Query 045873
Match_columns 868
No_of_seqs 442 out of 821
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 06:23:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045873.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045873hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03107 C1_2: C1 domain; Int 98.4 1.6E-07 3.4E-12 67.1 2.0 30 711-741 1-30 (30)
2 PF07649 C1_3: C1-like domain; 98.1 8.4E-07 1.8E-11 63.4 1.0 30 774-803 1-30 (30)
3 PF03107 C1_2: C1 domain; Int 97.9 5.3E-06 1.1E-10 59.2 1.4 28 832-859 1-30 (30)
4 PF07649 C1_3: C1-like domain; 97.7 8.4E-06 1.8E-10 58.2 0.6 29 540-568 1-30 (30)
5 cd02340 ZZ_NBR1_like Zinc fing 97.3 0.00024 5.1E-09 55.2 3.1 39 179-225 2-41 (43)
6 cd02340 ZZ_NBR1_like Zinc fing 96.9 0.00078 1.7E-08 52.3 3.1 39 541-585 2-41 (43)
7 cd02339 ZZ_Mind_bomb Zinc fing 96.3 0.0037 8.1E-08 49.0 3.0 41 179-225 2-43 (45)
8 cd02249 ZZ Zinc finger, ZZ typ 95.8 0.0083 1.8E-07 47.2 3.1 44 178-226 1-45 (46)
9 cd02337 ZZ_CBP Zinc finger, ZZ 95.7 0.0062 1.3E-07 46.8 1.8 37 115-167 2-39 (41)
10 cd02335 ZZ_ADA2 Zinc finger, Z 95.5 0.012 2.6E-07 47.0 2.9 35 236-270 2-37 (49)
11 cd02335 ZZ_ADA2 Zinc finger, Z 95.5 0.0097 2.1E-07 47.5 2.4 32 115-146 2-34 (49)
12 cd02339 ZZ_Mind_bomb Zinc fing 95.1 0.014 3.1E-07 45.7 2.1 40 541-585 2-43 (45)
13 cd02343 ZZ_EF Zinc finger, ZZ 94.9 0.015 3.3E-07 46.1 1.9 34 179-214 2-36 (48)
14 cd02338 ZZ_PCMF_like Zinc fing 94.9 0.024 5.2E-07 45.3 3.0 44 179-226 2-48 (49)
15 cd02344 ZZ_HERC2 Zinc finger, 94.5 0.037 8E-07 43.4 3.1 42 179-226 2-44 (45)
16 cd02341 ZZ_ZZZ3 Zinc finger, Z 94.5 0.039 8.4E-07 43.9 3.3 35 48-82 2-37 (48)
17 cd02334 ZZ_dystrophin Zinc fin 94.5 0.03 6.4E-07 44.8 2.6 44 179-225 2-47 (49)
18 cd02338 ZZ_PCMF_like Zinc fing 94.3 0.039 8.5E-07 44.1 2.9 44 541-586 2-48 (49)
19 cd02249 ZZ Zinc finger, ZZ typ 94.3 0.045 9.7E-07 43.1 3.2 33 48-82 2-34 (46)
20 cd02345 ZZ_dah Zinc finger, ZZ 94.1 0.03 6.5E-07 44.8 1.9 33 179-213 2-36 (49)
21 cd02341 ZZ_ZZZ3 Zinc finger, Z 94.0 0.043 9.3E-07 43.7 2.5 33 236-268 2-37 (48)
22 KOG0696 Serine/threonine prote 93.6 0.017 3.7E-07 64.6 -0.4 88 45-146 55-156 (683)
23 cd02344 ZZ_HERC2 Zinc finger, 93.1 0.077 1.7E-06 41.6 2.6 31 236-266 2-33 (45)
24 cd02342 ZZ_UBA_plant Zinc fing 92.9 0.059 1.3E-06 41.5 1.6 32 179-211 2-34 (43)
25 KOG1280 Uncharacterized conser 92.7 0.082 1.8E-06 57.8 3.1 49 234-282 8-57 (381)
26 cd02334 ZZ_dystrophin Zinc fin 92.6 0.085 1.8E-06 42.2 2.3 32 236-267 2-34 (49)
27 cd02342 ZZ_UBA_plant Zinc fing 92.5 0.063 1.4E-06 41.3 1.3 33 236-268 2-35 (43)
28 PF00130 C1_1: Phorbol esters/ 92.3 0.1 2.3E-06 42.0 2.5 36 413-448 9-45 (53)
29 PF00569 ZZ: Zinc finger, ZZ t 92.1 0.053 1.1E-06 42.7 0.5 32 113-145 4-37 (46)
30 smart00291 ZnF_ZZ Zinc-binding 92.1 0.17 3.7E-06 39.4 3.3 35 46-82 4-38 (44)
31 PF00130 C1_1: Phorbol esters/ 92.0 0.12 2.5E-06 41.7 2.4 33 469-501 11-45 (53)
32 KOG0957 PHD finger protein [Ge 91.6 0.068 1.5E-06 60.7 0.9 137 648-804 119-273 (707)
33 KOG0696 Serine/threonine prote 91.2 0.055 1.2E-06 60.7 -0.3 106 392-503 39-157 (683)
34 cd02345 ZZ_dah Zinc finger, ZZ 91.2 0.13 2.8E-06 41.2 1.8 32 541-572 2-35 (49)
35 KOG1280 Uncharacterized conser 91.1 0.15 3.3E-06 55.9 2.8 50 177-229 8-59 (381)
36 cd02343 ZZ_EF Zinc finger, ZZ 90.0 0.33 7.1E-06 38.6 3.1 37 48-86 2-38 (48)
37 PF00569 ZZ: Zinc finger, ZZ t 89.7 0.17 3.8E-06 39.8 1.4 33 539-571 4-38 (46)
38 smart00291 ZnF_ZZ Zinc-binding 89.6 0.22 4.8E-06 38.8 1.9 34 539-572 4-38 (44)
39 KOG0954 PHD finger protein [Ge 89.4 0.17 3.6E-06 60.3 1.5 123 648-804 271-411 (893)
40 KOG0956 PHD finger protein AF1 88.7 0.34 7.4E-06 57.3 3.4 127 48-210 7-156 (900)
41 cd00029 C1 Protein kinase C co 87.4 0.28 6.1E-06 38.6 1.2 34 113-146 11-46 (50)
42 KOG4582 Uncharacterized conser 87.2 0.35 7.7E-06 52.9 2.2 42 178-226 153-196 (278)
43 KOG4236 Serine/threonine prote 86.7 0.15 3.3E-06 58.9 -1.0 43 527-570 143-190 (888)
44 smart00109 C1 Protein kinase C 85.9 0.33 7.1E-06 37.9 0.9 34 113-146 11-45 (49)
45 KOG4236 Serine/threonine prote 85.4 0.21 4.5E-06 57.9 -0.7 36 469-504 156-193 (888)
46 cd02337 ZZ_CBP Zinc finger, ZZ 85.4 0.73 1.6E-05 35.5 2.5 29 49-80 3-31 (41)
47 PF13832 zf-HC5HC2H_2: PHD-zin 85.0 0.78 1.7E-05 42.8 3.1 89 650-749 2-93 (110)
48 PF00628 PHD: PHD-finger; Int 84.7 0.49 1.1E-05 37.7 1.4 33 650-684 1-33 (51)
49 cd00029 C1 Protein kinase C co 84.5 0.48 1E-05 37.3 1.2 33 469-501 11-45 (50)
50 KOG4582 Uncharacterized conser 84.2 0.65 1.4E-05 50.9 2.4 42 539-585 152-195 (278)
51 KOG0957 PHD finger protein [Ge 83.9 0.5 1.1E-05 54.0 1.4 131 48-209 121-273 (707)
52 smart00109 C1 Protein kinase C 83.4 0.51 1.1E-05 36.8 0.9 35 414-448 10-44 (49)
53 KOG0954 PHD finger protein [Ge 82.0 0.81 1.8E-05 54.8 2.2 123 288-447 271-411 (893)
54 KOG0955 PHD finger protein BR1 80.4 1.9 4.1E-05 54.8 4.7 122 649-804 220-361 (1051)
55 PF13832 zf-HC5HC2H_2: PHD-zin 75.7 3.4 7.4E-05 38.5 4.0 81 712-805 2-87 (110)
56 KOG0956 PHD finger protein AF1 74.7 3.4 7.4E-05 49.3 4.4 118 651-804 8-155 (900)
57 smart00249 PHD PHD zinc finger 73.1 3.6 7.7E-05 31.3 2.9 34 775-808 1-34 (47)
58 smart00249 PHD PHD zinc finger 70.9 5 0.00011 30.4 3.2 33 650-684 1-33 (47)
59 KOG1244 Predicted transcriptio 69.8 2.5 5.4E-05 45.2 1.6 99 235-362 225-332 (336)
60 PF00628 PHD: PHD-finger; Int 69.1 5.8 0.00012 31.4 3.3 32 290-321 1-32 (51)
61 PF13831 PHD_2: PHD-finger; PD 64.6 2.1 4.6E-05 32.0 -0.1 19 303-321 4-22 (36)
62 TIGR00622 ssl1 transcription f 63.7 12 0.00027 35.2 4.8 87 114-213 2-101 (112)
63 KOG0955 PHD finger protein BR1 58.7 10 0.00022 48.5 4.3 123 288-447 219-361 (1051)
64 TIGR01384 TFS_arch transcripti 58.5 13 0.00029 34.2 4.1 83 712-799 2-101 (104)
65 KOG1244 Predicted transcriptio 57.0 4.7 0.0001 43.2 0.9 101 595-720 225-332 (336)
66 KOG2807 RNA polymerase II tran 56.3 8.2 0.00018 42.5 2.6 49 161-210 311-362 (378)
67 PF02148 zf-UBP: Zn-finger in 53.0 7.4 0.00016 32.7 1.3 59 776-841 1-59 (63)
68 KOG0694 Serine/threonine prote 53.0 5.1 0.00011 48.3 0.4 97 46-146 169-276 (694)
69 KOG0457 Histone acetyltransfer 48.8 8 0.00017 44.2 1.1 35 113-147 14-49 (438)
70 cd02336 ZZ_RSC8 Zinc finger, Z 46.9 9.9 0.00022 29.9 1.0 31 115-146 2-33 (45)
71 KOG0457 Histone acetyltransfer 40.4 22 0.00047 40.8 2.9 44 49-94 17-63 (438)
72 PRK14890 putative Zn-ribbon RN 39.8 26 0.00057 29.2 2.5 49 415-493 7-57 (59)
73 PF02148 zf-UBP: Zn-finger in 39.0 9.6 0.00021 32.0 -0.1 57 542-604 1-59 (63)
74 KOG1512 PHD Zn-finger protein 35.5 15 0.00032 39.8 0.5 87 608-721 278-366 (381)
75 COG5114 Histone acetyltransfer 31.2 20 0.00044 39.3 0.7 34 114-147 6-40 (432)
76 PF13842 Tnp_zf-ribbon_2: DDE_ 31.1 36 0.00077 24.8 1.8 28 712-739 2-29 (32)
77 PF07282 OrfB_Zn_ribbon: Putat 29.7 59 0.0013 27.4 3.3 38 639-676 19-59 (69)
78 COG5141 PHD zinc finger-contai 29.5 29 0.00064 40.2 1.7 107 663-804 210-334 (669)
79 TIGR00622 ssl1 transcription f 28.9 84 0.0018 29.8 4.3 32 114-145 56-98 (112)
80 PF13831 PHD_2: PHD-finger; PD 28.9 34 0.00073 25.6 1.4 22 786-807 2-23 (36)
81 KOG0694 Serine/threonine prote 27.9 17 0.00037 44.0 -0.5 94 469-570 169-275 (694)
82 PF15499 Peptidase_C98: Ubiqui 26.4 53 0.0011 35.5 2.8 67 606-676 131-199 (275)
83 KOG1169 Diacylglycerol kinase 26.1 29 0.00063 42.0 0.9 96 112-211 43-147 (634)
84 KOG1512 PHD Zn-finger protein 25.2 34 0.00075 37.0 1.2 67 249-321 279-347 (381)
85 PF01363 FYVE: FYVE zinc finge 24.4 58 0.0013 27.5 2.2 43 347-390 4-46 (69)
86 PF11781 RRN7: RNA polymerase 23.8 34 0.00074 25.6 0.6 24 354-377 10-34 (36)
87 smart00396 ZnF_UBR1 Putative z 23.0 1.1E+02 0.0024 26.4 3.7 52 182-242 2-57 (71)
88 KOG2807 RNA polymerase II tran 22.5 50 0.0011 36.6 1.8 76 190-265 273-361 (378)
89 PF14446 Prok-RING_1: Prokaryo 22.3 57 0.0012 26.8 1.6 34 414-447 4-37 (54)
90 cd02336 ZZ_RSC8 Zinc finger, Z 21.9 81 0.0018 24.9 2.4 33 49-83 3-35 (45)
91 KOG2272 Focal adhesion protein 21.4 32 0.0007 36.6 0.1 29 351-379 119-148 (332)
92 PF10367 Vps39_2: Vacuolar sor 20.6 78 0.0017 28.8 2.5 32 414-447 77-108 (109)
No 1
>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=98.38 E-value=1.6e-07 Score=67.06 Aligned_cols=30 Identities=33% Similarity=0.844 Sum_probs=28.6
Q ss_pred eecccccccccCCCceEeCCCCCceeecccc
Q 045873 711 LRCEICKEERNPNHPSYGCVECECHAHVRCV 741 (868)
Q Consensus 711 ~~C~vC~~~~d~~~~~Y~C~~C~~~lH~~C~ 741 (868)
|||+||++++++.+ +|+|++|+++||++||
T Consensus 1 ~~C~~C~~~~~~~~-~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 1 FWCDVCRRKIDGFY-FYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCCcCCCE-eEEeCCCCCeEcCccC
Confidence 69999999999888 9999999999999997
No 2
>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=98.12 E-value=8.4e-07 Score=63.36 Aligned_cols=30 Identities=43% Similarity=0.924 Sum_probs=14.5
Q ss_pred cccccccccccCCCcEeeecCCceeehhhh
Q 045873 774 VVCYACEKLVRGQPTYGCDQCRFYLHKSCA 803 (868)
Q Consensus 774 ~~C~~C~~~i~~~~~y~C~~CdFilH~~CA 803 (868)
+.|++|.+++.++++|.|++|||+||++||
T Consensus 1 ~~C~~C~~~~~~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 1 FRCDACGKPIDGGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp ---TTTS----S--EEE-TTT-----HHHH
T ss_pred CcCCcCCCcCCCCceEECccCCCccChhcC
Confidence 469999999988899999999999999998
No 3
>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=97.87 E-value=5.3e-06 Score=59.24 Aligned_cols=28 Identities=43% Similarity=1.268 Sum_probs=26.4
Q ss_pred eeccccccccccE-EEeeCce-EEEeeeee
Q 045873 832 HECGACLKKLSGF-FYQCDNC-FVMDIDCA 859 (868)
Q Consensus 832 ~~C~~C~~~~~gf-~Y~c~~c-~~ldv~Ca 859 (868)
|+|++|+|.++|| +|.|..| |.||++||
T Consensus 1 ~~C~~C~~~~~~~~~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 1 FWCDVCRRKIDGFYFYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCCcCCCEeEEeCCCCCeEcCccC
Confidence 6899999999999 9999887 99999998
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=97.74 E-value=8.4e-06 Score=58.21 Aligned_cols=29 Identities=45% Similarity=1.032 Sum_probs=14.1
Q ss_pred cccccccccccC-CeeeeccCCcccccccc
Q 045873 540 AECQLCHKNIHG-TSYGCTPCMFNIHESCA 568 (868)
Q Consensus 540 ~~C~~C~~~i~~-~~Y~C~~Cdf~lH~~Ca 568 (868)
+.|++|++++.+ ..|.|.+|||+||++||
T Consensus 1 ~~C~~C~~~~~~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 1 FRCDACGKPIDGGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp ---TTTS----S--EEE-TTT-----HHHH
T ss_pred CcCCcCCCcCCCCceEECccCCCccChhcC
Confidence 479999999886 99999999999999997
No 5
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=97.26 E-value=0.00024 Score=55.16 Aligned_cols=39 Identities=28% Similarity=0.606 Sum_probs=31.9
Q ss_pred ccccCcCCCCCCCCcEEeccC-CCccccccCCCCccccCCCCCCCceE
Q 045873 179 KCKFCCKSIHGSQSYYCCGPC-NFYIHKSCSELPQQVRHPFHPCHSLT 225 (868)
Q Consensus 179 ~C~~C~~~~~~~~~~Y~C~~C-d~~~H~~C~~~p~~i~Hp~Hp~H~L~ 225 (868)
.|++|++++ .|.+|+|.+| ||+|+.+|.... .|+.||+.
