVEVSQP-EPYLIAAICGFKYTKRDDRQVVKLSFYFRADDIPETGYLNLMKPERARLEINPHLCPQPLSQ 221 (1229)
T ss_pred chhhhhhhhhhhhhccC-CccccccccCccccccccccccccccccccccCcccccccccCchhhhhccCCccCCCcchh
Confidence 45889999999988864 7788888877766554 56778888889999887 22 0 0113567
Q ss_pred eeeeeCccce-eecceeeeeeEEEeeecccccc------CCCCcceEEeeeeecccCccc
Q 027964 81 ELFLSDHYDV-QSAHTIEGKCTVHTFKNYTKLE------NVGAEDYFCRFEYKAATGGFT 133 (216)
Q Consensus 81 ELF~s~~~d~-~~~~~I~gkc~V~~~~~~~~~~------~~~~~~ffcr~~yd~~~~~f~ 133 (216)
|||.+.-.++ .+..+..|||.+....++..-. ....++||-..+|.+.+....
T Consensus 222 ~l~~s~l~~i~qppscp~gk~~~~~skd~~h~~~~n~p~~ld~~i~fk~agglpps~k~a 281 (1229)
T KOG2133|consen 222 ELFNSELQGITQPPSCPRGKGIAEYSKDVRHGGNTNAPFSLDNDIFFKCAGGLPPSTKPA 281 (1229)
T ss_pred hhhcccccCCCCCCcCCCCCceEEeecccccCCccCCCCcccceeeeecccCCCCCCCCC
Confidence 8888877744 8899999999988655553222 123455666677776655443
No 137
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=36.72 E-value=7 Score=36.65 Aligned_cols=34 Identities=21% Similarity=0.532 Sum_probs=26.2
Q ss_pred ceEeCccccceecCcCCCCChhhhcCCCeEEccccccccccc
Q 027964 152 LMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 193 (216)
Q Consensus 152 ~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~ 193 (216)
.-..|+.|..|||..|...... .||.|.+.....
T Consensus 530 ~~~rC~~C~avfH~~C~~r~s~--------~CPrC~R~q~r~ 563 (580)
T KOG1829|consen 530 NTRRCSTCLAVFHKKCLRRKSP--------CCPRCERRQKRA 563 (580)
T ss_pred cceeHHHHHHHHHHHHHhccCC--------CCCchHHHHHHh
Confidence 4477999999999999876442 299999876533
No 138
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=36.33 E-value=64 Score=22.12 Aligned_cols=28 Identities=29% Similarity=0.233 Sum_probs=18.9
Q ss_pred eEEccCCeEEEccCCCCCCCeEEEEeEEEE
Q 027964 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~ 50 (216)
.-++.||+|+|...+ ...--|.|+....
T Consensus 42 iwI~~GD~VlVe~~~--~~~~kg~Iv~r~~ 69 (83)
T smart00652 42 VWIRRGDIVLVDPWD--FQDVKADIIYKYT 69 (83)
T ss_pred EEEcCCCEEEEEecC--CCCCEEEEEEEeC
Confidence 457889999998764 2255666666554
No 139
>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=36.32 E-value=74 Score=21.14 Aligned_cols=25 Identities=24% Similarity=0.449 Sum_probs=14.3
Q ss_pred EccCCeEEEccCCCCCCCeEEEEeE
Q 027964 23 VRPGDCVLMRPADSDKPPYVARVEK 47 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~~I~~ 47 (216)
++.||.|++...+.....++.||..
T Consensus 32 ~~~GDiv~~~~~~~~~~~~vkRv~~ 56 (85)
T cd06530 32 PKRGDVVVFKSPGDPGKPIIKRVIG 56 (85)
T ss_pred CCCCCEEEEeCCCCCCCEEEEEEEE
Confidence 5556666666654223556666665
No 140
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=36.25 E-value=82 Score=24.92 Aligned_cols=46 Identities=26% Similarity=0.448 Sum_probs=36.4
Q ss_pred eEEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeeccccc
Q 027964 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEES 69 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~d~ 69 (216)
..+.+||.|-|..+. -..+.|+|.++..+ .+.+.+.|.-|-|+--+
T Consensus 122 ~~~e~Gd~VrI~~Gp--Fa~f~g~V~evd~e-k~~~~v~v~ifgr~tPV 167 (178)
T COG0250 122 VDFEPGDVVRIIDGP--FAGFKAKVEEVDEE-KGKLKVEVSIFGRPTPV 167 (178)
T ss_pred ccCCCCCEEEEeccC--CCCccEEEEEEcCc-CcEEEEEEEEeCCceEE
Confidence 578999999999987 67799999999874 35577777777776543
No 141
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=36.05 E-value=1.5e+02 Score=23.76 Aligned_cols=19 Identities=26% Similarity=0.801 Sum_probs=9.5
Q ss_pred EeCCCCCCCCceEeCcccc
Q 027964 142 KCEMPYNPDDLMVQCEGCK 160 (216)
Q Consensus 142 ~C~~~~~~~~~~i~C~~C~ 160 (216)
.|+.+.-..+.|..|..|+
T Consensus 154 rC~~~L~~~~~~l~Cp~Cg 172 (188)
T COG1096 154 RCRAPLVKKGNMLKCPNCG 172 (188)
T ss_pred CCCcceEEcCcEEECCCCC
Confidence 4555444444555555554
No 142
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=35.81 E-value=1.3e+02 Score=20.77 Aligned_cols=28 Identities=18% Similarity=0.258 Sum_probs=20.6
Q ss_pred eeEEEcCCCeEEccCCeEEEccCCCCCC
Q 027964 12 DSYNIKGTNKVVRPGDCVLMRPADSDKP 39 (216)
Q Consensus 12 ~~~~v~~~~~~~~vGD~V~v~~~~~~~~ 39 (216)
..+.+++.+...++||.|.|...-|-++
T Consensus 40 kk~~aHDe~n~~~~GD~V~I~e~RPlSK 67 (84)
T CHL00142 40 KKYLVHDEENECNIGDQVLIEETRPLSK 67 (84)
T ss_pred EEEEEeCCCCCCCCCCEEEEEEcCCCCC
Confidence 3566777666899999999998664433
No 143
>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=35.57 E-value=1.2e+02 Score=20.80 Aligned_cols=42 Identities=26% Similarity=0.336 Sum_probs=26.5
Q ss_pred EeEEEEcCCCCEEEEE---EEeecccccC-------CcccccCCCCeeeeeCcc
Q 027964 45 VEKIEADHRNNVKVRV---RWYYRPEESI-------GGRRQFHGAKELFLSDHY 88 (216)
Q Consensus 45 I~~i~~~~~g~~~v~v---~Wfyrp~d~~-------~~~~~~~~~~ELF~s~~~ 88 (216)
|.+.+...|.-+.|+. +|+| |.++. .|..+ -.+.|||+-+..
