Query 015009
Match_columns 414
No_of_seqs 164 out of 1189
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 02:13:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015009.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015009hhsearch_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 1.1E-45 2.3E-50 360.6 13.2 276 7-335 4-287 (287)
2 PLN03119 putative ADP-ribosyla 100.0 6.1E-42 1.3E-46 355.6 14.8 161 8-172 3-172 (648)
3 PLN03131 hypothetical protein; 100.0 7.1E-40 1.5E-44 342.5 12.6 158 8-169 3-169 (705)
4 PF01412 ArfGap: Putative GTPa 100.0 3.7E-38 8.1E-43 271.5 7.6 109 17-125 2-116 (116)
5 smart00105 ArfGap Putative GTP 100.0 1.4E-36 3E-41 260.6 9.6 103 26-128 1-110 (112)
6 COG5347 GTPase-activating prot 100.0 1.2E-33 2.6E-38 281.0 8.5 113 13-125 5-125 (319)
7 KOG0704 ADP-ribosylation facto 100.0 8.9E-30 1.9E-34 253.0 11.3 110 13-122 4-124 (386)
8 PLN03114 ADP-ribosylation fact 100.0 3.7E-29 8E-34 249.9 15.6 113 15-127 9-130 (395)
9 KOG0706 Predicted GTPase-activ 99.9 7.4E-28 1.6E-32 245.3 6.8 86 14-99 9-94 (454)
10 KOG0705 GTPase-activating prot 99.9 6.9E-26 1.5E-30 236.2 6.0 114 15-128 500-619 (749)
11 KOG0521 Putative GTPase activa 99.9 3.8E-23 8.2E-28 225.9 3.6 111 18-128 416-534 (785)
12 KOG0702 Predicted GTPase-activ 99.8 1.8E-19 3.9E-24 185.9 14.5 125 9-134 6-138 (524)
13 KOG0818 GTPase-activating prot 99.8 1E-19 2.2E-24 188.1 3.5 102 24-125 4-119 (669)
14 KOG1117 Rho- and Arf-GTPase ac 99.7 4.5E-18 9.7E-23 183.8 3.4 108 20-127 290-405 (1186)
15 KOG0521 Putative GTPase activa 94.5 0.0092 2E-07 67.1 -0.4 74 23-98 625-699 (785)
16 PF00643 zf-B_box: B-box zinc 79.4 1.2 2.7E-05 31.4 1.7 34 27-60 2-36 (42)
17 PRK00085 recO DNA repair prote 77.4 1.6 3.4E-05 41.6 2.2 31 25-55 146-177 (247)
18 PRK12495 hypothetical protein; 73.3 2 4.3E-05 42.1 1.7 39 15-57 27-67 (226)
19 TIGR00613 reco DNA repair prot 70.1 5.7 0.00012 37.7 4.1 33 25-57 144-177 (241)
20 PRK11019 hypothetical protein; 66.1 3.1 6.7E-05 35.3 1.2 36 27-63 35-72 (88)
21 KOG3362 Predicted BBOX Zn-fing 61.4 2.7 5.8E-05 38.9 -0.0 34 26-60 116-150 (156)
22 PF11781 RRN7: RNA polymerase 60.7 4.7 0.0001 28.7 1.1 27 26-55 6-32 (36)
23 COG1734 DksA DnaK suppressor p 60.1 5.3 0.00011 35.6 1.6 30 30-59 82-112 (120)
24 PRK11788 tetratricopeptide rep 59.0 6.5 0.00014 38.7 2.2 38 15-58 341-378 (389)
25 TIGR02419 C4_traR_proteo phage 58.7 5.9 0.00013 31.3 1.5 34 24-58 27-62 (63)
26 COG1381 RecO Recombinational D 56.3 5.8 0.00013 38.9 1.4 31 25-55 151-182 (251)
27 PRK13715 conjugal transfer pro 54.7 7.1 0.00015 31.9 1.4 33 28-60 34-67 (73)
28 smart00401 ZnF_GATA zinc finge 52.5 9 0.0002 29.1 1.6 37 27-63 2-40 (52)
29 PF01286 XPA_N: XPA protein N- 52.1 3.9 8.4E-05 29.1 -0.5 27 29-55 4-31 (34)
30 PF08271 TF_Zn_Ribbon: TFIIB z 51.2 3.6 7.9E-05 29.7 -0.7 27 30-57 2-28 (43)
31 PRK10778 dksA RNA polymerase-b 48.3 12 0.00026 34.4 2.0 38 24-61 107-145 (151)
32 PF00320 GATA: GATA zinc finge 47.3 10 0.00023 26.6 1.1 32 31-62 1-34 (36)
33 TIGR02890 spore_yteA sporulati 42.9 16 0.00034 34.0 1.9 34 26-60 84-119 (159)
34 PHA00080 DksA-like zinc finger 38.9 22 0.00048 28.9 2.0 35 25-60 28-64 (72)
35 cd00202 ZnF_GATA Zinc finger D 35.1 37 0.0008 26.1 2.6 33 30-62 1-35 (54)
36 PF01258 zf-dskA_traR: Prokary 33.6 6.9 0.00015 27.3 -1.5 29 30-58 5-34 (36)
37 PTZ00218 40S ribosomal protein 32.1 24 0.00053 27.6 1.1 39 26-69 14-52 (54)
38 cd07171 NR_DBD_ER DNA-binding 29.5 30 0.00064 28.7 1.3 31 27-60 2-32 (82)
39 cd07173 NR_DBD_AR DNA-binding 29.2 41 0.0009 27.8 2.1 31 27-60 2-32 (82)
40 PRK00423 tfb transcription ini 28.9 22 0.00047 36.0 0.5 33 26-59 9-41 (310)
41 COG2174 RPL34A Ribosomal prote 27.9 37 0.0008 29.3 1.6 33 24-56 30-79 (93)
42 cd06968 NR_DBD_ROR DNA-binding 27.2 38 0.00083 28.8 1.6 31 27-60 4-34 (95)
43 KOG0457 Histone acetyltransfer 27.0 69 0.0015 34.5 3.7 93 25-123 10-124 (438)
44 PF06752 E_Pc_C: Enhancer of P 26.5 40 0.00088 33.4 1.8 15 330-344 7-21 (230)
45 PF14803 Nudix_N_2: Nudix N-te 26.1 11 0.00024 26.6 -1.5 30 29-59 1-33 (34)
46 cd07170 NR_DBD_ERR DNA-binding 25.6 39 0.00085 28.9 1.4 30 28-60 4-33 (97)
47 cd07160 NR_DBD_LXR DNA-binding 25.0 40 0.00087 29.1 1.3 31 27-60 17-47 (101)
48 COG1997 RPL43A Ribosomal prote 24.7 44 0.00096 28.7 1.5 30 26-57 33-62 (89)
49 PF14471 DUF4428: Domain of un 24.7 36 0.00079 25.9 0.9 30 30-60 1-32 (51)
50 smart00782 PhnA_Zn_Ribbon PhnA 24.7 45 0.00097 25.2 1.4 33 23-56 3-44 (47)
51 COG0675 Transposase and inacti 24.3 19 0.00041 34.6 -0.8 24 27-57 308-331 (364)
52 PF04770 ZF-HD_dimer: ZF-HD pr 24.3 26 0.00056 28.0 0.1 31 30-61 20-52 (60)
53 PF07282 OrfB_Zn_ribbon: Putat 24.1 27 0.00058 27.1 0.1 28 27-56 27-54 (69)
54 TIGR02420 dksA RNA polymerase- 23.8 49 0.0011 28.5 1.7 31 25-55 77-108 (110)
55 cd07165 NR_DBD_DmE78_like DNA- 23.8 53 0.0011 26.9 1.8 27 31-60 1-27 (81)
56 COG1592 Rubrerythrin [Energy p 23.5 35 0.00075 32.2 0.7 22 9-30 112-133 (166)
57 smart00290 ZnF_UBP Ubiquitin C 23.3 58 0.0013 23.6 1.8 24 30-53 1-24 (50)
58 cd06966 NR_DBD_CAR DNA-binding 22.2 31 0.00067 29.3 0.1 29 29-60 1-29 (94)
59 PF13462 Thioredoxin_4: Thiore 22.0 50 0.0011 28.5 1.4 28 35-62 8-35 (162)
60 cd07162 NR_DBD_PXR DNA-binding 21.7 57 0.0012 27.1 1.6 28 30-60 1-28 (87)
61 cd07169 NR_DBD_GCNF_like DNA-b 21.1 52 0.0011 27.7 1.3 32 26-60 4-35 (90)
62 PF10764 Gin: Inhibitor of sig 21.0 42 0.0009 25.2 0.6 26 30-56 1-26 (46)
63 PF12760 Zn_Tnp_IS1595: Transp 20.6 79 0.0017 23.1 2.0 40 14-55 5-44 (46)
64 cd07158 NR_DBD_Ppar_like The D 20.0 64 0.0014 25.8 1.5 27 31-60 1-27 (73)
No 1
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=1.1e-45 Score=360.61 Aligned_cols=276 Identities=36% Similarity=0.516 Sum_probs=187.0
Q ss_pred ccHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCeeEcccchHhhHhhhHHhhcCCCccceeeecccCCCCHHHHHHHHh
Q 015009 7 VSKELNARHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQS 86 (414)
Q Consensus 7 ~sk~~~~r~~kiL~~Llk~PgNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~LG~hISkVKSlsLD~Wt~eeV~~L~~ 86 (414)
+.+...++++++|++||+.|+|++|||||+.+|+|||+|+|||||++|+||||+||+|||+||||+||.|++|+|+.|+.