T Consensus 2 ~Cd~C~~~i--~G~ry~C~~C~d~dLC~~C~~~~------~H~~H~f~ 41 (43)
T cd02340 2 ICDGCQGPI--VGVRYKCLVCPDYDLCESCEAKG------VHPEHAML 41 (43)
T ss_pred CCCCCCCcC--cCCeEECCCCCCccchHHhhCcC------CCCCCCEE
Confidence 699999854 7789999999 999999999755 34667765
No 6
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=96.92 E-value=0.00078 Score=52.29 Aligned_cols=39 Identities=33% Similarity=0.778 Sum_probs=33.1
Q ss_pred ccccccccccCCeeeeccC-CccccccccCCCceecCCCCCCCceE
Q 045873 541 ECQLCHKNIHGTSYGCTPC-MFNIHESCAELPQEVRHPFHPRHSLT 585 (868)
Q Consensus 541 ~C~~C~~~i~~~~Y~C~~C-df~lH~~Ca~lP~~i~H~~h~~HpL~ 585 (868)
.|++|+.+|.|..|+|.+| ||.|+..|...+ .| +.||+.
T Consensus 2 ~Cd~C~~~i~G~ry~C~~C~d~dLC~~C~~~~---~H---~~H~f~ 41 (43)
T cd02340 2 ICDGCQGPIVGVRYKCLVCPDYDLCESCEAKG---VH---PEHAML 41 (43)
T ss_pred CCCCCCCcCcCCeEECCCCCCccchHHhhCcC---CC---CCCCEE
Confidence 6999999888999999999 899999999866 34 456664
No 7
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=96.27 E-value=0.0037 Score=48.97 Aligned_cols=41 Identities=20% Similarity=0.399 Sum_probs=31.1
Q ss_pred ccccCcCCCCCCCCcEEeccC-CCccccccCCCCccccCCCCCCCceE
Q 045873 179 KCKFCCKSIHGSQSYYCCGPC-NFYIHKSCSELPQQVRHPFHPCHSLT 225 (868)
Q Consensus 179 ~C~~C~~~~~~~~~~Y~C~~C-d~~~H~~C~~~p~~i~Hp~Hp~H~L~ 225 (868)
.|++|++. .+.|.+|+|..| ||+|+++|..... -+|.|||.
T Consensus 2 ~Cd~C~~~-~i~G~RykC~~C~dyDLC~~C~~~~~-----H~~~H~f~ 43 (45)
T cd02339 2 ICDTCRKQ-GIIGIRWKCAECPNYDLCTTCYHGDK-----HDLEHRFY 43 (45)
T ss_pred CCCCCCCC-CcccCeEECCCCCCccchHHHhCCCC-----CCCCCCEE
Confidence 69999853 246789999999 9999999997421 24567764
No 8
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=95.81 E-value=0.0083 Score=47.25 Aligned_cols=44 Identities=36% Similarity=0.660 Sum_probs=32.8
Q ss_pred CccccCcCCCCCCCCcEEeccC-CCccccccCCCCccccCCCCCCCceEE
Q 045873 178 TKCKFCCKSIHGSQSYYCCGPC-NFYIHKSCSELPQQVRHPFHPCHSLTL 226 (868)
Q Consensus 178 ~~C~~C~~~~~~~~~~Y~C~~C-d~~~H~~C~~~p~~i~Hp~Hp~H~L~L 226 (868)
+.|++|++.+ .|.+|+|.+| ||+|..+|.....+ .|+ +.|+++.
T Consensus 1 ~~C~~C~~~i--~g~r~~C~~C~d~dLC~~Cf~~~~~-~H~--~~H~~~~ 45 (46)
T cd02249 1 YSCDGCLKPI--VGVRYHCLVCEDFDLCSSCYAKGKK-GHP--PDHSFTE 45 (46)
T ss_pred CCCcCCCCCC--cCCEEECCCCCCCcCHHHHHCcCcC-CCC--CCCCEeE
Confidence 3699999855 6689999999 69999999986652 232 1466653
No 9
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=95.68 E-value=0.0062 Score=46.79 Aligned_cols=37 Identities=24% Similarity=0.706 Sum_probs=29.7
Q ss_pred cCCcccccCCCCCceecCCC-CceeccccccccccccCCCcccccCCCCcCCCc
Q 045873 115 DCDYCDESHKDNPFLCCDFC-NFQIGAPCATTLIKYHRGQEEHIQHFSHRHPLI 167 (868)
Q Consensus 115 ~C~~C~k~~~~~~~y~C~~C-df~lh~~Ca~~~~~~~~~~~~~i~hf~H~H~L~ 167 (868)
+||.|.+ +.+ ..|+|..| ||||+..|.... .|+|.|.
T Consensus 2 ~C~~C~~-~~~-~r~~C~~C~dfDLC~~C~~~~--------------~H~H~~~ 39 (41)
T cd02337 2 TCNECKH-HVE-TRWHCTVCEDYDLCITCYNTK--------------NHPHKME 39 (41)
T ss_pred cCCCCCC-cCC-CceECCCCcchhhHHHHhCCC--------------CCCcccc
Confidence 5999988 444 45799999 999999999753 6788774
No 10
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=95.49 E-value=0.012 Score=47.05 Aligned_cols=35 Identities=40% Similarity=0.892 Sum_probs=30.5
Q ss_pred cccccccccCCCceEeCCCC-CCCCCccccCCCCCC
Q 045873 236 RCDACRSYIDLGMRYRCDDC-DFDMHPECMSLKPNI 270 (868)
Q Consensus 236 ~C~~C~~~~~~g~~Y~C~~C-~f~lh~~Ca~~P~~i 270 (868)
.|+.|++.+..|.+|+|.+| +|+|+..|.......
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~~~ 37 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAGAEI 37 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcCCC
Confidence 59999988877799999999 799999998877554
No 11
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=95.48 E-value=0.0097 Score=47.55 Aligned_cols=32 Identities=25% Similarity=0.685 Sum_probs=28.6
Q ss_pred cCCcccccCCCCCceecCCC-Cceecccccccc
Q 045873 115 DCDYCDESHKDNPFLCCDFC-NFQIGAPCATTL 146 (868)
Q Consensus 115 ~C~~C~k~~~~~~~y~C~~C-df~lh~~Ca~~~ 146 (868)
.|+.|++.+.+...|+|..| ||||++.|....
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g 34 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAG 34 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCc
Confidence 59999999988667899999 999999999865
No 12
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=95.08 E-value=0.014 Score=45.74 Aligned_cols=40 Identities=25% Similarity=0.696 Sum_probs=31.3
Q ss_pred ccccccc-cccCCeeeeccC-CccccccccCCCceecCCCCCCCceE
Q 045873 541 ECQLCHK-NIHGTSYGCTPC-MFNIHESCAELPQEVRHPFHPRHSLT 585 (868)
Q Consensus 541 ~C~~C~~-~i~~~~Y~C~~C-df~lH~~Ca~lP~~i~H~~h~~HpL~ 585 (868)
.|++|++ +|.|..|+|.+| ||+|++.|.... .| ++.||+.
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~~~---~H--~~~H~f~ 43 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAECPNYDLCTTCYHGD---KH--DLEHRFY 43 (45)
T ss_pred CCCCCCCCCcccCeEECCCCCCccchHHHhCCC---CC--CCCCCEE
Confidence 6999994 567999999999 899999999842 23 3456664
No 13
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=94.94 E-value=0.015 Score=46.06 Aligned_cols=34 Identities=21% Similarity=0.382 Sum_probs=28.7
Q ss_pred ccccCcCCCCCCCCcEEeccC-CCccccccCCCCccc
Q 045873 179 KCKFCCKSIHGSQSYYCCGPC-NFYIHKSCSELPQQV 214 (868)
Q Consensus 179 ~C~~C~~~~~~~~~~Y~C~~C-d~~~H~~C~~~p~~i 214 (868)
.||+|.+.. .+.+|+|.+| ||+|..+|...-.+.
T Consensus 2 ~CdgC~~~~--~~~RykCl~C~d~DlC~~Cf~~g~~~ 36 (48)
T cd02343 2 SCDGCDEIA--PWHRYRCLQCTDMDLCKTCFLGGVKP 36 (48)
T ss_pred CCCCCCCcC--CCceEECCCCCCchhHHHHHhCCccC
Confidence 599998754 5679999999 999999999876554
No 14
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=94.90 E-value=0.024 Score=45.35 Aligned_cols=44 Identities=18% Similarity=0.411 Sum_probs=33.3
Q ss_pred ccccCc-CCCCCCCCcEEeccC-CCccccccCCCCccccCCCC-CCCceEE
Q 045873 179 KCKFCC-KSIHGSQSYYCCGPC-NFYIHKSCSELPQQVRHPFH-PCHSLTL 226 (868)
Q Consensus 179 ~C~~C~-~~~~~~~~~Y~C~~C-d~~~H~~C~~~p~~i~Hp~H-p~H~L~L 226 (868)
.|++|+ .++ .|.+|+|..| ||+|..+|.....+. ..| +.||.++
T Consensus 2 ~C~~C~~~~i--~g~R~~C~~C~d~dlC~~Cf~~~~~~--~~H~~~H~~~~ 48 (49)
T cd02338 2 SCDGCGKSNF--TGRRYKCLICYDYDLCADCYDSGVTT--ERHLFDHPMQC 48 (49)
T ss_pred CCCCCcCCCc--EEeeEEeCCCCCCccchhHHhCCCcC--CCCCCCCCEEE
Confidence 699998 444 5789999999 999999999876542 233 3577765
No 15
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=94.53 E-value=0.037 Score=43.38 Aligned_cols=42 Identities=19% Similarity=0.445 Sum_probs=31.3
Q ss_pred ccccCcCCCCCCCCcEEeccC-CCccccccCCCCccccCCCCCCCceEE
Q 045873 179 KCKFCCKSIHGSQSYYCCGPC-NFYIHKSCSELPQQVRHPFHPCHSLTL 226 (868)
Q Consensus 179 ~C~~C~~~~~~~~~~Y~C~~C-d~~~H~~C~~~p~~i~Hp~Hp~H~L~L 226 (868)
.||+|+.. .+.|.+|+|..| ||+|.+.|...- .|+ +.|+|..
T Consensus 2 ~Cd~C~~~-pI~G~RykC~~C~dyDLC~~Cf~~~---~H~--~~H~F~r 44 (45)
T cd02344 2 TCDGCQMF-PINGPRFKCRNCDDFDFCENCFKTR---KHN--TRHTFGR 44 (45)
T ss_pred CCCCCCCC-CCccCeEECCCCCCccchHHhhCCC---CcC--CCCceee
Confidence 69999843 247789999999 899999999752 232 4677653
No 16
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=94.53 E-value=0.039 Score=43.91 Aligned_cols=35 Identities=23% Similarity=0.480 Sum_probs=30.8
Q ss_pred CCCCCCC-CCCCCceeeCcCCCCCcccchhhhcCCc
Q 045873 48 KCSACDR-QPSGSFYFCKQCWPKSPFFHKLCAELPR 82 (868)
Q Consensus 48 ~C~~C~~-~~~g~~Y~C~~C~~~~f~~H~~C~~~p~ 82 (868)
.|++|+. +|.|.-|+|.+|..|||+++++|...+.
T Consensus 2 ~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~~ 37 (48)
T cd02341 2 KCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKGE 37 (48)
T ss_pred CCCCCCCCccccceEECCCCCCCCCccCHHHHhCcC
Confidence 3888877 8999999999998778999999998775
No 17
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=94.51 E-value=0.03 Score=44.78 Aligned_cols=44 Identities=25% Similarity=0.486 Sum_probs=32.3
Q ss_pred ccccCcCCCCCCCCcEEeccC-CCccccccCCCCccc-cCCCCCCCceE
Q 045873 179 KCKFCCKSIHGSQSYYCCGPC-NFYIHKSCSELPQQV-RHPFHPCHSLT 225 (868)
Q Consensus 179 ~C~~C~~~~~~~~~~Y~C~~C-d~~~H~~C~~~p~~i-~Hp~Hp~H~L~ 225 (868)
.|++|++. ++.|.+|+|..| ||+|..+|...-.+. .|. +.||.+
T Consensus 2 ~Cd~C~~~-pi~g~RykC~~C~d~DLC~~Cf~~g~~~~~H~--~~Hp~~ 47 (49)
T cd02334 2 KCNICKEF-PITGFRYRCLKCFNYDLCQSCFFSGRTSKSHK--NSHPMK 47 (49)
T ss_pred CCCCCCCC-CceeeeEECCCCCCcCchHHHHhCCCcCCCCC--CCCCee
Confidence 69999853 236789999999 999999999765543 333 236654
No 18
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=94.31 E-value=0.039 Score=44.12 Aligned_cols=44 Identities=25% Similarity=0.617 Sum_probs=34.7
Q ss_pred cccccc-ccccCCeeeeccC-CccccccccCCCcee-cCCCCCCCceEE
Q 045873 541 ECQLCH-KNIHGTSYGCTPC-MFNIHESCAELPQEV-RHPFHPRHSLTV 586 (868)
Q Consensus 541 ~C~~C~-~~i~~~~Y~C~~C-df~lH~~Ca~lP~~i-~H~~h~~HpL~L 586 (868)
.|++|+ .+|.|..|+|.+| ||+|..+|.....+. .|. +.||.++
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~~~~~~~H~--~~H~~~~ 48 (49)
T cd02338 2 SCDGCGKSNFTGRRYKCLICYDYDLCADCYDSGVTTERHL--FDHPMQC 48 (49)
T ss_pred CCCCCcCCCcEEeeEEeCCCCCCccchhHHhCCCcCCCCC--CCCCEEE
Confidence 699999 6777999999999 999999999877543 232 2577664
No 19
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=94.27 E-value=0.045 Score=43.10 Aligned_cols=33 Identities=21% Similarity=0.439 Sum_probs=29.5
Q ss_pred CCCCCCCCCCCCceeeCcCCCCCcccchhhhcCCc
Q 045873 48 KCSACDRQPSGSFYFCKQCWPKSPFFHKLCAELPR 82 (868)
Q Consensus 48 ~C~~C~~~~~g~~Y~C~~C~~~~f~~H~~C~~~p~ 82 (868)
.|++|+..|.|..|+|.+|. +|+++.+|...+.
T Consensus 2 ~C~~C~~~i~g~r~~C~~C~--d~dLC~~Cf~~~~ 34 (46)
T cd02249 2 SCDGCLKPIVGVRYHCLVCE--DFDLCSSCYAKGK 34 (46)
T ss_pred CCcCCCCCCcCCEEECCCCC--CCcCHHHHHCcCc
Confidence 38889889999999999997 6999999998765
No 20
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=94.11 E-value=0.03 Score=44.78 Aligned_cols=33 Identities=24% Similarity=0.610 Sum_probs=27.9
Q ss_pred ccccCcC-CCCCCCCcEEeccC-CCccccccCCCCcc
Q 045873 179 KCKFCCK-SIHGSQSYYCCGPC-NFYIHKSCSELPQQ 213 (868)
Q Consensus 179 ~C~~C~~-~~~~~~~~Y~C~~C-d~~~H~~C~~~p~~ 213 (868)
.|++|++ ++ .|.+|+|..| ||+|..+|.....+
T Consensus 2 ~C~~C~~~~i--~g~R~~C~~C~dydLC~~Cf~~~~~ 36 (49)
T cd02345 2 SCSACRKQDI--SGIRFPCQVCRDYSLCLGCYTKGRE 36 (49)
T ss_pred cCCCCCCCCc--eEeeEECCCCCCcCchHHHHhCCCc
Confidence 5999987 54 6789999999 99999999986643
No 21
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=93.95 E-value=0.043 Score=43.69 Aligned_cols=33 Identities=36% Similarity=0.923 Sum_probs=27.6
Q ss_pred cccccccccCCCceEeCCCCC---CCCCccccCCCC
Q 045873 236 RCDACRSYIDLGMRYRCDDCD---FDMHPECMSLKP 268 (868)
Q Consensus 236 ~C~~C~~~~~~g~~Y~C~~C~---f~lh~~Ca~~P~ 268 (868)
.|+.|+.....|.+|+|.+|. |||+..|.....
T Consensus 2 ~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~~ 37 (48)
T cd02341 2 KCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKGE 37 (48)
T ss_pred CCCCCCCCccccceEECCCCCCCCCccCHHHHhCcC
Confidence 599999843348999999997 999999988765
No 22
>KOG0696 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=93.63 E-value=0.017 Score=64.59 Aligned_cols=88 Identities=23% Similarity=0.454 Sum_probs=60.4
Q ss_pred CCCCCCCCCCCCCCC---ceeeCcCCCCCcccchhhhcC-----Cccccccc----CCcceeeeccCccCCCCCCCCCCC
Q 045873 45 HPEKCSACDRQPSGS---FYFCKQCWPKSPFFHKLCAEL-----PRQIRIAL----RPHCVLRLRQESVGPDMSSFLSDK 112 (868)
Q Consensus 45 ~~~~C~~C~~~~~g~---~Y~C~~C~~~~f~~H~~C~~~-----p~~I~~~~----H~~h~L~l~~~~~~~~~~~~~~~~ 112 (868)
-|+.|++|...|||- |+.|.+|- |++|+.|.+. |..=+-+- ...|-.++.. ...
