Query 029867
Match_columns 186
No_of_seqs 208 out of 1629
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 04:54:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029867.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029867hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd04714 BAH_BAHCC1 BAH, or Bro 100.0 2.4E-30 5.3E-35 188.0 8.7 109 2-126 13-121 (121)
2 cd04716 BAH_plantDCM_I BAH, or 100.0 8.6E-29 1.9E-33 179.3 9.6 101 2-103 13-118 (122)
3 cd04718 BAH_plant_2 BAH, or Br 100.0 8.9E-30 1.9E-34 187.6 0.7 96 7-103 50-145 (148)
4 cd04717 BAH_polybromo BAH, or 99.9 1E-26 2.2E-31 169.1 8.7 103 2-104 13-118 (121)
5 smart00439 BAH Bromo adjacent 99.9 4.4E-25 9.6E-30 159.4 10.6 103 2-104 11-118 (120)
6 cd04709 BAH_MTA BAH, or Bromo 99.9 3.4E-25 7.5E-30 167.8 9.8 107 2-109 13-143 (164)
7 cd04370 BAH BAH, or Bromo Adja 99.9 3.6E-25 7.8E-30 160.0 8.3 98 7-104 20-121 (123)
8 cd04710 BAH_fungalPHD BAH, or 99.9 1.2E-24 2.6E-29 160.3 9.1 100 1-102 20-133 (135)
9 cd04713 BAH_plant_3 BAH, or Br 99.9 1.4E-24 3.1E-29 162.4 9.3 101 2-103 30-134 (146)
10 PF01426 BAH: BAH domain; Int 99.9 1.7E-24 3.6E-29 156.2 8.0 101 2-104 12-117 (119)
11 cd04711 BAH_Dnmt1_II BAH, or B 99.9 3.4E-24 7.4E-29 155.4 7.4 100 4-103 21-133 (137)
12 cd04721 BAH_plant_1 BAH, or Br 99.9 7.4E-24 1.6E-28 155.5 7.6 91 8-98 21-117 (130)
13 KOG1886 BAH domain proteins [T 99.9 6.8E-23 1.5E-27 174.5 9.8 156 1-160 59-219 (464)
14 cd04760 BAH_Dnmt1_I BAH, or Br 99.9 2.9E-22 6.2E-27 144.6 8.3 100 1-102 12-123 (124)
15 cd04712 BAH_DCM_I BAH, or Brom 99.9 3.7E-21 7.9E-26 141.2 10.9 91 8-103 31-126 (130)
16 cd04708 BAH_plantDCM_II BAH, o 99.9 2.9E-21 6.3E-26 149.9 9.9 97 7-103 39-143 (202)
17 cd04720 BAH_Orc1p_Yeast BAH, o 99.8 1.3E-20 2.8E-25 145.3 8.8 103 2-105 62-177 (179)
18 cd04715 BAH_Orc1p_like BAH, or 99.8 1E-19 2.2E-24 137.5 8.1 74 8-81 43-125 (159)
19 cd04719 BAH_Orc1p_animal BAH, 99.8 6.4E-20 1.4E-24 133.7 6.6 98 2-100 13-123 (128)
20 KOG1827 Chromatin remodeling c 99.4 5.4E-13 1.2E-17 118.2 5.5 108 4-111 202-312 (629)
21 PF00628 PHD: PHD-finger; Int 99.2 3E-12 6.4E-17 78.9 1.0 48 110-158 1-50 (51)
22 KOG1973 Chromatin remodeling p 99.1 1.8E-11 4E-16 100.5 2.6 52 106-162 217-271 (274)
23 smart00249 PHD PHD zinc finger 99.0 2.7E-10 5.8E-15 68.2 3.2 45 111-156 2-47 (47)
24 COG5034 TNG2 Chromatin remodel 99.0 1.6E-10 3.5E-15 91.8 2.8 49 106-159 219-270 (271)
25 KOG1632 Uncharacterized PHD Zn 98.7 6.8E-09 1.5E-13 87.8 2.2 112 51-163 4-117 (345)
26 KOG4323 Polycomb-like PHD Zn-f 98.4 1E-07 2.2E-12 82.4 2.3 55 106-161 169-226 (464)
27 KOG3554 Histone deacetylase co 98.0 3.5E-07 7.7E-12 78.5 -2.8 105 6-110 18-168 (693)
28 PF13831 PHD_2: PHD-finger; PD 97.5 1.2E-05 2.6E-10 45.7 -1.3 35 121-157 2-36 (36)
29 KOG1512 PHD Zn-finger protein 97.4 3.3E-05 7.1E-10 62.9 0.1 49 112-164 319-369 (381)
30 KOG0825 PHD Zn-finger protein 97.4 8.8E-05 1.9E-09 67.6 2.2 54 106-161 213-268 (1134)
31 KOG2752 Uncharacterized conser 97.2 0.00017 3.7E-09 59.5 2.1 37 104-140 124-166 (345)
32 KOG1244 Predicted transcriptio 97.2 0.00014 3.1E-09 58.9 1.2 49 109-159 282-331 (336)
33 KOG1844 PHD Zn-finger proteins 97.1 0.00027 5.9E-09 62.8 1.8 54 106-161 84-137 (508)
34 KOG0955 PHD finger protein BR1 97.0 0.0011 2.4E-08 63.1 5.2 53 108-163 220-273 (1051)
35 KOG1632 Uncharacterized PHD Zn 96.6 0.0001 2.2E-09 62.6 -4.2 64 106-169 237-306 (345)
36 KOG0954 PHD finger protein [Ge 96.4 0.0026 5.6E-08 58.0 3.1 52 107-161 270-323 (893)
37 KOG4299 PHD Zn-finger protein 96.2 0.0016 3.4E-08 58.3 0.6 53 110-163 255-309 (613)
38 KOG0957 PHD finger protein [Ge 95.8 0.0063 1.4E-07 53.4 2.7 53 106-159 542-598 (707)
39 cd04718 BAH_plant_2 BAH, or Br 95.4 0.011 2.5E-07 44.0 2.4 35 133-168 2-36 (148)
40 KOG1245 Chromatin remodeling c 94.3 0.0066 1.4E-07 59.9 -1.8 54 106-161 1106-1160(1404)
41 KOG0383 Predicted helicase [Ge 94.2 0.018 3.9E-07 53.0 1.0 50 107-161 46-96 (696)
42 KOG0957 PHD finger protein [Ge 93.0 0.082 1.8E-06 46.7 2.8 57 105-161 117-181 (707)
43 PF07496 zf-CW: CW-type Zinc F 92.6 0.048 1.1E-06 33.1 0.6 33 122-155 2-34 (50)
44 PF14446 Prok-RING_1: Prokaryo 92.2 0.094 2E-06 32.4 1.6 31 108-138 5-36 (54)
45 KOG2626 Histone H3 (Lys4) meth 91.7 0.16 3.5E-06 45.1 3.1 55 105-159 17-76 (544)
46 KOG1512 PHD Zn-finger protein 91.1 0.077 1.7E-06 43.6 0.5 38 121-158 277-316 (381)
47 PF07227 DUF1423: Protein of u 90.0 0.3 6.6E-06 42.6 3.2 50 112-161 133-194 (446)
48 COG5141 PHD zinc finger-contai 87.0 0.25 5.4E-06 43.6 0.7 47 109-158 194-242 (669)
49 KOG0956 PHD finger protein AF1 86.6 0.35 7.6E-06 44.4 1.4 54 108-164 6-62 (900)
50 PF13832 zf-HC5HC2H_2: PHD-zin 86.5 0.28 6E-06 34.4 0.6 31 107-140 54-87 (110)
51 COG5076 Transcription factor i 85.0 0.13 2.8E-06 44.1 -2.0 75 3-77 287-361 (371)
52 KOG4443 Putative transcription 85.0 0.21 4.5E-06 45.5 -0.8 37 121-157 161-200 (694)
53 PF13639 zf-RING_2: Ring finge 82.8 0.076 1.6E-06 31.0 -3.1 40 112-157 5-44 (44)
54 PF07649 C1_3: C1-like domain; 82.0 0.23 5E-06 26.6 -1.1 26 112-138 5-30 (30)
55 KOG4443 Putative transcription 80.4 0.53 1.1E-05 42.9 -0.0 42 120-161 32-73 (694)
56 PF15446 zf-PHD-like: PHD/FYVE 79.9 3 6.5E-05 31.9 3.9 44 120-163 14-64 (175)
57 PF13922 PHD_3: PHD domain of 79.5 0.3 6.5E-06 31.2 -1.3 32 106-142 31-62 (69)
58 KOG1473 Nucleosome remodeling 76.2 0.73 1.6E-05 44.6 -0.4 56 106-161 1121-1176(1414)
59 PF13771 zf-HC5HC2H: PHD-like 73.5 1.8 3.9E-05 29.0 1.1 32 108-142 36-70 (90)
60 COG5415 Predicted integral mem 72.1 3.5 7.6E-05 32.6 2.5 46 122-172 191-237 (251)
61 PF13341 RAG2_PHD: RAG2 PHD do 69.0 2.5 5.5E-05 27.4 0.9 34 122-155 29-67 (78)
62 PF02081 TrpBP: Tryptophan RNA 67.1 14 0.00031 24.0 4.1 47 28-74 19-65 (75)
63 PF13901 DUF4206: Domain of un 66.2 4.8 0.0001 31.6 2.2 31 121-161 170-200 (202)
64 PRK13251 transcription attenua 66.1 20 0.00042 23.3 4.6 48 27-74 18-65 (75)
65 PF04810 zf-Sec23_Sec24: Sec23 59.8 4.4 9.4E-05 23.2 0.7 34 123-161 2-35 (40)
66 COG4014 Uncharacterized protei 58.7 18 0.00038 24.7 3.5 28 11-38 22-52 (97)
67 PF03107 C1_2: C1 domain; Int 58.1 12 0.00026 19.8 2.3 26 112-138 5-30 (30)
68 cd00350 rubredoxin_like Rubred 57.6 9.1 0.0002 20.8 1.7 12 149-160 16-27 (33)
69 PF00130 C1_1: Phorbol esters/ 55.8 8.9 0.00019 22.8 1.7 35 107-141 10-46 (53)
70 KOG3799 Rab3 effector RIM1 and 55.5 3.4 7.4E-05 30.4 -0.3 61 108-169 65-127 (169)
71 PF10497 zf-4CXXC_R1: Zinc-fin 54.7 11 0.00023 26.6 2.1 35 127-161 31-72 (105)
72 cd00730 rubredoxin Rubredoxin; 53.6 11 0.00025 22.7 1.9 13 148-160 32-44 (50)
73 PF15446 zf-PHD-like: PHD/FYVE 53.0 12 0.00026 28.6 2.3 25 117-141 118-142 (175)
74 PF13913 zf-C2HC_2: zinc-finge 51.5 7.7 0.00017 19.7 0.7 14 122-135 1-14 (25)
75 PF09345 DUF1987: Domain of un 51.4 11 0.00023 26.3 1.7 17 24-40 75-91 (99)
76 PF09871 DUF2098: Uncharacteri 51.2 23 0.00051 24.2 3.3 28 11-39 16-46 (91)
77 PF07754 DUF1610: Domain of un 47.9 14 0.0003 18.8 1.3 11 147-157 13-23 (24)
78 PF05502 Dynactin_p62: Dynacti 45.4 16 0.00035 32.6 2.3 11 151-161 53-63 (483)
79 PF14901 Jiv90: Cleavage induc 43.5 6.4 0.00014 27.1 -0.4 49 121-174 3-51 (94)
80 KOG1829 Uncharacterized conser 43.2 3.7 8E-05 37.4 -2.1 34 120-161 528-561 (580)
81 cd06080 MUM1_like Mutated mela 42.4 29 0.00063 23.1 2.6 27 7-36 13-39 (80)
82 KOG4299 PHD Zn-finger protein 40.3 28 0.0006 31.9 2.9 50 108-161 47-97 (613)
83 PF07494 Reg_prop: Two compone 38.2 46 0.001 16.4 2.4 15 14-28 6-20 (24)
84 smart00109 C1 Protein kinase C 36.5 10 0.00022 21.7 -0.2 32 108-140 11-44 (49)
85 KOG1246 DNA-binding protein ju 35.9 45 0.00097 32.3 3.8 47 112-161 160-206 (904)
86 PF10367 Vps39_2: Vacuolar sor 35.3 34 0.00073 23.2 2.2 30 108-139 78-108 (109)
87 PF08921 DUF1904: Domain of un 35.0 15 0.00033 25.9 0.4 16 25-40 55-70 (108)
88 KOG2752 Uncharacterized conser 34.8 28 0.0006 29.4 1.9 51 108-161 53-103 (345)
89 PF11793 FANCL_C: FANCL C-term 34.7 12 0.00025 24.2 -0.2 52 112-163 7-68 (70)
90 TIGR00270 conserved hypothetic 33.5 23 0.00051 26.6 1.2 33 125-161 2-34 (154)
91 KOG2846 Predicted membrane pro 31.6 57 0.0012 27.7 3.3 56 122-182 219-275 (328)
92 PF09416 UPF1_Zn_bind: RNA hel 31.6 28 0.00061 26.2 1.3 19 120-138 11-29 (152)
93 PF14319 Zn_Tnp_IS91: Transpos 31.1 52 0.0011 23.2 2.6 38 112-161 32-71 (111)
94 KOG1705 Uncharacterized conser 30.5 17 0.00037 24.9 0.0 73 86-161 6-80 (110)
95 PF13717 zinc_ribbon_4: zinc-r 30.1 51 0.0011 18.2 2.0 11 124-134 3-13 (36)
96 PF05180 zf-DNL: DNL zinc fing 29.4 33 0.00071 22.1 1.2 17 117-133 23-39 (66)
97 KOG1244 Predicted transcriptio 28.9 17 0.00038 30.0 -0.2 39 120-158 243-283 (336)
98 KOG1952 Transcription factor N 28.9 16 0.00034 34.8 -0.5 55 107-161 190-247 (950)
99 KOG1941 Acetylcholine receptor 28.8 8.7 0.00019 33.4 -2.0 53 106-161 363-416 (518)
100 PF00301 Rubredoxin: Rubredoxi 28.5 29 0.00063 20.6 0.8 13 148-160 32-44 (47)
101 cd05834 HDGF_related The PWWP 27.9 74 0.0016 21.1 2.8 31 6-36 14-44 (83)
102 TIGR02098 MJ0042_CXXC MJ0042 f 27.7 51 0.0011 18.0 1.7 31 124-159 3-34 (38)
103 PF06220 zf-U1: U1 zinc finger 27.4 28 0.00061 19.6 0.6 11 125-135 5-16 (38)
104 KOG1473 Nucleosome remodeling 26.5 45 0.00098 33.0 2.1 38 120-158 353-390 (1414)
105 KOG3612 PHD Zn-finger protein 26.4 70 0.0015 29.1 3.1 42 120-161 69-110 (588)
106 PF13912 zf-C2H2_6: C2H2-type 26.3 33 0.00072 17.0 0.7 11 124-134 2-12 (27)
107 PF13719 zinc_ribbon_5: zinc-r 25.5 58 0.0013 18.0 1.7 30 124-158 3-33 (37)
108 PF02318 FYVE_2: FYVE-type zin 24.1 13 0.00029 26.4 -1.5 52 108-163 54-107 (118)
109 PF06701 MIB_HERC2: Mib_herc2; 23.6 62 0.0013 20.8 1.7 27 7-33 17-45 (68)
110 PF11910 NdhO: Cyanobacterial 23.2 1.5E+02 0.0032 19.0 3.3 29 3-37 22-54 (67)
111 KOG4628 Predicted E3 ubiquitin 22.5 74 0.0016 27.3 2.4 48 109-161 231-278 (348)
112 KOG2041 WD40 repeat protein [G 22.1 99 0.0021 29.5 3.3 52 104-159 1113-1165(1189)
113 smart00451 ZnF_U1 U1-like zinc 21.9 43 0.00093 17.7 0.6 11 124-134 4-14 (35)
114 PLN02294 cytochrome c oxidase 21.7 86 0.0019 24.1 2.4 37 108-144 117-162 (174)
115 PRK00398 rpoP DNA-directed RNA 21.5 1.7E+02 0.0037 16.7 3.3 32 123-163 3-34 (46)
116 PF14768 RPA_interact_C: Repli 20.9 1.3E+02 0.0028 19.9 2.9 26 107-133 55-80 (82)
117 PF11926 DUF3444: Domain of un 20.7 1.8E+02 0.0039 23.1 4.2 31 5-37 40-70 (217)
118 KOG2932 E3 ubiquitin ligase in 20.5 43 0.00092 28.3 0.6 18 110-127 92-110 (389)
119 PF00649 Copper-fist: Copper f 20.5 62 0.0013 18.6 1.1 14 148-161 6-19 (40)
120 KOG3896 Dynactin, subunit p62 20.3 78 0.0017 27.1 2.1 13 149-161 63-75 (449)
121 KOG3277 Uncharacterized conser 20.1 52 0.0011 24.9 0.9 24 116-139 97-129 (165)
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=99.97 E-value=2.4e-30 Score=187.98 Aligned_cols=109 Identities=47% Similarity=0.820 Sum_probs=96.6
Q ss_pred CCCCCCCCCeEEEEeEEeecCCCCEEEEEEEEeccccccCcccccCCCCeeEeeCCcceeeeceeeeeeEEEeeeccccc
Q 029867 2 RPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKL 81 (186)
Q Consensus 2 ~~~~~~~~~~iarI~~i~~~~~~~~~v~v~Wfyrp~d~~~~~~~~~~~~ELf~S~~~d~~~~~~I~gkc~V~~~~e~~~~ 81 (186)
.+++.+++||||+|++||++.+|+++|+|+|||||+||.+++++.++++|||+|+|.|++++++|.|||.|+++++|.++
T Consensus 13 ~~~~~~~~pyIgrI~~i~e~~~g~~~~~v~WfyrPeEt~~~~~~~~~~~EvF~S~~~d~~~~~~I~gkc~V~~~~ey~~~ 92 (121)
T cd04714 13 KSPGRPSLPYVARIESLWEDPEGNMVVRVKWYYRPEETKGGRKPNHGEKELFASDHQDENSVQTIEHKCYVLTFAEYERL 92 (121)
T ss_pred eCCCCCCCCEEEEEEEEEEcCCCCEEEEEEEEEcHHHccCcccccCCCCceEecCCcccccHHHhCcccEEEehhHheec
Confidence 45555588999999999999889999999999999999999888899999999999999999999999999999999877
Q ss_pred cccCCcceeEeeeeccccCcccCCCcceEEecCCCCCCCCceEeC
Q 029867 82 ENVGAEDYFCRFEYKAATGGFTPDRVAVYCKCEMPYNPDDLMVQC 126 (186)
Q Consensus 82 ~~~~~~~ffcr~~Yd~~~~~f~p~~~~~~C~C~~~~~~~~~~i~C 126 (186)
....+ ++..+...|+|..+|||+..||||
T Consensus 93 ~~~~~----------------~~~~~~d~~~Ce~~yn~~~~~~~c 121 (121)
T cd04714 93 ARVKK----------------KPQDGVDFYYCAGTYNPDTGMLKC 121 (121)
T ss_pred ccccC----------------CCCcCCCEEEEeccCCCCcCcccC
Confidence 65322 334567789999999999999998
No 2
>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=99.96 E-value=8.6e-29 Score=179.31 Aligned_cols=101 Identities=17% Similarity=0.366 Sum_probs=91.6
Q ss_pred CCCCCCCCCeEEEEeEEeecCCCCEEEEEEEEeccccccCcc-cccCCCCeeEeeCCcceeeeceeeeeeEEEeeecccc
Q 029867 2 RPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGR-RQFHGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTK 80 (186)
Q Consensus 2 ~~~~~~~~~~iarI~~i~~~~~~~~~v~v~Wfyrp~d~~~~~-~~~~~~~ELf~S~~~d~~~~~~I~gkc~V~~~~e~~~ 80 (186)
.+++ +++||||||++||++.+|..+++|+|||||+||..++ ...++++|||+|+|.|++|+++|.|||+|+++.++..
