Query psy1385
Match_columns 69
No_of_seqs 32 out of 34
Neff 2.4
Searched_HMMs 46136
Date Fri Aug 16 22:01:03 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1385.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1385hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00628 PHD: PHD-finger; Int 98.0 8.1E-06 1.8E-10 45.1 2.7 25 43-69 2-26 (51)
2 smart00249 PHD PHD zinc finger 97.4 7.7E-05 1.7E-09 38.5 1.6 25 43-69 2-26 (47)
3 PF14446 Prok-RING_1: Prokaryo 94.7 0.02 4.3E-07 34.9 1.5 29 40-69 5-33 (54)
4 PF07649 C1_3: C1-like domain; 92.2 0.092 2E-06 27.1 1.3 27 41-69 1-27 (30)
5 PF03604 DNA_RNApol_7kD: DNA d 90.5 0.11 2.3E-06 28.4 0.5 24 41-65 1-25 (32)
6 PF13639 zf-RING_2: Ring finge 90.3 0.2 4.3E-06 26.9 1.5 26 42-69 2-27 (44)
7 smart00659 RPOLCX RNA polymera 90.1 0.19 4.1E-06 28.8 1.4 24 40-64 2-26 (44)
8 PF03107 C1_2: C1 domain; Int 85.4 0.88 1.9E-05 23.6 2.0 26 41-68 1-26 (30)
9 PF07282 OrfB_Zn_ribbon: Putat 82.7 1.1 2.5E-05 25.8 2.0 30 39-69 27-58 (69)
10 PF13240 zinc_ribbon_2: zinc-r 81.5 0.67 1.4E-05 23.4 0.6 19 43-64 2-20 (23)
11 KOG3507|consensus 80.7 1.1 2.3E-05 28.4 1.4 29 35-64 15-44 (62)
12 PF04640 PLATZ: PLATZ transcri 79.9 1.8 3.8E-05 27.4 2.2 31 32-64 40-71 (72)
13 PF13832 zf-HC5HC2H_2: PHD-zin 78.3 1.9 4E-05 26.7 2.0 28 38-68 53-81 (110)
14 PF04770 ZF-HD_dimer: ZF-HD pr 77.6 1.3 2.8E-05 27.7 1.1 16 54-69 38-54 (60)
15 KOG4323|consensus 77.2 0.86 1.9E-05 37.3 0.3 28 41-69 169-197 (464)
16 PRK00398 rpoP DNA-directed RNA 76.6 1.8 3.8E-05 23.9 1.4 24 40-64 3-28 (46)
17 PF00130 C1_1: Phorbol esters/ 76.0 4.1 8.8E-05 22.3 2.8 30 39-69 10-40 (53)
18 PF11793 FANCL_C: FANCL C-term 75.7 1.4 3E-05 26.6 0.9 29 41-69 3-34 (70)
19 PF02591 DUF164: Putative zinc 73.5 2.1 4.6E-05 24.5 1.2 24 42-66 24-55 (56)
20 PF02085 Cytochrom_CIII: Class 71.9 1.1 2.3E-05 27.7 -0.3 39 23-64 16-54 (102)
21 COG1996 RPC10 DNA-directed RNA 66.2 2.9 6.3E-05 25.0 0.8 26 38-64 4-31 (49)
22 PF09416 UPF1_Zn_bind: RNA hel 64.5 5.4 0.00012 28.4 2.0 23 42-67 2-24 (152)
23 TIGR01566 ZF_HD_prot_N ZF-HD h 64.4 3.9 8.4E-05 25.2 1.1 17 53-69 33-50 (53)
24 cd04476 RPA1_DBD_C RPA1_DBD_C: 63.6 4.5 9.9E-05 26.7 1.4 24 41-65 35-59 (166)
25 KOG4718|consensus 62.7 1.3 2.9E-05 33.8 -1.4 30 36-69 177-206 (235)
26 PF05495 zf-CHY: CHY zinc fing 62.5 5.4 0.00012 24.1 1.5 27 40-67 41-71 (71)
27 KOG1973|consensus 62.3 4.3 9.3E-05 30.0 1.2 22 45-68 223-246 (274)
28 smart00451 ZnF_U1 U1-like zinc 61.2 3.7 8E-05 20.6 0.5 11 57-68 4-14 (35)
29 PF03119 DNA_ligase_ZBD: NAD-d 60.3 7.1 0.00015 20.3 1.5 21 42-62 1-23 (28)
30 PF13901 DUF4206: Domain of un 59.4 6.6 0.00014 27.7 1.7 29 40-69 152-184 (202)
31 cd07172 NR_DBD_GR_PR DNA-bindi 57.5 3.3 7.1E-05 25.6 -0.1 28 41-69 3-31 (78)
32 cd07163 NR_DBD_TLX DNA-binding 56.6 9 0.00019 24.3 1.8 29 40-69 6-35 (92)
33 cd07157 2DBD_NR_DBD1 The first 55.8 6.8 0.00015 24.6 1.1 27 42-69 2-29 (86)
34 cd06967 NR_DBD_TR2_like DNA-bi 53.8 8.2 0.00018 24.2 1.3 28 41-69 4-32 (87)
35 cd07173 NR_DBD_AR DNA-binding 53.5 2.6 5.6E-05 26.4 -1.0 30 39-69 2-32 (82)
36 COG2158 Uncharacterized protei 52.0 14 0.0003 25.7 2.3 30 38-69 40-73 (112)
37 KOG0957|consensus 51.3 4.5 9.7E-05 34.9 -0.3 28 39-68 543-570 (707)
38 PRK11088 rrmA 23S rRNA methylt 50.6 12 0.00027 26.3 1.9 25 40-65 2-26 (272)
39 PF13248 zf-ribbon_3: zinc-rib 50.1 7.3 0.00016 19.6 0.5 18 42-61 4-21 (26)
40 PF13894 zf-C2H2_4: C2H2-type 49.5 7.4 0.00016 17.2 0.4 12 41-52 1-12 (24)
41 PF13831 PHD_2: PHD-finger; PD 45.5 11 0.00023 20.5 0.7 15 54-69 2-16 (36)
42 PF00412 LIM: LIM domain; Int 45.2 28 0.0006 18.7 2.4 15 43-57 1-15 (58)
43 PF03966 Trm112p: Trm112p-like 44.7 19 0.00042 21.2 1.8 16 51-67 48-63 (68)
44 cd06965 NR_DBD_Ppar DNA-bindin 43.8 7 0.00015 24.3 -0.2 27 42-69 1-28 (84)
45 KOG2752|consensus 43.0 11 0.00025 30.2 0.9 41 25-68 114-159 (345)
46 cd07160 NR_DBD_LXR DNA-binding 43.0 18 0.00039 23.6 1.7 29 40-69 18-47 (101)
47 PF07191 zinc-ribbons_6: zinc- 43.0 19 0.00041 22.9 1.7 25 42-67 3-27 (70)
48 smart00744 RINGv The RING-vari 42.2 10 0.00022 21.6 0.3 24 43-69 2-30 (49)
49 TIGR00201 comF comF family pro 41.6 11 0.00024 25.6 0.5 22 43-67 1-22 (190)
50 PF13771 zf-HC5HC2H: PHD-like 41.2 28 0.00062 20.5 2.2 26 40-68 36-62 (90)
51 KOG4216|consensus 41.0 10 0.00022 31.6 0.3 30 39-69 45-75 (479)
52 cd06960 NR_DBD_HNF4A DNA-bindi 40.9 15 0.00033 22.1 1.0 14 55-69 14-27 (76)
53 PF10571 UPF0547: Uncharacteri 40.8 13 0.00029 19.2 0.6 21 42-65 2-22 (26)
54 PRK12411 cytidine deaminase; P 39.8 8.6 0.00019 25.8 -0.2 15 38-52 81-95 (132)
55 KOG1244|consensus 39.5 20 0.00043 28.8 1.7 25 42-68 283-307 (336)
56 PF14354 Lar_restr_allev: Rest 39.2 25 0.00055 19.7 1.7 26 39-65 2-37 (61)
57 cd06970 NR_DBD_PNR DNA-binding 38.9 17 0.00038 23.1 1.1 31 38-69 4-35 (92)
58 KOG1632|consensus 38.6 2.6 5.5E-05 32.5 -3.3 28 40-68 239-266 (345)
59 cd06963 NR_DBD_GR_like The DNA 38.2 9.8 0.00021 23.0 -0.1 26 43-69 1-27 (73)
60 PRK08298 cytidine deaminase; V 37.4 9.3 0.0002 26.0 -0.4 15 39-53 85-99 (136)
61 PF00105 zf-C4: Zinc finger, C 37.4 6.7 0.00015 22.9 -0.9 27 42-69 2-29 (70)
62 cd06968 NR_DBD_ROR DNA-binding 37.2 10 0.00022 24.3 -0.2 28 41-69 6-34 (95)
63 PRK06848 hypothetical protein; 36.1 11 0.00023 25.6 -0.2 16 38-53 92-107 (139)
64 PHA00733 hypothetical protein 35.7 35 0.00076 22.7 2.2 33 36-69 69-111 (128)
65 PRK12366 replication factor A; 35.1 22 0.00048 29.3 1.4 24 41-65 533-556 (637)
66 PF08646 Rep_fac-A_C: Replicat 34.8 25 0.00054 22.8 1.4 23 42-65 20-45 (146)
67 cd06956 NR_DBD_RXR DNA-binding 34.6 8.2 0.00018 23.6 -0.9 27 42-69 2-29 (77)
68 PRK11788 tetratricopeptide rep 34.5 32 0.00069 24.0 1.9 28 36-66 350-377 (389)
69 cd06959 NR_DBD_EcR_like The DN 34.2 11 0.00023 22.7 -0.4 26 43-69 2-28 (73)
70 cd07169 NR_DBD_GCNF_like DNA-b 34.1 9.9 0.00021 24.1 -0.6 29 40-69 6-35 (90)
71 KOG2593|consensus 33.3 31 0.00066 28.5 1.9 33 32-65 120-161 (436)
72 PF12678 zf-rbx1: RING-H2 zinc 32.6 39 0.00084 20.2 1.8 27 43-69 22-56 (73)
73 cd07156 NR_DBD_VDR_like The DN 32.5 17 0.00038 21.8 0.3 14 55-69 14-27 (72)
74 cd07158 NR_DBD_Ppar_like The D 31.4 10 0.00023 22.7 -0.8 14 55-69 14-27 (73)
75 PF00096 zf-C2H2: Zinc finger, 31.4 17 0.00038 16.6 0.1 12 41-52 1-12 (23)
76 smart00746 TRASH metallochaper 31.2 40 0.00088 14.9 1.4 10 43-52 1-10 (39)
77 smart00399 ZnF_C4 c4 zinc fing 30.9 20 0.00044 21.1 0.4 26 43-69 2-28 (70)
78 PF13912 zf-C2H2_6: C2H2-type 30.9 19 0.00042 17.1 0.3 13 40-52 1-13 (27)
79 KOG4218|consensus 30.2 16 0.00036 30.3 -0.1 27 42-69 17-44 (475)
80 cd07162 NR_DBD_PXR DNA-binding 30.2 13 0.00028 23.2 -0.6 26 43-69 2-28 (87)
81 PF12660 zf-TFIIIC: Putative z 30.2 32 0.00068 22.1 1.2 32 34-66 8-40 (99)
82 TIGR01384 TFS_arch transcripti 30.1 41 0.00088 20.8 1.7 13 39-51 15-27 (104)
83 KOG1829|consensus 29.8 11 0.00025 31.7 -1.1 27 40-69 511-543 (580)
84 KOG0383|consensus 29.6 20 0.00044 30.7 0.3 22 42-68 49-70 (696)
85 smart00132 LIM Zinc-binding do 29.5 40 0.00086 16.2 1.3 19 42-60 1-19 (39)
86 COG1579 Zn-ribbon protein, pos 29.0 23 0.0005 26.6 0.5 23 42-65 199-229 (239)
87 TIGR03831 YgiT_finger YgiT-typ 28.4 34 0.00073 17.7 1.0 15 39-53 31-45 (46)
88 KOG1802|consensus 28.2 44 0.00094 30.0 2.1 30 37-69 57-86 (935)
89 COG0295 Cdd Cytidine deaminase 28.0 23 0.0005 24.6 0.3 16 37-52 82-97 (134)
90 COG5188 PRP9 Splicing factor 3 27.7 19 0.00042 29.9 -0.1 22 47-69 229-250 (470)
91 PF06220 zf-U1: U1 zinc finger 27.6 24 0.00052 19.4 0.3 9 58-67 5-13 (38)
92 PF14421 LmjF365940-deam: A di 27.0 24 0.00052 26.4 0.3 18 33-50 147-164 (193)
93 KOG1512|consensus 26.9 29 0.00063 28.2 0.8 25 42-68 316-340 (381)
94 smart00109 C1 Protein kinase C 26.8 20 0.00043 18.4 -0.1 27 41-68 12-38 (49)
95 smart00834 CxxC_CXXC_SSSS Puta 26.7 30 0.00064 17.8 0.5 10 41-50 6-15 (41)
96 cd00350 rubredoxin_like Rubred 26.6 41 0.00089 17.5 1.1 13 41-53 2-14 (33)
97 PF08209 Sgf11: Sgf11 (transcr 26.3 29 0.00063 19.0 0.5 16 38-53 2-17 (33)
98 PRK05578 cytidine deaminase; V 25.5 17 0.00037 24.3 -0.6 15 38-52 81-95 (131)
99 PF13966 zf-RVT: zinc-binding 25.4 47 0.001 19.7 1.3 37 30-66 49-86 (86)
100 smart00531 TFIIE Transcription 25.2 37 0.0008 22.6 0.9 14 41-54 124-137 (147)
101 PF07227 DUF1423: Protein of u 25.0 62 0.0013 26.8 2.3 31 36-68 124-157 (446)
102 PF11331 DUF3133: Protein of u 25.0 36 0.00077 20.0 0.7 13 38-50 29-41 (46)
103 TIGR01374 soxD sarcosine oxida 24.4 38 0.00082 22.0 0.8 9 60-68 58-66 (84)
104 PF12773 DZR: Double zinc ribb 23.7 56 0.0012 17.6 1.3 19 40-60 29-47 (50)
105 smart00401 ZnF_GATA zinc finge 22.9 57 0.0012 18.7 1.3 27 40-67 3-35 (52)
106 cd06969 NR_DBD_NGFI-B DNA-bind 22.7 40 0.00087 20.4 0.7 27 42-69 2-29 (75)
107 COG0675 Transposase and inacti 22.5 1E+02 0.0022 20.8 2.7 29 37-69 306-334 (364)
108 cd07155 NR_DBD_ER_like DNA-bin 22.3 15 0.00032 22.3 -1.3 14 55-69 14-27 (75)
109 PHA03256 BDLF3; Provisional 22.3 22 0.00048 23.3 -0.6 7 63-69 25-31 (77)
110 TIGR02098 MJ0042_CXXC MJ0042 f 21.9 84 0.0018 16.2 1.7 24 41-65 3-33 (38)
111 PRK14892 putative transcriptio 21.9 79 0.0017 20.8 2.0 34 35-69 16-54 (99)
112 PF13842 Tnp_zf-ribbon_2: DDE_ 21.3 74 0.0016 16.8 1.5 13 55-68 15-27 (32)
113 PF14634 zf-RING_5: zinc-RING 21.2 72 0.0016 17.0 1.4 21 42-64 1-21 (44)
114 PF05605 zf-Di19: Drought indu 21.1 51 0.0011 18.4 0.8 12 40-51 31-42 (54)
115 PF01258 zf-dskA_traR: Prokary 21.0 24 0.00052 18.6 -0.5 21 43-64 6-31 (36)
116 smart00734 ZnF_Rad18 Rad18-lik 20.8 47 0.001 16.9 0.6 11 41-51 2-12 (26)
117 PRK09710 lar restriction allev 20.5 84 0.0018 19.8 1.8 15 38-52 4-18 (64)
118 cd00029 C1 Protein kinase C co 20.3 55 0.0012 17.0 0.8 26 42-68 13-39 (50)
119 cd06955 NR_DBD_VDR DNA-binding 20.2 48 0.0011 21.8 0.7 28 41-69 7-35 (107)
No 1
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=97.95 E-value=8.1e-06 Score=45.08 Aligned_cols=25 Identities=44% Similarity=1.220 Sum_probs=22.6
Q ss_pred ccccccccccCCceEEecccccceeeC
Q psy1385 43 CGICHKEVHDNDQAILCESGCNFWYHR 69 (69)
Q Consensus 43 CG~C~~eV~D~ddAI~CE~~C~~WFHR 69 (69)
|.+|++ ..++++.|.|+. |+.|||.