T Consensus 55 qPTfCsHCkDFiwGfgKQGfQCqvC~---fvvHkrChefVtF~CPGadkg~dtDdpr~kHkf~~~t-----------Yss 120 (683)
T KOG0696|consen 55 QPTFCSHCKDFIWGFGKQGFQCQVCC---FVVHKRCHEFVTFSCPGADKGPDTDDPRSKHKFKIHT-----------YSS 120 (683)
T ss_pred CCchhhhhhhheeccccCceeeeEEe---ehhhhhhcceEEEECCCCCCCCCCCCcccccceeeee-----------cCC
Confidence 367999999999987 69999994 8999999982 22211110 1112222211 112
Q ss_pred cccCCcccccCCCC--CceecCCCCceecccccccc
Q 045873 113 AFDCDYCDESHKDN--PFLCCDFCNFQIGAPCATTL 146 (868)
Q Consensus 113 ~~~C~~C~k~~~~~--~~y~C~~Cdf~lh~~Ca~~~ 146 (868)
--+|+-||.-+.+. ....|+.||.+||-.|....
T Consensus 121 PTFCDhCGsLLyGl~HQGmKC~~C~mNVH~rCv~nV 156 (683)
T KOG0696|consen 121 PTFCDHCGSLLYGLIHQGMKCDTCDMNVHHRCVENV 156 (683)
T ss_pred CchhhhHHHHHHHHHhcccccccccchHHHHHhhcC
Confidence 34799999988665 35799999999999999643
No 23
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=93.12 E-value=0.077 Score=41.61 Aligned_cols=31 Identities=35% Similarity=1.014 Sum_probs=26.4
Q ss_pred cccccccccCCCceEeCCCCC-CCCCccccCC
Q 045873 236 RCDACRSYIDLGMRYRCDDCD-FDMHPECMSL 266 (868)
Q Consensus 236 ~C~~C~~~~~~g~~Y~C~~C~-f~lh~~Ca~~ 266 (868)
.||.|+.....|.+|+|.+|. |||+..|-..
T Consensus 2 ~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~ 33 (45)
T cd02344 2 TCDGCQMFPINGPRFKCRNCDDFDFCENCFKT 33 (45)
T ss_pred CCCCCCCCCCccCeEECCCCCCccchHHhhCC
Confidence 599998754458999999995 9999999876
No 24
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=92.87 E-value=0.059 Score=41.50 Aligned_cols=32 Identities=13% Similarity=0.163 Sum_probs=26.6
Q ss_pred ccccCcCCCCCCCCcEEeccC-CCccccccCCCC
Q 045873 179 KCKFCCKSIHGSQSYYCCGPC-NFYIHKSCSELP 211 (868)
Q Consensus 179 ~C~~C~~~~~~~~~~Y~C~~C-d~~~H~~C~~~p 211 (868)
.||+|+.. ++.|.+|+|..| ||+|.+.|....
T Consensus 2 ~CDgCg~~-PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 2 QCDGCGVL-PITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCC-cccccceEeCCCCCCccHHHHhhhh
Confidence 69999853 347789999999 999999998754
No 25
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=92.72 E-value=0.082 Score=57.84 Aligned_cols=49 Identities=22% Similarity=0.455 Sum_probs=37.1
Q ss_pred cccccccccccCCCceEeCCCC-CCCCCccccCCCCCCCCCCCCcccEEE
Q 045873 234 WYRCDACRSYIDLGMRYRCDDC-DFDMHPECMSLKPNIKYPAHQHLLIVV 282 (868)
Q Consensus 234 ~~~C~~C~~~~~~g~~Y~C~~C-~f~lh~~Ca~~P~~i~~~~H~H~L~l~ 282 (868)
+..||+|++..-.+.+|+|-.| +|||+..|-..-..+..-.++||+..+
T Consensus 8 ~v~CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~~tt~~H~~dHPmqci 57 (381)
T KOG1280|consen 8 GVSCDGCGKTAFTFRRYKCLRCSDYDLCFSCYENGATTPIHDEDHPMQCI 57 (381)
T ss_pred CceeccccccceeeeeeEeeeecchhHHHHHhhcCCCCcccCCCCceeEE
Confidence 6789999987655679999999 699999997766555333357887643
No 26
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=92.63 E-value=0.085 Score=42.19 Aligned_cols=32 Identities=31% Similarity=0.967 Sum_probs=26.2
Q ss_pred cccccccccCCCceEeCCCC-CCCCCccccCCC
Q 045873 236 RCDACRSYIDLGMRYRCDDC-DFDMHPECMSLK 267 (868)
Q Consensus 236 ~C~~C~~~~~~g~~Y~C~~C-~f~lh~~Ca~~P 267 (868)
.|+.|+.....|++|+|.+| ||||+..|-..-
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g 34 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSG 34 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCC
Confidence 59999975434799999999 599999997654
No 27
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=92.48 E-value=0.063 Score=41.34 Aligned_cols=33 Identities=30% Similarity=0.584 Sum_probs=27.2
Q ss_pred cccccccccCCCceEeCCCC-CCCCCccccCCCC
Q 045873 236 RCDACRSYIDLGMRYRCDDC-DFDMHPECMSLKP 268 (868)
Q Consensus 236 ~C~~C~~~~~~g~~Y~C~~C-~f~lh~~Ca~~P~ 268 (868)
.||+|+.....|.+|+|..| ||||+..|-..+.
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~~ 35 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSRMG 35 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhhhc
Confidence 59999986555899999998 5999999977553
No 28
>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=92.30 E-value=0.1 Score=42.00 Aligned_cols=36 Identities=28% Similarity=0.709 Sum_probs=28.0
Q ss_pred cCCCcCccccccccc-CCCcEEecCCCcccccccCCC
Q 045873 413 NDDIECHACENLIIQ-GHSAYGCDPCRFYLHKSCFEL 448 (868)
Q Consensus 413 ~~~~~C~aC~~~~~~-~~~~Y~C~~C~F~lH~~C~~l 448 (868)
.....|+.|+..+++ ....|.|..|++++|++|+++
T Consensus 9 ~~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSK 45 (53)
T ss_dssp SSTEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCT
T ss_pred CCCCCCcccCcccCCCCCCeEEECCCCChHhhhhhhh
Confidence 346889999999942 246899999999999999974
No 29
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=92.10 E-value=0.053 Score=42.75 Aligned_cols=32 Identities=19% Similarity=0.594 Sum_probs=23.6
Q ss_pred cccCCcccc-cCCCCCceecCCC-Cceeccccccc
Q 045873 113 AFDCDYCDE-SHKDNPFLCCDFC-NFQIGAPCATT 145 (868)
Q Consensus 113 ~~~C~~C~k-~~~~~~~y~C~~C-df~lh~~Ca~~ 145 (868)
...|+.|++ .+.+. .|+|..| ||||+..|...
T Consensus 4 ~~~C~~C~~~~i~g~-Ry~C~~C~d~dLC~~C~~~ 37 (46)
T PF00569_consen 4 GYTCDGCGTDPIIGV-RYHCLVCPDYDLCEDCFSK 37 (46)
T ss_dssp SCE-SSS-SSSEESS-EEEESSSSS-EEEHHHHHH
T ss_pred CeECcCCCCCcCcCC-eEECCCCCCCchhhHHHhC
Confidence 457999999 44555 4799999 89999999975
No 30
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=92.06 E-value=0.17 Score=39.41 Aligned_cols=35 Identities=20% Similarity=0.417 Sum_probs=30.4
Q ss_pred CCCCCCCCCCCCCCceeeCcCCCCCcccchhhhcCCc
Q 045873 46 PEKCSACDRQPSGSFYFCKQCWPKSPFFHKLCAELPR 82 (868)
Q Consensus 46 ~~~C~~C~~~~~g~~Y~C~~C~~~~f~~H~~C~~~p~ 82 (868)
...|++|+..|.|.-|.|.+|. ||+++.+|...++
T Consensus 4 ~~~C~~C~~~i~g~ry~C~~C~--d~dlC~~Cf~~~~ 38 (44)
T smart00291 4 SYSCDTCGKPIVGVRYHCLVCP--DYDLCQSCFAKGS 38 (44)
T ss_pred CcCCCCCCCCCcCCEEECCCCC--CccchHHHHhCcC
Confidence 3468999889999999999997 6999999998664
No 31
>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=92.03 E-value=0.12 Score=41.74 Aligned_cols=33 Identities=24% Similarity=0.635 Sum_probs=26.7
Q ss_pred ccccccccceecCc--eeEeeccCCeeeccccccc
Q 045873 469 SERCTACGQQLKGN--AIYHCETCDFDLDLDCAAQ 501 (868)
Q Consensus 469 ~~~C~~C~~~~~g~--~~Y~C~~C~~~lh~~Ca~~ 501 (868)
...|++|++.+-|. .+|+|+.|++.+|.+|+..
T Consensus 11 ~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~ 45 (53)
T PF00130_consen 11 PTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSK 45 (53)
T ss_dssp TEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCT
T ss_pred CCCCcccCcccCCCCCCeEEECCCCChHhhhhhhh
Confidence 45899999999443 6799999999999999987
No 32
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=91.60 E-value=0.068 Score=60.66 Aligned_cols=137 Identities=22% Similarity=0.401 Sum_probs=85.7
Q ss_pred cccccccccCc--CCceeEEecCcceeeecccCCCCCCCcccccCCCcceEeeeCCcccCCCCCeeeccccccccc----
Q 045873 648 KSKCEACRCDI--EGTFFLRCVECKLNFHVQCGPDWLPPTVDQQHHDHPLTLTTGTIVKDNDGDLLRCEICKEERN---- 721 (868)
Q Consensus 648 ~~~C~~C~~~~--~~~~~y~C~~C~f~lH~~C~~~~lP~~i~~~~h~H~L~l~~g~~~~~~~g~~~~C~vC~~~~d---- 721 (868)
+.+|-+|-... ...-+..|..|+..+|..|-+ .-..+- +..|. .+.+.+.|.|+.|.-.|.
T Consensus 119 ~~iCcVClg~rs~da~ei~qCd~CGi~VHEgCYG--v~dn~s---------i~s~~--s~~stepWfCeaC~~Gvs~P~C 185 (707)
T KOG0957|consen 119 AVICCVCLGQRSVDAGEILQCDKCGINVHEGCYG--VLDNVS---------IPSGS--SDCSTEPWFCEACLYGVSLPHC 185 (707)
T ss_pred ceEEEEeecCccccccceeeccccCceecccccc--cccccc---------cCCCC--ccCCCCchhhhhHhcCCCCCcc
Confidence 34899996432 223489999999999999998 332222 22221 123445599999988775
Q ss_pred ----CCCceEeCCCCCceeecccccccCCcCCCCcceEeecceEE---EEe-cCCCccccccccccccccc--CCCcEee
Q 045873 722 ----PNHPSYGCVECECHAHVRCVITEVPSDEREKLNHFSHDHCL---FLV-GNQRDDDGVVCYACEKLVR--GQPTYGC 791 (868)
Q Consensus 722 ----~~~~~Y~C~~C~~~lH~~C~~~~~~~~~pg~~~~~~h~h~l---~l~-~n~~~~~~~~C~~C~~~i~--~~~~y~C 791 (868)
.+.|.|.=-+=+.-||.-||| ..||.-+ ..-|.+ .+. .+++--+.+.|.+|..+|. .+..-+|
T Consensus 186 ElCPn~~GifKetDigrWvH~iCAL-----YvpGVaf--g~~~~l~~Vtl~em~ysk~Gak~Cs~Ced~~fARtGvci~C 258 (707)
T KOG0957|consen 186 ELCPNRFGIFKETDIGRWVHAICAL-----YVPGVAF--GQTHTLCGVTLEEMDYSKFGAKTCSACEDKIFARTGVCIRC 258 (707)
T ss_pred ccCCCcCCcccccchhhHHHHHHHh-----hcCcccc--ccccccccccHHHhhhhhhccchhccccchhhhhcceeeec
Confidence 223344332333468999998 4577632 222222 221 1232234899999999986 4566666
Q ss_pred e--cCCceeehhhhc
Q 045873 792 D--QCRFYLHKSCAE 804 (868)
Q Consensus 792 ~--~CdFilH~~CA~ 804 (868)
. -|.-++|-+||.
T Consensus 259 daGMCk~YfHVTCAQ 273 (707)
T KOG0957|consen 259 DAGMCKEYFHVTCAQ 273 (707)
T ss_pred cchhhhhhhhhhHHh
Confidence 4 477889999995
No 33
>KOG0696 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=91.25 E-value=0.055 Score=60.71 Aligned_cols=106 Identities=28% Similarity=0.626 Sum_probs=71.7
Q ss_pred CCCcccccCccCccccccccccCCCcCcccccccc-cCCCcEEecCCCcccccccCCC-----CCceecc-----cCCCC
Q 045873 392 NTERHKHFSHHHLLVLLENERNDDIECHACENLII-QGHSAYGCDPCRFYLHKSCFEL-----PKVMKHI-----SDSHY 460 (868)
Q Consensus 392 ~i~~~kHFsH~H~L~l~~~~~~~~~~C~aC~~~~~-~~~~~Y~C~~C~F~lH~~C~~l-----Pr~i~h~-----~~~~~ 460 (868)
++.+.| +|.-..+++. .+..|+.|..-|+ .+...+.|..|.|++|+.|-+. |..=+-+ -..|-
T Consensus 39 nvhevk--~HkF~aRFFK----qPTfCsHCkDFiwGfgKQGfQCqvC~fvvHkrChefVtF~CPGadkg~dtDdpr~kHk 112 (683)
T KOG0696|consen 39 NVHEVK--SHKFIARFFK----QPTFCSHCKDFIWGFGKQGFQCQVCCFVVHKRCHEFVTFSCPGADKGPDTDDPRSKHK 112 (683)
T ss_pred chhhhc--cceeeehhcc----CCchhhhhhhheeccccCceeeeEEeehhhhhhcceEEEECCCCCCCCCCCCcccccc
Confidence 445667 7766656644 5788999988887 2346799999999999999873 2222211 11222
Q ss_pred ccccCCccccccccccceecCc--eeEeeccCCeeeccccccccC
Q 045873 461 LTLQNSSFSERCTACGQQLKGN--AIYHCETCDFDLDLDCAAQHP 503 (868)
Q Consensus 461 L~~~~~~~~~~C~~C~~~~~g~--~~Y~C~~C~~~lh~~Ca~~~~ 503 (868)
+.+......-.|+-|+.-+-|- .+-.|+.|+..+|-+|...-|
T Consensus 113 f~~~tYssPTFCDhCGsLLyGl~HQGmKC~~C~mNVH~rCv~nVP 157 (683)
T KOG0696|consen 113 FKIHTYSSPTFCDHCGSLLYGLIHQGMKCDTCDMNVHHRCVENVP 157 (683)
T ss_pred eeeeecCCCchhhhHHHHHHHHHhcccccccccchHHHHHhhcCC
Confidence 2222112244799999888775 457899999999999986633
No 34
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=91.24 E-value=0.13 Score=41.19 Aligned_cols=32 Identities=25% Similarity=0.746 Sum_probs=29.1
Q ss_pred ccccccc-cccCCeeeeccC-CccccccccCCCc
Q 045873 541 ECQLCHK-NIHGTSYGCTPC-MFNIHESCAELPQ 572 (868)
Q Consensus 541 ~C~~C~~-~i~~~~Y~C~~C-df~lH~~Ca~lP~ 572 (868)
.|++|.+ +|.|..|+|..| ||+|...|.....
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~dydLC~~Cf~~~~ 35 (49)
T cd02345 2 SCSACRKQDISGIRFPCQVCRDYSLCLGCYTKGR 35 (49)
T ss_pred cCCCCCCCCceEeeEECCCCCCcCchHHHHhCCC
Confidence 6999998 788999999999 9999999998765
No 35
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=91.06 E-value=0.15 Score=55.88 Aligned_cols=50 Identities=24% Similarity=0.416 Sum_probs=38.0
Q ss_pred CCccccCcCCCCCCCCcEEeccC-CCccccccCCCCccccCCCCC-CCceEEeec
Q 045873 177 DTKCKFCCKSIHGSQSYYCCGPC-NFYIHKSCSELPQQVRHPFHP-CHSLTLQNN 229 (868)
Q Consensus 177 ~~~C~~C~~~~~~~~~~Y~C~~C-d~~~H~~C~~~p~~i~Hp~Hp-~H~L~L~~~ 229 (868)
+..||||++.- ..+.+|+|+.| ||+|..+|.+.-.. -|.|+ .||+..+-.
