Query 022340
Match_columns 298
No_of_seqs 216 out of 1176
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 02:47:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022340.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022340hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0703 Predicted GTPase-activ 100.0 4.7E-45 1E-49 342.0 8.0 121 6-126 3-127 (287)
2 PLN03119 putative ADP-ribosyla 100.0 1.7E-41 3.6E-46 339.3 13.6 161 8-171 3-173 (648)
3 PF01412 ArfGap: Putative GTPa 100.0 3.6E-40 7.8E-45 271.8 7.2 109 17-125 2-116 (116)
4 PLN03131 hypothetical protein; 100.0 4.7E-39 1E-43 323.9 13.7 159 8-169 3-171 (705)
5 smart00105 ArfGap Putative GTP 100.0 1.2E-38 2.5E-43 261.6 9.2 103 26-128 1-110 (112)
6 COG5347 GTPase-activating prot 100.0 7.4E-36 1.6E-40 284.4 10.3 115 14-128 6-128 (319)
7 PLN03114 ADP-ribosylation fact 100.0 2E-29 4.4E-34 242.3 17.9 113 15-127 9-130 (395)
8 KOG0704 ADP-ribosylation facto 100.0 4.1E-31 8.9E-36 252.7 6.0 111 12-122 3-124 (386)
9 KOG0706 Predicted GTPase-activ 100.0 3.6E-29 7.8E-34 245.0 5.7 85 15-99 10-94 (454)
10 KOG0705 GTPase-activating prot 99.9 8.5E-28 1.9E-32 241.3 6.2 147 15-161 500-655 (749)
11 KOG0521 Putative GTPase activa 99.9 2.2E-24 4.8E-29 225.4 4.0 112 18-129 416-535 (785)
12 KOG0818 GTPase-activating prot 99.8 4.3E-21 9.3E-26 191.0 3.1 101 25-125 5-119 (669)
13 KOG1117 Rho- and Arf-GTPase ac 99.8 9.8E-20 2.1E-24 189.3 2.9 108 20-127 290-405 (1186)
14 KOG0702 Predicted GTPase-activ 99.7 1.1E-16 2.5E-21 159.1 13.3 125 7-132 4-136 (524)
15 KOG0521 Putative GTPase activa 95.6 0.003 6.5E-08 67.8 -0.4 72 24-97 626-698 (785)
16 PRK00085 recO DNA repair prote 85.0 0.55 1.2E-05 42.5 2.0 31 25-55 146-177 (247)
17 PRK12495 hypothetical protein; 79.3 1.2 2.6E-05 41.8 1.9 38 16-57 28-67 (226)
18 PF00643 zf-B_box: B-box zinc 78.1 1.5 3.2E-05 29.5 1.7 34 27-60 2-36 (42)
19 TIGR00613 reco DNA repair prot 76.4 1.7 3.7E-05 39.2 2.0 33 25-57 144-177 (241)
20 COG1734 DksA DnaK suppressor p 72.3 1.4 3.1E-05 37.5 0.5 35 26-60 78-113 (120)
21 COG1381 RecO Recombinational D 70.6 2.2 4.8E-05 39.8 1.4 31 25-55 151-182 (251)
22 TIGR02419 C4_traR_proteo phage 70.5 2.6 5.6E-05 31.9 1.5 35 24-58 27-62 (63)
23 PRK11019 hypothetical protein; 67.2 3.5 7.7E-05 33.4 1.7 37 27-64 35-73 (88)
24 PRK13715 conjugal transfer pro 63.4 5.1 0.00011 31.2 1.9 34 28-61 34-68 (73)
25 PF01286 XPA_N: XPA protein N- 58.4 2.7 5.9E-05 28.6 -0.4 27 29-55 4-31 (34)
26 PF11781 RRN7: RNA polymerase 58.0 4.9 0.00011 27.3 0.8 27 26-55 6-32 (36)
27 PRK10778 dksA RNA polymerase-b 57.2 6.9 0.00015 34.4 1.8 39 24-62 107-146 (151)
28 PRK11788 tetratricopeptide rep 54.5 11 0.00025 35.1 2.9 38 15-59 341-379 (389)
29 PHA00080 DksA-like zinc finger 53.9 9.1 0.0002 29.7 1.8 35 25-60 28-64 (72)
30 PF08271 TF_Zn_Ribbon: TFIIB z 52.5 4.1 8.8E-05 28.1 -0.3 26 30-56 2-27 (43)
31 smart00401 ZnF_GATA zinc finge 50.5 10 0.00022 27.5 1.5 37 27-63 2-40 (52)
32 PF01258 zf-dskA_traR: Prokary 50.1 2.5 5.3E-05 28.2 -1.6 30 29-58 4-34 (36)
33 KOG3362 Predicted BBOX Zn-fing 46.6 6.8 0.00015 34.8 0.1 34 26-60 116-150 (156)
34 TIGR02890 spore_yteA sporulati 46.2 16 0.00034 32.4 2.3 37 24-60 82-119 (159)
35 PF00320 GATA: GATA zinc finge 45.7 10 0.00022 25.5 0.8 32 31-62 1-34 (36)
36 TIGR02420 dksA RNA polymerase- 39.4 19 0.0004 29.6 1.6 31 25-55 77-108 (110)
37 cd07173 NR_DBD_AR DNA-binding 38.0 24 0.00052 27.9 2.0 31 27-60 2-32 (82)
38 cd07171 NR_DBD_ER DNA-binding 37.3 21 0.00045 28.2 1.5 31 27-60 2-32 (82)
39 PF10764 Gin: Inhibitor of sig 36.7 16 0.00034 26.2 0.7 26 30-56 1-26 (46)
40 KOG1029 Endocytic adaptor prot 35.0 2.6E+02 0.0057 31.5 9.6 27 228-267 179-205 (1118)
41 cd00202 ZnF_GATA Zinc finger D 34.5 36 0.00079 24.9 2.3 33 30-62 1-35 (54)
42 COG2174 RPL34A Ribosomal prote 33.5 25 0.00055 29.0 1.5 33 24-56 30-79 (93)
43 cd06968 NR_DBD_ROR DNA-binding 33.3 26 0.00056 28.4 1.5 31 27-60 4-34 (95)
44 cd07170 NR_DBD_ERR DNA-binding 32.3 25 0.00055 28.7 1.3 30 28-60 4-33 (97)
45 PF14471 DUF4428: Domain of un 32.2 21 0.00046 25.9 0.8 43 30-73 1-45 (51)
46 cd07160 NR_DBD_LXR DNA-binding 31.9 26 0.00057 28.8 1.3 31 27-60 17-47 (101)
47 smart00782 PhnA_Zn_Ribbon PhnA 30.4 31 0.00067 24.9 1.3 34 22-56 2-44 (47)
48 COG2158 Uncharacterized protei 30.0 19 0.00042 30.5 0.3 24 40-63 52-77 (112)
49 PF14803 Nudix_N_2: Nudix N-te 28.4 11 0.00025 25.4 -1.1 29 29-58 1-32 (34)
50 PF12156 ATPase-cat_bd: Putati 28.2 42 0.00091 26.7 1.9 32 30-61 2-39 (88)
51 cd07166 NR_DBD_REV_ERB DNA-bin 27.2 39 0.00084 27.0 1.6 30 28-60 3-32 (89)
52 cd06965 NR_DBD_Ppar DNA-bindin 26.4 38 0.00081 26.8 1.3 27 31-60 2-28 (84)
53 PF07282 OrfB_Zn_ribbon: Putat 26.4 23 0.0005 26.1 0.1 27 27-55 27-53 (69)
54 TIGR01385 TFSII transcription 26.2 50 0.0011 32.1 2.4 30 26-55 256-293 (299)
55 smart00290 ZnF_UBP Ubiquitin C 26.0 33 0.00072 23.6 0.9 23 30-52 1-23 (50)
56 cd06966 NR_DBD_CAR DNA-binding 25.6 26 0.00056 28.3 0.3 29 29-60 1-29 (94)
57 PRK00423 tfb transcription ini 25.1 30 0.00065 33.3 0.7 32 26-58 9-40 (310)
58 cd07162 NR_DBD_PXR DNA-binding 24.9 44 0.00096 26.5 1.5 28 30-60 1-28 (87)
59 cd07165 NR_DBD_DmE78_like DNA- 24.5 49 0.0011 25.8 1.7 27 31-60 1-27 (81)
60 cd07161 NR_DBD_EcR DNA-binding 24.2 44 0.00095 26.9 1.4 28 30-60 3-30 (91)
61 COG1997 RPL43A Ribosomal prote 24.0 46 0.001 27.3 1.4 31 25-57 32-62 (89)
62 KOG0457 Histone acetyltransfer 23.9 70 0.0015 33.0 3.0 95 25-123 10-124 (438)
63 PTZ00074 60S ribosomal protein 23.8 46 0.001 29.2 1.5 31 25-55 38-85 (135)
64 cd07169 NR_DBD_GCNF_like DNA-b 23.7 47 0.001 26.6 1.5 32 26-60 4-35 (90)
65 cd07158 NR_DBD_Ppar_like The D 23.2 50 0.0011 25.1 1.5 27 31-60 1-27 (73)
66 PF02318 FYVE_2: FYVE-type zin 22.6 68 0.0015 26.6 2.2 31 27-57 53-88 (118)
67 cd07155 NR_DBD_ER_like DNA-bin 22.6 56 0.0012 25.1 1.6 27 31-60 1-27 (75)
68 cd07172 NR_DBD_GR_PR DNA-bindi 22.6 49 0.0011 25.8 1.3 29 29-60 3-31 (78)
69 cd06956 NR_DBD_RXR DNA-binding 22.5 51 0.0011 25.5 1.4 28 30-60 2-29 (77)
70 COG0675 Transposase and inacti 22.3 25 0.00053 32.0 -0.5 22 29-57 310-331 (364)
71 TIGR00100 hypA hydrogenase nic 22.1 37 0.0008 28.3 0.6 46 24-74 66-113 (115)
72 PF12760 Zn_Tnp_IS1595: Transp 21.6 77 0.0017 22.0 2.0 31 24-55 14-44 (46)
73 PF13462 Thioredoxin_4: Thiore 21.3 49 0.0011 27.0 1.2 28 35-62 8-35 (162)
74 PRK04059 rpl34e 50S ribosomal 20.9 53 0.0011 26.8 1.2 31 26-56 32-79 (88)
75 cd03031 GRX_GRX_like Glutaredo 20.6 44 0.00095 29.1 0.7 36 17-61 88-123 (147)
76 cd06958 NR_DBD_COUP_TF DNA-bin 20.4 63 0.0014 24.7 1.5 27 31-60 1-27 (73)
77 PF14376 Haem_bd: Haem-binding 20.2 50 0.0011 28.2 1.0 21 18-42 35-55 (137)
No 1
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=4.7e-45 Score=341.97 Aligned_cols=121 Identities=57% Similarity=1.016 Sum_probs=113.7
Q ss_pred cccHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeecccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHH
Q 022340 6 NVSKELNAKHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQ 85 (298)
Q Consensus 6 ~~sk~l~ar~ekiL~~Ll~~PgNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~LG~hISkVKSltLD~Wt~eeV~~mk 85 (298)
.+.+...++++++|++||+.|+|+.|||||+++|+|||+|+|||||++|+||||+||+||||||||+||.|++|||+.|+
T Consensus 3 ~~~~~~~~~~~~~l~~Ll~~~~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~ 82 (287)
T KOG0703|consen 3 RVEKGSNERNKRRLRELLREPDNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMI 82 (287)
T ss_pred cccccccchHHHHHHHHHcCcccCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHH
Confidence 34446678999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccHHHHHHHhhcCCCCCChH----HHHHHHHHhhhcCccccCC
Q 022340 86 SMGNEKSNSYWEAELPPNYDRV----GIENFIRAKYEEKRWIPRG 126 (298)
Q Consensus 86 ~~GN~~aN~~wEa~lPp~~d~~----~~e~FIraKY~~k~F~~~~ 126 (298)
..||.+||+|||+.+|..+++. .+|+|||+||+.|+|+.++
T Consensus 83 ~~GN~~an~~~ea~~p~~~~~p~~d~~~e~FIR~KYE~kkf~~~~ 127 (287)
T KOG0703|consen 83 SMGNAKANSYYEAKLPDPFRRPGPDDLVEQFIRDKYERKKFLDPE 127 (287)
T ss_pred HHcchhhhhhccccCCccccCCChHHHHHHHHHHHHhhhhhccch
Confidence 9999999999999999877653 4999999999999999876
No 2