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 34456779999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hCchHHHHHHhhcCCCCCChh----HHHHHHHHHhhhcccccCCCCCCCCCCccccccccccCCCCCCCCCCCCCCCcch
Q 015009 87 MGNEKANSYWEAELPPNYDRV----GIENFIRAKYEEKRWVSRDGQANSPPRGLEEKASIHWQRPGEKSGHGYTDNSENL 162 (414)
Q Consensus 87 ~GN~~aN~iwea~lPp~~d~~----~~e~FIraKY~eKrf~~~~~~~~~ps~~~~ek~~~~~~r~~~~~g~~~~~s~~~~ 162 (414)
+||.++|.|||+++|..+++. .+|+|||+|||.|+|+.++..--...+..++... |...+..+.....+..
T Consensus 84 ~GN~~an~~~ea~~p~~~~~p~~d~~~e~FIR~KYE~kkf~~~~~~~~s~~~~~~~~~k----~~~~~~~~~~~s~s~~- 158 (287)
T KOG0703|consen 84 MGNAKANSYYEAKLPDPFRRPGPDDLVEQFIRDKYERKKFLDPEEDITSKPGSRDEESK----RSDKRSRKLSSSLSRS- 158 (287)
T ss_pred HcchhhhhhccccCCccccCCChHHHHHHHHHHHHhhhhhccchhhcccCCCccccccc----ccccCccccccchhhh-
Confidence 999999999999999887654 4999999999999999875111111112212111 1112222222222222
Q ss_pred hHhhhcCCCCCCCCCCccccccCCCCCCCCCCcccCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCcccchhhhhccCCC
Q 015009 163 SEERKHVQAPSTKDSVPAARISLPLPPRGPDQVVAITKPQQTESTVAPAGATNQSSDANLAVPPPKVDFASDLFDMLSGD 242 (414)
Q Consensus 163 f~er~~~~~~~~~~~~~a~r~~~~~~~k~~~~v~~~pkpq~~~p~~~~~~~~~~~~~~~~~~~~pk~~~~~dlf~mL~md 242 (414)
|-........ . ..++... . +.+ ....+...+.......++. +|+++|.++
T Consensus 159 ~~~~~r~~~~-------~--~~~~~~s------~--~~~------------~~~~~~~~~~~i~~~~~~~-~~~s~~n~~ 208 (287)
T KOG0703|consen 159 FVKSAREDQL-------K--YFLPKTS------Q--PVD------------DLATFQGPIASPHNLQTTY-SLNSTLNIF 208 (287)
T ss_pred hhhhcccccc-------c--cccccCC------C--Cch------------hhhhccCccccccchheee-ccccccccc
Confidence 2221111111 0 0000000 0 000 0011111123456666777 888887777
Q ss_pred CCCCCCccc----cccCcccccccccccccCcccccCCCcccccCCCCcccccccccCCCCCCCCCCCCCCcchhhhhHH
Q 015009 243 SPNENSSEA----ASADDNLWAGFQSAVETSTAEKKDSTKAVESSPQSATGIEDLFKDSPSLATPSSSEKPQKDLKNDIM 318 (414)
Q Consensus 243 ~~~e~~s~a----~~~dd~~~agFqsA~~~s~a~k~~~~~~~es~~~s~~g~edlFkds~~~~~~~~~~~~~k~~k~dIm 318 (414)
+ +..++ + +.+..|+.|+.+...-+ +...+..+..+....-.+.+ ++++.+..+. . . .|+
T Consensus 209 ~---~~~~~~~~~~-~~~~~~~~~~~~~~~~~-~~~~~~~~~~s~~~~f~~~~-~~~~~~~~~~----~------~-~~~ 271 (287)
T KOG0703|consen 209 G---SGKEAADSFT-LRAARFAPLAVAFSTVT-EDLVPFLQRNSLSEGFMEKT-LSKPKRWFGT----Q------Q-SKS 271 (287)
T ss_pred c---CccccCCCcc-cccccccccccccccCc-cccccccccccccccccCcc-cccccccccc----C------c-ccc
Confidence 7 22222 4 88899999999877666 66666666556555555555 7777333322 2 4 899
Q ss_pred HhhccCCcCCCchhhHH
Q 015009 319 SLFEKSNMVSPFAMHQQ 335 (414)
Q Consensus 319 sLfeks~~~spf~~~qq 335 (414)
+|| +-..+.||..++|
T Consensus 272 ~~~-~~~~~~~~~~~~~ 287 (287)
T KOG0703|consen 272 SLF-FLDGNVPFGSKES 287 (287)
T ss_pred ccc-cccccccccccCC
Confidence 999 9999999987764
No 2
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=100.00 E-value=6.1e-42 Score=355.64 Aligned_cols=161 Identities=29% Similarity=0.570 Sum_probs=149.4
Q ss_pred cHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCeeEcccchHhhHhhhHHhhcCCCccceeeecccCCCCHHHHHHHHhh
Q 015009 8 SKELNARHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSM 87 (414)
Q Consensus 8 sk~~~~r~~kiL~~Llk~PgNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~LG~hISkVKSlsLD~Wt~eeV~~L~~~ 87 (414)
|||+++|+++||++|+++|+|++|+|||..+|+|||++||||||+.|+||||+|| +|||||+||+|+++||++|+.+
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 5999999999999999999999
Q ss_pred CchHHHHHHhhcCCC-------CCChhHHHHHHHHHhhhcccccCCCCCCCCCCccccccccccCCCCCCCCCCCCCCCc
Q 015009 88 GNEKANSYWEAELPP-------NYDRVGIENFIRAKYEEKRWVSRDGQANSPPRGLEEKASIHWQRPGEKSGHGYTDNSE 160 (414)
Q Consensus 88 GN~~aN~iwea~lPp-------~~d~~~~e~FIraKY~eKrf~~~~~~~~~ps~~~~ek~~~~~~r~~~~~g~~~~~s~~ 160 (414)
||.++|+|||++|++ ..+...+++|||.||++|+|+.+...++++++.+++++++...|+ .++||+|++|++
T Consensus 80 GN~~AN~iyeanw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~~~~~~d~p~~~~~~~~~~~~~~~~-~~s~h~~s~sp~ 158 (648)
T PLN03119 80 GNQRAREIYLKNWDHQRQRLPENSNAERVREFIKNVYVQKKYAGANDADKPSKDSQDHVSSEDMTRR-ANSYHSYSQSPP 158 (648)
T ss_pred chHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhccCcCCCCCCcccccccccccccccc-cccCCCCCCCCC
Confidence 999999999998753 345567899999999999999999999999999999998876665 999999999998
Q ss_pred --chhHhhhcCCCC
Q 015009 161 --NLSEERKHVQAP 172 (414)
Q Consensus 161 --~~f~er~~~~~~ 172 (414)
++|||||..+-.
T Consensus 159 y~~~ye~rr~~~~~ 172 (648)
T PLN03119 159 YDYQYEERRYGKIP 172 (648)
T ss_pred cccchhhhhccccc
Confidence 889999987655
No 3
>PLN03131 hypothetical protein; Provisional
Probab=100.00 E-value=7.1e-40 Score=342.51 Aligned_cols=158 Identities=29% Similarity=0.538 Sum_probs=144.6
Q ss_pred cHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCeeEcccchHhhHhhhHHhhcCCCccceeeecccCCCCHHHHHHHHhh
Q 015009 8 SKELNARHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSM 87 (414)
Q Consensus 8 sk~~~~r~~kiL~~Llk~PgNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~LG~hISkVKSlsLD~Wt~eeV~~L~~~ 87 (414)
||+++++++++|++|+++|+|++|+|||+++|+|||++||||||+.|+||||+|| +|||||+||+|++++|++|+.+
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-------CCCChhHHHHHHHHHhhhcccccCCCCCCCCCCccccccccccCCCCCCCCCCCCCCCc
Q 015009 88 GNEKANSYWEAELP-------PNYDRVGIENFIRAKYEEKRWVSRDGQANSPPRGLEEKASIHWQRPGEKSGHGYTDNSE 160 (414)
Q Consensus 88 GN~~aN~iwea~lP-------p~~d~~~~e~FIraKY~eKrf~~~~~~~~~ps~~~~ek~~~~~~r~~~~~g~~~~~s~~ 160 (414)
||.++|+|||++|+ ...+...+++|||.||++|+|+.....++++...+..+..+...|+ ..++|+|++|+.