T Consensus 13 ~~~~-~~~~yi~rI~~i~e~~~g~~~~~v~WyyRpeet~~~r~~~~~~~rEvFlS~~~D~~pl~~I~~Kc~V~~~~~~~~ 91 (122)
T cd04716 13 QGGE-GEEPFICKITEFFEGTDGKTYFTAQWFYRAEDTVIERQATNHDKKRVFYSEIKNDNPLDCLISKVKILQVPPNVG 91 (122)
T ss_pred ECCC-CCCCEEEEEEEEEEcCCCceEEEEEEEEcHHHhccccccccCCCceEEEecccCccchhheeeeeEEEEeCCCCC
Confidence 3444 5899999999999998999999999999999999886 4688999999999999999999999999999999887
Q ss_pred c----cccCCcceeEeeeeccccCccc
Q 029867 81 L----ENVGAEDYFCRFEYKAATGGFT 103 (186)
Q Consensus 81 ~----~~~~~~~ffcr~~Yd~~~~~f~ 103 (186)
+ ...+.++|||++.|+....+|.
T Consensus 92 ~~~~~~~~~~~df~c~~~Y~~~~~tF~ 118 (122)
T cd04716 92 TKRKKPNSEKCDYYYDMEYCVPYSTFQ 118 (122)
T ss_pred cccccccCCCceEEEeeEeccchhheE
Confidence 6 5568999999999999998885
No 3
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.95 E-value=8.9e-30 Score=187.64 Aligned_cols=96 Identities=26% Similarity=0.516 Sum_probs=92.6
Q ss_pred CCCCeEEEEeEEeecCCCCEEEEEEEEeccccccCcccccCCCCeeEeeCCcceeeeceeeeeeEEEeeeccccccccCC
Q 029867 7 DKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLENVGA 86 (186)
Q Consensus 7 ~~~~~iarI~~i~~~~~~~~~v~v~Wfyrp~d~~~~~~~~~~~~ELf~S~~~d~~~~~~I~gkc~V~~~~e~~~~~~~~~ 86 (186)
+..+|||||++||++. |+.+++++|||||+||.+|++++++.+|||+|++.|++++++|.|+|.|+++++|.+++..+.
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 5679999999999986 899999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceeEeeeeccccCccc
Q 029867 87 EDYFCRFEYKAATGGFT 103 (186)
Q Consensus 87 ~~ffcr~~Yd~~~~~f~ 103 (186)
++|||++.||..++.|+
T Consensus 129 Dvy~Ce~~Yd~~~~~Fk 145 (148)
T cd04718 129 DVFLCEYEYDVHWQSFK 145 (148)
T ss_pred ceEEEEEEEhhhcCcee
Confidence 99999999999999986
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=99.94 E-value=1e-26 Score=169.12 Aligned_cols=103 Identities=25% Similarity=0.463 Sum_probs=92.3
Q ss_pred CCCCCCCCCeEEEEeEEeecCCCCEEEEEEEEeccccccCcccccCCCCeeEeeCCcceeeeceeeeeeEEEeeeccccc
Q 029867 2 RPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKL 81 (186)
Q Consensus 2 ~~~~~~~~~~iarI~~i~~~~~~~~~v~v~Wfyrp~d~~~~~~~~~~~~ELf~S~~~d~~~~~~I~gkc~V~~~~e~~~~ 81 (186)
.+++.+++||||+|.+||++.+|..+++|+|||||+||.++....++++|||+|++.|++++++|.|+|.|+++++|.+.
T Consensus 13 ~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~Wf~rP~et~~~~~~~~~~~Evfls~~~d~~~~~~I~~kc~Vl~~~~y~~~ 92 (121)
T cd04717 13 ANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGKCAVMDVKDYIKG 92 (121)
T ss_pred eCCCCCCCCEEEEEeEEEECCCCCEEEEEEEEeChHHccCCCccccccCceEEcCccccccHHHhcCeeEEEehHHHhcC
Confidence 34454478999999999999889999999999999999988888899999999999999999999999999999999877
Q ss_pred ccc---CCcceeEeeeeccccCcccC
Q 029867 82 ENV---GAEDYFCRFEYKAATGGFTP 104 (186)
Q Consensus 82 ~~~---~~~~ffcr~~Yd~~~~~f~p 104 (186)
... ..++|+|++.|+...+.|++
T Consensus 93 ~p~~~~~~dvy~ce~~y~~~~~~~~~ 118 (121)
T cd04717 93 RPTEISEEDVYVCESRYNESAKSFKK 118 (121)
T ss_pred CCCCCCCCCEEEEeEEECcccccEec
Confidence 643 46789999999999988864
No 5
>smart00439 BAH Bromo adjacent homology domain.
Probab=99.92 E-value=4.4e-25 Score=159.36 Aligned_cols=103 Identities=37% Similarity=0.733 Sum_probs=91.8
Q ss_pred CCCCCCCCCeEEEEeEEeecCCCC-EEEEEEEEeccccccCcccccCCCCeeEeeCCcceeeeceeeeeeEEEeeecccc
Q 029867 2 RPADSDKPPYVARVEKIEADHRNN-VKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTK 80 (186)
Q Consensus 2 ~~~~~~~~~~iarI~~i~~~~~~~-~~v~v~Wfyrp~d~~~~~~~~~~~~ELf~S~~~d~~~~~~I~gkc~V~~~~e~~~ 80 (186)
.++++++++|||+|.+||+..++. ++++|+|||||+||+++..+.++++|||+|++.+++++++|.|||.|++.+++..
T Consensus 11 ~~~~~~~~~~i~~I~~i~~~~~~~~~~~~v~Wf~rp~e~~~~~~~~~~~~Elf~s~~~~~i~~~~I~~kc~V~~~~~~~~ 90 (120)
T smart00439 11 EPDDADEPYYIGRIEEIFETKKNSEKMVRVRWFYRPEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGKCNVLSKSDYPG 90 (120)
T ss_pred eCCCCCCCCEEEEEEEEEECCCCCEEEEEEEEEEChhhccccccccCCCcceEEEccCccCChHHeeeEEEEEEcchhcc
Confidence 345556789999999999998888 8999999999999999888788999999999999999999999999999999976
Q ss_pred cccc----CCcceeEeeeeccccCcccC
Q 029867 81 LENV----GAEDYFCRFEYKAATGGFTP 104 (186)
Q Consensus 81 ~~~~----~~~~ffcr~~Yd~~~~~f~p 104 (186)
.... ..+.||||+.|+..++.|.+
T Consensus 91 ~~~~~~~~~~~~f~cr~~yd~~~~~f~~ 118 (120)
T smart00439 91 LRPEGKIGEPDVFFCESLYDPEKGAFKK 118 (120)
T ss_pred cccccCCCCCCeEEEEEEEccccCcccC
Confidence 6543 46899999999999888853
No 6
>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=99.92 E-value=3.4e-25 Score=167.81 Aligned_cols=107 Identities=22% Similarity=0.454 Sum_probs=91.9
Q ss_pred CCCCCCCCCeEEEEeEEeecCCCCEEEEEEEEeccccccCc----------------------ccccCCCCeeEeeCCcc
Q 029867 2 RPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGG----------------------RRQFHGAKELFLSDHYD 59 (186)
Q Consensus 2 ~~~~~~~~~~iarI~~i~~~~~~~~~v~v~Wfyrp~d~~~~----------------------~~~~~~~~ELf~S~~~d 59 (186)
.++ ++.|++||||++|+++.+|.+.|+|+|||||+|++.. ....++.+|||+|+|.|
T Consensus 13 ~~~-~~~Py~I~rI~e~~~~~~~~~~vkV~wfYRp~DI~~~~~~l~~~~r~~~~~~~~~~~~~~~~~~~~rELF~S~~~d 91 (164)
T cd04709 13 ESS-PNNPYLIRRIEELNKTARGHVEAKVVCYYRRRDIPDSLYQLADQHRRELEEKSDDLTPKQRHQLRHRELFLSRQVE 91 (164)
T ss_pred ECC-CCCCCEEEEEEEEEeCCCCCEEEEEEEEEChhHccchhhhhcccccccccccccccchhhhhccCcceeEEecccc
Confidence 344 4678899999999999999999999999999998642 12346899999999999
Q ss_pred eeeeceeeeeeEEEeeecccccccc--CCcceeEeeeeccccCcccCCCcce
Q 029867 60 VQSAHTIEGKCTVHTFKNYTKLENV--GAEDYFCRFEYKAATGGFTPDRVAV 109 (186)
Q Consensus 60 ~~~~~~I~gkc~V~~~~e~~~~~~~--~~~~ffcr~~Yd~~~~~f~p~~~~~ 109 (186)
.+|+++|+|||.|++++++..+... ..++|||+..||+.+++|..++..+
T Consensus 92 ~~p~~~IrGKC~V~~~~d~~~l~~~~~~~d~Ff~~~~YDP~~k~l~~~~gei 143 (164)
T cd04709 92 TLPATHIRGKCSVTLLNDTESARSYLAREDTFFYSLVYDPEQKTLLADQGEI 143 (164)
T ss_pred cccHHHeeeeEEEEEehhhhhhhhccCCCCEEEEEEEECCCCCeecccceeE
Confidence 9999999999999999999887654 5899999999999999998765443
No 7
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=99.92 E-value=3.6e-25 Score=160.02 Aligned_cols=98 Identities=40% Similarity=0.814 Sum_probs=89.3
Q ss_pred CCCCeEEEEeEEeecCCCCEEEEEEEEeccccccCcccccCCCCeeEeeCCcceeeeceeeeeeEEEeeecccccc----
Q 029867 7 DKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLE---- 82 (186)
Q Consensus 7 ~~~~~iarI~~i~~~~~~~~~v~v~Wfyrp~d~~~~~~~~~~~~ELf~S~~~d~~~~~~I~gkc~V~~~~e~~~~~---- 82 (186)
++++|||+|.+||++.++.++|+|+|||||+||..+....+.++|||+|++.+++++++|.|+|.|++..++.+..
T Consensus 20 ~~~~~i~~I~~i~~~~~~~~~~~v~wf~rp~e~~~~~~~~~~~~Elf~s~~~~~i~v~~I~gkc~V~~~~~~~~~~~~~~ 99 (123)
T cd04370 20 SDPPYIARIEELWEDTNGSKQVKVRWFYRPEETPKGLSPFALRRELFLSDHLDEIPVESIIGKCKVLFVSEFEGLKQRPN 99 (123)
T ss_pred CCCCEEEEEeeeeECCCCCEEEEEEEEEchhHhccccccccccceeEEecCccccCHHHhccccEEEechHhhccccccc
Confidence 4789999999999998899999999999999999988778899999999999999999999999999999987652
Q ss_pred ccCCcceeEeeeeccccCcccC
Q 029867 83 NVGAEDYFCRFEYKAATGGFTP 104 (186)
Q Consensus 83 ~~~~~~ffcr~~Yd~~~~~f~p 104 (186)
....++||||+.||..++.|.+
T Consensus 100 ~~~~~~f~~r~~yd~~~~~fk~ 121 (123)
T cd04370 100 KIDTDDFFCRLAYDPTTKEFKA 121 (123)
T ss_pred cCCCCeEEEEEEECcCcceEEe
Confidence 3467899999999999888764
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=99.91 E-value=1.2e-24 Score=160.33 Aligned_cols=100 Identities=23% Similarity=0.477 Sum_probs=86.2
Q ss_pred CCCCCCCCCCeEEEEeEEeecCC------------CCEEEEEEEEeccccccCcccccCCCCeeEeeCCcceeeeceeee
Q 029867 1 MRPADSDKPPYVARVEKIEADHR------------NNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEG 68 (186)
Q Consensus 1 ~~~~~~~~~~~iarI~~i~~~~~------------~~~~v~v~Wfyrp~d~~~~~~~~~~~~ELf~S~~~d~~~~~~I~g 68 (186)
|.|+++++|+|||||++|+...+ +...|+|+|||||+||..+. ..+.+|||+|+|.|++|+++|+|
T Consensus 20 v~~~~~~ePyyIgrI~e~~~~~~~~~~~~~~~~~~~~~~vrV~wfYRp~Di~~~~--~~d~relf~S~h~d~~p~~si~g 97 (135)
T cd04710 20 MSSEPPGEPYYIGRIMEFVPKHEFPSGIHARVFPASYFQVRLNWYYRPRDISRRV--VADSRLLYASMHSDICPIGSVRG 97 (135)
T ss_pred EecCCCCCCCEEEEEEEEEecCCCCccccccccCCCcEEEEEEEEeCHHHcCCcc--cCCceEEEEEeeEeeechHHEEe
Confidence 46788899999999999998532 23689999999999985443 56999999999999999999999
Q ss_pred eeEEEeeecccccccc--CCcceeEeeeeccccCcc
Q 029867 69 KCTVHTFKNYTKLENV--GAEDYFCRFEYKAATGGF 102 (186)
Q Consensus 69 kc~V~~~~e~~~~~~~--~~~~ffcr~~Yd~~~~~f 102 (186)
||+|.+.+++..++.. .++.|||...||..+.+|
T Consensus 98 KC~V~~~~di~~l~~~~~~~~~Fyf~~lyD~~~~r~ 133 (135)
T cd04710 98 KCTVRHRDQIPDLEEYKKRPNHFYFDQLFDRYILRY 133 (135)
T ss_pred EEEEEEecccchhhhhccCCCEEEEEeeeCcchhhc
Confidence 9999999998776543 578999999999988776
No 9
>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=99.91 E-value=1.4e-24 Score=162.38 Aligned_cols=101 Identities=27% Similarity=0.460 Sum_probs=86.9
Q ss_pred CCCCCCCCCeEEEEeEEeecCCCCEEEEEEEEeccccccCccc---ccCCCCeeEeeCCcceeeeceeeeeeEEEeeecc
Q 029867 2 RPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRR---QFHGAKELFLSDHYDVQSAHTIEGKCTVHTFKNY 78 (186)
Q Consensus 2 ~~~~~~~~~~iarI~~i~~~~~~~~~v~v~Wfyrp~d~~~~~~---~~~~~~ELf~S~~~d~~~~~~I~gkc~V~~~~e~ 78 (186)
.+++ +.+||||+|++||+..++.++|+|+|||||+||..... ..++++|||+|.|.|.+++++|.|||.|+.+.++
T Consensus 30 ~~~~-~~~pyI~~I~~i~~~~~~~~~v~V~WFyRpeEi~~~~~~~~~~~~~~ElF~S~~~d~~~~~~I~gkc~V~~~~~~ 108 (146)
T cd04713 30 VPED-DQKPYIAIIKDIYKQEEGSLKLEVQWLYRPEEIEKKKGGNWKAEDPRELFYSFHRDEVPAESVLHPCKVAFVPKG 108 (146)
T ss_pred eCCC-CCCCEEEEEEEEEEcCCCCEEEEEEeeECHHHhccccccccccCCCCeEEEeCCCCcCCHHHCcceeEEEECCcc
Confidence 3455 48899999999999888999999999999999975432 2346899999999999999999999999999888
Q ss_pred cccccc-CCcceeEeeeeccccCccc
Q 029867 79 TKLENV-GAEDYFCRFEYKAATGGFT 103 (186)
Q Consensus 79 ~~~~~~-~~~~ffcr~~Yd~~~~~f~ 103 (186)
.++... ...+||||..||..+++|.
T Consensus 109 ~~~~~~~~~~~F~cr~~yD~~~~~~~ 134 (146)
T cd04713 109 KQIPLRKGHSGFIVRRVYDNVNKKLW 134 (146)
T ss_pred ccCCccCCCCeEEEEEEEcCCCCcEe
Confidence 776654 5789999999999888775
No 10
>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=99.91 E-value=1.7e-24 Score=156.24 Aligned_cols=101 Identities=39% Similarity=0.794 Sum_probs=87.6
Q ss_pred CCCCCCCCCeEEEEeEEeecCCCC--EEEEEEEEeccccccCcccccCCCCeeEeeCCcceeeeceeeeeeEEEeeeccc
Q 029867 2 RPADSDKPPYVARVEKIEADHRNN--VKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYT 79 (186)
Q Consensus 2 ~~~~~~~~~~iarI~~i~~~~~~~--~~v~v~Wfyrp~d~~~~~~~~~~~~ELf~S~~~d~~~~~~I~gkc~V~~~~e~~ 79 (186)
.++++++++|||+|++||++.++. .+++|+|||||+||.. .....++|||+|++++.+++++|.|+|.|++..++.
