Query psy7971
Match_columns 276
No_of_seqs 255 out of 348
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 23:31:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7971.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7971hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4582|consensus 100.0 9.5E-31 2.1E-35 242.7 9.2 198 11-208 57-278 (278)
2 PF06701 MIB_HERC2: Mib_herc2; 100.0 6.1E-31 1.3E-35 196.7 5.3 68 157-224 1-68 (68)
3 PF06701 MIB_HERC2: Mib_herc2; 99.8 2.5E-21 5.5E-26 144.9 4.8 60 18-77 1-68 (68)
4 cd02344 ZZ_HERC2 Zinc finger, 99.7 4.6E-18 1E-22 117.7 2.9 45 86-130 1-45 (45)
5 cd02339 ZZ_Mind_bomb Zinc fing 99.6 6.7E-17 1.5E-21 111.9 2.9 45 86-130 1-45 (45)
6 cd02340 ZZ_NBR1_like Zinc fing 99.6 1.4E-15 3.1E-20 104.3 2.6 43 86-130 1-43 (43)
7 cd02334 ZZ_dystrophin Zinc fin 99.5 2.4E-15 5.2E-20 105.9 2.8 44 86-129 1-48 (49)
8 cd02341 ZZ_ZZZ3 Zinc finger, Z 99.5 2.8E-15 6.2E-20 105.1 2.9 45 86-130 1-48 (48)
9 PF00569 ZZ: Zinc finger, ZZ t 99.5 8.2E-15 1.8E-19 101.7 2.2 46 82-127 1-46 (46)
10 cd02338 ZZ_PCMF_like Zinc fing 99.5 2.6E-14 5.6E-19 100.6 3.5 44 86-129 1-48 (49)
11 cd02345 ZZ_dah Zinc finger, ZZ 99.5 2E-14 4.4E-19 101.1 2.4 45 86-130 1-49 (49)
12 cd02342 ZZ_UBA_plant Zinc fing 99.4 1.2E-13 2.6E-18 94.3 1.6 33 86-118 1-33 (43)
13 cd02249 ZZ Zinc finger, ZZ typ 99.3 4.4E-13 9.4E-18 92.8 2.6 44 86-130 1-46 (46)
14 cd02335 ZZ_ADA2 Zinc finger, Z 99.3 9.1E-13 2E-17 92.6 2.7 43 87-129 2-48 (49)
15 cd02343 ZZ_EF Zinc finger, ZZ 99.3 6.7E-13 1.5E-17 93.0 1.6 42 86-128 1-46 (48)
16 smart00291 ZnF_ZZ Zinc-binding 99.3 2.2E-12 4.7E-17 88.6 2.6 43 83-126 2-44 (44)
17 KOG1280|consensus 99.1 2.4E-11 5.2E-16 114.9 3.6 59 81-139 4-66 (381)
18 KOG4286|consensus 99.1 2.3E-11 5.1E-16 123.8 0.3 83 80-163 599-696 (966)
19 cd02337 ZZ_CBP Zinc finger, ZZ 99.0 8.3E-11 1.8E-15 80.0 0.9 39 86-128 1-39 (41)
20 KOG4301|consensus 98.3 6.9E-08 1.5E-12 91.8 -1.0 55 80-135 236-294 (434)
21 KOG0457|consensus 98.3 2.5E-07 5.4E-12 90.2 2.0 53 85-139 14-71 (438)
22 cd02336 ZZ_RSC8 Zinc finger, Z 97.9 9.1E-06 2E-10 56.4 2.3 40 86-126 1-40 (45)
23 COG5114 Histone acetyltransfer 97.8 6.4E-06 1.4E-10 78.1 1.6 54 85-139 5-62 (432)
24 KOG4582|consensus 96.1 0.0022 4.8E-08 60.1 1.1 95 152-246 59-166 (278)
25 PF07649 C1_3: C1-like domain; 93.8 0.027 5.8E-07 35.3 0.8 27 87-115 2-29 (30)
26 PF03107 C1_2: C1 domain; Int 89.1 0.34 7.3E-06 30.4 2.1 27 87-115 2-29 (30)
27 KOG1778|consensus 88.1 0.2 4.4E-06 48.0 0.9 43 85-131 169-211 (319)
28 PF02207 zf-UBR: Putative zinc 78.3 1.6 3.4E-05 32.6 2.0 35 98-133 11-48 (71)
29 PF00643 zf-B_box: B-box zinc 69.9 6.6 0.00014 25.7 3.2 40 85-130 3-42 (42)
30 smart00396 ZnF_UBR1 Putative z 52.7 14 0.0003 27.6 2.6 31 100-131 13-46 (71)
31 KOG4317|consensus 37.8 11 0.00023 36.5 -0.0 41 86-130 8-49 (383)
32 PF13842 Tnp_zf-ribbon_2: DDE_ 37.7 24 0.00051 22.5 1.6 27 87-114 2-29 (32)
33 cd00021 BBOX B-Box-type zinc f 36.8 37 0.00079 21.3 2.4 37 87-129 2-38 (39)
34 KOG2990|consensus 35.9 13 0.00029 35.4 0.3 19 85-103 52-70 (317)
35 PF07975 C1_4: TFIIH C1-like d 35.9 11 0.00023 26.9 -0.3 18 99-117 20-37 (51)
36 KOG2807|consensus 35.8 20 0.00044 34.8 1.5 31 86-117 331-361 (378)
37 KOG1280|consensus 34.5 23 0.0005 34.7 1.7 67 62-128 23-96 (381)
38 PF14445 Prok-RING_2: Prokaryo 34.1 4.1 8.8E-05 29.3 -2.6 33 85-117 7-49 (57)
39 PF14599 zinc_ribbon_6: Zinc-r 33.3 18 0.00039 26.6 0.6 28 85-112 30-60 (61)
40 cd06402 PB1_p62 The PB1 domain 32.0 7 0.00015 30.8 -1.9 34 26-65 49-82 (87)
41 COG5259 RSC8 RSC chromatin rem 31.2 20 0.00044 36.4 0.7 38 82-121 222-259 (531)
42 PF03811 Zn_Tnp_IS1: InsA N-te 29.7 37 0.00081 22.3 1.6 22 85-106 5-35 (36)
43 PF09862 DUF2089: Protein of u 28.3 39 0.00085 27.9 1.8 29 88-117 1-34 (113)
44 PF06507 Auxin_resp: Auxin res 26.0 1.1E+02 0.0023 23.9 3.8 60 126-189 10-71 (83)
45 PF00130 C1_1: Phorbol esters/ 25.8 51 0.0011 22.4 1.8 22 85-107 11-35 (53)
46 PF07754 DUF1610: Domain of un 25.7 46 0.001 20.2 1.3 19 88-106 1-22 (24)
47 cd00029 C1 Protein kinase C co 25.5 39 0.00084 22.3 1.1 22 84-106 10-34 (50)
48 smart00109 C1 Protein kinase C 24.3 43 0.00092 21.8 1.1 23 83-106 9-33 (49)
49 PF12760 Zn_Tnp_IS1595: Transp 23.6 58 0.0013 22.0 1.7 23 85-107 18-44 (46)
50 KOG1244|consensus 23.6 65 0.0014 30.8 2.5 67 69-135 227-316 (336)
51 TIGR00622 ssl1 transcription f 23.3 66 0.0014 26.5 2.3 30 86-117 56-97 (112)
52 PRK05585 yajC preprotein trans 23.1 1.3E+02 0.0029 24.2 4.0 37 9-57 47-83 (106)
53 PRK14890 putative Zn-ribbon RN 23.0 54 0.0012 24.1 1.5 32 86-117 8-44 (59)
54 smart00336 BBOX B-Box-type zin 21.9 1.2E+02 0.0026 19.2 2.9 37 86-128 4-40 (42)
55 PF08940 DUF1918: Domain of un 20.2 1.2E+02 0.0026 22.3 2.8 34 175-211 19-53 (58)
No 1
>KOG4582|consensus
Probab=99.97 E-value=9.5e-31 Score=242.65 Aligned_cols=198 Identities=35% Similarity=0.602 Sum_probs=175.7
Q ss_pred chhhccccceEEeCCCCccCCc---CCCCCceeEEEeeCC--------CC-ceEEEEcCCCCcceee----cCceeeeee
Q psy7971 11 RFAMEGVGARVIRGPDWKWGKQ---DGGDGHVGTVRNFES--------PE-EVVVVWDNGTAANYRC----AGAFDLRIL 74 (276)
Q Consensus 11 ~~~~~~vG~RVvRGpdWkWg~q---Dgg~g~vGtVv~~ss--------~e-evvV~WD~G~~~~YR~----~g~~DL~lv 74 (276)
++-...++.||++|.+|.|-.+ +...++++++..|.. .. .+.+.|+.....+++. .+..++.+.
