Query 022604
Match_columns 294
No_of_seqs 222 out of 1182
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 04:48:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022604.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022604hhsearch_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 5.3E-46 1.2E-50 347.7 9.0 120 7-126 4-127 (287)
2 PLN03119 putative ADP-ribosyla 100.0 6.4E-42 1.4E-46 341.6 13.5 165 8-175 3-177 (648)
3 PF01412 ArfGap: Putative GTPa 100.0 1.3E-40 2.8E-45 274.1 6.1 109 17-125 2-116 (116)
4 PLN03131 hypothetical protein; 100.0 1.5E-39 3.2E-44 326.8 13.0 159 8-169 3-171 (705)
5 smart00105 ArfGap Putative GTP 100.0 5E-39 1.1E-43 263.5 8.8 103 26-128 1-110 (112)
6 COG5347 GTPase-activating prot 100.0 2.3E-36 5E-41 287.4 9.0 115 14-128 6-128 (319)
7 PLN03114 ADP-ribosylation fact 100.0 7.2E-30 1.6E-34 244.9 18.8 113 15-127 9-130 (395)
8 KOG0704 ADP-ribosylation facto 100.0 1.9E-31 4.1E-36 254.5 4.4 110 13-122 4-124 (386)
9 KOG0706 Predicted GTPase-activ 100.0 1.5E-29 3.3E-34 247.2 4.4 86 14-99 9-94 (454)
10 KOG0705 GTPase-activating prot 99.9 4.4E-28 9.6E-33 242.8 4.6 118 15-132 500-623 (749)
11 KOG0521 Putative GTPase activa 99.9 1.1E-24 2.3E-29 227.5 4.1 112 18-129 416-535 (785)
12 KOG0818 GTPase-activating prot 99.8 7.1E-21 1.5E-25 189.0 2.6 101 25-125 5-119 (669)
13 KOG1117 Rho- and Arf-GTPase ac 99.8 6.1E-20 1.3E-24 190.4 2.0 108 20-127 290-405 (1186)
14 KOG0702 Predicted GTPase-activ 99.8 3.6E-18 7.7E-23 169.4 12.3 127 6-133 3-137 (524)
15 KOG0521 Putative GTPase activa 95.5 0.0031 6.6E-08 67.6 -0.4 72 24-97 626-698 (785)
16 PRK00085 recO DNA repair prote 84.9 0.46 1E-05 43.0 1.4 31 25-55 146-177 (247)
17 PF00643 zf-B_box: B-box zinc 76.5 1.1 2.3E-05 30.2 0.6 34 27-60 2-36 (42)
18 TIGR00613 reco DNA repair prot 75.2 1.4 3.1E-05 39.6 1.2 33 25-57 144-177 (241)
19 PRK12495 hypothetical protein; 75.2 1.3 2.8E-05 41.5 0.9 38 16-57 28-67 (226)
20 COG1734 DksA DnaK suppressor p 72.7 1.4 3.1E-05 37.4 0.6 35 26-60 78-113 (120)
21 COG1381 RecO Recombinational D 70.2 2 4.3E-05 40.0 0.9 31 25-55 151-182 (251)
22 TIGR02419 C4_traR_proteo phage 66.5 2.6 5.7E-05 31.7 0.8 34 24-58 27-62 (63)
23 PRK11019 hypothetical protein; 65.1 3.4 7.4E-05 33.4 1.2 37 27-64 35-73 (88)
24 PRK13715 conjugal transfer pro 58.6 5.5 0.00012 31.0 1.3 35 27-61 33-68 (73)
25 PRK10778 dksA RNA polymerase-b 56.2 6.3 0.00014 34.5 1.4 40 23-62 106-146 (151)
26 PF11781 RRN7: RNA polymerase 54.7 4 8.8E-05 27.7 -0.0 27 26-55 6-32 (36)
27 PRK11788 tetratricopeptide rep 52.8 7.9 0.00017 36.1 1.6 39 15-59 341-379 (389)
28 PF01286 XPA_N: XPA protein N- 52.6 2.8 6.1E-05 28.4 -1.0 27 29-55 4-31 (34)
29 PHA00080 DksA-like zinc finger 46.1 11 0.00024 29.2 1.2 35 25-60 28-64 (72)
30 TIGR02890 spore_yteA sporulati 43.2 14 0.0003 32.7 1.5 37 24-60 82-119 (159)
31 PF08271 TF_Zn_Ribbon: TFIIB z 42.4 3.7 8E-05 28.2 -1.8 27 30-57 2-28 (43)
32 PF01258 zf-dskA_traR: Prokary 41.7 2.7 5.8E-05 27.9 -2.5 30 29-58 4-34 (36)
33 KOG3362 Predicted BBOX Zn-fing 39.9 7.7 0.00017 34.4 -0.6 34 26-60 116-150 (156)
34 smart00401 ZnF_GATA zinc finge 39.8 12 0.00027 26.9 0.6 37 27-63 2-40 (52)
35 TIGR02420 dksA RNA polymerase- 37.1 20 0.00043 29.4 1.4 31 25-55 77-108 (110)
36 cd07173 NR_DBD_AR DNA-binding 35.9 24 0.00053 27.8 1.7 31 27-60 2-32 (82)
37 PF14471 DUF4428: Domain of un 34.4 17 0.00037 26.3 0.6 43 30-73 1-45 (51)
38 cd07171 NR_DBD_ER DNA-binding 34.0 20 0.00043 28.2 0.9 31 27-60 2-32 (82)
39 PF00320 GATA: GATA zinc finge 33.3 12 0.00026 25.1 -0.4 32 31-62 1-34 (36)
40 PF10764 Gin: Inhibitor of sig 32.5 15 0.00032 26.3 0.0 26 30-56 1-26 (46)
41 cd00202 ZnF_GATA Zinc finger D 32.1 43 0.00094 24.4 2.4 33 30-62 1-35 (54)
42 COG2174 RPL34A Ribosomal prote 30.5 25 0.00055 28.9 1.0 33 24-56 30-79 (93)
43 TIGR01385 TFSII transcription 29.2 28 0.00062 33.7 1.3 51 5-55 225-293 (299)
44 cd06968 NR_DBD_ROR DNA-binding 29.0 27 0.00058 28.3 0.9 31 27-60 4-34 (95)
45 cd07170 NR_DBD_ERR DNA-binding 28.6 25 0.00055 28.6 0.7 30 28-60 4-33 (97)
46 smart00290 ZnF_UBP Ubiquitin C 28.2 27 0.00058 24.1 0.7 23 30-52 1-23 (50)
47 smart00782 PhnA_Zn_Ribbon PhnA 27.9 29 0.00062 25.0 0.8 34 22-56 2-44 (47)
48 cd07160 NR_DBD_LXR DNA-binding 26.9 27 0.00059 28.7 0.6 31 27-60 17-47 (101)
49 COG2158 Uncharacterized protei 26.1 19 0.0004 30.5 -0.5 24 40-63 52-77 (112)
50 cd06965 NR_DBD_Ppar DNA-bindin 25.9 36 0.00079 26.8 1.2 27 31-60 2-28 (84)
51 PF12156 ATPase-cat_bd: Putati 25.8 41 0.00089 26.7 1.4 32 30-61 2-39 (88)
52 cd07166 NR_DBD_REV_ERB DNA-bin 25.7 46 0.001 26.5 1.7 30 28-60 3-32 (89)
53 KOG0457 Histone acetyltransfer 25.6 61 0.0013 33.3 2.9 95 25-123 10-124 (438)
54 PTZ00074 60S ribosomal protein 25.2 41 0.00088 29.4 1.4 32 25-56 38-86 (135)
55 cd07165 NR_DBD_DmE78_like DNA- 23.5 49 0.0011 25.8 1.5 27 31-60 1-27 (81)
56 PF07282 OrfB_Zn_ribbon: Putat 22.7 20 0.00043 26.4 -0.8 27 27-55 27-53 (69)
57 cd07155 NR_DBD_ER_like DNA-bin 22.0 55 0.0012 25.1 1.5 27 31-60 1-27 (75)
58 cd07162 NR_DBD_PXR DNA-binding 21.8 43 0.00094 26.5 0.9 28 30-60 1-28 (87)
59 cd07158 NR_DBD_Ppar_like The D 21.8 49 0.0011 25.1 1.2 27 31-60 1-27 (73)
60 cd06966 NR_DBD_CAR DNA-binding 21.7 26 0.00056 28.3 -0.4 29 29-60 1-29 (94)
61 PRK00423 tfb transcription ini 21.6 29 0.00062 33.3 -0.2 32 26-58 9-40 (310)
62 cd07161 NR_DBD_EcR DNA-binding 21.0 44 0.00096 26.8 0.8 28 30-60 3-30 (91)
63 TIGR00100 hypA hydrogenase nic 20.9 30 0.00065 28.7 -0.2 47 24-74 66-113 (115)
64 PF14376 Haem_bd: Haem-binding 20.3 50 0.0011 28.2 1.0 21 18-42 35-55 (137)
65 cd07169 NR_DBD_GCNF_like DNA-b 20.1 50 0.0011 26.4 0.9 32 26-60 4-35 (90)
No 1
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=5.3e-46 Score=347.74 Aligned_cols=120 Identities=58% Similarity=1.024 Sum_probs=113.1
Q ss_pred ccHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCccceeeecccCCCCHHHHHHHHh
Q 022604 7 VSKELNAKHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQS 86 (294)
Q Consensus 7 ~sk~l~ar~~kiL~~Ll~~PgNk~CADCga~~P~WaSvn~GVFVC~~CSGIHRsLG~hISkVKSltLD~Wt~eeV~~m~~ 86 (294)
+.+...++++++|++||+.|+|+.|||||+++|+|||+|+|||||++|+||||+||+||||||||+||.|++|||++|+.
