Query 023884
Match_columns 276
No_of_seqs 224 out of 1123
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 07:21:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023884.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023884hhsearch_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 4.6E-71 9.9E-76 516.7 13.7 215 3-275 6-221 (386)
2 COG5347 GTPase-activating prot 100.0 1.2E-38 2.7E-43 299.8 10.0 118 3-120 7-125 (319)
3 KOG0706 Predicted GTPase-activ 100.0 6.3E-38 1.4E-42 301.4 9.9 113 3-116 10-122 (454)
4 PLN03114 ADP-ribosylation fact 100.0 1.5E-37 3.2E-42 293.1 10.8 114 4-117 10-123 (395)
5 PF01412 ArfGap: Putative GTPa 100.0 2.1E-36 4.5E-41 247.2 8.7 114 5-122 2-115 (116)
6 KOG0703 Predicted GTPase-activ 100.0 7.3E-36 1.6E-40 275.9 7.8 115 3-124 12-127 (287)
7 smart00105 ArfGap Putative GTP 100.0 1.1E-34 2.3E-39 235.9 9.5 107 14-123 1-107 (112)
8 PLN03119 putative ADP-ribosyla 100.0 2E-29 4.4E-34 248.7 10.3 115 3-123 10-124 (648)
9 PLN03131 hypothetical protein; 100.0 2.2E-29 4.7E-34 250.1 9.7 114 3-122 10-123 (705)
10 KOG0705 GTPase-activating prot 99.9 3.6E-22 7.8E-27 197.5 7.6 113 4-123 501-616 (749)
11 KOG0521 Putative GTPase activa 99.8 1.2E-20 2.6E-25 195.5 2.5 81 7-87 417-497 (785)
12 KOG0818 GTPase-activating prot 99.7 1.2E-17 2.6E-22 163.6 3.9 108 12-123 4-119 (669)
13 KOG1117 Rho- and Arf-GTPase ac 99.6 4.8E-16 1E-20 159.4 3.2 94 9-102 291-398 (1186)
14 KOG0702 Predicted GTPase-activ 99.4 3.2E-13 6.9E-18 132.5 6.6 117 4-124 13-130 (524)
15 KOG0521 Putative GTPase activa 91.9 0.042 9.1E-07 58.4 -0.3 69 12-82 626-695 (785)
16 PRK00085 recO DNA repair prote 85.0 0.61 1.3E-05 42.0 2.2 39 6-44 139-178 (247)
17 TIGR00613 reco DNA repair prot 78.3 1.6 3.5E-05 39.0 2.5 40 6-45 137-177 (241)
18 PF00643 zf-B_box: B-box zinc 75.4 2.7 5.7E-05 27.7 2.3 34 15-48 2-36 (42)
19 COG1997 RPL43A Ribosomal prote 73.5 3.2 7E-05 32.9 2.6 41 3-45 21-62 (89)
20 PRK12495 hypothetical protein; 73.5 2.5 5.5E-05 38.8 2.4 29 13-45 39-67 (226)
21 COG1381 RecO Recombinational D 70.4 2.5 5.4E-05 38.9 1.7 37 7-43 145-182 (251)
22 PRK11019 hypothetical protein; 66.3 2 4.3E-05 34.0 0.1 37 15-52 35-73 (88)
23 PF08271 TF_Zn_Ribbon: TFIIB z 63.5 4 8.7E-05 27.4 1.2 26 18-44 2-27 (43)
24 PF00320 GATA: GATA zinc finge 63.4 4.8 0.0001 26.3 1.5 32 19-50 1-34 (36)
25 smart00401 ZnF_GATA zinc finge 62.0 7.6 0.00016 27.5 2.4 38 15-52 2-41 (52)
26 PF10764 Gin: Inhibitor of sig 59.1 5.5 0.00012 27.8 1.3 26 18-44 1-26 (46)
27 PF01286 XPA_N: XPA protein N- 55.5 4.4 9.6E-05 26.7 0.3 27 17-43 4-31 (34)
28 TIGR02419 C4_traR_proteo phage 54.8 5.3 0.00011 29.5 0.6 35 12-46 27-62 (63)
29 PF11781 RRN7: RNA polymerase 54.2 9.3 0.0002 25.2 1.6 27 14-43 6-32 (36)
30 PTZ00255 60S ribosomal protein 51.0 15 0.00033 29.3 2.7 39 3-43 22-61 (90)
31 cd07171 NR_DBD_ER DNA-binding 50.5 11 0.00023 29.2 1.7 31 15-48 2-32 (82)
32 PRK13715 conjugal transfer pro 46.0 8.6 0.00019 29.3 0.6 33 16-48 34-67 (73)
33 PF01258 zf-dskA_traR: Prokary 45.2 3.5 7.6E-05 26.8 -1.5 29 18-46 5-34 (36)
34 cd06968 NR_DBD_ROR DNA-binding 44.2 15 0.00032 29.2 1.7 31 15-48 4-34 (95)
35 cd07170 NR_DBD_ERR DNA-binding 43.8 14 0.0003 29.6 1.5 30 16-48 4-33 (97)
36 PTZ00218 40S ribosomal protein 42.8 10 0.00022 27.5 0.5 39 14-57 14-52 (54)