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=100.00 E-value=1.7e-41 Score=339.25 Aligned_cols=161 Identities=27% Similarity=0.515 Sum_probs=148.1
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeecccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhh
Q 022340 8 SKELNAKHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSM 87 (298)
Q Consensus 8 sk~l~ar~ekiL~~Ll~~PgNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~LG~hISkVKSltLD~Wt~eeV~~mk~~ 87 (298)
||+++++++++|++|++.|+|+.|||||+.+|.|||+|||||||+.|+||||.|| +|||||+||+|+++||++|+.+
T Consensus 3 SKR~qERnekILreLlklPgNk~CADCgs~~P~WASiNlGIFICi~CSGIHRsLG---hRVKSLSLDkWT~EEVe~Mk~g 79 (648)
T PLN03119 3 SKREEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREFT---HRVKSVSMSKFTSKEVEVLQNG 79 (648)
T ss_pred chHHHHHHHHHHHHHhhCcCCCccccCCCCCCCceeeccceEEeccchhhhccCC---ceeeccccCCCCHHHHHHHHHh
Confidence 6899999999999999999999999999999999999999999999999999998 4999999999999999999999
Q ss_pred ccHHHHHHHhhcCC-------CCCChHHHHHHHHHhhhcCccccCCCCCCCCCCCCcCccCCCCCCCCCCCCCCCCCCCC
Q 022340 88 GNEKSNSYWEAELP-------PNYDRVGIENFIRAKYEEKRWIPRGGNTKSPSRVSEEKASFHRPLPSSSGHRYTNNINR 160 (298)
Q Consensus 88 GN~~aN~~wEa~lP-------p~~d~~~~e~FIraKY~~k~F~~~~~~~~~~s~~~~~~~~~~~~~~~r~g~~~~ss~~~ 160 (298)
||.++|+|||++++ ...+...+++|||.||++|+|+.....+.++....+++.+...+.+.++||++.+|..|
T Consensus 80 GN~~AN~iyeanw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~~~~~~d~p~~~~~~~~~~~~~~~~~~s~h~~s~sp~y 159 (648)
T PLN03119 80 GNQRAREIYLKNWDHQRQRLPENSNAERVREFIKNVYVQKKYAGANDADKPSKDSQDHVSSEDMTRRANSYHSYSQSPPY 159 (648)
T ss_pred chHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhccCcCCCCCCcccccccccccccccccccCCCCCCCCCc
Confidence 99999999999874 33455678999999999999999999999888888999888888899999999999875
Q ss_pred ---ccccccCCCCC
Q 022340 161 ---VPDVRNIAHPP 171 (298)
Q Consensus 161 ---~~~~~~~~~~~ 171 (298)
+|||||+.+.-
T Consensus 160 ~~~ye~rr~~~~~~ 173 (648)
T PLN03119 160 DYQYEERRYGKIPL 173 (648)
T ss_pred ccchhhhhcccccc
Confidence 69999995543
No 3
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=100.00 E-value=3.6e-40 Score=271.77 Aligned_cols=109 Identities=57% Similarity=1.048 Sum_probs=90.7
Q ss_pred HHHHHHhcCCCCCCCcCCCCCCCCeeecccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHHHHHHH
Q 022340 17 KILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYW 96 (298)
Q Consensus 17 kiL~~Ll~~PgNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~LG~hISkVKSltLD~Wt~eeV~~mk~~GN~~aN~~w 96 (298)
++|+.|++.|+|+.|||||+++|+|||++||||||+.|+|+||.||+|||+||||+||+|++++|++|+.+||..+|++|
T Consensus 2 ~~l~~l~~~~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~VkSi~~d~w~~~ev~~~~~~GN~~~n~~~ 81 (116)
T PF01412_consen 2 KILRELLKKPGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRVKSITMDNWSPEEVQRMREGGNKRANSIW 81 (116)
T ss_dssp HHHHHHHCSTTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--EEETTTS---HHHHHHHHHSHHHHHHHHH
T ss_pred HHHHHHHcCcCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhccccccCCCCHHHHHHHHHHChHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCC------CCCChHHHHHHHHHhhhcCccccC
Q 022340 97 EAELP------PNYDRVGIENFIRAKYEEKRWIPR 125 (298)
Q Consensus 97 Ea~lP------p~~d~~~~e~FIraKY~~k~F~~~ 125 (298)
|++.+ +..+...+++||++||++++|+.+
T Consensus 82 e~~~~~~~~~~~~~~~~~~~~fI~~KY~~k~f~~~ 116 (116)
T PF01412_consen 82 EANSPPPKKPPPSSDQEKREQFIRAKYVEKAFISK 116 (116)
T ss_dssp TTTSTTTTTHCTTSHHHHHHHHHHHHHTTHTTS-C
T ss_pred HcCCCCCCCCCCCCcHHHHHHHHHHHHHhhhhccC
Confidence 99842 233456789999999999999863
No 4
>PLN03131 hypothetical protein; Provisional
Probab=100.00 E-value=4.7e-39 Score=323.86 Aligned_cols=159 Identities=28% Similarity=0.533 Sum_probs=140.5
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeecccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhh
Q 022340 8 SKELNAKHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSM 87 (298)
Q Consensus 8 sk~l~ar~ekiL~~Ll~~PgNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~LG~hISkVKSltLD~Wt~eeV~~mk~~ 87 (298)
||+++++++++|++|++.|+|+.|||||+++|.|||+|||||||+.|+||||.|| +|||||+||+|++++|++|+.+
T Consensus 3 SkkqqErnekiLreLlk~PgNk~CADCga~~P~WASiNlGIFICi~CSGIHRsLg---hRVKSVTLD~WtdeEV~~Mk~g 79 (705)
T PLN03131 3 SRKEEERNEKIIRGLMKLPPNRRCINCNSLGPQFVCTNFWTFICMTCSGIHREFT---HRVKSVSMSKFTSQDVEALQNG 79 (705)
T ss_pred chHHHHHHHHHHHHHhhCcCCCccccCCCCCCCeeEeccceEEchhchhhhcccC---cccccccCCCCCHHHHHHHHHh
Confidence 6789999999999999999999999999999999999999999999999999998 3999999999999999999999
Q ss_pred ccHHHHHHHhhcCC-------CCCChHHHHHHHHHhhhcCccccCCCCCCCCCCCCcCccCCCCCCCCCCCCCCCCCCCC
Q 022340 88 GNEKSNSYWEAELP-------PNYDRVGIENFIRAKYEEKRWIPRGGNTKSPSRVSEEKASFHRPLPSSSGHRYTNNINR 160 (298)
Q Consensus 88 GN~~aN~~wEa~lP-------p~~d~~~~e~FIraKY~~k~F~~~~~~~~~~s~~~~~~~~~~~~~~~r~g~~~~ss~~~ 160 (298)
||.++|+|||++++ .+.+...+++|||.||++|+|+.....+.++......+......++..++|++..|..|
T Consensus 80 GN~~AN~iyeanwd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa~~~s~d~pprd~q~~r~~e~e~rr~~syh~~SqSPpY 159 (705)
T PLN03131 80 GNQRAREIYLKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKYAGGKTHDKPPRDLQRIRSHEDETRRACSYHSYSQSPPY 159 (705)
T ss_pred ccHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhhhcCCCCCCCchhhhhhhcccccccccccccCCCcCCCc
Confidence 99999999998764 33455678999999999999999988877776666666666666777788888888776
Q ss_pred ---ccccccCCC
Q 022340 161 ---VPDVRNIAH 169 (298)
Q Consensus 161 ---~~~~~~~~~ 169 (298)
+|||||+-+
T Consensus 160 ~~~yedrRygk~ 171 (705)
T PLN03131 160 DFQYEDRRYGKQ 171 (705)
T ss_pred cccccccccccc
Confidence 689988643
No 5
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=100.00 E-value=1.2e-38 Score=261.60 Aligned_cols=103 Identities=57% Similarity=1.023 Sum_probs=96.0
Q ss_pred CCCCCCcCCCCCCCCeeecccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHHHHHHHhhcCCCCC-
Q 022340 26 PENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYWEAELPPNY- 104 (298)
Q Consensus 26 PgNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~LG~hISkVKSltLD~Wt~eeV~~mk~~GN~~aN~~wEa~lPp~~- 104 (298)
|+|+.|||||+++|+|+|++||||||+.|+|+||.||+|||+||||+||+|++++|++|+.+||.++|+|||+++++..
T Consensus 1 ~~N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~VkSl~md~w~~~~i~~~~~~GN~~~n~~~e~~~~~~~~ 80 (112)
T smart00105 1 PGNKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTLDTWTEEELRLLQKGGNENANSIWESNLDDFSL 80 (112)
T ss_pred CCCCcccCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCeeeecccCCCCHHHHHHHHHhhhHHHHHHHHhhCCcccc
Confidence 5899999999999999999999999999999999999999999999999999999999999999999999999986432
Q ss_pred ------ChHHHHHHHHHhhhcCccccCCCC
Q 022340 105 ------DRVGIENFIRAKYEEKRWIPRGGN 128 (298)
Q Consensus 105 ------d~~~~e~FIraKY~~k~F~~~~~~ 128 (298)
+...+++||++||++++|+...+.
T Consensus 81 ~~~~~~~~~~~~~fI~~KY~~k~f~~~~~~ 110 (112)
T smart00105 81 KPPDSDDQQKYESFIAAKYEEKLFVPPESA 110 (112)
T ss_pred CCCCCchHHHHHHHHHHHHHhhhccccccC
Confidence 356789999999999999987664
No 6
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=100.00 E-value=7.4e-36 Score=284.43 Aligned_cols=115 Identities=47% Similarity=0.905 Sum_probs=105.2
Q ss_pred HHHHHHHHHhcCCCCCCCcCCCCCCCCeeecccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHHHH
Q 022340 14 KHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSN 93 (298)
Q Consensus 14 r~ekiL~~Ll~~PgNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~LG~hISkVKSltLD~Wt~eeV~~mk~~GN~~aN 93 (298)
..+++|..|...++|+.|||||+++|+|+|+|||||||++||||||+||+|||+||||+||+|+.+||++|+.+||.+||
T Consensus 6 ~~~~~l~~l~~~~~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~wt~~~l~~m~~gGN~~a~ 85 (319)
T COG5347 6 EDRKLLKLLKSDSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWTEEELRRMEVGGNSNAN 85 (319)
T ss_pred HHHHHHHHHhhccccCccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeecccCCHHHHHHHHHhcchhhh
Confidence 45678888899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcC------C--CCCChHHHHHHHHHhhhcCccccCCCC
Q 022340 94 SYWEAEL------P--PNYDRVGIENFIRAKYEEKRWIPRGGN 128 (298)
Q Consensus 94 ~~wEa~l------P--p~~d~~~~e~FIraKY~~k~F~~~~~~ 128 (298)
.||+.++ | ..+|...+++||+.||+.++|+.....