T Consensus 80 GN~~AN~iyeanwd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa~~~s~d~pprd~q~~r~~e~e~rr-~~syh~~SqSPp 158 (705)
T PLN03131 80 GNQRAREIYLKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKYAGGKTHDKPPRDLQRIRSHEDETRR-ACSYHSYSQSPP 158 (705)
T ss_pred ccHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhhhcCCCCCCCchhhhhhhcccccccc-cccccCCCcCCC
Confidence 99999999999874 3345567899999999999999999888888888888888777887 789999999998
Q ss_pred --chhHhhhcC
Q 015009 161 --NLSEERKHV 169 (414)
Q Consensus 161 --~~f~er~~~ 169 (414)
++|||||..
T Consensus 159 Y~~~yedrRyg 169 (705)
T PLN03131 159 YDFQYEDRRYG 169 (705)
T ss_pred ccccccccccc
Confidence 579999763
No 4
>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=3.7e-38 Score=271.51 Aligned_cols=109 Identities=58% Similarity=1.053 Sum_probs=91.0
Q ss_pred HHHHHhhcCCCCCCCCCCCCCCCCeeEcccchHhhHhhhHHhhcCCCccceeeecccCCCCHHHHHHHHhhCchHHHHHH
Q 015009 17 KILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYW 96 (414)
Q Consensus 17 kiL~~Llk~PgNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~LG~hISkVKSlsLD~Wt~eeV~~L~~~GN~~aN~iw 96 (414)
++|+.|++.|+|++|+|||+++|+|||++||||||+.|+|+||+||+|||+||||+||+|++++|+.|+.+||.++|++|
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------CCCChhHHHHHHHHHhhhcccccC
Q 015009 97 EAELP------PNYDRVGIENFIRAKYEEKRWVSR 125 (414)
Q Consensus 97 ea~lP------p~~d~~~~e~FIraKY~eKrf~~~ 125 (414)
|++.+ +..+...+++||++||++++|+.+
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 233456799999999999999863
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=1.4e-36 Score=260.55 Aligned_cols=103 Identities=58% Similarity=1.018 Sum_probs=96.1
Q ss_pred CCCCCCCCCCCCCCCeeEcccchHhhHhhhHHhhcCCCccceeeecccCCCCHHHHHHHHhhCchHHHHHHhhcCCCCC-
Q 015009 26 PENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYWEAELPPNY- 104 (414)
Q Consensus 26 PgNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~LG~hISkVKSlsLD~Wt~eeV~~L~~~GN~~aN~iwea~lPp~~- 104 (414)
|+|++|||||+++|+|||++||||||+.|+|+||.||+|||+||||+||+|++++|++|+.+||.++|+|||+++++..
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 ------ChhHHHHHHHHHhhhcccccCCCC
Q 015009 105 ------DRVGIENFIRAKYEEKRWVSRDGQ 128 (414)
Q Consensus 105 ------d~~~~e~FIraKY~eKrf~~~~~~ 128 (414)
+...+++||+.||++++|+.+.+.
T Consensus 81 ~~~~~~~~~~~~~fI~~KY~~k~f~~~~~~ 110 (112)
T smart00105 81 KPPDSDDQQKYESFIAAKYEEKLFVPPESA 110 (112)
T ss_pred CCCCCchHHHHHHHHHHHHHhhhccccccC
Confidence 356799999999999999987654
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=1.2e-33 Score=281.00 Aligned_cols=113 Identities=47% Similarity=0.891 Sum_probs=104.5
Q ss_pred HHHHHHHHHhhcCCCCCCCCCCCCCCCCeeEcccchHhhHhhhHHhhcCCCccceeeecccCCCCHHHHHHHHhhCchHH
Q 015009 13 ARHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKA 92 (414)
Q Consensus 13 ~r~~kiL~~Llk~PgNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~LG~hISkVKSlsLD~Wt~eeV~~L~~~GN~~a 92 (414)
...+++|..|.+.++|+.|||||+++|+|||++||||||++|+||||+||+||++||||+||+|+.+||++|..+||.++
T Consensus 5 ~~~~~~l~~l~~~~~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~wt~~~l~~m~~gGN~~a 84 (319)
T COG5347 5 SEDRKLLKLLKSDSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWTEEELRRMEVGGNSNA 84 (319)
T ss_pred hHHHHHHHHHhhccccCccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeecccCCHHHHHHHHHhcchhh
Confidence 35678888889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhcCC--------CCCChhHHHHHHHHHhhhcccccC
Q 015009 93 NSYWEAELP--------PNYDRVGIENFIRAKYEEKRWVSR 125 (414)
Q Consensus 93 N~iwea~lP--------p~~d~~~~e~FIraKY~eKrf~~~ 125 (414)
|.||+.++- ..||..-+++||+.||+.++|...
T Consensus 85 ~~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~ 125 (319)
T COG5347 85 NRFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDD 125 (319)
T ss_pred hhHhccCCCcccccccccccCHHHHHHHHHHHHHhhhcccc
Confidence 999998642 345667799999999999999976
No 7
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=99.96 E-value=8.9e-30 Score=253.00 Aligned_cols=110 Identities=39% Similarity=0.740 Sum_probs=94.4
Q ss_pred HHHHHHHHHhhcCCCCCCCCCCCCCCCCeeEcccchHhhHhhhHHhhcCCCccceeeecccCCCCHHHHHHHHhhCchHH
Q 015009 13 ARHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKA 92 (414)
Q Consensus 13 ~r~~kiL~~Llk~PgNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~LG~hISkVKSlsLD~Wt~eeV~~L~~~GN~~a 92 (414)
.|.++.|.+|....+|+.|+||++.+|+|||++||||||++|+|+||.||+|||+|||||||+|.+.||+.|+.+||+++
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 46788888887778999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhcC--CCC------CCh---hHHHHHHHHHhhhccc
Q 015009 93 NSYWEAEL--PPN------YDR---VGIENFIRAKYEEKRW 122 (414)
Q Consensus 93 N~iwea~l--Pp~------~d~---~~~e~FIraKY~eKrf 122 (414)
+.|++.+- .+. |+- ..+++-|.+--+.+.|
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 99998652 222 221 2356667777777777
No 8
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.96 E-value=3.7e-29 Score=249.93 Aligned_cols=113 Identities=38% Similarity=0.666 Sum_probs=98.2
Q ss_pred HHHHHHHhhcCCCCCCCCCCCCCCCCeeEcccchHhhHhhhHHhhcCCCccceeeecccCCCCHHHHHHHHhhCchHHHH
Q 015009 15 HRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANS 94 (414)
Q Consensus 15 ~~kiL~~Llk~PgNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~LG~hISkVKSlsLD~Wt~eeV~~L~~~GN~~aN~ 94 (414)
..++|+.|+.+|+|++|+|||+++|+|+|++||||||+.|+||||.||+||++|||++||.|++++|++|+.+||.++|.
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 45679999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcC-CC------CCCh--hHHHHHHHHHhhhcccccCCC
Q 015009 95 YWEAEL-PP------NYDR--VGIENFIRAKYEEKRWVSRDG 127 (414)
Q Consensus 95 iwea~l-Pp------~~d~--~~~e~FIraKY~eKrf~~~~~ 127 (414)
||+.+. .. .|.- ..+.+-+.+|++++.+..+..
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 1221 234556888999998876543
No 9
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.94 E-value=7.4e-28 Score=245.27 Aligned_cols=86 Identities=45% Similarity=0.842 Sum_probs=83.0
Q ss_pred HHHHHHHHhhcCCCCCCCCCCCCCCCCeeEcccchHhhHhhhHHhhcCCCccceeeecccCCCCHHHHHHHHhhCchHHH
Q 015009 14 RHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKAN 93 (414)
Q Consensus 14 r~~kiL~~Llk~PgNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~LG~hISkVKSlsLD~Wt~eeV~~L~~~GN~~aN 93 (414)
....+++.|...++||.|+|||+++|+|+||+||||||+.|+++||+||+||++|||..||.|+.+||++|+.|||.+|+
T Consensus 9 d~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~ 88 (454)
T KOG0706|consen 9 DIQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANAR 88 (454)
T ss_pred hHHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHH
Confidence 45678899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhc
Q 015009 94 SYWEAE 99 (414)
Q Consensus 94 ~iwea~ 99 (414)
.|+..+
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=99.92 E-value=6.9e-26 Score=236.21 Aligned_cols=114 Identities=42% Similarity=0.841 Sum_probs=104.1
Q ss_pred HHHHHHHhhcCCCCCCCCCCCCCCCCeeEcccchHhhHhhhHHhhcCCCccceeeecccCCCCHHHHHHHHhhCchHHHH
Q 015009 15 HRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANS 94 (414)
Q Consensus 15 ~~kiL~~Llk~PgNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~LG~hISkVKSlsLD~Wt~eeV~~L~~~GN~~aN~ 94 (414)
....|+.+...+||.+|+||+.++|.|+|+|+|+.+|++|+||||.||.|+|+||||.||.|..|.+..|..+||+.||.
