Query 021042
Match_columns 318
No_of_seqs 235 out of 1120
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 07:09:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021042.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021042hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0704 ADP-ribosylation facto 100.0 1.2E-74 2.6E-79 552.1 14.1 240 3-305 6-246 (386)
2 COG5347 GTPase-activating prot 100.0 6E-38 1.3E-42 301.5 10.3 118 3-120 7-125 (319)
3 KOG0706 Predicted GTPase-activ 100.0 9.7E-38 2.1E-42 306.5 10.1 113 3-116 10-122 (454)
4 PLN03114 ADP-ribosylation fact 100.0 3.4E-37 7.4E-42 296.8 11.1 114 4-117 10-123 (395)
5 PF01412 ArfGap: Putative GTPa 100.0 3.8E-36 8.3E-41 250.7 9.2 114 5-122 2-115 (116)
6 KOG0703 Predicted GTPase-activ 100.0 1.1E-35 2.3E-40 280.7 8.1 115 3-124 12-127 (287)
7 smart00105 ArfGap Putative GTP 100.0 1.6E-34 3.4E-39 239.9 9.8 107 14-123 1-107 (112)
8 PLN03119 putative ADP-ribosyla 100.0 2.7E-29 5.8E-34 253.0 10.5 114 3-122 10-123 (648)
9 PLN03131 hypothetical protein; 100.0 3.2E-29 6.9E-34 254.1 10.1 114 3-122 10-123 (705)
10 KOG0705 GTPase-activating prot 99.9 4.1E-22 8.9E-27 201.2 6.5 113 4-123 501-616 (749)
11 KOG0521 Putative GTPase activa 99.8 2.7E-20 5.8E-25 197.1 2.5 81 7-87 417-497 (785)
12 KOG0818 GTPase-activating prot 99.7 5.8E-17 1.3E-21 162.1 4.3 111 11-125 3-121 (669)
13 KOG1117 Rho- and Arf-GTPase ac 99.5 6.3E-15 1.4E-19 154.5 3.3 80 8-87 290-371 (1186)
14 KOG0702 Predicted GTPase-activ 99.5 7.3E-14 1.6E-18 139.9 6.9 117 4-124 13-130 (524)
15 KOG0521 Putative GTPase activa 90.8 0.06 1.3E-06 58.6 -0.5 70 11-82 625-695 (785)
16 PRK00085 recO DNA repair prote 84.4 0.67 1.4E-05 42.6 2.3 38 7-44 140-178 (247)
17 PF00643 zf-B_box: B-box zinc 79.6 1.9 4.1E-05 29.1 2.6 34 15-48 2-36 (42)
18 TIGR00613 reco DNA repair prot 78.1 1.7 3.7E-05 39.8 2.6 39 7-45 138-177 (241)
19 PRK12495 hypothetical protein; 77.0 1.7 3.8E-05 40.8 2.3 29 13-45 39-67 (226)
20 COG1997 RPL43A Ribosomal prote 77.0 2.5 5.4E-05 34.4 2.9 43 2-46 20-63 (89)
21 COG1381 RecO Recombinational D 71.4 2.3 4.9E-05 40.1 1.6 32 12-43 150-182 (251)
22 PF08271 TF_Zn_Ribbon: TFIIB z 64.3 4.2 9.2E-05 28.0 1.4 27 18-45 2-28 (43)
23 PRK11019 hypothetical protein; 64.2 2.4 5.2E-05 34.4 0.2 37 15-52 35-73 (88)
24 PF00320 GATA: GATA zinc finge 63.3 5.6 0.00012 26.7 1.8 32 19-50 1-34 (36)
25 smart00401 ZnF_GATA zinc finge 61.3 7.7 0.00017 28.2 2.4 38 15-52 2-41 (52)
26 TIGR02419 C4_traR_proteo phage 58.5 3.8 8.2E-05 31.0 0.4 34 12-46 27-62 (63)
27 PF10764 Gin: Inhibitor of sig 56.7 7 0.00015 28.0 1.5 27 18-45 1-27 (46)
28 KOG0704 ADP-ribosylation facto 54.2 3.8 8.3E-05 41.0 -0.3 49 258-306 247-311 (386)
29 PTZ00255 60S ribosomal protein 53.2 15 0.00033 30.0 3.0 40 3-44 22-62 (90)
30 PF11781 RRN7: RNA polymerase 51.8 12 0.00026 25.4 1.9 27 14-43 6-32 (36)
31 cd07171 NR_DBD_ER DNA-binding 47.3 13 0.00027 29.5 1.7 31 15-48 2-32 (82)
32 PF01286 XPA_N: XPA protein N- 46.2 7.4 0.00016 26.3 0.2 27 17-43 4-31 (34)
33 COG1734 DksA DnaK suppressor p 45.3 7 0.00015 33.4 -0.0 30 18-47 82-112 (120)
34 PF01258 zf-dskA_traR: Prokary 45.3 3.8 8.2E-05 27.3 -1.3 29 18-46 5-34 (36)
35 PRK13715 conjugal transfer pro 44.2 9.6 0.00021 29.7 0.6 37 16-52 34-71 (73)
36 PF01780 Ribosomal_L37ae: Ribo 43.5 15 0.00033 30.0 1.7 40 3-44 21-61 (90)
37 PF07282 OrfB_Zn_ribbon: Putat 41.3 16 0.00034 27.2 1.4 28 15-44 27-54 (69)
38 cd06968 NR_DBD_ROR DNA-binding 40.9 18 0.0004 29.4 1.8 31 15-48 4-34 (95)
39 KOG0457 Histone acetyltransfer 39.7 24 0.00053 36.3 2.8 39 36-74 38-86 (438)
40 cd07170 NR_DBD_ERR DNA-binding 39.0 19 0.00041 29.5 1.6 30 16-48 4-33 (97)
41 PF14803 Nudix_N_2: Nudix N-te 38.8 13 0.00028 25.0 0.5 30 17-47 1-33 (34)
42 cd07173 NR_DBD_AR DNA-binding 38.6 19 0.00042 28.5 1.5 32 14-48 1-32 (82)
43 PF12760 Zn_Tnp_IS1595: Transp 36.8 41 0.00089 23.4 2.8 39 3-43 6-44 (46)
44 PRK00423 tfb transcription ini 35.9 24 0.00052 34.2 2.1 34 13-47 8-41 (310)
45 COG2158 Uncharacterized protei 35.6 15 0.00032 31.1 0.5 25 28-52 52-78 (112)
46 PHA00080 DksA-like zinc finger 35.1 20 0.00044 27.8 1.2 35 13-48 28-64 (72)
47 cd07169 NR_DBD_GCNF_like DNA-b 34.0 26 0.00056 28.2 1.6 32 14-48 4-35 (90)
48 cd07160 NR_DBD_LXR DNA-binding 33.1 28 0.0006 28.8 1.7 31 15-48 17-47 (101)
49 cd00202 ZnF_GATA Zinc finger D 32.4 28 0.00061 25.5 1.5 34 18-51 1-36 (54)
50 cd06966 NR_DBD_CAR DNA-binding 31.7 23 0.00049 28.8 1.0 29 17-48 1-29 (94)
51 COG2174 RPL34A Ribosomal prote 31.0 35 0.00076 28.1 1.9 34 11-44 29-79 (93)
52 KOG3362 Predicted BBOX Zn-fing 30.3 22 0.00048 31.6 0.7 34 14-48 116-150 (156)
53 PF14376 Haem_bd: Haem-binding 30.2 25 0.00055 30.2 1.1 14 17-30 42-55 (137)
54 PTZ00218 40S ribosomal protein 30.0 23 0.00049 26.4 0.6 39 14-57 14-52 (54)
55 smart00290 ZnF_UBP Ubiquitin C 29.6 40 0.00087 23.3 1.8 22 18-39 1-22 (50)
56 TIGR02890 spore_yteA sporulati 29.4 30 0.00064 30.8 1.4 34 14-48 84-119 (159)
57 smart00782 PhnA_Zn_Ribbon PhnA 28.5 38 0.00082 24.4 1.5 34 10-44 2-44 (47)
58 PRK10778 dksA RNA polymerase-b 28.3 36 0.00078 30.0 1.7 38 12-49 107-145 (151)
59 TIGR00280 L37a ribosomal prote 28.1 63 0.0014 26.5 2.9 40 3-44 21-61 (91)
60 PRK03976 rpl37ae 50S ribosomal 26.6 59 0.0013 26.6 2.5 40 3-44 22-62 (90)
61 cd07162 NR_DBD_PXR DNA-binding 26.0 45 0.00098 26.5 1.8 28 18-48 1-28 (87)
62 cd07168 NR_DBD_DHR4_like DNA-b 25.6 49 0.0011 26.6 1.9 31 15-48 5-35 (90)
63 cd07161 NR_DBD_EcR DNA-binding 25.2 48 0.001 26.7 1.8 29 17-48 2-30 (91)
64 cd06956 NR_DBD_RXR DNA-binding 25.2 52 0.0011 25.5 1.9 29 17-48 1-29 (77)
65 PF10281 Ish1: Putative stress 24.8 77 0.0017 21.2 2.5 20 62-92 2-21 (38)
66 COG0675 Transposase and inacti 24.7 31 0.00068 32.0 0.7 24 15-45 308-331 (364)
67 PF14471 DUF4428: Domain of un 23.7 30 0.00064 25.1 0.3 43 18-61 1-45 (51)
68 cd07156 NR_DBD_VDR_like The DN 23.5 51 0.0011 25.2 1.6 27 19-48 1-27 (72)
69 PHA02942 putative transposase; 22.9 40 0.00086 33.9 1.1 27 15-44 324-350 (383)
70 cd07172 NR_DBD_GR_PR DNA-bindi 22.8 57 0.0012 25.5 1.7 29 17-48 3-31 (78)
71 cd07165 NR_DBD_DmE78_like DNA- 22.7 45 0.00099 26.1 1.2 27 19-48 1-27 (81)
72 cd07158 NR_DBD_Ppar_like The D 22.6 51 0.0011 25.2 1.4 27 19-48 1-27 (73)
73 PF06689 zf-C4_ClpX: ClpX C4-t 22.6 79 0.0017 21.8 2.2 29 17-45 2-33 (41)
74 TIGR00382 clpX endopeptidase C 22.4 44 0.00094 34.1 1.2 29 16-44 7-37 (413)
75 cd07163 NR_DBD_TLX DNA-binding 22.3 40 0.00087 27.2 0.8 30 16-48 6-35 (92)
76 PF13119 DUF3973: Domain of un 22.0 41 0.00089 23.6 0.7 13 37-49 2-14 (41)
77 cd07157 2DBD_NR_DBD1 The first 21.8 34 0.00073 27.3 0.3 28 18-48 2-29 (86)
78 cd06965 NR_DBD_Ppar DNA-bindin 21.6 40 0.00087 26.7 0.7 27 19-48 2-28 (84)
79 cd06955 NR_DBD_VDR DNA-binding 21.0 55 0.0012 27.3 1.4 31 15-48 5-35 (107)
No 1
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=100.00 E-value=1.2e-74 Score=552.09 Aligned_cols=240 Identities=57% Similarity=0.930 Sum_probs=202.0
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 021042 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (318)
Q Consensus 3 a~~~L~~L~~~p~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~LGvhiS~VrSitmD~Ws~eel~~m~~gGN~~~n~ 82 (318)
+|+.|++|+...+|++||||+++|||||||+|||||||+|+|+||+||||||||||||||+|++.||++|++|||.++++
T Consensus 6 trr~L~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~~~e 85 (386)
T KOG0704|consen 6 TRRVLLELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNERFRE 85 (386)
T ss_pred HHHHHHhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchhHHH
Confidence 67777777777799999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcCCCCCC-ChhhhccchHHHHHHHHHHHHHcCCCCCCCcchhhhhccCCCCCCCCCccCCCCCCCCCCCCCCCCCC
Q 021042 83 FLSQYGIPKET-DIVTKYNTNAASIYRDRIQAIAEGRPWRDPPVVKETLNAGKSSSRPPLAQSASVGGVGRNGNYGNHGG 161 (318)
Q Consensus 83 ~~e~~~~~~~~-~i~~KY~s~aa~~yr~~L~a~~egr~w~~~p~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 161 (318)
||+.+++-++. +|++||++++|++||++|++++|||+|.+||.++|..++ ..++|. . .