T Consensus 2 C~vC~~-~~~~~~~i~C~~-C~~~~H~ 26 (51)
T PF00628_consen 2 CPVCGQ-SDDDGDMIQCDS-CNRWYHQ 26 (51)
T ss_dssp BTTTTS-SCTTSSEEEBST-TSCEEET
T ss_pred CcCCCC-cCCCCCeEEcCC-CChhhCc
Confidence 788998 888899999996 9999995
No 2
>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 PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=94.65 E-value=0.02 Score=34.90 Aligned_cols=29 Identities=34% Similarity=0.824 Sum_probs=26.8
Q ss_pred CccccccccccccCCceEEecccccceeeC
Q psy1385 40 IYPCGICHKEVHDNDQAILCESGCNFWYHR 69 (69)
Q Consensus 40 ~ypCG~C~~eV~D~ddAI~CE~~C~~WFHR 69 (69)
-..|-.|++.|.|.||.+.|.. |..=|||
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~-CgapyHR 33 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPE-CGAPYHR 33 (54)
T ss_pred CccChhhCCcccCCCCEEECCC-CCCcccH
Confidence 3579999999999999999999 9999998
No 4
>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=92.17 E-value=0.092 Score=27.10 Aligned_cols=27 Identities=26% Similarity=0.709 Sum_probs=10.2
Q ss_pred ccccccccccccCCceEEecccccceeeC
Q psy1385 41 YPCGICHKEVHDNDQAILCESGCNFWYHR 69 (69)
Q Consensus 41 ypCG~C~~eV~D~ddAI~CE~~C~~WFHR 69 (69)
+.|..|.+.+.. +-.-.|.. |++.+|.
T Consensus 1 ~~C~~C~~~~~~-~~~Y~C~~-Cdf~lH~ 27 (30)
T PF07649_consen 1 FRCDACGKPIDG-GWFYRCSE-CDFDLHE 27 (30)
T ss_dssp ---TTTS----S---EEE-TT-T-----H
T ss_pred CcCCcCCCcCCC-CceEECcc-CCCccCh
Confidence 479999999888 78888988 9999983
No 5
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=90.47 E-value=0.11 Score=28.43 Aligned_cols=24 Identities=38% Similarity=0.841 Sum_probs=18.5
Q ss_pred ccccccccccccC-CceEEecccccc
Q psy1385 41 YPCGICHKEVHDN-DQAILCESGCNF 65 (69)
Q Consensus 41 ypCG~C~~eV~D~-ddAI~CE~~C~~ 65 (69)
|.||.|+.+|... .|+|.|.- |..
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~-CG~ 25 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPE-CGH 25 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSS-SS-
T ss_pred CCCCcCCCeeEcCCCCcEECCc-CCC
Confidence 7899999999984 78899987 653
No 6
>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=90.28 E-value=0.2 Score=26.91 Aligned_cols=26 Identities=31% Similarity=0.791 Sum_probs=21.7
Q ss_pred cccccccccccCCceEEecccccceeeC
Q psy1385 42 PCGICHKEVHDNDQAILCESGCNFWYHR 69 (69)
Q Consensus 42 pCG~C~~eV~D~ddAI~CE~~C~~WFHR 69 (69)
.|.||.+++.+++..+... |.-.||+
T Consensus 2 ~C~IC~~~~~~~~~~~~l~--C~H~fh~ 27 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLP--CGHVFHR 27 (44)
T ss_dssp CETTTTCBHHTTSCEEEET--TSEEEEH
T ss_pred CCcCCChhhcCCCeEEEcc--CCCeeCH
Confidence 4999999999987777554 9999994
No 7
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=90.13 E-value=0.19 Score=28.77 Aligned_cols=24 Identities=33% Similarity=0.869 Sum_probs=19.9
Q ss_pred CccccccccccccC-CceEEeccccc
Q psy1385 40 IYPCGICHKEVHDN-DQAILCESGCN 64 (69)
Q Consensus 40 ~ypCG~C~~eV~D~-ddAI~CE~~C~ 64 (69)
.|.|+.|+.++.-+ .+.|.|-- |.
T Consensus 2 ~Y~C~~Cg~~~~~~~~~~irC~~-CG 26 (44)
T smart00659 2 IYICGECGRENEIKSKDVVRCRE-CG 26 (44)
T ss_pred EEECCCCCCEeecCCCCceECCC-CC
Confidence 58999999999875 78999975 54
No 8
>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=85.36 E-value=0.88 Score=23.63 Aligned_cols=26 Identities=23% Similarity=0.701 Sum_probs=21.7
Q ss_pred ccccccccccccCCceEEecccccceee
Q psy1385 41 YPCGICHKEVHDNDQAILCESGCNFWYH 68 (69)
Q Consensus 41 ypCG~C~~eV~D~ddAI~CE~~C~~WFH 68 (69)
|.|++|.+++.... .-.|+. |.+=+|
T Consensus 1 ~~C~~C~~~~~~~~-~Y~C~~-c~f~lh 26 (30)
T PF03107_consen 1 FWCDVCRRKIDGFY-FYHCSE-CCFTLH 26 (30)
T ss_pred CCCCCCCCCcCCCE-eEEeCC-CCCeEc
Confidence 57999999999877 999966 777666
No 9
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=82.71 E-value=1.1 Score=25.81 Aligned_cols=30 Identities=20% Similarity=0.533 Sum_probs=25.8
Q ss_pred CCcccccccccccc--CCceEEecccccceeeC
Q psy1385 39 PIYPCGICHKEVHD--NDQAILCESGCNFWYHR 69 (69)
Q Consensus 39 ~~ypCG~C~~eV~D--~ddAI~CE~~C~~WFHR 69 (69)
+...|..|+..+.+ .+....|.. |.+.+||
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~-Cg~~~~r 58 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPN-CGFEMDR 58 (69)
T ss_pred CccCccCcccccccccccceEEcCC-CCCEECc
Confidence 45569999999998 788999999 9999987
No 10
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=81.52 E-value=0.67 Score=23.40 Aligned_cols=19 Identities=37% Similarity=0.975 Sum_probs=15.1
Q ss_pred ccccccccccCCceEEeccccc
Q psy1385 43 CGICHKEVHDNDQAILCESGCN 64 (69)
Q Consensus 43 CG~C~~eV~D~ddAI~CE~~C~ 64 (69)
|..|+++|.| ++.+|.. |.
T Consensus 2 Cp~CG~~~~~--~~~fC~~-CG 20 (23)
T PF13240_consen 2 CPNCGAEIED--DAKFCPN-CG 20 (23)
T ss_pred CcccCCCCCC--cCcchhh-hC
Confidence 8899999976 6778876 54
No 11
>KOG3507|consensus
Probab=80.66 E-value=1.1 Score=28.43 Aligned_cols=29 Identities=34% Similarity=0.679 Sum_probs=22.0
Q ss_pred CCCCCCcccccccccccc-CCceEEeccccc
Q psy1385 35 PNAPPIYPCGICHKEVHD-NDQAILCESGCN 64 (69)
Q Consensus 35 ~~s~~~ypCG~C~~eV~D-~ddAI~CE~~C~ 64 (69)
....-+|.||.|+.|-.= --|+|.|-. |.
T Consensus 15 r~~~miYiCgdC~~en~lk~~D~irCRe-CG 44 (62)
T KOG3507|consen 15 RTATMIYICGDCGQENTLKRGDVIRCRE-CG 44 (62)
T ss_pred CcccEEEEeccccccccccCCCcEehhh-cc
Confidence 345568999999987543 589999987 64
No 12
>PF04640 PLATZ: PLATZ transcription factor; InterPro: IPR006734 This family includes a conserved region in several uncharacterised plant proteins.
Probab=79.88 E-value=1.8 Score=27.41 Aligned_cols=31 Identities=26% Similarity=0.633 Sum_probs=24.4
Q ss_pred CCCCCCC-CCccccccccccccCCceEEeccccc
Q psy1385 32 PQNPNAP-PIYPCGICHKEVHDNDQAILCESGCN 64 (69)
Q Consensus 32 ~q~~~s~-~~ypCG~C~~eV~D~ddAI~CE~~C~ 64 (69)
||+.... ....|-.|++.++|. .-+|-.+|.
T Consensus 40 pq~~~~~~~~~~C~~C~R~L~d~--~~fCSl~CK 71 (72)
T PF04640_consen 40 PQSRPSKGSGNICETCHRSLQDP--YRFCSLSCK 71 (72)
T ss_pred CcCCCCCCCCCccCCCCCCCCCC--CeEEeeeEE
Confidence 4554432 478999999999985 899999986
No 13
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=78.35 E-value=1.9 Score=26.74 Aligned_cols=28 Identities=32% Similarity=0.720 Sum_probs=23.5
Q ss_pred CCCccccccccccccCCceEEecc-cccceee
Q psy1385 38 PPIYPCGICHKEVHDNDQAILCES-GCNFWYH 68 (69)
Q Consensus 38 ~~~ypCG~C~~eV~D~ddAI~CE~-~C~~WFH 68 (69)
.....|.+|.+. .---|.|.. +|.++||
T Consensus 53 ~~~~~C~iC~~~---~G~~i~C~~~~C~~~fH 81 (110)
T PF13832_consen 53 RFKLKCSICGKS---GGACIKCSHPGCSTAFH 81 (110)
T ss_pred hcCCcCcCCCCC---CceeEEcCCCCCCcCCC
Confidence 357899999998 445789987 8999999
No 14
>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors. HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.