T Consensus 12 ~~~~~~~~~~v~~I~~i~~~~~~~~~~~~~v~Wf~rp~d~~~--~~~~~~~Elf~s~~~~~~~~~~I~gkc~V~~~~~~~ 89 (119)
T PF01426_consen 12 KPDDPPEPPYVARIEEIWEDKDGNKEKMVKVRWFYRPEDTSL--GKTFSPRELFLSDHCDDIPVESIRGKCNVLHLEDYE 89 (119)
T ss_dssp ECTSTTSEEEEEEEEEEEEETTTSEEEEEEEEEEEEGGGSTT--GGHSCTTEEEEEEEEEEEEGGGEEEEEEEEEHHHHT
T ss_pred eCCCCCCCCEEEEEEEEEcCCCCCEEEEEEEEEeECcccccc--cccCCCCEEEEECcEeEEehhhEEeeeEEEECCccc
Confidence 355667899999999999998887 9999999999999932 334456999999999999999999999999999987
Q ss_pred ccccc---CCcceeEeeeeccccCcccC
Q 029867 80 KLENV---GAEDYFCRFEYKAATGGFTP 104 (186)
Q Consensus 80 ~~~~~---~~~~ffcr~~Yd~~~~~f~p 104 (186)
+.... ..++|||++.||..++.|.+
T Consensus 90 ~~~~~~~~~~~~F~cr~~yd~~~~~f~~ 117 (119)
T PF01426_consen 90 QARPYGKEEPDTFFCRYAYDPQKKRFKK 117 (119)
T ss_dssp TGCCHCHHTTTEEEEEEEEETTTTEEEE
T ss_pred cccccccCCCCEEEEEEEEeCCcCEEeC
Confidence 76543 68999999999999998864
No 11
>cd04711 BAH_Dnmt1_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.90 E-value=3.4e-24 Score=155.42 Aligned_cols=100 Identities=25% Similarity=0.519 Sum_probs=83.4
Q ss_pred CCCCCCCeEEEEeEEeecCCC-------CEEEEEEEEeccccccCcccc-cC-CCCeeEeeCCcceeeeceeeeeeEEEe
Q 029867 4 ADSDKPPYVARVEKIEADHRN-------NVKVRVRWYYRPEESIGGRRQ-FH-GAKELFLSDHYDVQSAHTIEGKCTVHT 74 (186)
Q Consensus 4 ~~~~~~~~iarI~~i~~~~~~-------~~~v~v~Wfyrp~d~~~~~~~-~~-~~~ELf~S~~~d~~~~~~I~gkc~V~~ 74 (186)
-|.++|++||||++|....++ ..+|+|+|||||+||..+... ++ +.+|||+|+|.+++++++|.|||+|.+
T Consensus 21 ~d~~ePy~VgrI~eI~~~k~~~~k~~~~~ikvrV~~fYRPEdi~~g~~~ayhsDirevy~Sd~~~~~~~~~I~GKC~V~~ 100 (137)
T cd04711 21 LDAPEPFRIGRIKEIFCAKRSNGKPNESDIKLRINKFYRPENTHKGFKATYHADINMLYWSDEEATVDFSAVQGRCTVEY 100 (137)
T ss_pred CCCCCCcEEEEEEEEecCCCCCCCCCccceEEEEEEEecccccccccccccccceeeEEeecceeecChhhccceEEEEe
Confidence 467889999999999886432 368999999999999987533 44 559999999999999999999999997
Q ss_pred eecccc-c---cccCCcceeEeeeeccccCccc
Q 029867 75 FKNYTK-L---ENVGAEDYFCRFEYKAATGGFT 103 (186)
Q Consensus 75 ~~e~~~-~---~~~~~~~ffcr~~Yd~~~~~f~ 103 (186)
..+... + ...+++.|||+..|+++|+.|.
T Consensus 101 ~~di~~s~~~y~~~gpd~Fyf~~~Y~a~t~~F~ 133 (137)
T cd04711 101 GEDLPESVQEYSGGGPDRFYFLEAYNAKTKSFE 133 (137)
T ss_pred ccccchhHHHHhcCCCcceEEhhhhccccCccc
Confidence 655542 2 3357899999999999999997
No 12
>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=99.90 E-value=7.4e-24 Score=155.45 Aligned_cols=91 Identities=30% Similarity=0.495 Sum_probs=82.6
Q ss_pred CCCeEEEEeEEeecCCCCEEEEEEEEeccccccCccccc-CCCCeeEeeCCcceeeeceeeeeeEEEeeecccccccc--
Q 029867 8 KPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQF-HGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLENV-- 84 (186)
Q Consensus 8 ~~~~iarI~~i~~~~~~~~~v~v~Wfyrp~d~~~~~~~~-~~~~ELf~S~~~d~~~~~~I~gkc~V~~~~e~~~~~~~-- 84 (186)
+++|||+|++||++.+|.++|+|+||+||+||.++..+. +.++|||+|++.+.+++++|.|||.|++.++|.+....
T Consensus 21 ~~~~va~Ie~i~ed~~g~~~v~v~WF~~p~E~~~~~~~~~~~~~EvFlS~~~d~i~~~~I~gk~~Vls~~~y~k~~~~~~ 100 (130)
T cd04721 21 EDRYVAYIEDLYEDKKGSKMVKVRWFHTTDEVGAALSPDSVNPREIFLSPNLQVISVECIDGLATVLTREHYEKFQSVPK 100 (130)
T ss_pred CCcEEEEEEEEEEcCCCCEEEEEEEecCHHHhccccCCCCCCCCeEEEcCCccccchHHeeeeeEECCHHHHhhhhcccc
Confidence 678999999999998899999999999999999876555 89999999999999999999999999999999887643
Q ss_pred ---CCcceeEeeeeccc
Q 029867 85 ---GAEDYFCRFEYKAA 98 (186)
Q Consensus 85 ---~~~~ffcr~~Yd~~ 98 (186)
..++|+||..||..
T Consensus 101 ~~~~~~~f~C~~~~d~~ 117 (130)
T cd04721 101 NSSELQAYFCYRQIDNN 117 (130)
T ss_pred CccccccEEEEEEecCC
Confidence 25599999999975
No 13
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=99.88 E-value=6.8e-23 Score=174.54 Aligned_cols=156 Identities=34% Similarity=0.429 Sum_probs=138.5
Q ss_pred CCCCCCCCCCeEEEEeEEeecCC-CCEEEEEEEEeccccccCccccc---CCCCeeEeeCCcceeeeceeeeeeEEEeee
Q 029867 1 MRPADSDKPPYVARVEKIEADHR-NNVKVRVRWYYRPEESIGGRRQF---HGAKELFLSDHYDVQSAHTIEGKCTVHTFK 76 (186)
Q Consensus 1 ~~~~~~~~~~~iarI~~i~~~~~-~~~~v~v~Wfyrp~d~~~~~~~~---~~~~ELf~S~~~d~~~~~~I~gkc~V~~~~ 76 (186)
|.|++++.+||||+|..|+.... +.+.+.|+|||||+|+..+.... ..++|||+|.|.|.+++++|.++|.|.++.
T Consensus 59 lvped~~~pPyvaii~~i~a~~~g~~~k~ev~W~YrPee~~~~~~~~~~a~~~relF~SfH~De~~A~ti~~rC~V~fvp 138 (464)
T KOG1886|consen 59 LVPEDPGKPPYVAIIEDIYAQERGGNVKVEVQWFYRPEESEGGGSGKWGAKQPRELFLSFHEDEAFAETILHRCKVHFVP 138 (464)
T ss_pred ecCCCCCCCCeeEEEeeeeccccCCCcceecccccCCCccCCCCCCCcccCCCccccccccccchhhhhhcccceeeecc
Confidence 46889999999999999998765 58999999999999998765443 345699999999999999999999999999
Q ss_pred ccccccc-cCCcceeEeeeeccccCcccCCCcceEEecCCCCCCCCceEeCCCCCceecCCCCCCChhhhcCCCeEEccc
Q 029867 77 NYTKLEN-VGAEDYFCRFEYKAATGGFTPDRVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSD 155 (186)
Q Consensus 77 e~~~~~~-~~~~~ffcr~~Yd~~~~~f~p~~~~~~C~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~ 155 (186)
.+.++.+ .+.+.|+|+..||..++.+.......+|.|++..++...|.+|..|+.|+|..|++.... ++..+|..
T Consensus 139 ~~kqlp~~~~~~~f~~r~vYd~~~~~~~~~~~~~~~~~~k~e~d~~~~kt~~~~~~~~~p~~~~t~~~----~~~~~~~~ 214 (464)
T KOG1886|consen 139 AYKQLPNRVGHESFICRRVYDAVTSKLRKLRDGDFGDGQKLEIDMLVPKTGPRRGTLPDPKKVQTLNA----AASKRSQQ 214 (464)
T ss_pred ccccccccCCCCCcccccccccccccccCccccchhcccccCCccchhhhcccCCCCCCccccccccc----cccceecc
Confidence 9999877 689999999999999999998888999999999999999999999999999999998873 35678888
Q ss_pred Ccccc
Q 029867 156 CSSDV 160 (186)
Q Consensus 156 C~~~~ 160 (186)
|....
T Consensus 215 ~s~~~ 219 (464)
T KOG1886|consen 215 KSEIS 219 (464)
T ss_pred ccccc
Confidence 85443
No 14
>cd04760 BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.87 E-value=2.9e-22 Score=144.65 Aligned_cols=100 Identities=24% Similarity=0.410 Sum_probs=85.6
Q ss_pred CCCCCCCCCCeEEEEeEEeecCCCCEEEEEEEEeccccccCcccccCCCCeeEeeCCcceeeeceeeeeeEEEeeecccc
Q 029867 1 MRPADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTK 80 (186)
Q Consensus 1 ~~~~~~~~~~~iarI~~i~~~~~~~~~v~v~Wfyrp~d~~~~~~~~~~~~ELf~S~~~d~~~~~~I~gkc~V~~~~e~~~ 80 (186)
|.+++++.+||||+|+.||++.+|.++++++|||||+||..++. ++++|||+|++++.+++++|.+||+|+....-..
T Consensus 12 v~~~~~~~p~~I~rV~~mfe~~~g~k~~h~rWf~Rg~dTVlG~~--~~~kEvFlsd~c~d~~l~~I~~Kv~V~~~~p~~~ 89 (124)
T cd04760 12 VKPDDPTKPLYIARVTYMWKDSIGGKMFHAHWFCRGSDTVLGET--SDPLELFLVDECEDMALSSIHGKVNVIYKAPSEN 89 (124)
T ss_pred EecCCCCCCcEEEEEhhheecCCCCcEEEEEEEEECCccccccc--CCCcEEEeecccCCcchHHheeeeEEEEeCCCcc
Confidence 35677889999999999999999999999999999999999975 6899999999999999999999999997654311
Q ss_pred ------------ccccCCcceeEeeeeccccCcc
Q 029867 81 ------------LENVGAEDYFCRFEYKAATGGF 102 (186)
Q Consensus 81 ------------~~~~~~~~ffcr~~Yd~~~~~f 102 (186)
....+..+|||+.-|++...+|
T Consensus 90 w~~~~g~~~~~~~~~ddg~tffyq~~yd~~~arf 123 (124)
T cd04760 90 WSMEGGMDEEDEIFEDDGKTFFYQKWYDPECARF 123 (124)
T ss_pred hhhhcCCCCccccccCCCCeEEEEEeeChhhhcc
Confidence 1112567899999999987766
No 15
>cd04712 BAH_DCM_I BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.86 E-value=3.7e-21 Score=141.17 Aligned_cols=91 Identities=25% Similarity=0.404 Sum_probs=77.3
Q ss_pred CCCeEEEEeEEeecCCCCEEEEEEEEeccccccCcccccCCCCeeEeeCCcceeeec----eeeeeeEEEeeeccccccc
Q 029867 8 KPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAH----TIEGKCTVHTFKNYTKLEN 83 (186)
Q Consensus 8 ~~~~iarI~~i~~~~~~~~~v~v~Wfyrp~d~~~~~~~~~~~~ELf~S~~~d~~~~~----~I~gkc~V~~~~e~~~~~~ 83 (186)
.+|||++|+.||++.+|.++++++|||||+||.+++ .++++|||+|+|++.++++ .|.++|.|..+..+..
T Consensus 31 ~~~~i~~V~~~~e~~~g~~~~h~~W~yrp~eTv~g~--~~~~~ElFLSd~c~~~~~~~~~~~I~~k~~V~~~~~~~~--- 105 (130)
T cd04712 31 WLPLVQFVEYMKKGSDGSKMFHGRWLYRGCDTVLGN--YANERELFLTNECTCLELDLLSTEIKGVHKVDWSGTPWG--- 105 (130)
T ss_pred ccceEEEEEEeeecCCCceEEEEEEEEcchhccccc--cCCCceEEEeccccccccccccceeEEEEEEEEecCcCC---
Confidence 489999999999999999999999999999999997 7899999999999999999 9999999997766543
Q ss_pred cCCcceeEeeeec-cccCccc
Q 029867 84 VGAEDYFCRFEYK-AATGGFT 103 (186)
Q Consensus 84 ~~~~~ffcr~~Yd-~~~~~f~ 103 (186)
.+.++|||++.|. +..+.|.
T Consensus 106 ~~~~~~F~r~syy~~e~~~F~ 126 (130)
T cd04712 106 KGLPEFFVRQSYYWPERGAFT 126 (130)
T ss_pred cCCCCEEEEEEEECccCCceE
Confidence 2344455555554 4888875
No 16
>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=99.85 E-value=2.9e-21 Score=149.92 Aligned_cols=97 Identities=24% Similarity=0.449 Sum_probs=84.8
Q ss_pred CCCCeEEEEeEEeecCCC------CEEEEEEEEeccccccCcccccCCCCeeEeeCCcceeeeceeeeeeEEEeeecccc
Q 029867 7 DKPPYVARVEKIEADHRN------NVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTK 80 (186)
Q Consensus 7 ~~~~~iarI~~i~~~~~~------~~~v~v~Wfyrp~d~~~~~~~~~~~~ELf~S~~~d~~~~~~I~gkc~V~~~~e~~~ 80 (186)
..+++||||.+|+...++ ...|+|+|||||+||........+.+|||+|++.+++++++|.|||+|+...++.+
T Consensus 39 ~~p~~I~qI~ei~~~k~~~~~~~~~~~vrVrwFYRPEdt~~~~~y~sd~rely~Sde~~~~~~~~I~GKC~V~~~~d~~~ 118 (202)
T cd04708 39 LKAFVVCQVLEIVVEKESKQADVASTQVKVRRFYRPEDVSPEKAYASDIREVYYSEDTLTVPVEAVEGKCEVRKKSDLPD 118 (202)
T ss_pred CCCcEEEEEEEEEecccCCCCCCcceEEEEEEEechhhcCcccceecCceeEEEeccceeechhHcceEEEEEecCcchh
Confidence 358999999999985443 58999999999999966444455999999999999999999999999999999877
Q ss_pred ccc--cCCcceeEeeeeccccCccc
Q 029867 81 LEN--VGAEDYFCRFEYKAATGGFT 103 (186)
Q Consensus 81 ~~~--~~~~~ffcr~~Yd~~~~~f~ 103 (186)
+.. ...+.|||+..||+.++.|+
T Consensus 119 ~~~~~~~~~~Ffc~~~Yd~~tg~f~ 143 (202)
T cd04708 119 SDAPVIFEHVFFCELLYDPAKGSLK 143 (202)
T ss_pred hhccccCCCceEEEEEEcCCCCccC
Confidence 654 46899999999999999997
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=99.83 E-value=1.3e-20 Score=145.34 Aligned_cols=103 Identities=22% Similarity=0.335 Sum_probs=87.1
Q ss_pred CCCCCCCCCeEEEEeEEeecCC-CCEEEEEEEEeccccccCccc--c-------cCCCCeeEeeCCcceeeeceeeeeeE
Q 029867 2 RPADSDKPPYVARVEKIEADHR-NNVKVRVRWYYRPEESIGGRR--Q-------FHGAKELFLSDHYDVQSAHTIEGKCT 71 (186)
Q Consensus 2 ~~~~~~~~~~iarI~~i~~~~~-~~~~v~v~Wfyrp~d~~~~~~--~-------~~~~~ELf~S~~~d~~~~~~I~gkc~ 71 (186)
++++ +++||||.|.+|+.... +.+.+.|+|||||.|+..++. + ...++|||+|.|.|.+++.+|+|+|.
T Consensus 62 k~~~-~~~~~V~iI~ei~~~~~~~~v~i~v~Wy~r~~Ei~~~~~~~~~~~~~~~~~~~nElflT~~~d~i~l~~Ii~k~~ 140 (179)
T cd04720 62 KDDV-ANSPSVYLIHEIRLNTLNNEVELWVMWFLRWFEINPARYYKQFDPEFRSESNKNELYLTAELSEIKLKDIIDKAN 140 (179)
T ss_pred eCCC-CCCCEEEEEEEEEeCCCCCEEEEEEEEcCCHHHcccccccccccchhcccCCCceEEEecccceEEhhheeeeEE
Confidence 3444 47899999999998754 557999999999999976542 2 23379999999999999999999999
Q ss_pred EEeeecccccccc---CCcceeEeeeeccccCcccCC
Q 029867 72 VHTFKNYTKLENV---GAEDYFCRFEYKAATGGFTPD 105 (186)
Q Consensus 72 V~~~~e~~~~~~~---~~~~ffcr~~Yd~~~~~f~p~ 105 (186)
|++.++|.++... ...+||||+.|++.++.|.+.