T Consensus 86 FL~s~~~~~e~~~i~eKYns~aAa~yRdki~~laegr~w~d~~~~k~~~p~--~syt~a------~-~------------ 144 (386)
T KOG0704|consen 86 FLSSQGIYKETWPIREKYNSRAAALYRDKIAALAEGREWNDPPYLKEDNPA--QSYTSA------A-Q------------ 144 (386)
T ss_pred HHhhCccccccccHHHhhccHHHHHHHHHHHHHhcCCcccccccccccCcc--cccccC------C-C------------
Confidence 99999866654 999999999999999999999999999999999887531 122220 0 0
Q ss_pred CCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCCchhhhhHHHHHHHhhhhhhhhhHHhhhhhcCCCCCCCCC
Q 021042 162 WDSWDNDDFRSSNDMRRNQSVSDFRGGSGGMGGMPASRSKSTEDIYTRAELEASAANKEGFFSRKIAENEARPEGLPPSQ 241 (318)
Q Consensus 162 ~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~s~s~~~~y~~~q~~~~~~~~e~yFa~~~~~Na~rp~~lpPSQ 241 (318)
..+.+...+|+..|.+++++.+|.||++++.+|++|||+|||||
T Consensus 145 ------------------------------------~~~~ss~~~~~~sq~~~~~~~ke~~fa~~~~~n~srpd~lppsQ 188 (386)
T KOG0704|consen 145 ------------------------------------LGSKSSETIYTISQLSNSAAGKESYFAKRLSENQSRPDGLPPSQ 188 (386)
T ss_pred ------------------------------------cCCCcCCcccccccchhhhcchhHHHHHhcccccCCCCCCCccc
Confidence 00011112344455667788999999999999999999999999
Q ss_pred CCcccccCCCCCCCCCCcccchhhHHHHhhhhhhhHhHHHHHHHHhhhhcchhHHHHHhhhhcC
Q 021042 242 GGKYVGFGSTPPPTQRNTNSQGDVLSAVSQGFGRISLVAASAAQSAATVVQAGTREFTSKLFLS 305 (318)
Q Consensus 242 GGkY~GFG~tp~p~~~~~~~~~d~~~~ls~Gw~~fs~~a~~~~~~~~~v~~~g~~~~~~~~~~~ 305 (318)
||||+|||+|+.|||+.+ .++|+|+.|++||++||.+|++||. |++.+++.+. ||+|+
T Consensus 189 ggkY~GFGst~~~ppqs~-~~~~~~s~ls~Gws~~s~~as~~a~----~~~~~~~~~s-kvkeg 246 (386)
T KOG0704|consen 189 GGKYQGFGSTNAPPPQSN-SQDDAMSVLSSGWSRLSTGASSAAS----VGQTATQKAS-KVKEG 246 (386)
T ss_pred CCcccccCCCCCCCCccc-cccchhhhhccccccccchhhhhhh----hhhhhhhhhh-hhhhh
Confidence 999999999988887642 2338999999999999999998665 6666666665 77777
No 2
>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=6e-38 Score=301.49 Aligned_cols=118 Identities=39% Similarity=0.727 Sum_probs=110.5
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 021042 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (318)
Q Consensus 3 a~~~L~~L~~~p~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~LGvhiS~VrSitmD~Ws~eel~~m~~gGN~~~n~ 82 (318)
.+++|..|++.++|++|||||+++|+|||++||||||++||||||+|||||||||||+||.|+++||++|+.+||.++++
T Consensus 7 ~~~~l~~l~~~~~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~wt~~~l~~m~~gGN~~a~~ 86 (319)
T COG5347 7 DRKLLKLLKSDSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWTEEELRRMEVGGNSNANR 86 (319)
T ss_pred HHHHHHHHhhccccCccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeecccCCHHHHHHHHHhcchhhhh
Confidence 57788889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcCCCC-CCChhhhccchHHHHHHHHHHHHHcCCCC
Q 021042 83 FLSQYGIPK-ETDIVTKYNTNAASIYRDRIQAIAEGRPW 120 (318)
Q Consensus 83 ~~e~~~~~~-~~~i~~KY~s~aa~~yr~~L~a~~egr~w 120 (318)
||+.+++.. ..+|++||++..++.|++++..+.....|
T Consensus 87 ~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~ 125 (319)
T COG5347 87 FYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDD 125 (319)
T ss_pred HhccCCCcccccccccccCHHHHHHHHHHHHHhhhcccc
Confidence 999998874 47899999999999999888777776666
No 3
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=9.7e-38 Score=306.46 Aligned_cols=113 Identities=47% Similarity=0.938 Sum_probs=107.2
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 021042 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (318)
Q Consensus 3 a~~~L~~L~~~p~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~LGvhiS~VrSitmD~Ws~eel~~m~~gGN~~~n~ 82 (318)
...+++.|+.+++||+||||++++|+|+||+||||||++|+++||.||||||||||+.||.|+.+||++|+.|||.+++.
T Consensus 10 ~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~~ 89 (454)
T KOG0706|consen 10 IQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANARV 89 (454)
T ss_pred HHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHHH
Confidence 56789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcCCCCCCChhhhccchHHHHHHHHHHHHHc
Q 021042 83 FLSQYGIPKETDIVTKYNTNAASIYRDRIQAIAE 116 (318)
Q Consensus 83 ~~e~~~~~~~~~i~~KY~s~aa~~yr~~L~a~~e 116 (318)
||++|++.. .+++.||++++|..||++|..++.
T Consensus 90 FFkqhg~~t-~d~~aKY~SraA~~Yr~kl~~lv~ 122 (454)
T KOG0706|consen 90 FFKQHGCVT-LDANAKYNSRAAKLYREKLKKLVQ 122 (454)
T ss_pred HHHHcCCcc-hhhhhhhccHHHHHHHHHHHHHHH
Confidence 999998764 389999999999999999987664
No 4
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=100.00 E-value=3.4e-37 Score=296.78 Aligned_cols=114 Identities=46% Similarity=0.885 Sum_probs=109.5
Q ss_pred HHHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHHH
Q 021042 4 TRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTF 83 (318)
Q Consensus 4 ~~~L~~L~~~p~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~LGvhiS~VrSitmD~Ws~eel~~m~~gGN~~~n~~ 83 (318)
.++|++|+..|+|++|+||++++|+|||++||||||++|+|+||.||+||||||||+||.|+++||++|+.+||.++++|
T Consensus 10 ~~vfrkL~~kPgNk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~Ws~eqL~~Mk~GGN~rA~~f 89 (395)
T PLN03114 10 ISVFKKLKAKSDNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSSEQLKMMIYGGNNRAQVF 89 (395)
T ss_pred HHHHHHHHhCcCCCcCccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCCCCHHHHHHHHHhcCHHHHHH
Confidence 45799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcCCCCCCChhhhccchHHHHHHHHHHHHHcC
Q 021042 84 LSQYGIPKETDIVTKYNTNAASIYRDRIQAIAEG 117 (318)
Q Consensus 84 ~e~~~~~~~~~i~~KY~s~aa~~yr~~L~a~~eg 117 (318)
|++|++.....+++||++++|+.||++|++++++
T Consensus 90 F~qhG~~~~~~~~~KY~S~aA~~Yre~L~keVa~ 123 (395)
T PLN03114 90 FKQYGWSDGGKTEAKYTSRAADLYKQILAKEVAK 123 (395)
T ss_pred HHHcCCCCCCCcccccCCHHHHHHHHHHHHHHHH
Confidence 9999998878899999999999999999988765
No 5
>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=3.8e-36 Score=250.75 Aligned_cols=114 Identities=41% Similarity=0.810 Sum_probs=90.5
Q ss_pred HHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHHHH
Q 021042 5 RRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTFL 84 (318)
Q Consensus 5 ~~L~~L~~~p~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~LGvhiS~VrSitmD~Ws~eel~~m~~gGN~~~n~~~ 84 (318)
++|+.|++.|+|++|+|||+++|+|||++||||||++|+|+||.||+|||+||||+||.|+++||++|+.+||..+|++|
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 hhcCCCCCCChhhhccchHHHHHHHHHHHHHcCCCCCC
Q 021042 85 SQYGIPKETDIVTKYNTNAASIYRDRIQAIAEGRPWRD 122 (318)
Q Consensus 85 e~~~~~~~~~i~~KY~s~aa~~yr~~L~a~~egr~w~~ 122 (318)
+++. +.. ...-.......|+++|+++|+.+.|..