Probab=77.59 E-value=1.3 Score=27.74 Aligned_cols=16 Identities=38% Similarity=0.937 Sum_probs=13.8
Q ss_pred CceEEecc-cccceeeC
Q psy1385 54 DQAILCES-GCNFWYHR 69 (69)
Q Consensus 54 ddAI~CE~-~C~~WFHR 69 (69)
.+|+.|.+ ||++=|||
T Consensus 38 ~~al~CaACgCHRnFHR 54 (60)
T PF04770_consen 38 PEALKCAACGCHRNFHR 54 (60)
T ss_pred cccceecccCcchhccc
Confidence 57888888 89999998
No 15
>KOG4323|consensus
Probab=77.17 E-value=0.86 Score=37.29 Aligned_cols=28 Identities=25% Similarity=0.878 Sum_probs=22.2
Q ss_pred cccccccccccc-CCceEEecccccceeeC
Q psy1385 41 YPCGICHKEVHD-NDQAILCESGCNFWYHR 69 (69)
Q Consensus 41 ypCG~C~~eV~D-~ddAI~CE~~C~~WFHR 69 (69)
..|-.|..-+-- -..-|+|.. |+.|||+
T Consensus 169 ~qc~vC~~g~~~~~NrmlqC~~-C~~~fHq 197 (464)
T KOG4323|consen 169 LQCSVCYCGGPGAGNRMLQCDK-CRQWYHQ 197 (464)
T ss_pred ceeeeeecCCcCccceeeeecc-cccHHHH
Confidence 449999865544 359999999 9999995
No 16
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=76.57 E-value=1.8 Score=23.95 Aligned_cols=24 Identities=29% Similarity=0.776 Sum_probs=17.2
Q ss_pred CccccccccccccCCc--eEEeccccc
Q psy1385 40 IYPCGICHKEVHDNDQ--AILCESGCN 64 (69)
Q Consensus 40 ~ypCG~C~~eV~D~dd--AI~CE~~C~ 64 (69)
.|.|..|+.++.-++. ++.|.- |.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~-CG 28 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPY-CG 28 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCC-CC
Confidence 5789999988755433 688876 65
No 17
>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=75.97 E-value=4.1 Score=22.26 Aligned_cols=30 Identities=23% Similarity=0.475 Sum_probs=22.7
Q ss_pred CCcccccccccc-ccCCceEEecccccceeeC
Q psy1385 39 PIYPCGICHKEV-HDNDQAILCESGCNFWYHR 69 (69)
Q Consensus 39 ~~ypCG~C~~eV-~D~ddAI~CE~~C~~WFHR 69 (69)
..-.|..|.+.| ....+++.|+. |+.-.|+
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~-C~~~~H~ 40 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSW-CGLVCHK 40 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETT-TT-EEET
T ss_pred CCCCCcccCcccCCCCCCeEEECC-CCChHhh
Confidence 445799999999 33578999998 9999985
No 18
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=75.72 E-value=1.4 Score=26.61 Aligned_cols=29 Identities=28% Similarity=0.708 Sum_probs=10.6
Q ss_pred ccccccccccccCC--ceEEec-ccccceeeC
Q psy1385 41 YPCGICHKEVHDND--QAILCE-SGCNFWYHR 69 (69)
Q Consensus 41 ypCG~C~~eV~D~d--dAI~CE-~~C~~WFHR 69 (69)
-.|+||...+.+++ -.+.|+ ..|..=||+
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~ 34 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHL 34 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT----B-S
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccCCHHHH
Confidence 46999999988544 358897 469988885
No 19
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=73.50 E-value=2.1 Score=24.45 Aligned_cols=24 Identities=29% Similarity=0.793 Sum_probs=19.7
Q ss_pred ccccccccccc--------CCceEEecccccce
Q psy1385 42 PCGICHKEVHD--------NDQAILCESGCNFW 66 (69)
Q Consensus 42 pCG~C~~eV~D--------~ddAI~CE~~C~~W 66 (69)
.|+-|+..|.. .++-+.|+. |+++
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~-CgRi 55 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPN-CGRI 55 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcC-CCcc
Confidence 79999987765 478899999 9876
No 20
>PF02085 Cytochrom_CIII: Class III cytochrome C family; InterPro: IPR020942 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes []. Ambler [] recognised four classes of cytC. Class III comprises the low redox potential multiple haem cytochromes: cyt C7 (trihaem), C3 (tetrahaem), and high-molecular-weight cytC, HMC (hexadecahaem), with only 30-40 residues per haem group. The haem c groups, all bis-histidinyl coordinated, are structurally and functionally nonequivalent and present different redox potentials in the range 0 to -400 mV []. The 3D structures of a number of cyt C3 proteins have been determined. The proteins consist of 4-5 alpha-helices and 2 beta-strands wrapped around a compact core of four non-parallel haems, which present a relatively high degree of exposure to the solvent. The overall protein architecture, haem plane orientations and iron-iron distances are highly conserved [].; GO: 0009055 electron carrier activity, 0020037 heme binding; PDB: 1AQE_A 1CZJ_A 1H29_B 1GWS_A 2CVC_A 2KMY_A 1DUW_A 1UPD_A 1I77_A 1GMB_A ....
Probab=71.92 E-value=1.1 Score=27.66 Aligned_cols=39 Identities=18% Similarity=0.456 Sum_probs=30.2
Q ss_pred cCCCceeeCCCCCCCCCCccccccccccccCCceEEeccccc
Q psy1385 23 PENQAMVFNPQNPNAPPIYPCGICHKEVHDNDQAILCESGCN 64 (69)
Q Consensus 23 p~~~p~~fn~q~~~s~~~ypCG~C~~eV~D~ddAI~CE~~C~ 64 (69)
...+|+.|+-+-..+-. .|..||..+........|.. |+
T Consensus 16 ~~~~~V~F~H~~H~~~~--~C~~CHh~~~~~~~~~~C~~-CH 54 (102)
T PF02085_consen 16 NTKGPVAFSHSAHADAK--DCSTCHHKSAGGGSIESCMS-CH 54 (102)
T ss_dssp SSSSEEEEEHHHGTTST--GGGGTSTTCTTTSSSSSCTC-SS
T ss_pred cCCCCcccChHHHcCCC--ChhhCCCCCcCCCCcchHHH-hc
Confidence 37889999988777443 99999999666667777777 75
No 21
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=66.22 E-value=2.9 Score=24.98 Aligned_cols=26 Identities=31% Similarity=0.656 Sum_probs=20.8
Q ss_pred CCCcccccccccccc--CCceEEeccccc
Q psy1385 38 PPIYPCGICHKEVHD--NDQAILCESGCN 64 (69)
Q Consensus 38 ~~~ypCG~C~~eV~D--~ddAI~CE~~C~ 64 (69)
.-.|-|..|+++|.+ ..+.|.|.- |.
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~-Cg 31 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPY-CG 31 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCC-CC
Confidence 347999999999963 478999986 64
No 22
>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=64.53 E-value=5.4 Score=28.42 Aligned_cols=23 Identities=35% Similarity=1.143 Sum_probs=15.1
Q ss_pred cccccccccccCCceEEeccccccee
Q psy1385 42 PCGICHKEVHDNDQAILCESGCNFWY 67 (69)
Q Consensus 42 pCG~C~~eV~D~ddAI~CE~~C~~WF 67 (69)
.|-+|+ ++|-.-.+.|.. |++||
T Consensus 2 aC~YCG--~~~p~~vv~C~~-c~kWF 24 (152)
T PF09416_consen 2 ACAYCG--IHDPSCVVKCNT-CNKWF 24 (152)
T ss_dssp S-TTT------CCCEEEETT-TTEEE
T ss_pred CccccC--CCCcccEeEcCC-CCcEe
Confidence 466776 456668899998 99999
No 23
>TIGR01566 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich dimerization domain. This model describes a 54-residue domain found in the N-terminal region of plant proteins, the vast majority of which contain a ZF-HD class homeobox domain toward the C-terminus. The region between the two domains typically is rich in low complexity sequence. The companion ZF-HD homeobox domain is described in model TIGR01565.
Probab=64.42 E-value=3.9 Score=25.22 Aligned_cols=17 Identities=29% Similarity=0.915 Sum_probs=14.2
Q ss_pred CCceEEecc-cccceeeC
Q psy1385 53 NDQAILCES-GCNFWYHR 69 (69)
Q Consensus 53 ~ddAI~CE~-~C~~WFHR 69 (69)
+-+|+.|.+ +|++=|||
T Consensus 33 ~~~al~CaACgCHRnFHR 50 (53)
T TIGR01566 33 DPESLTCAACGCHRNFHR 50 (53)
T ss_pred CCcceeeeecCccccccc
Confidence 346888888 89999998
No 24
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=63.63 E-value=4.5 Score=26.71 Aligned_cols=24 Identities=33% Similarity=0.677 Sum_probs=19.1
Q ss_pred ccccccccccccCC-ceEEecccccc
Q psy1385 41 YPCGICHKEVHDND-QAILCESGCNF 65 (69)
Q Consensus 41 ypCG~C~~eV~D~d-dAI~CE~~C~~ 65 (69)
.-|..|.+-|.+++ +.-.|+. |+.
T Consensus 35 ~aC~~C~kkv~~~~~~~~~C~~-C~~ 59 (166)
T cd04476 35 PACPGCNKKVVEEGNGTYRCEK-CNK 59 (166)
T ss_pred ccccccCcccEeCCCCcEECCC-CCC
Confidence 35888999998876 8889987 764
No 25
>KOG4718|consensus
Probab=62.72 E-value=1.3 Score=33.81 Aligned_cols=30 Identities=47% Similarity=0.855 Sum_probs=25.0
Q ss_pred CCCCCccccccccccccCCceEEecccccceeeC
Q psy1385 36 NAPPIYPCGICHKEVHDNDQAILCESGCNFWYHR 69 (69)
Q Consensus 36 ~s~~~ypCG~C~~eV~D~ddAI~CE~~C~~WFHR 69 (69)
-++.++.|-+||+.|- +.|.|++ |+.=|||
T Consensus 177 y~dnlk~Cn~Ch~LvI---qg~rCg~-c~i~~h~ 206 (235)
T KOG4718|consen 177 YADNLKNCNLCHCLVI---QGIRCGS-CNIQYHR 206 (235)
T ss_pred hHHHHHHHhHhHHHhh---eeeccCc-ccchhhh
Confidence 3456889999999997 5799998 9888886
No 26
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=62.52 E-value=5.4 Score=24.13 Aligned_cols=27 Identities=22% Similarity=0.707 Sum_probs=12.8
Q ss_pred CccccccccccccCC----ceEEeccccccee
Q psy1385 40 IYPCGICHKEVHDND----QAILCESGCNFWY 67 (69)
Q Consensus 40 ~ypCG~C~~eV~D~d----dAI~CE~~C~~WF 67 (69)
..-||.|.++..-++ ....|.. |+.||
T Consensus 41 ~v~Cg~C~~~~~~~~~~c~~~~~C~~-C~~~~ 71 (71)
T PF05495_consen 41 RVICGKCRTEQPIDEYSCGADYFCPI-CGLYF 71 (71)
T ss_dssp EEEETTT--EEES-SBTT--SEEETT-TTEEE
T ss_pred CeECCCCCCccChhhhhcCCCccCcC-cCCCC
Confidence 455666666554433 1345555 66665
No 27
>KOG1973|consensus
Probab=62.26 E-value=4.3 Score=29.97 Aligned_cols=22 Identities=36% Similarity=1.007 Sum_probs=17.3
Q ss_pred ccccccccCCceEEecc-ccc-ceee
Q psy1385 45 ICHKEVHDNDQAILCES-GCN-FWYH 68 (69)
Q Consensus 45 ~C~~eV~D~ddAI~CE~-~C~-~WFH 68 (69)
+|. ...-.+-|.|+. .|. -|||
T Consensus 223 ~Cn--qvsyg~Mi~CDn~~C~~eWFH 246 (274)
T KOG1973|consen 223 ICN--QVSYGKMIGCDNPGCPIEWFH 246 (274)
T ss_pred Eec--ccccccccccCCCCCCcceEE
Confidence 566 344578999998 799 9999
No 28
>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=61.16 E-value=3.7 Score=20.56 Aligned_cols=11 Identities=27% Similarity=0.857 Sum_probs=8.4
Q ss_pred EEecccccceee
Q psy1385 57 ILCESGCNFWYH 68 (69)
Q Consensus 57 I~CE~~C~~WFH 68 (69)
..|+. |++||.