T Consensus 57 ~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~s~~k~~~~~~~~~~~~~~ 136 (278)
T KOG4582|consen 57 YSDEDGVGMRVVRGNDLFDVTNQRLADEIGHVNAVRSFNSAAPSSGSSTPATVPVPWDKIPRSIIKVLEKYQKLASLVIT 136 (278)
T ss_pred hhhccccceeEEecCCceEeecccCccccccccceeeeccccccccccCccccccccchhhhhhhhhhHHHhhhhhhhhh
Confidence 3445578999999999999999 555777788887732 22 3566799888888775 345677778
Q ss_pred cCCCCCCCCCC-----CcCCCCCCCceeeeeeeeccCCCCeeecccccCcccCCCceeEE---EeeCCCceeeecccccc
Q psy7971 75 DSAPTGVKHDG-----TMCDFCKQQPIYGIRWKCAECSNYDLCSICYHAEKHNLRHRFYR---INFPGSERVLLEPRRKS 146 (276)
Q Consensus 75 D~ap~~v~H~~-----v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~~H~~~H~f~r---i~~P~~~~V~lepRr~~ 146 (276)
++++.+..|++ +.||.|...+|+|.||||++|+|||||+.||....||.+|.|.| ..+|....+.+..++.+
T Consensus 137 ~~~~~~~~H~~~~~~~v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~~~h~~H~~lR~~t~~t~~~~~~~~~~p~~~ 216 (278)
T KOG4582|consen 137 LNPVVGEMHPNISKLSVPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGNEHHAAHAMLRLHTNETPFSGYVMLSSPPNP 216 (278)
T ss_pred cCCCccccCCCcccccccCCCccCCccccceeeecCCCccchhHHhhcCCCCCcccceeecccccCCCCcceeccCCCCc
Confidence 99999999999 99999998899999999999999999999999887889999999 88999999999999999
Q ss_pred CcceeeeeecCceEeecCCCccccCCCCCCCcceEEEeCCCCcCCCCceeEEEecCCCceee
Q psy7971 147 KKISVRGIFPGARVVRGVDWQWEDQDGGNGRRGKVNEVQDWSAASPRSAAYIVWDNGAKNLY 208 (276)
Q Consensus 147 ~~~~~~g~~~g~~v~rG~DW~w~dQDgg~g~~G~V~~~~~w~~~~~~~~v~V~Wd~g~~n~Y 208 (276)
......++++|..+.||++|+|++|+++++..|+|.++..|.+..+++.+.+-|+.|..+.|
T Consensus 217 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 278 (278)
T KOG4582|consen 217 VNLNKRPIFVGHSKVRGNDWYWTSLGGGEGRIGRVNEIVLWINGPRRSSAVVYWVMGSENDY 278 (278)
T ss_pred ccccccccccccccccccCCccccccCCCCCCccccccccccccccccceeeecCCCccCCC
Confidence 99899999999999999999999999999999999999999999999999999999988876
No 2
>PF06701 MIB_HERC2: Mib_herc2; InterPro: IPR010606 Mib is a RING ubiquitin ligase in the Notch pathway. Mib interacts with the intracellular domain of Delta to promote its ubiquitylation and internalisation. Cell transplantation studies suggest that mib function is essential in the signalling cell for efficient activation of Notch in neighbouring cells. This domain has been named 'mib/herc2 domain' in []and usually the protein also contains an E3 ligase domain (either Ring or Hect).; GO: 0004842 ubiquitin-protein ligase activity, 0046872 metal ion binding, 0016567 protein ubiquitination; PDB: 2DK3_A 3DKM_A.
Probab=99.96 E-value=6.1e-31 Score=196.67 Aligned_cols=68 Identities=57% Similarity=1.119 Sum_probs=48.4
Q ss_pred CceEeecCCCccccCCCCCCCcceEEEeCCCCcCCCCceeEEEecCCCceeeeeccCCeeeEEEeeCC
Q psy7971 157 GARVVRGVDWQWEDQDGGNGRRGKVNEVQDWSAASPRSAAYIVWDNGAKNLYRVGFEGMADLKVLNDA 224 (276)
Q Consensus 157 g~~v~rG~DW~w~dQDgg~g~~G~V~~~~~w~~~~~~~~v~V~Wd~g~~n~YR~G~~g~~Dl~~~~~~ 224 (276)
|+||+|||||+|+|||||+|++|||++|++|++.+++++|.|+||+|.+|+||+|++|+|||+++++|
T Consensus 1 G~rVvRGpDW~WgdQDGG~g~~GtV~~i~~~~~~~~~~~v~V~Wd~G~~~~YR~G~~G~~DL~~~~~a 68 (68)
T PF06701_consen 1 GARVVRGPDWKWGDQDGGEGHVGTVVSIRDWSSESPDGWVVVQWDNGTRNNYRVGYEGKYDLKVVDNA 68 (68)
T ss_dssp TSEEEE-TT--STTTTSSTT--EEE-S--------BTTEEEEEETTTEEEEEEBSCCC-B-EEE-T--
T ss_pred CCeeeeCcCCCccCcCCCCCcceEEEecccccccCCCCeEEEEeCCCCceeccccCCCCEEEEEecCC
Confidence 79999999999999999999999999999999999999999999999999999999999999999986
No 3
>PF06701 MIB_HERC2: Mib_herc2; InterPro: IPR010606 Mib is a RING ubiquitin ligase in the Notch pathway. Mib interacts with the intracellular domain of Delta to promote its ubiquitylation and internalisation. Cell transplantation studies suggest that mib function is essential in the signalling cell for efficient activation of Notch in neighbouring cells. This domain has been named 'mib/herc2 domain' in []and usually the protein also contains an E3 ligase domain (either Ring or Hect).; GO: 0004842 ubiquitin-protein ligase activity, 0046872 metal ion binding, 0016567 protein ubiquitination; PDB: 2DK3_A 3DKM_A.
Probab=99.83 E-value=2.5e-21 Score=144.85 Aligned_cols=60 Identities=63% Similarity=1.224 Sum_probs=44.2
Q ss_pred cceEEeCCCCccCCcCCCCCceeEEEee------CCCCceEEEEcCCCCcceee--cCceeeeeecCC
Q psy7971 18 GARVIRGPDWKWGKQDGGDGHVGTVRNF------ESPEEVVVVWDNGTAANYRC--AGAFDLRILDSA 77 (276)
Q Consensus 18 G~RVvRGpdWkWg~qDgg~g~vGtVv~~------ss~eevvV~WD~G~~~~YR~--~g~~DL~lvD~a 77 (276)
|+||||||||||++||||++++|||+++ +.++++.|+||++..++||+ +++|||+++++|
T Consensus 1 G~rVvRGpDW~WgdQDGG~g~~GtV~~i~~~~~~~~~~~v~V~Wd~G~~~~YR~G~~G~~DL~~~~~a 68 (68)
T PF06701_consen 1 GARVVRGPDWKWGDQDGGEGHVGTVVSIRDWSSESPDGWVVVQWDNGTRNNYRVGYEGKYDLKVVDNA 68 (68)
T ss_dssp TSEEEE-TT--STTTTSSTT--EEE-S--------BTTEEEEEETTTEEEEEEBSCCC-B-EEE-T--
T ss_pred CCeeeeCcCCCccCcCCCCCcceEEEecccccccCCCCeEEEEeCCCCceeccccCCCCEEEEEecCC
Confidence 7899999999999999999999999995 45678999999999999998 599999999875
No 4
>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=99.71 E-value=4.6e-18 Score=117.67 Aligned_cols=45 Identities=47% Similarity=1.068 Sum_probs=43.5
Q ss_pred CcCCCCCCCceeeeeeeeccCCCCeeecccccCcccCCCceeEEE
Q psy7971 86 TMCDFCKQQPIYGIRWKCAECSNYDLCSICYHAEKHNLRHRFYRI 130 (276)
Q Consensus 86 v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~~H~~~H~f~ri 130 (276)
|.||+|++.||.|.||||++|+|||||+.||.++.|+..|+|.||
T Consensus 1 V~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~~~H~~~H~F~ri 45 (45)
T cd02344 1 VTCDGCQMFPINGPRFKCRNCDDFDFCENCFKTRKHNTRHTFGRI 45 (45)
T ss_pred CCCCCCCCCCCccCeEECCCCCCccchHHhhCCCCcCCCCceeeC
Confidence 689999999999999999999999999999999999999999986
No 5
>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=99.65 E-value=6.7e-17 Score=111.92 Aligned_cols=45 Identities=67% Similarity=1.513 Sum_probs=43.1
Q ss_pred CcCCCCCCCceeeeeeeeccCCCCeeecccccCcccCCCceeEEE
Q psy7971 86 TMCDFCKQQPIYGIRWKCAECSNYDLCSICYHAEKHNLRHRFYRI 130 (276)
Q Consensus 86 v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~~H~~~H~f~ri 130 (276)
+.||+|++.||.|.||||++|+|||||+.||..+.|++.|+|+|+
T Consensus 1 i~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~~~~H~~~H~f~r~ 45 (45)
T cd02339 1 IICDTCRKQGIIGIRWKCAECPNYDLCTTCYHGDKHDLEHRFYRY 45 (45)