T Consensus 141 Vls~~ef~~~~~~~~~~~~~F~cR~~~d~~~~~F~~~ 177 (179)
T cd04720 141 VLSESEFNDLSTDDKNGERTFFCRYACEPDGEEFVWI 177 (179)
T ss_pred EecHHHhhhhcccccCCCceEEEEEEEeCCCCeEccc
Confidence 9999999877644 678999999999999988764
No 18
>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=99.80 E-value=1e-19 Score=137.50 Aligned_cols=74 Identities=26% Similarity=0.440 Sum_probs=64.8
Q ss_pred CCCeEEEEeEEeecCC--CCEEEEEEEEeccccccCccc--ccCCCCeeEeeCCc-----ceeeeceeeeeeEEEeeecc
Q 029867 8 KPPYVARVEKIEADHR--NNVKVRVRWYYRPEESIGGRR--QFHGAKELFLSDHY-----DVQSAHTIEGKCTVHTFKNY 78 (186)
Q Consensus 8 ~~~~iarI~~i~~~~~--~~~~v~v~Wfyrp~d~~~~~~--~~~~~~ELf~S~~~-----d~~~~~~I~gkc~V~~~~e~ 78 (186)
++||||+|.+||+..+ +.++++|+|||||+||..... ..++++|||+|.|. +++++++|.|||.|+++++|
T Consensus 43 ~~~yIgkI~~iwe~~~~~g~~~~~v~WfyRp~E~~~~~~~~~~~~~nEvFlS~~~d~~~~~~n~l~sI~gKC~Vl~~~ey 122 (159)
T cd04715 43 SEPYIGKIIKIYETAIDSGKKKVKVIWFFRPSEIRMELKGEPKRHINEVFLACGRGEGLANINLLESIIGKCNVVCISED 122 (159)
T ss_pred CCCEEEEEEEEEEcCCcCCceEEEEEeeeCHHHhccccccCcccCCCcEEEecCcCccccccCcHHHccceeEEEEehHh
Confidence 7899999999999865 889999999999999986432 46789999999986 56789999999999999999
Q ss_pred ccc
Q 029867 79 TKL 81 (186)
Q Consensus 79 ~~~ 81 (186)
.+.
T Consensus 123 ~~~ 125 (159)
T cd04715 123 FRN 125 (159)
T ss_pred hhC
Confidence 653
No 19
>cd04719 BAH_Orc1p_animal BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces cerevisiae Orc1p. Orc1 is part of the Yeast Sir1-origin recognition complex. The Orc1p BAH doman functions in epigenetic silencing. In vertebrates, a similar ORC protein complex exists, which has been shown essential for DNA replication in Xenopus laevis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.80 E-value=6.4e-20 Score=133.68 Aligned_cols=98 Identities=23% Similarity=0.318 Sum_probs=79.8
Q ss_pred CCCCCCCCCeEEEEeEEeecCCC---CEEEEEEEEeccccccCcc----cccCCCCeeEeeCCcc---eeeeceeeeeeE
Q 029867 2 RPADSDKPPYVARVEKIEADHRN---NVKVRVRWYYRPEESIGGR----RQFHGAKELFLSDHYD---VQSAHTIEGKCT 71 (186)
Q Consensus 2 ~~~~~~~~~~iarI~~i~~~~~~---~~~v~v~Wfyrp~d~~~~~----~~~~~~~ELf~S~~~d---~~~~~~I~gkc~ 71 (186)
+++++ ++||||+|++|+++.++ ...++|||||||+|++... .+..+++|||+|+|.+ .+.+++|.|+|.
T Consensus 13 ~~~d~-~~~yVAkI~~i~e~~~~~~~~~~~~VqWy~R~~Ev~~~~~~~~~~~~~~~EvF~~~~~~~~~~i~~etI~gkc~ 91 (128)
T cd04719 13 EGEDA-DGPDVARILHLYEDGNEDDDPKRAIVQWFSRPSEVPKNKRKLLGREPHSQEVFFYSRSSCDNDIDAETIIGKVR 91 (128)
T ss_pred ECCCC-CCCcEeeehhhhccccCCcccceEEEEcccChHHccccchhhccCCCCCcEEEEecCccccCcEeHHHcccEEE
Confidence 45554 78899999999998765 5799999999999997432 1345899999999875 899999999999
Q ss_pred EEeeecccccccc---CCcceeEeeeeccccC
Q 029867 72 VHTFKNYTKLENV---GAEDYFCRFEYKAATG 100 (186)
Q Consensus 72 V~~~~e~~~~~~~---~~~~ffcr~~Yd~~~~ 100 (186)
|+++.+|..+... ....||.+..++.+..
T Consensus 92 V~~~~~y~~l~~~~~~~~~~~F~r~~~~~k~~ 123 (128)
T cd04719 92 VEPVEPKTDLPETKKKTGGPLFVKRYWDTKTF 123 (128)
T ss_pred EEEcCCccchhhhccccCceEEEEEEeccccc
Confidence 9999999887632 3567888888887644
No 20
>KOG1827 consensus Chromatin remodeling complex RSC, subunit RSC1/Polybromo and related proteins [Chromatin structure and dynamics; Transcription]
Probab=99.37 E-value=5.4e-13 Score=118.22 Aligned_cols=108 Identities=20% Similarity=0.308 Sum_probs=96.3
Q ss_pred CCCCCCCeEEEEeEEeecCCCCEEEEEEEEeccccccCcccccCCCCeeEeeCCcceeeeceeeeeeEEEeeeccccccc
Q 029867 4 ADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLEN 83 (186)
Q Consensus 4 ~~~~~~~~iarI~~i~~~~~~~~~v~v~Wfyrp~d~~~~~~~~~~~~ELf~S~~~d~~~~~~I~gkc~V~~~~e~~~~~~ 83 (186)
.++..+|.|++|.++|+..+|..|+.+.|||||++|.+...+.+..+|+|.|......+++.|+|+|.|+.+.+|.....
T Consensus 202 ~~d~~~p~v~~Ier~w~~~dg~k~~~~~w~~rP~~T~H~a~r~F~k~Evfkt~~~~~~~~q~l~g~c~v~~~~~yi~~~p 281 (629)
T KOG1827|consen 202 PADNLKPIVAQIERLWKLPDGEKWPQGCWIYRPEETVHRADRKFYKQEVFKTSLYRDDLVQRLLGKCYVMKPTEYISGDP 281 (629)
T ss_pred cccccCCceeeecccccCcccccccceeEeeCCccCccccccchhcccceecccccccHHHHhhcceEEeehhHhhhcCc
Confidence 34447899999999999999999999999999999999988899999999999999999999999999999999987654
Q ss_pred c---CCcceeEeeeeccccCcccCCCcceEE
Q 029867 84 V---GAEDYFCRFEYKAATGGFTPDRVAVYC 111 (186)
Q Consensus 84 ~---~~~~ffcr~~Yd~~~~~f~p~~~~~~C 111 (186)
. ..+.|+|++.|+...+.|+.-.....|
T Consensus 282 ~~ls~~dv~lcesRyn~~~K~f~kirsw~~~ 312 (629)
T KOG1827|consen 282 ENLSEEDVFLCESRYNEQLKKFNKIRSWKAF 312 (629)
T ss_pred ccccccceeeEEeeeccchhhhccccCchhc
Confidence 3 678999999999999999865544444
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=99.21 E-value=3e-12 Score=78.91 Aligned_cols=48 Identities=29% Similarity=0.920 Sum_probs=39.7
Q ss_pred EE-ecCCCCCCCCceEeCCCCCceecCCCCCCChhhhcC-CCeEEcccCcc
Q 029867 110 YC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKK-LDHFLCSDCSS 158 (186)
Q Consensus 110 ~C-~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~~~~-~~~~~C~~C~~ 158 (186)
+| +|++ .++++.||+|+.|+.|||..|++++...... ...|+|+.|..
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 57 8999 4568999999999999999999999874332 23899999975
No 22
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=99.14 E-value=1.8e-11 Score=100.47 Aligned_cols=52 Identities=25% Similarity=0.843 Sum_probs=43.9
Q ss_pred CcceEEecCCCCCCCCceEeCCC--CC-ceecCCCCCCChhhhcCCCeEEcccCcccccc
Q 029867 106 RVAVYCKCEMPYNPDDLMVQCEG--CK-DWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA 162 (186)
Q Consensus 106 ~~~~~C~C~~~~~~~~~~i~C~~--C~-~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~ 162 (186)
.+..||+|.+. ..+.||.||. |. +|||+.|||+...+. +.|+|+.|......
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 47899999954 5799999996 99 999999999996543 57999999977653
No 23
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=99.01 E-value=1.6e-10 Score=91.80 Aligned_cols=49 Identities=31% Similarity=0.901 Sum_probs=41.4
Q ss_pred CcceEEecCCCCCCCCceEeCC--CCC-ceecCCCCCCChhhhcCCCeEEcccCccc
Q 029867 106 RVAVYCKCEMPYNPDDLMVQCE--GCK-DWFHPSCMGMTIEEAKKLDHFLCSDCSSD 159 (186)
Q Consensus 106 ~~~~~C~C~~~~~~~~~~i~C~--~C~-~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~ 159 (186)
.+.+||+|+++. -+.||.|| .|+ +|||+.|||+...+- ..|+|+.|...
T Consensus 219 ~e~lYCfCqqvS--yGqMVaCDn~nCkrEWFH~~CVGLk~pPK---G~WYC~eCk~~ 270 (271)
T COG5034 219 GEELYCFCQQVS--YGQMVACDNANCKREWFHLECVGLKEPPK---GKWYCPECKKA 270 (271)
T ss_pred CceeEEEecccc--cccceecCCCCCchhheeccccccCCCCC---CcEeCHHhHhc
Confidence 368999999984 78999999 696 999999999987542 58999999753
No 25
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=98.69 E-value=6.8e-09 Score=87.76 Aligned_cols=112 Identities=27% Similarity=0.449 Sum_probs=87.7
Q ss_pred eeEeeCCcceeeeceeeeeeEEEeeeccccccccCCcceeEeeeeccccCcccCCCcceEEecCCCCCCCCceEeCCCCC
Q 029867 51 ELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLENVGAEDYFCRFEYKAATGGFTPDRVAVYCKCEMPYNPDDLMVQCEGCK 130 (186)
Q Consensus 51 ELf~S~~~d~~~~~~I~gkc~V~~~~e~~~~~~~~~~~ffcr~~Yd~~~~~f~p~~~~~~C~C~~~~~~~~~~i~C~~C~ 130 (186)
+.+++.+...-....+.+.+...+...+... .....+......+....+.+.+.....+|.|..+.+++.+|++|+.|.
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~k~~~~~~~~a~~~~~~~~~~~~~p~~~~~~cd~C~ 82 (345)
T KOG1632|consen 4 IPKTSKTFSKTESDRRAPIAQKTTKPPKEPV-PIERPVPDVFRGRKGRRGGLLKALTQRYCKCYKPCDPDDLMEQCDLCE 82 (345)
T ss_pred cccccceecccccccccccccccccCCcCCC-CCCCCCcccccccccccccccHhhhhchhhcccccCchhhhhcccccc
Confidence 4455555555566666666666665555444 335566667777777777777777778999999999999999999999
Q ss_pred ceecCCC--CCCChhhhcCCCeEEcccCccccccc
Q 029867 131 DWFHPSC--MGMTIEEAKKLDHFLCSDCSSDVDAK 163 (186)
Q Consensus 131 ~W~H~~C--v~~~~~~~~~~~~~~C~~C~~~~~~~ 163 (186)
.|||..| ||++...+..++.|+|..|......+
T Consensus 83 ~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~~~~ 117 (345)
T KOG1632|consen 83 DWYHGECWEVGTAEKEAPKEDPKVCDECKEAQDGM 117 (345)
T ss_pred ccccccccccCchhhcCCccccccccccchhhhhh
Confidence 9999999 99999999999999999999888744
No 26
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=98.42 E-value=1e-07 Score=82.44 Aligned_cols=55 Identities=24% Similarity=0.680 Sum_probs=44.3
Q ss_pred CcceEEecCCCCCCCCceEeCCCCCceecCCCCCCChhhhc---CCCeEEcccCccccc
Q 029867 106 RVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAK---KLDHFLCSDCSSDVD 161 (186)
Q Consensus 106 ~~~~~C~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~~~---~~~~~~C~~C~~~~~ 161 (186)
..-.+|.|+++...+ .||||+.|+.|||..|......+.. ....|+|..|....+
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 346788999987655 9999999999999999987665322 224999999998887
No 27
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=98.03 E-value=3.5e-07 Score=78.51 Aligned_cols=105 Identities=25% Similarity=0.440 Sum_probs=83.5
Q ss_pred CCCCCeEEEEeEEeecCCCCEEEEEEEEeccccccCc---------c---------------------------------
Q 029867 6 SDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGG---------R--------------------------------- 43 (186)
Q Consensus 6 ~~~~~~iarI~~i~~~~~~~~~v~v~Wfyrp~d~~~~---------~--------------------------------- 43 (186)
.++|+.|-||+++....+|++-.+|--|||-.|+... +
T Consensus 18 ss~PYliRrIEELnKTa~GnVeAkvVc~~RRRDIs~~L~~lAD~~ar~~~~y~a~~~a~~~~e~e~EEe~e~p~~vdlt~ 97 (693)
T KOG3554|consen 18 SSNPYLIRRIEELNKTANGNVEAKVVCYLRRRDISSHLLKLADKHARRFDNYAAPEAAPEATEAEIEEESECPAPVDLTE 97 (693)
T ss_pred CCChHHHHHHHHHhccccCCcceEEEEEEEccchHHHHHHHHHHHhhhcccccCcccCcccchhhhhhhccCCCcCCCCH
Confidence 3568889999999999999999999999999987421 0
Q ss_pred --cccCCCCeeEeeCCcceeeeceeeeeeEEEeeeccccccc--cCCcceeEeeeeccccCcccCCCcceE
Q 029867 44 --RQFHGAKELFLSDHYDVQSAHTIEGKCTVHTFKNYTKLEN--VGAEDYFCRFEYKAATGGFTPDRVAVY 110 (186)
Q Consensus 44 --~~~~~~~ELf~S~~~d~~~~~~I~gkc~V~~~~e~~~~~~--~~~~~ffcr~~Yd~~~~~f~p~~~~~~ 110 (186)
+...--+|||+|.+.+..|+..|+|||.|.-+.+.+.+.. ...++||+...||+..+++-.++..+.
T Consensus 98 ~qrhqLrhrElFlsRQ~EsLPAthIRGKCsV~LLnete~~~~YL~~eDtFfySLVyDP~~kTLLADkGeIR 168 (693)
T KOG3554|consen 98 KQRHQLRHRELFLSRQSESLPATHIRGKCSVTLLNETESLQSYLEKEDTFFYSLVYDPNQKTLLADKGEIR 168 (693)
T ss_pred HHHHHHHHHHHHHhhhhccCchhhhccceeEEEecChHHHHhhccccceeEEEeeeccchhhhhccCccee
Confidence 0011236999999999999999999999999888776544 368899999999998888766554443
No 28
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=97.48 E-value=1.2e-05 Score=45.72 Aligned_cols=35 Identities=29% Similarity=0.771 Sum_probs=20.2
Q ss_pred CceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCc
Q 029867 121 DLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCS 157 (186)
Q Consensus 121 ~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~ 157 (186)
..||+|+.|....|.+|-|+...+.. +.|+|..|.
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~~~~~~--~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVSEVPDG--DDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-SS--SS-------HHH-
T ss_pred CceEEeCCCCCcCChhhCCcccCCCC--CcEECCcCC
Confidence 47999999999999999999987643 459998874
No 29
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.43 E-value=3.3e-05 Score=62.90 Aligned_cols=49 Identities=18% Similarity=0.429 Sum_probs=38.9
Q ss_pred ecCCCCCCCCceEeCCCCCceecCCCCCCChhhhcCCCeEEcc--cCcccccccc
Q 029867 112 KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCS--DCSSDVDAKR 164 (186)
Q Consensus 112 ~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~--~C~~~~~~~~ 164 (186)
||++|.. .++|+.||.|+.=||.-|||+...+. ..|+|. -|.+.....|
T Consensus 319 IC~~P~~-E~E~~FCD~CDRG~HT~CVGL~~lP~---G~WICD~~C~~~~~~t~R 369 (381)
T KOG1512|consen 319 ICLGPVI-ESEHLFCDVCDRGPHTLCVGLQDLPR---GEWICDMRCREATLNTTR 369 (381)
T ss_pred ccCCccc-chheeccccccCCCCccccccccccC---ccchhhhHHHHhcCCCCh
Confidence 8999875 78999999999999999999988764 579999 4444444333
No 30
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.38 E-value=8.8e-05 Score=67.64 Aligned_cols=54 Identities=24% Similarity=0.744 Sum_probs=42.5
Q ss_pred CcceEE-ecCCCCCCCCceEeCCCCCce-ecCCCCCCChhhhcCCCeEEcccCccccc
Q 029867 106 RVAVYC-KCEMPYNPDDLMVQCEGCKDW-FHPSCMGMTIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 106 ~~~~~C-~C~~~~~~~~~~i~C~~C~~W-~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 161 (186)
.....| ||..+ ++.+.|+.||.|+.- ||..|+.++..+.. +..|+|+.|.-..-
T Consensus 213 ~E~~~C~IC~~~-DpEdVLLLCDsCN~~~YH~YCLDPdl~eiP-~~eWYC~NC~dL~~ 268 (1134)
T KOG0825|consen 213 QEEVKCDICTVH-DPEDVLLLCDSCNKVYYHVYCLDPDLSESP-VNEWYCTNCSLLEI 268 (1134)
T ss_pred cccccceeeccC-ChHHhheeecccccceeeccccCccccccc-ccceecCcchhhhh
Confidence 455667 88886 468999999999865 99999999775442 36899999986543
No 31
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=97.23 E-value=0.00017 Score=59.45 Aligned_cols=37 Identities=41% Similarity=1.066 Sum_probs=31.1
Q ss_pred CCCcceEEecCCCCCC-----CCceEeCCCCCceec-CCCCCC
Q 029867 104 PDRVAVYCKCEMPYNP-----DDLMVQCEGCKDWFH-PSCMGM 140 (186)
Q Consensus 104 p~~~~~~C~C~~~~~~-----~~~~i~C~~C~~W~H-~~Cv~~ 140 (186)
.+....+|.|..+|++ ++.|+||..|..||| ..|+..
T Consensus 124 hNfqG~~C~Cd~~Ypdp~~~~e~~m~QC~iCEDWFHce~c~~~ 166 (345)
T KOG2752|consen 124 HNFQGLFCKCDTPYPDPVRTEEGEMLQCVICEDWFHCEGCMQA 166 (345)
T ss_pred hhhcceeEEecCCCCCccccccceeeeEEeccchhcccccCcc
Confidence 3457899999999976 479999999999999 777753
No 32
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=97.18 E-value=0.00014 Score=58.86 Aligned_cols=49 Identities=27% Similarity=0.709 Sum_probs=41.7
Q ss_pred eEE-ecCCCCCCCCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccc
Q 029867 109 VYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSD 159 (186)
Q Consensus 109 ~~C-~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~ 159 (186)
.+| ||+...| ++.++.||.|+.=||+-|+..+...+.. ..|.|..|...