T Consensus 82 e~~~-~~~---~~~~~~~~~~~~~~fI~~KY~~k~f~~ 115 (116)
T PF01412_consen 82 EANS-PPP---KKPPPSSDQEKREQFIRAKYVEKAFIS 115 (116)
T ss_dssp TTTS-TTT---TTHCTTSHHHHHHHHHHHHHTTHTTS-
T ss_pred HcCC-CCC---CCCCCCCcHHHHHHHHHHHHHhhhhcc
Confidence 9771 111 111223445678899999999999975
No 6
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=1.1e-35 Score=280.71 Aligned_cols=115 Identities=41% Similarity=0.815 Sum_probs=100.6
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 021042 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (318)
Q Consensus 3 a~~~L~~L~~~p~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~LGvhiS~VrSitmD~Ws~eel~~m~~gGN~~~n~ 82 (318)
.+++|++|++.|+|+.|+|||++.|+|||+++|||||+.|+||||.||||||+||||+||.|++|||+.|+..||.++|.
T Consensus 12 ~~~~l~~Ll~~~~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~~GN~~an~ 91 (287)
T KOG0703|consen 12 NKRRLRELLREPDNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMISMGNAKANS 91 (287)
T ss_pred HHHHHHHHHcCcccCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHHHcchhhhh
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcCCCCCCChhhhccchHHH-HHHHHHHHHHcCCCCCCCc
Q 021042 83 FLSQYGIPKETDIVTKYNTNAAS-IYRDRIQAIAEGRPWRDPP 124 (318)
Q Consensus 83 ~~e~~~~~~~~~i~~KY~s~aa~-~yr~~L~a~~egr~w~~~p 124 (318)
|||+. ++.. |+..-.. ..-.+|++|||-++|+++.
T Consensus 92 ~~ea~-~p~~------~~~p~~d~~~e~FIR~KYE~kkf~~~~ 127 (287)
T KOG0703|consen 92 YYEAK-LPDP------FRRPGPDDLVEQFIRDKYERKKFLDPE 127 (287)
T ss_pred hcccc-CCcc------ccCCChHHHHHHHHHHHHhhhhhccch
Confidence 99976 3322 2211111 3455899999999999875
No 7
>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=1.6e-34 Score=239.88 Aligned_cols=107 Identities=43% Similarity=0.775 Sum_probs=94.0
Q ss_pred CCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHHHHhhcCCCCCC
Q 021042 14 PGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTFLSQYGIPKET 93 (318)
Q Consensus 14 p~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~LGvhiS~VrSitmD~Ws~eel~~m~~gGN~~~n~~~e~~~~~~~~ 93 (318)
|+|++|+||++++|+|||++||||||++|+|+||.||+|||+||||+||+|+++||++|+.+||..+|+||+.+..+...
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 58999999999999999999999999999999999999999999999999999999999999999999999987644321
Q ss_pred ChhhhccchHHHHHHHHHHHHHcCCCCCCC
Q 021042 94 DIVTKYNTNAASIYRDRIQAIAEGRPWRDP 123 (318)
Q Consensus 94 ~i~~KY~s~aa~~yr~~L~a~~egr~w~~~ 123 (318)
.. -.......|+++|+.+|+.+.|+++
T Consensus 81 ~~---~~~~~~~~~~~fI~~KY~~k~f~~~ 107 (112)
T smart00105 81 KP---PDSDDQQKYESFIAAKYEEKLFVPP 107 (112)
T ss_pred CC---CCCchHHHHHHHHHHHHHhhhcccc
Confidence 11 1122356789999999999999874
No 8
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=99.96 E-value=2.7e-29 Score=252.99 Aligned_cols=114 Identities=24% Similarity=0.517 Sum_probs=96.9
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 021042 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (318)
Q Consensus 3 a~~~L~~L~~~p~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~LGvhiS~VrSitmD~Ws~eel~~m~~gGN~~~n~ 82 (318)
.+++|++|++.|+|++|+||++++|+|||++||||||++|+||||.|| | +||||+||+|+++||++|+.+||+++|+
T Consensus 10 nekILreLlklPgNk~CADCgs~~P~WASiNlGIFICi~CSGIHRsLG-h--RVKSLSLDkWT~EEVe~Mk~gGN~~AN~ 86 (648)
T PLN03119 10 NEKIIRGLMKLPPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREFT-H--RVKSVSMSKFTSKEVEVLQNGGNQRARE 86 (648)
T ss_pred HHHHHHHHhhCcCCCccccCCCCCCCceeeccceEEeccchhhhccCC-c--eeeccccCCCCHHHHHHHHHhchHHHHH
Confidence 467899999999999999999999999999999999999999999998 3 8999999999999999999999999999
Q ss_pred HHhhcCCCCCCChhhhccchHHHHHHHHHHHHHcCCCCCC
Q 021042 83 FLSQYGIPKETDIVTKYNTNAASIYRDRIQAIAEGRPWRD 122 (318)
Q Consensus 83 ~~e~~~~~~~~~i~~KY~s~aa~~yr~~L~a~~egr~w~~ 122 (318)
||+++..+....+. .....+..+++|+.+|+.|.|..
T Consensus 87 iyeanw~~~~~~~P---~~sD~e~lr~FIR~KYVeKRF~~ 123 (648)
T PLN03119 87 IYLKNWDHQRQRLP---ENSNAERVREFIKNVYVQKKYAG 123 (648)
T ss_pred HHHhhcccccCCCC---CCccHHHHHHHHHHHHhhhhccC
Confidence 99975322211111 11123456789999999999985
No 9
>PLN03131 hypothetical protein; Provisional
Probab=99.96 E-value=3.2e-29 Score=254.15 Aligned_cols=114 Identities=24% Similarity=0.516 Sum_probs=96.6
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 021042 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (318)
Q Consensus 3 a~~~L~~L~~~p~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~LGvhiS~VrSitmD~Ws~eel~~m~~gGN~~~n~ 82 (318)
.+++|++|++.|+|++|+||++++|+|||++||||||++|+||||.|| | +||||+||+|+++||++|+.+||+++|+
T Consensus 10 nekiLreLlk~PgNk~CADCga~~P~WASiNlGIFICi~CSGIHRsLg-h--RVKSVTLD~WtdeEV~~Mk~gGN~~AN~ 86 (705)
T PLN03131 10 NEKIIRGLMKLPPNRRCINCNSLGPQFVCTNFWTFICMTCSGIHREFT-H--RVKSVSMSKFTSQDVEALQNGGNQRARE 86 (705)
T ss_pred HHHHHHHHhhCcCCCccccCCCCCCCeeEeccceEEchhchhhhcccC-c--ccccccCCCCCHHHHHHHHHhccHHHHH
Confidence 467899999999999999999999999999999999999999999997 4 8999999999999999999999999999
Q ss_pred HHhhcCCCCCCChhhhccchHHHHHHHHHHHHHcCCCCCC
Q 021042 83 FLSQYGIPKETDIVTKYNTNAASIYRDRIQAIAEGRPWRD 122 (318)
Q Consensus 83 ~~e~~~~~~~~~i~~KY~s~aa~~yr~~L~a~~egr~w~~ 122 (318)
||+++.......+.. .......+++|+.+|+.|+|..
T Consensus 87 iyeanwd~~r~~lP~---~sd~ekrr~FIR~KYVeKRFa~ 123 (705)
T PLN03131 87 IYLKDWDQQRQRLPD---NSKVDKIREFIKDIYVDKKYAG 123 (705)
T ss_pred HHHhhcccccCCCCC---CccHHHHHHHHHHHHhhhhhhc
Confidence 999653222111211 1223456889999999999975
No 10
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.85 E-value=4.1e-22 Score=201.24 Aligned_cols=113 Identities=38% Similarity=0.682 Sum_probs=93.0
Q ss_pred HHHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHHH
Q 021042 4 TRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTF 83 (318)
Q Consensus 4 ~~~L~~L~~~p~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~LGvhiS~VrSitmD~Ws~eel~~m~~gGN~~~n~~ 83 (318)
+-.|+.|+..++|..|+||+.++|.|||+++|+.||++|+||||.||.|+|+|||+.||.|..|.+..|...||+.+|.+
T Consensus 501 a~a~qairn~rgn~~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl~~Vm~aiGN~~AN~v 580 (749)
T KOG0705|consen 501 AMALQAIRNMRGNSHCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVELLKVMSAIGNDLANSV 580 (749)
T ss_pred HHHHHHHhcCcCCceeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHHHHHHHHhhhhHHHHH
Confidence 34678899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Hhh--cCCCCCCChhhhccchHHHHH-HHHHHHHHcCCCCCCC
Q 021042 84 LSQ--YGIPKETDIVTKYNTNAASIY-RDRIQAIAEGRPWRDP 123 (318)
Q Consensus 84 ~e~--~~~~~~~~i~~KY~s~aa~~y-r~~L~a~~egr~w~~~ 123 (318)
||. .|..++. -+....- ..+|+++||.+.|..|
T Consensus 581 WE~~~~G~~KPs-------~~s~REEkErwIr~KYeqklFLaP 616 (749)
T KOG0705|consen 581 WEGSSQGQTKPS-------PDSSREEKERWIRAKYEQKLFLAP 616 (749)
T ss_pred hhhhccCCcCCC-------ccccHHHHHHHHHHHHHHHhhcCC
Confidence 995 2322211 1111111 2257777777777654
No 11
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.79 E-value=2.7e-20 Score=197.14 Aligned_cols=81 Identities=44% Similarity=0.882 Sum_probs=78.7
Q ss_pred HHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHHHHhh
Q 021042 7 LRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTFLSQ 86 (318)
Q Consensus 7 L~~L~~~p~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~LGvhiS~VrSitmD~Ws~eel~~m~~gGN~~~n~~~e~ 86 (318)
+..+++.|+|..|+|||++.|+|+|+|+||.+|++|+|+||.||||||+|||++||.|..+.+..|+..||..+|.+||+
T Consensus 417 ~~~vq~~pgN~~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~~~~l~~l~~~lgn~~~N~i~e~ 496 (785)
T KOG0521|consen 417 IEEVQSVPGNAQCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVWEPELLLLFKNLGNKYVNEIYEA 496 (785)
T ss_pred hhhhhcCCchhhhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhccCcHHHHHHHHhCcchhhhhhhc
Confidence 67789999999999999999999999999999999999999999999999999999999999999999999999999996
Q ss_pred c
Q 021042 87 Y 87 (318)
Q Consensus 87 ~ 87 (318)
.