T Consensus 4 ~~~~~~~~~~~~l~~Ll~~~~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~ 83 (287)
T KOG0703|consen 4 VEKGSNERNKRRLRELLREPDNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMIS 83 (287)
T ss_pred ccccccchHHHHHHHHHcCcccCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHH
Confidence 34466779999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccHHHHHHHhhcCCCCCChH----HHHHHHHHhhhcCccccCC
Q 022604 87 MGNEKSNSYWEAELPPNYDRV----GIENFIRAKYEEKRWIPRG 126 (294)
Q Consensus 87 ~GN~~aN~~wEa~lPp~~d~~----~~e~FIraKY~~k~F~~~~ 126 (294)
.||.+||.|||+.+|..+++. .+|+|||+|||.|+|+.++
T Consensus 84 ~GN~~an~~~ea~~p~~~~~p~~d~~~e~FIR~KYE~kkf~~~~ 127 (287)
T KOG0703|consen 84 MGNAKANSYYEAKLPDPFRRPGPDDLVEQFIRDKYERKKFLDPE 127 (287)
T ss_pred HcchhhhhhccccCCccccCCChHHHHHHHHHHHHhhhhhccch
Confidence 999999999999999877653 4999999999999999876
No 2
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=100.00 E-value=6.4e-42 Score=341.57 Aligned_cols=165 Identities=26% Similarity=0.502 Sum_probs=150.2
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCccceeeecccCCCCHHHHHHHHhh
Q 022604 8 SKELNAKHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSM 87 (294)
Q Consensus 8 sk~l~ar~~kiL~~Ll~~PgNk~CADCga~~P~WaSvn~GVFVC~~CSGIHRsLG~hISkVKSltLD~Wt~eeV~~m~~~ 87 (294)
||+++++++++|++|++.|+|+.|||||+.+|+|||+|||||||+.|+||||.|| +|||||+||+|++++|++|+.+
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 7899999999999999999999999999999999999999999999999999998 4999999999999999999999
Q ss_pred ccHHHHHHHhhcCC-------CCCChHHHHHHHHHhhhcCccccCCCCCCCCCCCCcCccCCCCCCCCCCCCcCCCCCCC
Q 022604 88 GNEKSNSYWEAELP-------PNYDRVGIENFIRAKYEEKRWIPRGGNTKSPSRVSEEKASFHRPLPSSSGHRYTNNINR 160 (294)
Q Consensus 88 GN~~aN~~wEa~lP-------p~~d~~~~e~FIraKY~~k~F~~~~~~~~~~s~~~~~~~~~~~~~~~r~G~~~~ss~~~ 160 (294)
||.++|+|||++++ ...+...+++|||.||++|+|+.....+.++....+++++...+.+.++||++.+|..|
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 33456678999999999999999999988888888889888888899999999999875
Q ss_pred ---cccccccCCCCCCCC
Q 022604 161 ---VPDVRNIAHPPNASN 175 (294)
Q Consensus 161 ---~~~~~~~~~~~~~~~ 175 (294)
+|+|||+-+.-....
T Consensus 160 ~~~ye~rr~~~~~~~~~~ 177 (648)
T PLN03119 160 DYQYEERRYGKIPLGFTG 177 (648)
T ss_pred ccchhhhhcccccccccc
Confidence 699999777654433
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=1.3e-40 Score=274.10 Aligned_cols=109 Identities=57% Similarity=1.048 Sum_probs=90.8
Q ss_pred HHHHHHhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHHHHHHH
Q 022604 17 KILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYW 96 (294)
Q Consensus 17 kiL~~Ll~~PgNk~CADCga~~P~WaSvn~GVFVC~~CSGIHRsLG~hISkVKSltLD~Wt~eeV~~m~~~GN~~aN~~w 96 (294)
++|++|++.|+|+.|||||+++|+|||++||||||+.|+|+||.||+|||+||||+||+|++++|++|+.+||..+|++|
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 022604 97 EAELP------PNYDRVGIENFIRAKYEEKRWIPR 125 (294)
Q Consensus 97 Ea~lP------p~~d~~~~e~FIraKY~~k~F~~~ 125 (294)
|++.+ +..+...+++||++||++++|+.+
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=1.5e-39 Score=326.80 Aligned_cols=159 Identities=28% Similarity=0.533 Sum_probs=139.7
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCccceeeecccCCCCHHHHHHHHhh
Q 022604 8 SKELNAKHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSM 87 (294)
Q Consensus 8 sk~l~ar~~kiL~~Ll~~PgNk~CADCga~~P~WaSvn~GVFVC~~CSGIHRsLG~hISkVKSltLD~Wt~eeV~~m~~~ 87 (294)
||+++++++++|++|++.|+|+.|||||+++|+|||+|||||||+.|+||||.|| +|||||+||+|++++|++|+.+
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 4999999999999999999999
Q ss_pred ccHHHHHHHhhcCC-------CCCChHHHHHHHHHhhhcCccccCCCCCCCCCCCCcCccCCCCCCCCCCCCcCCCCCCC
Q 022604 88 GNEKSNSYWEAELP-------PNYDRVGIENFIRAKYEEKRWIPRGGNTKSPSRVSEEKASFHRPLPSSSGHRYTNNINR 160 (294)
Q Consensus 88 GN~~aN~~wEa~lP-------p~~d~~~~e~FIraKY~~k~F~~~~~~~~~~s~~~~~~~~~~~~~~~r~G~~~~ss~~~ 160 (294)
||.++|+|||++|+ ...+...+++|||.||++|+|+.....++++......+.......+..++|++..|..|
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 022604 161 ---VPDVRNIAH 169 (294)
Q Consensus 161 ---~~~~~~~~~ 169 (294)
+|||||+-+
T Consensus 160 ~~~yedrRygk~ 171 (705)
T PLN03131 160 DFQYEDRRYGKQ 171 (705)
T ss_pred cccccccccccc
Confidence 689887443
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=5e-39 Score=263.46 Aligned_cols=103 Identities=57% Similarity=1.023 Sum_probs=96.1
Q ss_pred CCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHHHHHHHhhcCCCCC-
Q 022604 26 PENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYWEAELPPNY- 104 (294)
Q Consensus 26 PgNk~CADCga~~P~WaSvn~GVFVC~~CSGIHRsLG~hISkVKSltLD~Wt~eeV~~m~~~GN~~aN~~wEa~lPp~~- 104 (294)
|+|+.|||||+++|+|||++||||||+.|+|+||.||+|||+||||+||+|++++|++|+.+||.++|+|||+++|+..