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 44567888889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcC-----C-CCCChhHHHHHHHHHhhhcccccCCCC
Q 015009 95 YWEAEL-----P-PNYDRVGIENFIRAKYEEKRWVSRDGQ 128 (414)
Q Consensus 95 iwea~l-----P-p~~d~~~~e~FIraKY~eKrf~~~~~~ 128 (414)
+||..+ | +.+.++++|+|||+||++|.|......
T Consensus 580 vWE~~~~G~~KPs~~s~REEkErwIr~KYeqklFLaPl~~ 619 (749)
T KOG0705|consen 580 VWEGSSQGQTKPSPDSSREEKERWIRAKYEQKLFLAPLPC 619 (749)
T ss_pred HhhhhccCCcCCCccccHHHHHHHHHHHHHHHhhcCCCCC
Confidence 999753 2 345678999999999999999986654
No 11
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.87 E-value=3.8e-23 Score=225.90 Aligned_cols=111 Identities=48% Similarity=0.926 Sum_probs=102.2
Q ss_pred HHHHhhcCCCCCCCCCCCCCCCCeeEcccchHhhHhhhHHhhcCCCccceeeecccCCCCHHHHHHHHhhCchHHHHHHh
Q 015009 18 ILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYWE 97 (414)
Q Consensus 18 iL~~Llk~PgNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~LG~hISkVKSlsLD~Wt~eeV~~L~~~GN~~aN~iwe 97 (414)
.+..+.+.|+|..|+|||++.|+|+++|+||.+|++|+|+||+||+|||+|+||+||.|.++.+..++.+||..+|.+||
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 47788899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCC--------CChhHHHHHHHHHhhhcccccCCCC
Q 015009 98 AELPPN--------YDRVGIENFIRAKYEEKRWVSRDGQ 128 (414)
Q Consensus 98 a~lPp~--------~d~~~~e~FIraKY~eKrf~~~~~~ 128 (414)
+.++.. .++..++.||++||++++|..+...
T Consensus 496 ~~l~~~~~~~~~~~~~~~~r~~~i~~kyve~~F~~k~~~ 534 (785)
T KOG0521|consen 496 ALLPSYDSSKPTASSSRQAREAWIKAKYVERRFSVKEPQ 534 (785)
T ss_pred cccccccccCCCCccchhhhhHhhhcccceeeEeecccc
Confidence 998632 2356799999999999999876543
No 12
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.81 E-value=1.8e-19 Score=185.94 Aligned_cols=125 Identities=30% Similarity=0.573 Sum_probs=110.6
Q ss_pred HHHHHHHHHHHHHhhcCCCCCCCCCCCCCCC-CeeEcccchHhhHhhhHHhhcCCCccceeeecccCCCCHHHHHHHHhh
Q 015009 9 KELNARHRKILEGLLKLPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSM 87 (414)
Q Consensus 9 k~~~~r~~kiL~~Llk~PgNk~CADCGa~~P-~WaSvn~GVFlC~~CSgIHR~LG~hISkVKSlsLD~Wt~eeV~~L~~~ 87 (414)
|+.++.++++||+|+++|+|++|++|....+ +|+++.-|-|+|+.|+|.-|.|.. -+|||||+|.+|+..||..|+.+
T Consensus 6 ke~E~~~ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~~-ahRvksiSmttft~qevs~lQsh 84 (524)
T KOG0702|consen 6 KEDEYDYEKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLNP-AHRVKSISMTTFTDQEVSFLQSH 84 (524)
T ss_pred ccchhHHHHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccCCC-ccccceeeeeeccccchHHHhhc
Confidence 4444556999999999999999999999988 999999999999999999999864 47999999999999999999999
Q ss_pred CchHHHHHHhhc-------CCCCCChhHHHHHHHHHhhhcccccCCCCCCCCCC
Q 015009 88 GNEKANSYWEAE-------LPPNYDRVGIENFIRAKYEEKRWVSRDGQANSPPR 134 (414)
Q Consensus 88 GN~~aN~iwea~-------lPp~~d~~~~e~FIraKY~eKrf~~~~~~~~~ps~ 134 (414)
||+.+.+||..- +|+..+....++|||.||+.|+|+-.....+.++.
T Consensus 85 gNq~~k~i~fkl~D~q~S~vPD~rn~~~~kef~q~~y~~kr~~v~~n~~k~~s~ 138 (524)
T KOG0702|consen 85 GNQVCKEIWFKLFDFQRSNVPDSRNPQKVKEFQQEKYVKKRYYVPKNQMKIPSY 138 (524)
T ss_pred chhhhhhhhhcchhhhhccCCCcccchhhHHHHhhhhccceeecCccccccccc
Confidence 999999999753 57777778899999999999999987666554443
No 13
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.77 E-value=1e-19 Score=188.09 Aligned_cols=102 Identities=42% Similarity=0.804 Sum_probs=91.2
Q ss_pred cCCCCCCCCCCCCCCCCeeEcccchHhhHhhhHHhhcCCCccceeeecccCCCCHHHHHHHHhhCchHHHHHHhhcCCC-
Q 015009 24 KLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYWEAELPP- 102 (414)
Q Consensus 24 k~PgNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~LG~hISkVKSlsLD~Wt~eeV~~L~~~GN~~aN~iwea~lPp- 102 (414)
+...-+.|+|||+++|.|+|++-|+|||.+|+.+||.||.|||.||+|.-..|.++-|.+...+.|..+|.|||..|=+
T Consensus 4 ~~l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaNsIWEh~Lld~ 83 (669)
T KOG0818|consen 4 RLLSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGANSIWEHSLLDP 83 (669)
T ss_pred cchhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcchhhhhhccCc
Confidence 3456689999999999999999999999999999999999999999999999999999999999999999999987522
Q ss_pred -----------CCCh--hHHHHHHHHHhhhcccccC
Q 015009 103 -----------NYDR--VGIENFIRAKYEEKRWVSR 125 (414)
Q Consensus 103 -----------~~d~--~~~e~FIraKY~eKrf~~~ 125 (414)
..|. ..+++|||+||+...|+.+
T Consensus 84 st~~sg~rk~~pqD~~Hp~K~eFIkaKy~~LtFv~~ 119 (669)
T KOG0818|consen 84 ATIMSGRRKANPQDKVHPNKAEFIRAKYQMLAFVHR 119 (669)
T ss_pred hhhhcccCCCCCcCCCCccHHHHHHHHHHheeeecc
Confidence 1232 2489999999999999984
No 14
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.70 E-value=4.5e-18 Score=183.77 Aligned_cols=108 Identities=43% Similarity=0.802 Sum_probs=98.4
Q ss_pred HHhhcCCCCCCCCCCCCCCCCeeEcccchHhhHhhhHHhhcCCCccceeeecccCC--CCHHHHHHHHhhCchHHHHHHh
Q 015009 20 EGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDT--WLPEQVAFIQSMGNEKANSYWE 97 (414)
Q Consensus 20 ~~Llk~PgNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~LG~hISkVKSlsLD~--Wt~eeV~~L~~~GN~~aN~iwe 97 (414)
+++.....|+.|+|||+..|.|+++|+++.||-.|+|-||.||..+|+|+|++||. |+.+-|+++..+||.++|.||-
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 45667889999999999999999999999999999999999999999999999996 9999999999999999999999
Q ss_pred hcCCCCC------ChhHHHHHHHHHhhhcccccCCC
Q 015009 98 AELPPNY------DRVGIENFIRAKYEEKRWVSRDG 127 (414)
Q Consensus 98 a~lPp~~------d~~~~e~FIraKY~eKrf~~~~~ 127 (414)
.++|++. ....|++||..||.+.+|.....
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 33579999999999998876543
No 15
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=94.51 E-value=0.0092 Score=67.09 Aligned_cols=74 Identities=20% Similarity=0.237 Sum_probs=62.8
Q ss_pred hcCCCCCCCCCCCCC-CCCeeEcccchHhhHhhhHHhhcCCCccceeeecccCCCCHHHHHHHHhhCchHHHHHHhh
Q 015009 23 LKLPENRECADCKAK-GPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYWEA 98 (414)
Q Consensus 23 lk~PgNk~CADCGa~-~P~WaSvn~GVFlC~~CSgIHR~LG~hISkVKSlsLD~Wt~eeV~~L~~~GN~~aN~iwea 98 (414)
.....+-.|++|++. ...|+++++.+-+|+.|+++|+.++.|++..+++.|++..+ |..+..-|+...+..|..