T Consensus 282 k~csicgtsen-ddqllfcddcdrgyhmyclsppm~eppe-gswsc~KOG~~ 331 (336)
T KOG1244|consen 282 KYCSICGTSEN-DDQLLFCDDCDRGYHMYCLSPPMVEPPE-GSWSCHLCLEE 331 (336)
T ss_pred ceeccccCcCC-CceeEeecccCCceeeEecCCCcCCCCC-CchhHHHHHHH
Confidence 456 8888876 7889999999999999999998887654 68999999754
No 33
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=97.06 E-value=0.00027 Score=62.80 Aligned_cols=54 Identities=28% Similarity=0.704 Sum_probs=46.3
Q ss_pred CcceEEecCCCCCCCCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccc
Q 029867 106 RVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 106 ~~~~~C~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 161 (186)
.....|+|+..+..+++||+|+.|..|.|.-|+|...... .+.|.|..|....-
T Consensus 84 ~~~~~c~c~~~~~~~g~~i~c~~c~~Wqh~~C~g~~~~~~--p~~y~c~~c~~~~~ 137 (508)
T KOG1844|consen 84 REISRCDCGLEDDMEGLMIQCDWCGRWQHKICCGSFKSTK--PDKYVCEICTPRNK 137 (508)
T ss_pred CcccccccccccCCCceeeCCcccCcccCceeeeecCCCC--chhceeeeeccccc
Confidence 4678899999876589999999999999999999877654 47999999996654
No 34
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=96.99 E-value=0.0011 Score=63.12 Aligned_cols=53 Identities=26% Similarity=0.610 Sum_probs=41.4
Q ss_pred ceEEecCCCCCC-CCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccccc
Q 029867 108 AVYCKCEMPYNP-DDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 163 (186)
Q Consensus 108 ~~~C~C~~~~~~-~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~ 163 (186)
...|||...... ....++||+|+.-+|..|+|++..+ ...|+|-.|.......
T Consensus 220 ~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~ip---eg~WlCr~Cl~s~~~~ 273 (1051)
T KOG0955|consen 220 AVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPFIP---EGQWLCRRCLQSPQRP 273 (1051)
T ss_pred ccceeecccccCCCceEEEcCCCcchhhhhccCCCCCC---CCcEeehhhccCcCcc
Confidence 445699886543 3799999999999999999965543 3689999999877733
No 35
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=96.61 E-value=0.0001 Score=62.57 Aligned_cols=64 Identities=19% Similarity=0.569 Sum_probs=48.1
Q ss_pred CcceEE-ecCCCCCCCCceEeCCCCCceecCCCCCCChhhhcCCCe----EEcccCcc-ccccccccCCC
Q 029867 106 RVAVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDH----FLCSDCSS-DVDAKRSLNTF 169 (186)
Q Consensus 106 ~~~~~C-~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~----~~C~~C~~-~~~~~~~~~~~ 169 (186)
.....| .|+..+..+.+||.|+.|..|||+.||.+.......+.. |.|+.|.. ..+.++..+..
T Consensus 237 ~~~~~~~~cg~~~~~~~~~~~~~~~e~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~~~~~k~~~~~~~ 306 (345)
T KOG1632|consen 237 YSKLICDPCGLSDANKKFEICCDLCESWFHGDCVQIFEARKRLNEIRNEVYKCPHCTVLKFEKKRHDEMA 306 (345)
T ss_pred cccccccccCcchHHHHHHHHHHHHHHHhcccccccccchhhhhhhhccceecCceeecccchhhccchH
Confidence 345667 666666556899999999999999999999987666666 99999997 44434433333
No 36
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=96.40 E-value=0.0026 Score=58.00 Aligned_cols=52 Identities=27% Similarity=0.680 Sum_probs=43.0
Q ss_pred cceEE-ecCCCCCC-CCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccc
Q 029867 107 VAVYC-KCEMPYNP-DDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 107 ~~~~C-~C~~~~~~-~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 161 (186)
+...| +|+.++.. ..+||.||.|+.=.|..|.||.+.+. ..|.|..|.-...
T Consensus 270 edviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIle~p~---gpWlCr~Calg~~ 323 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGILEVPE---GPWLCRTCALGIE 323 (893)
T ss_pred ccceeceecCCCccccceeEEeccchhHHHHhhhceeecCC---CCeeehhccccCC
Confidence 56778 89988754 36999999999999999999988753 6799999986644
No 37
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.18 E-value=0.0016 Score=58.31 Aligned_cols=53 Identities=23% Similarity=0.635 Sum_probs=40.7
Q ss_pred EE-ecCCCCCCCCceEeCCCCCceecCCCCCCChh-hhcCCCeEEcccCccccccc
Q 029867 110 YC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIE-EAKKLDHFLCSDCSSDVDAK 163 (186)
Q Consensus 110 ~C-~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~-~~~~~~~~~C~~C~~~~~~~ 163 (186)
|| .|++...- ...|+||+|..-||..|+..+.. +....+.|+|+.|.-....+
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 78886543 56799999999999999998743 22233689999999776643
No 38
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=95.85 E-value=0.0063 Score=53.41 Aligned_cols=53 Identities=23% Similarity=0.631 Sum_probs=41.1
Q ss_pred CcceEE-ecCCCCCCCCceEeCCCCCceecCCCCCCChhhhcC---CCeEEcccCccc
Q 029867 106 RVAVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKK---LDHFLCSDCSSD 159 (186)
Q Consensus 106 ~~~~~C-~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~~~~---~~~~~C~~C~~~ 159 (186)
.....| ||....+ ....++||.|+.-||..|+..+...+.. -..|.|..|.+.
T Consensus 542 a~~ysCgiCkks~d-QHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECdk~ 598 (707)
T KOG0957|consen 542 AMNYSCGICKKSTD-QHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECDKN 598 (707)
T ss_pred ccceeeeeeccchh-hHHHhhcchhhceeeccccCCccccCcccccCcceeecccccc
Confidence 345568 8888654 6799999999999999999988875433 247999999433
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=95.43 E-value=0.011 Score=44.04 Aligned_cols=35 Identities=17% Similarity=0.585 Sum_probs=27.5
Q ss_pred ecCCCCCCChhhhcCCCeEEcccCccccccccccCC
Q 029867 133 FHPSCMGMTIEEAKKLDHFLCSDCSSDVDAKRSLNT 168 (186)
Q Consensus 133 ~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~~~~~~ 168 (186)
||+.|+..+...+.. ..|+||.|......+.....
T Consensus 2 ~H~~CL~Ppl~~~P~-g~W~Cp~C~~~~~~~~~~~~ 36 (148)
T cd04718 2 FHLCCLRPPLKEVPE-GDWICPFCEVEKSGQSAMPQ 36 (148)
T ss_pred cccccCCCCCCCCCC-CCcCCCCCcCCCCCCccccc
Confidence 899999999987665 57999999987765544443
No 40
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=94.27 E-value=0.0066 Score=59.88 Aligned_cols=54 Identities=22% Similarity=0.626 Sum_probs=43.4
Q ss_pred CcceEE-ecCCCCCCCCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccc
Q 029867 106 RVAVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 106 ~~~~~C-~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 161 (186)
.....| +|+.-. ....|+-|+.|..|+|.-|+.+....+.. ..|.|+.|...++
T Consensus 1106 ~~~~~c~~cr~k~-~~~~m~lc~~c~~~~h~~C~rp~~~~~~~-~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1106 AVNALCKVCRRKK-QDEKMLLCDECLSGFHLFCLRPALSSVPP-GDWMCPSCRKEHR 1160 (1404)
T ss_pred cchhhhhhhhhcc-cchhhhhhHhhhhhHHHHhhhhhhccCCc-CCccCCccchhhh
Confidence 345567 777654 36799999999999999999987776543 5799999998886
No 41
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=94.24 E-value=0.018 Score=52.98 Aligned_cols=50 Identities=24% Similarity=0.640 Sum_probs=38.2
Q ss_pred cceEE-ecCCCCCCCCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccc
Q 029867 107 VAVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 107 ~~~~C-~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 161 (186)
....| +|.. ++..+.|+.|-.|||..|++.+..+....+ |+|+.|.....
T Consensus 46 ~~e~c~ic~~----~g~~l~c~tC~~s~h~~cl~~pl~~~p~~~-~~c~Rc~~p~~ 96 (696)
T KOG0383|consen 46 EQEACRICAD----GGELLWCDTCPASFHASCLGPPLTPQPNGE-FICPRCFCPKN 96 (696)
T ss_pred hhhhhhhhcC----CCcEEEeccccHHHHHHccCCCCCcCCccc-eeeeeeccCCC
Confidence 34444 6665 567888999999999999998887766556 99999944333
No 42
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=92.96 E-value=0.082 Score=46.66 Aligned_cols=57 Identities=19% Similarity=0.503 Sum_probs=40.5
Q ss_pred CCcceEEecCCCCC-CCCceEeCCCCCceecCCCCCCChhhhcC-------CCeEEcccCccccc
Q 029867 105 DRVAVYCKCEMPYN-PDDLMVQCEGCKDWFHPSCMGMTIEEAKK-------LDHFLCSDCSSDVD 161 (186)
Q Consensus 105 ~~~~~~C~C~~~~~-~~~~~i~C~~C~~W~H~~Cv~~~~~~~~~-------~~~~~C~~C~~~~~ 161 (186)
.++.+.|+|=+-.. .-++.||||.|+.-.|..|.|+.+..... ...|+|..|.-...
T Consensus 117 kk~~iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~Gvs 181 (707)
T KOG0957|consen 117 KKAVICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYGVS 181 (707)
T ss_pred ccceEEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHhcCCC
Confidence 34557778865432 23799999999999999999987432111 14799999986554
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=92.56 E-value=0.048 Score=33.10 Aligned_cols=33 Identities=24% Similarity=0.485 Sum_probs=16.7
Q ss_pred ceEeCCCCCceecCCCCCCChhhhcCCCeEEccc
Q 029867 122 LMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSD 155 (186)
Q Consensus 122 ~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~ 155 (186)
..|||+.|.+|=... .++........+.|+|..
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 579999999998887 333221122335899976
No 44
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=92.21 E-value=0.094 Score=32.37 Aligned_cols=31 Identities=26% Similarity=0.686 Sum_probs=27.4
Q ss_pred ceEE-ecCCCCCCCCceEeCCCCCceecCCCC
Q 029867 108 AVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCM 138 (186)
Q Consensus 108 ~~~C-~C~~~~~~~~~~i~C~~C~~W~H~~Cv 138 (186)
...| +|+.+..+++..|.|..|+.=||-.|.
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 4456 889998889999999999999999997
No 45
>KOG2626 consensus Histone H3 (Lys4) methyltransferase complex, subunit CPS60/ASH2/BRE2 [Chromatin structure and dynamics; Transcription]
Probab=91.74 E-value=0.16 Score=45.08 Aligned_cols=55 Identities=25% Similarity=0.521 Sum_probs=43.0
Q ss_pred CCcceEEecCCCCCCCCceEeCCCCCceecCCCCCCChhh-----hcCCCeEEcccCccc
Q 029867 105 DRVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEE-----AKKLDHFLCSDCSSD 159 (186)
Q Consensus 105 ~~~~~~C~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~-----~~~~~~~~C~~C~~~ 159 (186)
.....+|+|+...+....-+||..|.+|+|..++-....- ..-.+.|.|..|...
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 3467899999999999999999999999998666443321 111268999999977
No 46
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=91.10 E-value=0.077 Score=43.64 Aligned_cols=38 Identities=26% Similarity=0.594 Sum_probs=31.4
Q ss_pred CceEeCCCCCceecCCCCCCChhhhcCC--CeEEcccCcc
Q 029867 121 DLMVQCEGCKDWFHPSCMGMTIEEAKKL--DHFLCSDCSS 158 (186)
Q Consensus 121 ~~~i~C~~C~~W~H~~Cv~~~~~~~~~~--~~~~C~~C~~ 158 (186)
..||.|..|..-+|..||.++...+..+ ..|.|..|.-
T Consensus 277 ~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~l 316 (381)
T KOG1512|consen 277 NSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSCEL 316 (381)
T ss_pred ccceeecccccCCCCcchhcCHHHHhHHhhcchhhcccHh
Confidence 5899999999999999999999865544 4787777753
No 47
>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=90.05 E-value=0.3 Score=42.63 Aligned_cols=50 Identities=18% Similarity=0.458 Sum_probs=34.7
Q ss_pred ecCCCCCC--CCceEeCCCCCceecCCCCCC--------Chhhhc--CCCeEEcccCccccc
Q 029867 112 KCEMPYNP--DDLMVQCEGCKDWFHPSCMGM--------TIEEAK--KLDHFLCSDCSSDVD 161 (186)
Q Consensus 112 ~C~~~~~~--~~~~i~C~~C~~W~H~~Cv~~--------~~~~~~--~~~~~~C~~C~~~~~ 161 (186)
+|.+-++. +-.+|.||.|+-|-|..|.-- +...+. ..-.|+|..|....+
T Consensus 133 iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~se 194 (446)
T PF07227_consen 133 ICSKFDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTSE 194 (446)
T ss_pred ccCCcccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChhh
Confidence 77764321 359999999999999999632 222111 123899999998877
No 48
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=87.02 E-value=0.25 Score=43.63 Aligned_cols=47 Identities=32% Similarity=0.786 Sum_probs=35.8
Q ss_pred eEE-ecCCCCCCC-CceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCcc
Q 029867 109 VYC-KCEMPYNPD-DLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSS 158 (186)
Q Consensus 109 ~~C-~C~~~~~~~-~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~ 158 (186)
-.| +|....+.+ .-.|.||+|+.-.|.+|.|+.-.+. ..|.|-.|.-
T Consensus 194 ~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~f~pe---G~WlCrkCi~ 242 (669)
T COG5141 194 DICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPE---GFWLCRKCIY 242 (669)
T ss_pred hhhHhccccccCCcceEEEecCcchhhhhhcccceecCc---chhhhhhhcc
Confidence 345 777777654 5889999999999999999977542 4677777763
No 49
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=86.62 E-value=0.35 Score=44.37 Aligned_cols=54 Identities=24% Similarity=0.616 Sum_probs=40.7
Q ss_pred ceEEecCCCCC-CCCceEeCC--CCCceecCCCCCCChhhhcCCCeEEcccCcccccccc
Q 029867 108 AVYCKCEMPYN-PDDLMVQCE--GCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAKR 164 (186)
Q Consensus 108 ~~~C~C~~~~~-~~~~~i~C~--~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~~ 164 (186)
.-.|+|-...- ++..+|-|| .|.+-.|-.|.||-.-+. ..|+|..|-....+.|
T Consensus 6 GGCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVPt---GpWfCrKCesqeraar 62 (900)
T KOG0956|consen 6 GGCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVPT---GPWFCRKCESQERAAR 62 (900)
T ss_pred cceeeecCcCCCccCceeeecCCCceeeeehhcceeEecCC---Cchhhhhhhhhhhhcc
Confidence 34688875321 356899999 699999999999987643 5799999987766554
No 50
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=86.52 E-value=0.28 Score=34.45 Aligned_cols=31 Identities=26% Similarity=0.753 Sum_probs=25.0
Q ss_pred cceEE-ecCCCCCCCCceEeCCC--CCceecCCCCCC
Q 029867 107 VAVYC-KCEMPYNPDDLMVQCEG--CKDWFHPSCMGM 140 (186)
Q Consensus 107 ~~~~C-~C~~~~~~~~~~i~C~~--C~~W~H~~Cv~~ 140 (186)
....| +|+.. .+..|+|.. |..+||..|...
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 34556 88886 788999997 999999999743
No 51
>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]
Probab=85.04 E-value=0.13 Score=44.14 Aligned_cols=75 Identities=13% Similarity=0.045 Sum_probs=61.4
Q ss_pred CCCCCCCCeEEEEeEEeecCCCCEEEEEEEEeccccccCcccccCCCCeeEeeCCcceeeeceeeeeeEEEeeec
Q 029867 3 PADSDKPPYVARVEKIEADHRNNVKVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHTFKN 77 (186)
Q Consensus 3 ~~~~~~~~~iarI~~i~~~~~~~~~v~v~Wfyrp~d~~~~~~~~~~~~ELf~S~~~d~~~~~~I~gkc~V~~~~e 77 (186)
+......|.++.+..+|.+.++..+.-+.|||+|+++.......+..+++......+........+.+.|...-+
T Consensus 287 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 361 (371)
T COG5076 287 PVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTDYYKNANVLEDFVIKKTR 361 (371)
T ss_pred cCCcccccchhhhhhcccccccchhhhhcccCCCccccccccchhhhcccccchhhhhhhhhccchhhhHhhhhh
Confidence 334457789999999999888888889999999998887777788888999988888888888888887765433
No 52
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=84.96 E-value=0.21 Score=45.47 Aligned_cols=37 Identities=32% Similarity=0.792 Sum_probs=30.2
Q ss_pred CceEeCCCCCceecCCCCCCChhhhc--CCC-eEEcccCc
Q 029867 121 DLMVQCEGCKDWFHPSCMGMTIEEAK--KLD-HFLCSDCS 157 (186)
Q Consensus 121 ~~~i~C~~C~~W~H~~Cv~~~~~~~~--~~~-~~~C~~C~ 157 (186)
..|++|+.|.+|.|..|.|+...... .+| .|.|..|+
T Consensus 161 ~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~CR 200 (694)
T KOG4443|consen 161 LPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTCR 200 (694)
T ss_pred hhhHHHHHhcccccCCCCccchHHHHHHhhhhhcccceee
Confidence 46799999999999999999876321 124 89999998
No 53
>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=82.82 E-value=0.076 Score=30.99 Aligned_cols=40 Identities=23% Similarity=0.544 Sum_probs=28.0
Q ss_pred ecCCCCCCCCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCc
Q 029867 112 KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCS 157 (186)
Q Consensus 112 ~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~ 157 (186)
||.....+++.++... |+-.||.+|+..-... ...||.|+
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 6777666567777777 9999999998644433 23888884
No 54
>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=82.05 E-value=0.23 Score=26.61 Aligned_cols=26 Identities=23% Similarity=0.635 Sum_probs=10.5
Q ss_pred ecCCCCCCCCceEeCCCCCceecCCCC
Q 029867 112 KCEMPYNPDDLMVQCEGCKDWFHPSCM 138 (186)
Q Consensus 112 ~C~~~~~~~~~~i~C~~C~~W~H~~Cv 138 (186)
.|+.+... .....|..|+-..|..|+
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 56666542 588899999999998773
No 55
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=80.39 E-value=0.53 Score=42.93 Aligned_cols=42 Identities=19% Similarity=0.483 Sum_probs=35.2
Q ss_pred CCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccc
Q 029867 120 DDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 120 ~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 161 (186)
.+.|..|..|..-||..||.+-...+....-|.|+.|+..+.