T Consensus 20 V~dTY~~vD~lVNvHf~~GrWm~-P~~~~Y~VGyNe~GLGp-K~~~ElyiVnk~ 71 (85)
T PF12503_consen 20 VFDTYHRVDPLVNVHFPNGRWMY-PEGYEYMVGYNESGLGP-KFDGELYIVNKD 71 (85)
T ss_pred eEEEEeeccccEEEEecCCceec-CCCeEEEeeecCCCCCc-CcCCeEEEEcCc
Confidence 6666665666666664 5999 88753 11111 357899998764
No 144
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=34.42 E-value=1.3e+02 Score=20.72 Aligned_cols=26 Identities=19% Similarity=0.276 Sum_probs=19.3
Q ss_pred eEEEcCCCeEEccCCeEEEccCCCCC
Q 027964 13 SYNIKGTNKVVRPGDCVLMRPADSDK 38 (216)
Q Consensus 13 ~~~v~~~~~~~~vGD~V~v~~~~~~~ 38 (216)
.+.+++.+...++||.|.|...-|-+
T Consensus 44 k~~aHD~~n~~k~GD~V~I~e~rPlS 69 (84)
T PRK05610 44 KYHAHDENNEAKIGDVVRIMETRPLS 69 (84)
T ss_pred EEEEECCCCCCCCCCEEEEEEcccCC
Confidence 55567666689999999999865433
No 145
>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=34.17 E-value=66 Score=21.71 Aligned_cols=28 Identities=25% Similarity=0.162 Sum_probs=18.5
Q ss_pred eEEccCCeEEEccCCCCCCCeEEEEeEEEE
Q 027964 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~~I~~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 467889999998665 2455666665543
No 146
>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=33.90 E-value=51 Score=26.62 Aligned_cols=22 Identities=18% Similarity=0.445 Sum_probs=12.9
Q ss_pred EEEcCCCeEEccCCeEEEccCC
Q 027964 14 YNIKGTNKVVRPGDCVLMRPAD 35 (216)
Q Consensus 14 ~~v~~~~~~~~vGD~V~v~~~~ 35 (216)
+-+.+.+..|++||.+.|.+.+
T Consensus 33 ldl~~~~l~Y~pGD~l~V~P~N 54 (219)
T PF00667_consen 33 LDLSDSGLSYQPGDHLGVYPPN 54 (219)
T ss_dssp EE-TTSTG---TT-EEEEE-SS
T ss_pred EEeCCCCCcccCCCEEEEEccC
Confidence 3345568999999999999998
No 147
>PF11132 SplA: Transcriptional regulator protein (SplA); InterPro: IPR022608 The SplA protein functions in trans as a negative regulator of the level of splB-lacZ expression in the developing forespore [].
Probab=33.76 E-value=30 Score=23.21 Aligned_cols=25 Identities=20% Similarity=0.262 Sum_probs=19.1
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeE
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEK 47 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~ 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 789999999988774 4456777765
No 148
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=33.67 E-value=31 Score=24.44 Aligned_cols=21 Identities=24% Similarity=0.271 Sum_probs=15.4
Q ss_pred EEccCCeEEEccCCCCCCCeE
Q 027964 22 VVRPGDCVLMRPADSDKPPYV 42 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I 42 (216)
.+++||.|++.+...++.++|
T Consensus 76 ~Lk~GD~V~ll~~~~gQ~yiV 96 (100)
T PF10844_consen 76 GLKVGDKVLLLRVQGGQKYIV 96 (100)
T ss_pred CCcCCCEEEEEEecCCCEEEE
Confidence 679999999999654444443
No 149
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=33.20 E-value=37 Score=23.64 Aligned_cols=29 Identities=28% Similarity=0.584 Sum_probs=20.5
Q ss_pred ceE-EeCCCCCCCCceEeCccccceecCcCCC
Q 027964 139 VYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMG 169 (216)
Q Consensus 139 ~~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv~ 169 (216)
..| +|+++.....+.+. -|+.-+|..|..
T Consensus 79 ~~C~vC~k~l~~~~f~~~--p~~~v~H~~C~~ 108 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVVF--PCGHVVHYSCIK 108 (109)
T ss_pred CCccCcCCcCCCceEEEe--CCCeEEeccccc
Confidence 346 99998866545555 345899999974
No 150
>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=33.04 E-value=60 Score=22.00 Aligned_cols=29 Identities=14% Similarity=0.247 Sum_probs=19.1
Q ss_pred eEEccCCeEEEccCCCCCCCeEEEEeEEEE
Q 027964 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~~I~~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 5678899999987651 2345666665554
No 151
>KOG3896 consensus Dynactin, subunit p62 [Cell motility]
Probab=32.83 E-value=50 Score=28.99 Aligned_cols=25 Identities=32% Similarity=0.724 Sum_probs=10.4
Q ss_pred eecCcCCC-CChhhhcCCCeEEccccc
Q 027964 162 WFHPSCMG-MTIEEAKKLDHFLCSDCS 187 (216)
Q Consensus 162 w~H~~Cv~-~~~~~~~~~~~~~C~~C~ 187 (216)
.|+..|+. ++..++ +..+-.|++|.
T Consensus 46 hfCp~CLEn~ps~EA-rlKKn~CAnCf 71 (449)
T KOG3896|consen 46 HFCPRCLENSPSPEA-RLKKNKCANCF 71 (449)
T ss_pred ccchhhccCCCchHH-Hhhhccccccc
Confidence 34455554 333333 33343444443
No 152
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=32.72 E-value=30 Score=18.01 Aligned_cols=11 Identities=27% Similarity=0.818 Sum_probs=8.4
Q ss_pred CCCeEEccccc
Q 027964 177 KLDHFLCSDCS 187 (216)
Q Consensus 177 ~~~~~~C~~C~ 187 (216)
+...|.|++|-
T Consensus 13 ~~v~f~CPnCG 23 (24)
T PF07754_consen 13 QAVPFPCPNCG 23 (24)
T ss_pred cCceEeCCCCC
Confidence 34689999994
No 153
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=32.00 E-value=23 Score=30.43 Aligned_cols=37 Identities=24% Similarity=0.436 Sum_probs=23.9
Q ss_pred CCCceEeCccccceecCcCCCCChhhhcCCCeEEccccccccccc
Q 027964 149 PDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 193 (216)
Q Consensus 149 ~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~ 193 (216)
|++.|+.|+.|+...+. .+.+. ..++|+.|..-..+.
T Consensus 34 p~~lw~kc~~C~~~~~~-------~~l~~-~~~vcp~c~~h~rlt 70 (296)
T CHL00174 34 YKHLWVQCENCYGLNYK-------KFLKS-KMNICEQCGYHLKMS 70 (296)
T ss_pred CCCCeeECCCccchhhH-------HHHHH-cCCCCCCCCCCcCCC
Confidence 57789999999753322 12211 357999998765544
No 154
>COG3257 GlxB Uncharacterized protein, possibly involved in glyoxylate utilization [General function prediction only]
Probab=31.84 E-value=1.5e+02 Score=24.46 Aligned_cols=46 Identities=15% Similarity=0.350 Sum_probs=28.3
Q ss_pred EcCCCeEEccCCeEEEccCCCCCCCeEEEEeEEEEcC-CCCEEEEEEEeecccccCCcc
Q 027964 16 IKGTNKVVRPGDCVLMRPADSDKPPYVARVEKIEADH-RNNVKVRVRWYYRPEESIGGR 73 (216)
Q Consensus 16 v~~~~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~-~g~~~v~v~Wfyrp~d~~~~~ 73 (216)
+.|.--.++.|+++|+.++.. |.-. ...--.++.|+-++-+...+.