T Consensus 625 ~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~~~~~ 699 (785)
T KOG0521|consen 625 VKASSDGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHHATAS 699 (785)
T ss_pred HHhccCccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchhhhhh
Confidence 344568899999876 78999999999999999999999999999999999988766 777777788777776653
No 16
>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=79.42 E-value=1.2 Score=31.36 Aligned_cols=34 Identities=12% Similarity=0.335 Sum_probs=29.5
Q ss_pred CCCCCCCCCCCCCCeeEcccchHhhHhhhHH-hhc
Q 015009 27 ENRECADCKAKGPRWASVNLGIFICMQCSGI-HRS 60 (414)
Q Consensus 27 gNk~CADCGa~~P~WaSvn~GVFlC~~CSgI-HR~ 60 (414)
.+..|..|+.....|.+.+-+++||..|... |+.
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 3578999999889999999999999999998 886
No 17
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=77.40 E-value=1.6 Score=41.62 Aligned_cols=31 Identities=32% Similarity=0.578 Sum_probs=26.7
Q ss_pred CCCCCCCCCCCCCCC-CeeEcccchHhhHhhh
Q 015009 25 LPENRECADCKAKGP-RWASVNLGIFICMQCS 55 (414)
Q Consensus 25 ~PgNk~CADCGa~~P-~WaSvn~GVFlC~~CS 55 (414)
.|.-..|+-||.... .|.+...|.++|..|.
T Consensus 146 ~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 146 GLDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred ccchhhHhcCCCCCCceEEecccCCccccccc
Confidence 466679999998754 7899999999999997
No 18
>PRK12495 hypothetical protein; Provisional
Probab=73.27 E-value=2 Score=42.12 Aligned_cols=39 Identities=26% Similarity=0.392 Sum_probs=28.6
Q ss_pred HHHHHHHhhc--CCCCCCCCCCCCCCCCeeEcccchHhhHhhhHH
Q 015009 15 HRKILEGLLK--LPENRECADCKAKGPRWASVNLGIFICMQCSGI 57 (414)
Q Consensus 15 ~~kiL~~Llk--~PgNk~CADCGa~~P~WaSvn~GVFlC~~CSgI 57 (414)
.+++-+.|++ ...+.+|-+||.+=|.+ -|+.+|..|..+
T Consensus 27 ~~~ma~lL~~gatmsa~hC~~CG~PIpa~----pG~~~Cp~CQ~~ 67 (226)
T PRK12495 27 TERMSELLLQGATMTNAHCDECGDPIFRH----DGQEFCPTCQQP 67 (226)
T ss_pred HHHHHHHHHhhcccchhhcccccCcccCC----CCeeECCCCCCc
Confidence 3444444454 47899999999998832 699999999744
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=70.11 E-value=5.7 Score=37.70 Aligned_cols=33 Identities=27% Similarity=0.497 Sum_probs=27.1
Q ss_pred CCCCCCCCCCCCCCC-CeeEcccchHhhHhhhHH
Q 015009 25 LPENRECADCKAKGP-RWASVNLGIFICMQCSGI 57 (414)
Q Consensus 25 ~PgNk~CADCGa~~P-~WaSvn~GVFlC~~CSgI 57 (414)
.|.-..|+.||..++ .|.++..|.|+|..|...
T Consensus 144 ~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 144 ALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred CcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 467789999998544 688999999999999753
No 20
>PRK11019 hypothetical protein; Provisional
Probab=66.09 E-value=3.1 Score=35.34 Aligned_cols=36 Identities=22% Similarity=0.553 Sum_probs=25.4
Q ss_pred CCCCCCCCCCCCC--CeeEcccchHhhHhhhHHhhcCCC
Q 015009 27 ENRECADCKAKGP--RWASVNLGIFICMQCSGIHRSLGV 63 (414)
Q Consensus 27 gNk~CADCGa~~P--~WaSvn~GVFlC~~CSgIHR~LG~ 63 (414)
.-.+|.|||.+=| +|--+. ++-.|+.|...+...+.
T Consensus 35 syg~C~~CG~~Ip~~Rl~A~P-~a~~Cv~Cq~~~E~~~k 72 (88)
T PRK11019 35 SLTECEECGEPIPEARRKAIP-GVRLCVACQQEKDLQQA 72 (88)
T ss_pred cCCeeCcCCCcCcHHHHhhcC-CccccHHHHHHHHHHHh
Confidence 4579999999733 343333 67899999998765443
No 21
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=61.38 E-value=2.7 Score=38.92 Aligned_cols=34 Identities=29% Similarity=0.640 Sum_probs=28.7
Q ss_pred CCCCCCCCCCCCCCCeeEcccchHhhH-hhhHHhhc
Q 015009 26 PENRECADCKAKGPRWASVNLGIFICM-QCSGIHRS 60 (414)
Q Consensus 26 PgNk~CADCGa~~P~WaSvn~GVFlC~-~CSgIHR~ 60 (414)
|--++|+-|| ...-|.+++.|.-+|. .|-.+|..
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 6677999999999985 89999965
No 22
>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=60.68 E-value=4.7 Score=28.71 Aligned_cols=27 Identities=26% Similarity=0.812 Sum_probs=23.4
Q ss_pred CCCCCCCCCCCCCCCeeEcccchHhhHhhh
Q 015009 26 PENRECADCKAKGPRWASVNLGIFICMQCS 55 (414)
Q Consensus 26 PgNk~CADCGa~~P~WaSvn~GVFlC~~CS 55 (414)
..|..|..|++. |....=|.++|.+|.
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCc
Confidence 456679999998 999999999999995
No 23
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=60.10 E-value=5.3 Score=35.63 Aligned_cols=30 Identities=17% Similarity=0.454 Sum_probs=20.7
Q ss_pred CCCCCCCCCC-CeeEcccchHhhHhhhHHhh
Q 015009 30 ECADCKAKGP-RWASVNLGIFICMQCSGIHR 59 (414)
Q Consensus 30 ~CADCGa~~P-~WaSvn~GVFlC~~CSgIHR 59 (414)
+|.+||.+=| .=.-.--+..+|+.|...|-
T Consensus 82 ~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~~E 112 (120)
T COG1734 82 ICEECGEPIPEARLEARPTARLCIECQERAE 112 (120)
T ss_pred chhccCCcCCHHHHhhCcchHHHHHHHHHHH
Confidence 8999999722 11222336789999998874
No 24
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=59.00 E-value=6.5 Score=38.72 Aligned_cols=38 Identities=18% Similarity=0.411 Sum_probs=29.3
Q ss_pred HHHHHHHhhcCCCCCCCCCCCCCCCCeeEcccchHhhHhhhHHh
Q 015009 15 HRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIH 58 (414)
Q Consensus 15 ~~kiL~~Llk~PgNk~CADCGa~~P~WaSvn~GVFlC~~CSgIH 58 (414)
-++.++..++......|-.||.....|. ++|..|.++|
T Consensus 341 ~~~~~~~~~~~~p~~~c~~cg~~~~~~~------~~c~~c~~~~ 378 (389)
T PRK11788 341 LRDLVGEQLKRKPRYRCRNCGFTARTLY------WHCPSCKAWE 378 (389)
T ss_pred HHHHHHHHHhCCCCEECCCCCCCCccce------eECcCCCCcc
Confidence 4666666655444455999999999996 7899998887
No 25
>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=58.73 E-value=5.9 Score=31.33 Aligned_cols=34 Identities=35% Similarity=0.638 Sum_probs=23.6
Q ss_pred cCCCCCCCCCCCCCCC--CeeEcccchHhhHhhhHHh
Q 015009 24 KLPENRECADCKAKGP--RWASVNLGIFICMQCSGIH 58 (414)
Q Consensus 24 k~PgNk~CADCGa~~P--~WaSvn~GVFlC~~CSgIH 58 (414)
..++..+|.|||..=| +|. .--|+..|+.|...+
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 3467789999999733 232 233788999998754
No 26
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=56.34 E-value=5.8 Score=38.86 Aligned_cols=31 Identities=32% Similarity=0.693 Sum_probs=27.0
Q ss_pred CCCCCCCCCCCCCC-CCeeEcccchHhhHhhh
Q 015009 25 LPENRECADCKAKG-PRWASVNLGIFICMQCS 55 (414)
Q Consensus 25 ~PgNk~CADCGa~~-P~WaSvn~GVFlC~~CS 55 (414)
.+.=..|+.||.+. +..++.-.|-++|..|.
T Consensus 151 ~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 151 GPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred ccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 35667899999985 57999999999999998
No 27
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=54.65 E-value=7.1 Score=31.87 Aligned_cols=33 Identities=18% Similarity=0.516 Sum_probs=22.3
Q ss_pred CCCCCCCCCCCCC-eeEcccchHhhHhhhHHhhc
Q 015009 28 NRECADCKAKGPR-WASVNLGIFICMQCSGIHRS 60 (414)
Q Consensus 28 Nk~CADCGa~~P~-WaSvn~GVFlC~~CSgIHR~ 60 (414)
..+|.|||..=|. =.-.--|+..|+.|...+-.