T Consensus 8 ~v~CdgC~k~~-~t~rrYkCL~C~DyDlC~sCyen~~t--t~~H~~dHPmqcil~ 59 (381)
T KOG1280|consen 8 GVSCDGCGKTA-FTFRRYKCLRCSDYDLCFSCYENGAT--TPIHDEDHPMQCILS 59 (381)
T ss_pred Cceeccccccc-eeeeeeEeeeecchhHHHHHhhcCCC--CcccCCCCceeEEee
Confidence 35899999764 35668999999 99999999987644 34444 388887543
No 36
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=89.96 E-value=0.33 Score=38.63 Aligned_cols=37 Identities=24% Similarity=0.314 Sum_probs=31.4
Q ss_pred CCCCCCCCCCCCceeeCcCCCCCcccchhhhcCCccccc
Q 045873 48 KCSACDRQPSGSFYFCKQCWPKSPFFHKLCAELPRQIRI 86 (868)
Q Consensus 48 ~C~~C~~~~~g~~Y~C~~C~~~~f~~H~~C~~~p~~I~~ 86 (868)
.|++|+..+.|.-|.|.+|. ||+++.+|...+.+.+.
T Consensus 2 ~CdgC~~~~~~~RykCl~C~--d~DlC~~Cf~~g~~~~~ 38 (48)
T cd02343 2 SCDGCDEIAPWHRYRCLQCT--DMDLCKTCFLGGVKPEG 38 (48)
T ss_pred CCCCCCCcCCCceEECCCCC--CchhHHHHHhCCccCCC
Confidence 37888887888889999997 69999999998887644
No 37
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=89.73 E-value=0.17 Score=39.82 Aligned_cols=33 Identities=27% Similarity=0.659 Sum_probs=25.3
Q ss_pred Ccccccccc-cccCCeeeeccC-CccccccccCCC
Q 045873 539 DAECQLCHK-NIHGTSYGCTPC-MFNIHESCAELP 571 (868)
Q Consensus 539 ~~~C~~C~~-~i~~~~Y~C~~C-df~lH~~Ca~lP 571 (868)
...|++|+. +|.|..|+|..| ||+|...|....
T Consensus 4 ~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~g 38 (46)
T PF00569_consen 4 GYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSKG 38 (46)
T ss_dssp SCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH-
T ss_pred CeECcCCCCCcCcCCeEECCCCCCCchhhHHHhCc
Confidence 357999998 677999999999 899999998653
No 38
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=89.65 E-value=0.22 Score=38.80 Aligned_cols=34 Identities=29% Similarity=0.707 Sum_probs=29.7
Q ss_pred CcccccccccccCCeeeeccC-CccccccccCCCc
Q 045873 539 DAECQLCHKNIHGTSYGCTPC-MFNIHESCAELPQ 572 (868)
Q Consensus 539 ~~~C~~C~~~i~~~~Y~C~~C-df~lH~~Ca~lP~ 572 (868)
...|++|+.+|.+..|+|..| ||+|..+|....+
T Consensus 4 ~~~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~~~ 38 (44)
T smart00291 4 SYSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAKGS 38 (44)
T ss_pred CcCCCCCCCCCcCCEEECCCCCCccchHHHHhCcC
Confidence 357999999888999999999 9999999987553
No 39
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=89.36 E-value=0.17 Score=60.31 Aligned_cols=123 Identities=22% Similarity=0.410 Sum_probs=78.6
Q ss_pred cccccccccCc--CCceeEEecCcceeeecccCCCCCCCcccccCCCcceEeeeCCcccCCCCCeeecccccccccC---
Q 045873 648 KSKCEACRCDI--EGTFFLRCVECKLNFHVQCGPDWLPPTVDQQHHDHPLTLTTGTIVKDNDGDLLRCEICKEERNP--- 722 (868)
Q Consensus 648 ~~~C~~C~~~~--~~~~~y~C~~C~f~lH~~C~~~~lP~~i~~~~h~H~L~l~~g~~~~~~~g~~~~C~vC~~~~d~--- 722 (868)
...|++|..+. .+.-.-.|..|+..+|..|.+ |- +.+.|. |-|.-|.-++-|
T Consensus 271 dviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyG--Il--------------------e~p~gp-WlCr~Calg~~ppCv 327 (893)
T KOG0954|consen 271 DVICDVCRSPDSEEANEMVFCDKCNICVHQACYG--IL--------------------EVPEGP-WLCRTCALGIEPPCV 327 (893)
T ss_pred cceeceecCCCccccceeEEeccchhHHHHhhhc--ee--------------------ecCCCC-eeehhccccCCCCee
Confidence 45899999764 344567799999999999999 32 233455 888888776543
Q ss_pred ----CCceEeCCCCC-ceeecccccccCCcCCCCcceEeecceEEEE------ecCCCcccccccccccccccCCCcEee
Q 045873 723 ----NHPSYGCVECE-CHAHVRCVITEVPSDEREKLNHFSHDHCLFL------VGNQRDDDGVVCYACEKLVRGQPTYGC 791 (868)
Q Consensus 723 ----~~~~Y~C~~C~-~~lH~~C~~~~~~~~~pg~~~~~~h~h~l~l------~~n~~~~~~~~C~~C~~~i~~~~~y~C 791 (868)
++|+-+=..=+ ..+|+.|||| .|+.+|. ..+.++- |+..+- ..+|.-|..+ .+..-+|
T Consensus 328 LCPkkGGamK~~~sgT~wAHvsCALw-----IPEVsie--~~ekmePItkfs~IpesRw--slvC~LCk~k--~GACIqC 396 (893)
T KOG0954|consen 328 LCPKKGGAMKPTKSGTKWAHVSCALW-----IPEVSIE--CPEKMEPITKFSHIPESRW--SLVCNLCKVK--SGACIQC 396 (893)
T ss_pred eccccCCcccccCCCCeeeEeeeeec-----cceeecc--CHhhcCcccccCCCcHHHH--HHHHHHhccc--CcceEEe
Confidence 12222211112 2699999998 3554431 1111111 122222 3689999988 5677888
Q ss_pred --ecCCceeehhhhc
Q 045873 792 --DQCRFYLHKSCAE 804 (868)
Q Consensus 792 --~~CdFilH~~CA~ 804 (868)
..|.=-.|..||-
T Consensus 397 s~k~C~t~fHv~CA~ 411 (893)
T KOG0954|consen 397 SNKTCRTAFHVTCAF 411 (893)
T ss_pred cccchhhhccchhhh
Confidence 4788889999993
No 40
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=88.68 E-value=0.34 Score=57.26 Aligned_cols=127 Identities=18% Similarity=0.527 Sum_probs=77.4
Q ss_pred CCCCC-CCCCC--CCceeeCc--CCCCCcccchhhhcCCcccccccCCcceeeeccCccCCCCCCCCCCCcccCCccccc
Q 045873 48 KCSAC-DRQPS--GSFYFCKQ--CWPKSPFFHKLCAELPRQIRIALRPHCVLRLRQESVGPDMSSFLSDKAFDCDYCDES 122 (868)
Q Consensus 48 ~C~~C-~~~~~--g~~Y~C~~--C~~~~f~~H~~C~~~p~~I~~~~H~~h~L~l~~~~~~~~~~~~~~~~~~~C~~C~k~ 122 (868)
.|=.| ++.-| ++--+|.- |. ..||+.|-..- ..| .+.|+|..|.+.
T Consensus 7 GCCVCSDErGWaeNPLVYCDG~nCs---VAVHQaCYGIv---qVP-----------------------tGpWfCrKCesq 57 (900)
T KOG0956|consen 7 GCCVCSDERGWAENPLVYCDGHNCS---VAVHQACYGIV---QVP-----------------------TGPWFCRKCESQ 57 (900)
T ss_pred ceeeecCcCCCccCceeeecCCCce---eeeehhcceeE---ecC-----------------------CCchhhhhhhhh
Confidence 34345 44444 44567765 75 68999998421 111 256889999875
Q ss_pred CCCCCceecCCCCce------------eccccccccccccCCCcccccCCCCcCCCcccccccccCCCccccCcCCCC--
Q 045873 123 HKDNPFLCCDFCNFQ------------IGAPCATTLIKYHRGQEEHIQHFSHRHPLILLEMELEAEDTKCKFCCKSIH-- 188 (868)
Q Consensus 123 ~~~~~~y~C~~Cdf~------------lh~~Ca~~~~~~~~~~~~~i~hf~H~H~L~~~~~~~~~~~~~C~~C~~~~~-- 188 (868)
--..+ ++|+-|-++ .|..||++.++...+-+-+ .=|..|...+.++.+-.|-.|.+.+-
T Consensus 58 eraar-vrCeLCP~kdGALKkTDn~GWAHVVCALYIPEVrFgNV~T------MEPIiLq~VP~dRfnKtCYIC~E~Grpn 130 (900)
T KOG0956|consen 58 ERAAR-VRCELCPHKDGALKKTDNGGWAHVVCALYIPEVRFGNVHT------MEPIILQDVPHDRFNKTCYICNEEGRPN 130 (900)
T ss_pred hhhcc-ceeecccCcccceecccCCCceEEEEEeeccceeeccccc------ccceeeccCchhhhcceeeeecccCCcc
Confidence 44444 699999554 7899998765332221111 33555554444444447999976532
Q ss_pred --CCCCcEEecc--CCCccccccCCC
Q 045873 189 --GSQSYYCCGP--CNFYIHKSCSEL 210 (868)
Q Consensus 189 --~~~~~Y~C~~--Cd~~~H~~C~~~ 210 (868)
..|....|+. |.-.||..||+.
T Consensus 131 kA~~GACMtCNKs~CkqaFHVTCAQ~ 156 (900)
T KOG0956|consen 131 KAAKGACMTCNKSGCKQAFHVTCAQR 156 (900)
T ss_pred ccccccceecccccchhhhhhhHhhh
Confidence 2344566764 788999999974
No 41
>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=87.37 E-value=0.28 Score=38.62 Aligned_cols=34 Identities=26% Similarity=0.519 Sum_probs=28.9
Q ss_pred cccCCcccccCCCC--CceecCCCCceecccccccc
Q 045873 113 AFDCDYCDESHKDN--PFLCCDFCNFQIGAPCATTL 146 (868)
Q Consensus 113 ~~~C~~C~k~~~~~--~~y~C~~Cdf~lh~~Ca~~~ 146 (868)
..+|++|++.+.+. ..|+|+.|++.+|..|+.+.
T Consensus 11 ~~~C~~C~~~i~~~~~~~~~C~~C~~~~H~~C~~~v 46 (50)
T cd00029 11 PTFCDVCRKSIWGLFKQGLRCSWCKVKCHKKCADKV 46 (50)
T ss_pred CCChhhcchhhhccccceeEcCCCCCchhhhhhccC
Confidence 34699999999863 56899999999999999754
No 42
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=87.22 E-value=0.35 Score=52.91 Aligned_cols=42 Identities=24% Similarity=0.586 Sum_probs=34.1
Q ss_pred CccccCcC-CCCCCCCcEEeccC-CCccccccCCCCccccCCCCCCCceEE
Q 045873 178 TKCKFCCK-SIHGSQSYYCCGPC-NFYIHKSCSELPQQVRHPFHPCHSLTL 226 (868)
Q Consensus 178 ~~C~~C~~-~~~~~~~~Y~C~~C-d~~~H~~C~~~p~~i~Hp~Hp~H~L~L 226 (868)
..||.|++ .+ .|.+|+|..| |++|.+.|.... +.|.+|+|.-
T Consensus 153 v~CD~C~~~~I--vG~RyKC~~C~dYDLCe~Ce~~~-----~~h~~H~~lR 196 (278)
T KOG4582|consen 153 VPCDNCGKPGI--VGARYKCTVCPDYDLCERCEAGN-----EHHAAHAMLR 196 (278)
T ss_pred ccCCCccCCcc--ccceeeecCCCccchhHHhhcCC-----CCCcccceee
Confidence 48999987 54 6789999999 999999998643 4677787765
No 43
>KOG4236 consensus Serine/threonine protein kinase PKC mu/PKD and related proteins [Signal transduction mechanisms]
Probab=86.72 E-value=0.15 Score=58.93 Aligned_cols=43 Identities=23% Similarity=0.478 Sum_probs=33.4
Q ss_pred cccccCEEeec--CCccccccccccc---CCeeeeccCCccccccccCC
Q 045873 527 SHYHYLTVLDV--GDAECQLCHKNIH---GTSYGCTPCMFNIHESCAEL 570 (868)
Q Consensus 527 sH~H~L~~l~~--~~~~C~~C~~~i~---~~~Y~C~~Cdf~lH~~Ca~l 570 (868)
.+||.|+ ... ....|+-|++-.. ....+|..|+..+|+.||..
T Consensus 143 i~PH~l~-vhSY~~PtFCD~CGEmL~GLvrQGlKC~gCglNyHKRCa~k 190 (888)
T KOG4236|consen 143 IRPHTLF-VHSYKAPTFCDFCGEMLFGLVRQGLKCEGCGLNYHKRCAFK 190 (888)
T ss_pred eecceee-eecccCchHHHHHHHHHHHHHHccccccCCCCcHhhhhhhc
Confidence 4678887 332 2678999998654 45789999999999999963
No 44
>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=85.90 E-value=0.33 Score=37.90 Aligned_cols=34 Identities=24% Similarity=0.493 Sum_probs=28.7
Q ss_pred cccCCcccccCCCCC-ceecCCCCceecccccccc
Q 045873 113 AFDCDYCDESHKDNP-FLCCDFCNFQIGAPCATTL 146 (868)
Q Consensus 113 ~~~C~~C~k~~~~~~-~y~C~~Cdf~lh~~Ca~~~ 146 (868)
..+|++|++.+.... .|+|+.|++.+|..|+.+.
T Consensus 11 ~~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~~v 45 (49)
T smart00109 11 PTKCCVCRKSIWGSFQGLRCSWCKVKCHKKCAEKV 45 (49)
T ss_pred CCCccccccccCcCCCCcCCCCCCchHHHHHHhhc
Confidence 347999999998653 6899999999999999754
No 45
>KOG4236 consensus Serine/threonine protein kinase PKC mu/PKD and related proteins [Signal transduction mechanisms]
Probab=85.43 E-value=0.21 Score=57.88 Aligned_cols=36 Identities=31% Similarity=0.671 Sum_probs=30.6
Q ss_pred ccccccccceecCc--eeEeeccCCeeeccccccccCC
Q 045873 469 SERCTACGQQLKGN--AIYHCETCDFDLDLDCAAQHPS 504 (868)
Q Consensus 469 ~~~C~~C~~~~~g~--~~Y~C~~C~~~lh~~Ca~~~~~ 504 (868)
.-.|+-|+.++-|- .+-+|.-|+...|.|||..+|+
T Consensus 156 PtFCD~CGEmL~GLvrQGlKC~gCglNyHKRCa~kipN 193 (888)
T KOG4236|consen 156 PTFCDFCGEMLFGLVRQGLKCEGCGLNYHKRCAFKIPN 193 (888)
T ss_pred chHHHHHHHHHHHHHHccccccCCCCcHhhhhhhcCCC
Confidence 45799999998775 4689999999999999988765
No 46
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=85.36 E-value=0.73 Score=35.47 Aligned_cols=29 Identities=17% Similarity=0.470 Sum_probs=24.4
Q ss_pred CCCCCCCCCCCceeeCcCCCCCcccchhhhcC
Q 045873 49 CSACDRQPSGSFYFCKQCWPKSPFFHKLCAEL 80 (868)
Q Consensus 49 C~~C~~~~~g~~Y~C~~C~~~~f~~H~~C~~~ 80 (868)
|++|.. +.|..|.|.+|. ||+++.+|...
T Consensus 3 C~~C~~-~~~~r~~C~~C~--dfDLC~~C~~~ 31 (41)
T cd02337 3 CNECKH-HVETRWHCTVCE--DYDLCITCYNT 31 (41)
T ss_pred CCCCCC-cCCCceECCCCc--chhhHHHHhCC
Confidence 777866 446789999998 69999999976
No 47
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=85.02 E-value=0.78 Score=42.82 Aligned_cols=89 Identities=21% Similarity=0.407 Sum_probs=55.3
Q ss_pred cccccccCcCCceeEEecCcceeeecccCCCCCCCcccccCC-CcceEeeeCCcccCCCCCeeecccccccccCCCceEe
Q 045873 650 KCEACRCDIEGTFFLRCVECKLNFHVQCGPDWLPPTVDQQHH-DHPLTLTTGTIVKDNDGDLLRCEICKEERNPNHPSYG 728 (868)
Q Consensus 650 ~C~~C~~~~~~~~~y~C~~C~f~lH~~C~~~~lP~~i~~~~h-~H~L~l~~g~~~~~~~g~~~~C~vC~~~~d~~~~~Y~ 728 (868)
.|..|... + ..++-..-+-.+|..||. |.|..+-.... .=++.+..- .....+ ..|.+|++. .+..=+
T Consensus 2 ~C~lC~~~--~-Galk~t~~~~WvHv~Cal-~~~~~~~~~~~~~~~v~~~~i---~~~~~~-~~C~iC~~~---~G~~i~ 70 (110)
T PF13832_consen 2 SCVLCPKR--G-GALKRTSDGQWVHVLCAL-WIPEVIFNNGESMEPVDISNI---PPSRFK-LKCSICGKS---GGACIK 70 (110)
T ss_pred ccEeCCCC--C-CcccCccCCcEEEeEccc-eeCccEEeechhcCcccceee---cchhcC-CcCcCCCCC---CceeEE
Confidence 47778743 2 245555557789999998 77866532211 112222111 112235 799999987 234567
Q ss_pred CCC--CCceeecccccccCCcCC
Q 045873 729 CVE--CECHAHVRCVITEVPSDE 749 (868)
Q Consensus 729 C~~--C~~~lH~~C~~~~~~~~~ 749 (868)
|.. |..++|+.||...+.+++
T Consensus 71 C~~~~C~~~fH~~CA~~~g~~~~ 93 (110)
T PF13832_consen 71 CSHPGCSTAFHPTCARKAGLYFE 93 (110)
T ss_pred cCCCCCCcCCCHHHHHHCCCeEE
Confidence 876 999999999986555443
No 48
>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=84.70 E-value=0.49 Score=37.66 Aligned_cols=33 Identities=21% Similarity=0.555 Sum_probs=27.5
Q ss_pred cccccccCcCCceeEEecCcceeeecccCCCCCCC
Q 045873 650 KCEACRCDIEGTFFLRCVECKLNFHVQCGPDWLPP 684 (868)
Q Consensus 650 ~C~~C~~~~~~~~~y~C~~C~f~lH~~C~~~~lP~ 684 (868)
+|.+|+..........|..|+-.+|..|+. +|.