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 022604 105 ------DRVGIENFIRAKYEEKRWIPRGGN 128 (294)
Q Consensus 105 ------d~~~~e~FIraKY~~k~F~~~~~~ 128 (294)
+...+++||++||++++|+...+.
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=2.3e-36 Score=287.42 Aligned_cols=115 Identities=47% Similarity=0.905 Sum_probs=105.5
Q ss_pred HHHHHHHHHhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHHHH
Q 022604 14 KHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSN 93 (294)
Q Consensus 14 r~~kiL~~Ll~~PgNk~CADCga~~P~WaSvn~GVFVC~~CSGIHRsLG~hISkVKSltLD~Wt~eeV~~m~~~GN~~aN 93 (294)
..+++|..|...++|+.|||||+++|+|||+|||||||++||||||+||+|||+||||+||+|+.++|++|+.+||.+||
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 45778888999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcC------C--CCCChHHHHHHHHHhhhcCccccCCCC
Q 022604 94 SYWEAEL------P--PNYDRVGIENFIRAKYEEKRWIPRGGN 128 (294)
Q Consensus 94 ~~wEa~l------P--p~~d~~~~e~FIraKY~~k~F~~~~~~ 128 (294)
.||+.++ | ..+|...+++||+.||+.++|+.....
T Consensus 86 ~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~~~~ 128 (319)
T COG5347 86 RFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDDSSS 128 (319)
T ss_pred hHhccCCCcccccccccccCHHHHHHHHHHHHHhhhccccccC
Confidence 9999864 2 245667899999999999999987444
No 7
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.97 E-value=7.2e-30 Score=244.91 Aligned_cols=113 Identities=37% Similarity=0.645 Sum_probs=96.9
Q ss_pred HHHHHHHHhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHHHHH
Q 022604 15 HRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNS 94 (294)
Q Consensus 15 ~~kiL~~Ll~~PgNk~CADCga~~P~WaSvn~GVFVC~~CSGIHRsLG~hISkVKSltLD~Wt~eeV~~m~~~GN~~aN~ 94 (294)
..++|+.|+..|+|+.|+|||+++|+|+|++||||||+.|+|+||.||+|||+|||++||.|++++|++|+.+||.++|.
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------CCCh--HHHHHHHHHhhhcCccccCCC
Q 022604 95 YWEAEL-PP------NYDR--VGIENFIRAKYEEKRWIPRGG 127 (294)
Q Consensus 95 ~wEa~l-Pp------~~d~--~~~e~FIraKY~~k~F~~~~~ 127 (294)
||+.+. .. .|.. ...-+.+.+|++.+.+.....
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 1211 122344888888888875544
No 8
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=99.97 E-value=1.9e-31 Score=254.51 Aligned_cols=110 Identities=39% Similarity=0.753 Sum_probs=94.8
Q ss_pred HHHHHHHHHHhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHHH
Q 022604 13 AKHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKS 92 (294)
Q Consensus 13 ar~~kiL~~Ll~~PgNk~CADCga~~P~WaSvn~GVFVC~~CSGIHRsLG~hISkVKSltLD~Wt~eeV~~m~~~GN~~a 92 (294)
.|.++.|..|....+|+.|+||++++|+|||++||||||++|||+||+||+|||+|||||||+|.+.||+.|+.+||.++
T Consensus 4 prtrr~L~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~~ 83 (386)
T KOG0704|consen 4 PRTRRVLLELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNERF 83 (386)
T ss_pred hHHHHHHHhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchhH
Confidence 47788888888888999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhcC------CC--CCCh---HHHHHHHHHhhhcCcc
Q 022604 93 NSYWEAEL------PP--NYDR---VGIENFIRAKYEEKRW 122 (294)
Q Consensus 93 N~~wEa~l------Pp--~~d~---~~~e~FIraKY~~k~F 122 (294)
+.|++..- |. .|+. ...++-|.+--+.+.|
T Consensus 84 ~eFL~s~~~~~e~~~i~eKYns~aAa~yRdki~~laegr~w 124 (386)
T KOG0704|consen 84 REFLSSQGIYKETWPIREKYNSRAAALYRDKIAALAEGREW 124 (386)
T ss_pred HHHHhhCccccccccHHHhhccHHHHHHHHHHHHHhcCCcc
Confidence 99998642 21 1221 2345667777777777
No 9
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.95 E-value=1.5e-29 Score=247.17 Aligned_cols=86 Identities=44% Similarity=0.842 Sum_probs=82.9
Q ss_pred HHHHHHHHHhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHHHH
Q 022604 14 KHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSN 93 (294)
Q Consensus 14 r~~kiL~~Ll~~PgNk~CADCga~~P~WaSvn~GVFVC~~CSGIHRsLG~hISkVKSltLD~Wt~eeV~~m~~~GN~~aN 93 (294)
..+.+++.|..++.|+.|||||+++|+|+||+||||||++||++||.||||||+|||..||+|+.+||+.|+.|||.+|+
T Consensus 9 d~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~ 88 (454)
T KOG0706|consen 9 DIQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANAR 88 (454)
T ss_pred hHHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHH
Confidence 34678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhc
Q 022604 94 SYWEAE 99 (294)
Q Consensus 94 ~~wEa~ 99 (294)
.|+..|
T Consensus 89 ~FFkqh 94 (454)
T KOG0706|consen 89 VFFKQH 94 (454)
T ss_pred HHHHHc
Confidence 999876
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=4.4e-28 Score=242.83 Aligned_cols=118 Identities=42% Similarity=0.850 Sum_probs=106.8
Q ss_pred HHHHHHHHhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHHHHH
Q 022604 15 HRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNS 94 (294)
Q Consensus 15 ~~kiL~~Ll~~PgNk~CADCga~~P~WaSvn~GVFVC~~CSGIHRsLG~hISkVKSltLD~Wt~eeV~~m~~~GN~~aN~ 94 (294)
....|+.|...+||..|+||+.++|.|+|+|+|+.||++|+||||.||+|+|+|+||.||.|..|.+..|..+||+.||.
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 34568888899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcC-----C-CCCChHHHHHHHHHhhhcCccccCCCCCCCC
Q 022604 95 YWEAEL-----P-PNYDRVGIENFIRAKYEEKRWIPRGGNTKSP 132 (294)
Q Consensus 95 ~wEa~l-----P-p~~d~~~~e~FIraKY~~k~F~~~~~~~~~~ 132 (294)
+||..+ | +.+.++++|+|||+||++|.|..+.....-+
T Consensus 580 vWE~~~~G~~KPs~~s~REEkErwIr~KYeqklFLaPl~~te~~ 623 (749)
T KOG0705|consen 580 VWEGSSQGQTKPSPDSSREEKERWIRAKYEQKLFLAPLPCTEEP 623 (749)
T ss_pred HhhhhccCCcCCCccccHHHHHHHHHHHHHHHhhcCCCCCCCCc
Confidence 999754 2 3445789999999999999999887765444
No 11
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.90 E-value=1.1e-24 Score=227.48 Aligned_cols=112 Identities=46% Similarity=0.889 Sum_probs=103.0
Q ss_pred HHHHHhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHHHHHHHh
Q 022604 18 ILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYWE 97 (294)
Q Consensus 18 iL~~Ll~~PgNk~CADCga~~P~WaSvn~GVFVC~~CSGIHRsLG~hISkVKSltLD~Wt~eeV~~m~~~GN~~aN~~wE 97 (294)
.+..+...|||..|+|||++.|+|+|+|+||.+|+.|+|+||+||+|||+|+||+||.|.++.+.+|+.+||..+|.+||
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 022604 98 AELPPN--------YDRVGIENFIRAKYEEKRWIPRGGNT 129 (294)
Q Consensus 98 a~lPp~--------~d~~~~e~FIraKY~~k~F~~~~~~~ 129 (294)
+.++.. .+...++.||++||++++|.......