T Consensus 497 ~ 497 (785)
T KOG0521|consen 497 L 497 (785)
T ss_pred c
Confidence 4
No 12
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.65 E-value=5.8e-17 Score=162.11 Aligned_cols=111 Identities=27% Similarity=0.481 Sum_probs=90.0
Q ss_pred hcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHHHHhhcCCC
Q 021042 11 QSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTFLSQYGIP 90 (318)
Q Consensus 11 ~~~p~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~LGvhiS~VrSitmD~Ws~eel~~m~~gGN~~~n~~~e~~~~~ 90 (318)
++...-++|+|||+++|.||||+-|+|||.+|..+||.||.|||.||++....|.++.|+++....|..+|.+||.+.++
T Consensus 3 k~~l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaNsIWEh~Lld 82 (669)
T KOG0818|consen 3 KRLLSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGANSIWEHSLLD 82 (669)
T ss_pred ccchhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcchhhhhhccC
Confidence 34456789999999999999999999999999999999999999999999999999999999999999999999976555
Q ss_pred CC--------CChhhhccchHHHHHHHHHHHHHcCCCCCCCcc
Q 021042 91 KE--------TDIVTKYNTNAASIYRDRIQAIAEGRPWRDPPV 125 (318)
Q Consensus 91 ~~--------~~i~~KY~s~aa~~yr~~L~a~~egr~w~~~p~ 125 (318)
.. ...++|-+... .+||+++|+-..|...++
T Consensus 83 ~st~~sg~rk~~pqD~~Hp~K----~eFIkaKy~~LtFv~~~~ 121 (669)
T KOG0818|consen 83 PATIMSGRRKANPQDKVHPNK----AEFIRAKYQMLAFVHRLP 121 (669)
T ss_pred chhhhcccCCCCCcCCCCccH----HHHHHHHHHheeeeccCC
Confidence 32 12234444332 346777777777776443
No 13
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.50 E-value=6.3e-15 Score=154.47 Aligned_cols=80 Identities=38% Similarity=0.677 Sum_probs=74.7
Q ss_pred HHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccC--CCCHHHHHHHHhcChHHHHHHHh
Q 021042 8 RDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMD--SWSEIQIKKMEAGGNERLNTFLS 85 (318)
Q Consensus 8 ~~L~~~p~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~LGvhiS~VrSitmD--~Ws~eel~~m~~gGN~~~n~~~e 85 (318)
..+-....|+.|+||+++.|.|||+|+++.||-.|+|-||+||.-+|+|||++|| .|+.+-|+++...||.++|.||.
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 3455678899999999999999999999999999999999999999999999999 59999999999999999999997
Q ss_pred hc
Q 021042 86 QY 87 (318)
Q Consensus 86 ~~ 87 (318)
.+
T Consensus 370 ~n 371 (1186)
T KOG1117|consen 370 GN 371 (1186)
T ss_pred cC
Confidence 53
No 14
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.46 E-value=7.3e-14 Score=139.88 Aligned_cols=117 Identities=18% Similarity=0.371 Sum_probs=96.8
Q ss_pred HHHHHHHhcCCCCCCccCCCCCCC-CceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 021042 4 TRRLRDLQSQPGNKICVDCAQKNP-QWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (318)
Q Consensus 4 ~~~L~~L~~~p~Nk~C~DCga~~P-~WaSv~~GiFICl~CsgiHR~LGvhiS~VrSitmD~Ws~eel~~m~~gGN~~~n~ 82 (318)
..+||.|+++|+|++|++|....+ +|++++-|-|+|+.|+|.-|+|.. -++||||+|..|++.|+..++.+||+.+++
T Consensus 13 ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~~-ahRvksiSmttft~qevs~lQshgNq~~k~ 91 (524)
T KOG0702|consen 13 EKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLNP-AHRVKSISMTTFTDQEVSFLQSHGNQVCKE 91 (524)
T ss_pred HHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccCCC-ccccceeeeeeccccchHHHhhcchhhhhh
Confidence 678999999999999999999888 999999999999999999999853 248999999999999999999999999999
Q ss_pred HHhhcCCCCCCChhhhccchHHHHHHHHHHHHHcCCCCCCCc
Q 021042 83 FLSQYGIPKETDIVTKYNTNAASIYRDRIQAIAEGRPWRDPP 124 (318)
Q Consensus 83 ~~e~~~~~~~~~i~~KY~s~aa~~yr~~L~a~~egr~w~~~p 124 (318)
+|-+.-......+. +.+.....|++|+.+|++++|+.++
T Consensus 92 i~fkl~D~q~S~vP---D~rn~~~~kef~q~~y~~kr~~v~~ 130 (524)
T KOG0702|consen 92 IWFKLFDFQRSNVP---DSRNPQKVKEFQQEKYVKKRYYVPK 130 (524)
T ss_pred hhhcchhhhhccCC---CcccchhhHHHHhhhhccceeecCc
Confidence 88542111111122 2233345789999999999999875
No 15
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=90.85 E-value=0.06 Score=58.61 Aligned_cols=70 Identities=14% Similarity=0.277 Sum_probs=56.6
Q ss_pred hcCCCCCCccCCCC-CCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 021042 11 QSQPGNKICVDCAQ-KNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (318)
Q Consensus 11 ~~~p~Nk~C~DCga-~~P~WaSv~~GiFICl~CsgiHR~LGvhiS~VrSitmD~Ws~eel~~m~~gGN~~~n~ 82 (318)
.....+-.|++|.+ ..-.|+++++.+-+|..|+++|+.++.|++..+++.+|...+ |.....-||..++.
T Consensus 625 ~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~ 695 (785)
T KOG0521|consen 625 VKASSDGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHH 695 (785)
T ss_pred HHhccCccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchh
Confidence 34445788999988 688899999999999999999999999999999999988887 44444445554444
No 16
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=84.39 E-value=0.67 Score=42.64 Aligned_cols=38 Identities=24% Similarity=0.419 Sum_probs=30.0
Q ss_pred HHHHhcCCCCCCccCCCCCCC-CceEeccceeeehhhhh
Q 021042 7 LRDLQSQPGNKICVDCAQKNP-QWASVSYGVFMCLECSG 44 (318)
Q Consensus 7 L~~L~~~p~Nk~C~DCga~~P-~WaSv~~GiFICl~Csg 44 (318)
|..+=-.|.-..|+-||.+.. .|.++..|.|+|..|..
T Consensus 140 L~~~G~~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~ 178 (247)
T PRK00085 140 LAELGYGLDLDHCAVCGAPGDHRYFSPKEGGAVCSECGD 178 (247)
T ss_pred HHHcCCccchhhHhcCCCCCCceEEecccCCcccccccC
Confidence 333444566789999999754 78999999999999973
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=79.64 E-value=1.9 Score=29.11 Aligned_cols=34 Identities=18% Similarity=0.387 Sum_probs=29.2
Q ss_pred CCCCccCCCCCCCCceEeccceeeehhhhhh-hcc
Q 021042 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGK-HRG 48 (318)
Q Consensus 15 ~Nk~C~DCga~~P~WaSv~~GiFICl~Csgi-HR~ 48 (318)
.+..|..|......+-..+-.++||..|... |+.
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 4678999998888899999999999999987 987
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=78.07 E-value=1.7 Score=39.77 Aligned_cols=39 Identities=28% Similarity=0.532 Sum_probs=30.2
Q ss_pred HHHHhcCCCCCCccCCCCCCC-CceEeccceeeehhhhhh
Q 021042 7 LRDLQSQPGNKICVDCAQKNP-QWASVSYGVFMCLECSGK 45 (318)
Q Consensus 7 L~~L~~~p~Nk~C~DCga~~P-~WaSv~~GiFICl~Csgi 45 (318)
|..+=-.|.-..|+.||..++ .+.++..|.|+|.+|...