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~--~~~ 33 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVG--PPE 33 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTST--SSH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCC--CCh
Confidence 478899765556689999999999999999 664
No 49
>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=84.52 E-value=0.48 Score=37.30 Aligned_cols=33 Identities=21% Similarity=0.535 Sum_probs=28.8
Q ss_pred ccccccccceecCc--eeEeeccCCeeeccccccc
Q 045873 469 SERCTACGQQLKGN--AIYHCETCDFDLDLDCAAQ 501 (868)
Q Consensus 469 ~~~C~~C~~~~~g~--~~Y~C~~C~~~lh~~Ca~~ 501 (868)
...|.+|++.+-+. .+|.|..|++.+|.+|+..
T Consensus 11 ~~~C~~C~~~i~~~~~~~~~C~~C~~~~H~~C~~~ 45 (50)
T cd00029 11 PTFCDVCRKSIWGLFKQGLRCSWCKVKCHKKCADK 45 (50)
T ss_pred CCChhhcchhhhccccceeEcCCCCCchhhhhhcc
Confidence 44799999999763 5799999999999999987
No 50
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=84.18 E-value=0.65 Score=50.87 Aligned_cols=42 Identities=31% Similarity=0.728 Sum_probs=34.1
Q ss_pred Ccccccccc-cccCCeeeeccC-CccccccccCCCceecCCCCCCCceE
Q 045873 539 DAECQLCHK-NIHGTSYGCTPC-MFNIHESCAELPQEVRHPFHPRHSLT 585 (868)
Q Consensus 539 ~~~C~~C~~-~i~~~~Y~C~~C-df~lH~~Ca~lP~~i~H~~h~~HpL~ 585 (868)
...|+.|.. +|.|..|+|.+| ||+|++.|-.-. +.|.+|+|.
T Consensus 152 ~v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~-----~~h~~H~~l 195 (278)
T KOG4582|consen 152 SVPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGN-----EHHAAHAML 195 (278)
T ss_pred cccCCCccCCccccceeeecCCCccchhHHhhcCC-----CCCccccee
Confidence 368999999 788999999999 999999998643 345566554
No 51
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=83.88 E-value=0.5 Score=53.97 Aligned_cols=131 Identities=24% Similarity=0.510 Sum_probs=78.4
Q ss_pred CCCCC-CCCC--CCCceeeCcCCCCCcccchhhhcCCcccccccCCcceeeeccCccCCCCCCCCCCCcccCCcccccCC
Q 045873 48 KCSAC-DRQP--SGSFYFCKQCWPKSPFFHKLCAELPRQIRIALRPHCVLRLRQESVGPDMSSFLSDKAFDCDYCDESHK 124 (868)
Q Consensus 48 ~C~~C-~~~~--~g~~Y~C~~C~~~~f~~H~~C~~~p~~I~~~~H~~h~L~l~~~~~~~~~~~~~~~~~~~C~~C~k~~~ 124 (868)
.|-.| |..+ -|+.-.|..|+ ..||..|-.-.....+++-. ......-|+|..|+-.+.
T Consensus 121 iCcVClg~rs~da~ei~qCd~CG---i~VHEgCYGv~dn~si~s~~----------------s~~stepWfCeaC~~Gvs 181 (707)
T KOG0957|consen 121 ICCVCLGQRSVDAGEILQCDKCG---INVHEGCYGVLDNVSIPSGS----------------SDCSTEPWFCEACLYGVS 181 (707)
T ss_pred EEEEeecCccccccceeeccccC---ceecccccccccccccCCCC----------------ccCCCCchhhhhHhcCCC
Confidence 34455 3333 24578899997 68999998644334443111 112234688999988766
Q ss_pred CCCceecCCC--Cce----------eccccccccccccCCCcccccCCCCcCCCccc---ccccccCC-CccccCcCCC-
Q 045873 125 DNPFLCCDFC--NFQ----------IGAPCATTLIKYHRGQEEHIQHFSHRHPLILL---EMELEAED-TKCKFCCKSI- 187 (868)
Q Consensus 125 ~~~~y~C~~C--df~----------lh~~Ca~~~~~~~~~~~~~i~hf~H~H~L~~~---~~~~~~~~-~~C~~C~~~~- 187 (868)
.. +|+.| .|. ||+.||++.... .|.--|.|... .......+ -.|.+|...+
T Consensus 182 ~P---~CElCPn~~GifKetDigrWvH~iCALYvpGV---------afg~~~~l~~Vtl~em~ysk~Gak~Cs~Ced~~f 249 (707)
T KOG0957|consen 182 LP---HCELCPNRFGIFKETDIGRWVHAICALYVPGV---------AFGQTHTLCGVTLEEMDYSKFGAKTCSACEDKIF 249 (707)
T ss_pred CC---ccccCCCcCCcccccchhhHHHHHHHhhcCcc---------ccccccccccccHHHhhhhhhccchhccccchhh
Confidence 53 88888 333 799999876422 22333344332 22111122 3699997443
Q ss_pred CCCCCcEEecc--CCCccccccCC
Q 045873 188 HGSQSYYCCGP--CNFYIHKSCSE 209 (868)
Q Consensus 188 ~~~~~~Y~C~~--Cd~~~H~~C~~ 209 (868)
...|+.-+|.. |.-+||..||+
T Consensus 250 ARtGvci~CdaGMCk~YfHVTCAQ 273 (707)
T KOG0957|consen 250 ARTGVCIRCDAGMCKEYFHVTCAQ 273 (707)
T ss_pred hhcceeeeccchhhhhhhhhhHHh
Confidence 34555666764 78899999997
No 52
>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=83.44 E-value=0.51 Score=36.79 Aligned_cols=35 Identities=26% Similarity=0.574 Sum_probs=29.1
Q ss_pred CCCcCcccccccccCCCcEEecCCCcccccccCCC
Q 045873 414 DDIECHACENLIIQGHSAYGCDPCRFYLHKSCFEL 448 (868)
Q Consensus 414 ~~~~C~aC~~~~~~~~~~Y~C~~C~F~lH~~C~~l 448 (868)
....|+.|+..++.....|.|..|++..|+.|+..
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~~ 44 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCKVKCHKKCAEK 44 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCCchHHHHHHhh
Confidence 35789999999983324799999999999999874
No 53
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=81.98 E-value=0.81 Score=54.77 Aligned_cols=123 Identities=20% Similarity=0.422 Sum_probs=73.3
Q ss_pred CccCCcCCCCC-C-CCcEEEeeccCceeecCCCCCCCCCCeeeeccCCCceeeeecCCccCCCCcCccccccccccCCCC
Q 045873 288 ESQCHGCSLDI-E-GTFFARCVECKLDFHVQCGPAPSLPPTVVHKSHSHPLSLIDKSETLGTDDATHLYCDACKEETNPS 365 (868)
Q Consensus 288 ~~~C~~Cg~~~-~-~~~~Y~C~~C~f~lH~~C~~lp~~~~~I~~~~H~H~L~l~~~~~~~~~~~~~~~~C~vC~~~~d~~ 365 (868)
.-.||+|.... + ..-.-.|..||..||+.|..+- ++|+ +.|.|..|.-.+..
T Consensus 271 dviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIl------------------------e~p~-gpWlCr~Calg~~p- 324 (893)
T KOG0954|consen 271 DVICDVCRSPDSEEANEMVFCDKCNICVHQACYGIL------------------------EVPE-GPWLCRTCALGIEP- 324 (893)
T ss_pred cceeceecCCCccccceeEEeccchhHHHHhhhcee------------------------ecCC-CCeeehhccccCCC-
Confidence 45799998652 1 2235669999999999997543 2332 56777777655432
Q ss_pred CCcccCCCCC------------cceeeecccceeeecCCCCcccccCccCcccccccc--ccCCCcCcccccccccCCCc
Q 045873 366 HPCYGCSECD------------QYYAHVRCVITEIHLDNTERHKHFSHHHLLVLLENE--RNDDIECHACENLIIQGHSA 431 (868)
Q Consensus 366 ~~~Y~C~~C~------------~~~~H~~C~~~~~~~d~i~~~kHFsH~H~L~l~~~~--~~~~~~C~aC~~~~~~~~~~ 431 (868)
-|..|+ .-..|+.||+-.|.+ .|+.++-. =|.+.++.. ..-...|+.|..... ..
T Consensus 325 ----pCvLCPkkGGamK~~~sgT~wAHvsCALwIPEV-sie~~ekm---ePItkfs~IpesRwslvC~LCk~k~G---AC 393 (893)
T KOG0954|consen 325 ----PCVLCPKKGGAMKPTKSGTKWAHVSCALWIPEV-SIECPEKM---EPITKFSHIPESRWSLVCNLCKVKSG---AC 393 (893)
T ss_pred ----CeeeccccCCcccccCCCCeeeEeeeeecccee-eccCHhhc---CcccccCCCcHHHHHHHHHHhcccCc---ce
Confidence 122232 122399999988888 66543300 122222200 011467999977764 44
Q ss_pred EEec--CCCcccccccCC
Q 045873 432 YGCD--PCRFYLHKSCFE 447 (868)
Q Consensus 432 Y~C~--~C~F~lH~~C~~ 447 (868)
-.|. .|-=.+|..||-
T Consensus 394 IqCs~k~C~t~fHv~CA~ 411 (893)
T KOG0954|consen 394 IQCSNKTCRTAFHVTCAF 411 (893)
T ss_pred EEecccchhhhccchhhh
Confidence 4553 466779999995
No 54
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=80.40 E-value=1.9 Score=54.80 Aligned_cols=122 Identities=24% Similarity=0.463 Sum_probs=79.7
Q ss_pred ccccccccCcCC--ceeEEecCcceeeecccCCCCCCCcccccCCCcceEeeeCCcccCCCCCeeecccccccccCCCce
Q 045873 649 SKCEACRCDIEG--TFFLRCVECKLNFHVQCGPDWLPPTVDQQHHDHPLTLTTGTIVKDNDGDLLRCEICKEERNPNHPS 726 (868)
Q Consensus 649 ~~C~~C~~~~~~--~~~y~C~~C~f~lH~~C~~~~lP~~i~~~~h~H~L~l~~g~~~~~~~g~~~~C~vC~~~~d~~~~~ 726 (868)
..|.+|...... .....|..|+..+|.+|.+ .|. ...|+ |-|--|-..-. +.
T Consensus 220 ~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cyg--i~~--------------------ipeg~-WlCr~Cl~s~~---~~ 273 (1051)
T KOG0955|consen 220 AVCCICLDGECQNSNVIVFCDGCNLAVHQECYG--IPF--------------------IPEGQ-WLCRRCLQSPQ---RP 273 (1051)
T ss_pred ccceeecccccCCCceEEEcCCCcchhhhhccC--CCC--------------------CCCCc-EeehhhccCcC---cc
Confidence 489999977544 4578899999999999999 662 13367 88887765433 22
Q ss_pred EeCCCC------------CceeecccccccCCcCCCCcceEeecceEEEEecCCCcc----cccccccccccccCCCcEe
Q 045873 727 YGCVEC------------ECHAHVRCVITEVPSDEREKLNHFSHDHCLFLVGNQRDD----DGVVCYACEKLVRGQPTYG 790 (868)
Q Consensus 727 Y~C~~C------------~~~lH~~C~~~~~~~~~pg~~~~~~h~h~l~l~~n~~~~----~~~~C~~C~~~i~~~~~y~ 790 (868)
-.|..| +..+|+-||+|. |+. .|.+..-++-+.+...- -+..|+.|+.+- .+.+-+
T Consensus 274 v~c~~cp~~~gAFkqt~dgrw~Hv~caiwi-----pev--~F~nt~~~E~I~~i~~i~~aRwkL~cy~cK~~~-~gaciq 345 (1051)
T KOG0955|consen 274 VRCLLCPSKGGAFKQTDDGRWAHVVCAIWI-----PEV--SFANTVFLEPIDSIENIPPARWKLTCYICKQKG-LGACIQ 345 (1051)
T ss_pred cceEeccCCCCcceeccCCceeeeehhhcc-----ccc--ccccchhhccccchhcCcHhhhhceeeeeccCC-CCccee
Confidence 344444 347999999973 443 33333212212221111 156899999883 477778
Q ss_pred ee--cCCceeehhhhc
Q 045873 791 CD--QCRFYLHKSCAE 804 (868)
Q Consensus 791 C~--~CdFilH~~CA~ 804 (868)
|. .|--..|-+||.
T Consensus 346 cs~~~c~~a~hvtca~ 361 (1051)
T KOG0955|consen 346 CSKANCYTAFHVTCAR 361 (1051)
T ss_pred cchhhhhhhhhhhhHh
Confidence 84 588889999994
No 55
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=75.72 E-value=3.4 Score=38.49 Aligned_cols=81 Identities=20% Similarity=0.351 Sum_probs=51.2
Q ss_pred ecccccccccCCCceEeCCCCCceeecccccccCCcCCCCcceEeecc-eEEE--EecCCCcccccccccccccccCCCc
Q 045873 712 RCEICKEERNPNHPSYGCVECECHAHVRCVITEVPSDEREKLNHFSHD-HCLF--LVGNQRDDDGVVCYACEKLVRGQPT 788 (868)
Q Consensus 712 ~C~vC~~~~d~~~~~Y~C~~C~~~lH~~C~~~~~~~~~pg~~~~~~h~-h~l~--l~~n~~~~~~~~C~~C~~~i~~~~~ 788 (868)
.|.+|.+. .|+..-..-+.-+|+.||+|. |+.++.-... .++. -+..+. . +..|..|..+ .+..
T Consensus 2 ~C~lC~~~----~Galk~t~~~~WvHv~Cal~~-----~~~~~~~~~~~~~v~~~~i~~~~-~-~~~C~iC~~~--~G~~ 68 (110)
T PF13832_consen 2 SCVLCPKR----GGALKRTSDGQWVHVLCALWI-----PEVIFNNGESMEPVDISNIPPSR-F-KLKCSICGKS--GGAC 68 (110)
T ss_pred ccEeCCCC----CCcccCccCCcEEEeEcccee-----CccEEeechhcCcccceeecchh-c-CCcCcCCCCC--Ccee
Confidence 46777764 345554445668999999973 4433221110 1122 122222 1 6899999988 6678
Q ss_pred Eeeec--CCceeehhhhcC
Q 045873 789 YGCDQ--CRFYLHKSCAEL 805 (868)
Q Consensus 789 y~C~~--CdFilH~~CA~l 805 (868)
-+|.. |+-.+|-+||-.
T Consensus 69 i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 69 IKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred EEcCCCCCCcCCCHHHHHH
Confidence 99976 999999999953
No 56
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=74.73 E-value=3.4 Score=49.31 Aligned_cols=118 Identities=25% Similarity=0.540 Sum_probs=72.2
Q ss_pred ccccccCcCCce----eEEe--cCcceeeecccCCCCCCCcccccCCCcceEeeeCCcccCCCCCeeecccccccccCCC
Q 045873 651 CEACRCDIEGTF----FLRC--VECKLNFHVQCGPDWLPPTVDQQHHDHPLTLTTGTIVKDNDGDLLRCEICKEERNPNH 724 (868)
Q Consensus 651 C~~C~~~~~~~~----~y~C--~~C~f~lH~~C~~~~lP~~i~~~~h~H~L~l~~g~~~~~~~g~~~~C~vC~~~~d~~~ 724 (868)
|-+|. .+..| ...| -.|..++|..|-. +- +-+.|. |.|.-||..-..