T Consensus 4 ~~C~~-C~~~~~ 14 (35)
T smart00451 4 FYCKL-CNVTFT 14 (35)
T ss_pred eEccc-cCCccC
Confidence 46888 888875
No 29
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=60.27 E-value=7.1 Score=20.35 Aligned_cols=21 Identities=19% Similarity=0.642 Sum_probs=12.7
Q ss_pred cccccccccc--cCCceEEeccc
Q psy1385 42 PCGICHKEVH--DNDQAILCESG 62 (69)
Q Consensus 42 pCG~C~~eV~--D~ddAI~CE~~ 62 (69)
.|..|+..|. +++-++.|..+
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~N~ 23 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCPNP 23 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE--C
T ss_pred CcCCCCCEeEcCCCCEeEECCCC
Confidence 3889999998 67778999753
No 30
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=59.41 E-value=6.6 Score=27.73 Aligned_cols=29 Identities=24% Similarity=0.687 Sum_probs=22.3
Q ss_pred Cccccccccc-ccc---CCceEEecccccceeeC
Q psy1385 40 IYPCGICHKE-VHD---NDQAILCESGCNFWYHR 69 (69)
Q Consensus 40 ~ypCG~C~~e-V~D---~ddAI~CE~~C~~WFHR 69 (69)
-|.|-+|+.. |-- .+.++.|+. |..=|||
T Consensus 152 GfiCe~C~~~~~IfPF~~~~~~~C~~-C~~v~H~ 184 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQIDTTVRCPK-CKSVFHK 184 (202)
T ss_pred CCCCccCCCCCCCCCCCCCCeeeCCc-Cccccch
Confidence 3789999853 322 468999999 9999996
No 31
>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers. DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p
Probab=57.46 E-value=3.3 Score=25.59 Aligned_cols=28 Identities=25% Similarity=0.669 Sum_probs=19.5
Q ss_pred ccccccccccccC-CceEEecccccceeeC
Q psy1385 41 YPCGICHKEVHDN-DQAILCESGCNFWYHR 69 (69)
Q Consensus 41 ypCG~C~~eV~D~-ddAI~CE~~C~~WFHR 69 (69)
-+|-+|+..-... =.++-|++ |...|.|
T Consensus 3 ~~C~VCg~~a~g~hyGv~sC~a-C~~FFRR 31 (78)
T cd07172 3 KICLVCSDEASGCHYGVLTCGS-CKVFFKR 31 (78)
T ss_pred CCCeecCCcCcceEECceeehh-hHHhHHH
Confidence 4588887654443 45677887 9988876
No 32
>cd07163 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=56.58 E-value=9 Score=24.29 Aligned_cols=29 Identities=21% Similarity=0.651 Sum_probs=21.3
Q ss_pred CccccccccccccC-CceEEecccccceeeC
Q psy1385 40 IYPCGICHKEVHDN-DQAILCESGCNFWYHR 69 (69)
Q Consensus 40 ~ypCG~C~~eV~D~-ddAI~CE~~C~~WFHR 69 (69)
.-+|-+|+..-+.. =.++-|++ |...|.|
T Consensus 6 ~~~C~VCg~~a~g~hyGv~sC~a-Ck~FFRR 35 (92)
T cd07163 6 DIPCKVCGDRSSGKHYGIYACDG-CSGFFKR 35 (92)
T ss_pred CCCCcccCCcCcccEECceeeee-eeeEEee
Confidence 45788998755553 45677888 9999987
No 33
>cd07157 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers. The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=55.82 E-value=6.8 Score=24.57 Aligned_cols=27 Identities=26% Similarity=0.753 Sum_probs=18.8
Q ss_pred cccccccccccC-CceEEecccccceeeC
Q psy1385 42 PCGICHKEVHDN-DQAILCESGCNFWYHR 69 (69)
Q Consensus 42 pCG~C~~eV~D~-ddAI~CE~~C~~WFHR 69 (69)
+|-+|+..-... =.++.|++ |...|.|
T Consensus 2 ~C~VCg~~a~g~hyGv~sC~a-Ck~FFRR 29 (86)
T cd07157 2 TCQVCGEPAAGFHHGAYVCEA-CKKFFMR 29 (86)
T ss_pred CCcccCCcCcccEECcceeeE-eeeEEec
Confidence 477787654442 35677888 9999987
No 34
>cd06967 NR_DBD_TR2_like DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. It has been shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or
Probab=53.83 E-value=8.2 Score=24.24 Aligned_cols=28 Identities=25% Similarity=0.650 Sum_probs=19.7
Q ss_pred ccccccccccccC-CceEEecccccceeeC
Q psy1385 41 YPCGICHKEVHDN-DQAILCESGCNFWYHR 69 (69)
Q Consensus 41 ypCG~C~~eV~D~-ddAI~CE~~C~~WFHR 69 (69)
-+|-+|+..-..- -.++.|++ |...|.|
T Consensus 4 ~~C~VCg~~~~g~hyGv~sC~a-C~~FFRR 32 (87)
T cd06967 4 ELCVVCGDKASGRHYGAVSCEG-CKGFFKR 32 (87)
T ss_pred CCCeecCCcCCcCEeCcceEee-eeeEeee
Confidence 3588887644443 45667887 9999987
No 35
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=53.52 E-value=2.6 Score=26.41 Aligned_cols=30 Identities=33% Similarity=0.740 Sum_probs=20.3
Q ss_pred CCccccccccccccC-CceEEecccccceeeC
Q psy1385 39 PIYPCGICHKEVHDN-DQAILCESGCNFWYHR 69 (69)
Q Consensus 39 ~~ypCG~C~~eV~D~-ddAI~CE~~C~~WFHR 69 (69)
+.-+|-+|+..-... =.++-|++ |...|.|
T Consensus 2 ~~~~C~VCg~~a~g~hyGv~sC~a-Ck~FFRR 32 (82)
T cd07173 2 PQKTCLICGDEASGCHYGALTCGS-CKVFFKR 32 (82)
T ss_pred CCCCCeecCCcCcceEECcchhhh-HHHHHHH
Confidence 344688898655553 45666777 9888875
No 36
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=52.00 E-value=14 Score=25.66 Aligned_cols=30 Identities=33% Similarity=0.855 Sum_probs=22.0
Q ss_pred CCCccccccccc--cccCCc--eEEecccccceeeC
Q psy1385 38 PPIYPCGICHKE--VHDNDQ--AILCESGCNFWYHR 69 (69)
Q Consensus 38 ~~~ypCG~C~~e--V~D~dd--AI~CE~~C~~WFHR 69 (69)
.|.|||..|..- |.|.+- .--|-- | .|.||
T Consensus 40 CPfYpc~~~~~gewi~~~~G~~VwSC~d-C-~~iH~ 73 (112)
T COG2158 40 CPFYPCENEELGEWISDSNGRKVWSCSD-C-HWIHR 73 (112)
T ss_pred cccccccccccCceeEcCCCCEEeeccc-c-ceecc
Confidence 578999999776 777655 666766 6 48886
No 37
>KOG0957|consensus
Probab=51.26 E-value=4.5 Score=34.87 Aligned_cols=28 Identities=39% Similarity=1.005 Sum_probs=23.6
Q ss_pred CCccccccccccccCCceEEecccccceee
Q psy1385 39 PIYPCGICHKEVHDNDQAILCESGCNFWYH 68 (69)
Q Consensus 39 ~~ypCG~C~~eV~D~ddAI~CE~~C~~WFH 68 (69)
..|.||||.+. +|-+--++|.. |+.-||
T Consensus 543 ~~ysCgiCkks-~dQHll~~CDt-C~lhYH 570 (707)
T KOG0957|consen 543 MNYSCGICKKS-TDQHLLTQCDT-CHLHYH 570 (707)
T ss_pred cceeeeeeccc-hhhHHHhhcch-hhceee
Confidence 47999999774 56677889999 999998
No 38
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=50.59 E-value=12 Score=26.31 Aligned_cols=25 Identities=20% Similarity=0.652 Sum_probs=21.0
Q ss_pred CccccccccccccCCceEEecccccc
Q psy1385 40 IYPCGICHKEVHDNDQAILCESGCNF 65 (69)
Q Consensus 40 ~ypCG~C~~eV~D~ddAI~CE~~C~~ 65 (69)
+|.|.+|++...-++....|+. .+.
T Consensus 2 ~~~CP~C~~~l~~~~~~~~C~~-~h~ 26 (272)
T PRK11088 2 SYQCPLCHQPLTLEENSWICPQ-NHQ 26 (272)
T ss_pred cccCCCCCcchhcCCCEEEcCC-CCC
Confidence 4889999999987888999998 443
No 39
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=50.11 E-value=7.3 Score=19.58 Aligned_cols=18 Identities=28% Similarity=0.639 Sum_probs=13.0
Q ss_pred cccccccccccCCceEEecc
Q psy1385 42 PCGICHKEVHDNDQAILCES 61 (69)
Q Consensus 42 pCG~C~~eV~D~ddAI~CE~ 61 (69)
.|..|++++.+ ++-+|..
T Consensus 4 ~Cp~Cg~~~~~--~~~fC~~ 21 (26)
T PF13248_consen 4 FCPNCGAEIDP--DAKFCPN 21 (26)
T ss_pred CCcccCCcCCc--ccccChh
Confidence 58899996654 6667765
No 40
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=49.54 E-value=7.4 Score=17.22 Aligned_cols=12 Identities=33% Similarity=0.930 Sum_probs=7.3
Q ss_pred cccccccccccc
Q psy1385 41 YPCGICHKEVHD 52 (69)
Q Consensus 41 ypCG~C~~eV~D 52 (69)
|.|.+|.+...+
T Consensus 1 ~~C~~C~~~~~~ 12 (24)
T PF13894_consen 1 FQCPICGKSFRS 12 (24)
T ss_dssp EE-SSTS-EESS
T ss_pred CCCcCCCCcCCc
Confidence 678888877655
No 41
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=45.52 E-value=11 Score=20.55 Aligned_cols=15 Identities=27% Similarity=0.864 Sum_probs=7.6
Q ss_pred CceEEecccccceeeC
Q psy1385 54 DQAILCESGCNFWYHR 69 (69)
Q Consensus 54 ddAI~CE~~C~~WFHR 69 (69)
++-|.|.. |+..+|+
T Consensus 2 n~ll~C~~-C~v~VH~ 16 (36)
T PF13831_consen 2 NPLLFCDN-CNVAVHQ 16 (36)
T ss_dssp CEEEE-SS-S--EEEH
T ss_pred CceEEeCC-CCCcCCh
Confidence 35567765 7777774
No 42
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=45.20 E-value=28 Score=18.70 Aligned_cols=15 Identities=27% Similarity=0.640 Sum_probs=9.1
Q ss_pred ccccccccccCCceE
Q psy1385 43 CGICHKEVHDNDQAI 57 (69)
Q Consensus 43 CG~C~~eV~D~ddAI 57 (69)
|..|++.|.+++..|
T Consensus 1 C~~C~~~I~~~~~~~ 15 (58)
T PF00412_consen 1 CARCGKPIYGTEIVI 15 (58)
T ss_dssp BTTTSSBESSSSEEE
T ss_pred CCCCCCCccCcEEEE
Confidence 566777777655443
No 43
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=44.68 E-value=19 Score=21.16 Aligned_cols=16 Identities=19% Similarity=0.524 Sum_probs=13.0
Q ss_pred ccCCceEEeccccccee
Q psy1385 51 HDNDQAILCESGCNFWY 67 (69)
Q Consensus 51 ~D~ddAI~CE~~C~~WF 67 (69)
+-.+..+.|.. |++||
T Consensus 48 ~i~eg~L~Cp~-c~r~Y 63 (68)
T PF03966_consen 48 EIVEGELICPE-CGREY 63 (68)
T ss_dssp ETTTTEEEETT-TTEEE
T ss_pred cccCCEEEcCC-CCCEE
Confidence 34578899988 99998
No 44
>cd06965 NR_DBD_Ppar DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive gene
Probab=43.80 E-value=7 Score=24.33 Aligned_cols=27 Identities=22% Similarity=0.634 Sum_probs=15.8
Q ss_pred cccccccccccC-CceEEecccccceeeC
Q psy1385 42 PCGICHKEVHDN-DQAILCESGCNFWYHR 69 (69)
Q Consensus 42 pCG~C~~eV~D~-ddAI~CE~~C~~WFHR 69 (69)
+|-+|+..-+.. -.++.|++ |...|.|
T Consensus 1 ~C~VCg~~~~g~hyGv~sC~a-Ck~FFRR 28 (84)
T cd06965 1 ECRVCGDKASGFHYGVHACEG-CKGFFRR 28 (84)
T ss_pred CCcccCccCcceEEChhhhhh-hhhheee
Confidence 356665433332 34566776 8887765
No 45
>KOG2752|consensus
Probab=43.02 E-value=11 Score=30.22 Aligned_cols=41 Identities=22% Similarity=0.472 Sum_probs=32.2
Q ss_pred CCceeeCCCCCCCCCCcccccccccccc-----CCceEEecccccceee
Q psy1385 25 NQAMVFNPQNPNAPPIYPCGICHKEVHD-----NDQAILCESGCNFWYH 68 (69)
Q Consensus 25 ~~p~~fn~q~~~s~~~ypCG~C~~eV~D-----~ddAI~CE~~C~~WFH 68 (69)
+++-+.|.-|.+..+.|. +|.....| +..-++|.. |--|||
T Consensus 114 ~~~n~~N~YNhNfqG~~C--~Cd~~Ypdp~~~~e~~m~QC~i-CEDWFH 159 (345)
T KOG2752|consen 114 DAENSENLYNHNFQGLFC--KCDTPYPDPVRTEEGEMLQCVI-CEDWFH 159 (345)
T ss_pred ccccchhhhhhhhcceeE--EecCCCCCccccccceeeeEEe-ccchhc
Confidence 455677788888888884 89988888 345678888 888999
No 46
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=43.02 E-value=18 Score=23.56 Aligned_cols=29 Identities=21% Similarity=0.595 Sum_probs=20.9
Q ss_pred CccccccccccccC-CceEEecccccceeeC
Q psy1385 40 IYPCGICHKEVHDN-DQAILCESGCNFWYHR 69 (69)
Q Consensus 40 ~ypCG~C~~eV~D~-ddAI~CE~~C~~WFHR 69 (69)
.-+|-+|+..-..- =.++.|++ |...|.|
T Consensus 18 ~~~C~VCg~~a~g~hyGv~sC~a-Ck~FFRR 47 (101)
T cd07160 18 NEVCSVCGDKASGFHYNVLSCEG-CKGFFRR 47 (101)
T ss_pred CCCCeecCCcCcceEECcceehh-hhhhhhh
Confidence 44699998755543 35667887 9999987
No 47
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=42.96 E-value=19 Score=22.86 Aligned_cols=25 Identities=28% Similarity=0.624 Sum_probs=14.5
Q ss_pred cccccccccccCCceEEeccccccee
Q psy1385 42 PCGICHKEVHDNDQAILCESGCNFWY 67 (69)
Q Consensus 42 pCG~C~~eV~D~ddAI~CE~~C~~WF 67 (69)
.|..|+.++.-+.....|+. |+.=|
T Consensus 3 ~CP~C~~~L~~~~~~~~C~~-C~~~~ 27 (70)
T PF07191_consen 3 TCPKCQQELEWQGGHYHCEA-CQKDY 27 (70)
T ss_dssp B-SSS-SBEEEETTEEEETT-T--EE
T ss_pred cCCCCCCccEEeCCEEECcc-ccccc
Confidence 47777777666667777777 76544
No 48
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=42.20 E-value=10 Score=21.55 Aligned_cols=24 Identities=33% Similarity=0.786 Sum_probs=13.1
Q ss_pred ccccccccccCCceEEeccccc-----ceeeC
Q psy1385 43 CGICHKEVHDNDQAILCESGCN-----FWYHR 69 (69)
Q Consensus 43 CG~C~~eV~D~ddAI~CE~~C~-----~WFHR 69 (69)
|-||.. ..++++.+ ...|. .|+|+
T Consensus 2 CrIC~~-~~~~~~~l--~~PC~C~G~~~~vH~ 30 (49)
T smart00744 2 CRICHD-EGDEGDPL--VSPCRCKGSLKYVHQ 30 (49)
T ss_pred ccCCCC-CCCCCCee--EeccccCCchhHHHH
Confidence 778877 22233333 34453 78884
No 49
>TIGR00201 comF comF family protein. This protein is found in species that do (Bacillus subtilis, Haemophilus influenzae) or do not (E. coli, Borrelia burgdorferi) have described systems for natural transformation with exogenous DNA. It is involved in competence for transformation in Bacillus subtilis.