T ss_pred CCCCCCCCCCcccCeEECCCCCCccchHHHhCCCCCCCCCCEEeC
Confidence 589999999999999999999999999999999999999999875
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=99.56 E-value=1.4e-15 Score=104.26 Aligned_cols=43 Identities=42% Similarity=1.003 Sum_probs=40.4
Q ss_pred CcCCCCCCCceeeeeeeeccCCCCeeecccccCcccCCCceeEEE
Q psy7971 86 TMCDFCKQQPIYGIRWKCAECSNYDLCSICYHAEKHNLRHRFYRI 130 (276)
Q Consensus 86 v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~~H~~~H~f~ri 130 (276)
|.||+|++ +|.|.||||++|+|||||+.||..+.| +.|+|+++
T Consensus 1 v~Cd~C~~-~i~G~ry~C~~C~d~dLC~~C~~~~~H-~~H~f~~~ 43 (43)
T cd02340 1 VICDGCQG-PIVGVRYKCLVCPDYDLCESCEAKGVH-PEHAMLKI 43 (43)
T ss_pred CCCCCCCC-cCcCCeEECCCCCCccchHHhhCcCCC-CCCCEEeC
Confidence 68999996 999999999999999999999999988 99999875
No 7
>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=99.54 E-value=2.4e-15 Score=105.95 Aligned_cols=44 Identities=39% Similarity=1.002 Sum_probs=40.4
Q ss_pred CcCCCCCCCceeeeeeeeccCCCCeeecccccCc----ccCCCceeEE
Q psy7971 86 TMCDFCKQQPIYGIRWKCAECSNYDLCSICYHAE----KHNLRHRFYR 129 (276)
Q Consensus 86 v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~----~H~~~H~f~r 129 (276)
|.||+|++.||.|+||||+.|+|||||+.||..+ .|...|||.+
T Consensus 1 ~~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~~~~~H~~~Hp~~e 48 (49)
T cd02334 1 AKCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRTSKSHKNSHPMKE 48 (49)
T ss_pred CCCCCCCCCCceeeeEECCCCCCcCchHHHHhCCCcCCCCCCCCCeec
Confidence 5899999999999999999999999999999864 6889999865
No 8
>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=99.54 E-value=2.8e-15 Score=105.13 Aligned_cols=45 Identities=38% Similarity=0.880 Sum_probs=42.3
Q ss_pred CcCCCCCCCceeeeeeeeccCC--CCeeecccccCc-ccCCCceeEEE
Q psy7971 86 TMCDFCKQQPIYGIRWKCAECS--NYDLCSICYHAE-KHNLRHRFYRI 130 (276)
Q Consensus 86 v~Cd~C~~~pI~G~RykC~~C~--dfDLC~~C~~~~-~H~~~H~f~ri 130 (276)
+.||+|++.||.|+||+|++|+ |||||+.||.++ .|+..|+|.+|
T Consensus 1 y~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~~~H~~~H~~~~i 48 (48)
T cd02341 1 FKCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKGESHQEDHWLVKI 48 (48)
T ss_pred CCCCCCCCCccccceEECCCCCCCCCccCHHHHhCcCCCCCCCceeeC
Confidence 4799999999999999999999 999999999988 89999999875
No 9
>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=99.49 E-value=8.2e-15 Score=101.65 Aligned_cols=46 Identities=39% Similarity=1.021 Sum_probs=36.5
Q ss_pred CCCCCcCCCCCCCceeeeeeeeccCCCCeeecccccCcccCCCcee
Q psy7971 82 KHDGTMCDFCKQQPIYGIRWKCAECSNYDLCSICYHAEKHNLRHRF 127 (276)
Q Consensus 82 ~H~~v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~~H~~~H~f 127 (276)
.|.++.||+|+..||.|.||+|++|+|||||+.||..+.++..|++
T Consensus 1 ~h~~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~g~~~~~H~~ 46 (46)
T PF00569_consen 1 IHHGYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSKGRHSHNHKM 46 (46)
T ss_dssp -CSSCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH--H-SSSSE
T ss_pred CCCCeECcCCCCCcCcCCeEECCCCCCCchhhHHHhCcCCCCCcCc
Confidence 4889999999988999999999999999999999999887778864
No 10
>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=99.47 E-value=2.6e-14 Score=100.56 Aligned_cols=44 Identities=36% Similarity=0.840 Sum_probs=40.6
Q ss_pred CcCCCCCCCceeeeeeeeccCCCCeeecccccCc----ccCCCceeEE
Q psy7971 86 TMCDFCKQQPIYGIRWKCAECSNYDLCSICYHAE----KHNLRHRFYR 129 (276)
Q Consensus 86 v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~----~H~~~H~f~r 129 (276)
|.||+|++.||.|.||||+.|+|||||+.||..+ .|.++|+|..
T Consensus 1 i~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~~~~~~~H~~~H~~~~ 48 (49)
T cd02338 1 VSCDGCGKSNFTGRRYKCLICYDYDLCADCYDSGVTTERHLFDHPMQC 48 (49)
T ss_pred CCCCCCcCCCcEEeeEEeCCCCCCccchhHHhCCCcCCCCCCCCCEEE
Confidence 5899999999999999999999999999999976 7888999864
No 11
>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=99.46 E-value=2e-14 Score=101.11 Aligned_cols=45 Identities=40% Similarity=0.943 Sum_probs=40.7
Q ss_pred CcCCCCCCCceeeeeeeeccCCCCeeecccccCc----ccCCCceeEEE
Q psy7971 86 TMCDFCKQQPIYGIRWKCAECSNYDLCSICYHAE----KHNLRHRFYRI 130 (276)
Q Consensus 86 v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~----~H~~~H~f~ri 130 (276)
+.||+|.+.||.|+||+|++|+|||||..||..+ .|++.|+|..+
T Consensus 1 ~~C~~C~~~~i~g~R~~C~~C~dydLC~~Cf~~~~~~~~H~~~H~~~~~ 49 (49)
T cd02345 1 LSCSACRKQDISGIRFPCQVCRDYSLCLGCYTKGRETKRHNSLHIMYEL 49 (49)
T ss_pred CcCCCCCCCCceEeeEECCCCCCcCchHHHHhCCCcCCCCCCCCCcccC
Confidence 4799999889999999999999999999999964 69999999653
No 12
>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=99.38 E-value=1.2e-13 Score=94.33 Aligned_cols=33 Identities=42% Similarity=0.899 Sum_probs=31.6
Q ss_pred CcCCCCCCCceeeeeeeeccCCCCeeecccccC
Q psy7971 86 TMCDFCKQQPIYGIRWKCAECSNYDLCSICYHA 118 (276)
Q Consensus 86 v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~ 118 (276)
|.||+|.+.||.|.||||+.|+|||||+.||..
T Consensus 1 I~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~ 33 (43)
T cd02342 1 IQCDGCGVLPITGPRYKSKVKEDYDLCTICFSR 33 (43)
T ss_pred CCCCCCCCCcccccceEeCCCCCCccHHHHhhh
Confidence 689999999999999999999999999999975
No 13
>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=99.34 E-value=4.4e-13 Score=92.84 Aligned_cols=44 Identities=43% Similarity=0.985 Sum_probs=40.3
Q ss_pred CcCCCCCCCceeeeeeeeccCCCCeeecccccCc--ccCCCceeEEE
Q psy7971 86 TMCDFCKQQPIYGIRWKCAECSNYDLCSICYHAE--KHNLRHRFYRI 130 (276)
Q Consensus 86 v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~--~H~~~H~f~ri 130 (276)
+.||+|.+ +|.|.||+|+.|+|||||..||..+ .|.+.|+|.++
T Consensus 1 ~~C~~C~~-~i~g~r~~C~~C~d~dLC~~Cf~~~~~~H~~~H~~~~~ 46 (46)
T cd02249 1 YSCDGCLK-PIVGVRYHCLVCEDFDLCSSCYAKGKKGHPPDHSFTEI 46 (46)
T ss_pred CCCcCCCC-CCcCCEEECCCCCCCcCHHHHHCcCcCCCCCCCCEeEC
Confidence 47999996 9999999999999999999999987 88889999764
No 14
>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=99.31 E-value=9.1e-13 Score=92.56 Aligned_cols=43 Identities=42% Similarity=0.927 Sum_probs=39.6
Q ss_pred cCCCCCCCceeeeeeeeccCCCCeeecccccCc----ccCCCceeEE
Q psy7971 87 MCDFCKQQPIYGIRWKCAECSNYDLCSICYHAE----KHNLRHRFYR 129 (276)
Q Consensus 87 ~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~----~H~~~H~f~r 129 (276)
.||+|.+.++.|.||+|++|+|||||..||..+ .|.+.|+|..