T Consensus 496 ~~l~~~~~~~~~~~~~~~~r~~~i~~kyve~~F~~k~~~~ 535 (785)
T KOG0521|consen 496 ALLPSYDSSKPTASSSRQAREAWIKAKYVERRFSVKEPQI 535 (785)
T ss_pred cccccccccCCCCccchhhhhHhhhcccceeeEeecccch
Confidence 998742 23557899999999999998776554
No 12
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.81 E-value=7.1e-21 Score=189.02 Aligned_cols=101 Identities=41% Similarity=0.795 Sum_probs=90.3
Q ss_pred CCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHHHHHHHhhcCCCC-
Q 022604 25 LPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYWEAELPPN- 103 (294)
Q Consensus 25 ~PgNk~CADCga~~P~WaSvn~GVFVC~~CSGIHRsLG~hISkVKSltLD~Wt~eeV~~m~~~GN~~aN~~wEa~lPp~- 103 (294)
...-+.|+|||+++|.|+|++-|+|||.+|..+||+||.|||.||+|.-..|.++.|.+...+.|..+|.|||..|=+.
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 4456789999999999999999999999999999999999999999999999999999999999999999999876221
Q ss_pred -----------CCh--HHHHHHHHHhhhcCccccC
Q 022604 104 -----------YDR--VGIENFIRAKYEEKRWIPR 125 (294)
Q Consensus 104 -----------~d~--~~~e~FIraKY~~k~F~~~ 125 (294)
.|. ...++|||+||+...|+.+
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=6.1e-20 Score=190.41 Aligned_cols=108 Identities=41% Similarity=0.786 Sum_probs=98.2
Q ss_pred HHHhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCccceeeecccCC--CCHHHHHHHHhhccHHHHHHHh
Q 022604 20 DGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDT--WLPEQVAVIQSMGNEKSNSYWE 97 (294)
Q Consensus 20 ~~Ll~~PgNk~CADCga~~P~WaSvn~GVFVC~~CSGIHRsLG~hISkVKSltLD~--Wt~eeV~~m~~~GN~~aN~~wE 97 (294)
+++.....|+.|+|||++.|.|+|+|++|.||-.|+|-||+||..+|+|+|++||. |+.+-|+++..+||.++|.||-
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 45667789999999999999999999999999999999999999999999999997 9999999999999999999999
Q ss_pred hcCCCCC------ChHHHHHHHHHhhhcCccccCCC
Q 022604 98 AELPPNY------DRVGIENFIRAKYEEKRWIPRGG 127 (294)
Q Consensus 98 a~lPp~~------d~~~~e~FIraKY~~k~F~~~~~ 127 (294)
+++|++. ....+++||.+||.+..|-....
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 9998754 24578999999999998865433
No 14
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.76 E-value=3.6e-18 Score=169.38 Aligned_cols=127 Identities=30% Similarity=0.549 Sum_probs=113.0
Q ss_pred cccHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCC-CeeecchhHHHHHHhhhhhhcCCCccceeeecccCCCCHHHHHHH
Q 022604 6 NVSKELNAKHRKILDGLLKLPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVI 84 (294)
Q Consensus 6 ~~sk~l~ar~~kiL~~Ll~~PgNk~CADCga~~P-~WaSvn~GVFVC~~CSGIHRsLG~hISkVKSltLD~Wt~eeV~~m 84 (294)
...|+.+..++++|+.|+++|+|++|++|....+ +|+++.-|-|+|+.|+|+-|.|.. -+|||||+|.+++..+|..|
T Consensus 3 ~~~ke~E~~~ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~~-ahRvksiSmttft~qevs~l 81 (524)
T KOG0702|consen 3 GYKKEDEYDYEKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLNP-AHRVKSISMTTFTDQEVSFL 81 (524)
T ss_pred cccccchhHHHHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccCCC-ccccceeeeeeccccchHHH
Confidence 3456766777999999999999999999999988 999999999999999999999975 57999999999999999999
Q ss_pred HhhccHHHHHHHhhc-------CCCCCChHHHHHHHHHhhhcCccccCCCCCCCCC
Q 022604 85 QSMGNEKSNSYWEAE-------LPPNYDRVGIENFIRAKYEEKRWIPRGGNTKSPS 133 (294)
Q Consensus 85 ~~~GN~~aN~~wEa~-------lPp~~d~~~~e~FIraKY~~k~F~~~~~~~~~~s 133 (294)
+.+||+.+.++|... +|+..+....++|||.||+.|+|+........++
T Consensus 82 QshgNq~~k~i~fkl~D~q~S~vPD~rn~~~~kef~q~~y~~kr~~v~~n~~k~~s 137 (524)
T KOG0702|consen 82 QSHGNQVCKEIWFKLFDFQRSNVPDSRNPQKVKEFQQEKYVKKRYYVPKNQMKIPS 137 (524)
T ss_pred hhcchhhhhhhhhcchhhhhccCCCcccchhhHHHHhhhhccceeecCcccccccc
Confidence 999999999999753 5777778889999999999999997666555443
No 15
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=95.53 E-value=0.0031 Score=67.60 Aligned_cols=72 Identities=21% Similarity=0.237 Sum_probs=61.0
Q ss_pred cCCCCCCCcCCCCC-CCCeeecchhHHHHHHhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhccHHHHHHHh
Q 022604 24 KLPENRECADCKAK-GPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYWE 97 (294)
Q Consensus 24 ~~PgNk~CADCga~-~P~WaSvn~GVFVC~~CSGIHRsLG~hISkVKSltLD~Wt~eeV~~m~~~GN~~aN~~wE 97 (294)
....+..|++|++. ...|+++++.+.+|+.|+++|+.++.+++...++.|++..+ |......|+...+..|.
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 78899999999999999999999999999999999998777 77777667776666554
No 16
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=84.88 E-value=0.46 Score=42.98 Aligned_cols=31 Identities=32% Similarity=0.578 Sum_probs=27.0
Q ss_pred CCCCCCCcCCCCCCC-CeeecchhHHHHHHhh
Q 022604 25 LPENRECADCKAKGP-RWASVNLGIFICMQCS 55 (294)
Q Consensus 25 ~PgNk~CADCga~~P-~WaSvn~GVFVC~~CS 55 (294)
.|.-..|+-||.+.. .|.+..-|.|+|..|.
T Consensus 146 ~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 146 GLDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred ccchhhHhcCCCCCCceEEecccCCccccccc
Confidence 566789999998754 7899999999999997
No 17
>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=76.52 E-value=1.1 Score=30.17 Aligned_cols=34 Identities=12% Similarity=0.335 Sum_probs=29.4
Q ss_pred CCCCCcCCCCCCCCeeecchhHHHHHHhhhh-hhc
Q 022604 27 ENRECADCKAKGPRWASVNLGIFICMQCSGI-HRS 60 (294)
Q Consensus 27 gNk~CADCga~~P~WaSvn~GVFVC~~CSGI-HRs 60 (294)
.+..|..|+.....+.+.+-+++||..|... |+.