T Consensus 34 ~~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~E~ 67 (73)
T PRK13715 34 VYLCEACGNPIPEARRKIFPGVTLCVECQAYQER 67 (73)
T ss_pred cccHhhcCCcCCHHHHhcCCCcCCCHHHHHHHHH
Confidence 4689999997432 11222378899999886643
No 28
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=52.53 E-value=9 Score=29.10 Aligned_cols=37 Identities=24% Similarity=0.587 Sum_probs=30.7
Q ss_pred CCCCCCCCCCC-CCCeeEcccch-HhhHhhhHHhhcCCC
Q 015009 27 ENRECADCKAK-GPRWASVNLGI-FICMQCSGIHRSLGV 63 (414)
Q Consensus 27 gNk~CADCGa~-~P~WaSvn~GV-FlC~~CSgIHR~LG~ 63 (414)
..+.|..|+.. .|.|=....|- +||-.|.-..+..+.
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~ 40 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCC
Confidence 45789999987 68898888886 999999888877654
No 29
>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=52.10 E-value=3.9 Score=29.10 Aligned_cols=27 Identities=19% Similarity=0.582 Sum_probs=16.8
Q ss_pred CCCCCCCCC-CCCeeEcccchHhhHhhh
Q 015009 29 RECADCKAK-GPRWASVNLGIFICMQCS 55 (414)
Q Consensus 29 k~CADCGa~-~P~WaSvn~GVFlC~~CS 55 (414)
..|.+||.. .-+|..-+|+.-||..|.
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 678999999999999994
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=51.19 E-value=3.6 Score=29.71 Aligned_cols=27 Identities=22% Similarity=0.600 Sum_probs=21.0
Q ss_pred CCCCCCCCCCCeeEcccchHhhHhhhHH
Q 015009 30 ECADCKAKGPRWASVNLGIFICMQCSGI 57 (414)
Q Consensus 30 ~CADCGa~~P~WaSvn~GVFlC~~CSgI 57 (414)
+|-.||+.. ....-..|-++|..|..+
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 599999977 455677899999999543
No 31
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=48.34 E-value=12 Score=34.44 Aligned_cols=38 Identities=13% Similarity=0.270 Sum_probs=24.3
Q ss_pred cCCCCCCCCCCCCCCC-CeeEcccchHhhHhhhHHhhcC
Q 015009 24 KLPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRSL 61 (414)
Q Consensus 24 k~PgNk~CADCGa~~P-~WaSvn~GVFlC~~CSgIHR~L 61 (414)
..+.--+|-+||.+=| .=.-+--++.+|+.|...|-..
T Consensus 107 ~~gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~E~~ 145 (151)
T PRK10778 107 EDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIR 145 (151)
T ss_pred hCCCCceeccCCCcccHHHHhcCCCccccHHHHHHHHHH
Confidence 4567779999998711 1111122457899999977643
No 32
>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=47.29 E-value=10 Score=26.62 Aligned_cols=32 Identities=25% Similarity=0.694 Sum_probs=23.7
Q ss_pred CCCCCCC-CCCeeEcccchH-hhHhhhHHhhcCC
Q 015009 31 CADCKAK-GPRWASVNLGIF-ICMQCSGIHRSLG 62 (414)
Q Consensus 31 CADCGa~-~P~WaSvn~GVF-lC~~CSgIHR~LG 62 (414)
|.+|+.. .|.|=....|-. ||-.|.-.+|..|
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 8899987 699998888877 9999988877654
No 33
>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=42.92 E-value=16 Score=33.98 Aligned_cols=34 Identities=15% Similarity=0.333 Sum_probs=21.9
Q ss_pred CCCCCCCCCCCC--CCCeeEcccchHhhHhhhHHhhc
Q 015009 26 PENRECADCKAK--GPRWASVNLGIFICMQCSGIHRS 60 (414)
Q Consensus 26 PgNk~CADCGa~--~P~WaSvn~GVFlC~~CSgIHR~ 60 (414)
..=-+|.+||.. ..++-.+. ++-.|+.|...+-.
T Consensus 84 G~YG~Ce~CGe~I~~~RL~a~P-~a~~Ci~Cq~~~E~ 119 (159)
T TIGR02890 84 GTYGICEVCGKPIPYERLEAIP-TATTCVECQNRKEV 119 (159)
T ss_pred CCCCeecccCCcccHHHHhhCC-CcchhHHHHHHhhh
Confidence 444579999986 12222222 46789999987643
No 34
>PHA00080 DksA-like zinc finger domain containing protein
Probab=38.94 E-value=22 Score=28.91 Aligned_cols=35 Identities=26% Similarity=0.563 Sum_probs=23.8
Q ss_pred CCCCCCCCCCCCCC--CCeeEcccchHhhHhhhHHhhc
Q 015009 25 LPENRECADCKAKG--PRWASVNLGIFICMQCSGIHRS 60 (414)
Q Consensus 25 ~PgNk~CADCGa~~--P~WaSvn~GVFlC~~CSgIHR~ 60 (414)
..+..+|.|||..= .+|.-+. |+..|+.|...+-.
T Consensus 28 ~~~~~~C~~Cg~~Ip~~Rl~a~P-~~~~Cv~Cq~~~E~ 64 (72)
T PHA00080 28 APSATHCEECGDPIPEARREAVP-GCRTCVSCQEILEL 64 (72)
T ss_pred CCCCCEecCCCCcCcHHHHHhCC-CccCcHHHHHHHHH
Confidence 35566899999873 3343333 56779999987643
No 35
>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=35.14 E-value=37 Score=26.09 Aligned_cols=33 Identities=24% Similarity=0.637 Sum_probs=27.3
Q ss_pred CCCCCCCC-CCCeeEcc-cchHhhHhhhHHhhcCC
Q 015009 30 ECADCKAK-GPRWASVN-LGIFICMQCSGIHRSLG 62 (414)
Q Consensus 30 ~CADCGa~-~P~WaSvn-~GVFlC~~CSgIHR~LG 62 (414)
.|..|+.. -|.|=... -+..||-.|.-..+..|
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~ 35 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG 35 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC
Confidence 59999987 58888765 78899999988777766
No 36
>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=33.57 E-value=6.9 Score=27.27 Aligned_cols=29 Identities=24% Similarity=0.563 Sum_probs=16.2
Q ss_pred CCCCCCCCCC-CeeEcccchHhhHhhhHHh
Q 015009 30 ECADCKAKGP-RWASVNLGIFICMQCSGIH 58 (414)
Q Consensus 30 ~CADCGa~~P-~WaSvn~GVFlC~~CSgIH 58 (414)
.|.+||..=+ .=.-+--|..+|..|...|
T Consensus 5 ~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~~ 34 (36)
T PF01258_consen 5 ICEDCGEPIPEERLVAVPGATLCVECQERR 34 (36)
T ss_dssp B-TTTSSBEEHHHHHHCTTECS-HHHHHHH
T ss_pred CccccCChHHHHHHHhCCCcEECHHHhCcc
Confidence 5999997611 1112223678899998765
No 37
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=32.12 E-value=24 Score=27.60 Aligned_cols=39 Identities=23% Similarity=0.422 Sum_probs=28.0
Q ss_pred CCCCCCCCCCCCCCCeeEcccchHhhHhhhHHhhcCCCccceee
Q 015009 26 PENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVR 69 (414)
Q Consensus 26 PgNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~LG~hISkVK 69 (414)
+|-+.|.-||... -+--.||..+|..|- |++...|.++|
T Consensus 14 kGsr~C~vCg~~~--gliRkygL~~CRqCF---Re~A~~iGF~K 52 (54)
T PTZ00218 14 KGSRQCRVCSNRH--GLIRKYGLNVCRQCF---RENAELIGFHK 52 (54)
T ss_pred CCCCeeecCCCcc--hhhhhcCcchhhHHH---HHhhHhcCeee
Confidence 5778999999864 344589999999996 44444444544
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=29.54 E-value=30 Score=28.66 Aligned_cols=31 Identities=19% Similarity=0.613 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCCCCeeEcccchHhhHhhhHHhhc
Q 015009 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (414)
Q Consensus 27 gNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~ 60 (414)
.|..|.=||.... ...||++.|..|.++.|-
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 4677999997553 468999999999998874
No 39
>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=29.18 E-value=41 Score=27.84 Aligned_cols=31 Identities=16% Similarity=0.540 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCCCCeeEcccchHhhHhhhHHhhc
Q 015009 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (414)
Q Consensus 27 gNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~ 60 (414)
..+.|.=||.... ...||++.|..|.++.|-
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 4567999997654 468999999999998874
No 40
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=28.93 E-value=22 Score=35.96 Aligned_cols=33 Identities=18% Similarity=0.462 Sum_probs=23.6
Q ss_pred CCCCCCCCCCCCCCCeeEcccchHhhHhhhHHhh
Q 015009 26 PENRECADCKAKGPRWASVNLGIFICMQCSGIHR 59 (414)
Q Consensus 26 PgNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR 59 (414)
.....|-+||... --....-|-.||..|.-|..