T Consensus 138 L~~~G~~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 138 LQILGYALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred HHHcCCCcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 333444667789999998544 688999999999999764
No 19
>PRK12495 hypothetical protein; Provisional
Probab=77.03 E-value=1.7 Score=40.78 Aligned_cols=29 Identities=21% Similarity=0.399 Sum_probs=23.9
Q ss_pred CCCCCCccCCCCCCCCceEeccceeeehhhhhh
Q 021042 13 QPGNKICVDCAQKNPQWASVSYGVFMCLECSGK 45 (318)
Q Consensus 13 ~p~Nk~C~DCga~~P~WaSv~~GiFICl~Csgi 45 (318)
...++.|-+||.+-|.. -|+.+|..|..+
T Consensus 39 tmsa~hC~~CG~PIpa~----pG~~~Cp~CQ~~ 67 (226)
T PRK12495 39 TMTNAHCDECGDPIFRH----DGQEFCPTCQQP 67 (226)
T ss_pred ccchhhcccccCcccCC----CCeeECCCCCCc
Confidence 44799999999999932 699999999855
No 20
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=77.02 E-value=2.5 Score=34.40 Aligned_cols=43 Identities=21% Similarity=0.622 Sum_probs=32.1
Q ss_pred hHHHHHHHH-hcCCCCCCccCCCCCCCCceEeccceeeehhhhhhh
Q 021042 2 AATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKH 46 (318)
Q Consensus 2 ~a~~~L~~L-~~~p~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiH 46 (318)
..|+..++| .....-..|-.|+.+ .---+..||+.|..|--.-
T Consensus 20 ~~Rrrv~~ie~~~~~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 20 KLRRRVKEIEAQQRAKHVCPFCGRT--TVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred HHHHHHHHHHHHHhcCCcCCCCCCc--ceeeeccCeEEcCCCCCee
Confidence 356666665 445567799999998 5567789999999996543
No 21
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=71.39 E-value=2.3 Score=40.15 Aligned_cols=32 Identities=28% Similarity=0.665 Sum_probs=27.4
Q ss_pred cCCCCCCccCCCCCC-CCceEeccceeeehhhh
Q 021042 12 SQPGNKICVDCAQKN-PQWASVSYGVFMCLECS 43 (318)
Q Consensus 12 ~~p~Nk~C~DCga~~-P~WaSv~~GiFICl~Cs 43 (318)
-.+.=..|+.||.+. |...|+..|-++|.+|+
T Consensus 150 ~~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 150 IGPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred CccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 345667899999974 47999999999999999
No 22
>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=64.26 E-value=4.2 Score=28.04 Aligned_cols=27 Identities=22% Similarity=0.502 Sum_probs=21.5
Q ss_pred CccCCCCCCCCceEeccceeeehhhhhh
Q 021042 18 ICVDCAQKNPQWASVSYGVFMCLECSGK 45 (318)
Q Consensus 18 ~C~DCga~~P~WaSv~~GiFICl~Csgi 45 (318)
+|-.||+.. .-....-|-++|..|--+
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 699999977 566678999999999543
No 23
>PRK11019 hypothetical protein; Provisional
Probab=64.16 E-value=2.4 Score=34.44 Aligned_cols=37 Identities=19% Similarity=0.510 Sum_probs=25.7
Q ss_pred CCCCccCCCCCCC--CceEeccceeeehhhhhhhccCCCc
Q 021042 15 GNKICVDCAQKNP--QWASVSYGVFMCLECSGKHRGLGVH 52 (318)
Q Consensus 15 ~Nk~C~DCga~~P--~WaSv~~GiFICl~CsgiHR~LGvh 52 (318)
.-..|.|||.+=| .+.-+. ++-.|++|...+-..+.|
T Consensus 35 syg~C~~CG~~Ip~~Rl~A~P-~a~~Cv~Cq~~~E~~~k~ 73 (88)
T PRK11019 35 SLTECEECGEPIPEARRKAIP-GVRLCVACQQEKDLQQAA 73 (88)
T ss_pred cCCeeCcCCCcCcHHHHhhcC-CccccHHHHHHHHHHHhH
Confidence 4579999999755 343333 677899999877654444
No 24
>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=63.33 E-value=5.6 Score=26.68 Aligned_cols=32 Identities=28% Similarity=0.726 Sum_probs=23.5
Q ss_pred ccCCCC-CCCCceEecccee-eehhhhhhhccCC
Q 021042 19 CVDCAQ-KNPQWASVSYGVF-MCLECSGKHRGLG 50 (318)
Q Consensus 19 C~DCga-~~P~WaSv~~GiF-ICl~CsgiHR~LG 50 (318)
|..|+. ..|.|=....|-. ||-.|--.+|..+
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 889998 5899998888888 9999988777543
No 25
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=61.31 E-value=7.7 Score=28.15 Aligned_cols=38 Identities=21% Similarity=0.531 Sum_probs=31.0
Q ss_pred CCCCccCCCC-CCCCceEeccce-eeehhhhhhhccCCCc
Q 021042 15 GNKICVDCAQ-KNPQWASVSYGV-FMCLECSGKHRGLGVH 52 (318)
Q Consensus 15 ~Nk~C~DCga-~~P~WaSv~~Gi-FICl~CsgiHR~LGvh 52 (318)
....|..|+. ..|+|=.-..|- +||-.|.-..+..+..
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC
Confidence 4678999998 589998888886 9999999877765543
No 26
>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=58.49 E-value=3.8 Score=31.00 Aligned_cols=34 Identities=26% Similarity=0.558 Sum_probs=23.2
Q ss_pred cCCCCCCccCCCCCCCC--ceEeccceeeehhhhhhh
Q 021042 12 SQPGNKICVDCAQKNPQ--WASVSYGVFMCLECSGKH 46 (318)
Q Consensus 12 ~~p~Nk~C~DCga~~P~--WaSv~~GiFICl~CsgiH 46 (318)
..++...|.|||.+=|. +.- --|+..|.+|...|
T Consensus 27 ~~~s~g~C~~Cg~~Ip~~Rl~a-~p~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 27 IGPSLRECEDCGEPIPEARREA-LPGVTRCVSCQEIL 62 (63)
T ss_pred cCCCCCeeccCCCcChHHHHhh-cCCcCCcHHHHhhc
Confidence 34567799999996542 222 23678899998754
No 27
>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=56.65 E-value=7 Score=27.97 Aligned_cols=27 Identities=26% Similarity=0.819 Sum_probs=20.7
Q ss_pred CccCCCCCCCCceEeccceeeehhhhhh
Q 021042 18 ICVDCAQKNPQWASVSYGVFMCLECSGK 45 (318)
Q Consensus 18 ~C~DCga~~P~WaSv~~GiFICl~Csgi 45 (318)
+|+=|+.+.+. --.=+|.|||.+|-.-
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~~ 27 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEKE 27 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHHH
Confidence 48889988776 4445889999999753
No 28
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=54.24 E-value=3.8 Score=41.00 Aligned_cols=49 Identities=18% Similarity=0.254 Sum_probs=35.0
Q ss_pred CcccchhhHHHHh-h----h---hhhhHhHHHH-HHHH--hhhhcch-----hHHHHHhhhhcCc
Q 021042 258 NTNSQGDVLSAVS-Q----G---FGRISLVAAS-AAQS--AATVVQA-----GTREFTSKLFLSE 306 (318)
Q Consensus 258 ~~~~~~d~~~~ls-~----G---w~~fs~~a~~-~~~~--~~~v~~~-----g~~~~~~~~~~~~ 306 (318)
.++++.|||++|+ | | |++|+.++.. +... .++|++| |..++++-++.++
T Consensus 247 l~~~~s~~v~~va~k~t~vG~r~W~~ls~~~sq~~e~fq~~~s~g~~~~qn~~~~n~~sn~~~g~ 311 (386)
T KOG0704|consen 247 LDDFVSDPVGTVASKVTEVGTRGWGLLSAAVSQSVEDFQDSESVGGPYYQNSGQGNFSSNSKRGG 311 (386)
T ss_pred hhhhcccchhhhhhhcccccccchhhhHHhhccccccccccCccCCccccccccccccccccccc
Confidence 3689999999999 5 4 9999977744 5555 7888887 5555555554443
No 29
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=53.22 E-value=15 Score=30.04 Aligned_cols=40 Identities=20% Similarity=0.549 Sum_probs=30.7
Q ss_pred HHHHHHHH-hcCCCCCCccCCCCCCCCceEeccceeeehhhhh
Q 021042 3 ATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECSG 44 (318)
Q Consensus 3 a~~~L~~L-~~~p~Nk~C~DCga~~P~WaSv~~GiFICl~Csg 44 (318)
.|+.+++| .....-..|.-||........+ ||+-|..|.-
T Consensus 22 lRK~v~kie~~q~a~y~CpfCgk~~vkR~a~--GIW~C~~C~~ 62 (90)
T PTZ00255 22 LRKQIKKIEISQHAKYFCPFCGKHAVKRQAV--GIWRCKGCKK 62 (90)
T ss_pred HHHHHHHHHHHHhCCccCCCCCCCceeeeee--EEEEcCCCCC
Confidence 46667776 5566778999999877666655 9999999964
No 30
>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=51.79 E-value=12 Score=25.39 Aligned_cols=27 Identities=26% Similarity=0.728 Sum_probs=23.1
Q ss_pred CCCCCccCCCCCCCCceEeccceeeehhhh
Q 021042 14 PGNKICVDCAQKNPQWASVSYGVFMCLECS 43 (318)
Q Consensus 14 p~Nk~C~DCga~~P~WaSv~~GiFICl~Cs 43 (318)
..|..|..|++. |....=|-++|..|-
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 888899999999885
No 31
>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=47.29 E-value=13 Score=29.50 Aligned_cols=31 Identities=23% Similarity=0.651 Sum_probs=25.6
Q ss_pred CCCCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 021042 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 15 ~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~ 48 (318)
.|..|.-|+.+. ....||++.|..|.+..|-
T Consensus 2 ~~~~C~VCg~~~---~g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 2 DTHFCAVCSDYA---SGYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CCCCCeecCCcC---cceEECceeehhhHHhHHH
Confidence 467899999754 3579999999999998874
No 32
>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=46.15 E-value=7.4 Score=26.32 Aligned_cols=27 Identities=15% Similarity=0.533 Sum_probs=16.4
Q ss_pred CCccCCCCC-CCCceEeccceeeehhhh
Q 021042 17 KICVDCAQK-NPQWASVSYGVFMCLECS 43 (318)
Q Consensus 17 k~C~DCga~-~P~WaSv~~GiFICl~Cs 43 (318)
..|.+|+.+ .=.|..-+|+.-+|..|.