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 18
>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=75.20 E-value=1.4 Score=39.64 Aligned_cols=33 Identities=27% Similarity=0.497 Sum_probs=27.6
Q ss_pred CCCCCCCcCCCCCCC-CeeecchhHHHHHHhhhh
Q 022604 25 LPENRECADCKAKGP-RWASVNLGIFICMQCSGI 57 (294)
Q Consensus 25 ~PgNk~CADCga~~P-~WaSvn~GVFVC~~CSGI 57 (294)
.|.-..|+.||..++ .|.+...|.|+|..|.+.
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 19
>PRK12495 hypothetical protein; Provisional
Probab=75.18 E-value=1.3 Score=41.49 Aligned_cols=38 Identities=24% Similarity=0.397 Sum_probs=28.1
Q ss_pred HHHHHHHhc--CCCCCCCcCCCCCCCCeeecchhHHHHHHhhhh
Q 022604 16 RKILDGLLK--LPENRECADCKAKGPRWASVNLGIFICMQCSGI 57 (294)
Q Consensus 16 ~kiL~~Ll~--~PgNk~CADCga~~P~WaSvn~GVFVC~~CSGI 57 (294)
+++-+.|++ ...+..|-+||.+=|.+ -|+.+|..|..+
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 334444444 47899999999998832 699999999654
No 20
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=72.70 E-value=1.4 Score=37.35 Aligned_cols=35 Identities=14% Similarity=0.349 Sum_probs=23.3
Q ss_pred CCCCCCcCCCCCCC-CeeecchhHHHHHHhhhhhhc
Q 022604 26 PENRECADCKAKGP-RWASVNLGIFICMQCSGIHRS 60 (294)
Q Consensus 26 PgNk~CADCga~~P-~WaSvn~GVFVC~~CSGIHRs 60 (294)
..-.+|.+||.+=| .=.-.--+..+|+.|...|-.
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 34458999999732 122233468999999987743
No 21
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=70.23 E-value=2 Score=40.04 Aligned_cols=31 Identities=32% Similarity=0.693 Sum_probs=27.4
Q ss_pred CCCCCCCcCCCCCC-CCeeecchhHHHHHHhh
Q 022604 25 LPENRECADCKAKG-PRWASVNLGIFICMQCS 55 (294)
Q Consensus 25 ~PgNk~CADCga~~-P~WaSvn~GVFVC~~CS 55 (294)
.+.=..|+.||.+. +..++.-.|-++|..|.
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=66.54 E-value=2.6 Score=31.72 Aligned_cols=34 Identities=35% Similarity=0.638 Sum_probs=23.8
Q ss_pred cCCCCCCCcCCCCCCC--CeeecchhHHHHHHhhhhh
Q 022604 24 KLPENRECADCKAKGP--RWASVNLGIFICMQCSGIH 58 (294)
Q Consensus 24 ~~PgNk~CADCga~~P--~WaSvn~GVFVC~~CSGIH 58 (294)
..++...|.|||.+=| ++. ..-|+..|+.|...+
T Consensus 27 ~~~s~g~C~~Cg~~Ip~~Rl~-a~p~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 27 IGPSLRECEDCGEPIPEARRE-ALPGVTRCVSCQEIL 62 (63)
T ss_pred cCCCCCeeccCCCcChHHHHh-hcCCcCCcHHHHhhc
Confidence 4567889999999743 222 233788899997654
No 23
>PRK11019 hypothetical protein; Provisional
Probab=65.06 E-value=3.4 Score=33.42 Aligned_cols=37 Identities=22% Similarity=0.518 Sum_probs=26.3
Q ss_pred CCCCCcCCCCCCC--CeeecchhHHHHHHhhhhhhcCCCc
Q 022604 27 ENRECADCKAKGP--RWASVNLGIFICMQCSGIHRSLGVH 64 (294)
Q Consensus 27 gNk~CADCga~~P--~WaSvn~GVFVC~~CSGIHRsLG~h 64 (294)
...+|.|||.+=| .+..+ -|+-.|+.|...+-..+.|
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 34333 3788999999987655444
No 24
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=58.60 E-value=5.5 Score=30.97 Aligned_cols=35 Identities=17% Similarity=0.467 Sum_probs=23.2
Q ss_pred CCCCCcCCCCCCCC-eeecchhHHHHHHhhhhhhcC
Q 022604 27 ENRECADCKAKGPR-WASVNLGIFICMQCSGIHRSL 61 (294)
Q Consensus 27 gNk~CADCga~~P~-WaSvn~GVFVC~~CSGIHRsL 61 (294)
+...|.|||.+=|. =.-.--|+..|+.|...+-.-
T Consensus 33 ~~~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~E~~ 68 (73)
T PRK13715 33 PVYLCEACGNPIPEARRKIFPGVTLCVECQAYQERQ 68 (73)
T ss_pred CcccHhhcCCcCCHHHHhcCCCcCCCHHHHHHHHHH
Confidence 34689999997442 112233788999998876543
No 25
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=56.17 E-value=6.3 Score=34.55 Aligned_cols=40 Identities=13% Similarity=0.265 Sum_probs=25.8
Q ss_pred hcCCCCCCCcCCCCCCC-CeeecchhHHHHHHhhhhhhcCC
Q 022604 23 LKLPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRSLG 62 (294)
Q Consensus 23 l~~PgNk~CADCga~~P-~WaSvn~GVFVC~~CSGIHRsLG 62 (294)
+..+.-.+|-+||.+=| .=.-+--++..|+.|...|-..+
T Consensus 106 i~~gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~E~~~ 146 (151)
T PRK10778 106 VEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIRE 146 (151)
T ss_pred HhCCCCceeccCCCcccHHHHhcCCCccccHHHHHHHHHHh
Confidence 34577899999998711 11111224678999998876443
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=54.66 E-value=4 Score=27.67 Aligned_cols=27 Identities=26% Similarity=0.812 Sum_probs=22.7
Q ss_pred CCCCCCcCCCCCCCCeeecchhHHHHHHhh
Q 022604 26 PENRECADCKAKGPRWASVNLGIFICMQCS 55 (294)
Q Consensus 26 PgNk~CADCga~~P~WaSvn~GVFVC~~CS 55 (294)
..|..|..|++. |....=|-|+|.+|-
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
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=52.85 E-value=7.9 Score=36.12 Aligned_cols=39 Identities=18% Similarity=0.406 Sum_probs=28.8
Q ss_pred HHHHHHHHhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhh
Q 022604 15 HRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHR 59 (294)
Q Consensus 15 ~~kiL~~Ll~~PgNk~CADCga~~P~WaSvn~GVFVC~~CSGIHR 59 (294)
.++.++..+.......|-.||.....|. ++|-.|.+.|-
T Consensus 341 ~~~~~~~~~~~~p~~~c~~cg~~~~~~~------~~c~~c~~~~~ 379 (389)
T PRK11788 341 LRDLVGEQLKRKPRYRCRNCGFTARTLY------WHCPSCKAWET 379 (389)
T ss_pred HHHHHHHHHhCCCCEECCCCCCCCccce------eECcCCCCccC
Confidence 4556665555433355999999999995 78999988873
No 28
>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=52.63 E-value=2.8 Score=28.42 Aligned_cols=27 Identities=19% Similarity=0.582 Sum_probs=16.6
Q ss_pred CCCcCCCCC-CCCeeecchhHHHHHHhh
Q 022604 29 RECADCKAK-GPRWASVNLGIFICMQCS 55 (294)
Q Consensus 29 k~CADCga~-~P~WaSvn~GVFVC~~CS 55 (294)
..|.+||.. .-+|..-+|+.-||..|-
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 567999999999999994
No 29
>PHA00080 DksA-like zinc finger domain containing protein
Probab=46.14 E-value=11 Score=29.16 Aligned_cols=35 Identities=29% Similarity=0.619 Sum_probs=23.9
Q ss_pred CCCCCCCcCCCCCCC--CeeecchhHHHHHHhhhhhhc
Q 022604 25 LPENRECADCKAKGP--RWASVNLGIFICMQCSGIHRS 60 (294)
Q Consensus 25 ~PgNk~CADCga~~P--~WaSvn~GVFVC~~CSGIHRs 60 (294)
..+..+|.|||.+=| .|..+ -|+..|+.|...+-.