T Consensus 32 ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~ 73 (694)
T KOG4443|consen 32 AGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEA 73 (694)
T ss_pred cCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeeee
Confidence 468999999999999999997776665556799999987665
No 56
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=79.92 E-value=3 Score=31.86 Aligned_cols=44 Identities=23% Similarity=0.558 Sum_probs=30.5
Q ss_pred CCceEeCCCCCceecCCCCCCChhh-------hcCCCeEEcccCccccccc
Q 029867 120 DDLMVQCEGCKDWFHPSCMGMTIEE-------AKKLDHFLCSDCSSDVDAK 163 (186)
Q Consensus 120 ~~~~i~C~~C~~W~H~~Cv~~~~~~-------~~~~~~~~C~~C~~~~~~~ 163 (186)
.+.||.|.+|..-||-.|+|.-... ..+...--|-.|......|
T Consensus 14 kG~Lv~CQGCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~~~kK 64 (175)
T PF15446_consen 14 KGPLVYCQGCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGIAHKK 64 (175)
T ss_pred CCCeEEcCccChHHHhhhcCCccccceeeEEEcCCceEEechhhcChhhcc
Confidence 5799999999999999999976542 1111244566666555444
No 57
>PF13922 PHD_3: PHD domain of transcriptional enhancer, Asx
Probab=79.46 E-value=0.3 Score=31.20 Aligned_cols=32 Identities=28% Similarity=0.863 Sum_probs=26.8
Q ss_pred CcceEEecCCCCCCCCceEeCCCCCceecCCCCCCCh
Q 029867 106 RVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTI 142 (186)
Q Consensus 106 ~~~~~C~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~ 142 (186)
.....|.|... -||-|..|+.+-|.+|+|.+.
T Consensus 31 ~~~~~C~C~Lk-----AMi~Cq~CGAFCHDDCIgpsk 62 (69)
T PF13922_consen 31 STSNKCACSLK-----AMIMCQGCGAFCHDDCIGPSK 62 (69)
T ss_pred ccccccccchH-----HHHHHhhccchhccccccHHH
Confidence 34567888763 799999999999999999876
No 58
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=76.23 E-value=0.73 Score=44.58 Aligned_cols=56 Identities=23% Similarity=0.551 Sum_probs=44.5
Q ss_pred CcceEEecCCCCCCCCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccc
Q 029867 106 RVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 106 ~~~~~C~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 161 (186)
..+..=+|..|++|+...|.|-.|..|+|..-|.+....-...-.+.|-.|++.+.
T Consensus 1121 ~~p~~~i~~~p~~pg~~~i~~~~~~~~~~~~~v~ln~s~~p~~~~~k~~~~~ri~~ 1176 (1414)
T KOG1473|consen 1121 LSPVCFICTLPYNPGLTYIHCTVCMTWGHKEAVKLNSSPIPEVVGFKCCQCRRIRS 1176 (1414)
T ss_pred CCccccceeeccCCCCCcceEEEeeccCcceeEecCCCcchHHhhhhHHhhhccCC
Confidence 33443399999999999999999999999999988776443335788888887655
No 59
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=73.50 E-value=1.8 Score=29.00 Aligned_cols=32 Identities=25% Similarity=0.646 Sum_probs=24.9
Q ss_pred ceEE-ecCCCCCCCCceEeCC--CCCceecCCCCCCCh
Q 029867 108 AVYC-KCEMPYNPDDLMVQCE--GCKDWFHPSCMGMTI 142 (186)
Q Consensus 108 ~~~C-~C~~~~~~~~~~i~C~--~C~~W~H~~Cv~~~~ 142 (186)
...| +|+.+ .+-.|+|. .|...||..|.....
T Consensus 36 ~~~C~~C~~~---~Ga~i~C~~~~C~~~fH~~CA~~~~ 70 (90)
T PF13771_consen 36 KLKCSICKKK---GGACIGCSHPGCSRSFHVPCARKAG 70 (90)
T ss_pred CCCCcCCCCC---CCeEEEEeCCCCCcEEChHHHccCC
Confidence 4456 77765 57999998 699999999986544
No 60
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=72.05 E-value=3.5 Score=32.62 Aligned_cols=46 Identities=17% Similarity=0.422 Sum_probs=30.2
Q ss_pred ceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccc-cccccCCCCCC
Q 029867 122 LMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD-AKRSLNTFSVS 172 (186)
Q Consensus 122 ~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~-~~~~~~~~~~~ 172 (186)
.-+-|..|. .|..|+.+.+.+. +.|+|+.|....+ .++..+.....
T Consensus 191 ~alIC~~C~--hhngl~~~~ek~~---~efiC~~Cn~~n~~~~~~~dsn~~~ 237 (251)
T COG5415 191 KALICPQCH--HHNGLYRLAEKPI---IEFICPHCNHKNDEVKEREDSNEAK 237 (251)
T ss_pred hhhcccccc--ccccccccccccc---hheecccchhhcCcccccccchhhc
Confidence 345566664 5778888877653 5899999998884 44444443333
No 61
>PF13341 RAG2_PHD: RAG2 PHD domain; PDB: 2JWO_A 2V86_B 2V85_B 2V87_A 2V83_C 2V89_A 2V88_A.
Probab=68.98 E-value=2.5 Score=27.39 Aligned_cols=34 Identities=24% Similarity=0.697 Sum_probs=18.6
Q ss_pred ceEeCCCC-CceecCCCCCCChhhh----cCCCeEEccc
Q 029867 122 LMVQCEGC-KDWFHPSCMGMTIEEA----KKLDHFLCSD 155 (186)
Q Consensus 122 ~~i~C~~C-~~W~H~~Cv~~~~~~~----~~~~~~~C~~ 155 (186)
-||.|..= +-|.|..|+.+++... +...+|+|..
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 68888743 5899999999998632 2235788864
No 62
>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=67.13 E-value=14 Score=23.98 Aligned_cols=47 Identities=21% Similarity=0.169 Sum_probs=35.7
Q ss_pred EEEEEEeccccccCcccccCCCCeeEeeCCcceeeeceeeeeeEEEe
Q 029867 28 VRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHT 74 (186)
Q Consensus 28 v~v~Wfyrp~d~~~~~~~~~~~~ELf~S~~~d~~~~~~I~gkc~V~~ 74 (186)
|.|.=+-|-.||.-......+..||.....++-..+-.|+|++.|++
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 55666778888865544556899999999999999999999999985
No 63
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=66.22 E-value=4.8 Score=31.63 Aligned_cols=31 Identities=35% Similarity=0.791 Sum_probs=25.6
Q ss_pred CceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccc
Q 029867 121 DLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 121 ~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 161 (186)
+..++|+.|+.-||..|..- -.||.|.+...
T Consensus 170 ~~~~~C~~C~~v~H~~C~~~----------~~CpkC~R~~~ 200 (202)
T PF13901_consen 170 DTTVRCPKCKSVFHKSCFRK----------KSCPKCARRQK 200 (202)
T ss_pred CCeeeCCcCccccchhhcCC----------CCCCCcHhHhc
Confidence 47899999999999999972 13999987664
No 64
>PRK13251 transcription attenuation protein MtrB; Provisional
Probab=66.05 E-value=20 Score=23.32 Aligned_cols=48 Identities=21% Similarity=0.192 Sum_probs=38.8
Q ss_pred EEEEEEEeccccccCcccccCCCCeeEeeCCcceeeeceeeeeeEEEe
Q 029867 27 KVRVRWYYRPEESIGGRRQFHGAKELFLSDHYDVQSAHTIEGKCTVHT 74 (186)
Q Consensus 27 ~v~v~Wfyrp~d~~~~~~~~~~~~ELf~S~~~d~~~~~~I~gkc~V~~ 74 (186)
-|.|.=+-|..||.-......+..||.+...++...+-.|+|++.|++
T Consensus 18 gV~vIgltrg~dtkfhhtEkLDkGEVmiaqftehtsaiKirGkA~I~t 65 (75)
T PRK13251 18 GVNVIGLTRGKDTKFHHTEKLDKGEVMIAQFTEHTSAIKIRGKAEIQT 65 (75)
T ss_pred CeEEEEEecCCCccchhhhhcCCCcEEEEEeecceeEEEEeceEEEEe
Confidence 356666778888865444556899999999999999999999999985
No 65
>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=59.83 E-value=4.4 Score=23.17 Aligned_cols=34 Identities=21% Similarity=0.605 Sum_probs=16.6
Q ss_pred eEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccc
Q 029867 123 MVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 123 ~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 161 (186)
.+.|..|+...-.-|.-.. ....|.|+.|....+
T Consensus 2 p~rC~~C~aylNp~~~~~~-----~~~~w~C~~C~~~N~ 35 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDD-----GGKTWICNFCGTKNP 35 (40)
T ss_dssp S-B-TTT--BS-TTSEEET-----TTTEEEETTT--EEE
T ss_pred ccccCCCCCEECCcceEcC-----CCCEEECcCCCCcCC
Confidence 3567777665555443222 236899999987655
No 66
>COG4014 Uncharacterized protein conserved in archaea [Function unknown]
Probab=58.69 E-value=18 Score=24.69 Aligned_cols=28 Identities=29% Similarity=0.436 Sum_probs=22.3
Q ss_pred eEEEEeEEeecCCCCEEEEEE---EEecccc
Q 029867 11 YVARVEKIEADHRNNVKVRVR---WYYRPEE 38 (186)
Q Consensus 11 ~iarI~~i~~~~~~~~~v~v~---Wfyrp~d 38 (186)
-+|+|..|.++.+|..||.+- .+||+.=
T Consensus 22 TvgrV~dIkkdEdG~~WV~LdstdLwYre~~ 52 (97)
T COG4014 22 TVGRVVDIKKDEDGDIWVVLDSTDLWYREHY 52 (97)
T ss_pred ceeeEEEEEeecCCceEEEEecCCceecccc
Confidence 479999999999999999874 4566643
No 67
>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=58.06 E-value=12 Score=19.79 Aligned_cols=26 Identities=19% Similarity=0.393 Sum_probs=19.0
Q ss_pred ecCCCCCCCCceEeCCCCCceecCCCC
Q 029867 112 KCEMPYNPDDLMVQCEGCKDWFHPSCM 138 (186)
Q Consensus 112 ~C~~~~~~~~~~i~C~~C~~W~H~~Cv 138 (186)
+|++.-++.. ...|+.|.--.|..|+
T Consensus 5 ~C~~~~~~~~-~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 5 VCRRKIDGFY-FYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCcCCCE-eEEeCCCCCeEcCccC
Confidence 5666544333 8899999988898885
No 68
>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=57.59 E-value=9.1 Score=20.79 Aligned_cols=12 Identities=17% Similarity=0.656 Sum_probs=9.2
Q ss_pred CeEEcccCcccc
Q 029867 149 DHFLCSDCSSDV 160 (186)
Q Consensus 149 ~~~~C~~C~~~~ 160 (186)
+.|.||.|....
T Consensus 16 ~~~~CP~Cg~~~ 27 (33)
T cd00350 16 APWVCPVCGAPK 27 (33)
T ss_pred CCCcCcCCCCcH
Confidence 569999997643
No 69
>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=55.80 E-value=8.9 Score=22.83 Aligned_cols=35 Identities=20% Similarity=0.425 Sum_probs=24.7
Q ss_pred cceEE-ecCCCC-CCCCceEeCCCCCceecCCCCCCC
Q 029867 107 VAVYC-KCEMPY-NPDDLMVQCEGCKDWFHPSCMGMT 141 (186)
Q Consensus 107 ~~~~C-~C~~~~-~~~~~~i~C~~C~~W~H~~Cv~~~ 141 (186)
...+| +|+..- ......+.|..|+.-.|.+|+..-
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 35567 777654 235688999999999999998643
No 70
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=55.47 E-value=3.4 Score=30.39 Aligned_cols=61 Identities=21% Similarity=0.418 Sum_probs=39.6
Q ss_pred ceEE-ecCCCCCCCCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCcccccc-ccccCCC
Q 029867 108 AVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDA-KRSLNTF 169 (186)
Q Consensus 108 ~~~C-~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~-~~~~~~~ 169 (186)
.-.| ||...--.|+----|.-|..-+-..|-|--...... ..|.|+.|....++ -+...||
T Consensus 65 datC~IC~KTKFADG~GH~C~YCq~r~CARCGGrv~lrsNK-v~wvcnlc~k~q~il~ksg~wf 127 (169)
T KOG3799|consen 65 DATCGICHKTKFADGCGHNCSYCQTRFCARCGGRVSLRSNK-VMWVCNLCRKQQEILTKSGAWF 127 (169)
T ss_pred CcchhhhhhcccccccCcccchhhhhHHHhcCCeeeeccCc-eEEeccCCcHHHHHHHhcchHH
Confidence 3345 776654445555567778888888888755444322 57999999998883 2334444
No 71
>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=54.75 E-value=11 Score=26.55 Aligned_cols=35 Identities=20% Similarity=0.548 Sum_probs=21.5
Q ss_pred CCC---CceecCCCCCC----ChhhhcCCCeEEcccCccccc
Q 029867 127 EGC---KDWFHPSCMGM----TIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 127 ~~C---~~W~H~~Cv~~----~~~~~~~~~~~~C~~C~~~~~ 161 (186)
..| ..-|=..|+-. ...++.....|.||.|...-.
T Consensus 31 ~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~CrgiCn 72 (105)
T PF10497_consen 31 SSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGICN 72 (105)
T ss_pred CCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCCeeC
Confidence 455 67777777632 222333336899999987444
No 72
>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=53.63 E-value=11 Score=22.71 Aligned_cols=13 Identities=23% Similarity=0.733 Sum_probs=10.4
Q ss_pred CCeEEcccCcccc
Q 029867 148 LDHFLCSDCSSDV 160 (186)
Q Consensus 148 ~~~~~C~~C~~~~ 160 (186)
.+.|.||.|....
T Consensus 32 p~~w~CP~C~a~K 44 (50)
T cd00730 32 PDDWVCPVCGAGK 44 (50)
T ss_pred CCCCCCCCCCCcH
Confidence 4789999998654
No 73
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=53.00 E-value=12 Score=28.60 Aligned_cols=25 Identities=24% Similarity=0.623 Sum_probs=22.1
Q ss_pred CCCCCceEeCCCCCceecCCCCCCC
Q 029867 117 YNPDDLMVQCEGCKDWFHPSCMGMT 141 (186)
Q Consensus 117 ~~~~~~~i~C~~C~~W~H~~Cv~~~ 141 (186)
.|++..|..|..|+.-||+..+...
T Consensus 118 nN~~nVLFRC~~C~RawH~~HLP~~ 142 (175)
T PF15446_consen 118 NNPDNVLFRCTSCHRAWHFEHLPPP 142 (175)
T ss_pred cChhheEEecCCccceeehhhCCCC
Confidence 5778899999999999999998764
No 74
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=51.46 E-value=7.7 Score=19.73 Aligned_cols=14 Identities=36% Similarity=0.764 Sum_probs=10.3
Q ss_pred ceEeCCCCCceecC
Q 029867 122 LMVQCEGCKDWFHP 135 (186)
Q Consensus 122 ~~i~C~~C~~W~H~ 135 (186)
.|++|..|++.|..
T Consensus 1 ~l~~C~~CgR~F~~ 14 (25)
T PF13913_consen 1 ELVPCPICGRKFNP 14 (25)
T ss_pred CCCcCCCCCCEECH
Confidence 36788888887743
No 75
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=51.43 E-value=11 Score=26.28 Aligned_cols=17 Identities=35% Similarity=0.761 Sum_probs=13.9
Q ss_pred CCEEEEEEEEecccccc
Q 029867 24 NNVKVRVRWYYRPEESI 40 (186)
Q Consensus 24 ~~~~v~v~Wfyrp~d~~ 40 (186)
....|+|+|||.++|..
T Consensus 75 ~g~~V~v~Wyyd~dD~~ 91 (99)
T PF09345_consen 75 KGGKVTVNWYYDEDDED 91 (99)
T ss_pred cCCcEEEEEEECCCCch
Confidence 34789999999998764
No 76
>PF09871 DUF2098: Uncharacterized protein conserved in archaea (DUF2098); InterPro: IPR019209 This family of proteins have no known function.
Probab=51.19 E-value=23 Score=24.22 Aligned_cols=28 Identities=29% Similarity=0.449 Sum_probs=21.2
Q ss_pred eEEEEeEEeecCCCCEEEEE---EEEeccccc
Q 029867 11 YVARVEKIEADHRNNVKVRV---RWYYRPEES 39 (186)
Q Consensus 11 ~iarI~~i~~~~~~~~~v~v---~Wfyrp~d~ 39 (186)
-+|+|.+|-. .++..||.+ .-||||.-+
T Consensus 16 T~G~V~diK~-ed~~~wv~LD~t~L~Yr~~~L 46 (91)
T PF09871_consen 16 TVGKVVDIKE-EDGETWVLLDSTDLYYRPDYL 46 (91)
T ss_pred eEEEEEEEEE-eCCCeEEEEccCCceeeccee
Confidence 3799999954 477899988 577888654
No 77
>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=47.89 E-value=14 Score=18.84 Aligned_cols=11 Identities=27% Similarity=0.818 Sum_probs=8.6
Q ss_pred CCCeEEcccCc
Q 029867 147 KLDHFLCSDCS 157 (186)
Q Consensus 147 ~~~~~~C~~C~ 157 (186)
....|.||+|-
T Consensus 13 ~~v~f~CPnCG 23 (24)
T PF07754_consen 13 QAVPFPCPNCG 23 (24)
T ss_pred cCceEeCCCCC
Confidence 34689999994
No 78
>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=45.36 E-value=16 Score=32.62 Aligned_cols=11 Identities=36% Similarity=0.715 Sum_probs=5.1
Q ss_pred EEcccCccccc
Q 029867 151 FLCSDCSSDVD 161 (186)
Q Consensus 151 ~~C~~C~~~~~ 161 (186)
|.||.|...-.