T Consensus 8 CCVCS--DErGWaeNPLVYCDG~nCsVAVHQaCYG--Iv--------------------qVPtGp-WfCrKCesqera-- 60 (900)
T KOG0956|consen 8 CCVCS--DERGWAENPLVYCDGHNCSVAVHQACYG--IV--------------------QVPTGP-WFCRKCESQERA-- 60 (900)
T ss_pred eeeec--CcCCCccCceeeecCCCceeeeehhcce--eE--------------------ecCCCc-hhhhhhhhhhhh--
Confidence 66776 33333 2337 4689999999987 21 223466 999999876532
Q ss_pred ceEeCCCCCc------------eeecccccccCCcCCCCcceEeecce---EE--EEecCCCcccccccccccccc--c-
Q 045873 725 PSYGCVECEC------------HAHVRCVITEVPSDEREKLNHFSHDH---CL--FLVGNQRDDDGVVCYACEKLV--R- 784 (868)
Q Consensus 725 ~~Y~C~~C~~------------~lH~~C~~~~~~~~~pg~~~~~~h~h---~l--~l~~n~~~~~~~~C~~C~~~i--~- 784 (868)
-...|+-|.. -.||-||| | .||.- |-.-+ ++ ..|+-++. ++.|++|...- +
T Consensus 61 arvrCeLCP~kdGALKkTDn~GWAHVVCAL----Y-IPEVr--FgNV~TMEPIiLq~VP~dRf--nKtCYIC~E~Grpnk 131 (900)
T KOG0956|consen 61 ARVRCELCPHKDGALKKTDNGGWAHVVCAL----Y-IPEVR--FGNVHTMEPIILQDVPHDRF--NKTCYICNEEGRPNK 131 (900)
T ss_pred ccceeecccCcccceecccCCCceEEEEEe----e-cccee--ecccccccceeeccCchhhh--cceeeeecccCCccc
Confidence 2367777754 38999998 2 35542 22222 33 22444443 79999998642 2
Q ss_pred --CCCcEeee--cCCceeehhhhc
Q 045873 785 --GQPTYGCD--QCRFYLHKSCAE 804 (868)
Q Consensus 785 --~~~~y~C~--~CdFilH~~CA~ 804 (868)
.+.+-.|. .|.-.+|-+||.
T Consensus 132 A~~GACMtCNKs~CkqaFHVTCAQ 155 (900)
T KOG0956|consen 132 AAKGACMTCNKSGCKQAFHVTCAQ 155 (900)
T ss_pred cccccceecccccchhhhhhhHhh
Confidence 23444552 466789999996
No 57
>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 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 KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=69.83 E-value=2.5 Score=45.17 Aligned_cols=99 Identities=24% Similarity=0.510 Sum_probs=64.2
Q ss_pred cccccc-ccc---cCCCc---eEeCCCCCCCCCccccCCCCCC--CCCCCCcccEEEecCCCCccCCcCCCCCCCCcEEE
Q 045873 235 YRCDAC-RSY---IDLGM---RYRCDDCDFDMHPECMSLKPNI--KYPAHQHLLIVVEDMSYESQCHGCSLDIEGTFFAR 305 (868)
Q Consensus 235 ~~C~~C-~~~---~~~g~---~Y~C~~C~f~lh~~Ca~~P~~i--~~~~H~H~L~l~~~~~~~~~C~~Cg~~~~~~~~Y~ 305 (868)
..||.| |.. -..|+ .-.|+.|+-+-|+.|..-..++ ..++-.-+-+ .-.-|++||+...+.....
T Consensus 225 ~YCDFclgdsr~nkkt~~peelvscsdcgrsghpsclqft~nm~~avk~yrwqci------eck~csicgtsenddqllf 298 (336)
T KOG1244|consen 225 PYCDFCLGDSRENKKTGMPEELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCI------ECKYCSICGTSENDDQLLF 298 (336)
T ss_pred cccceeccccccccccCCchhhcchhhcCCCCCcchhhhhHHHHHHHHhheeeee------ecceeccccCcCCCceeEe
Confidence 358988 322 12343 5789999999999997655433 2221100000 0235999997654555667
Q ss_pred eeccCceeecCCCCCCCCCCeeeeccCCCceeeeecCCccCCCCcCccccccccccC
Q 045873 306 CVECKLDFHVQCGPAPSLPPTVVHKSHSHPLSLIDKSETLGTDDATHLYCDACKEET 362 (868)
Q Consensus 306 C~~C~f~lH~~C~~lp~~~~~I~~~~H~H~L~l~~~~~~~~~~~~~~~~C~vC~~~~ 362 (868)
|..||=-.|+=|.+-| +.+|.+|.|.|.+|-+++
T Consensus 299 cddcdrgyhmyclspp-----------------------m~eppegswsc~KOG~~~ 332 (336)
T KOG1244|consen 299 CDDCDRGYHMYCLSPP-----------------------MVEPPEGSWSCHLCLEEL 332 (336)
T ss_pred ecccCCceeeEecCCC-----------------------cCCCCCCchhHHHHHHHH
Confidence 9999999999997644 134557889999997665
No 60
>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=69.11 E-value=5.8 Score=31.44 Aligned_cols=32 Identities=22% Similarity=0.536 Sum_probs=26.9
Q ss_pred cCCcCCCCCCCCcEEEeeccCceeecCCCCCC
Q 045873 290 QCHGCSLDIEGTFFARCVECKLDFHVQCGPAP 321 (868)
Q Consensus 290 ~C~~Cg~~~~~~~~Y~C~~C~f~lH~~C~~lp 321 (868)
+|.+||+....+..-.|..|+-.+|..|+.++
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~ 32 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPP 32 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSS
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCC
Confidence 37889886556778889999999999999876
No 61
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=64.57 E-value=2.1 Score=31.97 Aligned_cols=19 Identities=21% Similarity=0.564 Sum_probs=12.6
Q ss_pred EEEeeccCceeecCCCCCC
Q 045873 303 FARCVECKLDFHVQCGPAP 321 (868)
Q Consensus 303 ~Y~C~~C~f~lH~~C~~lp 321 (868)
...|..|++.+|.+|-...
T Consensus 4 ll~C~~C~v~VH~~CYGv~ 22 (36)
T PF13831_consen 4 LLFCDNCNVAVHQSCYGVS 22 (36)
T ss_dssp EEE-SSS--EEEHHHHT-S
T ss_pred eEEeCCCCCcCChhhCCcc
Confidence 5679999999999996554
No 62
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=63.66 E-value=12 Score=35.21 Aligned_cols=87 Identities=16% Similarity=0.371 Sum_probs=47.5
Q ss_pred ccCCcccccCCCCCceecCCCCceeccccccccccccCCCcccccCCCCcCCCccccccc---ccCCCccccCcCCCCC-
Q 045873 114 FDCDYCDESHKDNPFLCCDFCNFQIGAPCATTLIKYHRGQEEHIQHFSHRHPLILLEMEL---EAEDTKCKFCCKSIHG- 189 (868)
Q Consensus 114 ~~C~~C~k~~~~~~~y~C~~Cdf~lh~~Ca~~~~~~~~~~~~~i~hf~H~H~L~~~~~~~---~~~~~~C~~C~~~~~~- 189 (868)
..|..|+.++-+... .|.+|+.-|-++=-+ .+ -+.|--||..+...+ ......|.||......
T Consensus 2 Y~CPrC~skvC~LP~-~CpiCgLtLVss~HL--AR----------SyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~ 68 (112)
T TIGR00622 2 YFCPQCRAKVCELPV-ECPICGLTLILSTHL--AR----------SYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKP 68 (112)
T ss_pred ccCCCCCCCccCCCC-cCCcCCCEEeccchH--HH----------hhhccCCCcccccccccccCCCCcccCcCCCCCCc
Confidence 357788887766663 777775444221000 00 123444555443211 0111259999764321
Q ss_pred ---------CCCcEEeccCCCccccccCCCCcc
Q 045873 190 ---------SQSYYCCGPCNFYIHKSCSELPQQ 213 (868)
Q Consensus 190 ---------~~~~Y~C~~Cd~~~H~~C~~~p~~ 213 (868)
...+|+|..|...|..+|-...-|
T Consensus 69 ~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 69 PVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHE 101 (112)
T ss_pred ccccccccccccceeCCCCCCccccccchhhhh
Confidence 123899999998888888754433
No 63
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=58.66 E-value=10 Score=48.54 Aligned_cols=123 Identities=21% Similarity=0.475 Sum_probs=75.3
Q ss_pred CccCCcCCCCC-C-CCcEEEeeccCceeecCCCCCCCCCCeeeeccCCCceeeeecCCccCCCCcCccccccccccCCCC
Q 045873 288 ESQCHGCSLDI-E-GTFFARCVECKLDFHVQCGPAPSLPPTVVHKSHSHPLSLIDKSETLGTDDATHLYCDACKEETNPS 365 (868)
Q Consensus 288 ~~~C~~Cg~~~-~-~~~~Y~C~~C~f~lH~~C~~lp~~~~~I~~~~H~H~L~l~~~~~~~~~~~~~~~~C~vC~~~~d~~ 365 (868)
...|.+|.... . ....-.|..||..+|++|...|- | -+|+|.|.-|...-..
T Consensus 219 D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~----i---------------------peg~WlCr~Cl~s~~~- 272 (1051)
T KOG0955|consen 219 DAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPF----I---------------------PEGQWLCRRCLQSPQR- 272 (1051)
T ss_pred CccceeecccccCCCceEEEcCCCcchhhhhccCCCC----C---------------------CCCcEeehhhccCcCc-
Confidence 45899996542 2 13346699999999999987552 1 2357777777655432
Q ss_pred CCcccCCCCCc-----------ceeeecccceeeecCCCCcccccCccCccccccccccC-----CCcCcccccccccCC
Q 045873 366 HPCYGCSECDQ-----------YYAHVRCVITEIHLDNTERHKHFSHHHLLVLLENERND-----DIECHACENLIIQGH 429 (868)
Q Consensus 366 ~~~Y~C~~C~~-----------~~~H~~C~~~~~~~d~i~~~kHFsH~H~L~l~~~~~~~-----~~~C~aC~~~~~~~~ 429 (868)
.-.|..|+. -..|+.||+-.+.+ +|.+.+.|..+.+.+.+ ...|-.|..... +
T Consensus 273 --~v~c~~cp~~~gAFkqt~dgrw~Hv~caiwipev-------~F~nt~~~E~I~~i~~i~~aRwkL~cy~cK~~~~--g 341 (1051)
T KOG0955|consen 273 --PVRCLLCPSKGGAFKQTDDGRWAHVVCAIWIPEV-------SFANTVFLEPIDSIENIPPARWKLTCYICKQKGL--G 341 (1051)
T ss_pred --ccceEeccCCCCcceeccCCceeeeehhhccccc-------ccccchhhccccchhcCcHhhhhceeeeeccCCC--C
Confidence 244555531 12388887765555 44544433333222221 467888877664 3
Q ss_pred CcEEecC--CCcccccccCC
Q 045873 430 SAYGCDP--CRFYLHKSCFE 447 (868)
Q Consensus 430 ~~Y~C~~--C~F~lH~~C~~ 447 (868)
..-.|.+ |.=.+|-+||.
T Consensus 342 aciqcs~~~c~~a~hvtca~ 361 (1051)
T KOG0955|consen 342 ACIQCSKANCYTAFHVTCAR 361 (1051)
T ss_pred cceecchhhhhhhhhhhhHh
Confidence 5556653 77789999985
No 64
>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=58.48 E-value=13 Score=34.21 Aligned_cols=83 Identities=17% Similarity=0.344 Sum_probs=44.6
Q ss_pred ecccccccccCCCceEeCCCCCceeecc----cccccCCcCCCCcceEeecceEEEEecCCCcccccccccccccc----
Q 045873 712 RCEICKEERNPNHPSYGCVECECHAHVR----CVITEVPSDEREKLNHFSHDHCLFLVGNQRDDDGVVCYACEKLV---- 783 (868)
Q Consensus 712 ~C~vC~~~~d~~~~~Y~C~~C~~~lH~~----C~~~~~~~~~pg~~~~~~h~h~l~l~~n~~~~~~~~C~~C~~~i---- 783 (868)
-|..|...+.+....+.|..|++....+ .+.......+....+.+..+ ..+..... ...|..|...-
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~----~~~~~~~~-~~~Cp~Cg~~~a~f~ 76 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCGYEKEKKPEDDYKVTEKVKHKIKETIIIREE----DSETLPTT-RVECPKCGHKEAYYW 76 (104)
T ss_pred CCcccCcccccCCCeEECcCCCCccccccccccEEEEEeccccccceeeccc----cccCCCcc-cCCCCCCCCCeeEEE
Confidence 3777888887777788899998864432 22111000000111111111 01111122 46899998753
Q ss_pred ---------cCCCcEeeecCCceee
Q 045873 784 ---------RGQPTYGCDQCRFYLH 799 (868)
Q Consensus 784 ---------~~~~~y~C~~CdFilH 799 (868)
....||.|+.|++.+.
T Consensus 77 ~~Q~RsadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 77 LLQTRRADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred EeccCCCCCCcEEEEEeCCCCCeeE
Confidence 1346999999997654
No 65
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=56.96 E-value=4.7 Score=43.15 Aligned_cols=101 Identities=26% Similarity=0.516 Sum_probs=63.9
Q ss_pred cccccceecc--c--CC---ceEEcCCcCcccccccccCcccceecCCcceEEEEecCCCcccccccccCcCCceeEEec
Q 045873 595 YFCDACRFDV--K--PG---LRYRCDECDFDLHLECLSLKANIRYEDHQHLLILIENMSCKSKCEACRCDIEGTFFLRCV 667 (868)
Q Consensus 595 ~~C~~C~~~~--~--~g---~~Y~C~~C~~~lH~~Ca~~p~p~~~~~H~H~L~l~~~~~~~~~C~~C~~~~~~~~~y~C~ 667 (868)
..|+.|-... + .| -.-.|++|+-+-|+.|.......+..-- ++...=.+-+.|++||.....+..+-|.