T Consensus 98 ~~G~th~l~eggyaylPpgs~------------~~~~N~~~~~~rfhw~rk~Y~~VdG~ 144 (264)
T COG3257 98 AEGKTHALREGGYAYLPPGSG------------WTLRNAQKEDSRFHWIRKRYQPVEGV 144 (264)
T ss_pred EcCeEEEeccCCeEEeCCCCc------------ceEeeccCCceEEEEEeecceeecCc
Confidence 344444678899999988751 1111 122447788888887776553
No 155
>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=31.58 E-value=55 Score=21.12 Aligned_cols=25 Identities=24% Similarity=0.340 Sum_probs=16.0
Q ss_pred eEEccCCeEEEccCCCCCCCeEEEEeE
Q 027964 21 KVVRPGDCVLMRPADSDKPPYVARVEK 47 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~~I~~ 47 (216)
.-++.||+|+|...+ ...--|+|..
T Consensus 40 iwI~~GD~V~V~~~~--~d~~kG~Ii~ 64 (65)
T PF01176_consen 40 IWIKRGDFVLVEPSP--YDKVKGRIIY 64 (65)
T ss_dssp C---TTEEEEEEEST--TCTTEEEEEE
T ss_pred EecCCCCEEEEEecc--cCCCeEEEEE
Confidence 357889999999865 2366777754
No 156
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=31.40 E-value=85 Score=21.04 Aligned_cols=37 Identities=19% Similarity=0.369 Sum_probs=24.1
Q ss_pred eEEEcCCCeEEccCCeEEEccCCCC---CCCeEEEEeEEE
Q 027964 13 SYNIKGTNKVVRPGDCVLMRPADSD---KPPYVARVEKIE 49 (216)
Q Consensus 13 ~~~v~~~~~~~~vGD~V~v~~~~~~---~~~~I~~I~~i~ 49 (216)
.|.+..+.-.|+|||.+.+..=+++ .....++|..|.
T Consensus 19 tfEiRkNDRdf~VGD~L~L~E~~~~~YTGr~~~~~Ityi~ 58 (72)
T PF12961_consen 19 TFEIRKNDRDFQVGDILVLREWDNGEYTGREIEAEITYIT 58 (72)
T ss_pred eEEEEecCCCCCCCCEEEEEEecCCCccccEEEEEEEEEe
Confidence 4666666678999999998775422 223455565554
No 157
>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=31.09 E-value=68 Score=22.47 Aligned_cols=23 Identities=17% Similarity=0.018 Sum_probs=19.9
Q ss_pred ccCCeEEEccCCCCCCCeEEEEeEE
Q 027964 24 RPGDCVLMRPADSDKPPYVARVEKI 48 (216)
Q Consensus 24 ~vGD~V~v~~~~~~~~~~I~~I~~i 48 (216)
.+||.|...-.. .+.|-|+|.+-
T Consensus 2 ~~GdlVWaK~~g--~pwWPa~V~~~ 24 (95)
T cd05838 2 LYGDIVWAKLGN--FRWWPAIICDP 24 (95)
T ss_pred CcCCEEEEECCC--CCCCCeEEcCh
Confidence 479999999887 79999999874
No 158
>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=30.80 E-value=1.1e+02 Score=25.85 Aligned_cols=44 Identities=18% Similarity=0.252 Sum_probs=35.3
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeecccc
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEE 68 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~d 68 (216)
.+.+||.|.|..+. -.-+.|.|.++.. ..+.+.|.+.+|-|.--
T Consensus 205 ~f~vGd~VrI~dGP--F~GfeG~I~eid~-~k~Rv~VlV~IfGR~Tp 248 (258)
T TIGR01956 205 KFRVGNFVKIVDGP--FKGIVGKIKKIDQ-EKKKAIVEVEILGKSVD 248 (258)
T ss_pred CCCCCCEEEEEecC--CCCcEEEEEEEeC-CCCEEEEEEEecCCcEE
Confidence 47899999999987 5678899999876 35668888888877643
No 159
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=30.48 E-value=47 Score=32.24 Aligned_cols=51 Identities=25% Similarity=0.641 Sum_probs=33.5
Q ss_pred CCCcceE-EeCCCCCCCCceEeCccccceecCcCCCCChhhhcCCCeEEccccccc
Q 027964 135 DRVAVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSD 189 (216)
Q Consensus 135 ~~~~~~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~ 1165 (1189)
T KOG2041|consen 1114 NSAKVDCSVCGAKIDPY--DLQCSECQTKF-PVCIASGRPITDN-IFWLCPRCKHR 1165 (1189)
T ss_pred CccceeeeecCCcCCcc--CCCChhhcCcC-ceeeccCCccccc-eEEEccccccc
Confidence 3455667 788876543 36899998755 5677554433322 37999999864
No 160
>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=30.25 E-value=33 Score=22.10 Aligned_cols=57 Identities=23% Similarity=0.416 Sum_probs=29.0
Q ss_pred cCCCCcceE-EeCCCCCCCCceEeCccccceecCcCCCCChhhh-----cCCCeEEccccccc
Q 027964 133 TPDRVAVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEA-----KKLDHFLCSDCSSD 189 (216)
Q Consensus 133 ~p~~~~~~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~-----~~~~~~~C~~C~~~ 189 (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 345556677 6888775445557799999999999987543221 11236788888654
No 161
>PF02559 CarD_CdnL_TRCF: CarD-like/TRCF domain; InterPro: IPR003711 The bacterium Myxococcus xanthus responds to blue light by producing carotenoids. It also responds to starvation conditions by developing fruiting bodies, where the cells differentiate into myxospores. Each response entails the transcriptional activation of a separate set of genes. A single gene, carD, is required for the activation of both light- and starvation-inducible genes []. The predicted protein contains four repeats of a DNA-binding domain present in mammalian high mobility group I(Y) proteins and other nuclear proteins from animals and plants. Other peptide stretches on CarD also resemble functional domains typical of eukaryotic transcription factors, including a very acidic region and a leucine zipper. High mobility group yI(Y) proteins are known to bind the minor groove of A+T-rich DNA [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3MLQ_H 2EYQ_A.
Probab=30.13 E-value=72 Score=22.14 Aligned_cols=24 Identities=33% Similarity=0.429 Sum_probs=18.6
Q ss_pred EccCCeEEEccCCCCCCCeEEEEeEEEEcC
Q 027964 23 VRPGDCVLMRPADSDKPPYVARVEKIEADH 52 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~ 52 (216)
|++||.|.-...+ ||+|..|....