T Consensus 86 ~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~~~~ 128 (319)
T COG5347 86 RFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDDSSS 128 (319)
T ss_pred hHhccCCCcccccccccccCHHHHHHHHHHHHHhhhccccccC
Confidence 9999864 2 345667899999999999999976444
No 7
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.97 E-value=2e-29 Score=242.34 Aligned_cols=113 Identities=37% Similarity=0.639 Sum_probs=96.5
Q ss_pred HHHHHHHHhcCCCCCCCcCCCCCCCCeeecccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHHHHH
Q 022340 15 HRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNS 94 (298)
Q Consensus 15 ~ekiL~~Ll~~PgNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~LG~hISkVKSltLD~Wt~eeV~~mk~~GN~~aN~ 94 (298)
..++|+.|+..|+|+.|+|||+++|+|+|+|||||||+.|+|+||.||+|||+|||++||.|++++|++|+.+||.++|.
T Consensus 9 ~~~vfrkL~~kPgNk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~Ws~eqL~~Mk~GGN~rA~~ 88 (395)
T PLN03114 9 KISVFKKLKAKSDNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSSEQLKMMIYGGNNRAQV 88 (395)
T ss_pred HHHHHHHHHhCcCCCcCccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCCCCHHHHHHHHHhcCHHHHH
Confidence 35679999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcC-CC------CCChH--HHHHHHHHhhhcCccccCCC
Q 022340 95 YWEAEL-PP------NYDRV--GIENFIRAKYEEKRWIPRGG 127 (298)
Q Consensus 95 ~wEa~l-Pp------~~d~~--~~e~FIraKY~~k~F~~~~~ 127 (298)
||+.+. .. .|... ..-+.+.+|++.+.+.....
T Consensus 89 fF~qhG~~~~~~~~~KY~S~aA~~Yre~L~keVa~~~a~~~~ 130 (395)
T PLN03114 89 FFKQYGWSDGGKTEAKYTSRAADLYKQILAKEVAKSKAEEEL 130 (395)
T ss_pred HHHHcCCCCCCCcccccCCHHHHHHHHHHHHHHHHhhhcccc
Confidence 998763 11 12211 22344888888888875443
No 8
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=99.97 E-value=4.1e-31 Score=252.71 Aligned_cols=111 Identities=39% Similarity=0.749 Sum_probs=95.6
Q ss_pred HHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeecccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHH
Q 022340 12 NAKHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEK 91 (298)
Q Consensus 12 ~ar~ekiL~~Ll~~PgNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~LG~hISkVKSltLD~Wt~eeV~~mk~~GN~~ 91 (298)
..+.++.|..|....+|+.|+||+++||+|||++||||||++|||+||+||+|||+|||||||+|.+.||+.|+.+||.+
T Consensus 3 sprtrr~L~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~ 82 (386)
T KOG0704|consen 3 SPRTRRVLLELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNER 82 (386)
T ss_pred ChHHHHHHHhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchh
Confidence 34778888888888899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcC------CC--CCCh---HHHHHHHHHhhhcCcc
Q 022340 92 SNSYWEAEL------PP--NYDR---VGIENFIRAKYEEKRW 122 (298)
Q Consensus 92 aN~~wEa~l------Pp--~~d~---~~~e~FIraKY~~k~F 122 (298)
++.|++..- |. .|+. ...++-|.+--+.+.|
T Consensus 83 ~~eFL~s~~~~~e~~~i~eKYns~aAa~yRdki~~laegr~w 124 (386)
T KOG0704|consen 83 FREFLSSQGIYKETWPIREKYNSRAAALYRDKIAALAEGREW 124 (386)
T ss_pred HHHHHhhCccccccccHHHhhccHHHHHHHHHHHHHhcCCcc
Confidence 999998652 21 1221 2346667777777777
No 9
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.95 E-value=3.6e-29 Score=245.02 Aligned_cols=85 Identities=45% Similarity=0.850 Sum_probs=82.4
Q ss_pred HHHHHHHHhcCCCCCCCcCCCCCCCCeeecccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHHHHH
Q 022340 15 HRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNS 94 (298)
Q Consensus 15 ~ekiL~~Ll~~PgNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~LG~hISkVKSltLD~Wt~eeV~~mk~~GN~~aN~ 94 (298)
.+.+++.|..+++|+.|||||+++|.|+||+||||||++||++||+||+|||+|||..||+|+.+||+.|+.|||.+|+.
T Consensus 10 ~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~~ 89 (454)
T KOG0706|consen 10 IQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANARV 89 (454)
T ss_pred HHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHHH
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhc
Q 022340 95 YWEAE 99 (298)
Q Consensus 95 ~wEa~ 99 (298)
|+..+
T Consensus 90 FFkqh 94 (454)
T KOG0706|consen 90 FFKQH 94 (454)
T ss_pred HHHHc
Confidence 99876
No 10
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.94 E-value=8.5e-28 Score=241.28 Aligned_cols=147 Identities=36% Similarity=0.667 Sum_probs=117.7
Q ss_pred HHHHHHHHhcCCCCCCCcCCCCCCCCeeecccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHHHHH
Q 022340 15 HRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNS 94 (298)
Q Consensus 15 ~ekiL~~Ll~~PgNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~LG~hISkVKSltLD~Wt~eeV~~mk~~GN~~aN~ 94 (298)
....|+.|...+||..|+||+.++|.|+|+|+|+.||++|+||||.||+|+|+|+||.||.|..|.+..|..+||+.||+
T Consensus 500 ea~a~qairn~rgn~~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl~~Vm~aiGN~~AN~ 579 (749)
T KOG0705|consen 500 EAMALQAIRNMRGNSHCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVELLKVMSAIGNDLANS 579 (749)
T ss_pred hHHHHHHHhcCcCCceeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHHHHHHHHhhhhHHHH
Confidence 44568888999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcC-----C-CCCChHHHHHHHHHhhhcCccccCCCCCCCCCCCCcCc---cCCCCCCCCCCCCCCCCCCCCc
Q 022340 95 YWEAEL-----P-PNYDRVGIENFIRAKYEEKRWIPRGGNTKSPSRVSEEK---ASFHRPLPSSSGHRYTNNINRV 161 (298)
Q Consensus 95 ~wEa~l-----P-p~~d~~~~e~FIraKY~~k~F~~~~~~~~~~s~~~~~~---~~~~~~~~~r~g~~~~ss~~~~ 161 (298)
+||..+ | +.+.++++|+|||+||++|.|..+.....-+-++.--. ....++....+.|+++..++..
T Consensus 580 vWE~~~~G~~KPs~~s~REEkErwIr~KYeqklFLaPl~~te~~lgqqLl~A~~~~Dl~t~~lLLAhg~~~e~~~t 655 (749)
T KOG0705|consen 580 VWEGSSQGQTKPSPDSSREEKERWIRAKYEQKLFLAPLPCTEEPLGQQLLRAVAAEDLQTAILLLAHGSREEVNET 655 (749)
T ss_pred HhhhhccCCcCCCccccHHHHHHHHHHHHHHHhhcCCCCCCCCchHHHHHHHHHHHHHHHHHHHHhccCchhhhcc
Confidence 999753 2 34457889999999999999998877655443321111 1111233334556666555543
No 11
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.89 E-value=2.2e-24 Score=225.41 Aligned_cols=112 Identities=46% Similarity=0.889 Sum_probs=102.6
Q ss_pred HHHHHhcCCCCCCCcCCCCCCCCeeecccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHHHHHHHh
Q 022340 18 ILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYWE 97 (298)
Q Consensus 18 iL~~Ll~~PgNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~LG~hISkVKSltLD~Wt~eeV~~mk~~GN~~aN~~wE 97 (298)
.+..+...|||..|+|||++.|+|+|+|+||.+|++|+|+||+||+|||+|+||+||.|.++.+.+|+.+||..+|.+||
T Consensus 416 ~~~~vq~~pgN~~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~~~~l~~l~~~lgn~~~N~i~e 495 (785)
T KOG0521|consen 416 VIEEVQSVPGNAQCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVWEPELLLLFKNLGNKYVNEIYE 495 (785)
T ss_pred hhhhhhcCCchhhhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhccCcHHHHHHHHhCcchhhhhhh
Confidence 37788899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCC--------CChHHHHHHHHHhhhcCccccCCCCC
Q 022340 98 AELPPN--------YDRVGIENFIRAKYEEKRWIPRGGNT 129 (298)
Q Consensus 98 a~lPp~--------~d~~~~e~FIraKY~~k~F~~~~~~~ 129 (298)
+.++.. .+...++.||++||++++|..+....
T Consensus 496 ~~l~~~~~~~~~~~~~~~~r~~~i~~kyve~~F~~k~~~~ 535 (785)
T KOG0521|consen 496 ALLPSYDSSKPTASSSRQAREAWIKAKYVERRFSVKEPQI 535 (785)
T ss_pred cccccccccCCCCccchhhhhHhhhcccceeeEeecccch
Confidence 998742 23456899999999999998765543
No 12
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.81 E-value=4.3e-21 Score=190.97 Aligned_cols=101 Identities=41% Similarity=0.795 Sum_probs=90.4
Q ss_pred CCCCCCCcCCCCCCCCeeecccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHHHHHHHhhcCCCC-
Q 022340 25 LPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYWEAELPPN- 103 (298)
Q Consensus 25 ~PgNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~LG~hISkVKSltLD~Wt~eeV~~mk~~GN~~aN~~wEa~lPp~- 103 (298)
...-+.|+|||+++|.|+|+|-|+|||.+|+.+||+||.|||.||+|....|.++-|.+...+.|..+|.|||..|=+.