Probab=41.59 E-value=11 Score=25.55 Aligned_cols=22 Identities=27% Similarity=0.930 Sum_probs=13.4
Q ss_pred ccccccccccCCceEEeccccccee
Q psy1385 43 CGICHKEVHDNDQAILCESGCNFWY 67 (69)
Q Consensus 43 CG~C~~eV~D~ddAI~CE~~C~~WF 67 (69)
|..|++++... ..+|+. |..|+
T Consensus 1 C~~C~~~~~~~--~~~C~~-C~~~~ 22 (190)
T TIGR00201 1 CSLCGRPYQSV--HALCRQ-CGSWR 22 (190)
T ss_pred CCccccccccc--cCCchh-hCCcc
Confidence 66677766542 356777 76653
No 50
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=41.17 E-value=28 Score=20.50 Aligned_cols=26 Identities=35% Similarity=0.835 Sum_probs=21.5
Q ss_pred CccccccccccccCCceEEecc-cccceee
Q psy1385 40 IYPCGICHKEVHDNDQAILCES-GCNFWYH 68 (69)
Q Consensus 40 ~ypCG~C~~eV~D~ddAI~CE~-~C~~WFH 68 (69)
...|-+|.+. .--.|.|.. +|...||
T Consensus 36 ~~~C~~C~~~---~Ga~i~C~~~~C~~~fH 62 (90)
T PF13771_consen 36 KLKCSICKKK---GGACIGCSHPGCSRSFH 62 (90)
T ss_pred CCCCcCCCCC---CCeEEEEeCCCCCcEEC
Confidence 4689999866 357899987 8999999
No 51
>KOG4216|consensus
Probab=40.96 E-value=10 Score=31.61 Aligned_cols=30 Identities=33% Similarity=0.759 Sum_probs=21.8
Q ss_pred CCccccccccccccC-CceEEecccccceeeC
Q psy1385 39 PIYPCGICHKEVHDN-DQAILCESGCNFWYHR 69 (69)
Q Consensus 39 ~~ypCG~C~~eV~D~-ddAI~CE~~C~~WFHR 69 (69)
.+.||-+|+---.-- =-.|-||+ |.-+|-|
T Consensus 45 EvIPCKiCGDKSSGiHYGVITCEG-CKGFFRR 75 (479)
T KOG4216|consen 45 EIIPCKICGDKSSGIHYGVITCEG-CKGFFRR 75 (479)
T ss_pred EEEeeeeccCCCCcceeeeEeecc-chHhhhh
Confidence 478999997432221 26799999 9999876
No 52
>cd06960 NR_DBD_HNF4A DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is
Probab=40.94 E-value=15 Score=22.13 Aligned_cols=14 Identities=21% Similarity=0.802 Sum_probs=9.7
Q ss_pred ceEEecccccceeeC
Q psy1385 55 QAILCESGCNFWYHR 69 (69)
Q Consensus 55 dAI~CE~~C~~WFHR 69 (69)
.++.|++ |...|.|
T Consensus 14 gv~~C~a-C~~FFrR 27 (76)
T cd06960 14 GVLSCNG-CKGFFRR 27 (76)
T ss_pred Ccceeee-ehheeCc
Confidence 4566777 8887766
No 53
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=40.78 E-value=13 Score=19.21 Aligned_cols=21 Identities=33% Similarity=0.887 Sum_probs=16.1
Q ss_pred cccccccccccCCceEEecccccc
Q psy1385 42 PCGICHKEVHDNDQAILCESGCNF 65 (69)
Q Consensus 42 pCG~C~~eV~D~ddAI~CE~~C~~ 65 (69)
.|..|.++|.. .+..|.. |..
T Consensus 2 ~CP~C~~~V~~--~~~~Cp~-CG~ 22 (26)
T PF10571_consen 2 TCPECGAEVPE--SAKFCPH-CGY 22 (26)
T ss_pred cCCCCcCCchh--hcCcCCC-CCC
Confidence 48899999966 7778876 654
No 54
>PRK12411 cytidine deaminase; Provisional
Probab=39.83 E-value=8.6 Score=25.83 Aligned_cols=15 Identities=33% Similarity=1.012 Sum_probs=12.5
Q ss_pred CCCcccccccccccc
Q psy1385 38 PPIYPCGICHKEVHD 52 (69)
Q Consensus 38 ~~~ypCG~C~~eV~D 52 (69)
....|||.|.+-+.+
T Consensus 81 ~~~sPCG~CRQ~l~E 95 (132)
T PRK12411 81 RPVPPCGACRQVMVE 95 (132)
T ss_pred CCcCCchhHHHHHHH
Confidence 457899999998877
No 55
>KOG1244|consensus
Probab=39.49 E-value=20 Score=28.76 Aligned_cols=25 Identities=40% Similarity=0.975 Sum_probs=20.3
Q ss_pred cccccccccccCCceEEecccccceee
Q psy1385 42 PCGICHKEVHDNDQAILCESGCNFWYH 68 (69)
Q Consensus 42 pCG~C~~eV~D~ddAI~CE~~C~~WFH 68 (69)
.|-||+..-+| ||-++|.- |++=||
T Consensus 283 ~csicgtsend-dqllfcdd-cdrgyh 307 (336)
T KOG1244|consen 283 YCSICGTSEND-DQLLFCDD-CDRGYH 307 (336)
T ss_pred eeccccCcCCC-ceeEeecc-cCCcee
Confidence 47788876555 78899999 999988
No 56
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=39.21 E-value=25 Score=19.70 Aligned_cols=26 Identities=19% Similarity=0.516 Sum_probs=17.2
Q ss_pred CCcccccccccccc---C-----C--ceEEecccccc
Q psy1385 39 PIYPCGICHKEVHD---N-----D--QAILCESGCNF 65 (69)
Q Consensus 39 ~~ypCG~C~~eV~D---~-----d--dAI~CE~~C~~ 65 (69)
.+.||..|+....- + + -.|.|.. |..
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~-Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTD-CGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCC-CCC
Confidence 46889999854332 1 1 4688988 865
No 57
>cd06970 NR_DBD_PNR DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of the nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hing
Probab=38.92 E-value=17 Score=23.14 Aligned_cols=31 Identities=19% Similarity=0.551 Sum_probs=22.0
Q ss_pred CCCccccccccccccC-CceEEecccccceeeC
Q psy1385 38 PPIYPCGICHKEVHDN-DQAILCESGCNFWYHR 69 (69)
Q Consensus 38 ~~~ypCG~C~~eV~D~-ddAI~CE~~C~~WFHR 69 (69)
++.-+|-+|+..-+.. -.++-|++ |...|.|
T Consensus 4 ~p~~~C~VCg~~a~g~hyGv~sC~a-Ck~FFRR 35 (92)
T cd06970 4 NPGLLCRVCGDTSSGKHYGIYACNG-CSGFFKR 35 (92)
T ss_pred CCCCCCeecCCcCcccEECccEEee-eeeEeee
Confidence 3444699998765554 34666887 9999987
No 58
>KOG1632|consensus
Probab=38.55 E-value=2.6 Score=32.52 Aligned_cols=28 Identities=25% Similarity=0.705 Sum_probs=23.6
Q ss_pred CccccccccccccCCceEEecccccceee
Q psy1385 40 IYPCGICHKEVHDNDQAILCESGCNFWYH 68 (69)
Q Consensus 40 ~ypCG~C~~eV~D~ddAI~CE~~C~~WFH 68 (69)
-+.|+.|+....-+...|.|.. |..|||
T Consensus 239 ~~~~~~cg~~~~~~~~~~~~~~-~e~w~~ 266 (345)
T KOG1632|consen 239 KLICDPCGLSDANKKFEICCDL-CESWFH 266 (345)
T ss_pred cccccccCcchHHHHHHHHHHH-HHHHhc
Confidence 4789999976555588899999 999999
No 59
>cd06963 NR_DBD_GR_like The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family of NRs includes four types of nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). The receptors bind to common DNA elements containing a partial palindrome of the core sequence 5'-TGTTCT-3' with a 3bp spacer. These four receptors regulate some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family have high sequence homology and sha
Probab=38.24 E-value=9.8 Score=23.05 Aligned_cols=26 Identities=31% Similarity=0.777 Sum_probs=14.4
Q ss_pred ccccccccccC-CceEEecccccceeeC
Q psy1385 43 CGICHKEVHDN-DQAILCESGCNFWYHR 69 (69)
Q Consensus 43 CG~C~~eV~D~-ddAI~CE~~C~~WFHR 69 (69)
|-+|+..-... -.++-|++ |...|.|
T Consensus 1 C~VCg~~a~~~hygv~sC~a-Ck~FFRR 27 (73)
T cd06963 1 CLICGDEASGCHYGVLTCGS-CKVFFKR 27 (73)
T ss_pred CcccCccCcceEECceeehh-hhHhHHH
Confidence 34454433332 34566777 8877765
No 60
>PRK08298 cytidine deaminase; Validated
Probab=37.40 E-value=9.3 Score=26.03 Aligned_cols=15 Identities=27% Similarity=0.833 Sum_probs=12.2
Q ss_pred CCccccccccccccC
Q psy1385 39 PIYPCGICHKEVHDN 53 (69)
Q Consensus 39 ~~ypCG~C~~eV~D~ 53 (69)
...|||.|.+-+.+-
T Consensus 85 ~~sPCG~CRQvl~Ef 99 (136)
T PRK08298 85 VLSPCGVCQERLFYW 99 (136)
T ss_pred ccCCChhHHHHHHHh
Confidence 478999999877764
No 61
>PF00105 zf-C4: Zinc finger, C4 type (two domains); InterPro: IPR001628 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences, connected via a linker region to a C-terminal ligand-binding domain (IPR000536 from INTERPRO). In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The DNA-binding domain can elicit either an activating or repressing effect by binding to specific regions of the DNA known as hormone-response elements [, ]. These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension, where residues in the first zinc module determine the specificity of the DNA recognition and residues in the second zinc module are involved in dimerisation. The DNA-binding domain is furthermore involved in several other functions including nuclear localisation, and interaction with transcription factors and co-activators []. 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 two C4-type zinc finger modules involved in DNA-binding. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1DSZ_A 1LO1_A 3M9E_F 2EBL_A 1GA5_B 1A6Y_B 1HLZ_B 1HRA_A 1KB6_B 1KB4_B ....
Probab=37.35 E-value=6.7 Score=22.90 Aligned_cols=27 Identities=19% Similarity=0.773 Sum_probs=18.2
Q ss_pred ccccccccccc-CCceEEecccccceeeC
Q psy1385 42 PCGICHKEVHD-NDQAILCESGCNFWYHR 69 (69)
Q Consensus 42 pCG~C~~eV~D-~ddAI~CE~~C~~WFHR 69 (69)
.|-+|...-.. .-.++-|++ |..+|-|
T Consensus 2 ~C~VCg~~~~~~~ygv~sC~~-C~~FFrR 29 (70)
T PF00105_consen 2 KCKVCGDPASGYHYGVLSCNA-CKMFFRR 29 (70)
T ss_dssp BSTTTSSBESEEETTEEEEHH-HHHHHHH
T ss_pred CCeECCCccCccccccccccc-ceeeeee
Confidence 47788765443 346677887 8888754
No 62
>cd06968 NR_DBD_ROR DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RORS are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum particularly in the regulation of the maturation and survival of Purkinje cells. RORbe
Probab=37.20 E-value=10 Score=24.28 Aligned_cols=28 Identities=32% Similarity=0.771 Sum_probs=19.1
Q ss_pred ccccccccccccC-CceEEecccccceeeC
Q psy1385 41 YPCGICHKEVHDN-DQAILCESGCNFWYHR 69 (69)
Q Consensus 41 ypCG~C~~eV~D~-ddAI~CE~~C~~WFHR 69 (69)
-+|-+|+..-..- -.++.|++ |...|.|
T Consensus 6 ~~C~VCg~~~~g~hyGv~sC~a-C~~FFRR 34 (95)
T cd06968 6 IPCKICGDKSSGIHYGVITCEG-CKGFFRR 34 (95)
T ss_pred cCCcccCCcCcceEECceeehh-hHHhhHH
Confidence 4788887644332 34667887 9888876
No 63
>PRK06848 hypothetical protein; Validated
Probab=36.07 E-value=11 Score=25.62 Aligned_cols=16 Identities=31% Similarity=0.750 Sum_probs=13.0
Q ss_pred CCCccccccccccccC
Q psy1385 38 PPIYPCGICHKEVHDN 53 (69)
Q Consensus 38 ~~~ypCG~C~~eV~D~ 53 (69)
....|||.|.+-+.+-
T Consensus 92 ~~~~PCG~CRQvl~E~ 107 (139)
T PRK06848 92 WVVSPCGACRELISDY 107 (139)
T ss_pred CccCCChhhHHHHHHh
Confidence 4688999999888763
No 64
>PHA00733 hypothetical protein
Probab=35.73 E-value=35 Score=22.67 Aligned_cols=33 Identities=18% Similarity=0.525 Sum_probs=23.0
Q ss_pred CCCCCccccccccccccC----------CceEEecccccceeeC
Q psy1385 36 NAPPIYPCGICHKEVHDN----------DQAILCESGCNFWYHR 69 (69)
Q Consensus 36 ~s~~~ypCG~C~~eV~D~----------ddAI~CE~~C~~WFHR 69 (69)
.+...|.|..|.+..... .....|+. |.+||-+
T Consensus 69 ~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~-CgK~F~~ 111 (128)
T PHA00733 69 KAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPV-CGKEFRN 111 (128)
T ss_pred CCCCCccCCCCCCcCCCHHHHHHHHhcCCcCccCCC-CCCccCC
Confidence 345579999999875541 23458888 9999853
No 65
>PRK12366 replication factor A; Reviewed
Probab=35.06 E-value=22 Score=29.28 Aligned_cols=24 Identities=38% Similarity=0.815 Sum_probs=20.2
Q ss_pred ccccccccccccCCceEEecccccc
Q psy1385 41 YPCGICHKEVHDNDQAILCESGCNF 65 (69)
Q Consensus 41 ypCG~C~~eV~D~ddAI~CE~~C~~ 65 (69)
.-|..|.+-|.+++..-.||. |+.