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 479999994 667999999999999995
No 33
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=45.28 E-value=7 Score=33.39 Aligned_cols=30 Identities=23% Similarity=0.665 Sum_probs=20.1
Q ss_pred CccCCCCCCCC-ceEeccceeeehhhhhhhc
Q 021042 18 ICVDCAQKNPQ-WASVSYGVFMCLECSGKHR 47 (318)
Q Consensus 18 ~C~DCga~~P~-WaSv~~GiFICl~CsgiHR 47 (318)
+|.+||.+=|. =.-.--+..+|++|.-.|-
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 89999997431 1122235788999998764
No 34
>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=45.26 E-value=3.8 Score=27.30 Aligned_cols=29 Identities=31% Similarity=0.787 Sum_probs=16.7
Q ss_pred CccCCCCCCCC-ceEeccceeeehhhhhhh
Q 021042 18 ICVDCAQKNPQ-WASVSYGVFMCLECSGKH 46 (318)
Q Consensus 18 ~C~DCga~~P~-WaSv~~GiFICl~CsgiH 46 (318)
.|.+||.+=|. -.-+--+..+|..|+..|
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 49999985321 112223678899998765
No 35
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=44.21 E-value=9.6 Score=29.74 Aligned_cols=37 Identities=24% Similarity=0.536 Sum_probs=23.8
Q ss_pred CCCccCCCCCCCCc-eEeccceeeehhhhhhhccCCCc
Q 021042 16 NKICVDCAQKNPQW-ASVSYGVFMCLECSGKHRGLGVH 52 (318)
Q Consensus 16 Nk~C~DCga~~P~W-aSv~~GiFICl~CsgiHR~LGvh 52 (318)
...|.|||.+=|.= .-.--|+..|++|...+-.-+.|
T Consensus 34 ~~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~E~~~~~ 71 (73)
T PRK13715 34 VYLCEACGNPIPEARRKIFPGVTLCVECQAYQERQRKH 71 (73)
T ss_pred cccHhhcCCcCCHHHHhcCCCcCCCHHHHHHHHHHhcc
Confidence 45899999975521 11223788899998866543333
No 36
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=43.51 E-value=15 Score=29.98 Aligned_cols=40 Identities=23% Similarity=0.563 Sum_probs=29.6
Q ss_pred HHHHHHHH-hcCCCCCCccCCCCCCCCceEeccceeeehhhhh
Q 021042 3 ATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECSG 44 (318)
Q Consensus 3 a~~~L~~L-~~~p~Nk~C~DCga~~P~WaSv~~GiFICl~Csg 44 (318)
.|+.+.+| ......-.|.-||.... --+..|||-|..|--
T Consensus 21 lRK~vkkie~~q~~ky~Cp~Cgk~~v--kR~a~GIW~C~~C~~ 61 (90)
T PF01780_consen 21 LRKRVKKIEISQHAKYTCPFCGKTSV--KRVATGIWKCKKCGK 61 (90)
T ss_dssp HHHHHHHHHHHHHS-BEESSSSSSEE--EEEETTEEEETTTTE
T ss_pred HHHHHHHHHHHHhCCCcCCCCCCcee--EEeeeEEeecCCCCC
Confidence 45666665 45667889999999874 455789999999974
No 37
>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=41.27 E-value=16 Score=27.22 Aligned_cols=28 Identities=29% Similarity=0.623 Sum_probs=23.5
Q ss_pred CCCCccCCCCCCCCceEeccceeeehhhhh
Q 021042 15 GNKICVDCAQKNPQWASVSYGVFMCLECSG 44 (318)
Q Consensus 15 ~Nk~C~DCga~~P~WaSv~~GiFICl~Csg 44 (318)
--+.|..||..... ..+.-+|.|..|--
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 46789999998887 77888999999854
No 38
>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=40.91 E-value=18 Score=29.40 Aligned_cols=31 Identities=32% Similarity=0.692 Sum_probs=25.6
Q ss_pred CCCCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 021042 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 15 ~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~ 48 (318)
++..|.-||.+. ....||++.|..|.+..|-
T Consensus 4 ~~~~C~VCg~~~---~g~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 4 EVIPCKICGDKS---SGIHYGVITCEGCKGFFRR 34 (95)
T ss_pred cccCCcccCCcC---cceEECceeehhhHHhhHH
Confidence 567899999865 4468999999999998874
No 39
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=39.71 E-value=24 Score=36.25 Aligned_cols=39 Identities=26% Similarity=0.451 Sum_probs=22.3
Q ss_pred eeeehhhhhhhccCCCcc-----cceeecc----cCCCCH-HHHHHHHh
Q 021042 36 VFMCLECSGKHRGLGVHI-----SFVRSVT----MDSWSE-IQIKKMEA 74 (318)
Q Consensus 36 iFICl~CsgiHR~LGvhi-----S~VrSit----mD~Ws~-eel~~m~~ 74 (318)
.+||+.|-..--.+|+|- -.|...+ --.|+. |||++++.
T Consensus 38 fdLCl~CFs~GaE~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLea 86 (438)
T KOG0457|consen 38 FDLCLQCFSVGAETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLEA 86 (438)
T ss_pred cchhHHHHhcccccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHHH
Confidence 578999986544455542 1233312 136886 66776654
No 40
>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=39.01 E-value=19 Score=29.52 Aligned_cols=30 Identities=23% Similarity=0.674 Sum_probs=24.5
Q ss_pred CCCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 021042 16 NKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 16 Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~ 48 (318)
+..|.-|+.+. ....||++.|..|.+..|-
T Consensus 4 ~~~C~VCg~~a---~g~hyGv~sC~aCk~FFRR 33 (97)
T cd07170 4 KRLCLVCGDIA---SGYHYGVASCEACKAFFKR 33 (97)
T ss_pred CCCCeecCCcC---cceEECceeehhhhHHHHH
Confidence 35799999765 3568999999999998874
No 41
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=38.78 E-value=13 Score=25.03 Aligned_cols=30 Identities=20% Similarity=0.404 Sum_probs=15.5
Q ss_pred CCccCCCCCCCCceEe---ccceeeehhhhhhhc
Q 021042 17 KICVDCAQKNPQWASV---SYGVFMCLECSGKHR 47 (318)
Q Consensus 17 k~C~DCga~~P~WaSv---~~GiFICl~CsgiHR 47 (318)
|.|-.||.+ -.+.-+ +.--++|..|.-||-
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 578899986 233322 445678999998883
No 42
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=38.56 E-value=19 Score=28.50 Aligned_cols=32 Identities=25% Similarity=0.657 Sum_probs=25.7
Q ss_pred CCCCCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 021042 14 PGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 14 p~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~ 48 (318)
|..+.|.-|+.+.- ...||++-|..|.+..|-
T Consensus 1 ~~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 32 (82)
T cd07173 1 PPQKTCLICGDEAS---GCHYGALTCGSCKVFFKR 32 (82)
T ss_pred CCCCCCeecCCcCc---ceEECcchhhhHHHHHHH
Confidence 34677999997553 578999999999998874
No 43
>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=36.79 E-value=41 Score=23.45 Aligned_cols=39 Identities=18% Similarity=0.514 Sum_probs=26.3
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhh
Q 021042 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECS 43 (318)
Q Consensus 3 a~~~L~~L~~~p~Nk~C~DCga~~P~WaSv~~GiFICl~Cs 43 (318)
+.+.|.+|+ -+..-+|.-||....-+..- .+.|-|-.|.
T Consensus 6 c~~~l~~~R-W~~g~~CP~Cg~~~~~~~~~-~~~~~C~~C~ 44 (46)
T PF12760_consen 6 CREYLEEIR-WPDGFVCPHCGSTKHYRLKT-RGRYRCKACR 44 (46)
T ss_pred HHHHHHHhc-CCCCCCCCCCCCeeeEEeCC-CCeEECCCCC
Confidence 455565554 44557899999985544433 6889998884
No 44
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=35.87 E-value=24 Score=34.25 Aligned_cols=34 Identities=15% Similarity=0.438 Sum_probs=24.5
Q ss_pred CCCCCCccCCCCCCCCceEeccceeeehhhhhhhc
Q 021042 13 QPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHR 47 (318)
Q Consensus 13 ~p~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR 47 (318)
......|.+||..+ -=....-|-.||.+|--|..
T Consensus 8 ~~~~~~Cp~Cg~~~-iv~d~~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 8 EEEKLVCPECGSDK-LIYDYERGEIVCADCGLVIE 41 (310)
T ss_pred cccCCcCcCCCCCC-eeEECCCCeEeecccCCccc
Confidence 34566899999743 22345789999999987543
No 45
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=35.58 E-value=15 Score=31.06 Aligned_cols=25 Identities=40% Similarity=0.781 Sum_probs=21.9
Q ss_pred CceEeccc--eeeehhhhhhhccCCCc
Q 021042 28 QWASVSYG--VFMCLECSGKHRGLGVH 52 (318)
Q Consensus 28 ~WaSv~~G--iFICl~CsgiHR~LGvh 52 (318)
.|++-.-| |+-|.+|--|||.-++.
T Consensus 52 ewi~~~~G~~VwSC~dC~~iH~ke~~~ 78 (112)
T COG2158 52 EWISDSNGRKVWSCSDCHWIHRKEGAE 78 (112)
T ss_pred ceeEcCCCCEEeeccccceecccchHH
Confidence 89999999 99999999999975543
No 46
>PHA00080 DksA-like zinc finger domain containing protein
Probab=35.12 E-value=20 Score=27.79 Aligned_cols=35 Identities=23% Similarity=0.561 Sum_probs=23.1
Q ss_pred CCCCCCccCCCCCCC--CceEeccceeeehhhhhhhcc
Q 021042 13 QPGNKICVDCAQKNP--QWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 13 ~p~Nk~C~DCga~~P--~WaSv~~GiFICl~CsgiHR~ 48 (318)
.+....|.|||.+=| .+.-+. ++..|++|...+-.
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 345568999999643 333333 56679999986543
No 47
>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=34.02 E-value=26 Score=28.20 Aligned_cols=32 Identities=22% Similarity=0.742 Sum_probs=26.2
Q ss_pred CCCCCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 021042 14 PGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 14 p~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~ 48 (318)
.+++.|.-|+.+. ....||+..|..|.+..|-
T Consensus 4 ~~~~~C~VCg~~a---~g~hyGv~sC~aCk~FFRR 35 (90)
T cd07169 4 AEQRTCLICGDRA---TGLHYGIISCEGCKGFFKR 35 (90)
T ss_pred ccCCCCeecCCcC---cceEECcceehhhHHHHHH
Confidence 4677899999754 4568999999999998874
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=33.05 E-value=28 Score=28.78 Aligned_cols=31 Identities=35% Similarity=0.832 Sum_probs=25.6
Q ss_pred CCCCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 021042 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 15 ~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~ 48 (318)
.+..|.-|+.+.- ...||+..|..|.+..|-
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 4678999997543 568999999999998874
No 49
>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=32.45 E-value=28 Score=25.49 Aligned_cols=34 Identities=26% Similarity=0.647 Sum_probs=27.9
Q ss_pred CccCCCC-CCCCceEec-cceeeehhhhhhhccCCC
Q 021042 18 ICVDCAQ-KNPQWASVS-YGVFMCLECSGKHRGLGV 51 (318)
Q Consensus 18 ~C~DCga-~~P~WaSv~-~GiFICl~CsgiHR~LGv 51 (318)
+|..|+. .-|+|=... -+..||-.|.-..+..|.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~ 36 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGV 36 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCC
Confidence 5999998 578898765 788999999988877664
No 50
>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=31.74 E-value=23 Score=28.78 Aligned_cols=29 Identities=28% Similarity=0.615 Sum_probs=23.1
Q ss_pred CCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 021042 17 KICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 17 k~C~DCga~~P~WaSv~~GiFICl~CsgiHR~ 48 (318)
+.|.-||.+.- ...||++.|..|.+..|-
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 46888987533 458999999999998874
No 51
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=30.98 E-value=35 Score=28.07 Aligned_cols=34 Identities=21% Similarity=0.636 Sum_probs=24.2
Q ss_pred hcCCCCCCccCCCCCC--------CCc---------eEeccceeeehhhhh
Q 021042 11 QSQPGNKICVDCAQKN--------PQW---------ASVSYGVFMCLECSG 44 (318)
Q Consensus 11 ~~~p~Nk~C~DCga~~--------P~W---------aSv~~GiFICl~Csg 44 (318)
.+.+.--+|+|||.+- ++. .+=.||-.+|..|..