T Consensus 28 ~~~~~~C~~Cg~~Ip~~Rl~a~-P~~~~Cv~Cq~~~E~ 64 (72)
T PHA00080 28 APSATHCEECGDPIPEARREAV-PGCRTCVSCQEILEL 64 (72)
T ss_pred CCCCCEecCCCCcCcHHHHHhC-CCccCcHHHHHHHHH
Confidence 456679999999733 33322 367789999887643
No 30
>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=43.18 E-value=14 Score=32.67 Aligned_cols=37 Identities=14% Similarity=0.228 Sum_probs=23.4
Q ss_pred cCCCCCCCcCCCCCCC-CeeecchhHHHHHHhhhhhhc
Q 022604 24 KLPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRS 60 (294)
Q Consensus 24 ~~PgNk~CADCga~~P-~WaSvn~GVFVC~~CSGIHRs 60 (294)
....-.+|.+||.+=| .=.-+--++-.|+.|...+-.
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 3456678999998611 111122246789999987644
No 31
>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=42.44 E-value=3.7 Score=28.21 Aligned_cols=27 Identities=22% Similarity=0.600 Sum_probs=20.4
Q ss_pred CCcCCCCCCCCeeecchhHHHHHHhhhh
Q 022604 30 ECADCKAKGPRWASVNLGIFICMQCSGI 57 (294)
Q Consensus 30 ~CADCga~~P~WaSvn~GVFVC~~CSGI 57 (294)
.|-.||+.. .-..-.-|-++|..|.-+
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-BB
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCCCE
Confidence 588999977 455667899999999433
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=41.65 E-value=2.7 Score=27.94 Aligned_cols=30 Identities=23% Similarity=0.533 Sum_probs=16.6
Q ss_pred CCCcCCCCCCC-CeeecchhHHHHHHhhhhh
Q 022604 29 RECADCKAKGP-RWASVNLGIFICMQCSGIH 58 (294)
Q Consensus 29 k~CADCga~~P-~WaSvn~GVFVC~~CSGIH 58 (294)
..|.+||..=+ .=.-+--|..+|..|+..|
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 35999998622 1112223677899998765
No 33
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=39.86 E-value=7.7 Score=34.42 Aligned_cols=34 Identities=29% Similarity=0.669 Sum_probs=27.2
Q ss_pred CCCCCCcCCCCCCCCeeecchhHHHH-HHhhhhhhc
Q 022604 26 PENRECADCKAKGPRWASVNLGIFIC-MQCSGIHRS 60 (294)
Q Consensus 26 PgNk~CADCga~~P~WaSvn~GVFVC-~~CSGIHRs 60 (294)
|--+.|+-|| -...|.+++.|.-+| ..|-++|..
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 666689999999888 478888854
No 34
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=39.76 E-value=12 Score=26.95 Aligned_cols=37 Identities=24% Similarity=0.587 Sum_probs=29.8
Q ss_pred CCCCCcCCCCC-CCCeeecchhH-HHHHHhhhhhhcCCC
Q 022604 27 ENRECADCKAK-GPRWASVNLGI-FICMQCSGIHRSLGV 63 (294)
Q Consensus 27 gNk~CADCga~-~P~WaSvn~GV-FVC~~CSGIHRsLG~ 63 (294)
....|..|+.. .|.|=.-..|- +||-.|.-..+..|.
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 999999777776654
No 35
>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=37.10 E-value=20 Score=29.39 Aligned_cols=31 Identities=19% Similarity=0.410 Sum_probs=18.5
Q ss_pred CCCCCCCcCCCCCCC-CeeecchhHHHHHHhh
Q 022604 25 LPENRECADCKAKGP-RWASVNLGIFICMQCS 55 (294)
Q Consensus 25 ~PgNk~CADCga~~P-~WaSvn~GVFVC~~CS 55 (294)
.+.-.+|.|||.+=| .=.-.--++..|+.|.
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 456689999998722 1111112356788885
No 36
>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=35.93 E-value=24 Score=27.76 Aligned_cols=31 Identities=16% Similarity=0.540 Sum_probs=25.5
Q ss_pred CCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhc
Q 022604 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (294)
Q Consensus 27 gNk~CADCga~~P~WaSvn~GVFVC~~CSGIHRs 60 (294)
..+.|.=||...- ...||++.|..|.+..|-
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 4567999998665 458999999999998875
No 37
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=34.36 E-value=17 Score=26.32 Aligned_cols=43 Identities=23% Similarity=0.413 Sum_probs=25.1
Q ss_pred CCcCCCCCCCCe--eecchhHHHHHHhhhhhhcCCCccceeeeccc
Q 022604 30 ECADCKAKGPRW--ASVNLGIFICMQCSGIHRSLGVHISKVRSATL 73 (294)
Q Consensus 30 ~CADCga~~P~W--aSvn~GVFVC~~CSGIHRsLG~hISkVKSltL 73 (294)
.|+=||..-.-. +-+.=| +||-.|..--..+...+..++++++
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 488888864333 345567 8999998654444333333344444
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=34.03 E-value=20 Score=28.22 Aligned_cols=31 Identities=19% Similarity=0.613 Sum_probs=25.6
Q ss_pred CCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhc
Q 022604 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (294)
Q Consensus 27 gNk~CADCga~~P~WaSvn~GVFVC~~CSGIHRs 60 (294)
.|..|.=||.... ...||++.|..|.+..|-
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 4678999997654 468999999999998865
No 39
>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=33.27 E-value=12 Score=25.05 Aligned_cols=32 Identities=25% Similarity=0.694 Sum_probs=22.6
Q ss_pred CcCCCCC-CCCeeecchhHH-HHHHhhhhhhcCC
Q 022604 31 CADCKAK-GPRWASVNLGIF-ICMQCSGIHRSLG 62 (294)
Q Consensus 31 CADCga~-~P~WaSvn~GVF-VC~~CSGIHRsLG 62 (294)
|..|+.. .|.|=....|-. ||-.|.-.+|..|
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 699988887776 9999977766544
No 40
>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=32.54 E-value=15 Score=26.29 Aligned_cols=26 Identities=27% Similarity=0.630 Sum_probs=19.2
Q ss_pred CCcCCCCCCCCeeecchhHHHHHHhhh
Q 022604 30 ECADCKAKGPRWASVNLGIFICMQCSG 56 (294)
Q Consensus 30 ~CADCga~~P~WaSvn~GVFVC~~CSG 56 (294)
.|.=|+..... .-.=+|.|||..|-.
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 334479999999943
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=32.09 E-value=43 Score=24.44 Aligned_cols=33 Identities=24% Similarity=0.637 Sum_probs=26.4
Q ss_pred CCcCCCCC-CCCeeecc-hhHHHHHHhhhhhhcCC
Q 022604 30 ECADCKAK-GPRWASVN-LGIFICMQCSGIHRSLG 62 (294)
Q Consensus 30 ~CADCga~-~P~WaSvn-~GVFVC~~CSGIHRsLG 62 (294)
.|..|+.. -|.|=... -+..||-.|.--.+..|
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 78899999977666666
No 42
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=30.51 E-value=25 Score=28.90 Aligned_cols=33 Identities=27% Similarity=0.589 Sum_probs=22.9
Q ss_pred cCCCCCCCcCCCCCC-------C----------CeeecchhHHHHHHhhh
Q 022604 24 KLPENRECADCKAKG-------P----------RWASVNLGIFICMQCSG 56 (294)
Q Consensus 24 ~~PgNk~CADCga~~-------P----------~WaSvn~GVFVC~~CSG 56 (294)
+.++--.|++||.+- | .=++=.||-.+|..|..