T Consensus 2 f~~GD~VVh~~~G------v~~i~~i~~~~ 25 (98)
T PF02559_consen 2 FKIGDYVVHPNHG------VGRIEGIEEIE 25 (98)
T ss_dssp --TTSEEEETTTE------EEEEEEEEEEE
T ss_pred CCCCCEEEECCCc------eEEEEEEEEEe
Confidence 6789999887776 99999998754
No 162
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=30.03 E-value=50 Score=21.28 Aligned_cols=46 Identities=17% Similarity=0.454 Sum_probs=25.7
Q ss_pred ceE-EeCCCCCCCCce--EeCccccceecCcCCCCChhhhcCCCeEEcccccc
Q 027964 139 VYC-KCEMPYNPDDLM--VQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSS 188 (216)
Q Consensus 139 ~~C-~C~~~~~~~~~~--i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~ 188 (216)
..| .|+....+++.. -.|..|++--=..|..-.. +...|.|++|--
T Consensus 10 ~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~CRk----~g~~Y~Cp~CGF 58 (61)
T COG2888 10 PVCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKCRK----LGNPYRCPKCGF 58 (61)
T ss_pred ceeccCCCEeccCCceeEeeCCCCCceeeehhhhHHH----cCCceECCCcCc
Confidence 355 566655455543 4477777544444433322 224789998854
No 163
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=29.86 E-value=23 Score=20.84 Aligned_cols=11 Identities=18% Similarity=1.014 Sum_probs=8.1
Q ss_pred CeEEccccccc
Q 027964 179 DHFLCSDCSSD 189 (216)
Q Consensus 179 ~~~~C~~C~~~ 189 (216)
+.++|..|...
T Consensus 23 ~~~IC~~Cv~~ 33 (41)
T PF06689_consen 23 GAYICDECVEQ 33 (41)
T ss_dssp SEEEEHHHHHH
T ss_pred CcEECHHHHHH
Confidence 47889888753
No 164
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=29.37 E-value=15 Score=31.05 Aligned_cols=37 Identities=30% Similarity=0.680 Sum_probs=26.9
Q ss_pred CceEeCccccceecCcCCCCChhhhc--CCCeEEccccc
Q 027964 151 DLMVQCEGCKDWFHPSCMGMTIEEAK--KLDHFLCSDCS 187 (216)
Q Consensus 151 ~~~i~C~~C~~w~H~~Cv~~~~~~~~--~~~~~~C~~C~ 187 (216)
+++|.|..|+.-=|++|+..+..... .-.-|.|-.|.
T Consensus 244 eelvscsdcgrsghpsclqft~nm~~avk~yrwqcieck 282 (336)
T KOG1244|consen 244 EELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECK 282 (336)
T ss_pred hhhcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeecc
Confidence 57799999999999999998865421 22456655554
No 165
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.34 E-value=39 Score=28.71 Aligned_cols=49 Identities=20% Similarity=0.396 Sum_probs=32.6
Q ss_pred CcceE-EeCCCCCCCCceEeCccccceecCcCCCCChhhhcCCCeEEccccccccc
Q 027964 137 VAVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 191 (216)
Q Consensus 137 ~~~~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 191 (216)
..+.| +|+.+. .-.|+. .-|+.-|+.-|+.-+..-. ..|.|+.|...-.
T Consensus 238 ~~~~C~~Cg~~P--tiP~~~-~~C~HiyCY~Ci~ts~~~~---asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 238 SDTECPVCGEPP--TIPHVI-GKCGHIYCYYCIATSRLWD---ASFTCPLCGENVE 287 (298)
T ss_pred CCceeeccCCCC--CCCeee-ccccceeehhhhhhhhcch---hhcccCccCCCCc
Confidence 45677 888763 333322 1277799999998766432 3689999987644
No 166
>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=28.19 E-value=64 Score=20.43 Aligned_cols=25 Identities=28% Similarity=0.314 Sum_probs=16.2
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEE
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~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 368999999975431 2 255666654
No 167
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=27.88 E-value=31 Score=29.60 Aligned_cols=38 Identities=18% Similarity=0.519 Sum_probs=24.9
Q ss_pred CCCCceEeCccccceecCcCCCCChhhhcCCCeEEccccccccccc
Q 027964 148 NPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 193 (216)
Q Consensus 148 ~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~ 193 (216)
-|++.|+.|+.|+...+.+ +.+. +.++|+.|..-..+.
T Consensus 22 ~~~~~~~~c~~c~~~~~~~-------~l~~-~~~vc~~c~~h~rl~ 59 (292)
T PRK05654 22 VPEGLWTKCPSCGQVLYRK-------ELEA-NLNVCPKCGHHMRIS 59 (292)
T ss_pred CCCCCeeECCCccchhhHH-------HHHh-cCCCCCCCCCCeeCC
Confidence 3677899999997644322 1211 347999998766543
No 168
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=27.39 E-value=1.2e+02 Score=22.14 Aligned_cols=40 Identities=23% Similarity=0.268 Sum_probs=29.1
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeeccc
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPE 67 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~ 67 (216)
-+..||.|.+..++ ..+++.++.+ ..|+..++|.-.-...
T Consensus 25 glA~gDvV~~~~~~--g~~~~~~~v~----~sGnsTiRv~~~~~~~ 64 (117)
T PF14085_consen 25 GLALGDVVRAEPDD--GELWFQKVVE----SSGNSTIRVIFDDPGP 64 (117)
T ss_pred CCCCCCEEEEEeCC--CeEEEEEEEe----cCCCEEEEEEEcCCcc
Confidence 46889999999997 6677766655 6788888885443333
No 169
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=27.19 E-value=4.3e+02 Score=23.22 Aligned_cols=38 Identities=24% Similarity=0.251 Sum_probs=28.1
Q ss_pred CeEEccCCeEEEccCC--CCCCCeEEEEeEEEEcCCCCEE
Q 027964 20 NKVVRPGDCVLMRPAD--SDKPPYVARVEKIEADHRNNVK 57 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~--~~~~~~I~~I~~i~~~~~g~~~ 57 (216)
+..+++||.|.-..-+ -+....||+|.++..+..|...
T Consensus 258 ~~di~~GD~lVTSGlgGvfP~Gl~Vg~V~~V~~~~~g~~~ 297 (337)
T PRK14872 258 GKTLRVGDILVTTGLDGVFPPGLLVATVTKVLPPREGACS 297 (337)
T ss_pred CCCcCCCCEEEECCCCCcCCCCCEEEEEEEEEECCCCCee
Confidence 4688999887666533 2466899999999997766543
No 170
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=27.05 E-value=46 Score=23.69 Aligned_cols=17 Identities=35% Similarity=0.761 Sum_probs=13.7
Q ss_pred CCEEEEEEEeecccccC
Q 027964 54 NNVKVRVRWYYRPEESI 70 (216)
Q Consensus 54 g~~~v~v~Wfyrp~d~~ 70 (216)
....|+|+|||.++|..
T Consensus 75 ~g~~V~v~Wyyd~dD~~ 91 (99)
T PF09345_consen 75 KGGKVTVNWYYDEDDED 91 (99)
T ss_pred cCCcEEEEEEECCCCch
Confidence 34789999999988754
No 171
>PF08921 DUF1904: Domain of unknown function (DUF1904); InterPro: IPR015017 This entry represents a family of hypothetical bacterial proteins. ; PDB: 1U9D_B.
Probab=26.99 E-value=26 Score=25.40 Aligned_cols=17 Identities=29% Similarity=0.411 Sum_probs=10.0
Q ss_pred CCEEEEEEEeecccccC
Q 027964 54 NNVKVRVRWYYRPEESI 70 (216)
Q Consensus 54 g~~~v~v~Wfyrp~d~~ 70 (216)
+..+|+|.||-|+.++.