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~~~~~H~~~H~~~~ 48 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAGAEIGKHRNDHNYRV 48 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcCCCCCCCCCCCeEe
Confidence 699999999999999999999999999999975 7999999864
No 15
>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=99.30 E-value=6.7e-13 Score=93.01 Aligned_cols=42 Identities=31% Similarity=0.757 Sum_probs=36.7
Q ss_pred CcCCCCCCCceeeeeeeeccCCCCeeecccccC----cccCCCceeE
Q psy7971 86 TMCDFCKQQPIYGIRWKCAECSNYDLCSICYHA----EKHNLRHRFY 128 (276)
Q Consensus 86 v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~----~~H~~~H~f~ 128 (276)
|.||+|.. .+.|+||||+.|+|||||+.||.. +.|..+|+|.
T Consensus 1 i~CdgC~~-~~~~~RykCl~C~d~DlC~~Cf~~g~~~~~H~~~Hpm~ 46 (48)
T cd02343 1 ISCDGCDE-IAPWHRYRCLQCTDMDLCKTCFLGGVKPEGHEDDHEMV 46 (48)
T ss_pred CCCCCCCC-cCCCceEECCCCCCchhHHHHHhCCccCCCCCCCCCcc
Confidence 57999996 688999999999999999999996 4677888874
No 16
>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=99.27 E-value=2.2e-12 Score=88.65 Aligned_cols=43 Identities=37% Similarity=0.965 Sum_probs=38.8
Q ss_pred CCCCcCCCCCCCceeeeeeeeccCCCCeeecccccCcccCCCce
Q psy7971 83 HDGTMCDFCKQQPIYGIRWKCAECSNYDLCSICYHAEKHNLRHR 126 (276)
Q Consensus 83 H~~v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~~H~~~H~ 126 (276)
|..+.|+.|++ +|.|.||+|+.|+|||||..||..+.|...|.
T Consensus 2 ~~~~~C~~C~~-~i~g~ry~C~~C~d~dlC~~Cf~~~~~~~~h~ 44 (44)
T smart00291 2 HHSYSCDTCGK-PIVGVRYHCLVCPDYDLCQSCFAKGSAGGEHE 44 (44)
T ss_pred CCCcCCCCCCC-CCcCCEEECCCCCCccchHHHHhCcCcCCCCC
Confidence 55799999997 99999999999999999999999888776663
No 17
>KOG1280|consensus
Probab=99.14 E-value=2.4e-11 Score=114.94 Aligned_cols=59 Identities=32% Similarity=0.619 Sum_probs=53.6
Q ss_pred CCCCCCcCCCCCCCceeeeeeeeccCCCCeeecccccCc----ccCCCceeEEEeeCCCceee
Q psy7971 81 VKHDGTMCDFCKQQPIYGIRWKCAECSNYDLCSICYHAE----KHNLRHRFYRINFPGSERVL 139 (276)
Q Consensus 81 v~H~~v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~----~H~~~H~f~ri~~P~~~~V~ 139 (276)
..|.+|.||+|.+..+.|.||||+.|.|||||..||.++ .|..+||+..|..+.+...+
T Consensus 4 ~rHe~v~CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~~tt~~H~~dHPmqcil~~~dfeL~ 66 (381)
T KOG1280|consen 4 SRHEGVSCDGCGKTAFTFRRYKCLRCSDYDLCFSCYENGATTPIHDEDHPMQCILSRVDFELY 66 (381)
T ss_pred CCcCCceeccccccceeeeeeEeeeecchhHHHHHhhcCCCCcccCCCCceeEEeeccceeeE
Confidence 469999999999999999999999999999999999964 69999999999999876544
No 18
>KOG4286|consensus
Probab=99.07 E-value=2.3e-11 Score=123.83 Aligned_cols=83 Identities=28% Similarity=0.563 Sum_probs=67.8
Q ss_pred CCCCCCCcCCCCCCCceeeeeeeeccCCCCeeecccccC----cccCCCceeEEEeeCCCceeeeccc-----------c
Q psy7971 80 GVKHDGTMCDFCKQQPIYGIRWKCAECSNYDLCSICYHA----EKHNLRHRFYRINFPGSERVLLEPR-----------R 144 (276)
Q Consensus 80 ~v~H~~v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~----~~H~~~H~f~ri~~P~~~~V~lepR-----------r 144 (276)
..+|. .+|++|+++||+|+||+|+.|+|||||..||.. +.|.+.|||.++.+|...+..+... +
T Consensus 599 ~~kH~-~kCniCk~~pIvG~RyR~l~~fn~dlCq~CF~sgraak~hk~~~pM~Ey~~~tts~~d~rdfak~L~nkfr~~~ 677 (966)
T KOG4286|consen 599 TAKHQ-AKCNICKECPIIGFRYRSLKHFNYDICQSCFFSGRAAKGHKMHYPMVEYCTPTTSGEDVRDFAKVLKNKFRTKR 677 (966)
T ss_pred HHHhh-hhcchhhhCccceeeeeehhhcChhHHhhHhhhcccccCCCCCCCceeeeCCCCChhhHHHHHHHHHhhhccch
Confidence 46776 899999999999999999999999999999985 5799999999999998876644322 1
Q ss_pred ccCcceeeeeecCceEeec
Q psy7971 145 KSKKISVRGIFPGARVVRG 163 (276)
Q Consensus 145 ~~~~~~~~g~~~g~~v~rG 163 (276)
...+.+.+|+.|-+.|..|
T Consensus 678 ~~a~~~rrGylpvq~~~e~ 696 (966)
T KOG4286|consen 678 YFAKHPRRGYLPVQTVLEG 696 (966)
T ss_pred hhhcccccCCccchhcccc
Confidence 2235556888888887766
No 19
>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=99.01 E-value=8.3e-11 Score=79.96 Aligned_cols=39 Identities=38% Similarity=1.054 Sum_probs=33.2
Q ss_pred CcCCCCCCCceeeeeeeeccCCCCeeecccccCcccCCCceeE
Q psy7971 86 TMCDFCKQQPIYGIRWKCAECSNYDLCSICYHAEKHNLRHRFY 128 (276)
Q Consensus 86 v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~~H~~~H~f~ 128 (276)
..||+|.. +.|.||+|+.|+|||||..||.+..| .|.+.
T Consensus 1 y~C~~C~~--~~~~r~~C~~C~dfDLC~~C~~~~~H--~H~~~ 39 (41)
T cd02337 1 YTCNECKH--HVETRWHCTVCEDYDLCITCYNTKNH--PHKME 39 (41)
T ss_pred CcCCCCCC--cCCCceECCCCcchhhHHHHhCCCCC--Ccccc
Confidence 36999985 66899999999999999999998776 56654
No 20
>KOG4301|consensus
Probab=98.33 E-value=6.9e-08 Score=91.84 Aligned_cols=55 Identities=29% Similarity=0.788 Sum_probs=50.4
Q ss_pred CCCCCCCcCCCCCCCceeeeeeeeccCCCCeeecccccC----cccCCCceeEEEeeCCC
Q psy7971 80 GVKHDGTMCDFCKQQPIYGIRWKCAECSNYDLCSICYHA----EKHNLRHRFYRINFPGS 135 (276)
Q Consensus 80 ~v~H~~v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~----~~H~~~H~f~ri~~P~~ 135 (276)
++.|| +.|+.|...+|.|+||+|..|.+|.||+.||.. +.|+..|.|.++....+
T Consensus 236 nv~hp-v~cs~c~srs~~gfry~cq~C~nyqlcq~cfwrG~~g~~hsnqh~mke~Ss~ks 294 (434)
T KOG4301|consen 236 NVFHP-VECSYCRSRSMMGFRYRCQQCHNYQLCQQCFWRGHAGGSHSNQHQMKEYSSWKS 294 (434)
T ss_pred ccCCC-ccCcceecccccchhhhHhhcCCccccchhhccccCCCCcchHHHHHHhhcccC
Confidence 68888 999999999999999999999999999999985 57999999988887765
No 21
>KOG0457|consensus
Probab=98.30 E-value=2.5e-07 Score=90.20 Aligned_cols=53 Identities=43% Similarity=0.859 Sum_probs=42.6
Q ss_pred CCcCCCCCCCceee-eeeeeccCCCCeeecccccC----cccCCCceeEEEeeCCCceee
Q psy7971 85 GTMCDFCKQQPIYG-IRWKCAECSNYDLCSICYHA----EKHNLRHRFYRINFPGSERVL 139 (276)
Q Consensus 85 ~v~Cd~C~~~pI~G-~RykC~~C~dfDLC~~C~~~----~~H~~~H~f~ri~~P~~~~V~ 139 (276)
.+.||+|. .-|.| +|.||++|+|||||-.||.. +.|+..|++ +|..+.+.++.
T Consensus 14 ky~C~~C~-~dit~~i~ikCaeCp~fdLCl~CFs~GaE~~~H~~~H~Y-rim~~~s~~i~ 71 (438)
T KOG0457|consen 14 KYNCDYCS-LDITGLIRIKCAECPDFDLCLQCFSVGAETGKHQNDHPY-RIMDTNSFPIL 71 (438)
T ss_pred CCCCccHh-HHhccceEEEeecCCCcchhHHHHhcccccCCCCCCCCc-eeecCCCCCCC
Confidence 36899999 55666 56999999999999999995 589999998 66666554443
No 22
>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=97.86 E-value=9.1e-06 Score=56.39 Aligned_cols=40 Identities=23% Similarity=0.565 Sum_probs=33.7
Q ss_pred CcCCCCCCCceeeeeeeeccCCCCeeecccccCcccCCCce
Q psy7971 86 TMCDFCKQQPIYGIRWKCAECSNYDLCSICYHAEKHNLRHR 126 (276)
Q Consensus 86 v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~~H~~~H~ 126 (276)
+.|+.|+ ..+..+||+|+.+.+||||..||..+.....|.