T Consensus 5 ~l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaNsIWEh~Lld~s 84 (669)
T KOG0818|consen 5 LLSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGANSIWEHSLLDPA 84 (669)
T ss_pred chhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcchhhhhhccCch
Confidence 4556789999999999999999999999999999999999999999999999999999999999999999999876221
Q ss_pred -----------CCh--HHHHHHHHHhhhcCccccC
Q 022340 104 -----------YDR--VGIENFIRAKYEEKRWIPR 125 (298)
Q Consensus 104 -----------~d~--~~~e~FIraKY~~k~F~~~ 125 (298)
.|. ..+++|||+||+...|+.+
T Consensus 85 t~~sg~rk~~pqD~~Hp~K~eFIkaKy~~LtFv~~ 119 (669)
T KOG0818|consen 85 TIMSGRRKANPQDKVHPNKAEFIRAKYQMLAFVHR 119 (669)
T ss_pred hhhcccCCCCCcCCCCccHHHHHHHHHHheeeecc
Confidence 122 2478999999999999974
No 13
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.77 E-value=9.8e-20 Score=189.28 Aligned_cols=108 Identities=41% Similarity=0.786 Sum_probs=97.8
Q ss_pred HHHhcCCCCCCCcCCCCCCCCeeecccchHhhHhhhhhhhcCCCccceeeecccCC--CCHHHHHHHHhhccHHHHHHHh
Q 022340 20 DGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDT--WLPEQVAVIQSMGNEKSNSYWE 97 (298)
Q Consensus 20 ~~Ll~~PgNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~LG~hISkVKSltLD~--Wt~eeV~~mk~~GN~~aN~~wE 97 (298)
+++.....|+.|+|||++.|.|+|+|++|.||-.|+|-||+||..+|+|+|++||. |+.+-|+++..+||.++|.||-
T Consensus 290 eriW~ne~nr~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~Fwa 369 (1186)
T KOG1117|consen 290 ERIWLNEENRECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANRFWA 369 (1186)
T ss_pred HHHHhccccccccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCcccccccc
Confidence 35566789999999999999999999999999999999999999999999999997 9999999999999999999999
Q ss_pred hcCCCCC------ChHHHHHHHHHhhhcCccccCCC
Q 022340 98 AELPPNY------DRVGIENFIRAKYEEKRWIPRGG 127 (298)
Q Consensus 98 a~lPp~~------d~~~~e~FIraKY~~k~F~~~~~ 127 (298)
.++|++. ....+++||.+||.+..|-....
T Consensus 370 ~nl~~~e~lh~dssp~~r~~fi~~Kykeg~fRk~~~ 405 (1186)
T KOG1117|consen 370 GNLPPNEHLHPDSSPSTRRQFIKEKYKEGKFRKEHP 405 (1186)
T ss_pred cCCCCccccCCCCCcchhhhHHHHHhhccccccccc
Confidence 9998764 23568999999999998865433
No 14
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.70 E-value=1.1e-16 Score=159.10 Aligned_cols=125 Identities=30% Similarity=0.560 Sum_probs=110.8
Q ss_pred ccHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCC-CeeecccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHH
Q 022340 7 VSKELNAKHRKILDGLLKLPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQ 85 (298)
Q Consensus 7 ~sk~l~ar~ekiL~~Ll~~PgNk~CADCGa~~P-~WaSln~GVFlC~~CSgiHR~LG~hISkVKSltLD~Wt~eeV~~mk 85 (298)
..|+.+..++++|+.|+++|+|++|++|....+ +|+++.-|-|+|+.|+|+-|.|.. -++|||++|.+++..+|..|+
T Consensus 4 ~~ke~E~~~ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~~-ahRvksiSmttft~qevs~lQ 82 (524)
T KOG0702|consen 4 YKKEDEYDYEKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLNP-AHRVKSISMTTFTDQEVSFLQ 82 (524)
T ss_pred ccccchhHHHHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccCCC-ccccceeeeeeccccchHHHh
Confidence 456666777999999999999999999999987 999999999999999999999864 469999999999999999999
Q ss_pred hhccHHHHHHHhh-------cCCCCCChHHHHHHHHHhhhcCccccCCCCCCCC
Q 022340 86 SMGNEKSNSYWEA-------ELPPNYDRVGIENFIRAKYEEKRWIPRGGNTKSP 132 (298)
Q Consensus 86 ~~GN~~aN~~wEa-------~lPp~~d~~~~e~FIraKY~~k~F~~~~~~~~~~ 132 (298)
.+||+.+.++|.. .+|+..+....++|||.||+.++|+-.......+
T Consensus 83 shgNq~~k~i~fkl~D~q~S~vPD~rn~~~~kef~q~~y~~kr~~v~~n~~k~~ 136 (524)
T KOG0702|consen 83 SHGNQVCKEIWFKLFDFQRSNVPDSRNPQKVKEFQQEKYVKKRYYVPKNQMKIP 136 (524)
T ss_pred hcchhhhhhhhhcchhhhhccCCCcccchhhHHHHhhhhccceeecCccccccc
Confidence 9999999999975 3577777788999999999999999665555444
No 15
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=95.56 E-value=0.003 Score=67.75 Aligned_cols=72 Identities=21% Similarity=0.237 Sum_probs=61.5
Q ss_pred cCCCCCCCcCCCCC-CCCeeecccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHHHHHHHh
Q 022340 24 KLPENRECADCKAK-GPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYWE 97 (298)
Q Consensus 24 ~~PgNk~CADCGa~-~P~WaSln~GVFlC~~CSgiHR~LG~hISkVKSltLD~Wt~eeV~~mk~~GN~~aN~~wE 97 (298)
....+..|++|++. ...|+++|+.+-+|+.|+++|+.++.+++...++.|++..+ |..+...|+...+..|.
T Consensus 626 ~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~~~~ 698 (785)
T KOG0521|consen 626 KASSDGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHHATA 698 (785)
T ss_pred HhccCccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchhhhh
Confidence 34568899999985 78999999999999999999999999999999999998776 77777777777666554
No 16
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=85.01 E-value=0.55 Score=42.53 Aligned_cols=31 Identities=32% Similarity=0.578 Sum_probs=27.1
Q ss_pred CCCCCCCcCCCCCCC-CeeecccchHhhHhhh
Q 022340 25 LPENRECADCKAKGP-RWASVNLGIFICMQCS 55 (298)
Q Consensus 25 ~PgNk~CADCGa~~P-~WaSln~GVFlC~~CS 55 (298)
.|.-..|+-||.+.. .|.+..-|.|+|..|.
T Consensus 146 ~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 146 GLDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred ccchhhHhcCCCCCCceEEecccCCccccccc
Confidence 567789999998854 7899999999999997
No 17
>PRK12495 hypothetical protein; Provisional
Probab=79.31 E-value=1.2 Score=41.81 Aligned_cols=38 Identities=24% Similarity=0.397 Sum_probs=28.5
Q ss_pred HHHHHHHhc--CCCCCCCcCCCCCCCCeeecccchHhhHhhhhh
Q 022340 16 RKILDGLLK--LPENRECADCKAKGPRWASVNLGIFICMQCSGI 57 (298)
Q Consensus 16 ekiL~~Ll~--~PgNk~CADCGa~~P~WaSln~GVFlC~~CSgi 57 (298)
+++-+.|++ ...+..|-+||.+-|.+ -|+.+|..|..+
T Consensus 28 ~~ma~lL~~gatmsa~hC~~CG~PIpa~----pG~~~Cp~CQ~~ 67 (226)
T PRK12495 28 ERMSELLLQGATMTNAHCDECGDPIFRH----DGQEFCPTCQQP 67 (226)
T ss_pred HHHHHHHHhhcccchhhcccccCcccCC----CCeeECCCCCCc
Confidence 344444554 47899999999999832 699999999644
No 18
>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=78.14 E-value=1.5 Score=29.49 Aligned_cols=34 Identities=12% Similarity=0.335 Sum_probs=29.3
Q ss_pred CCCCCcCCCCCCCCeeecccchHhhHhhhhh-hhc
Q 022340 27 ENRECADCKAKGPRWASVNLGIFICMQCSGI-HRS 60 (298)
Q Consensus 27 gNk~CADCGa~~P~WaSln~GVFlC~~CSgi-HR~ 60 (298)
.+..|..|+.....+.+.+-+++||..|... |+.
T Consensus 2 ~~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~ 36 (42)
T PF00643_consen 2 QEPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG 36 (42)
T ss_dssp SSSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT
T ss_pred cCccCccCCccceEEEecCCCCccCccCCCCCCCC
Confidence 3578999999889999999999999999988 877
No 19
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=76.43 E-value=1.7 Score=39.25 Aligned_cols=33 Identities=27% Similarity=0.497 Sum_probs=27.6
Q ss_pred CCCCCCCcCCCCCCC-CeeecccchHhhHhhhhh
Q 022340 25 LPENRECADCKAKGP-RWASVNLGIFICMQCSGI 57 (298)
Q Consensus 25 ~PgNk~CADCGa~~P-~WaSln~GVFlC~~CSgi 57 (298)
.|.-..|+.||..++ .|.+...|.|+|..|...
T Consensus 144 ~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 144 ALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred CcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 577789999998544 688999999999999764
No 20
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=72.34 E-value=1.4 Score=37.47 Aligned_cols=35 Identities=14% Similarity=0.349 Sum_probs=23.4
Q ss_pred CCCCCCcCCCCCCC-CeeecccchHhhHhhhhhhhc
Q 022340 26 PENRECADCKAKGP-RWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 26 PgNk~CADCGa~~P-~WaSln~GVFlC~~CSgiHR~ 60 (298)
..-.+|.+||.+=| .=.-.--+..+|+.|...|-.
T Consensus 78 gtYG~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~~E~ 113 (120)
T COG1734 78 GTYGICEECGEPIPEARLEARPTARLCIECQERAER 113 (120)
T ss_pred CCccchhccCCcCCHHHHhhCcchHHHHHHHHHHHH
Confidence 34458999999722 122233468999999987743
No 21
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=70.62 E-value=2.2 Score=39.77 Aligned_cols=31 Identities=32% Similarity=0.693 Sum_probs=27.4
Q ss_pred CCCCCCCcCCCCCC-CCeeecccchHhhHhhh
Q 022340 25 LPENRECADCKAKG-PRWASVNLGIFICMQCS 55 (298)
Q Consensus 25 ~PgNk~CADCGa~~-P~WaSln~GVFlC~~CS 55 (298)
.+.=..|+.||.+. +...+.-.|-++|.+|.
T Consensus 151 ~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 151 GPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred ccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 46668999999985 57999999999999998
No 22
>TIGR02419 C4_traR_proteo phage/conjugal plasmid C-4 type zinc finger protein, TraR family. Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA.