T Consensus 54 ~~pfVEV~WF~R~qe~q 70 (108)
T PF08921_consen 54 GYPFVEVLWFDRGQEVQ 70 (108)
T ss_dssp ---EEEEEES---HHHH
T ss_pred cceeEEEEEecCCHHHH
Confidence 34689999999999975
No 172
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=26.96 E-value=72 Score=30.76 Aligned_cols=54 Identities=30% Similarity=0.599 Sum_probs=33.7
Q ss_pred CCCcceE-EeCCCCCCC----CceEeCc--cccceecCcCCCCC----hhh-hcCCCeEEcccccc
Q 027964 135 DRVAVYC-KCEMPYNPD----DLMVQCE--GCKDWFHPSCMGMT----IEE-AKKLDHFLCSDCSS 188 (216)
Q Consensus 135 ~~~~~~C-~C~~~~~~~----~~~i~C~--~C~~w~H~~Cv~~~----~~~-~~~~~~~~C~~C~~ 188 (216)
++..+.| ||.+...+. +--.+|- +|+.-||..|...- +++ ......-+|-.|..
T Consensus 114 dRfnKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE~gn~~dNVKYCGYCk~ 179 (900)
T KOG0956|consen 114 DRFNKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEEEGNISDNVKYCGYCKY 179 (900)
T ss_pred hhhcceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceeccccccccceechhHHH
Confidence 3445567 787764333 3345676 79999999998543 222 11224678999975
No 173
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=26.66 E-value=26 Score=30.27 Aligned_cols=30 Identities=23% Similarity=0.690 Sum_probs=18.9
Q ss_pred eE-EeCCCCCCCCceEeCccccceecCcCCCCCh
Q 027964 140 YC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTI 172 (216)
Q Consensus 140 ~C-~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~ 172 (216)
+| .|+.|-.-.+.||-|+ .-|+.+|.....
T Consensus 92 fCd~Cd~PI~IYGRmIPCk---HvFCl~CAr~~~ 122 (389)
T KOG2932|consen 92 FCDRCDFPIAIYGRMIPCK---HVFCLECARSDS 122 (389)
T ss_pred eecccCCcceeeecccccc---hhhhhhhhhcCc
Confidence 45 5666665577888765 356666665543
No 174
>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=26.21 E-value=39 Score=28.88 Aligned_cols=37 Identities=16% Similarity=0.540 Sum_probs=24.5
Q ss_pred CCCCceEeCccccceecCcCCCCChhhhcCCCeEEcccccccccc
Q 027964 148 NPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (216)
Q Consensus 148 ~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (216)
-|++.|+.|+.|+...+. .+.+. ..++|+.|..-..+
T Consensus 21 ~~~~~~~~c~~c~~~~~~-------~~l~~-~~~vc~~c~~h~rl 57 (285)
T TIGR00515 21 VPEGVWTKCPKCGQVLYT-------KELER-NLEVCPKCDHHMRM 57 (285)
T ss_pred CCCCCeeECCCCcchhhH-------HHHHh-hCCCCCCCCCcCcC
Confidence 367789999999764432 22211 34799999876554
No 175
>PF04322 DUF473: Protein of unknown function (DUF473); InterPro: IPR007417 This is a family of uncharacterised archaeal proteins.
Probab=26.16 E-value=1.1e+02 Score=22.64 Aligned_cols=29 Identities=31% Similarity=0.512 Sum_probs=22.1
Q ss_pred EEccCCeEEEccCC-----CCCCCeEEEEeEEEE
Q 027964 22 VVRPGDCVLMRPAD-----SDKPPYVARVEKIEA 50 (216)
Q Consensus 22 ~~~vGD~V~v~~~~-----~~~~~~I~~I~~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 45899999999865 345567888887765
No 176
>COG1773 Rubredoxin [Energy production and conversion]
Probab=25.55 E-value=57 Score=20.68 Aligned_cols=12 Identities=25% Similarity=0.877 Sum_probs=9.8
Q ss_pred CCCeEEcccccc
Q 027964 177 KLDHFLCSDCSS 188 (216)
Q Consensus 177 ~~~~~~C~~C~~ 188 (216)
.++.|.|+.|.-
T Consensus 33 lPd~w~CP~Cg~ 44 (55)
T COG1773 33 LPDDWVCPECGV 44 (55)
T ss_pred CCCccCCCCCCC
Confidence 357899999985
No 177
>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=25.53 E-value=89 Score=25.56 Aligned_cols=28 Identities=32% Similarity=0.487 Sum_probs=16.8
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEE
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~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 57999999994433 36778888888876
No 178
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=25.35 E-value=24 Score=24.50 Aligned_cols=63 Identities=21% Similarity=0.424 Sum_probs=35.4
Q ss_pred CCcceEEeeeeecccCcccCCCCcceEEeCCCCCCCCceEeCccccceecCcCCCCChhhhcCCCeEEcccccccccc
Q 027964 115 GAEDYFCRFEYKAATGGFTPDRVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 192 (216)
Q Consensus 115 ~~~~ffcr~~yd~~~~~f~p~~~~~~C~C~~~~~~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 192 (216)
.+..-+||..||..- | .|.-|.+ +-..+. ..|..-||+.|+-.=.... . .+-.||.|++.-..
T Consensus 21 dd~CgICr~~fdg~C----p-------~Ck~Pgd-~Cplv~-g~C~H~FH~hCI~kWl~~~-~-~~~~CPmCR~~w~~ 83 (85)
T PF12861_consen 21 DDVCGICRMPFDGCC----P-------DCKFPGD-DCPLVW-GKCSHNFHMHCILKWLSTQ-S-SKGQCPMCRQPWKF 83 (85)
T ss_pred CCceeeEecccccCC----C-------CccCCCC-CCceee-ccCccHHHHHHHHHHHccc-c-CCCCCCCcCCeeee
Confidence 344577887776431 1 2444432 112232 3599999999985322211 1 13489999987554
No 179
>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=25.32 E-value=30 Score=26.69 Aligned_cols=17 Identities=29% Similarity=0.917 Sum_probs=13.3
Q ss_pred CceEeCccccceecCcC
Q 027964 151 DLMVQCEGCKDWFHPSC 167 (216)
Q Consensus 151 ~~~i~C~~C~~w~H~~C 167 (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 46799999999998644
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=25.18 E-value=1.6e+02 Score=22.54 Aligned_cols=45 Identities=18% Similarity=0.271 Sum_probs=34.5
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeeccccc
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEES 69 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~d~ 69 (216)
.+.+||-|.|..+. -.-+.|.|.++.. .++.+.+.+.+|-+...+
T Consensus 119 ~~~~G~~V~I~~Gp--f~G~~g~v~~~~~-~~~r~~V~v~~~g~~~~v 163 (172)
T TIGR00922 119 DFEVGEQVRVNDGP--FANFTGTVEEVDY-EKSKLKVSVSIFGRETPV 163 (172)
T ss_pred CCCCCCEEEEeecC--CCCcEEEEEEEcC-CCCEEEEEEEECCCceEE
Confidence 47899999999886 5677899988743 455688888888776544
No 181
>PRK06424 transcription factor; Provisional
Probab=25.10 E-value=33 Score=26.19 Aligned_cols=32 Identities=25% Similarity=0.433 Sum_probs=17.4
Q ss_pred CccccceecCcCCCCChhhhcCCCeEEccccccccc
Q 027964 156 CEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 191 (216)
Q Consensus 156 C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 191 (216)
|+.|+.-.... ..+-.+.+ .--+|..|.+.-.