T Consensus 533 ~aCp~CnkKv~~~~g~~~C~~-c~~ 556 (637)
T PRK12366 533 YLCPNCRKRVEEVDGEYICEF-CGE 556 (637)
T ss_pred ecccccCeEeEcCCCcEECCC-CCC
Confidence 468899999998778889999 864
No 66
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=34.81 E-value=25 Score=22.77 Aligned_cols=23 Identities=43% Similarity=0.925 Sum_probs=14.1
Q ss_pred ccc--ccccccccC-CceEEecccccc
Q psy1385 42 PCG--ICHKEVHDN-DQAILCESGCNF 65 (69)
Q Consensus 42 pCG--~C~~eV~D~-ddAI~CE~~C~~ 65 (69)
-|. .|.+-|..+ +..-.|+. |+.
T Consensus 20 aC~~~~C~kKv~~~~~~~y~C~~-C~~ 45 (146)
T PF08646_consen 20 ACPNEKCNKKVTENGDGSYRCEK-CNK 45 (146)
T ss_dssp E-TSTTTS-B-EEETTTEEEETT-TTE
T ss_pred CCCCccCCCEeecCCCcEEECCC-CCC
Confidence 366 788887776 45778877 764
No 67
>cd06956 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor, or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear rec
Probab=34.64 E-value=8.2 Score=23.56 Aligned_cols=27 Identities=26% Similarity=0.683 Sum_probs=17.2
Q ss_pred cccccccccccC-CceEEecccccceeeC
Q psy1385 42 PCGICHKEVHDN-DQAILCESGCNFWYHR 69 (69)
Q Consensus 42 pCG~C~~eV~D~-ddAI~CE~~C~~WFHR 69 (69)
+|-+|+..-..- -.++-|++ |...|.|
T Consensus 2 ~C~VC~~~~~g~hygv~sC~a-C~~FFRR 29 (77)
T cd06956 2 ICAICGDRASGKHYGVYSCEG-CKGFFKR 29 (77)
T ss_pred CCcccCCcCcceEECceeehh-HHHHHHH
Confidence 477777544443 34566777 8887765
No 68
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=34.50 E-value=32 Score=24.01 Aligned_cols=28 Identities=29% Similarity=0.675 Sum_probs=21.2
Q ss_pred CCCCCccccccccccccCCceEEecccccce
Q psy1385 36 NAPPIYPCGICHKEVHDNDQAILCESGCNFW 66 (69)
Q Consensus 36 ~s~~~ypCG~C~~eV~D~ddAI~CE~~C~~W 66 (69)
...+.|-|..|+.-... =.-.|+. |..|
T Consensus 350 ~~~p~~~c~~cg~~~~~--~~~~c~~-c~~~ 377 (389)
T PRK11788 350 KRKPRYRCRNCGFTART--LYWHCPS-CKAW 377 (389)
T ss_pred hCCCCEECCCCCCCCcc--ceeECcC-CCCc
Confidence 45567889999876655 5567888 9988
No 69
>cd06959 NR_DBD_EcR_like The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: Ecdysone receptor (EcR), Liver X receptor (LXR) and Farnesoid X receptor (FXR). The DNA binding activity is regulated by their corresponding ligands. The ligands for EcR are ecdysteroids; LXR is regulated by oxidized cholesterol derivatives or oxysterols; and bile acids control FXR's activities. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcR-like receptors have a central well conserved DNA binding domai
Probab=34.24 E-value=11 Score=22.73 Aligned_cols=26 Identities=23% Similarity=0.687 Sum_probs=15.3
Q ss_pred ccccccccccC-CceEEecccccceeeC
Q psy1385 43 CGICHKEVHDN-DQAILCESGCNFWYHR 69 (69)
Q Consensus 43 CG~C~~eV~D~-ddAI~CE~~C~~WFHR 69 (69)
|-+|+..-... -.++.|++ |...|.|
T Consensus 2 C~vCg~~~~~~hygv~sC~a-C~~FFRR 28 (73)
T cd06959 2 CVVCGDKASGFHYGVLSCEG-CKGFFRR 28 (73)
T ss_pred CceeCCcCcceEECceeehh-hHHHHHH
Confidence 55565443332 34566777 8888765
No 70
>cd07169 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=34.08 E-value=9.9 Score=24.07 Aligned_cols=29 Identities=28% Similarity=0.567 Sum_probs=19.6
Q ss_pred CccccccccccccC-CceEEecccccceeeC
Q psy1385 40 IYPCGICHKEVHDN-DQAILCESGCNFWYHR 69 (69)
Q Consensus 40 ~ypCG~C~~eV~D~-ddAI~CE~~C~~WFHR 69 (69)
.-+|-+|...-... =.++.|++ |...|.|
T Consensus 6 ~~~C~VCg~~a~g~hyGv~sC~a-Ck~FFRR 35 (90)
T cd07169 6 QRTCLICGDRATGLHYGIISCEG-CKGFFKR 35 (90)
T ss_pred CCCCeecCCcCcceEECcceehh-hHHHHHH
Confidence 34588887654443 45677887 9888876
No 71
>KOG2593|consensus
Probab=33.34 E-value=31 Score=28.49 Aligned_cols=33 Identities=21% Similarity=0.465 Sum_probs=25.1
Q ss_pred CCCCCCCCCcccccccccccc---------CCceEEecccccc
Q psy1385 32 PQNPNAPPIYPCGICHKEVHD---------NDQAILCESGCNF 65 (69)
Q Consensus 32 ~q~~~s~~~ypCG~C~~eV~D---------~ddAI~CE~~C~~ 65 (69)
.++......|-|++|.+...+ .+....|+- |+.
T Consensus 120 ~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~-C~g 161 (436)
T KOG2593|consen 120 LRDDTNVAGYVCPNCQKKYTSLEALQLLDNETGEFHCEN-CGG 161 (436)
T ss_pred hhhccccccccCCccccchhhhHHHHhhcccCceEEEec-CCC
Confidence 355667788999999998655 367888988 863
No 72
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=32.64 E-value=39 Score=20.23 Aligned_cols=27 Identities=26% Similarity=0.671 Sum_probs=18.7
Q ss_pred ccccccccccC--------CceEEecccccceeeC
Q psy1385 43 CGICHKEVHDN--------DQAILCESGCNFWYHR 69 (69)
Q Consensus 43 CG~C~~eV~D~--------ddAI~CE~~C~~WFHR 69 (69)
|+||.+++.|. ++...--+.|+=-||+
T Consensus 22 C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~ 56 (73)
T PF12678_consen 22 CAICREPLEDPCPECQAPQDECPIVWGPCGHIFHF 56 (73)
T ss_dssp ETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEH
T ss_pred ccccChhhhChhhhhcCCccccceEecccCCCEEH
Confidence 99999999663 2344444568888884
No 73
>cd07156 NR_DBD_VDR_like The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemi
Probab=32.48 E-value=17 Score=21.76 Aligned_cols=14 Identities=36% Similarity=0.973 Sum_probs=9.1
Q ss_pred ceEEecccccceeeC
Q psy1385 55 QAILCESGCNFWYHR 69 (69)
Q Consensus 55 dAI~CE~~C~~WFHR 69 (69)
.++-|++ |...|.|
T Consensus 14 gv~sC~a-C~~FFRR 27 (72)
T cd07156 14 NAMTCEG-CKGFFRR 27 (72)
T ss_pred Ccceehh-hhhhhch
Confidence 4555666 7777765
No 74
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=31.40 E-value=10 Score=22.66 Aligned_cols=14 Identities=29% Similarity=0.748 Sum_probs=9.0
Q ss_pred ceEEecccccceeeC
Q psy1385 55 QAILCESGCNFWYHR 69 (69)
Q Consensus 55 dAI~CE~~C~~WFHR 69 (69)
.++.|++ |...|.|
T Consensus 14 Gv~~C~a-C~~FFRR 27 (73)
T cd07158 14 GVHSCEG-CKGFFRR 27 (73)
T ss_pred CcchhhH-HHHHHhh
Confidence 4555666 7777765
No 75
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=31.39 E-value=17 Score=16.61 Aligned_cols=12 Identities=42% Similarity=0.971 Sum_probs=8.8
Q ss_pred cccccccccccc
Q psy1385 41 YPCGICHKEVHD 52 (69)
Q Consensus 41 ypCG~C~~eV~D 52 (69)
|.|.+|++...+
T Consensus 1 y~C~~C~~~f~~ 12 (23)
T PF00096_consen 1 YKCPICGKSFSS 12 (23)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCccCC
Confidence 678888876654
No 76
>smart00746 TRASH metallochaperone-like domain.
Probab=31.18 E-value=40 Score=14.90 Aligned_cols=10 Identities=30% Similarity=1.065 Sum_probs=7.0
Q ss_pred cccccccccc
Q psy1385 43 CGICHKEVHD 52 (69)
Q Consensus 43 CG~C~~eV~D 52 (69)
|..|++.|.+
T Consensus 1 c~~C~~~~~~ 10 (39)
T smart00746 1 CSFCGKDIYN 10 (39)
T ss_pred CCCCCCCccC
Confidence 6677777763
No 77
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=30.89 E-value=20 Score=21.12 Aligned_cols=26 Identities=19% Similarity=0.627 Sum_probs=13.6
Q ss_pred ccccccccccC-CceEEecccccceeeC
Q psy1385 43 CGICHKEVHDN-DQAILCESGCNFWYHR 69 (69)
Q Consensus 43 CG~C~~eV~D~-ddAI~CE~~C~~WFHR 69 (69)
|-+|+..-+.. -.++.|++ |...|.|
T Consensus 2 C~vC~~~~~~~hygv~~C~a-C~~FFRR 28 (70)
T smart00399 2 CCVCGDHASGFHFGVCSCRA-CKAFFRR 28 (70)
T ss_pred CeEeCCcCcccEeCCcEech-hhhhhhh
Confidence 44554332222 23456776 7777765
No 78
>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=30.87 E-value=19 Score=17.07 Aligned_cols=13 Identities=23% Similarity=0.629 Sum_probs=8.5
Q ss_pred Ccccccccccccc
Q psy1385 40 IYPCGICHKEVHD 52 (69)
Q Consensus 40 ~ypCG~C~~eV~D 52 (69)
+|.|..|.+...+
T Consensus 1 ~~~C~~C~~~F~~ 13 (27)
T PF13912_consen 1 PFECDECGKTFSS 13 (27)
T ss_dssp SEEETTTTEEESS
T ss_pred CCCCCccCCccCC
Confidence 3677777776554
No 79
>KOG4218|consensus
Probab=30.19 E-value=16 Score=30.29 Aligned_cols=27 Identities=30% Similarity=0.784 Sum_probs=21.6
Q ss_pred cccccccccccCCceE-EecccccceeeC
Q psy1385 42 PCGICHKEVHDNDQAI-LCESGCNFWYHR 69 (69)
Q Consensus 42 pCG~C~~eV~D~ddAI-~CE~~C~~WFHR 69 (69)
-|..|+..|.--+..+ -||+ |..+|-|
T Consensus 17 lCPVCGDkVSGYHYGLLTCES-CKGFFKR 44 (475)
T KOG4218|consen 17 LCPVCGDKVSGYHYGLLTCES-CKGFFKR 44 (475)
T ss_pred ccccccCccccceeeeeehhh-hhhHHHH
Confidence 5899999998877665 5887 9988865
No 80
>cd07162 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers. DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding
Probab=30.19 E-value=13 Score=23.24 Aligned_cols=26 Identities=27% Similarity=0.763 Sum_probs=14.8
Q ss_pred ccccccccccC-CceEEecccccceeeC
Q psy1385 43 CGICHKEVHDN-DQAILCESGCNFWYHR 69 (69)
Q Consensus 43 CG~C~~eV~D~-ddAI~CE~~C~~WFHR 69 (69)
|-+|+..-+.. -.++-|++ |...|.|
T Consensus 2 C~VCg~~~~g~hygv~sC~a-C~~FFRR 28 (87)
T cd07162 2 CRVCGDRATGYHFNAMTCEG-CKGFFRR 28 (87)
T ss_pred CcccCCcCcceEECcceehh-hHHHHHh
Confidence 55665543332 33556776 8777765
No 81
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=30.18 E-value=32 Score=22.05 Aligned_cols=32 Identities=28% Similarity=0.687 Sum_probs=7.5
Q ss_pred CCCCCCCccccccccccc-cCCceEEecccccce
Q psy1385 34 NPNAPPIYPCGICHKEVH-DNDQAILCESGCNFW 66 (69)
Q Consensus 34 ~~~s~~~ypCG~C~~eV~-D~ddAI~CE~~C~~W 66 (69)
+...+-.-.|-+|++.|. ++.+.+.|+. -|+|
T Consensus 8 ~~~~~i~E~C~~C~~~i~~~~~~~~~C~~-GH~w 40 (99)
T PF12660_consen 8 GPGLPIFEKCPICGAPIPFDDLDEAQCEN-GHVW 40 (99)
T ss_dssp ---------------------SSEEE-TT-S-EE
T ss_pred cccccccccccccccccccCCcCEeECCC-CCEE
Confidence 344445578999999997 4557788998 5776
No 82
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=30.06 E-value=41 Score=20.76 Aligned_cols=13 Identities=31% Similarity=0.664 Sum_probs=8.7
Q ss_pred CCccccccccccc
Q psy1385 39 PIYPCGICHKEVH 51 (69)
Q Consensus 39 ~~ypCG~C~~eV~ 51 (69)
..+.|..|..+..