T Consensus 225 ~YCDFclgdsr~nkkt~~peelvscsdcgrsghpsclqft~nm~~avk----~yrwqcieck~csicgtsenddqllfcd 300 (336)
T KOG1244|consen 225 PYCDFCLGDSRENKKTGMPEELVSCSDCGRSGHPSCLQFTANMIAAVK----TYRWQCIECKYCSICGTSENDDQLLFCD 300 (336)
T ss_pred cccceeccccccccccCCchhhcchhhcCCCCCcchhhhhHHHHHHHH----hheeeeeecceeccccCcCCCceeEeec
Confidence 3588883321 1 23 3357999999999999765433221100 0000111225789999776666788899
Q ss_pred CcceeeecccCCCCCCCcccccCCCcceEeeeCCcccCCCCCeeecccccccc
Q 045873 668 ECKLNFHVQCGPDWLPPTVDQQHHDHPLTLTTGTIVKDNDGDLLRCEICKEER 720 (868)
Q Consensus 668 ~C~f~lH~~C~~~~lP~~i~~~~h~H~L~l~~g~~~~~~~g~~~~C~vC~~~~ 720 (868)
.||=-+|+.|.+ -| .+ +-+.|. |+|-.|-+++
T Consensus 301 dcdrgyhmycls--pp-m~-----------------eppegs-wsc~KOG~~~ 332 (336)
T KOG1244|consen 301 DCDRGYHMYCLS--PP-MV-----------------EPPEGS-WSCHLCLEEL 332 (336)
T ss_pred ccCCceeeEecC--CC-cC-----------------CCCCCc-hhHHHHHHHH
Confidence 999999999998 33 11 224477 9999996654
No 66
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=56.29 E-value=8.2 Score=42.48 Aligned_cols=49 Identities=22% Similarity=0.385 Sum_probs=29.3
Q ss_pred CCcCCCccccccccc--CC-CccccCcCCCCCCCCcEEeccCCCccccccCCC
Q 045873 161 SHRHPLILLEMELEA--ED-TKCKFCCKSIHGSQSYYCCGPCNFYIHKSCSEL 210 (868)
Q Consensus 161 ~H~H~L~~~~~~~~~--~~-~~C~~C~~~~~~~~~~Y~C~~Cd~~~H~~C~~~ 210 (868)
.|--||.++...+.. .+ ..|.+|..... ++.+|+|..|.-.|...|--+
T Consensus 311 hhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~-~~~~y~C~~Ck~~FCldCDv~ 362 (378)
T KOG2807|consen 311 HHLFPLKPFVEIPETEYNGSRFCFACQGELL-SSGRYRCESCKNVFCLDCDVF 362 (378)
T ss_pred HhhcCCcchhhccccccCCCcceeeeccccC-CCCcEEchhccceeeccchHH
Confidence 345666665443221 11 24999943222 344899999888888888643
No 67
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=53.01 E-value=7.4 Score=32.66 Aligned_cols=59 Identities=17% Similarity=0.233 Sum_probs=34.2
Q ss_pred cccccccccCCCcEeeecCCceeehhhhcCCccccccccccceEEeecCCCCCcceeecccccccc
Q 045873 776 CYACEKLVRGQPTYGCDQCRFYLHKSCAELPRQIQHALHRHSLILKSHTDEGTKEDHECGACLKKL 841 (868)
Q Consensus 776 C~~C~~~i~~~~~y~C~~CdFilH~~CA~lPr~k~h~~h~h~ltL~~~~~~~~~~~~~C~~C~~~~ 841 (868)
|..|... .+..|.|.+|.++..-.=.+--.+++..-..|+|.+...+ ...||-+|..++
T Consensus 1 C~~C~~~--~~~lw~CL~Cg~~~C~~~~~~Ha~~H~~~~~H~l~v~~~~-----~~i~C~~C~~~v 59 (63)
T PF02148_consen 1 CSVCGST--NSNLWLCLTCGYVGCGRYSNGHALKHYKETGHPLAVSLST-----GSIWCYACDDYV 59 (63)
T ss_dssp -SSSHTC--SSSEEEETTTS-EEETTTSTSHHHHHHHHHT--EEEETTT-----TCEEETTTTEEE
T ss_pred CCCCCCc--CCceEEeCCCCcccccCCcCcHHHHhhcccCCeEEEECCC-----CeEEEcCCCcEE
Confidence 5667754 4567999999999877322212223333335999997643 346888887654
No 68
>KOG0694 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=52.97 E-value=5.1 Score=48.33 Aligned_cols=97 Identities=23% Similarity=0.391 Sum_probs=61.6
Q ss_pred CCCCCCCCCCCCCC---ceeeCcCCCCCcccchhhhcCC--cc--ccc-ccCCcceee-eccCccCCCCCCCCCCCcccC
Q 045873 46 PEKCSACDRQPSGS---FYFCKQCWPKSPFFHKLCAELP--RQ--IRI-ALRPHCVLR-LRQESVGPDMSSFLSDKAFDC 116 (868)
Q Consensus 46 ~~~C~~C~~~~~g~---~Y~C~~C~~~~f~~H~~C~~~p--~~--I~~-~~H~~h~L~-l~~~~~~~~~~~~~~~~~~~C 116 (868)
++.|+.|.+.+||. +|.|..|. +++||+|+.+- .. ++. ++-|.-.+. ++- .-.|.+.....++..+|
T Consensus 169 pt~Cs~C~kFi~gL~kqGyQCqvC~---~vvHKkCh~kvv~~C~~~~~~n~e~q~~~~~~~~-~~Phrf~~~~~q~ptFc 244 (694)
T KOG0694|consen 169 PTFCSWCQKFIWGLRKQGYQCQVCW---RVVHKKCHVKVVTLCDFLDNLNSEPQGFLFEFTF-RNPHRFVKLNRQRPTFC 244 (694)
T ss_pred cchhhhhhhheeccCCCceEEeeee---ehHhhhhHHHHHHhccCcCccCcCCccccccccc-cCCCcchhhhccCccHH
Confidence 46799998988884 89999997 79999999832 11 121 222211111 100 00011111133456689
Q ss_pred CcccccCCCCC--ceecCCCCceecccccccc
Q 045873 117 DYCDESHKDNP--FLCCDFCNFQIGAPCATTL 146 (868)
Q Consensus 117 ~~C~k~~~~~~--~y~C~~Cdf~lh~~Ca~~~ 146 (868)
+-||..+.... ...|+.|.-++|..|+...
T Consensus 245 ~hCGs~L~r~~qqGlkCs~Cg~n~H~~c~~~v 276 (694)
T KOG0694|consen 245 DHCGSVLYRLRQQGLKCSTCGRNVHNRCVENL 276 (694)
T ss_pred HhcchhhhhhcccCeeehhhhccccHHHHHhc
Confidence 99999887652 5699999999999999654
No 69
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=48.81 E-value=8 Score=44.24 Aligned_cols=35 Identities=23% Similarity=0.606 Sum_probs=31.2
Q ss_pred cccCCcccccCCCCCceecCCC-Cceeccccccccc
Q 045873 113 AFDCDYCDESHKDNPFLCCDFC-NFQIGAPCATTLI 147 (868)
Q Consensus 113 ~~~C~~C~k~~~~~~~y~C~~C-df~lh~~Ca~~~~ 147 (868)
...|+.|-+.+.+...++|-.| ||||++.|++..+
T Consensus 14 ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs~Ga 49 (438)
T KOG0457|consen 14 KYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSVGA 49 (438)
T ss_pred CCCCccHhHHhccceEEEeecCCCcchhHHHHhccc
Confidence 4579999999999987899999 8999999998654
No 70
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=46.89 E-value=9.9 Score=29.94 Aligned_cols=31 Identities=10% Similarity=0.161 Sum_probs=26.4
Q ss_pred cCCcccccCCCCCceecCCC-Cceecccccccc
Q 045873 115 DCDYCDESHKDNPFLCCDFC-NFQIGAPCATTL 146 (868)
Q Consensus 115 ~C~~C~k~~~~~~~y~C~~C-df~lh~~Ca~~~ 146 (868)
.|+.|+...... +|||... ||+|+..|....
T Consensus 2 ~C~~Cg~D~t~v-ryh~~~~~~~dLC~~CF~~G 33 (45)
T cd02336 2 HCFTCGNDCTRV-RYHNLKAKKYDLCPSCYQEG 33 (45)
T ss_pred cccCCCCccCce-EEEecCCCccccChHHHhCc
Confidence 599999999854 5799999 899999999754
No 71
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=40.36 E-value=22 Score=40.83 Aligned_cols=44 Identities=16% Similarity=0.317 Sum_probs=34.8
Q ss_pred CCCCCCCCCCCc-eeeCcCCCCCcccchhhhcCCcccc-c-ccCCccee
Q 045873 49 CSACDRQPSGSF-YFCKQCWPKSPFFHKLCAELPRQIR-I-ALRPHCVL 94 (868)
Q Consensus 49 C~~C~~~~~g~~-Y~C~~C~~~~f~~H~~C~~~p~~I~-~-~~H~~h~L 94 (868)
|+.|...+.|.. ..|.+|. +|+++-.|...+.++. | +.||-.+.
T Consensus 17 C~~C~~dit~~i~ikCaeCp--~fdLCl~CFs~GaE~~~H~~~H~Yrim 63 (438)
T KOG0457|consen 17 CDYCSLDITGLIRIKCAECP--DFDLCLQCFSVGAETGKHQNDHPYRIM 63 (438)
T ss_pred CccHhHHhccceEEEeecCC--CcchhHHHHhcccccCCCCCCCCceee
Confidence 777878788875 8999996 6999999999998883 3 56666543
No 72
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=39.79 E-value=26 Score=29.20 Aligned_cols=49 Identities=27% Similarity=0.653 Sum_probs=33.1
Q ss_pred CCcCcccccccccC--CCcEEecCCCcccccccCCCCCceecccCCCCccccCCccccccccccceecCceeEeeccCCe
Q 045873 415 DIECHACENLIIQG--HSAYGCDPCRFYLHKSCFELPKVMKHISDSHYLTLQNSSFSERCTACGQQLKGNAIYHCETCDF 492 (868)
Q Consensus 415 ~~~C~aC~~~~~~~--~~~Y~C~~C~F~lH~~C~~lPr~i~h~~~~~~L~~~~~~~~~~C~~C~~~~~g~~~Y~C~~C~~ 492 (868)
...|..|+..|... ..-+.|..|+=.+ .+.|.-||++.+ .|.|..|+|
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~~---------------------------I~RC~~CRk~~~---~Y~CP~CGF 56 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEVI---------------------------IYRCEKCRKQSN---PYTCPKCGF 56 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCee---------------------------EeechhHHhcCC---ceECCCCCC
Confidence 34688888777522 2457787775331 357888998753 599999987
Q ss_pred e
Q 045873 493 D 493 (868)
Q Consensus 493 ~ 493 (868)
.
T Consensus 57 ~ 57 (59)
T PRK14890 57 E 57 (59)
T ss_pred c
Confidence 4
No 73
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=38.96 E-value=9.6 Score=31.97 Aligned_cols=57 Identities=23% Similarity=0.470 Sum_probs=36.5
Q ss_pred cccccccccCCeeeeccCCccccccccCCCc--eecCCCCCCCceEEEecccccccccccceecc
Q 045873 542 CQLCHKNIHGTSYGCTPCMFNIHESCAELPQ--EVRHPFHPRHSLTVQENTFQSRYFCDACRFDV 604 (868)
Q Consensus 542 C~~C~~~i~~~~Y~C~~Cdf~lH~~Ca~lP~--~i~H~~h~~HpL~L~~~~~~~~~~C~~C~~~~ 604 (868)
|+.|... ....|.|.+|++++.- ..+. ..+|..-..|+|.+.... ...||-.|+..+
T Consensus 1 C~~C~~~-~~~lw~CL~Cg~~~C~---~~~~~Ha~~H~~~~~H~l~v~~~~--~~i~C~~C~~~v 59 (63)
T PF02148_consen 1 CSVCGST-NSNLWLCLTCGYVGCG---RYSNGHALKHYKETGHPLAVSLST--GSIWCYACDDYV 59 (63)
T ss_dssp -SSSHTC-SSSEEEETTTS-EEET---TTSTSHHHHHHHHHT--EEEETTT--TCEEETTTTEEE
T ss_pred CCCCCCc-CCceEEeCCCCccccc---CCcCcHHHHhhcccCCeEEEECCC--CeEEEcCCCcEE
Confidence 5677754 5678999999988765 3221 234555557899987654 567999998766
No 74
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=35.53 E-value=15 Score=39.76 Aligned_cols=87 Identities=18% Similarity=0.287 Sum_probs=57.9
Q ss_pred ceEEcCCcCcccccccccCcccceecCCcceEEEEecCCCcccccccccCcCCceeEEecCcceeeecccCCCCCCCccc
Q 045873 608 LRYRCDECDFDLHLECLSLKANIRYEDHQHLLILIENMSCKSKCEACRCDIEGTFFLRCVECKLNFHVQCGPDWLPPTVD 687 (868)
Q Consensus 608 ~~Y~C~~C~~~lH~~Ca~~p~p~~~~~H~H~L~l~~~~~~~~~C~~C~~~~~~~~~y~C~~C~f~lH~~C~~~~lP~~i~ 687 (868)
-+-.|+.|...-|+.|+..++-+...- -++...=.+=.+|.+|+++...+-..-|..||=-.|.-|++ |-
T Consensus 278 S~I~C~~C~~~~HP~Ci~M~~elv~~~----KTY~W~C~~C~lC~IC~~P~~E~E~~FCD~CDRG~HT~CVG--L~---- 347 (381)
T KOG1512|consen 278 SWIVCKPCATRPHPYCVAMIPELVGQY----KTYFWKCSSCELCRICLGPVIESEHLFCDVCDRGPHTLCVG--LQ---- 347 (381)
T ss_pred cceeecccccCCCCcchhcCHHHHhHH----hhcchhhcccHhhhccCCcccchheeccccccCCCCccccc--cc----
Confidence 345799999999999987765443210 01222222335788888876555567799999888999998 42
Q ss_pred ccCCCcceEeeeCCcccCCCCCeeecc--ccccccc
Q 045873 688 QQHHDHPLTLTTGTIVKDNDGDLLRCE--ICKEERN 721 (868)
Q Consensus 688 ~~~h~H~L~l~~g~~~~~~~g~~~~C~--vC~~~~d 721 (868)
.++.|. |-|+ -|++.++
T Consensus 348 ----------------~lP~G~-WICD~~C~~~~~~ 366 (381)
T KOG1512|consen 348 ----------------DLPRGE-WICDMRCREATLN 366 (381)
T ss_pred ----------------cccCcc-chhhhHHHHhcCC
Confidence 246677 9998 4555443
No 75
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=31.18 E-value=20 Score=39.27 Aligned_cols=34 Identities=29% Similarity=0.660 Sum_probs=30.2
Q ss_pred ccCCcccccCCCCCceecCCC-Cceeccccccccc
Q 045873 114 FDCDYCDESHKDNPFLCCDFC-NFQIGAPCATTLI 147 (868)
Q Consensus 114 ~~C~~C~k~~~~~~~y~C~~C-df~lh~~Ca~~~~ 147 (868)
.-|++|-..+....+.+|..| +|||++.|.+..+
T Consensus 6 ~hCdvC~~d~T~~~~i~C~eC~~~DLC~pCF~~g~ 40 (432)
T COG5114 6 IHCDVCFLDMTDLTFIKCNECPAVDLCLPCFVNGI 40 (432)
T ss_pred eeehHHHHhhhcceeeeeecccccceehhhhhccc
Confidence 469999999988878999999 9999999998654
No 76
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=31.09 E-value=36 Score=24.80 Aligned_cols=28 Identities=25% Similarity=0.810 Sum_probs=20.9
Q ss_pred ecccccccccCCCceEeCCCCCceeecc
Q 045873 712 RCEICKEERNPNHPSYGCVECECHAHVR 739 (868)
Q Consensus 712 ~C~vC~~~~d~~~~~Y~C~~C~~~lH~~ 739 (868)
.|-||.++-+.+.-.|+|+.|++.|+..
T Consensus 2 rC~vC~~~k~rk~T~~~C~~C~v~lC~~ 29 (32)
T PF13842_consen 2 RCKVCSKKKRRKDTRYMCSKCDVPLCVE 29 (32)
T ss_pred CCeECCcCCccceeEEEccCCCCcccCC
Confidence 4778877666566889999998777653
No 77
>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=29.71 E-value=59 Score=27.43 Aligned_cols=38 Identities=11% Similarity=0.397 Sum_probs=27.5
Q ss_pred EEEEecCCCcccccccccCcCC---ceeEEecCcceeeecc
Q 045873 639 LILIENMSCKSKCEACRCDIEG---TFFLRCVECKLNFHVQ 676 (868)
Q Consensus 639 L~l~~~~~~~~~C~~C~~~~~~---~~~y~C~~C~f~lH~~ 676 (868)
+..+.+..++.+|..||..... ...|.|..|++..+.+
T Consensus 19 v~~v~~~~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 19 VVEVDEAYTSQTCPRCGHRNKKRRSGRVFTCPNCGFEMDRD 59 (69)
T ss_pred EEEECCCCCccCccCcccccccccccceEEcCCCCCEECcH
Confidence 4444555567899999977543 3479999999987764
No 78
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=29.51 E-value=29 Score=40.22 Aligned_cols=107 Identities=22% Similarity=0.436 Sum_probs=67.0
Q ss_pred eEEecCcceeeecccCCCCCCCcccccCCCcceEeeeCCcccCCCCCeeecccccccccCCCceEeCCCCCc--------
Q 045873 663 FLRCVECKLNFHVQCGPDWLPPTVDQQHHDHPLTLTTGTIVKDNDGDLLRCEICKEERNPNHPSYGCVECEC-------- 734 (868)
Q Consensus 663 ~y~C~~C~f~lH~~C~~~~lP~~i~~~~h~H~L~l~~g~~~~~~~g~~~~C~vC~~~~d~~~~~Y~C~~C~~-------- 734 (868)
.-.|..|+..+|..|-+ +|- .++|+ |-|.-| +-..+-+=.|.-|..
T Consensus 210 iVfCdgC~i~VHq~CYG--I~f--------------------~peG~-WlCrkC---i~~~~~i~~C~fCps~dGaFkqT 263 (669)
T COG5141 210 IVFCDGCEICVHQSCYG--IQF--------------------LPEGF-WLCRKC---IYGEYQIRCCSFCPSSDGAFKQT 263 (669)
T ss_pred EEEecCcchhhhhhccc--cee--------------------cCcch-hhhhhh---cccccceeEEEeccCCCCceeec
Confidence 56699999999999999 551 23466 755444 444445555655532
Q ss_pred ----eeecccccccCCcCCCCcceEeecceEEEEecCC---Ccc-cccccccccccccCCCcEeee--cCCceeehhhhc
Q 045873 735 ----HAHVRCVITEVPSDEREKLNHFSHDHCLFLVGNQ---RDD-DGVVCYACEKLVRGQPTYGCD--QCRFYLHKSCAE 804 (868)
Q Consensus 735 ----~lH~~C~~~~~~~~~pg~~~~~~h~h~l~l~~n~---~~~-~~~~C~~C~~~i~~~~~y~C~--~CdFilH~~CA~ 804 (868)
-.|+-||++- |+. .|+|-+.+..+.|. +.+ ....|..|+++ ++..-+|. .|=-.-|-+||-
T Consensus 264 ~dgrW~H~iCA~~~-----pel--sF~~l~~~dpI~~i~sVs~srwkl~C~iCk~~--~GtcIqCs~~nC~~aYHVtCAr 334 (669)
T COG5141 264 SDGRWGHVICAMFN-----PEL--SFGHLLSKDPIDNIASVSSSRWKLGCLICKEF--GGTCIQCSYFNCTRAYHVTCAR 334 (669)
T ss_pred cCCchHhHhHHHhc-----chh--ccccccccchhhhhcccchhhHhheeeEEccc--Ccceeeecccchhhhhhhhhhh
Confidence 4799999862 443 45555444444432 222 35689999987 56655553 355568999994
No 79
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.94 E-value=84 Score=29.76 Aligned_cols=32 Identities=16% Similarity=0.296 Sum_probs=24.6
Q ss_pred ccCCcccccCCCC-----------CceecCCCCceeccccccc
Q 045873 114 FDCDYCDESHKDN-----------PFLCCDFCNFQIGAPCATT 145 (868)
Q Consensus 114 ~~C~~C~k~~~~~-----------~~y~C~~Cdf~lh~~Ca~~ 145 (868)
..|-.|.+.+.+. ..|.|..|.-+.+++|-..