T Consensus 1 y~C~~Cg-~D~t~vryh~~~~~~~dLC~~CF~~G~f~~~~~ 40 (45)
T cd02336 1 YHCFTCG-NDCTRVRYHNLKAKKYDLCPSCYQEGRFPSNFQ 40 (45)
T ss_pred CcccCCC-CccCceEEEecCCCccccChHHHhCcCCCCCCc
Confidence 4699999 555679999999999999999999887665554
No 23
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.83 E-value=6.4e-06 Score=78.08 Aligned_cols=54 Identities=28% Similarity=0.417 Sum_probs=43.7
Q ss_pred CCcCCCCCCCceeeeeeeeccCCCCeeecccccC----cccCCCceeEEEeeCCCceee
Q psy7971 85 GTMCDFCKQQPIYGIRWKCAECSNYDLCSICYHA----EKHNLRHRFYRINFPGSERVL 139 (276)
Q Consensus 85 ~v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~----~~H~~~H~f~ri~~P~~~~V~ 139 (276)
.+.||.|.+.-..-++.+|..|++||||-.||.+ +.|++.|++.-| .-.+-++.
T Consensus 5 k~hCdvC~~d~T~~~~i~C~eC~~~DLC~pCF~~g~~tg~H~pyH~YRii-etnsypI~ 62 (432)
T COG5114 5 KIHCDVCFLDMTDLTFIKCNECPAVDLCLPCFVNGIETGVHSPYHGYRII-ETNSYPIG 62 (432)
T ss_pred eeeehHHHHhhhcceeeeeecccccceehhhhhccccccccCCCCCeeEe-eccCcccc
Confidence 3679999977777899999999999999999985 689999998444 44444443
No 24
>KOG4582|consensus
Probab=96.09 E-value=0.0022 Score=60.08 Aligned_cols=95 Identities=20% Similarity=0.162 Sum_probs=76.7
Q ss_pred eeeecCceEeecCCCccccCCCCC---CCcceEEEeCC---CCcCCCCceeEEEecCCCceeeeec--cCCeeeEEEeeC
Q psy7971 152 RGIFPGARVVRGVDWQWEDQDGGN---GRRGKVNEVQD---WSAASPRSAAYIVWDNGAKNLYRVG--FEGMADLKVLND 223 (276)
Q Consensus 152 ~g~~~g~~v~rG~DW~w~dQDgg~---g~~G~V~~~~~---w~~~~~~~~v~V~Wd~g~~n~YR~G--~~g~~Dl~~~~~ 223 (276)
....++.+|+||.||.|-.+...+ ++.+++.+... -+.+.....+.+.||.....+|+.+ +.+..+|..+.+
T Consensus 59 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~s~~k~~~~~~~~~~~~~~~~ 138 (278)
T KOG4582|consen 59 DEDGVGMRVVRGNDLFDVTNQRLADEIGHVNAVRSFNSAAPSSGSSTPATVPVPWDKIPRSIIKVLEKYQKLASLVITLN 138 (278)
T ss_pred hccccceeEEecCCceEeecccCccccccccceeeeccccccccccCccccccccchhhhhhhhhhHHHhhhhhhhhhcC
Confidence 457789999999999999994444 45555554322 2335567778899999999999999 599999999999
Q ss_pred Cccccccch-----hhhhhhccCCchhh
Q psy7971 224 AKALRHHTL-----SQLRLLRDVPDVGK 246 (276)
Q Consensus 224 ~~~~~~h~~-----t~~~ll~~~p~~~~ 246 (276)
+..+.+|.. +.||-|..-|++|-
T Consensus 139 ~~~~~~H~~~~~~~v~CD~C~~~~IvG~ 166 (278)
T KOG4582|consen 139 PVVGEMHPNISKLSVPCDNCGKPGIVGA 166 (278)
T ss_pred CCccccCCCcccccccCCCccCCccccc
Confidence 999999998 99999999888775
No 25
>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=93.76 E-value=0.027 Score=35.34 Aligned_cols=27 Identities=44% Similarity=1.143 Sum_probs=12.5
Q ss_pred cCCCCCCCceee-eeeeeccCCCCeeeccc
Q psy7971 87 MCDFCKQQPIYG-IRWKCAECSNYDLCSIC 115 (276)
Q Consensus 87 ~Cd~C~~~pI~G-~RykC~~C~dfDLC~~C 115 (276)
.|+.|+ .++.+ .-|.|..| ||+|...|
T Consensus 2 ~C~~C~-~~~~~~~~Y~C~~C-df~lH~~C 29 (30)
T PF07649_consen 2 RCDACG-KPIDGGWFYRCSEC-DFDLHEEC 29 (30)
T ss_dssp --TTTS-----S--EEE-TTT------HHH
T ss_pred cCCcCC-CcCCCCceEECccC-CCccChhc
Confidence 599999 67777 99999999 88887776
No 26
>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=89.10 E-value=0.34 Score=30.42 Aligned_cols=27 Identities=37% Similarity=1.041 Sum_probs=23.0
Q ss_pred cCCCCCCCceeee-eeeeccCCCCeeeccc
Q psy7971 87 MCDFCKQQPIYGI-RWKCAECSNYDLCSIC 115 (276)
Q Consensus 87 ~Cd~C~~~pI~G~-RykC~~C~dfDLC~~C 115 (276)
.|+.|. ..+.|. .|+|..|. |+|-..|
T Consensus 2 ~C~~C~-~~~~~~~~Y~C~~c~-f~lh~~C 29 (30)
T PF03107_consen 2 WCDVCR-RKIDGFYFYHCSECC-FTLHVRC 29 (30)
T ss_pred CCCCCC-CCcCCCEeEEeCCCC-CeEcCcc
Confidence 699998 678888 99999998 8887766
No 27
>KOG1778|consensus
Probab=88.10 E-value=0.2 Score=48.05 Aligned_cols=43 Identities=28% Similarity=0.750 Sum_probs=34.5
Q ss_pred CCcCCCCCCCceeeeeeeeccCCCCeeecccccCcccCCCceeEEEe
Q psy7971 85 GTMCDFCKQQPIYGIRWKCAECSNYDLCSICYHAEKHNLRHRFYRIN 131 (276)
Q Consensus 85 ~v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~~H~~~H~f~ri~ 131 (276)
...|..|...- ..+|.|..|++||+|..||....| .|.+....
T Consensus 169 ~~~c~~c~~~~--~~~~~c~~~~d~d~~~~~~~k~~h--~h~~~~~~ 211 (319)
T KOG1778|consen 169 AYTCPICKLEV--LTAWHCEVCPDYDRCRACEEKPLH--PHLYEAME 211 (319)
T ss_pred eeecCcccccc--ccccccccCCchhhhhcccCCCCC--Ccchhccc
Confidence 47899998443 789999999999999999998875 56654443
No 28
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 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 N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=78.29 E-value=1.6 Score=32.57 Aligned_cols=35 Identities=26% Similarity=0.585 Sum_probs=25.9
Q ss_pred eeeeeeccCCC---CeeecccccCcccCCCceeEEEeeC
Q psy7971 98 GIRWKCAECSN---YDLCSICYHAEKHNLRHRFYRINFP 133 (276)
Q Consensus 98 G~RykC~~C~d---fDLC~~C~~~~~H~~~H~f~ri~~P 133 (276)
-.-|+|..|.. .-+|..||....|. .|.+..+...
T Consensus 11 q~~y~C~tC~~~~~~~iC~~CF~~~~H~-gH~~~~~~~~ 48 (71)
T PF02207_consen 11 QIFYRCLTCSLDESSGICEECFANSCHE-GHRVVYYRSS 48 (71)
T ss_dssp -EEEEETTTBSSTT-BBEHHHHCTSGGG-GSSEEEEE--
T ss_pred CEEEECccCCCCCCEEEchhhCCCCCcC-CCcEEEEEeC
Confidence 35689999964 78899999988875 9998877765
No 29
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=69.89 E-value=6.6 Score=25.69 Aligned_cols=40 Identities=28% Similarity=0.640 Sum_probs=29.0
Q ss_pred CCcCCCCCCCceeeeeeeeccCCCCeeecccccCcccCCCceeEEE
Q psy7971 85 GTMCDFCKQQPIYGIRWKCAECSNYDLCSICYHAEKHNLRHRFYRI 130 (276)
Q Consensus 85 ~v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~~H~~~H~f~ri 130 (276)
...|+.|...+ ..|-|..|.. -+|..|.... | ..|.+..|
T Consensus 3 ~~~C~~H~~~~---~~~~C~~C~~-~~C~~C~~~~-H-~~H~~~~i 42 (42)
T PF00643_consen 3 EPKCPEHPEEP---LSLFCEDCNE-PLCSECTVSG-H-KGHKIVPI 42 (42)
T ss_dssp SSB-SSTTTSB---EEEEETTTTE-EEEHHHHHTS-T-TTSEEEEC
T ss_pred CccCccCCccc---eEEEecCCCC-ccCccCCCCC-C-CCCEEeEC
Confidence 35677777433 6788999987 5999999877 5 46887653
No 30
>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=52.65 E-value=14 Score=27.64 Aligned_cols=31 Identities=26% Similarity=0.637 Sum_probs=22.8
Q ss_pred eeeeccCCC---CeeecccccCcccCCCceeEEEe
Q psy7971 100 RWKCAECSN---YDLCSICYHAEKHNLRHRFYRIN 131 (276)
Q Consensus 100 RykC~~C~d---fDLC~~C~~~~~H~~~H~f~ri~ 131 (276)
-|+|..|.- .-+|..||....| ..|.+..+.