Probab=70.48 E-value=2.6 Score=31.85 Aligned_cols=35 Identities=31% Similarity=0.575 Sum_probs=24.1
Q ss_pred cCCCCCCCcCCCCCCCC-eeecccchHhhHhhhhhh
Q 022340 24 KLPENRECADCKAKGPR-WASVNLGIFICMQCSGIH 58 (298)
Q Consensus 24 ~~PgNk~CADCGa~~P~-WaSln~GVFlC~~CSgiH 58 (298)
..++...|.|||.+=|. =.-..-|+..|+.|...+
T Consensus 27 ~~~s~g~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 27 IGPSLRECEDCGEPIPEARREALPGVTRCVSCQEIL 62 (63)
T ss_pred cCCCCCeeccCCCcChHHHHhhcCCcCCcHHHHhhc
Confidence 45678899999997432 112234788999998754
No 23
>PRK11019 hypothetical protein; Provisional
Probab=67.23 E-value=3.5 Score=33.44 Aligned_cols=37 Identities=22% Similarity=0.518 Sum_probs=26.2
Q ss_pred CCCCCcCCCCCCC--CeeecccchHhhHhhhhhhhcCCCc
Q 022340 27 ENRECADCKAKGP--RWASVNLGIFICMQCSGIHRSLGVH 64 (298)
Q Consensus 27 gNk~CADCGa~~P--~WaSln~GVFlC~~CSgiHR~LG~h 64 (298)
...+|.|||.+=| .+..+ -|+-.|+.|...+...+.|
T Consensus 35 syg~C~~CG~~Ip~~Rl~A~-P~a~~Cv~Cq~~~E~~~k~ 73 (88)
T PRK11019 35 SLTECEECGEPIPEARRKAI-PGVRLCVACQQEKDLQQAA 73 (88)
T ss_pred cCCeeCcCCCcCcHHHHhhc-CCccccHHHHHHHHHHHhH
Confidence 4679999999744 33332 3788999999987655443
No 24
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=63.44 E-value=5.1 Score=31.24 Aligned_cols=34 Identities=18% Similarity=0.485 Sum_probs=23.1
Q ss_pred CCCCcCCCCCCCC-eeecccchHhhHhhhhhhhcC
Q 022340 28 NRECADCKAKGPR-WASVNLGIFICMQCSGIHRSL 61 (298)
Q Consensus 28 Nk~CADCGa~~P~-WaSln~GVFlC~~CSgiHR~L 61 (298)
...|.|||.+=|. =.-.--|+..|+.|...+-.-
T Consensus 34 ~~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~E~~ 68 (73)
T PRK13715 34 VYLCEACGNPIPEARRKIFPGVTLCVECQAYQERQ 68 (73)
T ss_pred cccHhhcCCcCCHHHHhcCCCcCCCHHHHHHHHHH
Confidence 4689999997442 112234789999998876443
No 25
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=58.45 E-value=2.7 Score=28.58 Aligned_cols=27 Identities=19% Similarity=0.582 Sum_probs=16.8
Q ss_pred CCCcCCCCC-CCCeeecccchHhhHhhh
Q 022340 29 RECADCKAK-GPRWASVNLGIFICMQCS 55 (298)
Q Consensus 29 k~CADCGa~-~P~WaSln~GVFlC~~CS 55 (298)
..|.+||.. .-+|..-+|+.-||..|-
T Consensus 4 ~~C~eC~~~f~dSyL~~~F~~~VCD~CR 31 (34)
T PF01286_consen 4 PKCDECGKPFMDSYLLNNFDLPVCDKCR 31 (34)
T ss_dssp EE-TTT--EES-SSCCCCTS-S--TTT-
T ss_pred chHhHhCCHHHHHHHHHhCCcccccccc
Confidence 469999987 677999999999999994
No 26
>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=58.02 E-value=4.9 Score=27.33 Aligned_cols=27 Identities=26% Similarity=0.812 Sum_probs=22.7
Q ss_pred CCCCCCcCCCCCCCCeeecccchHhhHhhh
Q 022340 26 PENRECADCKAKGPRWASVNLGIFICMQCS 55 (298)
Q Consensus 26 PgNk~CADCGa~~P~WaSln~GVFlC~~CS 55 (298)
..|..|..|++. |...+=|.|+|.+|-
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCc
Confidence 345679999998 888899999999994
No 27
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=57.15 E-value=6.9 Score=34.41 Aligned_cols=39 Identities=13% Similarity=0.256 Sum_probs=25.7
Q ss_pred cCCCCCCCcCCCCCCC-CeeecccchHhhHhhhhhhhcCC
Q 022340 24 KLPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRSLG 62 (298)
Q Consensus 24 ~~PgNk~CADCGa~~P-~WaSln~GVFlC~~CSgiHR~LG 62 (298)
..+.-.+|-+||.+=| .=.-+--++..|+.|...|-..+
T Consensus 107 ~~gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~E~~~ 146 (151)
T PRK10778 107 EDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIRE 146 (151)
T ss_pred hCCCCceeccCCCcccHHHHhcCCCccccHHHHHHHHHHh
Confidence 4577899999999711 11112224678999998776443
No 28
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=54.47 E-value=11 Score=35.10 Aligned_cols=38 Identities=21% Similarity=0.495 Sum_probs=28.8
Q ss_pred HHHHHHHHhc-CCCCCCCcCCCCCCCCeeecccchHhhHhhhhhhh
Q 022340 15 HRKILDGLLK-LPENRECADCKAKGPRWASVNLGIFICMQCSGIHR 59 (298)
Q Consensus 15 ~ekiL~~Ll~-~PgNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR 59 (298)
.++.++..+. .|. ..|-.||.....|. ++|-.|.+.|-
T Consensus 341 ~~~~~~~~~~~~p~-~~c~~cg~~~~~~~------~~c~~c~~~~~ 379 (389)
T PRK11788 341 LRDLVGEQLKRKPR-YRCRNCGFTARTLY------WHCPSCKAWET 379 (389)
T ss_pred HHHHHHHHHhCCCC-EECCCCCCCCccce------eECcCCCCccC
Confidence 4556665555 455 45999999999994 79999988873
No 29
>PHA00080 DksA-like zinc finger domain containing protein
Probab=53.94 E-value=9.1 Score=29.71 Aligned_cols=35 Identities=26% Similarity=0.565 Sum_probs=24.1
Q ss_pred CCCCCCCcCCCCCCC--CeeecccchHhhHhhhhhhhc
Q 022340 25 LPENRECADCKAKGP--RWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 25 ~PgNk~CADCGa~~P--~WaSln~GVFlC~~CSgiHR~ 60 (298)
..+..+|.|||.+=| .|.. .-|+..|+.|...+-.
T Consensus 28 ~~~~~~C~~Cg~~Ip~~Rl~a-~P~~~~Cv~Cq~~~E~ 64 (72)
T PHA00080 28 APSATHCEECGDPIPEARREA-VPGCRTCVSCQEILEL 64 (72)
T ss_pred CCCCCEecCCCCcCcHHHHHh-CCCccCcHHHHHHHHH
Confidence 456679999999733 3322 2367789999887643
No 30
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=52.47 E-value=4.1 Score=28.08 Aligned_cols=26 Identities=23% Similarity=0.584 Sum_probs=20.3
Q ss_pred CCcCCCCCCCCeeecccchHhhHhhhh
Q 022340 30 ECADCKAKGPRWASVNLGIFICMQCSG 56 (298)
Q Consensus 30 ~CADCGa~~P~WaSln~GVFlC~~CSg 56 (298)
+|-.||+.. .-..-.-|-++|..|.-
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-B
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCCC
Confidence 689999977 45566789999999943
No 31
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=50.46 E-value=10 Score=27.48 Aligned_cols=37 Identities=24% Similarity=0.587 Sum_probs=30.0
Q ss_pred CCCCCcCCCCC-CCCeeecccch-HhhHhhhhhhhcCCC
Q 022340 27 ENRECADCKAK-GPRWASVNLGI-FICMQCSGIHRSLGV 63 (298)
Q Consensus 27 gNk~CADCGa~-~P~WaSln~GV-FlC~~CSgiHR~LG~ 63 (298)
....|..|+.. .|.|=.-..|- +||-.|.-..+..|.
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~ 40 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCC
Confidence 35789999986 68898888886 999999877776654
No 32
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=50.09 E-value=2.5 Score=28.21 Aligned_cols=30 Identities=23% Similarity=0.533 Sum_probs=17.4
Q ss_pred CCCcCCCCCCC-CeeecccchHhhHhhhhhh
Q 022340 29 RECADCKAKGP-RWASVNLGIFICMQCSGIH 58 (298)
Q Consensus 29 k~CADCGa~~P-~WaSln~GVFlC~~CSgiH 58 (298)
.+|.+||..=+ .=.-+.-|..+|..|+..|
T Consensus 4 g~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~~ 34 (36)
T PF01258_consen 4 GICEDCGEPIPEERLVAVPGATLCVECQERR 34 (36)
T ss_dssp SB-TTTSSBEEHHHHHHCTTECS-HHHHHHH
T ss_pred CCccccCChHHHHHHHhCCCcEECHHHhCcc
Confidence 45999998622 1122233788999998765
No 33
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=46.56 E-value=6.8 Score=34.85 Aligned_cols=34 Identities=29% Similarity=0.669 Sum_probs=27.7
Q ss_pred CCCCCCcCCCCCCCCeeecccchHhh-Hhhhhhhhc
Q 022340 26 PENRECADCKAKGPRWASVNLGIFIC-MQCSGIHRS 60 (298)
Q Consensus 26 PgNk~CADCGa~~P~WaSln~GVFlC-~~CSgiHR~ 60 (298)
|--+.|+-|| -...|.+++.|.-.| ..|-++|..
T Consensus 116 P~r~fCaVCG-~~S~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 116 PLRKFCAVCG-YDSKYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred CcchhhhhcC-CCchhHHHhcCCceeechhhhhccc
Confidence 4557899999 667799999999888 578888854
No 34
>TIGR02890 spore_yteA sporulation protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to PFAM family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. The function of proteins in this family is unknown. YteA was detected in mature spores of Bacillus subtilis by Kuwana, et al., and appears to be expressed under control of sigma-K.
Probab=46.18 E-value=16 Score=32.42 Aligned_cols=37 Identities=11% Similarity=0.132 Sum_probs=23.8
Q ss_pred cCCCCCCCcCCCCCC-CCeeecccchHhhHhhhhhhhc
Q 022340 24 KLPENRECADCKAKG-PRWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 24 ~~PgNk~CADCGa~~-P~WaSln~GVFlC~~CSgiHR~ 60 (298)
....-.+|.+||.+= +.=.-+--++-.|+.|...+-.
T Consensus 82 ~~G~YG~Ce~CGe~I~~~RL~a~P~a~~Ci~Cq~~~E~ 119 (159)
T TIGR02890 82 ENGTYGICEVCGKPIPYERLEAIPTATTCVECQNRKEV 119 (159)
T ss_pred hCCCCCeecccCCcccHHHHhhCCCcchhHHHHHHhhh
Confidence 345667899999871 1111222257789999987644
No 35
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=45.73 E-value=10 Score=25.49 Aligned_cols=32 Identities=25% Similarity=0.694 Sum_probs=23.0
Q ss_pred CcCCCCC-CCCeeecccchH-hhHhhhhhhhcCC
Q 022340 31 CADCKAK-GPRWASVNLGIF-ICMQCSGIHRSLG 62 (298)
Q Consensus 31 CADCGa~-~P~WaSln~GVF-lC~~CSgiHR~LG 62 (298)
|.+|+.. .|.|=....|-. ||-.|.-.+|..|
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~ 34 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYG 34 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhC
Confidence 8899986 699998888877 9999977776654
No 36
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=39.44 E-value=19 Score=29.59 Aligned_cols=31 Identities=19% Similarity=0.410 Sum_probs=19.0
Q ss_pred CCCCCCCcCCCCCCC-CeeecccchHhhHhhh
Q 022340 25 LPENRECADCKAKGP-RWASVNLGIFICMQCS 55 (298)
Q Consensus 25 ~PgNk~CADCGa~~P-~WaSln~GVFlC~~CS 55 (298)
.+.-.+|.|||.+=| .=.-.--++..|+.|.