T Consensus 3 CE~CG~~~~~~-~~v~ieg~---~l~vC~~Ca~~G~ 34 (144)
T PRK06424 3 CEMCGKKVPQT-TKVMIDGA---ILNVCDDCAKFGT 34 (144)
T ss_pred ccccCcccCCc-eEEEEcCe---eeehhHHHHHcCC
Confidence 88886644433 22222222 3468999986433
No 182
>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=24.98 E-value=2.3e+02 Score=21.46 Aligned_cols=45 Identities=20% Similarity=0.176 Sum_probs=27.2
Q ss_pred CeEEccCCeEEEccCCC--CCCCeEEEEeEEEEcCCC-CEEEEEEEee
Q 027964 20 NKVVRPGDCVLMRPADS--DKPPYVARVEKIEADHRN-NVKVRVRWYY 64 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~~--~~~~~I~~I~~i~~~~~g-~~~v~v~Wfy 64 (216)
+..+++||.|+-..-+. +....||+|.++.....+ ...+.+.=+.
T Consensus 91 ~~~i~~GD~V~TSG~~~~fP~Gi~VG~V~~v~~~~~~~~~~~~v~p~~ 138 (152)
T PF04085_consen 91 DADIKKGDIVVTSGLGGIFPPGIPVGTVSSVEPDKSGLFKEVYVKPAV 138 (152)
T ss_dssp TS---TT-EEEEE-TTSSS-CCEEEEEEEEEECTTTCCCEEEEEEESS
T ss_pred CCCCCCCCEEEECCCCCcCCCCCEEEEEEEEEeCCCCcEEEEEEEECC
Confidence 45889999999765442 345799999999987654 3556665443
No 183
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=24.88 E-value=1.2e+02 Score=21.72 Aligned_cols=26 Identities=27% Similarity=0.229 Sum_probs=13.9
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEE
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIE 49 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~ 49 (216)
-+..||+|+|...+- ..-=|+|+..+
T Consensus 59 wI~~GD~VlVe~~~~--~~~kg~Iv~r~ 84 (100)
T PRK04012 59 WIREGDVVIVAPWDF--QDEKADIIWRY 84 (100)
T ss_pred EecCCCEEEEEeccc--CCCEEEEEEEc
Confidence 456677777766441 13345555444
No 184
>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=24.80 E-value=46 Score=21.96 Aligned_cols=24 Identities=25% Similarity=0.421 Sum_probs=17.0
Q ss_pred eeeEEEcCCCeEEccCCeEEEccC
Q 027964 11 LDSYNIKGTNKVVRPGDCVLMRPA 34 (216)
Q Consensus 11 y~~~~v~~~~~~~~vGD~V~v~~~ 34 (216)
.+.+.+++.+....+||.|.|...
T Consensus 32 ~kk~~aHD~~~~~~vGD~V~I~e~ 55 (69)
T PF00366_consen 32 TKKYMAHDENNICKVGDKVRIREC 55 (69)
T ss_dssp EEEEEEE-TTSSSTTTSEEEEEEE
T ss_pred cccEEEeCCccCCCCCCEEEEEee
Confidence 446777776667789999998653
No 185
>PRK04980 hypothetical protein; Provisional
Probab=24.13 E-value=1.2e+02 Score=21.85 Aligned_cols=37 Identities=16% Similarity=0.307 Sum_probs=21.2
Q ss_pred EEEcC-CCeEEccCCeEEEccCCCCCCCeEEEEeEEEE
Q 027964 14 YNIKG-TNKVVRPGDCVLMRPADSDKPPYVARVEKIEA 50 (216)
Q Consensus 14 ~~v~~-~~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~ 50 (216)
+++.. ....+++||.|.|.....+.+.-..+|.++..
T Consensus 22 iTiRd~se~~~~~G~~~~V~~~e~g~~~c~ieI~sV~~ 59 (102)
T PRK04980 22 ITIRDESESHFKPGDVLRVGTFEDDRYFCTIEVLSVSP 59 (102)
T ss_pred EEeeCCcccCCCCCCEEEEEECCCCcEEEEEEEEEEEE
Confidence 44433 34579999999997544223333444555544
No 186
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=23.94 E-value=40 Score=28.69 Aligned_cols=37 Identities=19% Similarity=0.586 Sum_probs=25.4
Q ss_pred CCCceEeCccccceecCcCCCCChhhhcCCCeEEccccccccccc
Q 027964 149 PDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 193 (216)
Q Consensus 149 ~~~~~i~C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~ 193 (216)
+++.|+.|..|+...|.+ +.+. +.++|+.|..-..+.
T Consensus 24 ~e~lw~KCp~c~~~~y~~-------eL~~-n~~vcp~c~~h~ri~ 60 (294)
T COG0777 24 PEGLWTKCPSCGEMLYRK-------ELES-NLKVCPKCGHHMRIS 60 (294)
T ss_pred CCCceeECCCccceeeHH-------HHHh-hhhcccccCcccccC
Confidence 378999999997544422 1111 468999999876655
No 187
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=23.65 E-value=38 Score=17.28 Aligned_cols=10 Identities=30% Similarity=0.976 Sum_probs=7.5
Q ss_pred eCccccceec
Q 027964 155 QCEGCKDWFH 164 (216)
Q Consensus 155 ~C~~C~~w~H 164 (216)
.|+.|+..|.
T Consensus 3 ~C~~C~~~F~ 12 (27)
T PF13912_consen 3 ECDECGKTFS 12 (27)
T ss_dssp EETTTTEEES
T ss_pred CCCccCCccC
Confidence 6888888774
No 188
>PF14353 CpXC: CpXC protein
Probab=22.92 E-value=63 Score=23.67 Aligned_cols=40 Identities=18% Similarity=0.453 Sum_probs=21.9
Q ss_pred EeCccccceecC---cCCCCChhh-------hcCCCeEEccccccccccc
Q 027964 154 VQCEGCKDWFHP---SCMGMTIEE-------AKKLDHFLCSDCSSDVDAK 193 (216)
Q Consensus 154 i~C~~C~~w~H~---~Cv~~~~~~-------~~~~~~~~C~~C~~~~~~~ 193 (216)
|.|..|+.-|.. .-|+....+ ...+..+.||.|.......
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecC
Confidence 457777665553 333333221 1224578888888776543
No 189
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=22.78 E-value=27 Score=23.03 Aligned_cols=18 Identities=39% Similarity=0.909 Sum_probs=10.7
Q ss_pred CCCCCCceEeCcccccee
Q 027964 146 PYNPDDLMVQCEGCKDWF 163 (216)
Q Consensus 146 ~~~~~~~~i~C~~C~~w~ 163 (216)
.|..+-..|+|++|+.|.