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 456777899999861 1 11244689999999954
No 43
>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=29.20 E-value=28 Score=33.73 Aligned_cols=51 Identities=22% Similarity=0.410 Sum_probs=31.0
Q ss_pred ccccHHHHHHHHHHHHHHh----------cCCCCCCCcCCCCCCCCeeec-------c-hhHHHHHHhh
Q 022604 5 ANVSKELNAKHRKILDGLL----------KLPENRECADCKAKGPRWASV-------N-LGIFICMQCS 55 (294)
Q Consensus 5 ~~~sk~l~ar~~kiL~~Ll----------~~PgNk~CADCga~~P~WaSv-------n-~GVFVC~~CS 55 (294)
.=.|+++....+++.+.-+ ...+...|..||.....|.-+ . --.|+|..|.
T Consensus 225 Emas~e~k~~~e~~~ke~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg 293 (299)
T TIGR01385 225 EMASAELKQEREEITKENLFEAQGAKIQKAVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECG 293 (299)
T ss_pred HcCCHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCC
Confidence 3345555555555444321 234567999999999888744 1 1245888885
No 44
>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=29.01 E-value=27 Score=28.27 Aligned_cols=31 Identities=29% Similarity=0.703 Sum_probs=25.6
Q ss_pred CCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhc
Q 022604 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (294)
Q Consensus 27 gNk~CADCga~~P~WaSvn~GVFVC~~CSGIHRs 60 (294)
.+..|.=||...-. ..||++.|..|.+..|-
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 46679999987644 58999999999999875
No 45
>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=28.58 E-value=25 Score=28.58 Aligned_cols=30 Identities=20% Similarity=0.540 Sum_probs=24.6
Q ss_pred CCCCcCCCCCCCCeeecchhHHHHHHhhhhhhc
Q 022604 28 NRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (294)
Q Consensus 28 Nk~CADCga~~P~WaSvn~GVFVC~~CSGIHRs 60 (294)
+..|.=||...-. ..||++.|..|.+..|-
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 58999999999999875
No 46
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=28.18 E-value=27 Score=24.06 Aligned_cols=23 Identities=22% Similarity=0.541 Sum_probs=17.9
Q ss_pred CCcCCCCCCCCeeecchhHHHHH
Q 022604 30 ECADCKAKGPRWASVNLGIFICM 52 (294)
Q Consensus 30 ~CADCga~~P~WaSvn~GVFVC~ 52 (294)
+|.+|+..+.-|+++.-|-..|.
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c~ 23 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGCG 23 (50)
T ss_pred CcccCCCcCCeEEecCCCCcccC
Confidence 59999988888888876666663
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=27.88 E-value=29 Score=25.00 Aligned_cols=34 Identities=24% Similarity=0.653 Sum_probs=22.2
Q ss_pred HhcCCCCCCCcCCCCCCC--Ce-------eecchhHHHHHHhhh
Q 022604 22 LLKLPENRECADCKAKGP--RW-------ASVNLGIFICMQCSG 56 (294)
Q Consensus 22 Ll~~PgNk~CADCga~~P--~W-------aSvn~GVFVC~~CSG 56 (294)
|+++.+| .|-=||+..+ .| .+..-.|+||..|.+
T Consensus 2 L~~Rs~~-kCELC~a~~~L~vy~Vpp~~~~~~d~~iliC~tC~~ 44 (47)
T smart00782 2 LLARCES-KCELCGSDSPLVVYAVPPSSDVTADNSVMLCDTCHS 44 (47)
T ss_pred hhHHcCC-cccCcCCCCCceEEecCCCCCCCccceeeechHHHH
Confidence 3444444 4999998643 12 234668999999965
No 48
>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=26.93 E-value=27 Score=28.67 Aligned_cols=31 Identities=26% Similarity=0.677 Sum_probs=25.8
Q ss_pred CCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhc
Q 022604 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (294)
Q Consensus 27 gNk~CADCga~~P~WaSvn~GVFVC~~CSGIHRs 60 (294)
.+..|.=||...- ...||+..|..|.+..|-
T Consensus 17 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 47 (101)
T cd07160 17 GNEVCSVCGDKAS---GFHYNVLSCEGCKGFFRR 47 (101)
T ss_pred CCCCCeecCCcCc---ceEECcceehhhhhhhhh
Confidence 4678999998665 458999999999998875
No 49
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=26.13 E-value=19 Score=30.51 Aligned_cols=24 Identities=38% Similarity=0.826 Sum_probs=21.6
Q ss_pred Ceeecchh--HHHHHHhhhhhhcCCC
Q 022604 40 RWASVNLG--IFICMQCSGIHRSLGV 63 (294)
Q Consensus 40 ~WaSvn~G--VFVC~~CSGIHRsLG~ 63 (294)
.|++-.-| |.-|.+|--|||.-+.
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 50
>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=25.94 E-value=36 Score=26.77 Aligned_cols=27 Identities=30% Similarity=0.783 Sum_probs=22.0
Q ss_pred CcCCCCCCCCeeecchhHHHHHHhhhhhhc
Q 022604 31 CADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (294)
Q Consensus 31 CADCga~~P~WaSvn~GVFVC~~CSGIHRs 60 (294)
|.=||...-. ..||++.|..|.+..|-
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 7778876544 47999999999999876
No 51
>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=25.78 E-value=41 Score=26.71 Aligned_cols=32 Identities=22% Similarity=0.510 Sum_probs=23.7
Q ss_pred CCcCCCCCCC---Ceeecchh---HHHHHHhhhhhhcC
Q 022604 30 ECADCKAKGP---RWASVNLG---IFICMQCSGIHRSL 61 (294)
Q Consensus 30 ~CADCga~~P---~WaSvn~G---VFVC~~CSGIHRsL 61 (294)
.|..||.+-| .|...--| .|-|..|.+|...|
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 52
>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=25.68 E-value=46 Score=26.51 Aligned_cols=30 Identities=27% Similarity=0.629 Sum_probs=24.4
Q ss_pred CCCCcCCCCCCCCeeecchhHHHHHHhhhhhhc
Q 022604 28 NRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (294)
Q Consensus 28 Nk~CADCga~~P~WaSvn~GVFVC~~CSGIHRs 60 (294)
+..|.=||.+.-. ..||++.|..|.+..|-
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 4569999986654 47999999999998875
No 53
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=25.56 E-value=61 Score=33.30 Aligned_cols=95 Identities=14% Similarity=0.288 Sum_probs=44.7
Q ss_pred CCCCCCCcC-CCCC--CCCeeecchh--HHHHHHhhhhhhcCCCcc-----ceeeecc----cCCCCH-HHHHHHHh---
Q 022604 25 LPENRECAD-CKAK--GPRWASVNLG--IFICMQCSGIHRSLGVHI-----SKVRSAT----LDTWLP-EQVAVIQS--- 86 (294)
Q Consensus 25 ~PgNk~CAD-Cga~--~P~WaSvn~G--VFVC~~CSGIHRsLG~hI-----SkVKSlt----LD~Wt~-eeV~~m~~--- 86 (294)
.+|++.|+| |-.- +...+.+.-+ .+||+.|-..=-.+|+|- --|...+ --.|+. ||+.+|..
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 355544433 6542 3333322222 589999977655555541 1222212 124985 67777763
Q ss_pred --hccHHHHHHHhhcCCCCCChHHHHHHHHHhhhcCccc
Q 022604 87 --MGNEKSNSYWEAELPPNYDRVGIENFIRAKYEEKRWI 123 (294)
Q Consensus 87 --~GN~~aN~~wEa~lPp~~d~~~~e~FIraKY~~k~F~ 123 (294)
+||=. .|=+ ++- .-+..+.+++-...|++.-+.