T Consensus 29 kK~~~~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~ 79 (93)
T COG2174 29 KKKPTIPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVR 79 (93)
T ss_pred eccCCCCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHHH
Confidence 4567778999999851 112 234599999999975
No 52
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=30.26 E-value=22 Score=31.61 Aligned_cols=34 Identities=26% Similarity=0.622 Sum_probs=26.6
Q ss_pred CCCCCccCCCCCCCCceEeccceeeeh-hhhhhhcc
Q 021042 14 PGNKICVDCAQKNPQWASVSYGVFMCL-ECSGKHRG 48 (318)
Q Consensus 14 p~Nk~C~DCga~~P~WaSv~~GiFICl-~CsgiHR~ 48 (318)
|--+.|+-||-..+ |.+++.|.-+|. .|-.+|..
T Consensus 116 P~r~fCaVCG~~S~-ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 116 PLRKFCAVCGYDSK-YSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred CcchhhhhcCCCch-hHHHhcCCceeechhhhhccc
Confidence 55678999995444 999999998885 67778764
No 53
>PF14376 Haem_bd: Haem-binding domain
Probab=30.15 E-value=25 Score=30.23 Aligned_cols=14 Identities=29% Similarity=0.847 Sum_probs=11.5
Q ss_pred CCccCCCCCCCCce
Q 021042 17 KICVDCAQKNPQWA 30 (318)
Q Consensus 17 k~C~DCga~~P~Wa 30 (318)
+-|.||++.+..|.
T Consensus 42 ~~CydCHSn~T~~P 55 (137)
T PF14376_consen 42 NSCYDCHSNNTRYP 55 (137)
T ss_pred ccccccCCCCCCCc
Confidence 46999999877765
No 54
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=30.04 E-value=23 Score=26.44 Aligned_cols=39 Identities=23% Similarity=0.539 Sum_probs=27.4
Q ss_pred CCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCccccee
Q 021042 14 PGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVR 57 (318)
Q Consensus 14 p~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~LGvhiS~Vr 57 (318)
++-+.|.-||.+. =+--.||..||..|-.- +-..|.|||
T Consensus 14 kGsr~C~vCg~~~--gliRkygL~~CRqCFRe---~A~~iGF~K 52 (54)
T PTZ00218 14 KGSRQCRVCSNRH--GLIRKYGLNVCRQCFRE---NAELIGFHK 52 (54)
T ss_pred CCCCeeecCCCcc--hhhhhcCcchhhHHHHH---hhHhcCeee
Confidence 4678999999854 23448999999999743 334555554
No 55
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=29.58 E-value=40 Score=23.32 Aligned_cols=22 Identities=23% Similarity=0.646 Sum_probs=14.1
Q ss_pred CccCCCCCCCCceEeccceeee
Q 021042 18 ICVDCAQKNPQWASVSYGVFMC 39 (318)
Q Consensus 18 ~C~DCga~~P~WaSv~~GiFIC 39 (318)
+|.+|+..+.-|+++.-+-..|
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c 22 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGC 22 (50)
T ss_pred CcccCCCcCCeEEecCCCCccc
Confidence 5999998776555554444444
No 56
>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=29.37 E-value=30 Score=30.83 Aligned_cols=34 Identities=21% Similarity=0.532 Sum_probs=21.2
Q ss_pred CCCCCccCCCCCCC--CceEeccceeeehhhhhhhcc
Q 021042 14 PGNKICVDCAQKNP--QWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 14 p~Nk~C~DCga~~P--~WaSv~~GiFICl~CsgiHR~ 48 (318)
..=-.|.+||.+=| +.--+. .+-.|+.|...+-.
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 34457999999522 222222 35679999987643
No 57
>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=28.47 E-value=38 Score=24.38 Aligned_cols=34 Identities=24% Similarity=0.615 Sum_probs=22.5
Q ss_pred HhcCCCCCCccCCCCCCC--Cc-------eEeccceeeehhhhh
Q 021042 10 LQSQPGNKICVDCAQKNP--QW-------ASVSYGVFMCLECSG 44 (318)
Q Consensus 10 L~~~p~Nk~C~DCga~~P--~W-------aSv~~GiFICl~Csg 44 (318)
|+.+.+|+ |-=|++..+ .| .+..-.|+||..|..
T Consensus 2 L~~Rs~~k-CELC~a~~~L~vy~Vpp~~~~~~d~~iliC~tC~~ 44 (47)
T smart00782 2 LLARCESK-CELCGSDSPLVVYAVPPSSDVTADNSVMLCDTCHS 44 (47)
T ss_pred hhHHcCCc-ccCcCCCCCceEEecCCCCCCCccceeeechHHHH
Confidence 34444444 999998543 12 245678999999975
No 58
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=28.30 E-value=36 Score=30.04 Aligned_cols=38 Identities=11% Similarity=0.187 Sum_probs=23.9
Q ss_pred cCCCCCCccCCCCCCCC-ceEeccceeeehhhhhhhccC
Q 021042 12 SQPGNKICVDCAQKNPQ-WASVSYGVFMCLECSGKHRGL 49 (318)
Q Consensus 12 ~~p~Nk~C~DCga~~P~-WaSv~~GiFICl~CsgiHR~L 49 (318)
..+.--.|.+||.+=|. =.-+--++..|+.|...|-..
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 44667799999996221 111112356799999887643
No 59
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=28.13 E-value=63 Score=26.53 Aligned_cols=40 Identities=23% Similarity=0.582 Sum_probs=29.8
Q ss_pred HHHHHHHH-hcCCCCCCccCCCCCCCCceEeccceeeehhhhh
Q 021042 3 ATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECSG 44 (318)
Q Consensus 3 a~~~L~~L-~~~p~Nk~C~DCga~~P~WaSv~~GiFICl~Csg 44 (318)
.|+.+++| .....-..|.-|+..... -+..||+-|..|--
T Consensus 21 lRK~v~kie~~q~a~y~CpfCgk~~vk--R~a~GIW~C~~C~~ 61 (91)
T TIGR00280 21 LRRQVKKIEIQQKAKYVCPFCGKKTVK--RGSTGIWTCRKCGA 61 (91)
T ss_pred HHHHHHHHHHHHhcCccCCCCCCCceE--EEeeEEEEcCCCCC
Confidence 46666676 456677899999976644 45779999999964
No 60
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=26.59 E-value=59 Score=26.61 Aligned_cols=40 Identities=20% Similarity=0.623 Sum_probs=29.8
Q ss_pred HHHHHHHH-hcCCCCCCccCCCCCCCCceEeccceeeehhhhh
Q 021042 3 ATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECSG 44 (318)
Q Consensus 3 a~~~L~~L-~~~p~Nk~C~DCga~~P~WaSv~~GiFICl~Csg 44 (318)
.|+.+++| .....-..|.-|+...... +..||+-|..|.-
T Consensus 22 lRK~v~kie~~q~a~y~CpfCgk~~vkR--~a~GIW~C~~C~~ 62 (90)
T PRK03976 22 IRKRVADIEEKMRAKHVCPVCGRPKVKR--VGTGIWECRKCGA 62 (90)
T ss_pred HHHHHHHHHHHHhcCccCCCCCCCceEE--EEEEEEEcCCCCC
Confidence 46666666 4566778999998766654 4679999999864
No 61
>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=25.99 E-value=45 Score=26.52 Aligned_cols=28 Identities=25% Similarity=0.692 Sum_probs=22.1
Q ss_pred CccCCCCCCCCceEeccceeeehhhhhhhcc
Q 021042 18 ICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 18 ~C~DCga~~P~WaSv~~GiFICl~CsgiHR~ 48 (318)
.|.-||.+.- ...||++.|..|.+..|-
T Consensus 1 ~C~VCg~~~~---g~hygv~sC~aC~~FFRR 28 (87)
T cd07162 1 ICRVCGDRAT---GYHFNAMTCEGCKGFFRR 28 (87)
T ss_pred CCcccCCcCc---ceEECcceehhhHHHHHh
Confidence 4777887544 358999999999998764
No 62
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor 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. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=25.57 E-value=49 Score=26.56 Aligned_cols=31 Identities=29% Similarity=0.778 Sum_probs=25.1
Q ss_pred CCCCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 021042 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 15 ~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~ 48 (318)
..+.|.-||.+. ....||+..|..|....|-
T Consensus 5 ~~~~C~VCg~~~---~g~hyGv~sC~aCk~FFRR 35 (90)
T cd07168 5 SPKLCSICEDKA---TGLHYGIITCEGCKGFFKR 35 (90)
T ss_pred cCCCCcccCCcC---cceEECceehhhhhHhhhh
Confidence 456799999754 3579999999999998874
No 63
>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=25.20 E-value=48 Score=26.73 Aligned_cols=29 Identities=24% Similarity=0.750 Sum_probs=23.1
Q ss_pred CCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 021042 17 KICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 17 k~C~DCga~~P~WaSv~~GiFICl~CsgiHR~ 48 (318)
..|.-||.+.- ...||++.|..|.+..|-
T Consensus 2 ~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 30 (91)
T cd07161 2 ELCLVCGDRAS---GYHYNALTCEGCKGFFRR 30 (91)
T ss_pred CCCeeCCCcCc---ceEECceeehhhHHHHHH
Confidence 35888987544 468999999999998873
No 64
>cd06956 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor, or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear rec
Probab=25.15 E-value=52 Score=25.53 Aligned_cols=29 Identities=31% Similarity=0.833 Sum_probs=23.0
Q ss_pred CCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 021042 17 KICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 17 k~C~DCga~~P~WaSv~~GiFICl~CsgiHR~ 48 (318)
+.|.-|+.+.- ...||++.|..|.+..|-
T Consensus 1 ~~C~VC~~~~~---g~hygv~sC~aC~~FFRR 29 (77)
T cd06956 1 HICAICGDRAS---GKHYGVYSCEGCKGFFKR 29 (77)
T ss_pred CCCcccCCcCc---ceEECceeehhHHHHHHH
Confidence 35888887544 468999999999998864
No 65
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=24.79 E-value=77 Score=21.19 Aligned_cols=20 Identities=40% Similarity=0.893 Sum_probs=14.3
Q ss_pred CCCCHHHHHHHHhcChHHHHHHHhhcCCCCC
Q 021042 62 DSWSEIQIKKMEAGGNERLNTFLSQYGIPKE 92 (318)
Q Consensus 62 D~Ws~eel~~m~~gGN~~~n~~~e~~~~~~~ 92 (318)
|.|++++|+ .||+.|++...