T Consensus 77 ~g~yG~C~~Cge~I~~~RL~a~P~a~~Cv~Cq 108 (110)
T TIGR02420 77 DGEYGYCEECGEEIGLRRLEARPTATLCIDCK 108 (110)
T ss_pred CCCCCchhccCCcccHHHHhhCCCccccHHhH
Confidence 456689999999722 1111122456788885
No 37
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=38.02 E-value=24 Score=27.90 Aligned_cols=31 Identities=16% Similarity=0.540 Sum_probs=25.5
Q ss_pred CCCCCcCCCCCCCCeeecccchHhhHhhhhhhhc
Q 022340 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 27 gNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~ 60 (298)
..+.|.=||.+.. ...||+..|..|.+..|-
T Consensus 2 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 32 (82)
T cd07173 2 PQKTCLICGDEAS---GCHYGALTCGSCKVFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECcchhhhHHHHHHH
Confidence 4567999998765 458999999999998875
No 38
>cd07171 NR_DBD_ER DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ER interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Estrogen receptor is a transcription regulator that mediates the biological effects of hormone estrogen. The binding of estrogen to the receptor triggers the dimerization and the binding of the receptor dimer to estrogen response element, which is a palindromic inverted repeat: 5'GGTCAnnnTGACC-3', of target genes. Through ER, estrogen regulates development, reproduction and homeostasis. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well-conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserv
Probab=37.31 E-value=21 Score=28.21 Aligned_cols=31 Identities=19% Similarity=0.613 Sum_probs=25.6
Q ss_pred CCCCCcCCCCCCCCeeecccchHhhHhhhhhhhc
Q 022340 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 27 gNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~ 60 (298)
.|..|.=||.... ...||++.|..|.+..|-
T Consensus 2 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 2 DTHFCAVCSDYAS---GYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 4678999997664 468999999999998865
No 39
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=36.66 E-value=16 Score=26.24 Aligned_cols=26 Identities=27% Similarity=0.630 Sum_probs=19.4
Q ss_pred CCcCCCCCCCCeeecccchHhhHhhhh
Q 022340 30 ECADCKAKGPRWASVNLGIFICMQCSG 56 (298)
Q Consensus 30 ~CADCGa~~P~WaSln~GVFlC~~CSg 56 (298)
.|.=|+..... .-.=+|.|||..|-.
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHH
Confidence 47888888776 334579999999943
No 40
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=34.97 E-value=2.6e+02 Score=31.48 Aligned_cols=27 Identities=41% Similarity=0.522 Sum_probs=17.3
Q ss_pred hhhccCCCCCCCCCCCCCCCCCCCCCCccccchhhccccc
Q 022340 228 QHKKQNSEPAVPKYEPPKQEASTTPQRKVDYATDLFNLLC 267 (298)
Q Consensus 228 ~~~~~~~~~~~~~~~~~~~~~~~~~~~kvd~atdlf~~l~ 267 (298)
..+.|-+|=||| -+.|..| +-|||-|.
T Consensus 179 ~s~~q~~eWAVp------------~~~klKY-~QlFNa~D 205 (1118)
T KOG1029|consen 179 ESVNQLEEWAVP------------QHNKLKY-RQLFNALD 205 (1118)
T ss_pred hhhhhhhhcccc------------chhhhHH-HHHhhhcc
Confidence 334455666776 3567777 57999773
No 41
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=34.49 E-value=36 Score=24.91 Aligned_cols=33 Identities=24% Similarity=0.637 Sum_probs=26.5
Q ss_pred CCcCCCCC-CCCeeecc-cchHhhHhhhhhhhcCC
Q 022340 30 ECADCKAK-GPRWASVN-LGIFICMQCSGIHRSLG 62 (298)
Q Consensus 30 ~CADCGa~-~P~WaSln-~GVFlC~~CSgiHR~LG 62 (298)
.|..|+.. -|.|=... -+..||-.|.-..+..|
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~ 35 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG 35 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC
Confidence 59999986 57888765 78899999977767666
No 42
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=33.51 E-value=25 Score=28.98 Aligned_cols=33 Identities=27% Similarity=0.566 Sum_probs=23.1
Q ss_pred cCCCCCCCcCCCCCC-------C-C---------eeecccchHhhHhhhh
Q 022340 24 KLPENRECADCKAKG-------P-R---------WASVNLGIFICMQCSG 56 (298)
Q Consensus 24 ~~PgNk~CADCGa~~-------P-~---------WaSln~GVFlC~~CSg 56 (298)
+.++--.|+|||.+- | + =.+=.||-.+|..|..
T Consensus 30 K~~~~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~ 79 (93)
T COG2174 30 KKPTIPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVR 79 (93)
T ss_pred ccCCCCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHHH
Confidence 457778999999861 1 1 1234689999999954
No 43
>cd06968 NR_DBD_ROR DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RORS are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum particularly in the regulation of the maturation and survival of Purkinje cells. RORbe
Probab=33.35 E-value=26 Score=28.45 Aligned_cols=31 Identities=29% Similarity=0.703 Sum_probs=25.7
Q ss_pred CCCCCcCCCCCCCCeeecccchHhhHhhhhhhhc
Q 022340 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 27 gNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~ 60 (298)
.+..|.=||..... ..||++.|..|.+..|-
T Consensus 4 ~~~~C~VCg~~~~g---~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 4 EVIPCKICGDKSSG---IHYGVITCEGCKGFFRR 34 (95)
T ss_pred cccCCcccCCcCcc---eEECceeehhhHHhhHH
Confidence 46679999987654 58999999999998874
No 44
>cd07170 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription
Probab=32.25 E-value=25 Score=28.69 Aligned_cols=30 Identities=20% Similarity=0.540 Sum_probs=24.6
Q ss_pred CCCCcCCCCCCCCeeecccchHhhHhhhhhhhc
Q 022340 28 NRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 28 Nk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~ 60 (298)
+..|.=||..... ..||++.|..|.+..|-
T Consensus 4 ~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 33 (97)
T cd07170 4 KRLCLVCGDIASG---YHYGVASCEACKAFFKR 33 (97)
T ss_pred CCCCeecCCcCcc---eEECceeehhhhHHHHH
Confidence 3569999987654 58999999999998875
No 45
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=32.24 E-value=21 Score=25.92 Aligned_cols=43 Identities=23% Similarity=0.413 Sum_probs=25.0
Q ss_pred CCcCCCCCCCCe--eecccchHhhHhhhhhhhcCCCccceeeeccc
Q 022340 30 ECADCKAKGPRW--ASVNLGIFICMQCSGIHRSLGVHISKVRSATL 73 (298)
Q Consensus 30 ~CADCGa~~P~W--aSln~GVFlC~~CSgiHR~LG~hISkVKSltL 73 (298)
.|+=||..-.-. +-+.=| +||-.|..--..+...+..++++++
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl~~~~~~~~~~~~~t~ 45 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKLSGFFSDVKIKKNLTL 45 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHhcCcccchhhhhhccH
Confidence 488888874433 345557 8999998644443333333344444
No 46
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=31.85 E-value=26 Score=28.84 Aligned_cols=31 Identities=26% Similarity=0.662 Sum_probs=25.8
Q ss_pred CCCCCcCCCCCCCCeeecccchHhhHhhhhhhhc
Q 022340 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 27 gNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~ 60 (298)
++..|.=||..... ..||+..|..|.+..|-
T Consensus 17 ~~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 47 (101)
T cd07160 17 GNEVCSVCGDKASG---FHYNVLSCEGCKGFFRR 47 (101)
T ss_pred CCCCCeecCCcCcc---eEECcceehhhhhhhhh
Confidence 46789999986654 58999999999998875
No 47
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=30.43 E-value=31 Score=24.93 Aligned_cols=34 Identities=24% Similarity=0.642 Sum_probs=22.2
Q ss_pred HhcCCCCCCCcCCCCCCC--Ce-------eecccchHhhHhhhh
Q 022340 22 LLKLPENRECADCKAKGP--RW-------ASVNLGIFICMQCSG 56 (298)
Q Consensus 22 Ll~~PgNk~CADCGa~~P--~W-------aSln~GVFlC~~CSg 56 (298)
|+++.+ ..|-=||+..+ .| .+..-.|+||..|.+
T Consensus 2 L~~Rs~-~kCELC~a~~~L~vy~Vpp~~~~~~d~~iliC~tC~~ 44 (47)
T smart00782 2 LLARCE-SKCELCGSDSPLVVYAVPPSSDVTADNSVMLCDTCHS 44 (47)
T ss_pred hhHHcC-CcccCcCCCCCceEEecCCCCCCCccceeeechHHHH
Confidence 334444 44999998643 12 244668999999975
No 48
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=30.04 E-value=19 Score=30.50 Aligned_cols=24 Identities=38% Similarity=0.826 Sum_probs=21.6
Q ss_pred Ceeecccc--hHhhHhhhhhhhcCCC
Q 022340 40 RWASVNLG--IFICMQCSGIHRSLGV 63 (298)
Q Consensus 40 ~WaSln~G--VFlC~~CSgiHR~LG~ 63 (298)
.|++-.-| |.-|.+|--|||.-+.
T Consensus 52 ewi~~~~G~~VwSC~dC~~iH~ke~~ 77 (112)
T COG2158 52 EWISDSNGRKVWSCSDCHWIHRKEGA 77 (112)
T ss_pred ceeEcCCCCEEeeccccceecccchH
Confidence 89999889 9999999999998664
No 49
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=28.44 E-value=11 Score=25.38 Aligned_cols=29 Identities=21% Similarity=0.455 Sum_probs=14.5
Q ss_pred CCCcCCCCCCCCeeec---ccchHhhHhhhhhh
Q 022340 29 RECADCKAKGPRWASV---NLGIFICMQCSGIH 58 (298)
Q Consensus 29 k~CADCGa~~P~WaSl---n~GVFlC~~CSgiH 58 (298)
+.|-.||.+- .+... +.-=++|..|..||
T Consensus 1 kfC~~CG~~l-~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 1 KFCPQCGGPL-ERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp -B-TTT--B--EEE--TT-SS-EEEETTTTEEE
T ss_pred CccccccChh-hhhcCCCCCccceECCCCCCEE
Confidence 4788898872 22211 34456888898887
No 50
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=28.22 E-value=42 Score=26.73 Aligned_cols=32 Identities=22% Similarity=0.510 Sum_probs=23.6
Q ss_pred CCcCCCCCCC---Ceeecccc---hHhhHhhhhhhhcC
Q 022340 30 ECADCKAKGP---RWASVNLG---IFICMQCSGIHRSL 61 (298)
Q Consensus 30 ~CADCGa~~P---~WaSln~G---VFlC~~CSgiHR~L 61 (298)
.|..||.+-| .|...--| .|-|..|.+|...|
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~~~i 39 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVYQLI 39 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccccccHHHHHHHHHH
Confidence 6999999876 34333334 89999999998653
No 51
>cd07166 NR_DBD_REV_ERB DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers. DNA-binding domain of REV-ERB receptor- like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. REV-ERB receptors are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. REV-ERB receptors bind as a monomer to a (A/G)GGTCA half-site with a 5' AT-rich extension or as a homodimer to a direct repeat 2 element (AGGTCA sequence with a 2-bp spacer), indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target genes. The porphyr
Probab=27.17 E-value=39 Score=27.01 Aligned_cols=30 Identities=27% Similarity=0.629 Sum_probs=24.4
Q ss_pred CCCCcCCCCCCCCeeecccchHhhHhhhhhhhc
Q 022340 28 NRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 28 Nk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~ 60 (298)
+..|.=||.+.-. ..||++.|..|.+..|-
T Consensus 3 ~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 32 (89)
T cd07166 3 VVLCKVCGDKASG---FHYGVHACEGCKGFFRR 32 (89)
T ss_pred CCCCcccCccCcc---eEEChhhhhhHhhEecc
Confidence 4569999987654 47999999999998775
No 52
>cd06965 NR_DBD_Ppar DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive gene
Probab=26.44 E-value=38 Score=26.76 Aligned_cols=27 Identities=30% Similarity=0.783 Sum_probs=22.0
Q ss_pred CcCCCCCCCCeeecccchHhhHhhhhhhhc
Q 022340 31 CADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 31 CADCGa~~P~WaSln~GVFlC~~CSgiHR~ 60 (298)
|.=||..... ..||++.|..|.+..|-
T Consensus 2 C~VCg~~~~g---~hyGv~sC~aCk~FFRR 28 (84)
T cd06965 2 CRVCGDKASG---FHYGVHACEGCKGFFRR 28 (84)
T ss_pred CcccCccCcc---eEEChhhhhhhhhheee
Confidence 7778876554 47999999999999875
No 53
>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=26.43 E-value=23 Score=26.11 Aligned_cols=27 Identities=19% Similarity=0.655 Sum_probs=22.4
Q ss_pred CCCCCcCCCCCCCCeeecccchHhhHhhh
Q 022340 27 ENRECADCKAKGPRWASVNLGIFICMQCS 55 (298)
Q Consensus 27 gNk~CADCGa~~P~WaSln~GVFlC~~CS 55 (298)
--+.|..||..... ..+-.+|.|..|.