T Consensus 22 aY~~GvViv~C~gC~~~H 39 (66)
T PF05180_consen 22 AYHKGVVIVQCPGCKNRH 39 (66)
T ss_dssp HHHTSEEEEE-TTS--EE
T ss_pred HHhCCeEEEECCCCccee
Confidence 444566789999998863
No 190
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=22.73 E-value=47 Score=18.23 Aligned_cols=11 Identities=18% Similarity=1.017 Sum_probs=7.8
Q ss_pred CeEEccccccc
Q 027964 179 DHFLCSDCSSD 189 (216)
Q Consensus 179 ~~~~C~~C~~~ 189 (216)
..|+|+.|..+
T Consensus 18 ~~~vCp~C~~e 28 (30)
T PF08274_consen 18 ELLVCPECGHE 28 (30)
T ss_dssp SSEEETTTTEE
T ss_pred CEEeCCccccc
Confidence 56888888654
No 191
>COG4127 Uncharacterized conserved protein [Function unknown]
Probab=22.68 E-value=53 Score=28.03 Aligned_cols=41 Identities=17% Similarity=0.319 Sum_probs=29.9
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEcC---C--CCEEEEEEEe
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADH---R--NNVKVRVRWY 63 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~---~--g~~~v~v~Wf 63 (216)
+++.||-|.+.... ...++||+|.+=++-. . -.....|.|.
T Consensus 72 eI~KGDlvi~y~k~-~r~y~IGkVtsdYEy~p~~~~~i~hTrkVkWL 117 (318)
T COG4127 72 EIQKGDLVITYSKS-NRTYLIGKVTSDYEYHPEWLEGIGHTRKVKWL 117 (318)
T ss_pred HhccCcEEEeeccc-CceEEEEEecCCcccCccccccCchhhHhHHh
Confidence 68899999999976 4789999998766521 1 1144667776
No 192
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=22.50 E-value=3.4e+02 Score=22.58 Aligned_cols=42 Identities=21% Similarity=0.179 Sum_probs=29.8
Q ss_pred eEEccCCeEEEccCCC--CCCCeEEEEeEEEEcCCC-CEEEEEEE
Q 027964 21 KVVRPGDCVLMRPADS--DKPPYVARVEKIEADHRN-NVKVRVRW 62 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~--~~~~~I~~I~~i~~~~~g-~~~v~v~W 62 (216)
..+++||.|+-..-+. +....||+|.++..+.++ ...+.+.=
T Consensus 213 ~~i~~GD~VvTSGl~g~fP~Gi~VG~V~~v~~~~~~~~~~~~v~p 257 (276)
T PRK13922 213 ADIKVGDLVVTSGLGGIFPAGLPVGKVTSVERDDYGLFKTVYVKP 257 (276)
T ss_pred CCCCCCCEEEECCCCCcCCCCCEEEEEEEEEeCCCCCeeEEEEEE
Confidence 4689999998887542 356799999999776554 24455543
No 193
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=22.47 E-value=2.2e+02 Score=19.18 Aligned_cols=29 Identities=28% Similarity=0.444 Sum_probs=22.5
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEc
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEAD 51 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~ 51 (216)
.+++||.|++.|... .....++|.+|...
T Consensus 26 ~v~~g~~v~~~P~~~-g~~~~~~V~sI~~~ 54 (87)
T cd03694 26 VIRLGDTLLLGPDQD-GSFRPVTVKSIHRN 54 (87)
T ss_pred EEeCCCEEEECCCCC-CCEeEEEEEEEEEC
Confidence 899999999999741 23467899998764
No 194
>cd05841 BS69_related The PWWP domain is part of BS69 protein, a nuclear protein that specifically binds adenoviral E1A and Epstein-Barr viral EBNA2 proteins, suppressing their transactivation functions. BS69 is a multi-domain protein, containing bromo, PHD, PWWP, and MYND domains. The specific role of the PWWP domain within BS69 is not clearly identified, but BS69 functions in chromatin remodeling, consistent with other PWWP-containing proteins. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=22.46 E-value=1.5e+02 Score=20.41 Aligned_cols=39 Identities=23% Similarity=0.367 Sum_probs=28.1
Q ss_pred EccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeecccc
Q 027964 23 VRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEE 68 (216)
Q Consensus 23 ~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~d 68 (216)
...||.|.-.-.+ -++|-|+|.+.. + ..+.|++|--..+
T Consensus 7 ~~p~dLVwAK~kG--yp~WPAkV~~~~---~--~~~~V~FFG~t~~ 45 (83)
T cd05841 7 RPPHELVWAKLKG--FPYWPAKVMRVE---D--NQVDVRFFGGQHD 45 (83)
T ss_pred CCCCCEEEEeCCC--CCCCCEEEeecC---C--CeEEEEEcCCCCC
Confidence 3578888888776 799999998732 1 4577888873333
No 195
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=22.45 E-value=2.5e+02 Score=19.55 Aligned_cols=27 Identities=15% Similarity=0.199 Sum_probs=18.7
Q ss_pred eEEEcCCCeEEccCCeEEEccCCCCCC
Q 027964 13 SYNIKGTNKVVRPGDCVLMRPADSDKP 39 (216)
Q Consensus 13 ~~~v~~~~~~~~vGD~V~v~~~~~~~~ 39 (216)
.+-++.....+++||.|.|...-|.+.
T Consensus 46 K~~aHde~~~~k~GD~V~I~EtRPLSK 72 (87)
T COG0186 46 KYHAHDECNEAKVGDIVRIAETRPLSK 72 (87)
T ss_pred eeEeecccccCCCCCEEEEEEccccCC
Confidence 444555566789999999988655443
No 196
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=22.30 E-value=1.9e+02 Score=23.59 Aligned_cols=71 Identities=18% Similarity=0.107 Sum_probs=45.0
Q ss_pred CeEEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeecccc---------cCCcccccCCCCeeeeeCccce
Q 027964 20 NKVVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEE---------SIGGRRQFHGAKELFLSDHYDV 90 (216)
Q Consensus 20 ~~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~d---------~~~~~~~~~~~~ELF~s~~~d~ 90 (216)
...+..||.|-|..+- ++--+|.|..+....+.-+.=-++|=||-.- +.....+.+..+.|.|-+..|.