T Consensus 15 ~~~~C~~C~~~~~ 27 (104)
T TIGR01384 15 GVYVCPSCGYEKE 27 (104)
T ss_pred CeEECcCCCCccc
Confidence 3677888885543
No 83
>KOG1829|consensus
Probab=29.83 E-value=11 Score=31.65 Aligned_cols=27 Identities=22% Similarity=0.693 Sum_probs=17.6
Q ss_pred Ccccccccccccc------CCceEEecccccceeeC
Q psy1385 40 IYPCGICHKEVHD------NDQAILCESGCNFWYHR 69 (69)
Q Consensus 40 ~ypCG~C~~eV~D------~ddAI~CE~~C~~WFHR 69 (69)
-|.|-+| ..+| .+....|+. |..|||+
T Consensus 511 gfiCe~C--q~~~iiyPF~~~~~~rC~~-C~avfH~ 543 (580)
T KOG1829|consen 511 GFICELC--QHNDIIYPFETRNTRRCST-CLAVFHK 543 (580)
T ss_pred eeeeeec--cCCCcccccccccceeHHH-HHHHHHH
Confidence 4667777 2222 355566777 9999995
No 84
>KOG0383|consensus
Probab=29.56 E-value=20 Score=30.73 Aligned_cols=22 Identities=32% Similarity=0.985 Sum_probs=15.7
Q ss_pred cccccccccccCCceEEecccccceee
Q psy1385 42 PCGICHKEVHDNDQAILCESGCNFWYH 68 (69)
Q Consensus 42 pCG~C~~eV~D~ddAI~CE~~C~~WFH 68 (69)
-|++|. |.-..|.|++ |..|||
T Consensus 49 ~c~ic~----~~g~~l~c~t-C~~s~h 70 (696)
T KOG0383|consen 49 ACRICA----DGGELLWCDT-CPASFH 70 (696)
T ss_pred hhhhhc----CCCcEEEecc-ccHHHH
Confidence 355553 4456778888 999999
No 85
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=29.53 E-value=40 Score=16.25 Aligned_cols=19 Identities=16% Similarity=0.412 Sum_probs=13.7
Q ss_pred cccccccccccCCceEEec
Q psy1385 42 PCGICHKEVHDNDQAILCE 60 (69)
Q Consensus 42 pCG~C~~eV~D~ddAI~CE 60 (69)
.|..|++.|.+++..+.-.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~ 19 (39)
T smart00132 1 KCAGCGKPIRGGELVLRAL 19 (39)
T ss_pred CccccCCcccCCcEEEEeC
Confidence 3788999998876665543
No 86
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=29.02 E-value=23 Score=26.64 Aligned_cols=23 Identities=30% Similarity=0.863 Sum_probs=18.3
Q ss_pred ccccccccccc--------CCceEEecccccc
Q psy1385 42 PCGICHKEVHD--------NDQAILCESGCNF 65 (69)
Q Consensus 42 pCG~C~~eV~D--------~ddAI~CE~~C~~ 65 (69)
-||-|+..+.+ +|+-+.|.. |.+
T Consensus 199 ~C~GC~m~l~~~~~~~V~~~d~iv~CP~-CgR 229 (239)
T COG1579 199 VCGGCHMKLPSQTLSKVRKKDEIVFCPY-CGR 229 (239)
T ss_pred cccCCeeeecHHHHHHHhcCCCCccCCc-cch
Confidence 59999987766 588889988 765
No 87
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=28.39 E-value=34 Score=17.70 Aligned_cols=15 Identities=33% Similarity=0.651 Sum_probs=11.9
Q ss_pred CCccccccccccccC
Q psy1385 39 PIYPCGICHKEVHDN 53 (69)
Q Consensus 39 ~~ypCG~C~~eV~D~ 53 (69)
+.+-|..|++++.|.
T Consensus 31 p~~~C~~CGE~~~~~ 45 (46)
T TIGR03831 31 PALVCPQCGEEYLDA 45 (46)
T ss_pred CccccccCCCEeeCC
Confidence 456699999998875
No 88
>KOG1802|consensus
Probab=28.19 E-value=44 Score=30.04 Aligned_cols=30 Identities=23% Similarity=0.739 Sum_probs=24.3
Q ss_pred CCCCccccccccccccCCceEEecccccceeeC
Q psy1385 37 APPIYPCGICHKEVHDNDQAILCESGCNFWYHR 69 (69)
Q Consensus 37 s~~~ypCG~C~~eV~D~ddAI~CE~~C~~WFHR 69 (69)
..+.+-|-.|+ +.|..-.|.|.. |.+||=|
T Consensus 57 ~~~~~~c~Ycg--i~~p~~v~kc~~-c~Kwfcn 86 (935)
T KOG1802|consen 57 KLPEHACAYCG--ISEPACVIKCNT-CGKWFCN 86 (935)
T ss_pred ccchhhhhhcc--CCCchheeeccc-cCceeec
Confidence 56688899997 567778999995 9999953
No 89
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=28.01 E-value=23 Score=24.58 Aligned_cols=16 Identities=31% Similarity=1.020 Sum_probs=13.0
Q ss_pred CCCCcccccccccccc
Q psy1385 37 APPIYPCGICHKEVHD 52 (69)
Q Consensus 37 s~~~ypCG~C~~eV~D 52 (69)
..+.-|||.|.+-+.+
T Consensus 82 ~~~~sPCG~CRQ~i~E 97 (134)
T COG0295 82 GKPVSPCGACRQVLAE 97 (134)
T ss_pred CCCcCCcHHHHHHHHH
Confidence 5678899999987765
No 90
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=27.73 E-value=19 Score=29.91 Aligned_cols=22 Identities=18% Similarity=0.267 Sum_probs=17.7
Q ss_pred ccccccCCceEEecccccceeeC
Q psy1385 47 HKEVHDNDQAILCESGCNFWYHR 69 (69)
Q Consensus 47 ~~eV~D~ddAI~CE~~C~~WFHR 69 (69)
.++-.|.-.+|.|+- |++||-|
T Consensus 229 ~~~g~~~~~~~YC~~-C~r~f~~ 250 (470)
T COG5188 229 GMEGAEWFPKVYCVK-CGREFSR 250 (470)
T ss_pred ccchhhhccceeeHh-hhhHhhh
Confidence 455667788999999 9999954
No 91
>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=27.64 E-value=24 Score=19.41 Aligned_cols=9 Identities=22% Similarity=0.940 Sum_probs=3.7
Q ss_pred Eeccccccee
Q psy1385 58 LCESGCNFWY 67 (69)
Q Consensus 58 ~CE~~C~~WF 67 (69)
.|+= |+.||
T Consensus 5 yCdy-C~~~~ 13 (38)
T PF06220_consen 5 YCDY-CKKYL 13 (38)
T ss_dssp B-TT-T--B-
T ss_pred eccc-cccee
Confidence 5777 88887
No 92
>PF14421 LmjF365940-deam: A distinct subfamily of CDD/CDA-like deaminases
Probab=26.95 E-value=24 Score=26.42 Aligned_cols=18 Identities=28% Similarity=0.948 Sum_probs=13.4
Q ss_pred CCCCCCCCcccccccccc
Q psy1385 33 QNPNAPPIYPCGICHKEV 50 (69)
Q Consensus 33 q~~~s~~~ypCG~C~~eV 50 (69)
....++|.+|||.|.+-+
T Consensus 147 s~~~~NPL~PCGaC~ewL 164 (193)
T PF14421_consen 147 SPRDPNPLFPCGACKEWL 164 (193)
T ss_pred CCCCCCCCCcchHHHHHH
Confidence 345568899999998643
No 93
>KOG1512|consensus
Probab=26.92 E-value=29 Score=28.19 Aligned_cols=25 Identities=28% Similarity=0.705 Sum_probs=20.5
Q ss_pred cccccccccccCCceEEecccccceee
Q psy1385 42 PCGICHKEVHDNDQAILCESGCNFWYH 68 (69)
Q Consensus 42 pCG~C~~eV~D~ddAI~CE~~C~~WFH 68 (69)
-|-||.+-+++ ++-++|.. |++=||
T Consensus 316 lC~IC~~P~~E-~E~~FCD~-CDRG~H 340 (381)
T KOG1512|consen 316 LCRICLGPVIE-SEHLFCDV-CDRGPH 340 (381)
T ss_pred hhhccCCcccc-hheecccc-ccCCCC
Confidence 47788887775 57899999 999888
No 94
>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=26.79 E-value=20 Score=18.41 Aligned_cols=27 Identities=26% Similarity=0.630 Sum_probs=19.4
Q ss_pred ccccccccccccCCceEEecccccceee
Q psy1385 41 YPCGICHKEVHDNDQAILCESGCNFWYH 68 (69)
Q Consensus 41 ypCG~C~~eV~D~ddAI~CE~~C~~WFH 68 (69)
--|-.|.+.+-...+++.|.. |+.=.|
T Consensus 12 ~~C~~C~~~i~~~~~~~~C~~-C~~~~H 38 (49)
T smart00109 12 TKCCVCRKSIWGSFQGLRCSW-CKVKCH 38 (49)
T ss_pred CCccccccccCcCCCCcCCCC-CCchHH
Confidence 358888888876556888876 766544
No 95
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=26.65 E-value=30 Score=17.77 Aligned_cols=10 Identities=30% Similarity=0.816 Sum_probs=5.6
Q ss_pred cccccccccc
Q psy1385 41 YPCGICHKEV 50 (69)
Q Consensus 41 ypCG~C~~eV 50 (69)
|.|..|++++
T Consensus 6 y~C~~Cg~~f 15 (41)
T smart00834 6 YRCEDCGHTF 15 (41)
T ss_pred EEcCCCCCEE
Confidence 5566666533
No 96
>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=26.61 E-value=41 Score=17.54 Aligned_cols=13 Identities=23% Similarity=0.631 Sum_probs=7.2
Q ss_pred ccccccccccccC
Q psy1385 41 YPCGICHKEVHDN 53 (69)
Q Consensus 41 ypCG~C~~eV~D~ 53 (69)
|.|.+|+-.+..+
T Consensus 2 ~~C~~CGy~y~~~ 14 (33)
T cd00350 2 YVCPVCGYIYDGE 14 (33)
T ss_pred EECCCCCCEECCC
Confidence 5566666555443
No 97
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=26.25 E-value=29 Score=19.02 Aligned_cols=16 Identities=25% Similarity=0.590 Sum_probs=10.9
Q ss_pred CCCccccccccccccC
Q psy1385 38 PPIYPCGICHKEVHDN 53 (69)
Q Consensus 38 ~~~ypCG~C~~eV~D~ 53 (69)
...+.|.+|.+.|.-+
T Consensus 2 ~~~~~C~nC~R~v~a~ 17 (33)
T PF08209_consen 2 SPYVECPNCGRPVAAS 17 (33)
T ss_dssp S-EEE-TTTSSEEEGG
T ss_pred CCeEECCCCcCCcchh
Confidence 4568899999988653
No 98
>PRK05578 cytidine deaminase; Validated
Probab=25.48 E-value=17 Score=24.35 Aligned_cols=15 Identities=33% Similarity=1.037 Sum_probs=11.8
Q ss_pred CCCcccccccccccc
Q psy1385 38 PPIYPCGICHKEVHD 52 (69)
Q Consensus 38 ~~~ypCG~C~~eV~D 52 (69)
....|||.|.+-+.|
T Consensus 81 ~~~sPCG~CRQ~l~e 95 (131)
T PRK05578 81 EPLSPCGRCRQVLAE 95 (131)
T ss_pred CccCccHHHHHHHHH
Confidence 357899999887765
No 99
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=25.37 E-value=47 Score=19.73 Aligned_cols=37 Identities=19% Similarity=0.299 Sum_probs=26.0
Q ss_pred eCCCCCCCCCCcccccccccccc-CCceEEecccccce
Q psy1385 30 FNPQNPNAPPIYPCGICHKEVHD-NDQAILCESGCNFW 66 (69)
Q Consensus 30 fn~q~~~s~~~ypCG~C~~eV~D-~ddAI~CE~~C~~W 66 (69)
.|-+...-.....|..|..+..| ++=-+.|..+.+.|
T Consensus 49 ~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~~~W 86 (86)
T PF13966_consen 49 DNLQRRGIQVDPICPLCGNEEETIEHLFFHCPFARELW 86 (86)
T ss_pred hhhhccCCccCCccccCCCccccccceeccCcCccccC
Confidence 34444555667899999998877 45666787777666
No 100
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=25.16 E-value=37 Score=22.62 Aligned_cols=14 Identities=29% Similarity=0.937 Sum_probs=7.8
Q ss_pred ccccccccccccCC
Q psy1385 41 YPCGICHKEVHDND 54 (69)
Q Consensus 41 ypCG~C~~eV~D~d 54 (69)
|.|..|+.++..+|
T Consensus 124 f~Cp~Cg~~l~~~d 137 (147)
T smart00531 124 FTCPRCGEELEEDD 137 (147)
T ss_pred EECCCCCCEEEEcC
Confidence 55666665555443
No 101
>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=25.02 E-value=62 Score=26.77 Aligned_cols=31 Identities=35% Similarity=0.683 Sum_probs=23.1
Q ss_pred CCCCCccccccccccccC---CceEEecccccceee
Q psy1385 36 NAPPIYPCGICHKEVHDN---DQAILCESGCNFWYH 68 (69)
Q Consensus 36 ~s~~~ypCG~C~~eV~D~---ddAI~CE~~C~~WFH 68 (69)
.=.....|-+|++ +.++ =-+|.|+. |.-|=|
T Consensus 124 gFC~~C~C~iC~k-fD~~~n~~~Wi~Cd~-CgH~cH 157 (446)
T PF07227_consen 124 GFCRRCMCCICSK-FDDNKNTCSWIGCDV-CGHWCH 157 (446)
T ss_pred CccccCCccccCC-cccCCCCeeEEeccC-CCceeh
Confidence 3345678999999 4333 35899997 999988
No 102
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=25.01 E-value=36 Score=19.98 Aligned_cols=13 Identities=23% Similarity=0.675 Sum_probs=9.7
Q ss_pred CCCcccccccccc
Q psy1385 38 PPIYPCGICHKEV 50 (69)
Q Consensus 38 ~~~ypCG~C~~eV 50 (69)
.....||.|++.+
T Consensus 29 ~~klrCGaCs~vl 41 (46)
T PF11331_consen 29 QQKLRCGACSEVL 41 (46)
T ss_pred eeEEeCCCCceeE
Confidence 3467799998765
No 103
>TIGR01374 soxD sarcosine oxidase, delta subunit family, heterotetrameric form. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) form
Probab=24.44 E-value=38 Score=22.04 Aligned_cols=9 Identities=33% Similarity=1.342 Sum_probs=6.9
Q ss_pred cccccceee
Q psy1385 60 ESGCNFWYH 68 (69)
Q Consensus 60 E~~C~~WFH 68 (69)
..||.+||.