T Consensus 90 ~G~GNW~--dIA~-hIG-tKtkeeck~hy~k~fv~s~~~ 124 (438)
T KOG0457|consen 90 YGFGNWQ--DIAD-HIG-TKTKEECKEHYLKHFVNSPIF 124 (438)
T ss_pred hCCCcHH--HHHH-HHc-ccchHHHHHHHHHHHhcCccc
Confidence 36621 1100 111 123344555555666665443
No 54
>PTZ00074 60S ribosomal protein L34; Provisional
Probab=25.20 E-value=41 Score=29.41 Aligned_cols=32 Identities=25% Similarity=0.523 Sum_probs=21.9
Q ss_pred CCCCCCCcCCCCC-----------------CCCeeecchhHHHHHHhhh
Q 022604 25 LPENRECADCKAK-----------------GPRWASVNLGIFICMQCSG 56 (294)
Q Consensus 25 ~PgNk~CADCga~-----------------~P~WaSvn~GVFVC~~CSG 56 (294)
.+.--.|+|||.+ .-.-++=.||-.+|..|--
T Consensus 38 ~~~~pkC~~cg~~L~GI~~~Rp~e~~rlsK~~KtvsRaYGG~lC~~CVr 86 (135)
T PTZ00074 38 KSSGPKCGDCGKVLAGIKALRPTEYKQLSRRERTVSRAYGGVLCHKCVR 86 (135)
T ss_pred CCCCCCCCCCCCccCCccCCchHHHHHccccCCCccCCCccchhHHHHH
Confidence 3444569999986 1123455789999999943
No 55
>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=23.54 E-value=49 Score=25.78 Aligned_cols=27 Identities=30% Similarity=0.732 Sum_probs=21.2
Q ss_pred CcCCCCCCCCeeecchhHHHHHHhhhhhhc
Q 022604 31 CADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (294)
Q Consensus 31 CADCga~~P~WaSvn~GVFVC~~CSGIHRs 60 (294)
|.=||...-. ..||+..|..|.+..|-
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 5557765543 48999999999998875
No 56
>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=22.74 E-value=20 Score=26.40 Aligned_cols=27 Identities=19% Similarity=0.655 Sum_probs=22.2
Q ss_pred CCCCCcCCCCCCCCeeecchhHHHHHHhh
Q 022604 27 ENRECADCKAKGPRWASVNLGIFICMQCS 55 (294)
Q Consensus 27 gNk~CADCga~~P~WaSvn~GVFVC~~CS 55 (294)
.-+.|..||..... ..+-.+|.|..|.
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 45789999998877 6777899999984
No 57
>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=22.03 E-value=55 Score=25.08 Aligned_cols=27 Identities=19% Similarity=0.583 Sum_probs=21.0
Q ss_pred CcCCCCCCCCeeecchhHHHHHHhhhhhhc
Q 022604 31 CADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (294)
Q Consensus 31 CADCga~~P~WaSvn~GVFVC~~CSGIHRs 60 (294)
|.=||.+.. ...||+..|..|.+..|-
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 358999999999998865
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=21.84 E-value=43 Score=26.45 Aligned_cols=28 Identities=21% Similarity=0.625 Sum_probs=22.5
Q ss_pred CCcCCCCCCCCeeecchhHHHHHHhhhhhhc
Q 022604 30 ECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (294)
Q Consensus 30 ~CADCga~~P~WaSvn~GVFVC~~CSGIHRs 60 (294)
.|.=||..... ..||++.|..|.+..|-
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 37778876554 48999999999998865
No 59
>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=21.84 E-value=49 Score=25.11 Aligned_cols=27 Identities=30% Similarity=0.773 Sum_probs=21.0
Q ss_pred CcCCCCCCCCeeecchhHHHHHHhhhhhhc
Q 022604 31 CADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (294)
Q Consensus 31 CADCga~~P~WaSvn~GVFVC~~CSGIHRs 60 (294)
|.=||.+.-. ..||++.|..|.+..|-
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 5557765543 58999999999999875
No 60
>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=21.75 E-value=26 Score=28.27 Aligned_cols=29 Identities=24% Similarity=0.592 Sum_probs=23.4
Q ss_pred CCCcCCCCCCCCeeecchhHHHHHHhhhhhhc
Q 022604 29 RECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (294)
Q Consensus 29 k~CADCga~~P~WaSvn~GVFVC~~CSGIHRs 60 (294)
+.|.=||.+... ..||++.|..|.+..|-
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 358889876554 48999999999998875
No 61
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=21.61 E-value=29 Score=33.32 Aligned_cols=32 Identities=19% Similarity=0.471 Sum_probs=22.5
Q ss_pred CCCCCCcCCCCCCCCeeecchhHHHHHHhhhhh
Q 022604 26 PENRECADCKAKGPRWASVNLGIFICMQCSGIH 58 (294)
Q Consensus 26 PgNk~CADCga~~P~WaSvn~GVFVC~~CSGIH 58 (294)
.....|-+||.... =....-|-.||..|.-|-
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 34567999997432 224567999999997754
No 62
>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=21.00 E-value=44 Score=26.80 Aligned_cols=28 Identities=21% Similarity=0.602 Sum_probs=23.1
Q ss_pred CCcCCCCCCCCeeecchhHHHHHHhhhhhhc
Q 022604 30 ECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (294)
Q Consensus 30 ~CADCga~~P~WaSvn~GVFVC~~CSGIHRs 60 (294)
.|.=||.+.-. ..||++.|..|.+..|-
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 48889876554 58999999999998874
No 63
>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=20.94 E-value=30 Score=28.74 Aligned_cols=47 Identities=23% Similarity=0.555 Sum_probs=27.6
Q ss_pred cCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhh-hcCCCccceeeecccC
Q 022604 24 KLPENRECADCKAKGPRWASVNLGIFICMQCSGIH-RSLGVHISKVRSATLD 74 (294)
Q Consensus 24 ~~PgNk~CADCga~~P~WaSvn~GVFVC~~CSGIH-RsLG~hISkVKSltLD 74 (294)
..|.--.|.+||.. ..+..-.|.|-.|.+.. +.++-+==+|++|.++
T Consensus 66 ~~p~~~~C~~Cg~~----~~~~~~~~~CP~Cgs~~~~i~~G~El~I~~ie~~ 113 (115)
T TIGR00100 66 DEPVECECEDCSEE----VSPEIDLYRCPKCHGIMLQVRAGKELNLKSIEVE 113 (115)
T ss_pred eeCcEEEcccCCCE----EecCCcCccCcCCcCCCcEEecCCeEEEEEEEEE
Confidence 45788899999943 23322358899998754 2222122245665543
No 64
>PF14376 Haem_bd: Haem-binding domain
Probab=20.32 E-value=50 Score=28.18 Aligned_cols=21 Identities=29% Similarity=0.686 Sum_probs=14.2
Q ss_pred HHHHHhcCCCCCCCcCCCCCCCCee
Q 022604 18 ILDGLLKLPENRECADCKAKGPRWA 42 (294)
Q Consensus 18 iL~~Ll~~PgNk~CADCga~~P~Wa 42 (294)
.+..|++ +-|.||++.++.|-
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 46999999876654
No 65
>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=20.07 E-value=50 Score=26.40 Aligned_cols=32 Identities=28% Similarity=0.754 Sum_probs=26.0
Q ss_pred CCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhc
Q 022604 26 PENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (294)
Q Consensus 26 PgNk~CADCga~~P~WaSvn~GVFVC~~CSGIHRs 60 (294)
..+..|.=||.... ...||+..|..|.+..|-
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
Done!