T Consensus 27 TSq~C~~CG~~~~~--~~~~r~~~C~~Cg 53 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK--RRSGRVFTCPNCG 53 (69)
T ss_pred CccCccCccccccc--ccccceEEcCCCC
Confidence 34789999998877 6778899999984
No 54
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=26.20 E-value=50 Score=32.11 Aligned_cols=30 Identities=20% Similarity=0.517 Sum_probs=21.9
Q ss_pred CCCCCCcCCCCCCCCeeec-------c-cchHhhHhhh
Q 022340 26 PENRECADCKAKGPRWASV-------N-LGIFICMQCS 55 (298)
Q Consensus 26 PgNk~CADCGa~~P~WaSl-------n-~GVFlC~~CS 55 (298)
.+...|..||.....|.-+ . --.|+|..|.
T Consensus 256 t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg 293 (299)
T TIGR01385 256 TDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECG 293 (299)
T ss_pred cccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCC
Confidence 4568999999998888744 1 1256899885
No 55
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=25.99 E-value=33 Score=23.65 Aligned_cols=23 Identities=22% Similarity=0.541 Sum_probs=17.7
Q ss_pred CCcCCCCCCCCeeecccchHhhH
Q 022340 30 ECADCKAKGPRWASVNLGIFICM 52 (298)
Q Consensus 30 ~CADCGa~~P~WaSln~GVFlC~ 52 (298)
+|.+|+..+.-|+++.-|-..|.
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c~ 23 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGCG 23 (50)
T ss_pred CcccCCCcCCeEEecCCCCcccC
Confidence 59999988878887776666663
No 56
>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian
Probab=25.61 E-value=26 Score=28.35 Aligned_cols=29 Identities=24% Similarity=0.592 Sum_probs=23.5
Q ss_pred CCCcCCCCCCCCeeecccchHhhHhhhhhhhc
Q 022340 29 RECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 29 k~CADCGa~~P~WaSln~GVFlC~~CSgiHR~ 60 (298)
+.|.=||.+... ..||++.|..|.+..|-
T Consensus 1 ~~C~VCg~~a~g---~hyGv~sC~aC~~FFRR 29 (94)
T cd06966 1 KICGVCGDKALG---YNFNAITCESCKAFFRR 29 (94)
T ss_pred CCCeeCCCcCcc---eEECcceeeeehheehh
Confidence 458889876554 48999999999998875
No 57
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=25.11 E-value=30 Score=33.25 Aligned_cols=32 Identities=19% Similarity=0.471 Sum_probs=22.6
Q ss_pred CCCCCCcCCCCCCCCeeecccchHhhHhhhhhh
Q 022340 26 PENRECADCKAKGPRWASVNLGIFICMQCSGIH 58 (298)
Q Consensus 26 PgNk~CADCGa~~P~WaSln~GVFlC~~CSgiH 58 (298)
.....|-+||.... =....-|-.||.+|.-|-
T Consensus 9 ~~~~~Cp~Cg~~~i-v~d~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 9 EEKLVCPECGSDKL-IYDYERGEIVCADCGLVI 40 (310)
T ss_pred ccCCcCcCCCCCCe-eEECCCCeEeecccCCcc
Confidence 44567999997432 224567999999997644
No 58
>cd07162 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers. DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding
Probab=24.87 E-value=44 Score=26.48 Aligned_cols=28 Identities=21% Similarity=0.625 Sum_probs=22.6
Q ss_pred CCcCCCCCCCCeeecccchHhhHhhhhhhhc
Q 022340 30 ECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 30 ~CADCGa~~P~WaSln~GVFlC~~CSgiHR~ 60 (298)
.|.=||..... ..||++.|..|.+..|-
T Consensus 1 ~C~VCg~~~~g---~hygv~sC~aC~~FFRR 28 (87)
T cd07162 1 ICRVCGDRATG---YHFNAMTCEGCKGFFRR 28 (87)
T ss_pred CCcccCCcCcc---eEECcceehhhHHHHHh
Confidence 37778876654 48999999999998865
No 59
>cd07165 NR_DBD_DmE78_like DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two C4-type zinc fingers. DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. The SmE78 may be involved in transduction of an ecdysone signal in S. mansoni,
Probab=24.55 E-value=49 Score=25.85 Aligned_cols=27 Identities=30% Similarity=0.732 Sum_probs=21.2
Q ss_pred CcCCCCCCCCeeecccchHhhHhhhhhhhc
Q 022340 31 CADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 31 CADCGa~~P~WaSln~GVFlC~~CSgiHR~ 60 (298)
|.=||..... ..||+..|..|.+..|-
T Consensus 1 C~VCg~~~~g---~hyG~~sC~aC~~FFRR 27 (81)
T cd07165 1 CKVCGDKASG---YHYGVTSCEGCKGFFRR 27 (81)
T ss_pred CCccCccCcc---eEECchhhhhHHHHHHh
Confidence 5567765543 48999999999998875
No 60
>cd07161 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers. DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs h
Probab=24.22 E-value=44 Score=26.90 Aligned_cols=28 Identities=21% Similarity=0.602 Sum_probs=23.1
Q ss_pred CCcCCCCCCCCeeecccchHhhHhhhhhhhc
Q 022340 30 ECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 30 ~CADCGa~~P~WaSln~GVFlC~~CSgiHR~ 60 (298)
.|.=||.+... ..||++.|..|.+..|-
T Consensus 3 ~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 30 (91)
T cd07161 3 LCLVCGDRASG---YHYNALTCEGCKGFFRR 30 (91)
T ss_pred CCeeCCCcCcc---eEECceeehhhHHHHHH
Confidence 48889976654 58999999999998864
No 61
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=24.00 E-value=46 Score=27.31 Aligned_cols=31 Identities=19% Similarity=0.495 Sum_probs=24.1
Q ss_pred CCCCCCCcCCCCCCCCeeecccchHhhHhhhhh
Q 022340 25 LPENRECADCKAKGPRWASVNLGIFICMQCSGI 57 (298)
Q Consensus 25 ~PgNk~CADCGa~~P~WaSln~GVFlC~~CSgi 57 (298)
.-.-..|-.|+.+ .---+..||..|..|-..
T Consensus 32 ~~~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~~ 62 (89)
T COG1997 32 QRAKHVCPFCGRT--TVKRIATGIWKCRKCGAK 62 (89)
T ss_pred HhcCCcCCCCCCc--ceeeeccCeEEcCCCCCe
Confidence 3456789999998 445678899999999543
No 62
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=23.94 E-value=70 Score=32.98 Aligned_cols=95 Identities=14% Similarity=0.288 Sum_probs=44.6
Q ss_pred CCCCCCCcC-CCCC--CCCeeecccc--hHhhHhhhhhhhcCCCcc-----ceeeecc----cCCCCH-HHHHHHHh---
Q 022340 25 LPENRECAD-CKAK--GPRWASVNLG--IFICMQCSGIHRSLGVHI-----SKVRSAT----LDTWLP-EQVAVIQS--- 86 (298)
Q Consensus 25 ~PgNk~CAD-CGa~--~P~WaSln~G--VFlC~~CSgiHR~LG~hI-----SkVKSlt----LD~Wt~-eeV~~mk~--- 86 (298)
.+|++.|+| |-.- +...+.+.-. .+||+.|-..=-.+|.|- --|...+ --.|+. ||+.+|..
T Consensus 10 ~~g~ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLea~~t 89 (438)
T KOG0457|consen 10 DPGGKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSVGAETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLEAAET 89 (438)
T ss_pred cCCCCCCCccHhHHhccceEEEeecCCCcchhHHHHhcccccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHHHHHH
Confidence 455554443 6543 3333322222 589999986544454441 1233212 124985 67777763
Q ss_pred --hccHHHHHHHhhcCCCCCChHHHHHHHHHhhhcCccc
Q 022340 87 --MGNEKSNSYWEAELPPNYDRVGIENFIRAKYEEKRWI 123 (298)
Q Consensus 87 --~GN~~aN~~wEa~lPp~~d~~~~e~FIraKY~~k~F~ 123 (298)
.||=. .|=+ ++ ..-+..+.+++-...|++..+.
T Consensus 90 ~G~GNW~--dIA~-hI-GtKtkeeck~hy~k~fv~s~~~ 124 (438)
T KOG0457|consen 90 YGFGNWQ--DIAD-HI-GTKTKEECKEHYLKHFVNSPIF 124 (438)
T ss_pred hCCCcHH--HHHH-HH-cccchHHHHHHHHHHHhcCccc
Confidence 36621 1111 01 1123344555555666665443
No 63
>PTZ00074 60S ribosomal protein L34; Provisional
Probab=23.77 E-value=46 Score=29.15 Aligned_cols=31 Identities=26% Similarity=0.514 Sum_probs=21.6
Q ss_pred CCCCCCCcCCCCCC-----------------CCeeecccchHhhHhhh
Q 022340 25 LPENRECADCKAKG-----------------PRWASVNLGIFICMQCS 55 (298)
Q Consensus 25 ~PgNk~CADCGa~~-----------------P~WaSln~GVFlC~~CS 55 (298)
.+.--.|.|||.+- -.-++=.||-.+|..|-
T Consensus 38 ~~~~pkC~~cg~~L~GI~~~Rp~e~~rlsK~~KtvsRaYGG~lC~~CV 85 (135)
T PTZ00074 38 KSSGPKCGDCGKVLAGIKALRPTEYKQLSRRERTVSRAYGGVLCHKCV 85 (135)
T ss_pred CCCCCCCCCCCCccCCccCCchHHHHHccccCCCccCCCccchhHHHH
Confidence 34445799999861 12345578999999994
No 64
>cd07169 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=23.72 E-value=47 Score=26.61 Aligned_cols=32 Identities=28% Similarity=0.754 Sum_probs=26.1
Q ss_pred CCCCCCcCCCCCCCCeeecccchHhhHhhhhhhhc
Q 022340 26 PENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 26 PgNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~ 60 (298)
.++..|.=||.+.. ...||+..|..|.+..|-
T Consensus 4 ~~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (90)
T cd07169 4 AEQRTCLICGDRAT---GLHYGIISCEGCKGFFKR 35 (90)
T ss_pred ccCCCCeecCCcCc---ceEECcceehhhHHHHHH
Confidence 45677999998654 458999999999998865
No 65
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=23.23 E-value=50 Score=25.11 Aligned_cols=27 Identities=30% Similarity=0.773 Sum_probs=21.0
Q ss_pred CcCCCCCCCCeeecccchHhhHhhhhhhhc
Q 022340 31 CADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 31 CADCGa~~P~WaSln~GVFlC~~CSgiHR~ 60 (298)
|.=||.+... ..||++.|..|.+..|-
T Consensus 1 C~VCg~~~~g---~hyGv~~C~aC~~FFRR 27 (73)
T cd07158 1 CKVCGDKASG---FHYGVHSCEGCKGFFRR 27 (73)
T ss_pred CcccCccCcc---eEECcchhhHHHHHHhh
Confidence 5557765553 58999999999998875
No 66
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=22.64 E-value=68 Score=26.56 Aligned_cols=31 Identities=23% Similarity=0.490 Sum_probs=21.3
Q ss_pred CCCCCcCCCCC-----CCCeeecccchHhhHhhhhh
Q 022340 27 ENRECADCKAK-----GPRWASVNLGIFICMQCSGI 57 (298)
Q Consensus 27 gNk~CADCGa~-----~P~WaSln~GVFlC~~CSgi 57 (298)
+...|+-|+.+ +..-.+..-.--||..|...