T Consensus 13 ~y~C~tC~~~~~~~iC~~Cf~~~~H-~gH~~~~~~ 46 (71)
T smart00396 13 IYRCKTCGLDPTCVLCSDCFRSNCH-KGHDYSLKT 46 (71)
T ss_pred EEECcCCCCCCCEeEChHHCCCCCC-CCCCEEEEE
Confidence 399999962 4589999998887 578864443
No 31
>KOG4317|consensus
Probab=37.80 E-value=11 Score=36.54 Aligned_cols=41 Identities=37% Similarity=0.902 Sum_probs=28.3
Q ss_pred CcCCCCCCCceeeeeeeeccCCCCeeecc-cccCcccCCCceeEEE
Q psy7971 86 TMCDFCKQQPIYGIRWKCAECSNYDLCSI-CYHAEKHNLRHRFYRI 130 (276)
Q Consensus 86 v~Cd~C~~~pI~G~RykC~~C~dfDLC~~-C~~~~~H~~~H~f~ri 130 (276)
..|-.|..++ .+|+|-.| |+-+|+- ||-+.+|.-...|+|-
T Consensus 8 ~~C~ic~vq~---~~YtCPRC-n~~YCsl~CYr~h~~~CsE~Fyrd 49 (383)
T KOG4317|consen 8 LACGICGVQK---REYTCPRC-NLLYCSLKCYRNHKHSCSEKFYRD 49 (383)
T ss_pred eecccccccc---ccccCCCC-CccceeeeeecCCCccchHHHHHH
Confidence 4555565444 67999999 4557876 9988777666667653
No 32
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=37.70 E-value=24 Score=22.54 Aligned_cols=27 Identities=26% Similarity=0.782 Sum_probs=18.9
Q ss_pred cCCCCCCCceee-eeeeeccCCCCeeecc
Q psy7971 87 MCDFCKQQPIYG-IRWKCAECSNYDLCSI 114 (276)
Q Consensus 87 ~Cd~C~~~pI~G-~RykC~~C~dfDLC~~ 114 (276)
.|..|.+..+.- ++|.|..| +--||..
T Consensus 2 rC~vC~~~k~rk~T~~~C~~C-~v~lC~~ 29 (32)
T PF13842_consen 2 RCKVCSKKKRRKDTRYMCSKC-DVPLCVE 29 (32)
T ss_pred CCeECCcCCccceeEEEccCC-CCcccCC
Confidence 366776655543 89999999 4667754
No 33
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=36.81 E-value=37 Score=21.32 Aligned_cols=37 Identities=27% Similarity=0.497 Sum_probs=22.3
Q ss_pred cCCCCCCCceeeeeeeeccCCCCeeecccccCcccCCCceeEE
Q psy7971 87 MCDFCKQQPIYGIRWKCAECSNYDLCSICYHAEKHNLRHRFYR 129 (276)
Q Consensus 87 ~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~~H~~~H~f~r 129 (276)
.|+.+...+ ..|-|..|... +|..|.... | ..|.+..
T Consensus 2 ~C~~H~~~~---~~~fC~~~~~~-iC~~C~~~~-H-~~H~~~~ 38 (39)
T cd00021 2 LCDEHGEEP---LSLFCETDRAL-LCVDCDLSV-H-SGHRRVP 38 (39)
T ss_pred CCCccCCcc---eEEEeCccChh-hhhhcChhh-c-CCCCEee
Confidence 355554333 23556666553 899998765 5 5887654
No 34
>KOG2990|consensus
Probab=35.91 E-value=13 Score=35.40 Aligned_cols=19 Identities=32% Similarity=0.683 Sum_probs=13.6
Q ss_pred CCcCCCCCCCceeeeeeee
Q psy7971 85 GTMCDFCKQQPIYGIRWKC 103 (276)
Q Consensus 85 ~v~Cd~C~~~pI~G~RykC 103 (276)
+|.|++|....-.|+||--
T Consensus 52 nIWC~gC~nhIgmGvRyNA 70 (317)
T KOG2990|consen 52 NIWCDGCKNHIGMGVRYNA 70 (317)
T ss_pred chhhccHHHhhhccceech
Confidence 6999999854445777744
No 35
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=35.90 E-value=11 Score=26.92 Aligned_cols=18 Identities=33% Similarity=0.934 Sum_probs=11.1
Q ss_pred eeeeeccCCCCeeeccccc
Q psy7971 99 IRWKCAECSNYDLCSICYH 117 (276)
Q Consensus 99 ~RykC~~C~dfDLC~~C~~ 117 (276)
.||+|..|... +|..|-.
T Consensus 20 ~~y~C~~C~~~-FC~dCD~ 37 (51)
T PF07975_consen 20 SRYRCPKCKNH-FCIDCDV 37 (51)
T ss_dssp EEE--TTTT---B-HHHHH
T ss_pred CeEECCCCCCc-cccCcCh
Confidence 79999999874 8998864
No 36
>KOG2807|consensus
Probab=35.78 E-value=20 Score=34.85 Aligned_cols=31 Identities=26% Similarity=0.711 Sum_probs=25.4
Q ss_pred CcCCCCCCCceeeeeeeeccCCCCeeeccccc
Q psy7971 86 TMCDFCKQQPIYGIRWKCAECSNYDLCSICYH 117 (276)
Q Consensus 86 v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~ 117 (276)
-.|-+|+.....+.||+|..|.++ +|..|--
T Consensus 331 ~~Cf~C~~~~~~~~~y~C~~Ck~~-FCldCDv 361 (378)
T KOG2807|consen 331 RFCFACQGELLSSGRYRCESCKNV-FCLDCDV 361 (378)
T ss_pred cceeeeccccCCCCcEEchhccce-eeccchH
Confidence 349999766777899999999986 8888853
No 37
>KOG1280|consensus
Probab=34.53 E-value=23 Score=34.68 Aligned_cols=67 Identities=13% Similarity=0.041 Sum_probs=43.9
Q ss_pred ceeecCceeeee----ecCCCCCCCCC--CCcCCCCCCCceeeeeeeeccCCCCeeecccccCc-ccCCCceeE
Q psy7971 62 NYRCAGAFDLRI----LDSAPTGVKHD--GTMCDFCKQQPIYGIRWKCAECSNYDLCSICYHAE-KHNLRHRFY 128 (276)
Q Consensus 62 ~YR~~g~~DL~l----vD~ap~~v~H~--~v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~-~H~~~H~f~ 128 (276)
.|+|.-++|..+ +++......|+ +..|..|....+.+.+++|..|..++.|-.|=.-+ -|-.+|+|.
T Consensus 23 rYkCL~C~DyDlC~sCyen~~tt~~H~~dHPmqcil~~~dfeL~f~Ge~i~~y~~qSftCPyC~~~Gfte~~f~ 96 (381)
T KOG1280|consen 23 RYKCLRCSDYDLCFSCYENGATTPIHDEDHPMQCILSRVDFELYFGGEPISHYDPQSFTCPYCGIMGFTERQFG 96 (381)
T ss_pred eeEeeeecchhHHHHHhhcCCCCcccCCCCceeEEeeccceeeEecCccccccccccccCCcccccccchhHHH
Confidence 455555555444 44543333443 67888898889999999999999999988875532 233344443
No 38
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=34.10 E-value=4.1 Score=29.27 Aligned_cols=33 Identities=36% Similarity=1.014 Sum_probs=23.3
Q ss_pred CCcCCCCCC-Cceeee-------eeeeccCC--CCeeeccccc
Q psy7971 85 GTMCDFCKQ-QPIYGI-------RWKCAECS--NYDLCSICYH 117 (276)
Q Consensus 85 ~v~Cd~C~~-~pI~G~-------RykC~~C~--dfDLC~~C~~ 117 (276)
...||-|.. .|+.+. ||-|..|- .|-+|..|-.