T Consensus 70 dw~ff~GDtVeVlvGk--DkGkqG~Vtqv~r~~s~VvV~gln~k~r~~gsekeg~pgtivk~EaPlhvsk~VmLvdp~d~ 147 (236)
T KOG1708|consen 70 DWHFFFGDTVEVLVGK--DKGKQGEVTQVIRHRSWVVVKGLNTKYRHMGSEKEGEPGTIVKSEAPLHVSKQVMLVDPEDD 147 (236)
T ss_pred ceeEecCCEEEEEecc--cCCccceEEEEeecCceEEEcccchhhhhhcccccCCCceEEeecCCceecceeEEECcccc
Confidence 4789999999999986 5677899999888554433333446554321 1111334445556777777666
Q ss_pred ee
Q 027964 91 QS 92 (216)
Q Consensus 91 ~~ 92 (216)
.+
T Consensus 148 q~ 149 (236)
T KOG1708|consen 148 QP 149 (236)
T ss_pred CC
Confidence 54
No 197
>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=22.26 E-value=1.1e+02 Score=20.37 Aligned_cols=23 Identities=22% Similarity=0.362 Sum_probs=17.5
Q ss_pred eEEEcCCCeEEccCCeEEEccCC
Q 027964 13 SYNIKGTNKVVRPGDCVLMRPAD 35 (216)
Q Consensus 13 ~~~v~~~~~~~~vGD~V~v~~~~ 35 (216)
.+.+++.+...++||.|.|..--
T Consensus 39 k~~aHD~~~~~k~GD~V~I~ecr 61 (71)
T TIGR03635 39 KYHAHDENNECKVGDVVRIIETR 61 (71)
T ss_pred EEEEECCCCCCCCCCEEEEEEcC
Confidence 45566666679999999998764
No 198
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=22.03 E-value=1.3e+02 Score=25.28 Aligned_cols=30 Identities=27% Similarity=0.377 Sum_probs=20.8
Q ss_pred eEEccCCeEEEccCCCCCCCeEEEEeEEEEc
Q 027964 21 KVVRPGDCVLMRPADSDKPPYVARVEKIEAD 51 (216)
Q Consensus 21 ~~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~ 51 (216)
...+|||.++....+ ++.+|-|.|.+|-..
T Consensus 67 ~~WkvGd~C~A~~s~-Dg~~Y~A~I~~i~~~ 96 (264)
T PF06003_consen 67 KKWKVGDKCMAVYSE-DGQYYPATIESIDEE 96 (264)
T ss_dssp T---TT-EEEEE-TT-TSSEEEEEEEEEETT
T ss_pred cCCCCCCEEEEEECC-CCCEEEEEEEEEcCC
Confidence 488999999988864 478999999999764
No 199
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=21.50 E-value=1.5e+02 Score=22.41 Aligned_cols=42 Identities=10% Similarity=0.001 Sum_probs=31.9
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEcCCCCEEEEEEEeeccc
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPE 67 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~~~g~~~v~v~Wfyrp~ 67 (216)
.+..||.|.|..+. -.-+.|.|.++. ..+.+.+.+.+|-|..
T Consensus 108 ~~~~G~~V~V~~GP--f~g~~g~v~~~~--~~~r~~v~l~~~gr~~ 149 (159)
T TIGR01955 108 LPYKGDKVRITDGA--FAGFEAIFLEPD--GEKRSMLLLNMIGKQI 149 (159)
T ss_pred CCCCCCEEEEeccC--CCCcEEEEEEEC--CCceEEEEEhhhCCce
Confidence 47899999999986 567899999975 3345777777776653
No 200
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=21.49 E-value=48 Score=26.94 Aligned_cols=41 Identities=12% Similarity=0.280 Sum_probs=26.9
Q ss_pred eEeCccccceecCcCCCCChhhh----------------cCCCeEEccccccccccc
Q 027964 153 MVQCEGCKDWFHPSCMGMTIEEA----------------KKLDHFLCSDCSSDVDAK 193 (216)
Q Consensus 153 ~i~C~~C~~w~H~~Cv~~~~~~~----------------~~~~~~~C~~C~~~~~~~ 193 (216)
-+.|+.|+.-|...=|..+.... --.+.|+||.|--..-..
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 36789998888877775542211 112579999998765544
No 201
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=21.24 E-value=1.9e+02 Score=17.43 Aligned_cols=28 Identities=32% Similarity=0.442 Sum_probs=22.5
Q ss_pred EEccCCeEEEccCCCCCCCeEEEEeEEEEc
Q 027964 22 VVRPGDCVLMRPADSDKPPYVARVEKIEAD 51 (216)
Q Consensus 22 ~~~vGD~V~v~~~~~~~~~~I~~I~~i~~~ 51 (216)
.+++|+.|.+.. . ++..|=|+|+++..+
T Consensus 2 ~~~~G~~~~a~~-~-d~~wyra~I~~~~~~ 29 (57)
T smart00333 2 TFKVGDKVAARW-E-DGEWYRARIIKVDGE 29 (57)
T ss_pred CCCCCCEEEEEe-C-CCCEEEEEEEEECCC
Confidence 367899999988 3 478999999998764
No 202
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=21.05 E-value=43 Score=18.16 Aligned_cols=11 Identities=27% Similarity=0.585 Sum_probs=8.6
Q ss_pred EeCccccceec
Q 027964 154 VQCEGCKDWFH 164 (216)
Q Consensus 154 i~C~~C~~w~H 164 (216)
..|+.|+.||.
T Consensus 4 ~~C~~C~~~~~ 14 (35)
T smart00451 4 FYCKLCNVTFT 14 (35)
T ss_pred eEccccCCccC
Confidence 35889988886
No 203
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=20.58 E-value=71 Score=18.14 Aligned_cols=31 Identities=16% Similarity=0.529 Sum_probs=14.8
Q ss_pred EeCccccceecCcCCCCChhh-hcCCCeEEccccccc
Q 027964 154 VQCEGCKDWFHPSCMGMTIEE-AKKLDHFLCSDCSSD 189 (216)
Q Consensus 154 i~C~~C~~w~H~~Cv~~~~~~-~~~~~~~~C~~C~~~ 189 (216)
|+|+.|+.-|. ++.+. +.....-.|+.|...
T Consensus 3 i~CP~C~~~f~-----v~~~~l~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 3 ITCPNCQTRFR-----VPDDKLPAGGRKVRCPKCGHV 34 (37)
T ss_pred EECCCCCceEE-----cCHHHcccCCcEEECCCCCcE
Confidence 56666666553 22221 112235566666543
No 204
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=20.43 E-value=17 Score=20.39 Aligned_cols=30 Identities=20% Similarity=0.434 Sum_probs=19.9
Q ss_pred CccccceecCcCCCCChhhhcCCCeEEccccccc
Q 027964 156 CEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSD 189 (216)
Q Consensus 156 C~~C~~w~H~~Cv~~~~~~~~~~~~~~C~~C~~~ 189 (216)
-..|+..||..|+..-... ....|+.|...
T Consensus 15 ~~~C~H~~c~~C~~~~~~~----~~~~Cp~C~~~ 44 (45)
T cd00162 15 LLPCGHVFCRSCIDKWLKS----GKNTCPLCRTP 44 (45)
T ss_pred ecCCCChhcHHHHHHHHHh----CcCCCCCCCCc
Confidence 3458888999998643332 24578888653
No 205
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=20.10 E-value=1.1e+02 Score=18.85 Aligned_cols=21 Identities=24% Similarity=0.227 Sum_probs=15.6
Q ss_pred CCceEeCccccceecCcCCCC
Q 027964 150 DDLMVQCEGCKDWFHPSCMGM 170 (216)
Q Consensus 150 ~~~~i~C~~C~~w~H~~Cv~~ 170 (216)
+...+.|..|+.-|...|...
T Consensus 37 ~~~~v~C~~C~~~fC~~C~~~ 57 (64)
T smart00647 37 GCNRVTCPKCGFSFCFRCKVP 57 (64)
T ss_pred CCCeeECCCCCCeECCCCCCc
Confidence 456788888888887777543
Done!