T Consensus 9 ~~~~~Cp~Cg~~~-iv~d~~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 9 EEKLVCPECGSDK-LIYDYERGEIVCADCGLVIE 41 (310)
T ss_pred ccCCcCcCCCCCC-eeEECCCCeEeecccCCccc
Confidence 4456899999742 22345679999999987653
No 41
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=27.93 E-value=37 Score=29.31 Aligned_cols=33 Identities=24% Similarity=0.561 Sum_probs=23.3
Q ss_pred cCCCCCCCCCCCCC--------CCCe---------eEcccchHhhHhhhH
Q 015009 24 KLPENRECADCKAK--------GPRW---------ASVNLGIFICMQCSG 56 (414)
Q Consensus 24 k~PgNk~CADCGa~--------~P~W---------aSvn~GVFlC~~CSg 56 (414)
+.++--.|+|||.+ ..++ ++=.||-.+|..|..
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 45667789999986 1111 234789999999975
No 42
>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=27.22 E-value=38 Score=28.79 Aligned_cols=31 Identities=29% Similarity=0.718 Sum_probs=25.2
Q ss_pred CCCCCCCCCCCCCCeeEcccchHhhHhhhHHhhc
Q 015009 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (414)
Q Consensus 27 gNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~ 60 (414)
++..|.=||.... ...||++.|..|.++.|-
T Consensus 4 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 4 EVIPCKICGDKSS---GIHYGVITCEGCKGFFRR 34 (95)
T ss_pred cccCCcccCCcCc---ceEECceeehhhHHhhHH
Confidence 4667999998654 357999999999999874
No 43
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=26.97 E-value=69 Score=34.50 Aligned_cols=93 Identities=15% Similarity=0.300 Sum_probs=48.4
Q ss_pred CCCCCCCCC-CCCC--CCCeeEcccc--hHhhHhhhHHhhcCCCcc-----ceeeecc----cCCCCH-HHHHHHHh---
Q 015009 25 LPENRECAD-CKAK--GPRWASVNLG--IFICMQCSGIHRSLGVHI-----SKVRSAT----LDTWLP-EQVAFIQS--- 86 (414)
Q Consensus 25 ~PgNk~CAD-CGa~--~P~WaSvn~G--VFlC~~CSgIHR~LG~hI-----SkVKSls----LD~Wt~-eeV~~L~~--- 86 (414)
.++++.|+| |-.. +...+...-+ ..||+.|-..=-++|.|- -.|...+ --.|+. ||+++|..
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 456665554 6543 4443433222 479999987555555441 1222212 225986 57777754
Q ss_pred --hCc--hHHHHHHhhcCCCCCChhHHHHHHHHHhhhcccc
Q 015009 87 --MGN--EKANSYWEAELPPNYDRVGIENFIRAKYEEKRWV 123 (414)
Q Consensus 87 --~GN--~~aN~iwea~lPp~~d~~~~e~FIraKY~eKrf~ 123 (414)
+|| +.|+.|= .-+....+++-...|++-.+.
T Consensus 90 ~G~GNW~dIA~hIG------tKtkeeck~hy~k~fv~s~~~ 124 (438)
T KOG0457|consen 90 YGFGNWQDIADHIG------TKTKEECKEHYLKHFVNSPIF 124 (438)
T ss_pred hCCCcHHHHHHHHc------ccchHHHHHHHHHHHhcCccc
Confidence 377 2333221 223345566666777765444
No 44
>PF06752 E_Pc_C: Enhancer of Polycomb C-terminus; InterPro: IPR009607 This entry represents the C terminus of eukaryotic enhancer of polycomb proteins, which have roles in heterochromatin formation []. This family contains several conserved motifs.
Probab=26.48 E-value=40 Score=33.36 Aligned_cols=15 Identities=47% Similarity=0.762 Sum_probs=10.5
Q ss_pred chhhHHHHHHHHHHH
Q 015009 330 FAMHQQQLTMLAQQQ 344 (414)
Q Consensus 330 f~~~qqq~~~~~qqq 344 (414)
|--|||||+.|-.||
T Consensus 7 yQqHQqQL~~MQkQQ 21 (230)
T PF06752_consen 7 YQQHQQQLVLMQKQQ 21 (230)
T ss_pred HHHHHHHHHHHHHHH
Confidence 456888888885544
No 45
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=26.07 E-value=11 Score=26.63 Aligned_cols=30 Identities=20% Similarity=0.443 Sum_probs=14.1
Q ss_pred CCCCCCCCCCCCeeEc---ccchHhhHhhhHHhh
Q 015009 29 RECADCKAKGPRWASV---NLGIFICMQCSGIHR 59 (414)
Q Consensus 29 k~CADCGa~~P~WaSv---n~GVFlC~~CSgIHR 59 (414)
|+|-.||.+ .++... +.-=++|..|..||-
T Consensus 1 kfC~~CG~~-l~~~ip~gd~r~R~vC~~Cg~IhY 33 (34)
T PF14803_consen 1 KFCPQCGGP-LERRIPEGDDRERLVCPACGFIHY 33 (34)
T ss_dssp -B-TTT--B--EEE--TT-SS-EEEETTTTEEE-
T ss_pred CccccccCh-hhhhcCCCCCccceECCCCCCEEe
Confidence 578899886 222222 333457888888773
No 46
>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=25.60 E-value=39 Score=28.91 Aligned_cols=30 Identities=20% Similarity=0.555 Sum_probs=24.3
Q ss_pred CCCCCCCCCCCCCeeEcccchHhhHhhhHHhhc
Q 015009 28 NRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (414)
Q Consensus 28 Nk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~ 60 (414)
+..|.=||.... ...||++.|..|.++.|-
T Consensus 4 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 33 (97)
T cd07170 4 KRLCLVCGDIAS---GYHYGVASCEACKAFFKR 33 (97)
T ss_pred CCCCeecCCcCc---ceEECceeehhhhHHHHH
Confidence 356999997654 458999999999999874
No 47
>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=25.01 E-value=40 Score=29.10 Aligned_cols=31 Identities=26% Similarity=0.677 Sum_probs=25.5
Q ss_pred CCCCCCCCCCCCCCeeEcccchHhhHhhhHHhhc
Q 015009 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (414)
Q Consensus 27 gNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~ 60 (414)
.+..|.=||.... ...||+..|..|.++.|-
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 4678999997654 458999999999998874
No 48
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=24.74 E-value=44 Score=28.65 Aligned_cols=30 Identities=20% Similarity=0.530 Sum_probs=23.5
Q ss_pred CCCCCCCCCCCCCCCeeEcccchHhhHhhhHH
Q 015009 26 PENRECADCKAKGPRWASVNLGIFICMQCSGI 57 (414)
Q Consensus 26 PgNk~CADCGa~~P~WaSvn~GVFlC~~CSgI 57 (414)
..--.|-.|+.+ .---+..||+.|..|...
T Consensus 33 ~~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~~ 62 (89)
T COG1997 33 RAKHVCPFCGRT--TVKRIATGIWKCRKCGAK 62 (89)
T ss_pred hcCCcCCCCCCc--ceeeeccCeEEcCCCCCe
Confidence 345679999998 555678999999999643
No 49
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=24.74 E-value=36 Score=25.91 Aligned_cols=30 Identities=27% Similarity=0.542 Sum_probs=19.7
Q ss_pred CCCCCCCCCCCe--eEcccchHhhHhhhHHhhc
Q 015009 30 ECADCKAKGPRW--ASVNLGIFICMQCSGIHRS 60 (414)
Q Consensus 30 ~CADCGa~~P~W--aSvn~GVFlC~~CSgIHR~ 60 (414)
.|+=||..-.-. +-+.=| +||..|..--..
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl~~ 32 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKLSG 32 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHhcC
Confidence 488888874333 345557 899999864333
No 50
>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=24.67 E-value=45 Score=25.23 Aligned_cols=33 Identities=24% Similarity=0.656 Sum_probs=21.8
Q ss_pred hcCCCCCCCCCCCCCCC--Cee-------EcccchHhhHhhhH
Q 015009 23 LKLPENRECADCKAKGP--RWA-------SVNLGIFICMQCSG 56 (414)
Q Consensus 23 lk~PgNk~CADCGa~~P--~Wa-------Svn~GVFlC~~CSg 56 (414)
+++-+| .|-=||+..+ .|. +..-.|+||..|..
T Consensus 3 ~~Rs~~-kCELC~a~~~L~vy~Vpp~~~~~~d~~iliC~tC~~ 44 (47)
T smart00782 3 LARCES-KCELCGSDSPLVVYAVPPSSDVTADNSVMLCDTCHS 44 (47)
T ss_pred hHHcCC-cccCcCCCCCceEEecCCCCCCCccceeeechHHHH
Confidence 344444 4999998753 222 34668999999964
No 51
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.31 E-value=19 Score=34.56 Aligned_cols=24 Identities=21% Similarity=0.653 Sum_probs=19.7
Q ss_pred CCCCCCCCCCCCCCeeEcccchHhhHhhhHH
Q 015009 27 ENRECADCKAKGPRWASVNLGIFICMQCSGI 57 (414)
Q Consensus 27 gNk~CADCGa~~P~WaSvn~GVFlC~~CSgI 57 (414)
.-+.|.-||. +.-+.|.|..|...