T Consensus 7 ry~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~deYY~CksC~G 49 (57)
T PF14445_consen 7 RYSCDLCNSSHPISELRQCVLCGRWACNSCWQDEYYTCKSCNG 49 (57)
T ss_pred hHhHHhhcccCcHHHHHHHhhhchhhhhhhhhhhHhHHHhhhc
Confidence 467888853 455554 79999994 6788888854
No 39
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=33.25 E-value=18 Score=26.63 Aligned_cols=28 Identities=21% Similarity=0.623 Sum_probs=12.5
Q ss_pred CCcCCCCCCCceeeee---eeeccCCCCeee
Q psy7971 85 GTMCDFCKQQPIYGIR---WKCAECSNYDLC 112 (276)
Q Consensus 85 ~v~Cd~C~~~pI~G~R---ykC~~C~dfDLC 112 (276)
.|.|+.|....-.-+. .||..|..|+-+
T Consensus 30 ~IlCNDC~~~s~v~fH~lg~KC~~C~SYNT~ 60 (61)
T PF14599_consen 30 WILCNDCNAKSEVPFHFLGHKCSHCGSYNTR 60 (61)
T ss_dssp EEEESSS--EEEEE--TT----TTTS---EE
T ss_pred EEECCCCCCccceeeeHhhhcCCCCCCcccC
Confidence 4889999865433332 388888888754
No 40
>cd06402 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=32.01 E-value=7 Score=30.77 Aligned_cols=34 Identities=24% Similarity=0.479 Sum_probs=25.5
Q ss_pred CCccCCcCCCCCceeEEEeeCCCCceEEEEcCCCCcceee
Q psy7971 26 DWKWGKQDGGDGHVGTVRNFESPEEVVVVWDNGTAANYRC 65 (276)
Q Consensus 26 dWkWg~qDgg~g~vGtVv~~ss~eevvV~WD~G~~~~YR~ 65 (276)
.-||.|.|| +.+.|++++++.++........+|+
T Consensus 49 tlky~DeeG------DlvtIssdeEL~~A~~~~~~~~~Rl 82 (87)
T cd06402 49 QLFWKDEEG------DLVAFSSDEELVMALGSLNDDTFRI 82 (87)
T ss_pred EEEEECCCC------CEEeecCHHHHHHHHHcCCCCcEEE
Confidence 468999885 7899999999888766655555553
No 41
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=31.22 E-value=20 Score=36.38 Aligned_cols=38 Identities=26% Similarity=0.718 Sum_probs=30.2
Q ss_pred CCCCCcCCCCCCCceeeeeeeeccCCCCeeecccccCccc
Q psy7971 82 KHDGTMCDFCKQQPIYGIRWKCAECSNYDLCSICYHAEKH 121 (276)
Q Consensus 82 ~H~~v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~~H 121 (276)
.|+ ..|+.|+ .--.-.||+=+.-..|++|..||..+..
T Consensus 222 ~~~-~~C~~cG-~~~~~t~y~nlra~~~n~C~~C~~qg~f 259 (531)
T COG5259 222 KHP-SSCSCCG-NKSFNTRYHNLRAEKYNSCSECYDQGRF 259 (531)
T ss_pred cCC-ceeeccC-ccccchhhhhhhhhhcccchHHHhcCcC
Confidence 343 8899998 4445678998888999999999997654
No 42
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=29.71 E-value=37 Score=22.33 Aligned_cols=22 Identities=27% Similarity=0.933 Sum_probs=14.6
Q ss_pred CCcCCCCCCCc-ee-------e-eeeeeccC
Q psy7971 85 GTMCDFCKQQP-IY-------G-IRWKCAEC 106 (276)
Q Consensus 85 ~v~Cd~C~~~p-I~-------G-~RykC~~C 106 (276)
.|.|-.|+... +. | -||+|..|
T Consensus 5 ~v~CP~C~s~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 5 DVHCPRCQSTEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeeCCCCCCCCcceeCCCCCCCCEeEecCcC
Confidence 36777787543 22 2 49999988
No 43
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=28.33 E-value=39 Score=27.87 Aligned_cols=29 Identities=24% Similarity=0.607 Sum_probs=23.1
Q ss_pred CCCCCCCceeeeeeeeccCC-----CCeeeccccc
Q psy7971 88 CDFCKQQPIYGIRWKCAECS-----NYDLCSICYH 117 (276)
Q Consensus 88 Cd~C~~~pI~G~RykC~~C~-----dfDLC~~C~~ 117 (276)
|-.|+ .++.=.|++|..|. +|.+|.-++-
T Consensus 1 CPvCg-~~l~vt~l~C~~C~t~i~G~F~l~~~~~L 34 (113)
T PF09862_consen 1 CPVCG-GELVVTRLKCPSCGTEIEGEFELPWFARL 34 (113)
T ss_pred CCCCC-CceEEEEEEcCCCCCEEEeeeccchhhcC
Confidence 77888 67777899999997 6888777664
No 44
>PF06507 Auxin_resp: Auxin response factor; InterPro: IPR010525 This pattern represents a conserved region of auxin-responsive transcription factors. The plant hormone auxin (indole-3-acetic acid) can regulate the gene expression of several families, including Aux/IAA, GH3 and SAUR families. Two related families of proteins, Aux/IAA proteins (IPR003311 from INTERPRO) and the auxin response factors (ARF), are key regulators of auxin-modulated gene expression []. There are multiple ARF proteins, some of which activate, while others repress transcription. ARF proteins bind to auxin-responsive cis-acting promoter elements (AuxREs) using an N-terminal DNA-binding domain. It is thought that Aux/IAA proteins activate transcription by modifying ARF activity through the C-terminal protein-protein interaction domains (IPR011525 from INTERPRO) found in both Aux/IAA and ARF proteins. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0009725 response to hormone stimulus, 0005634 nucleus
Probab=25.97 E-value=1.1e+02 Score=23.87 Aligned_cols=60 Identities=22% Similarity=0.289 Sum_probs=38.6
Q ss_pred eeEEEeeCC-CceeeeccccccCcceeeeeecCceEeecCCCccccCCCCCC-CcceEEEeCCCCc
Q psy7971 126 RFYRINFPG-SERVLLEPRRKSKKISVRGIFPGARVVRGVDWQWEDQDGGNG-RRGKVNEVQDWSA 189 (276)
Q Consensus 126 ~f~ri~~P~-~~~V~lepRr~~~~~~~~g~~~g~~v~rG~DW~w~dQDgg~g-~~G~V~~~~~w~~ 189 (276)
+|.-+..|- +.+.++-|+.+..+.....+.+|.|+.= ....+|..+- -.|||+.|.+.++
T Consensus 10 ~F~V~Y~PRa~~sEFVV~~~k~~~al~~~~~~GmRfkM----~fE~eds~~~~~~GtI~~v~~~dp 71 (83)
T PF06507_consen 10 PFEVFYYPRASPSEFVVPASKYDKALNHPWSVGMRFKM----RFETEDSSERRWQGTIVGVSDLDP 71 (83)
T ss_pred eEEEEECCCCCCcceEEEHHHHHHHhcCCCCCCcEEEE----EeccCCCccceeeeEEeEeeccCC
Confidence 455555554 3445555555554544567889999865 3667776664 4899999976653
No 45
>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=25.77 E-value=51 Score=22.38 Aligned_cols=22 Identities=32% Similarity=0.729 Sum_probs=15.6
Q ss_pred CCcCCCCCCCce---eeeeeeeccCC
Q psy7971 85 GTMCDFCKQQPI---YGIRWKCAECS 107 (276)
Q Consensus 85 ~v~Cd~C~~~pI---~G~RykC~~C~ 107 (276)
...|+.|+ ..| ...-|+|..|.