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 67899999975 45556667777778887666
No 67
>cd07155 NR_DBD_ER_like DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. E
Probab=22.60 E-value=56 Score=25.09 Aligned_cols=27 Identities=19% Similarity=0.583 Sum_probs=21.0
Q ss_pred CcCCCCCCCCeeecccchHhhHhhhhhhhc
Q 022340 31 CADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 31 CADCGa~~P~WaSln~GVFlC~~CSgiHR~ 60 (298)
|.=||.+.. ...||+..|..|.+..|-
T Consensus 1 C~VC~~~~~---g~hygv~sC~aCk~FFRR 27 (75)
T cd07155 1 CLVCGDIAS---GYHYGVASCEACKAFFKR 27 (75)
T ss_pred CcccCccCc---ceEEChhhhhhhHHHHHH
Confidence 556776544 358999999999998864
No 68
>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers. DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p
Probab=22.57 E-value=49 Score=25.80 Aligned_cols=29 Identities=17% Similarity=0.598 Sum_probs=23.6
Q ss_pred CCCcCCCCCCCCeeecccchHhhHhhhhhhhc
Q 022340 29 RECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 29 k~CADCGa~~P~WaSln~GVFlC~~CSgiHR~ 60 (298)
..|.=||..... ..||+..|..|.+..|-
T Consensus 3 ~~C~VCg~~a~g---~hyGv~sC~aC~~FFRR 31 (78)
T cd07172 3 KICLVCSDEASG---CHYGVLTCGSCKVFFKR 31 (78)
T ss_pred CCCeecCCcCcc---eEECceeehhhHHhHHH
Confidence 468889976554 59999999999998864
No 69
>cd06956 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor, or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear rec
Probab=22.50 E-value=51 Score=25.47 Aligned_cols=28 Identities=25% Similarity=0.746 Sum_probs=23.0
Q ss_pred CCcCCCCCCCCeeecccchHhhHhhhhhhhc
Q 022340 30 ECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 30 ~CADCGa~~P~WaSln~GVFlC~~CSgiHR~ 60 (298)
.|.=||.+... ..||+..|..|.+..|-
T Consensus 2 ~C~VC~~~~~g---~hygv~sC~aC~~FFRR 29 (77)
T cd06956 2 ICAICGDRASG---KHYGVYSCEGCKGFFKR 29 (77)
T ss_pred CCcccCCcCcc---eEECceeehhHHHHHHH
Confidence 58888876654 58999999999998865
No 70
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.31 E-value=25 Score=32.02 Aligned_cols=22 Identities=23% Similarity=0.700 Sum_probs=18.8
Q ss_pred CCCcCCCCCCCCeeecccchHhhHhhhhh
Q 022340 29 RECADCKAKGPRWASVNLGIFICMQCSGI 57 (298)
Q Consensus 29 k~CADCGa~~P~WaSln~GVFlC~~CSgi 57 (298)
+.|.-||. +.-+.|.|..|...
T Consensus 310 ~~C~~cg~-------~~~r~~~C~~cg~~ 331 (364)
T COG0675 310 KTCPCCGH-------LSGRLFKCPRCGFV 331 (364)
T ss_pred ccccccCC-------ccceeEECCCCCCe
Confidence 89999999 66789999999653
No 71
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=22.15 E-value=37 Score=28.26 Aligned_cols=46 Identities=26% Similarity=0.640 Sum_probs=27.6
Q ss_pred cCCCCCCCcCCCCCCCCeeecccchHhhHhhhhhh-hcC-CCccceeeecccC
Q 022340 24 KLPENRECADCKAKGPRWASVNLGIFICMQCSGIH-RSL-GVHISKVRSATLD 74 (298)
Q Consensus 24 ~~PgNk~CADCGa~~P~WaSln~GVFlC~~CSgiH-R~L-G~hISkVKSltLD 74 (298)
..|.--.|.+||.. ..+..-.|.|-.|.+.. +.+ |.. =+|++|.++
T Consensus 66 ~~p~~~~C~~Cg~~----~~~~~~~~~CP~Cgs~~~~i~~G~E-l~I~~ie~~ 113 (115)
T TIGR00100 66 DEPVECECEDCSEE----VSPEIDLYRCPKCHGIMLQVRAGKE-LNLKSIEVE 113 (115)
T ss_pred eeCcEEEcccCCCE----EecCCcCccCcCCcCCCcEEecCCe-EEEEEEEEE
Confidence 35778899999943 22322358899998754 222 322 256665543
No 72
>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=21.64 E-value=77 Score=22.02 Aligned_cols=31 Identities=19% Similarity=0.550 Sum_probs=22.6
Q ss_pred cCCCCCCCcCCCCCCCCeeecccchHhhHhhh
Q 022340 24 KLPENRECADCKAKGPRWASVNLGIFICMQCS 55 (298)
Q Consensus 24 ~~PgNk~CADCGa~~P~WaSln~GVFlC~~CS 55 (298)
+.++.-+|-.||.....++. +.+.|-|-.|.
T Consensus 14 RW~~g~~CP~Cg~~~~~~~~-~~~~~~C~~C~ 44 (46)
T PF12760_consen 14 RWPDGFVCPHCGSTKHYRLK-TRGRYRCKACR 44 (46)
T ss_pred cCCCCCCCCCCCCeeeEEeC-CCCeEECCCCC
Confidence 45666889999998554443 36888888883
No 73
>PF13462 Thioredoxin_4: Thioredoxin; PDB: 3FEU_A 3HZ8_A 3DVW_A 3A3T_E 3GMF_A 1Z6M_A 3GYK_C 3BCK_A 3BD2_A 3BCI_A ....
Probab=21.28 E-value=49 Score=27.00 Aligned_cols=28 Identities=18% Similarity=0.322 Sum_probs=22.6
Q ss_pred CCCCCCeeecccchHhhHhhhhhhhcCC
Q 022340 35 KAKGPRWASVNLGIFICMQCSGIHRSLG 62 (298)
Q Consensus 35 Ga~~P~WaSln~GVFlC~~CSgiHR~LG 62 (298)
|.++..+.-+-|+-|.|.-|...|..++
T Consensus 8 G~~~a~~~v~~f~d~~Cp~C~~~~~~~~ 35 (162)
T PF13462_consen 8 GNPDAPITVTEFFDFQCPHCAKFHEELE 35 (162)
T ss_dssp S-TTTSEEEEEEE-TTSHHHHHHHHHHH
T ss_pred cCCCCCeEEEEEECCCCHhHHHHHHHHh
Confidence 5677788889999999999999998764
No 74
>PRK04059 rpl34e 50S ribosomal protein L34e; Validated
Probab=20.87 E-value=53 Score=26.78 Aligned_cols=31 Identities=23% Similarity=0.549 Sum_probs=21.0
Q ss_pred CCCCCCcCCCCCCC-----------------CeeecccchHhhHhhhh
Q 022340 26 PENRECADCKAKGP-----------------RWASVNLGIFICMQCSG 56 (298)
Q Consensus 26 PgNk~CADCGa~~P-----------------~WaSln~GVFlC~~CSg 56 (298)
+.--.|+|||..-. .-++=.||-.+|..|--
T Consensus 32 ~~~pkC~~c~~~L~Gi~~~Rp~~~~rlsK~~K~vsRaYGG~lc~~cvr 79 (88)
T PRK04059 32 PSKAKCAICGKPLNGVPRGRPVEIRKLGKTEKRPERPYGGYLCPKCLK 79 (88)
T ss_pred CCCCcCCCCCCccCCccCcchHHHHhcccccCCcccCcCceecHHHHH
Confidence 44456999998611 23455789999998853
No 75
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=20.60 E-value=44 Score=29.15 Aligned_cols=36 Identities=22% Similarity=0.577 Sum_probs=24.3
Q ss_pred HHHHHHhcCCCCCCCcCCCCCCCCeeecccchHhhHhhhhhhhcC
Q 022340 17 KILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSL 61 (298)
Q Consensus 17 kiL~~Ll~~PgNk~CADCGa~~P~WaSln~GVFlC~~CSgiHR~L 61 (298)
++|+.+....+...|.-||. ++..+|..|.|-|+.+
T Consensus 88 ~lL~~~~~~~~~~~C~~Cgg---------~rfv~C~~C~Gs~k~~ 123 (147)
T cd03031 88 KLLKGIRARAGGGVCEGCGG---------ARFVPCSECNGSCKVF 123 (147)
T ss_pred HHHhhcccccCCCCCCCCCC---------cCeEECCCCCCcceEE
Confidence 33444433445667999984 3456899999999875
No 76
>cd06958 NR_DBD_COUP_TF DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. COUP-TFs homodimerize or heterodimerize with retinoid X receptor (RXR) and a few other nuclear receptors and bind to a variety of response elements that are composed of imperfect AGGTCA direct or inverted repeats with various spacings. COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone recept
Probab=20.40 E-value=63 Score=24.66 Aligned_cols=27 Identities=26% Similarity=0.695 Sum_probs=20.8
Q ss_pred CcCCCCCCCCeeecccchHhhHhhhhhhhc
Q 022340 31 CADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (298)
Q Consensus 31 CADCGa~~P~WaSln~GVFlC~~CSgiHR~ 60 (298)
|.=||..... ..||+..|..|.+..|-
T Consensus 1 C~VCg~~~~g---~hygv~sC~aC~~FFRR 27 (73)
T cd06958 1 CVVCGDKSSG---KHYGQFTCEGCKSFFKR 27 (73)
T ss_pred CCccCccCcc---eEEChhhhhhhhhhhhh
Confidence 5557765553 48999999999998864
No 77
>PF14376 Haem_bd: Haem-binding domain
Probab=20.20 E-value=50 Score=28.22 Aligned_cols=21 Identities=29% Similarity=0.686 Sum_probs=14.5
Q ss_pred HHHHHhcCCCCCCCcCCCCCCCCee
Q 022340 18 ILDGLLKLPENRECADCKAKGPRWA 42 (298)
Q Consensus 18 iL~~Ll~~PgNk~CADCGa~~P~Wa 42 (298)
.+..|++ +-|.||++.++.|-
T Consensus 35 ~v~~il~----~~CydCHSn~T~~P 55 (137)
T PF14376_consen 35 EVKIILK----NSCYDCHSNNTRYP 55 (137)
T ss_pred HHHHHHH----ccccccCCCCCCCc
Confidence 3445554 46999999877664
Done!