T Consensus 308 tS~~C~~cg~-------~~~r~~~C~~cg~~ 331 (364)
T COG0675 308 TSKTCPCCGH-------LSGRLFKCPRCGFV 331 (364)
T ss_pred CcccccccCC-------ccceeEECCCCCCe
Confidence 3379999999 67889999999763
No 52
>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors. HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.
Probab=24.27 E-value=26 Score=28.01 Aligned_cols=31 Identities=26% Similarity=0.509 Sum_probs=24.7
Q ss_pred CCCC-CCCCCCC-eeEcccchHhhHhhhHHhhcC
Q 015009 30 ECAD-CKAKGPR-WASVNLGIFICMQCSGIHRSL 61 (414)
Q Consensus 30 ~CAD-CGa~~P~-WaSvn~GVFlC~~CSgIHR~L 61 (414)
.+.| |+.--|. +..-+...+.|..| |.||+|
T Consensus 20 ~a~DGCgEFm~~~g~eg~~~al~CaAC-gCHRnF 52 (60)
T PF04770_consen 20 HAVDGCGEFMPSPGEEGTPEALKCAAC-GCHRNF 52 (60)
T ss_pred cccccccccccCCCCCCCcccceeccc-Ccchhc
Confidence 3666 8888777 76667888999999 789987
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=24.06 E-value=27 Score=27.09 Aligned_cols=28 Identities=18% Similarity=0.570 Sum_probs=22.8
Q ss_pred CCCCCCCCCCCCCCeeEcccchHhhHhhhH
Q 015009 27 ENRECADCKAKGPRWASVNLGIFICMQCSG 56 (414)
Q Consensus 27 gNk~CADCGa~~P~WaSvn~GVFlC~~CSg 56 (414)
--+.|..||..... ..+-.+|.|..|.-
T Consensus 27 TSq~C~~CG~~~~~--~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK--RRSGRVFTCPNCGF 54 (69)
T ss_pred CccCccCccccccc--ccccceEEcCCCCC
Confidence 45789999998777 77888999999853
No 54
>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=23.83 E-value=49 Score=28.49 Aligned_cols=31 Identities=19% Similarity=0.410 Sum_probs=17.9
Q ss_pred CCCCCCCCCCCCCCC-CeeEcccchHhhHhhh
Q 015009 25 LPENRECADCKAKGP-RWASVNLGIFICMQCS 55 (414)
Q Consensus 25 ~PgNk~CADCGa~~P-~WaSvn~GVFlC~~CS 55 (414)
.+.-.+|.|||.+=| .=.-.-=++..|+.|.
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 345679999998721 1111111346788885
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=23.83 E-value=53 Score=26.95 Aligned_cols=27 Identities=30% Similarity=0.749 Sum_probs=21.0
Q ss_pred CCCCCCCCCCeeEcccchHhhHhhhHHhhc
Q 015009 31 CADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (414)
Q Consensus 31 CADCGa~~P~WaSvn~GVFlC~~CSgIHR~ 60 (414)
|.=||.... ...||+..|..|.++.|-
T Consensus 1 C~VCg~~~~---g~hyG~~sC~aC~~FFRR 27 (81)
T cd07165 1 CKVCGDKAS---GYHYGVTSCEGCKGFFRR 27 (81)
T ss_pred CCccCccCc---ceEECchhhhhHHHHHHh
Confidence 556776544 358999999999998884
No 56
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=23.50 E-value=35 Score=32.20 Aligned_cols=22 Identities=27% Similarity=0.490 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHhhcCCCCCC
Q 015009 9 KELNARHRKILEGLLKLPENRE 30 (414)
Q Consensus 9 k~~~~r~~kiL~~Llk~PgNk~ 30 (414)
.+.+.+|.+.++.+|..+.+..
T Consensus 112 ~~~Ek~H~~~~~~~Le~~~~~~ 133 (166)
T COG1592 112 AKAEKRHAEMFRGLLERLEEGK 133 (166)
T ss_pred HHHHHHHHHHHHHHHHhhhcCC
Confidence 4567789999999998876554
No 57
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=23.30 E-value=58 Score=23.55 Aligned_cols=24 Identities=21% Similarity=0.540 Sum_probs=19.1
Q ss_pred CCCCCCCCCCCeeEcccchHhhHh
Q 015009 30 ECADCKAKGPRWASVNLGIFICMQ 53 (414)
Q Consensus 30 ~CADCGa~~P~WaSvn~GVFlC~~ 53 (414)
+|.+|+..+.-|+++.-|-..|..
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c~~ 24 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGCGR 24 (50)
T ss_pred CcccCCCcCCeEEecCCCCcccCC
Confidence 599999988888888877777743
No 58
>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=22.20 E-value=31 Score=29.26 Aligned_cols=29 Identities=24% Similarity=0.608 Sum_probs=22.9
Q ss_pred CCCCCCCCCCCCeeEcccchHhhHhhhHHhhc
Q 015009 29 RECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (414)
Q Consensus 29 k~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~ 60 (414)
+.|.=||.... ...||++.|..|.++.|-
T Consensus 1 ~~C~VCg~~a~---g~hyGv~sC~aC~~FFRR 29 (94)
T cd06966 1 KICGVCGDKAL---GYNFNAITCESCKAFFRR 29 (94)
T ss_pred CCCeeCCCcCc---ceEECcceeeeehheehh
Confidence 45888887544 348999999999998874
No 59
>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=22.01 E-value=50 Score=28.47 Aligned_cols=28 Identities=18% Similarity=0.322 Sum_probs=22.4
Q ss_pred CCCCCCeeEcccchHhhHhhhHHhhcCC
Q 015009 35 KAKGPRWASVNLGIFICMQCSGIHRSLG 62 (414)
Q Consensus 35 Ga~~P~WaSvn~GVFlC~~CSgIHR~LG 62 (414)
|.++..+..+=|.-|.|..|...|+.++
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 5667788889999999999999998763
No 60
>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=21.71 E-value=57 Score=27.13 Aligned_cols=28 Identities=21% Similarity=0.625 Sum_probs=22.1
Q ss_pred CCCCCCCCCCCeeEcccchHhhHhhhHHhhc
Q 015009 30 ECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (414)
Q Consensus 30 ~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~ 60 (414)
.|.=||..... ..||++.|..|.++.|-
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 37778876543 48999999999998874
No 61
>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=21.15 E-value=52 Score=27.69 Aligned_cols=32 Identities=28% Similarity=0.754 Sum_probs=25.8
Q ss_pred CCCCCCCCCCCCCCCeeEcccchHhhHhhhHHhhc
Q 015009 26 PENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (414)
Q Consensus 26 PgNk~CADCGa~~P~WaSvn~GVFlC~~CSgIHR~ 60 (414)
.++..|.=||.... ...||+..|..|.++.|-
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 45677999997653 458999999999998874
No 62
>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=21.05 E-value=42 Score=25.22 Aligned_cols=26 Identities=27% Similarity=0.630 Sum_probs=18.9
Q ss_pred CCCCCCCCCCCeeEcccchHhhHhhhH
Q 015009 30 ECADCKAKGPRWASVNLGIFICMQCSG 56 (414)
Q Consensus 30 ~CADCGa~~P~WaSvn~GVFlC~~CSg 56 (414)
.|.=|+..... --+=+|.|||..|-.
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHH
Confidence 47778887666 334478999999953
No 63
>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=20.65 E-value=79 Score=23.08 Aligned_cols=40 Identities=23% Similarity=0.493 Sum_probs=25.6
Q ss_pred HHHHHHHHhhcCCCCCCCCCCCCCCCCeeEcccchHhhHhhh
Q 015009 14 RHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCS 55 (414)
Q Consensus 14 r~~kiL~~Llk~PgNk~CADCGa~~P~WaSvn~GVFlC~~CS 55 (414)
.-.+.|+.+. =++.-+|--||.....+.. +.+.|-|-.|.
T Consensus 5 ~c~~~l~~~R-W~~g~~CP~Cg~~~~~~~~-~~~~~~C~~C~ 44 (46)
T PF12760_consen 5 ACREYLEEIR-WPDGFVCPHCGSTKHYRLK-TRGRYRCKACR 44 (46)
T ss_pred HHHHHHHHhc-CCCCCCCCCCCCeeeEEeC-CCCeEECCCCC
Confidence 3444555443 3455889999998544443 36888888884
No 64
>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=20.02 E-value=64 Score=25.78 Aligned_cols=27 Identities=30% Similarity=0.773 Sum_probs=20.7
Q ss_pred CCCCCCCCCCeeEcccchHhhHhhhHHhhc
Q 015009 31 CADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (414)
Q Consensus 31 CADCGa~~P~WaSvn~GVFlC~~CSgIHR~ 60 (414)
|.=||..... ..||++.|..|.+..|-
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 5557665443 58999999999999874
Done!