T Consensus 56 ~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~f 98 (112)
T TIGR00622 56 RFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVF 98 (112)
T ss_pred CcccCcCCCCCCcccccccccccccceeCCCCCCccccccchh
Confidence 4699999977532 2479999988888888753
No 80
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=28.93 E-value=34 Score=25.59 Aligned_cols=22 Identities=32% Similarity=0.773 Sum_probs=15.5
Q ss_pred CCcEeeecCCceeehhhhcCCc
Q 045873 786 QPTYGCDQCRFYLHKSCAELPR 807 (868)
Q Consensus 786 ~~~y~C~~CdFilH~~CA~lPr 807 (868)
++...|..|+...|++|.+++.
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~~ 23 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVSE 23 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-SS
T ss_pred CceEEeCCCCCcCChhhCCccc
Confidence 3568999999999999999877
No 81
>KOG0694 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=27.92 E-value=17 Score=44.04 Aligned_cols=94 Identities=18% Similarity=0.407 Sum_probs=60.1
Q ss_pred ccccccccceecC--ceeEeeccCCeeeccccccccCC----Ccc-ccccCCCCcccCCCcccccccc--ccCEEeec-C
Q 045873 469 SERCTACGQQLKG--NAIYHCETCDFDLDLDCAAQHPS----IKL-EWKASSDDHDENRDGIRHYSHY--HYLTVLDV-G 538 (868)
Q Consensus 469 ~~~C~~C~~~~~g--~~~Y~C~~C~~~lh~~Ca~~~~~----~~l-~~~peee~f~~i~~~i~H~sH~--H~L~~l~~-~ 538 (868)
...|++|++.+-| ...|.|..|..++|.+|+...-. ... ..+|+..-+. +.+. |....++. .
T Consensus 169 pt~Cs~C~kFi~gL~kqGyQCqvC~~vvHKkCh~kvv~~C~~~~~~n~e~q~~~~~--------~~~~~Phrf~~~~~q~ 240 (694)
T KOG0694|consen 169 PTFCSWCQKFIWGLRKQGYQCQVCWRVVHKKCHVKVVTLCDFLDNLNSEPQGFLFE--------FTFRNPHRFVKLNRQR 240 (694)
T ss_pred cchhhhhhhheeccCCCceEEeeeeehHhhhhHHHHHHhccCcCccCcCCcccccc--------ccccCCCcchhhhccC
Confidence 4579999998877 34699999999999999976311 111 2222110011 2222 42221222 3
Q ss_pred Cccccccccccc---CCeeeeccCCccccccccCC
Q 045873 539 DAECQLCHKNIH---GTSYGCTPCMFNIHESCAEL 570 (868)
Q Consensus 539 ~~~C~~C~~~i~---~~~Y~C~~Cdf~lH~~Ca~l 570 (868)
...|+-|+.-.. .....|..|.-..|..|+..
T Consensus 241 ptFc~hCGs~L~r~~qqGlkCs~Cg~n~H~~c~~~ 275 (694)
T KOG0694|consen 241 PTFCDHCGSVLYRLRQQGLKCSTCGRNVHNRCVEN 275 (694)
T ss_pred ccHHHhcchhhhhhcccCeeehhhhccccHHHHHh
Confidence 567888887543 45688999999999999864
No 82
>PF15499 Peptidase_C98: Ubiquitin-specific peptidase-like, SUMO isopeptidase
Probab=26.38 E-value=53 Score=35.47 Aligned_cols=67 Identities=15% Similarity=0.307 Sum_probs=41.5
Q ss_pred CCceEEcCCcCcccccccccCcccceec-CCcceEEEEecCCCcccccccccCc-CCceeEEecCcceeeecc
Q 045873 606 PGLRYRCDECDFDLHLECLSLKANIRYE-DHQHLLILIENMSCKSKCEACRCDI-EGTFFLRCVECKLNFHVQ 676 (868)
Q Consensus 606 ~g~~Y~C~~C~~~lH~~Ca~~p~p~~~~-~H~H~L~l~~~~~~~~~C~~C~~~~-~~~~~y~C~~C~f~lH~~ 676 (868)
..|-+.|+.|++..-.+|......|.-- .-.|||--. -...|+.|+... ...-+|.=..=-|++|+.
T Consensus 131 f~WeFeC~~Cg~~~~~R~~K~L~TFtnv~pdwhPLnA~----h~~pCn~C~~ksQ~rkMvlekv~~vfmLHFV 199 (275)
T PF15499_consen 131 FSWEFECSQCGHKYQNRCTKTLVTFTNVIPDWHPLNAV----HFGPCNSCNSKSQRRKMVLEKVPPVFMLHFV 199 (275)
T ss_pred eEEEEEccccCChhhhhheeeecccCCCCCCCCccccc----ccCCCcccCChHHhHhhhhhcCchhhhhhhh
Confidence 4688999999999999998776666432 223666332 234799998542 111234434445666664
No 83
>KOG1169 consensus Diacylglycerol kinase [Lipid transport and metabolism; Signal transduction mechanisms]
Probab=26.07 E-value=29 Score=41.96 Aligned_cols=96 Identities=19% Similarity=0.258 Sum_probs=55.9
Q ss_pred CcccCCcccccCCCCCceecCCCCceeccccccccccc-----cCCCcccccCCCCcCCCcccccccccCCCccccCcCC
Q 045873 112 KAFDCDYCDESHKDNPFLCCDFCNFQIGAPCATTLIKY-----HRGQEEHIQHFSHRHPLILLEMELEAEDTKCKFCCKS 186 (868)
Q Consensus 112 ~~~~C~~C~k~~~~~~~y~C~~Cdf~lh~~Ca~~~~~~-----~~~~~~~i~hf~H~H~L~~~~~~~~~~~~~C~~C~~~ 186 (868)
++.+|.+|.+..... ...|+.|++.++..|......+ ..+.......-.|.|...+.... ....|..|.+.
T Consensus 43 ~~~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~s~~~~~~~~~~~~~~~k~~~~~~~~~~~~~---~~~~c~~c~~~ 118 (634)
T KOG1169|consen 43 RQMVCCVCLWSEMAP-SVDCDVDGGVSHEECVSGAASDCPLLVLLGFENQRHKTDGDHVWRPKHLW---KPAYCFVCPKS 118 (634)
T ss_pred hhhhhhhhhhccccc-ccceeccccchhhhhhcccccchHHHHHHHhhhhhhhccCceeccCCCCC---CCceEEecccc
Confidence 445899999954433 4689999999999998654322 11111111111233443332221 12356666544
Q ss_pred CCC----CCCcEEeccCCCccccccCCCC
Q 045873 187 IHG----SQSYYCCGPCNFYIHKSCSELP 211 (868)
Q Consensus 187 ~~~----~~~~Y~C~~Cd~~~H~~C~~~p 211 (868)
... ...++.|..|....|+.|...+
T Consensus 119 c~~~~~~~~~g~~C~~C~~~vh~~C~~~~ 147 (634)
T KOG1169|consen 119 CGSCGVGIKQGLCCDWCGRTVHERCVRRA 147 (634)
T ss_pred ccchhhcccCceeeccccchHHHHHHhhc
Confidence 311 2236999999999999998744
No 84
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=25.19 E-value=34 Score=37.04 Aligned_cols=67 Identities=21% Similarity=0.379 Sum_probs=46.6
Q ss_pred eEeCCCCCCCCCccccCCCCCC--CCCCCCcccEEEecCCCCccCCcCCCCCCCCcEEEeeccCceeecCCCCCC
Q 045873 249 RYRCDDCDFDMHPECMSLKPNI--KYPAHQHLLIVVEDMSYESQCHGCSLDIEGTFFARCVECKLDFHVQCGPAP 321 (868)
Q Consensus 249 ~Y~C~~C~f~lh~~Ca~~P~~i--~~~~H~H~L~l~~~~~~~~~C~~Cg~~~~~~~~Y~C~~C~f~lH~~C~~lp 321 (868)
.-+|+.|...-||.|...|..+ ..|+- ...- ..-..|.+|+......-...|..||=-+|.-|+.|.
T Consensus 279 ~I~C~~C~~~~HP~Ci~M~~elv~~~KTY-----~W~C-~~C~lC~IC~~P~~E~E~~FCD~CDRG~HT~CVGL~ 347 (381)
T KOG1512|consen 279 WIVCKPCATRPHPYCVAMIPELVGQYKTY-----FWKC-SSCELCRICLGPVIESEHLFCDVCDRGPHTLCVGLQ 347 (381)
T ss_pred ceeecccccCCCCcchhcCHHHHhHHhhc-----chhh-cccHhhhccCCcccchheeccccccCCCCccccccc
Confidence 5799999999999998887554 22310 0000 113468888877544445669999999999998775
No 85
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=24.41 E-value=58 Score=27.46 Aligned_cols=43 Identities=19% Similarity=0.366 Sum_probs=26.3
Q ss_pred CCCcCccccccccccCCCCCCcccCCCCCcceeeecccceeeec
Q 045873 347 TDDATHLYCDACKEETNPSHPCYGCSECDQYYAHVRCVITEIHL 390 (868)
Q Consensus 347 ~~~~~~~~C~vC~~~~d~~~~~Y~C~~C~~~~~H~~C~~~~~~~ 390 (868)
.++.....|.+|+++......-++|..|+..+. .+|.....++
T Consensus 4 ~~d~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC-~~Cs~~~~~~ 46 (69)
T PF01363_consen 4 VPDSEASNCMICGKKFSLFRRRHHCRNCGRVVC-SSCSSQRIPL 46 (69)
T ss_dssp SSGGG-SB-TTT--B-BSSS-EEE-TTT--EEE-CCCS-EEEEE
T ss_pred CCCCCCCcCcCcCCcCCCceeeEccCCCCCEEC-CchhCCEEcc
Confidence 445556679999999988889999999999998 8888776655
No 86
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=23.79 E-value=34 Score=25.60 Aligned_cols=24 Identities=21% Similarity=0.534 Sum_probs=19.0
Q ss_pred ccccccccCC-CCCCcccCCCCCcc
Q 045873 354 YCDACKEETN-PSHPCYGCSECDQY 377 (868)
Q Consensus 354 ~C~vC~~~~d-~~~~~Y~C~~C~~~ 377 (868)
.|++|+.... ...|+|.|..|+..
T Consensus 10 ~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 10 PCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred cCCCCCCeEeEccCCEEEhhhCceE
Confidence 4999998853 55799999998743
No 87
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=23.03 E-value=1.1e+02 Score=26.41 Aligned_cols=52 Identities=23% Similarity=0.552 Sum_probs=30.9
Q ss_pred cCcCCCCCCCCcEEeccCCC----ccccccCCCCccccCCCCCCCceEEeecCCccccccccccc
Q 045873 182 FCCKSIHGSQSYYCCGPCNF----YIHKSCSELPQQVRHPFHPCHSLTLQNNDLSEWYRCDACRS 242 (868)
Q Consensus 182 ~C~~~~~~~~~~Y~C~~Cd~----~~H~~C~~~p~~i~Hp~Hp~H~L~L~~~~~~~~~~C~~C~~ 242 (868)
.|+.........|+|.+|.. .+..+|++ +.-|++|.+.+..... ++.|| ||.
T Consensus 2 ~C~~~~~~~~~~y~C~tC~~~~~~~iC~~Cf~------~~~H~gH~~~~~~~~~--~~~CD-CG~ 57 (71)
T smart00396 2 VCTYKFTGGEVIYRCKTCGLDPTCVLCSDCFR------SNCHKGHDYSLKTSRG--SGICD-CGD 57 (71)
T ss_pred CCCCccCCCCEEEECcCCCCCCCEeEChHHCC------CCCCCCCCEEEEEecC--CEEEC-CCC
Confidence 35543333445799999964 45566654 2257899988877532 24454 554
No 88
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=22.50 E-value=50 Score=36.63 Aligned_cols=76 Identities=21% Similarity=0.384 Sum_probs=42.9
Q ss_pred CCCcEEeccCCCcccc---ccCC------CCccccCCCCCCCceEEeecCC----cccccccccccccCCCceEeCCCCC
Q 045873 190 SQSYYCCGPCNFYIHK---SCSE------LPQQVRHPFHPCHSLTLQNNDL----SEWYRCDACRSYIDLGMRYRCDDCD 256 (868)
Q Consensus 190 ~~~~Y~C~~Cd~~~H~---~C~~------~p~~i~Hp~Hp~H~L~L~~~~~----~~~~~C~~C~~~~~~g~~Y~C~~C~ 256 (868)
++.+|.|.+|.-.... +|-- +.+.+.-.+|.--||+-..+-+ .+...|-+|+.....+.+|+|..|.
T Consensus 273 ~~~Gy~CP~CkakvCsLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck 352 (378)
T KOG2807|consen 273 SGGGYFCPQCKAKVCSLPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCK 352 (378)
T ss_pred ccCceeCCcccCeeecCCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhcc
Confidence 3447999998654432 2221 1112222234334555433211 1133599995555445699999998
Q ss_pred CCCCccccC
Q 045873 257 FDMHPECMS 265 (868)
Q Consensus 257 f~lh~~Ca~ 265 (868)
-.++..|-.
T Consensus 353 ~~FCldCDv 361 (378)
T KOG2807|consen 353 NVFCLDCDV 361 (378)
T ss_pred ceeeccchH
Confidence 888888854
No 89
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=22.29 E-value=57 Score=26.83 Aligned_cols=34 Identities=24% Similarity=0.669 Sum_probs=29.4
Q ss_pred CCCcCcccccccccCCCcEEecCCCcccccccCC
Q 045873 414 DDIECHACENLIIQGHSAYGCDPCRFYLHKSCFE 447 (868)
Q Consensus 414 ~~~~C~aC~~~~~~~~~~Y~C~~C~F~lH~~C~~ 447 (868)
....|.+|++++..++..-.|.+|.=..|+.|.+
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~ 37 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWE 37 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHh
Confidence 3578999999995447889999999999999986
No 90
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=21.89 E-value=81 Score=24.89 Aligned_cols=33 Identities=15% Similarity=0.172 Sum_probs=27.9
Q ss_pred CCCCCCCCCCCceeeCcCCCCCcccchhhhcCCcc
Q 045873 49 CSACDRQPSGSFYFCKQCWPKSPFFHKLCAELPRQ 83 (868)
Q Consensus 49 C~~C~~~~~g~~Y~C~~C~~~~f~~H~~C~~~p~~ 83 (868)
|+.|+.......|+|.... +++|+..|...++.
T Consensus 3 C~~Cg~D~t~vryh~~~~~--~~dLC~~CF~~G~f 35 (45)
T cd02336 3 CFTCGNDCTRVRYHNLKAK--KYDLCPSCYQEGRF 35 (45)
T ss_pred ccCCCCccCceEEEecCCC--ccccChHHHhCcCC
Confidence 7888888888889999986 69999999987653
No 91
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=21.44 E-value=32 Score=36.65 Aligned_cols=29 Identities=17% Similarity=0.551 Sum_probs=19.5
Q ss_pred CccccccccccCC-CCCCcccCCCCCccee
Q 045873 351 THLYCDACKEETN-PSHPCYGCSECDQYYA 379 (868)
Q Consensus 351 ~~~~C~vC~~~~d-~~~~~Y~C~~C~~~~~ 379 (868)
+.--|..|.++.. .-.|-|.|..|..-++
T Consensus 119 gr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD 148 (332)
T KOG2272|consen 119 GRALCRECNQKEKAKGRGRYVCQKCHAHID 148 (332)
T ss_pred chHHhhhhhhhhcccccceeehhhhhhhcc
Confidence 3445888877764 3367888888875553
No 92
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=20.56 E-value=78 Score=28.76 Aligned_cols=32 Identities=25% Similarity=0.646 Sum_probs=25.8
Q ss_pred CCCcCcccccccccCCCcEEecCCCcccccccCC
Q 045873 414 DDIECHACENLIIQGHSAYGCDPCRFYLHKSCFE 447 (868)
Q Consensus 414 ~~~~C~aC~~~~~~~~~~Y~C~~C~F~lH~~C~~ 447 (868)
....|..|+.++. .+.+.=.+|+-++|..|++
T Consensus 77 ~~~~C~vC~k~l~--~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLG--NSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCC--CceEEEeCCCeEEeccccc
Confidence 3678999999998 3555556788999999985
Done!