T Consensus 2 dtWs~~~L~-----------~wL~~~gi~~~ 21 (38)
T PF10281_consen 2 DTWSDSDLK-----------SWLKSHGIPVP 21 (38)
T ss_pred CCCCHHHHH-----------HHHHHcCCCCC
Confidence 678887765 47888887654
No 66
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.75 E-value=31 Score=31.96 Aligned_cols=24 Identities=29% Similarity=0.599 Sum_probs=20.0
Q ss_pred CCCCccCCCCCCCCceEeccceeeehhhhhh
Q 021042 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGK 45 (318)
Q Consensus 15 ~Nk~C~DCga~~P~WaSv~~GiFICl~Csgi 45 (318)
--+.|.-||. +.-..|.|..|...
T Consensus 308 tS~~C~~cg~-------~~~r~~~C~~cg~~ 331 (364)
T COG0675 308 TSKTCPCCGH-------LSGRLFKCPRCGFV 331 (364)
T ss_pred CcccccccCC-------ccceeEECCCCCCe
Confidence 3489999999 66789999999863
No 67
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=23.69 E-value=30 Score=25.14 Aligned_cols=43 Identities=21% Similarity=0.557 Sum_probs=25.4
Q ss_pred CccCCCCCCCCce--EeccceeeehhhhhhhccCCCcccceeeccc
Q 021042 18 ICVDCAQKNPQWA--SVSYGVFMCLECSGKHRGLGVHISFVRSVTM 61 (318)
Q Consensus 18 ~C~DCga~~P~Wa--Sv~~GiFICl~CsgiHR~LGvhiS~VrSitm 61 (318)
.|+=||..-.-.- -+.=| +||-+|...-..+-..+..++++|+
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 4888888644433 34556 8999999765443323233344444
No 68
>cd07156 NR_DBD_VDR_like The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of vitamin D receptors (VDR) 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. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemi
Probab=23.53 E-value=51 Score=25.20 Aligned_cols=27 Identities=22% Similarity=0.652 Sum_probs=20.4
Q ss_pred ccCCCCCCCCceEeccceeeehhhhhhhcc
Q 021042 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 19 C~DCga~~P~WaSv~~GiFICl~CsgiHR~ 48 (318)
|.-|+.+.- ...||++.|..|.+..|-
T Consensus 1 C~VC~~~~~---g~hygv~sC~aC~~FFRR 27 (72)
T cd07156 1 CGVCGDRAT---GYHFNAMTCEGCKGFFRR 27 (72)
T ss_pred CCccCccCc---ccEECcceehhhhhhhch
Confidence 555666444 358999999999998874
No 69
>PHA02942 putative transposase; Provisional
Probab=22.89 E-value=40 Score=33.92 Aligned_cols=27 Identities=22% Similarity=0.538 Sum_probs=20.6
Q ss_pred CCCCccCCCCCCCCceEeccceeeehhhhh
Q 021042 15 GNKICVDCAQKNPQWASVSYGVFMCLECSG 44 (318)
Q Consensus 15 ~Nk~C~DCga~~P~WaSv~~GiFICl~Csg 44 (318)
--+.|..||...+ .++-.+|.|..|--
T Consensus 324 TSq~Cs~CG~~~~---~l~~r~f~C~~CG~ 350 (383)
T PHA02942 324 SSVSCPKCGHKMV---EIAHRYFHCPSCGY 350 (383)
T ss_pred CCccCCCCCCccC---cCCCCEEECCCCCC
Confidence 3478999998765 34556899999975
No 70
>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers. DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p
Probab=22.81 E-value=57 Score=25.50 Aligned_cols=29 Identities=31% Similarity=0.763 Sum_probs=23.4
Q ss_pred CCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 021042 17 KICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 17 k~C~DCga~~P~WaSv~~GiFICl~CsgiHR~ 48 (318)
+.|.-|+.+. ....||++-|..|.+..|-
T Consensus 3 ~~C~VCg~~a---~g~hyGv~sC~aC~~FFRR 31 (78)
T cd07172 3 KICLVCSDEA---SGCHYGVLTCGSCKVFFKR 31 (78)
T ss_pred CCCeecCCcC---cceEECceeehhhHHhHHH
Confidence 5688898754 3469999999999998863
No 71
>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=22.72 E-value=45 Score=26.11 Aligned_cols=27 Identities=37% Similarity=0.775 Sum_probs=21.0
Q ss_pred ccCCCCCCCCceEeccceeeehhhhhhhcc
Q 021042 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 19 C~DCga~~P~WaSv~~GiFICl~CsgiHR~ 48 (318)
|.-||.+.- ...||++.|..|....|-
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 556776443 469999999999998874
No 72
>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=22.62 E-value=51 Score=25.20 Aligned_cols=27 Identities=37% Similarity=0.816 Sum_probs=20.5
Q ss_pred ccCCCCCCCCceEeccceeeehhhhhhhcc
Q 021042 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 19 C~DCga~~P~WaSv~~GiFICl~CsgiHR~ 48 (318)
|.-|+.+.- ...||++.|..|.+..|-
T Consensus 1 C~VCg~~~~---g~hyGv~~C~aC~~FFRR 27 (73)
T cd07158 1 CKVCGDKAS---GFHYGVHSCEGCKGFFRR 27 (73)
T ss_pred CcccCccCc---ceEECcchhhHHHHHHhh
Confidence 555666443 368999999999998874
No 73
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=22.60 E-value=79 Score=21.77 Aligned_cols=29 Identities=28% Similarity=0.638 Sum_probs=16.9
Q ss_pred CCccCCCCCCC---CceEeccceeeehhhhhh
Q 021042 17 KICVDCAQKNP---QWASVSYGVFMCLECSGK 45 (318)
Q Consensus 17 k~C~DCga~~P---~WaSv~~GiFICl~Csgi 45 (318)
++|.=||.+.. .-++-.-+++||.+|.-.
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNGAYICDECVEQ 33 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-SEEEEHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCCcEECHHHHHH
Confidence 56888988654 334445579999999853
No 74
>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.
Probab=22.36 E-value=44 Score=34.14 Aligned_cols=29 Identities=24% Similarity=0.590 Sum_probs=20.9
Q ss_pred CCCccCCCCCCCCceEecc--ceeeehhhhh
Q 021042 16 NKICVDCAQKNPQWASVSY--GVFMCLECSG 44 (318)
Q Consensus 16 Nk~C~DCga~~P~WaSv~~--GiFICl~Csg 44 (318)
+..|--||.+..+--.+-. ++|||.+|..
T Consensus 7 ~~~c~fc~~~~~~~~~~~~~~~~~ic~~c~~ 37 (413)
T TIGR00382 7 TLYCSFCGKSQDEVRKLIAGPGVYICDECIE 37 (413)
T ss_pred CeecCCCCCChhhcccccCCCCCcCCCchHH
Confidence 4489999997555433333 4899999985
No 75
>cd07163 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. DNA-binding domain of Tailless (TLX) 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. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX 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=22.33 E-value=40 Score=27.17 Aligned_cols=30 Identities=27% Similarity=0.744 Sum_probs=24.7
Q ss_pred CCCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 021042 16 NKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 16 Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~ 48 (318)
|..|.-|+.+.- ...||+..|..|.+..|-
T Consensus 6 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (92)
T cd07163 6 DIPCKVCGDRSS---GKHYGIYACDGCSGFFKR 35 (92)
T ss_pred CCCCcccCCcCc---ccEECceeeeeeeeEEee
Confidence 678999997544 468999999999998874
No 76
>PF13119 DUF3973: Domain of unknown function (DUF3973)
Probab=21.96 E-value=41 Score=23.65 Aligned_cols=13 Identities=31% Similarity=0.887 Sum_probs=10.8
Q ss_pred eeehhhhhhhccC
Q 021042 37 FMCLECSGKHRGL 49 (318)
Q Consensus 37 FICl~CsgiHR~L 49 (318)
|-|+.|+.+|-.-
T Consensus 2 yYCi~Cs~~h~e~ 14 (41)
T PF13119_consen 2 YYCINCSEIHHEK 14 (41)
T ss_pred EEEEEhHHhHHhh
Confidence 6799999999753
No 77
>cd07157 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers. The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) 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. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=21.82 E-value=34 Score=27.28 Aligned_cols=28 Identities=21% Similarity=0.552 Sum_probs=22.7
Q ss_pred CccCCCCCCCCceEeccceeeehhhhhhhcc
Q 021042 18 ICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 18 ~C~DCga~~P~WaSv~~GiFICl~CsgiHR~ 48 (318)
.|.-||.+. ....||++.|..|.+..|-
T Consensus 2 ~C~VCg~~a---~g~hyGv~sC~aCk~FFRR 29 (86)
T cd07157 2 TCQVCGEPA---AGFHHGAYVCEACKKFFMR 29 (86)
T ss_pred CCcccCCcC---cccEECcceeeEeeeEEec
Confidence 488888754 3569999999999998874
No 78
>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=21.59 E-value=40 Score=26.67 Aligned_cols=27 Identities=37% Similarity=0.821 Sum_probs=21.6
Q ss_pred ccCCCCCCCCceEeccceeeehhhhhhhcc
Q 021042 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 19 C~DCga~~P~WaSv~~GiFICl~CsgiHR~ 48 (318)
|.-||.+.- ...||++.|..|.+.+|-
T Consensus 2 C~VCg~~~~---g~hyGv~sC~aCk~FFRR 28 (84)
T cd06965 2 CRVCGDKAS---GFHYGVHACEGCKGFFRR 28 (84)
T ss_pred CcccCccCc---ceEEChhhhhhhhhheee
Confidence 777886543 457999999999999874
No 79
>cd06955 NR_DBD_VDR DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of core
Probab=20.96 E-value=55 Score=27.34 Aligned_cols=31 Identities=23% Similarity=0.608 Sum_probs=24.9
Q ss_pred CCCCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 021042 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (318)
Q Consensus 15 ~Nk~C~DCga~~P~WaSv~~GiFICl~CsgiHR~ 48 (318)
..+.|.-|+.+.- ...||++.|..|.+..|-
T Consensus 5 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (107)
T cd06955 5 VPRICGVCGDRAT---GFHFNAMTCEGCKGFFRR 35 (107)
T ss_pred CCCCCeecCCcCc---ccEECcceeeeecceecc
Confidence 3467999997544 468999999999998874
Done!