T Consensus 53 f~CP~C~~~L~ 63 (483)
T PF05502_consen 53 FDCPICFSPLS 63 (483)
T ss_pred ccCCCCCCcce
Confidence 44555544333
No 79
>PF14901 Jiv90: Cleavage inducing molecular chaperone
Probab=43.54 E-value=6.4 Score=27.15 Aligned_cols=49 Identities=16% Similarity=0.169 Sum_probs=36.8
Q ss_pred CceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccccccccCCCCCCCC
Q 029867 121 DLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAKRSLNTFSVSPS 174 (186)
Q Consensus 121 ~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~~~~~~~~~~~~ 174 (186)
..-|.|+.|+.+-...++..+... .-.|..|...++++-.-.|...+..
T Consensus 3 ~n~i~C~~C~~~H~r~~t~r~~~~-----AR~C~~C~~~H~Ak~gDiWaE~~~~ 51 (94)
T PF14901_consen 3 SNTIRCDKCGGKHKRIETDRPPSA-----ARYCQDCKIRHPAKEGDIWAESSSL 51 (94)
T ss_pred cceeechhhCCeeeeEEecCchhh-----hHhHHHhhhhcccccCCeEEEeccc
Confidence 356889999988887777776654 3589999999998877766665543
No 80
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=43.20 E-value=3.7 Score=37.38 Aligned_cols=34 Identities=21% Similarity=0.539 Sum_probs=27.1
Q ss_pred CCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccc
Q 029867 120 DDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 120 ~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 161 (186)
.+....|+.|..|||-.|...... .||.|.+...
T Consensus 528 ~~~~~rC~~C~avfH~~C~~r~s~--------~CPrC~R~q~ 561 (580)
T KOG1829|consen 528 TRNTRRCSTCLAVFHKKCLRRKSP--------CCPRCERRQK 561 (580)
T ss_pred cccceeHHHHHHHHHHHHHhccCC--------CCCchHHHHH
Confidence 456789999999999999865442 2999998766
No 81
>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=42.42 E-value=29 Score=23.14 Aligned_cols=27 Identities=22% Similarity=0.255 Sum_probs=21.6
Q ss_pred CCCCeEEEEeEEeecCCCCEEEEEEEEecc
Q 029867 7 DKPPYVARVEKIEADHRNNVKVRVRWYYRP 36 (186)
Q Consensus 7 ~~~~~iarI~~i~~~~~~~~~v~v~Wfyrp 36 (186)
+=|+|-|+|.++... ...+.|.||--.
T Consensus 13 g~P~WPa~I~~~~~~---~~k~~V~FfG~~ 39 (80)
T cd06080 13 GYPWWPAVIKSISRK---KQKARVNFIGDN 39 (80)
T ss_pred CCCCCCEEEeeecCC---CCEEEEEEeCCC
Confidence 458999999998643 568889999777
No 82
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=40.29 E-value=28 Score=31.95 Aligned_cols=50 Identities=24% Similarity=0.539 Sum_probs=36.2
Q ss_pred ceEE-ecCCCCCCCCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccc
Q 029867 108 AVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 108 ~~~C-~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 161 (186)
+..| +|.. ++....|+.|..-||..|.+....+......|.|..|....+
T Consensus 47 ~ts~~~~~~----~gn~~~~~~~~~s~h~~~~~~~~sp~~~~~~~~~~~~~~~~~ 97 (613)
T KOG4299|consen 47 ATSCGICKS----GGNLLCCDHCPASFHLECDKPPLSPDLKGSEINCSRCPKGRE 97 (613)
T ss_pred hhhcchhhh----cCCccccccCccccchhccCcccCcccccccccccCCCcccc
Confidence 4455 4444 566779999999999999998887544455777777776433
No 83
>PF07494 Reg_prop: Two component regulator propeller; InterPro: IPR011110 A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats. These repeats show homology to members of IPR002372 from INTERPRO and IPR001680 from INTERPRO indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=38.25 E-value=46 Score=16.44 Aligned_cols=15 Identities=20% Similarity=0.266 Sum_probs=11.2
Q ss_pred EEeEEeecCCCCEEE
Q 029867 14 RVEKIEADHRNNVKV 28 (186)
Q Consensus 14 rI~~i~~~~~~~~~v 28 (186)
.|..|.++++|..||
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 377888999998876
No 84
>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=36.46 E-value=10 Score=21.71 Aligned_cols=32 Identities=22% Similarity=0.446 Sum_probs=22.4
Q ss_pred ceEE-ecCCCCCCCC-ceEeCCCCCceecCCCCCC
Q 029867 108 AVYC-KCEMPYNPDD-LMVQCEGCKDWFHPSCMGM 140 (186)
Q Consensus 108 ~~~C-~C~~~~~~~~-~~i~C~~C~~W~H~~Cv~~ 140 (186)
..+| +|+...- .. ..+.|..|+.-.|..|+..
T Consensus 11 ~~~C~~C~~~i~-~~~~~~~C~~C~~~~H~~C~~~ 44 (49)
T smart00109 11 PTKCCVCRKSIW-GSFQGLRCSWCKVKCHKKCAEK 44 (49)
T ss_pred CCCccccccccC-cCCCCcCCCCCCchHHHHHHhh
Confidence 4456 6666532 22 3688999999999999754
No 85
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=35.95 E-value=45 Score=32.26 Aligned_cols=47 Identities=19% Similarity=0.635 Sum_probs=36.7
Q ss_pred ecCCCCCCCCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccc
Q 029867 112 KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 112 ~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 161 (186)
.|....++ ... +|+.|.+=+|..|..+....... ..|.|+.|.....
T Consensus 160 ~~~k~~~~-~~~-~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 206 (904)
T KOG1246|consen 160 TCSKGKEE-KLL-LCDSCDDSYHTYCLRPPLTRVPD-GDWRCPKCIPTPE 206 (904)
T ss_pred ccccCCCc-cce-ecccccCcccccccCCCCCcCCc-CcccCCccccccc
Confidence 55555444 445 99999999999999998887666 4577999998855
No 86
>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=35.28 E-value=34 Score=23.17 Aligned_cols=30 Identities=23% Similarity=0.400 Sum_probs=21.5
Q ss_pred ceEE-ecCCCCCCCCceEeCCCCCceecCCCCC
Q 029867 108 AVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMG 139 (186)
Q Consensus 108 ~~~C-~C~~~~~~~~~~i~C~~C~~W~H~~Cv~ 139 (186)
...| +|+++-....+.+..+ +.-+|..|..
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~--~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPC--GHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceEEEeCC--CeEEeccccc
Confidence 3447 9999887666666644 4889999974
No 87
>PF08921 DUF1904: Domain of unknown function (DUF1904); InterPro: IPR015017 This entry represents a family of hypothetical bacterial proteins. ; PDB: 1U9D_B.
Probab=35.00 E-value=15 Score=25.94 Aligned_cols=16 Identities=31% Similarity=0.428 Sum_probs=10.1
Q ss_pred CEEEEEEEEecccccc
Q 029867 25 NVKVRVRWYYRPEESI 40 (186)
Q Consensus 25 ~~~v~v~Wfyrp~d~~ 40 (186)
-++|.|.||-|+.|+.
T Consensus 55 ~pfVEV~WF~R~qe~q 70 (108)
T PF08921_consen 55 YPFVEVLWFDRGQEVQ 70 (108)
T ss_dssp --EEEEEES---HHHH
T ss_pred ceeEEEEEecCCHHHH
Confidence 3689999999999985
No 88
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=34.83 E-value=28 Score=29.37 Aligned_cols=51 Identities=14% Similarity=0.193 Sum_probs=38.7
Q ss_pred ceEEecCCCCCCCCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccc
Q 029867 108 AVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 108 ~~~C~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 161 (186)
...|+|-.+....+.|++|-.|.-|+|..-.++..-.- ..|.|.-|..+.+
T Consensus 53 Q~l~sClTC~P~~~~agvC~~C~~~CH~~H~lveL~tK---R~FrCDCg~sk~g 103 (345)
T KOG2752|consen 53 QALFSCLTCTPAPEMAGVCYACSLSCHDGHELVELYTK---RNFRCDCGNSKFG 103 (345)
T ss_pred cceeEeecccCChhhceeEEEeeeeecCCceeeecccc---CCccccccccccc
Confidence 34566666654556999999999999999877655321 5799998888877
No 89
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=34.68 E-value=12 Score=24.19 Aligned_cols=52 Identities=21% Similarity=0.215 Sum_probs=19.7
Q ss_pred ecCCCCC--CCCceEeCC--CCCceecCCCCCCChh---hh---cCCCeEEcccCccccccc
Q 029867 112 KCEMPYN--PDDLMVQCE--GCKDWFHPSCMGMTIE---EA---KKLDHFLCSDCSSDVDAK 163 (186)
Q Consensus 112 ~C~~~~~--~~~~~i~C~--~C~~W~H~~Cv~~~~~---~~---~~~~~~~C~~C~~~~~~~ 163 (186)
||-.... ....-+.|+ .|..-||..|+---.. .. -......||.|......+
T Consensus 7 IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~ 68 (70)
T PF11793_consen 7 ICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS 68 (70)
T ss_dssp SS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred cCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence 5554322 234568897 8999999999953211 11 112367899998776543
No 90
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=33.45 E-value=23 Score=26.58 Aligned_cols=33 Identities=21% Similarity=0.551 Sum_probs=20.8
Q ss_pred eCCCCCceecCCCCCCChhhhcCCCeEEcccCccccc
Q 029867 125 QCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 125 ~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 161 (186)
+|+.|+.=..+....+..+.+ .-..|..|. +.+
T Consensus 2 ~CEiCG~~i~~~~~~v~iega---~l~vC~~C~-k~G 34 (154)
T TIGR00270 2 NCEICGRKIKGKGFKIVIEGS---EMTVCGECR-KFG 34 (154)
T ss_pred ccccCCCccCCCCeEEEEcCe---EEehhhhHH-hcC
Confidence 378887766666554444444 347888888 444
No 91
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=31.60 E-value=57 Score=27.68 Aligned_cols=56 Identities=21% Similarity=0.380 Sum_probs=32.2
Q ss_pred ceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccccccc-cCCCCCCCCccCCCCcc
Q 029867 122 LMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAKRS-LNTFSVSPSVEAKVEPK 182 (186)
Q Consensus 122 ~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~~~-~~~~~~~~~~~~~~~~~ 182 (186)
.-+-|..|+ .|..|+... +.+ .-.|+|+.|....+.++. .+....+...++.+--|
T Consensus 219 yALIC~~C~--~HNGla~~e--e~~-yi~F~C~~Cn~LN~~~k~~e~s~~~~~~a~ps~s~k 275 (328)
T KOG2846|consen 219 YALICSQCH--HHNGLARKE--EYE-YITFRCPHCNALNPAKKSPENSLEAPQPAPPSSSSK 275 (328)
T ss_pred hhhcchhhc--cccCcCChh--hcC-ceEEECccccccCCCcCCcccccccCCCCCcccccC
Confidence 334455554 366665542 222 248999999988885544 55555555555544433
No 92
>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=31.57 E-value=28 Score=26.19 Aligned_cols=19 Identities=26% Similarity=0.747 Sum_probs=14.2
Q ss_pred CCceEeCCCCCceecCCCC
Q 029867 120 DDLMVQCEGCKDWFHPSCM 138 (186)
Q Consensus 120 ~~~~i~C~~C~~W~H~~Cv 138 (186)
..-.++|..|++||--.=-
T Consensus 11 p~~vv~C~~c~kWFCNg~~ 29 (152)
T PF09416_consen 11 PSCVVKCNTCNKWFCNGRG 29 (152)
T ss_dssp CCCEEEETTTTEEEES--T
T ss_pred cccEeEcCCCCcEeecCCC
Confidence 4678999999999976543
No 93
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=31.12 E-value=52 Score=23.18 Aligned_cols=38 Identities=21% Similarity=0.489 Sum_probs=26.1
Q ss_pred ecCCCCCCCCceEeCCCCC--ceecCCCCCCChhhhcCCCeEEcccCccccc
Q 029867 112 KCEMPYNPDDLMVQCEGCK--DWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 112 ~C~~~~~~~~~~i~C~~C~--~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 161 (186)
.|+... -+.....|+.|+ ...-.+| ..-.||.|.....
T Consensus 32 ~Crt~~-~G~~~~~C~~Cg~~~~~~~SC-----------k~R~CP~C~~~~~ 71 (111)
T PF14319_consen 32 ACRTEA-LGFHRYRCEDCGHEKIVYNSC-----------KNRHCPSCQAKAT 71 (111)
T ss_pred hcCCcc-CCcceeecCCCCceEEecCcc-----------cCcCCCCCCChHH
Confidence 466654 378899999996 3444467 2348999986654
No 94
>KOG1705 consensus Uncharacterized conserved protein, contains CXXC motifs [Function unknown]
Probab=30.46 E-value=17 Score=24.90 Aligned_cols=73 Identities=19% Similarity=0.479 Sum_probs=46.5
Q ss_pred CcceeEeeeeccccCcccCCCcceEE-ecCCCCCCCCceEeCCCCC-ceecCCCCCCChhhhcCCCeEEcccCccccc
Q 029867 86 AEDYFCRFEYKAATGGFTPDRVAVYC-KCEMPYNPDDLMVQCEGCK-DWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 86 ~~~ffcr~~Yd~~~~~f~p~~~~~~C-~C~~~~~~~~~~i~C~~C~-~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 161 (186)
++..+|+..--...+.+- .+-.--| ||+..--|....--||.|. --|...|+........ +.|+|..|.+..-
T Consensus 6 pDLi~CrkQPGi~~G~LC-EkCDgkC~ICDS~VRP~tlVRiC~eC~~Gs~q~~ciic~~~gV~--d~~yc~ectr~ek 80 (110)
T KOG1705|consen 6 PDLIMCRKQPGIAIGRLC-EKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGVGVS--DAYYCKECTRQEK 80 (110)
T ss_pred CcEEEEecCCCchhhhhH-HhcCCcccccccccccceeeeeehhcCCccccCceEEecCCccc--chHHHHHHHhhcc
Confidence 445566654333333321 1223344 7887777788888899996 6788888876664433 6899999986544
No 95
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=30.14 E-value=51 Score=18.24 Aligned_cols=11 Identities=18% Similarity=0.884 Sum_probs=5.5
Q ss_pred EeCCCCCceec
Q 029867 124 VQCEGCKDWFH 134 (186)
Q Consensus 124 i~C~~C~~W~H 134 (186)
|.|+.|+.=|.
T Consensus 3 i~Cp~C~~~y~ 13 (36)
T PF13717_consen 3 ITCPNCQAKYE 13 (36)
T ss_pred EECCCCCCEEe
Confidence 45555555443
No 96
>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=29.37 E-value=33 Score=22.06 Aligned_cols=17 Identities=41% Similarity=0.956 Sum_probs=10.6
Q ss_pred CCCCCceEeCCCCCcee
Q 029867 117 YNPDDLMVQCEGCKDWF 133 (186)
Q Consensus 117 ~~~~~~~i~C~~C~~W~ 133 (186)
|.-+-..|+|++|+.|.
T Consensus 23 Y~~GvViv~C~gC~~~H 39 (66)
T PF05180_consen 23 YHKGVVIVQCPGCKNRH 39 (66)
T ss_dssp HHTSEEEEE-TTS--EE
T ss_pred HhCCeEEEECCCCccee
Confidence 44567899999999764
No 97
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=28.93 E-value=17 Score=30.00 Aligned_cols=39 Identities=31% Similarity=0.640 Sum_probs=29.3
Q ss_pred CCceEeCCCCCceecCCCCCCChhh--hcCCCeEEcccCcc
Q 029867 120 DDLMVQCEGCKDWFHPSCMGMTIEE--AKKLDHFLCSDCSS 158 (186)
Q Consensus 120 ~~~~i~C~~C~~W~H~~Cv~~~~~~--~~~~~~~~C~~C~~ 158 (186)
.+++|.|..|+.-=|.+|+..+... +..-..|.|-.|.-
T Consensus 243 peelvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~ 283 (336)
T KOG1244|consen 243 PEELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKY 283 (336)
T ss_pred chhhcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeecce
Confidence 3689999999999999999887753 22235677766653
No 98
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=28.92 E-value=16 Score=34.82 Aligned_cols=55 Identities=22% Similarity=0.445 Sum_probs=40.9
Q ss_pred cceEE-ecCCCCCCCCceEeCCCCCceecCCCCCCC--hhhhcCCCeEEcccCccccc
Q 029867 107 VAVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMT--IEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 107 ~~~~C-~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~--~~~~~~~~~~~C~~C~~~~~ 161 (186)
....| ||-..-+....|-.|.+|-..||..|+.-= ..+....+.|.||.|.....
T Consensus 190 ~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~ 247 (950)
T KOG1952|consen 190 RKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSK 247 (950)
T ss_pred CceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhc
Confidence 45567 888777788899999999999999998621 12233347999999995444
No 99
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=28.78 E-value=8.7 Score=33.35 Aligned_cols=53 Identities=21% Similarity=0.472 Sum_probs=38.5
Q ss_pred CcceEE-ecCCCCCCCCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccc
Q 029867 106 RVAVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 106 ~~~~~C-~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 161 (186)
....+| .|+..+....+-.|=--|.-.||..|+---... -..-.||.|+.-..
T Consensus 363 e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~---n~~rsCP~CrklrS 416 (518)
T KOG1941|consen 363 ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN---NGTRSCPNCRKLRS 416 (518)
T ss_pred HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh---CCCCCCccHHHHHh
Confidence 357789 899877666677777789999999998632221 24569999996555
No 100
>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=28.51 E-value=29 Score=20.65 Aligned_cols=13 Identities=23% Similarity=0.713 Sum_probs=8.0
Q ss_pred CCeEEcccCcccc
Q 029867 148 LDHFLCSDCSSDV 160 (186)
Q Consensus 148 ~~~~~C~~C~~~~ 160 (186)
.+.|.||.|....
T Consensus 32 p~~w~CP~C~a~K 44 (47)
T PF00301_consen 32 PDDWVCPVCGAPK 44 (47)
T ss_dssp -TT-B-TTTSSBG
T ss_pred CCCCcCcCCCCcc
Confidence 4689999998653
No 101
>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=27.91 E-value=74 Score=21.12 Aligned_cols=31 Identities=23% Similarity=0.237 Sum_probs=23.4
Q ss_pred CCCCCeEEEEeEEeecCCCCEEEEEEEEecc
Q 029867 6 SDKPPYVARVEKIEADHRNNVKVRVRWYYRP 36 (186)
Q Consensus 6 ~~~~~~iarI~~i~~~~~~~~~v~v~Wfyrp 36 (186)
.+=|+|=|+|.+.-........+.|+||-..