T Consensus 11 ~~~C~~C~-~~i~g~~~~g~~C~~C~ 35 (53)
T PF00130_consen 11 PTYCDVCG-KFIWGLGKQGYRCSWCG 35 (53)
T ss_dssp TEB-TTSS-SBECSSSSCEEEETTTT
T ss_pred CCCCcccC-cccCCCCCCeEEECCCC
Confidence 47899999 666 45578888775
No 46
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=25.69 E-value=46 Score=20.16 Aligned_cols=19 Identities=26% Similarity=0.926 Sum_probs=11.7
Q ss_pred CCCCCC--Ccee-eeeeeeccC
Q psy7971 88 CDFCKQ--QPIY-GIRWKCAEC 106 (276)
Q Consensus 88 Cd~C~~--~pI~-G~RykC~~C 106 (276)
|..|.. .|.. +.+|+|-+|
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnC 22 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNC 22 (24)
T ss_pred CccCCCcccCcccCceEeCCCC
Confidence 555642 2222 778999888
No 47
>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=25.52 E-value=39 Score=22.28 Aligned_cols=22 Identities=36% Similarity=1.045 Sum_probs=16.0
Q ss_pred CCCcCCCCCCCceee---eeeeeccC
Q psy7971 84 DGTMCDFCKQQPIYG---IRWKCAEC 106 (276)
Q Consensus 84 ~~v~Cd~C~~~pI~G---~RykC~~C 106 (276)
....|+.|. ..|.| .-|+|..|
T Consensus 10 ~~~~C~~C~-~~i~~~~~~~~~C~~C 34 (50)
T cd00029 10 KPTFCDVCR-KSIWGLFKQGLRCSWC 34 (50)
T ss_pred CCCChhhcc-hhhhccccceeEcCCC
Confidence 346799998 66776 56777776
No 48
>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=24.25 E-value=43 Score=21.80 Aligned_cols=23 Identities=30% Similarity=0.852 Sum_probs=15.7
Q ss_pred CCCCcCCCCCCCceeee--eeeeccC
Q psy7971 83 HDGTMCDFCKQQPIYGI--RWKCAEC 106 (276)
Q Consensus 83 H~~v~Cd~C~~~pI~G~--RykC~~C 106 (276)
+....|+.|+ ..|.+. -++|..|
T Consensus 9 ~~~~~C~~C~-~~i~~~~~~~~C~~C 33 (49)
T smart00109 9 KKPTKCCVCR-KSIWGSFQGLRCSWC 33 (49)
T ss_pred CCCCCccccc-cccCcCCCCcCCCCC
Confidence 3346899999 567664 5666666
No 49
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=23.60 E-value=58 Score=22.01 Aligned_cols=23 Identities=26% Similarity=0.803 Sum_probs=16.2
Q ss_pred CCcCCCCCCC---ceee-eeeeeccCC
Q psy7971 85 GTMCDFCKQQ---PIYG-IRWKCAECS 107 (276)
Q Consensus 85 ~v~Cd~C~~~---pI~G-~RykC~~C~ 107 (276)
++.|--|+.. .|.. .+|+|..|-
T Consensus 18 g~~CP~Cg~~~~~~~~~~~~~~C~~C~ 44 (46)
T PF12760_consen 18 GFVCPHCGSTKHYRLKTRGRYRCKACR 44 (46)
T ss_pred CCCCCCCCCeeeEEeCCCCeEECCCCC
Confidence 5678888743 4555 789998884
No 50
>KOG1244|consensus
Probab=23.58 E-value=65 Score=30.81 Aligned_cols=67 Identities=22% Similarity=0.495 Sum_probs=42.6
Q ss_pred eeeeeecC---CCCCCCCCCCcCCCCCCCc--------------eeeeeeeeccCCCCeeecccccCc------ccCCCc
Q psy7971 69 FDLRILDS---APTGVKHDGTMCDFCKQQP--------------IYGIRWKCAECSNYDLCSICYHAE------KHNLRH 125 (276)
Q Consensus 69 ~DL~lvD~---ap~~v~H~~v~Cd~C~~~p--------------I~G~RykC~~C~dfDLC~~C~~~~------~H~~~H 125 (276)
+|+-+-|+ ..+++.-.-|.|..|+... +.-.||+|..|.-..+|.+-...+ .-+...
T Consensus 227 CDFclgdsr~nkkt~~peelvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~csicgtsenddqllfcddcdrgy 306 (336)
T KOG1244|consen 227 CDFCLGDSRENKKTGMPEELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGTSENDDQLLFCDDCDRGY 306 (336)
T ss_pred cceeccccccccccCCchhhcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeecceeccccCcCCCceeEeecccCCce
Confidence 35555443 4556666778899887532 345699999998766666654421 223455
Q ss_pred eeEEEeeCCC
Q psy7971 126 RFYRINFPGS 135 (276)
Q Consensus 126 ~f~ri~~P~~ 135 (276)
.|+.+..|..
T Consensus 307 hmyclsppm~ 316 (336)
T KOG1244|consen 307 HMYCLSPPMV 316 (336)
T ss_pred eeEecCCCcC
Confidence 5778877764
No 51
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.33 E-value=66 Score=26.55 Aligned_cols=30 Identities=33% Similarity=0.752 Sum_probs=21.8
Q ss_pred CcCCCCCCCcee------------eeeeeeccCCCCeeeccccc
Q psy7971 86 TMCDFCKQQPIY------------GIRWKCAECSNYDLCSICYH 117 (276)
Q Consensus 86 v~Cd~C~~~pI~------------G~RykC~~C~dfDLC~~C~~ 117 (276)
..|-+|.+ ++. -.||+|..|... +|..|-.
T Consensus 56 ~~C~~C~~-~f~~~~~~~~~~~~~~~~y~C~~C~~~-FC~dCD~ 97 (112)
T TIGR00622 56 RFCFGCQG-PFPKPPVSPFDELKDSHRYVCAVCKNV-FCVDCDV 97 (112)
T ss_pred CcccCcCC-CCCCcccccccccccccceeCCCCCCc-cccccch
Confidence 46999984 222 359999999874 8888854
No 52
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=23.11 E-value=1.3e+02 Score=24.24 Aligned_cols=37 Identities=16% Similarity=0.336 Sum_probs=27.5
Q ss_pred ccchhhccccceEEeCCCCccCCcCCCCCceeEEEeeCCCCceEEEEcC
Q psy7971 9 ANRFAMEGVGARVIRGPDWKWGKQDGGDGHVGTVRNFESPEEVVVVWDN 57 (276)
Q Consensus 9 ~~~~~~~~vG~RVvRGpdWkWg~qDgg~g~vGtVv~~ss~eevvV~WD~ 57 (276)
.+...++++|.||+..- |-.|+|+++.. +.+.+.-+.
T Consensus 47 ~~~~~~Lk~Gd~VvT~g-----------Gi~G~Vv~i~~-~~v~lei~~ 83 (106)
T PRK05585 47 KKMLSSLAKGDEVVTNG-----------GIIGKVTKVSE-DFVIIELND 83 (106)
T ss_pred HHHHHhcCCCCEEEECC-----------CeEEEEEEEeC-CEEEEEECC
Confidence 34567889999999864 78999999864 456655443
No 53
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=22.96 E-value=54 Score=24.14 Aligned_cols=32 Identities=22% Similarity=0.700 Sum_probs=21.4
Q ss_pred CcCCCCCCC--cee-eeeeeeccCCCC--eeeccccc
Q psy7971 86 TMCDFCKQQ--PIY-GIRWKCAECSNY--DLCSICYH 117 (276)
Q Consensus 86 v~Cd~C~~~--pI~-G~RykC~~C~df--DLC~~C~~ 117 (276)
..|..|+.. |.- +.+|.|-+|-.. --|..|-.
T Consensus 8 ~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk 44 (59)
T PRK14890 8 PKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCEKCRK 44 (59)
T ss_pred ccccCCCCcccCCCccCEeeCCCCCCeeEeechhHHh
Confidence 478899832 223 689999999653 23777754
No 54
>smart00336 BBOX B-Box-type zinc finger.
Probab=21.95 E-value=1.2e+02 Score=19.16 Aligned_cols=37 Identities=32% Similarity=0.734 Sum_probs=22.5
Q ss_pred CcCCCCCCCceeeeeeeeccCCCCeeecccccCcccCCCceeE
Q psy7971 86 TMCDFCKQQPIYGIRWKCAECSNYDLCSICYHAEKHNLRHRFY 128 (276)
Q Consensus 86 v~Cd~C~~~pI~G~RykC~~C~dfDLC~~C~~~~~H~~~H~f~ 128 (276)
..|..|...+ ..|-|..|... +|..|... .| ..|+..
T Consensus 4 ~~C~~h~~~~---~~~~C~~c~~~-iC~~C~~~-~H-~~H~~~ 40 (42)
T smart00336 4 PKCDSHGDEP---AEFFCEECGAL-LCRTCDEA-EH-RGHTVV 40 (42)
T ss_pred CcCCCCCCCc---eEEECCCCCcc-cccccChh-hc-CCCcee
Confidence 4566665333 23447777654 79999876 54 577754
No 55
>PF08940 DUF1918: Domain of unknown function (DUF1918); InterPro: IPR015035 This domain is found in various hypothetical bacterial proteins, and has no known function. ; PDB: 2A7Y_A.
Probab=20.18 E-value=1.2e+02 Score=22.30 Aligned_cols=34 Identities=32% Similarity=0.580 Sum_probs=18.8
Q ss_pred CCCcceEEEeCCCCcCCCCceeEEEecC-CCceeeeec
Q psy7971 175 NGRRGKVNEVQDWSAASPRSAAYIVWDN-GAKNLYRVG 211 (276)
Q Consensus 175 ~g~~G~V~~~~~w~~~~~~~~v~V~Wd~-g~~n~YR~G 211 (276)
....|.|+|+++-.- .|. -.|+|+. |....+=-|
T Consensus 19 ~~r~GeIveV~g~dG-~PP--Y~VRw~D~Ghe~lv~PG 53 (58)
T PF08940_consen 19 PDRHGEIVEVRGPDG-SPP--YLVRWDDTGHESLVFPG 53 (58)
T ss_dssp -EEEEEEEE-S-SSS--S---EEEEETTTTEEEEE---
T ss_pred CCcEeEEEEEECCCC-CCC--EEEEecCCCcEEEEeCC
Confidence 346789999986432 222 5899998 877665444
Done!