T Consensus 58 ~~GC~~Wf~ 66 (84)
T TIGR01374 58 SGGCRRWFN 66 (84)
T ss_pred CCCCcCeEE
Confidence 457999985
No 104
>PF12773 DZR: Double zinc ribbon
Probab=23.74 E-value=56 Score=17.59 Aligned_cols=19 Identities=26% Similarity=0.415 Sum_probs=10.1
Q ss_pred CccccccccccccCCceEEec
Q psy1385 40 IYPCGICHKEVHDNDQAILCE 60 (69)
Q Consensus 40 ~ypCG~C~~eV~D~ddAI~CE 60 (69)
...|..|++++.. ++.+|.
T Consensus 29 ~~~C~~Cg~~~~~--~~~fC~ 47 (50)
T PF12773_consen 29 KKICPNCGAENPP--NAKFCP 47 (50)
T ss_pred CCCCcCCcCCCcC--CcCccC
Confidence 4556666666443 444444
No 105
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=22.87 E-value=57 Score=18.68 Aligned_cols=27 Identities=22% Similarity=0.672 Sum_probs=17.5
Q ss_pred Ccccccccccccc------CCceEEeccccccee
Q psy1385 40 IYPCGICHKEVHD------NDQAILCESGCNFWY 67 (69)
Q Consensus 40 ~ypCG~C~~eV~D------~ddAI~CE~~C~~WF 67 (69)
...|..|...-.- ....++|++ |..+|
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCna-Cgl~~ 35 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNA-CGLYY 35 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeec-ccHHH
Confidence 4678888754332 133499997 88765
No 106
>cd06969 NR_DBD_NGFI-B DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B. DNA-binding domain (DBD) of the orphan nuclear receptor, nerve growth factor-induced-B (NGFI-B) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NGFI-B interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. NGFI-B is a member of the nuclear-steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcrip
Probab=22.70 E-value=40 Score=20.37 Aligned_cols=27 Identities=22% Similarity=0.621 Sum_probs=17.8
Q ss_pred cccccccccccC-CceEEecccccceeeC
Q psy1385 42 PCGICHKEVHDN-DQAILCESGCNFWYHR 69 (69)
Q Consensus 42 pCG~C~~eV~D~-ddAI~CE~~C~~WFHR 69 (69)
+|-+|+..-... -.++-|++ |...|.|
T Consensus 2 ~C~VCg~~~~g~hyGv~sC~a-C~~FFRR 29 (75)
T cd06969 2 LCAVCGDNAACQHYGVRTCEG-CKGFFKR 29 (75)
T ss_pred CCeecCCcCcceEECcceeee-eeeeeee
Confidence 467776544443 34566777 9998876
No 107
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.51 E-value=1e+02 Score=20.81 Aligned_cols=29 Identities=21% Similarity=0.423 Sum_probs=20.5
Q ss_pred CCCCccccccccccccCCceEEecccccceeeC
Q psy1385 37 APPIYPCGICHKEVHDNDQAILCESGCNFWYHR 69 (69)
Q Consensus 37 s~~~ypCG~C~~eV~D~ddAI~CE~~C~~WFHR 69 (69)
+.+.-.|..|+. -.+....|.. |..=+||
T Consensus 306 ~~tS~~C~~cg~---~~~r~~~C~~-cg~~~~r 334 (364)
T COG0675 306 YYTSKTCPCCGH---LSGRLFKCPR-CGFVHDR 334 (364)
T ss_pred CCCcccccccCC---ccceeEECCC-CCCeehh
Confidence 344456777877 3457788988 8887776
No 108
>cd07155 NR_DBD_ER_like DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. E
Probab=22.33 E-value=15 Score=22.26 Aligned_cols=14 Identities=29% Similarity=0.866 Sum_probs=8.4
Q ss_pred ceEEecccccceeeC
Q psy1385 55 QAILCESGCNFWYHR 69 (69)
Q Consensus 55 dAI~CE~~C~~WFHR 69 (69)
.++.|++ |...|.|
T Consensus 14 gv~sC~a-Ck~FFRR 27 (75)
T cd07155 14 GVASCEA-CKAFFKR 27 (75)
T ss_pred Chhhhhh-hHHHHHH
Confidence 3455666 7766654
No 109
>PHA03256 BDLF3; Provisional
Probab=22.32 E-value=22 Score=23.33 Aligned_cols=7 Identities=14% Similarity=0.135 Sum_probs=6.0
Q ss_pred ccceeeC
Q psy1385 63 CNFWYHR 69 (69)
Q Consensus 63 C~~WFHR 69 (69)
|+.||||
T Consensus 25 ~~~ff~r 31 (77)
T PHA03256 25 LLSWDPT 31 (77)
T ss_pred HHHHcCC
Confidence 7889987
No 110
>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=21.89 E-value=84 Score=16.18 Aligned_cols=24 Identities=21% Similarity=0.625 Sum_probs=12.6
Q ss_pred ccccccccccc-------cCCceEEecccccc
Q psy1385 41 YPCGICHKEVH-------DNDQAILCESGCNF 65 (69)
Q Consensus 41 ypCG~C~~eV~-------D~ddAI~CE~~C~~ 65 (69)
+.|..|+..+. ++...+.|-. |+.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~-C~~ 33 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGK-CGH 33 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCC-CCC
Confidence 45677776321 2233477766 653
No 111
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=21.86 E-value=79 Score=20.83 Aligned_cols=34 Identities=29% Similarity=0.643 Sum_probs=21.9
Q ss_pred CCCCCCcccccccccccc-----CCceEEecccccceeeC
Q psy1385 35 PNAPPIYPCGICHKEVHD-----NDQAILCESGCNFWYHR 69 (69)
Q Consensus 35 ~~s~~~ypCG~C~~eV~D-----~ddAI~CE~~C~~WFHR 69 (69)
.+.+..|.|..|++.... +---+.|.. |..-|+|
T Consensus 16 ~klpt~f~CP~Cge~~v~v~~~k~~~h~~C~~-CG~y~~~ 54 (99)
T PRK14892 16 PKLPKIFECPRCGKVSISVKIKKNIAIITCGN-CGLYTEF 54 (99)
T ss_pred cCCCcEeECCCCCCeEeeeecCCCcceEECCC-CCCccCE
Confidence 455678999999943331 234677877 8766543
No 112
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=21.25 E-value=74 Score=16.84 Aligned_cols=13 Identities=15% Similarity=0.534 Sum_probs=7.5
Q ss_pred ceEEecccccceee
Q psy1385 55 QAILCESGCNFWYH 68 (69)
Q Consensus 55 dAI~CE~~C~~WFH 68 (69)
-.+.|+. |+.|++
T Consensus 15 T~~~C~~-C~v~lC 27 (32)
T PF13842_consen 15 TRYMCSK-CDVPLC 27 (32)
T ss_pred eEEEccC-CCCccc
Confidence 4556666 666554
No 113
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=21.23 E-value=72 Score=17.02 Aligned_cols=21 Identities=19% Similarity=0.613 Sum_probs=12.6
Q ss_pred cccccccccccCCceEEeccccc
Q psy1385 42 PCGICHKEVHDNDQAILCESGCN 64 (69)
Q Consensus 42 pCG~C~~eV~D~ddAI~CE~~C~ 64 (69)
.|++|.+++.+++. ..-.+|.
T Consensus 1 ~C~~C~~~~~~~~~--~~l~~Cg 21 (44)
T PF14634_consen 1 HCNICFEKYSEERR--PRLTSCG 21 (44)
T ss_pred CCcCcCccccCCCC--eEEcccC
Confidence 38899999944333 3334443
No 114
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=21.10 E-value=51 Score=18.44 Aligned_cols=12 Identities=33% Similarity=0.642 Sum_probs=7.1
Q ss_pred Cccccccccccc
Q psy1385 40 IYPCGICHKEVH 51 (69)
Q Consensus 40 ~ypCG~C~~eV~ 51 (69)
.+.|.+|.+.+.
T Consensus 31 ~v~CPiC~~~~~ 42 (54)
T PF05605_consen 31 NVVCPICSSRVT 42 (54)
T ss_pred CccCCCchhhhh
Confidence 466666665544
No 115
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=21.04 E-value=24 Score=18.56 Aligned_cols=21 Identities=29% Similarity=0.784 Sum_probs=15.3
Q ss_pred ccccccccccC-----CceEEeccccc
Q psy1385 43 CGICHKEVHDN-----DQAILCESGCN 64 (69)
Q Consensus 43 CG~C~~eV~D~-----ddAI~CE~~C~ 64 (69)
|-.|++.|.+. ..+++|-. |+
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~-C~ 31 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVE-CQ 31 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HH-HH
T ss_pred ccccCChHHHHHHHhCCCcEECHH-Hh
Confidence 88999999884 78888876 65
No 116
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=20.79 E-value=47 Score=16.87 Aligned_cols=11 Identities=36% Similarity=0.960 Sum_probs=8.9
Q ss_pred ccccccccccc
Q psy1385 41 YPCGICHKEVH 51 (69)
Q Consensus 41 ypCG~C~~eV~ 51 (69)
..|.+|.+.|.
T Consensus 2 v~CPiC~~~v~ 12 (26)
T smart00734 2 VQCPVCFREVP 12 (26)
T ss_pred CcCCCCcCccc
Confidence 46999999884
No 117
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=20.54 E-value=84 Score=19.76 Aligned_cols=15 Identities=20% Similarity=0.483 Sum_probs=11.5
Q ss_pred CCCcccccccccccc
Q psy1385 38 PPIYPCGICHKEVHD 52 (69)
Q Consensus 38 ~~~ypCG~C~~eV~D 52 (69)
..+-||..|..++.+
T Consensus 4 d~lKPCPFCG~~~~~ 18 (64)
T PRK09710 4 DNVKPCPFCGCPSVT 18 (64)
T ss_pred ccccCCCCCCCceeE
Confidence 456789999887766
No 118
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=20.30 E-value=55 Score=16.96 Aligned_cols=26 Identities=27% Similarity=0.678 Sum_probs=19.0
Q ss_pred cccccccccccC-CceEEecccccceee
Q psy1385 42 PCGICHKEVHDN-DQAILCESGCNFWYH 68 (69)
Q Consensus 42 pCG~C~~eV~D~-ddAI~CE~~C~~WFH 68 (69)
-|-.|.+.+..- .+++.|+. |+.=.|
T Consensus 13 ~C~~C~~~i~~~~~~~~~C~~-C~~~~H 39 (50)
T cd00029 13 FCDVCRKSIWGLFKQGLRCSW-CKVKCH 39 (50)
T ss_pred ChhhcchhhhccccceeEcCC-CCCchh
Confidence 488888888754 58888877 776555
No 119
>cd06955 NR_DBD_VDR DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of core
Probab=20.16 E-value=48 Score=21.80 Aligned_cols=28 Identities=29% Similarity=0.726 Sum_probs=20.5
Q ss_pred ccccccccccccC-CceEEecccccceeeC
Q psy1385 41 YPCGICHKEVHDN-DQAILCESGCNFWYHR 69 (69)
Q Consensus 41 ypCG~C~~eV~D~-ddAI~CE~~C~~WFHR 69 (69)
-+|-+|+..-... =.++-|++ |...|.|
T Consensus 7 ~~C~VCg~~a~g~hyGv~sC~a-Ck~FFRR 35 (107)
T cd06955 7 RICGVCGDRATGFHFNAMTCEG-CKGFFRR 35 (107)
T ss_pred CCCeecCCcCcccEECcceeee-ecceecc
Confidence 4599998755553 35667877 9999987
Done!