T Consensus 14 kGyp~WPa~I~~~~~~~~~~~~~~V~FfGt~ 44 (83)
T cd05834 14 KGYPAWPARVDEPEDWKPPGKKYPVYFFGTH 44 (83)
T ss_pred CCCCCCCEEEecccccCCCCCEEEEEEeCCC
Confidence 4568999999998764344567889999854
No 102
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=27.74 E-value=51 Score=18.05 Aligned_cols=31 Identities=23% Similarity=0.544 Sum_probs=15.8
Q ss_pred EeCCCCCceecCCCCCCChhhh-cCCCeEEcccCccc
Q 029867 124 VQCEGCKDWFHPSCMGMTIEEA-KKLDHFLCSDCSSD 159 (186)
Q Consensus 124 i~C~~C~~W~H~~Cv~~~~~~~-~~~~~~~C~~C~~~ 159 (186)
+.|..|+..|= ++.... .......|+.|...
T Consensus 3 ~~CP~C~~~~~-----v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFR-----VVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEE-----eCHHHcCCCCCEEECCCCCCE
Confidence 66777766542 222221 11235777777643
No 103
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=27.40 E-value=28 Score=19.63 Aligned_cols=11 Identities=36% Similarity=1.062 Sum_probs=4.2
Q ss_pred eCCCCCcee-cC
Q 029867 125 QCEGCKDWF-HP 135 (186)
Q Consensus 125 ~C~~C~~W~-H~ 135 (186)
-||-|+.|+ |.
T Consensus 5 yCdyC~~~~~~d 16 (38)
T PF06220_consen 5 YCDYCKKYLTHD 16 (38)
T ss_dssp B-TTT--B-S--
T ss_pred ecccccceecCC
Confidence 589999998 54
No 104
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=26.51 E-value=45 Score=33.03 Aligned_cols=38 Identities=18% Similarity=0.353 Sum_probs=31.1
Q ss_pred CCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCcc
Q 029867 120 DDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSS 158 (186)
Q Consensus 120 ~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~ 158 (186)
.+..++|+.|..-||..||-.+...... ..|-|..|..
T Consensus 353 ~~~~lc~Et~prvvhlEcv~hP~~~~~s-~~~e~evc~~ 390 (1414)
T KOG1473|consen 353 LGDLLCCETCPRVVHLECVFHPRFAVPS-AFWECEVCNI 390 (1414)
T ss_pred ccceeecccCCceEEeeecCCccccCCC-ccchhhhhhh
Confidence 5678999999999999999887765433 6799999873
No 105
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=26.40 E-value=70 Score=29.06 Aligned_cols=42 Identities=14% Similarity=0.090 Sum_probs=33.7
Q ss_pred CCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccc
Q 029867 120 DDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 120 ~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 161 (186)
.+..+-|+.|.+-||..|...........+.|.|+.|.....
T Consensus 69 pg~vl~c~vc~Rs~h~~c~sp~~q~r~~s~p~~~p~p~s~k~ 110 (588)
T KOG3612|consen 69 PGAVLKCIVCHRSFHENCQSPDPQKRNYSVPSDKPQPYSFKV 110 (588)
T ss_pred CcceeeeehhhccccccccCcchhhccccccccCCcccccCC
Confidence 467788999999999999988776555556888888876655
No 106
>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=26.26 E-value=33 Score=17.04 Aligned_cols=11 Identities=27% Similarity=0.891 Sum_probs=8.0
Q ss_pred EeCCCCCceec
Q 029867 124 VQCEGCKDWFH 134 (186)
Q Consensus 124 i~C~~C~~W~H 134 (186)
.+|+.|++.|.
T Consensus 2 ~~C~~C~~~F~ 12 (27)
T PF13912_consen 2 FECDECGKTFS 12 (27)
T ss_dssp EEETTTTEEES
T ss_pred CCCCccCCccC
Confidence 36888887774
No 107
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=25.53 E-value=58 Score=18.04 Aligned_cols=30 Identities=17% Similarity=0.541 Sum_probs=14.1
Q ss_pred EeCCCCCceecCCCCCCChhh-hcCCCeEEcccCcc
Q 029867 124 VQCEGCKDWFHPSCMGMTIEE-AKKLDHFLCSDCSS 158 (186)
Q Consensus 124 i~C~~C~~W~H~~Cv~~~~~~-~~~~~~~~C~~C~~ 158 (186)
|+|..|+.-|.. +++. +.....-.|+.|..
T Consensus 3 i~CP~C~~~f~v-----~~~~l~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 3 ITCPNCQTRFRV-----PDDKLPAGGRKVRCPKCGH 33 (37)
T ss_pred EECCCCCceEEc-----CHHHcccCCcEEECCCCCc
Confidence 566666655532 2221 11224566666653
No 108
>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=24.12 E-value=13 Score=26.43 Aligned_cols=52 Identities=21% Similarity=0.448 Sum_probs=35.1
Q ss_pred ceEE-ecCCCCCC-CCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccccc
Q 029867 108 AVYC-KCEMPYNP-DDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 163 (186)
Q Consensus 108 ~~~C-~C~~~~~~-~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~ 163 (186)
...| .|+.+... ...-..|..|+..+-.+|-..... ...|+|..|....+++
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~~~----~~~WlC~vC~k~rel~ 107 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYSKK----EPIWLCKVCQKQRELK 107 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEETSS----SCCEEEHHHHHHHHHH
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCcCCC----CCCEEChhhHHHHHHH
Confidence 4567 67665321 233489999999999999776322 2579999999988854
No 109
>PF06701 MIB_HERC2: Mib_herc2; InterPro: IPR010606 Mib is a RING ubiquitin ligase in the Notch pathway. Mib interacts with the intracellular domain of Delta to promote its ubiquitylation and internalisation. Cell transplantation studies suggest that mib function is essential in the signalling cell for efficient activation of Notch in neighbouring cells. This domain has been named 'mib/herc2 domain' in []and usually the protein also contains an E3 ligase domain (either Ring or Hect).; GO: 0004842 ubiquitin-protein ligase activity, 0046872 metal ion binding, 0016567 protein ubiquitination; PDB: 2DK3_A 3DKM_A.
Probab=23.61 E-value=62 Score=20.84 Aligned_cols=27 Identities=22% Similarity=0.212 Sum_probs=13.9
Q ss_pred CCCCeEEEEeEEee--cCCCCEEEEEEEE
Q 029867 7 DKPPYVARVEKIEA--DHRNNVKVRVRWY 33 (186)
Q Consensus 7 ~~~~~iarI~~i~~--~~~~~~~v~v~Wf 33 (186)
+.+..+|.|++|.. ......+|.|+|-
T Consensus 17 GG~g~~GtV~~i~~~~~~~~~~~v~V~Wd 45 (68)
T PF06701_consen 17 GGEGHVGTVVSIRDWSSESPDGWVVVQWD 45 (68)
T ss_dssp SSTT--EEE-S--------BTTEEEEEET
T ss_pred CCCCcceEEEecccccccCCCCeEEEEeC
Confidence 34678999999833 2234579999994
No 110
>PF11910 NdhO: Cyanobacterial and plant NDH-1 subunit O; InterPro: IPR020905 NAD(P)H-quinone oxidoreductase (NDH-1) shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. It couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. NDH-1 can be composed of about 15 different subunits, although different subcomplexes with different compositions have been identified which probably have different functions. This entry represents subunit O. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process, 0005886 plasma membrane
Probab=23.17 E-value=1.5e+02 Score=19.03 Aligned_cols=29 Identities=28% Similarity=0.509 Sum_probs=17.4
Q ss_pred CCCCCCCCeE----EEEeEEeecCCCCEEEEEEEEeccc
Q 029867 3 PADSDKPPYV----ARVEKIEADHRNNVKVRVRWYYRPE 37 (186)
Q Consensus 3 ~~~~~~~~~i----arI~~i~~~~~~~~~v~v~Wfyrp~ 37 (186)
++|+.-|.|| |-|..|.. .+..|+| ++|.
T Consensus 22 ASD~~~P~Yife~~GEvl~ikg-----dYa~vr~-~~Pt 54 (67)
T PF11910_consen 22 ASDPRPPSYIFEGPGEVLDIKG-----DYAQVRF-RVPT 54 (67)
T ss_pred hcCCCCCcceecCCCeEEEecC-----CEEEEEe-cCCC
Confidence 3454455555 34444443 4888999 8885
No 111
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.45 E-value=74 Score=27.29 Aligned_cols=48 Identities=21% Similarity=0.496 Sum_probs=35.1
Q ss_pred eEEecCCCCCCCCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccc
Q 029867 109 VYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVD 161 (186)
Q Consensus 109 ~~C~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~ 161 (186)
..+||-..|.+++...- --|+--||..||..=.... .=.||.|.+...
T Consensus 231 ~CaIClEdY~~GdklRi-LPC~H~FH~~CIDpWL~~~----r~~CPvCK~di~ 278 (348)
T KOG4628|consen 231 TCAICLEDYEKGDKLRI-LPCSHKFHVNCIDPWLTQT----RTFCPVCKRDIR 278 (348)
T ss_pred eEEEeecccccCCeeeE-ecCCCchhhccchhhHhhc----CccCCCCCCcCC
Confidence 44599998876665444 7899999999997655432 247999998655
No 112
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=22.10 E-value=99 Score=29.46 Aligned_cols=52 Identities=27% Similarity=0.695 Sum_probs=34.2
Q ss_pred CCCcceEE-ecCCCCCCCCceEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccc
Q 029867 104 PDRVAVYC-KCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSD 159 (186)
Q Consensus 104 p~~~~~~C-~C~~~~~~~~~~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~ 159 (186)
|+...+.| .|+.+-+| .-.||..|+.=| ..|+.....-.+. -.|.|+.|...
T Consensus 1113 ~~~~~vdc~~cg~~i~~--~~~~c~ec~~kf-P~CiasG~pIt~~-~fWlC~~CkH~ 1165 (1189)
T KOG2041|consen 1113 PNSAKVDCSVCGAKIDP--YDLQCSECQTKF-PVCIASGRPITDN-IFWLCPRCKHR 1165 (1189)
T ss_pred CCccceeeeecCCcCCc--cCCCChhhcCcC-ceeeccCCccccc-eEEEccccccc
Confidence 45567788 88887643 446899998655 4566543333222 38999999754
No 113
>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=21.88 E-value=43 Score=17.69 Aligned_cols=11 Identities=27% Similarity=0.585 Sum_probs=8.5
Q ss_pred EeCCCCCceec
Q 029867 124 VQCEGCKDWFH 134 (186)
Q Consensus 124 i~C~~C~~W~H 134 (186)
..|+.|+.||.
T Consensus 4 ~~C~~C~~~~~ 14 (35)
T smart00451 4 FYCKLCNVTFT 14 (35)
T ss_pred eEccccCCccC
Confidence 35888988876
No 114
>PLN02294 cytochrome c oxidase subunit Vb
Probab=21.70 E-value=86 Score=24.09 Aligned_cols=37 Identities=16% Similarity=0.270 Sum_probs=26.3
Q ss_pred ceEEecCCCCCC---------CCceEeCCCCCceecCCCCCCChhh
Q 029867 108 AVYCKCEMPYNP---------DDLMVQCEGCKDWFHPSCMGMTIEE 144 (186)
Q Consensus 108 ~~~C~C~~~~~~---------~~~~i~C~~C~~W~H~~Cv~~~~~~ 144 (186)
-+-|.|+.+.+. .+....|..|+.||=..=||.....
T Consensus 117 iVGCtg~~~eDsh~v~Wf~L~kGkp~RCpeCG~~fkL~~vG~~~~~ 162 (174)
T PLN02294 117 IVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFELEVVGPGGPP 162 (174)
T ss_pred EEeeCCCCCCCCceeEEEEecCCCceeCCCCCCEEEEEEeCCCCCC
Confidence 445888644322 3466789999999999998876653
No 115
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=21.53 E-value=1.7e+02 Score=16.74 Aligned_cols=32 Identities=19% Similarity=0.270 Sum_probs=19.2
Q ss_pred eEeCCCCCceecCCCCCCChhhhcCCCeEEcccCccccccc
Q 029867 123 MVQCEGCKDWFHPSCMGMTIEEAKKLDHFLCSDCSSDVDAK 163 (186)
Q Consensus 123 ~i~C~~C~~W~H~~Cv~~~~~~~~~~~~~~C~~C~~~~~~~ 163 (186)
.+.|..|+.-+... + ....+.||.|......+
T Consensus 3 ~y~C~~CG~~~~~~-------~--~~~~~~Cp~CG~~~~~~ 34 (46)
T PRK00398 3 EYKCARCGREVELD-------E--YGTGVRCPYCGYRILFK 34 (46)
T ss_pred EEECCCCCCEEEEC-------C--CCCceECCCCCCeEEEc
Confidence 45677776655442 1 11268999998766544
No 116
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=20.89 E-value=1.3e+02 Score=19.90 Aligned_cols=26 Identities=15% Similarity=0.175 Sum_probs=18.1
Q ss_pred cceEEecCCCCCCCCceEeCCCCCcee
Q 029867 107 VAVYCKCEMPYNPDDLMVQCEGCKDWF 133 (186)
Q Consensus 107 ~~~~C~C~~~~~~~~~~i~C~~C~~W~ 133 (186)
.+.+.+-..... ...++.|+.|+.|.
T Consensus 55 ~p~F~v~~~~~~-~~L~~~C~~Cd~~~ 80 (82)
T PF14768_consen 55 TPQFSVEPGFGE-SSLYMSCEACDFLE 80 (82)
T ss_pred CCEEEEecCCCc-hhheeECCCCCcce
Confidence 345555555444 38999999999874
No 117
>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=20.72 E-value=1.8e+02 Score=23.14 Aligned_cols=31 Identities=29% Similarity=0.622 Sum_probs=24.0
Q ss_pred CCCCCCeEEEEeEEeecCCCCEEEEEEEEeccc
Q 029867 5 DSDKPPYVARVEKIEADHRNNVKVRVRWYYRPE 37 (186)
Q Consensus 5 ~~~~~~~iarI~~i~~~~~~~~~v~v~Wfyrp~ 37 (186)
..+-|-|.|+|.++... +...|+|.|+-.-.
T Consensus 40 ~D~mPR~Ya~I~kV~~~--~~Fkl~i~wLe~~~ 70 (217)
T PF11926_consen 40 DDGMPRYYARIKKVDSS--NPFKLHITWLEPCP 70 (217)
T ss_pred CCCCeeeEEEEEEEecC--CCeEEEEEEccccC
Confidence 34678899999999875 34699999987554
No 118
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=20.52 E-value=43 Score=28.33 Aligned_cols=18 Identities=28% Similarity=1.001 Sum_probs=13.4
Q ss_pred EE-ecCCCCCCCCceEeCC
Q 029867 110 YC-KCEMPYNPDDLMVQCE 127 (186)
Q Consensus 110 ~C-~C~~~~~~~~~~i~C~ 127 (186)
+| .|+.|..-.+.||-|+
T Consensus 92 fCd~Cd~PI~IYGRmIPCk 110 (389)
T KOG2932|consen 92 FCDRCDFPIAIYGRMIPCK 110 (389)
T ss_pred eecccCCcceeeecccccc
Confidence 45 6777766678999887
No 119
>PF00649 Copper-fist: Copper fist DNA binding domain; InterPro: IPR001083 Some fungal transcription factors contain an N-terminal domain, the copper fist, which seems to be involved in copper-dependent DNA-binding [, ]. These proteins activate the transcription of the metallothionein gene in response to copper. Metallothionein maintains copper levels in yeast [, ]. The copper fist domain, which is similar in structure to metallothionein itself, undergoes a large conformational change on copper-binding that allows DNA-binding. The domain contains a conserved array of zinc-binding residues (Cys-X2-Cys-X8-Cys-X-His) and forms a three-stranded antiparallel beta-sheet with two short helical segments that project from one end of the beta-sheet []. Conserved residues form a basic patch that may be important for DNA binding. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0005507 copper ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1CO4_A.
Probab=20.46 E-value=62 Score=18.62 Aligned_cols=14 Identities=14% Similarity=0.532 Sum_probs=12.2
Q ss_pred CCeEEcccCccccc
Q 029867 148 LDHFLCSDCSSDVD 161 (186)
Q Consensus 148 ~~~~~C~~C~~~~~ 161 (186)
..+|.|..|.+.+.
T Consensus 6 g~KyAC~~CirGHR 19 (40)
T PF00649_consen 6 GEKYACESCIRGHR 19 (40)
T ss_dssp TEEEEETTTTTTSG
T ss_pred CeEEEhhhhhCccc
Confidence 46899999999887
No 120
>KOG3896 consensus Dynactin, subunit p62 [Cell motility]
Probab=20.30 E-value=78 Score=27.13 Aligned_cols=13 Identities=15% Similarity=0.396 Sum_probs=6.8
Q ss_pred CeEEcccCccccc
Q 029867 149 DHFLCSDCSSDVD 161 (186)
Q Consensus 149 ~~~~C~~C~~~~~ 161 (186)
.+-.|++|.....
T Consensus 63 KKn~CAnCfDCP~ 75 (449)
T KOG3896|consen 63 KKNKCANCFDCPK 75 (449)
T ss_pred hhccccccccCcc
Confidence 4555555555444
No 121
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.09 E-value=52 Score=24.85 Aligned_cols=24 Identities=42% Similarity=0.937 Sum_probs=17.8
Q ss_pred CCCCCCceEeCCCCCc---------eecCCCCC
Q 029867 116 PYNPDDLMVQCEGCKD---------WFHPSCMG 139 (186)
Q Consensus 116 ~~~~~~~~i~C~~C~~---------W~H~~Cv~ 139 (186)
.|..+-..|||++|+. |||..=+.
T Consensus 97 AY~~GvVivqC~gC~~~HliaDnL~~F~d~~~~ 129 (165)
T KOG3277|consen 97 AYEKGVVIVQCPGCKNHHLIADNLGWFHDLKGK 129 (165)
T ss_pred hhhCceEEEECCCCccceeehhhhccccccccc
Confidence 3444679999999974 88876554
Done!