37 KOG0457 Histone acetyltransfer 42.2 22 0.00047 35.8 2.8 63 12-74 9-86 (438)
38 PHA00080 DksA-like zinc finger 41.0 15 0.00032 27.9 1.2 34 13-47 28-63 (72)
39 COG1734 DksA DnaK suppressor p 40.9 9.4 0.0002 31.8 0.1 30 18-47 82-112 (120)
40 cd07173 NR_DBD_AR DNA-binding 40.8 18 0.00038 28.0 1.6 31 15-48 2-32 (82)
41 PF07282 OrfB_Zn_ribbon: Putat 40.7 15 0.00032 26.7 1.1 27 15-43 27-53 (69)
42 PF12760 Zn_Tnp_IS1595: Transp 40.7 30 0.00066 23.5 2.6 39 3-43 6-44 (46)
43 COG2158 Uncharacterized protei 40.3 11 0.00023 31.1 0.3 25 28-52 52-78 (112)
44 cd07160 NR_DBD_LXR DNA-binding 39.8 20 0.00044 28.8 1.9 31 15-48 17-47 (101)
45 cd07169 NR_DBD_GCNF_like DNA-b 38.9 21 0.00045 28.1 1.8 32 14-48 4-35 (90)
46 cd06966 NR_DBD_CAR DNA-binding 38.5 15 0.00033 29.0 1.0 29 17-48 1-29 (94)
47 PF01780 Ribosomal_L37ae: Ribo 38.2 17 0.00037 29.0 1.2 39 3-43 21-60 (90)
48 PF14803 Nudix_N_2: Nudix N-te 37.3 13 0.00027 24.4 0.3 30 17-47 1-33 (34)
49 KOG3362 Predicted BBOX Zn-fing 35.8 16 0.00035 31.7 0.7 34 14-48 116-150 (156)
50 PRK00423 tfb transcription ini 35.4 23 0.0005 33.5 1.8 33 13-46 8-40 (310)
51 KOG3507 DNA-directed RNA polym 34.6 19 0.0004 26.8 0.8 22 18-42 22-43 (62)
52 cd00202 ZnF_GATA Zinc finger D 34.0 26 0.00057 25.0 1.5 34 18-51 1-36 (54)
53 TIGR00382 clpX endopeptidase C 32.7 23 0.00049 35.3 1.3 30 15-44 6-37 (413)
54 cd07161 NR_DBD_EcR DNA-binding 32.2 29 0.00064 27.3 1.6 29 17-48 2-30 (91)
55 cd07162 NR_DBD_PXR DNA-binding 31.9 31 0.00067 26.8 1.7 28 18-48 1-28 (87)
56 cd06956 NR_DBD_RXR DNA-binding 31.6 33 0.0007 26.0 1.8 28 18-48 2-29 (77)
57 smart00290 ZnF_UBP Ubiquitin C 31.0 38 0.00082 22.9 1.9 22 18-39 1-22 (50)
58 cd07166 NR_DBD_REV_ERB DNA-bin 30.9 25 0.00054 27.5 1.0 30 16-48 3-32 (89)
59 cd07163 NR_DBD_TLX DNA-binding 30.8 23 0.0005 27.9 0.8 30 16-48 6-35 (92)
60 TIGR02890 spore_yteA sporulati 30.5 23 0.00051 30.7 0.9 41 6-48 77-119 (159)
61 cd07172 NR_DBD_GR_PR DNA-bindi 30.2 33 0.00072 26.1 1.6 29 17-48 3-31 (78)
62 PF10281 Ish1: Putative stress 30.0 65 0.0014 21.0 2.8 21 62-93 2-22 (38)
63 COG2174 RPL34A Ribosomal prote 29.7 37 0.0008 27.2 1.8 34 11-44 29-79 (93)
64 cd07156 NR_DBD_VDR_like The DN 29.5 35 0.00076 25.5 1.6 27 19-48 1-27 (72)
65 PF14471 DUF4428: Domain of un 29.3 20 0.00044 25.3 0.2 43 18-61 1-45 (51)
66 PRK10778 dksA RNA polymerase-b 29.1 35 0.00076 29.4 1.7 38 12-49 107-145 (151)
67 PF14376 Haem_bd: Haem-binding 29.1 28 0.0006 29.3 1.1 14 17-30 42-55 (137)
68 smart00782 PhnA_Zn_Ribbon PhnA 28.7 34 0.00074 24.0 1.3 34 10-44 2-44 (47)
69 cd06955 NR_DBD_VDR DNA-binding 28.6 28 0.0006 28.4 1.0 31 15-48 5-35 (107)
70 cd07165 NR_DBD_DmE78_like DNA- 28.4 31 0.00068 26.4 1.2 27 19-48 1-27 (81)
71 cd07158 NR_DBD_Ppar_like The D 27.9 35 0.00076 25.4 1.4 27 19-48 1-27 (73)
72 cd06965 NR_DBD_Ppar DNA-bindin 27.8 30 0.00065 26.7 1.0 27 19-48 2-28 (84)
73 cd07168 NR_DBD_DHR4_like DNA-b 27.0 46 0.001 26.0 1.9 31 15-48 5-35 (90)
74 cd07179 2DBD_NR_DBD2 The secon 26.8 40 0.00087 25.3 1.5 27 19-48 1-27 (74)
75 PF06689 zf-C4_ClpX: ClpX C4-t 26.6 53 0.0012 22.0 1.9 28 17-44 2-32 (41)
76 COG0675 Transposase and inacti 25.7 28 0.0006 31.6 0.5 22 16-44 309-330 (364)
77 TIGR00280 L37a ribosomal prote 25.3 64 0.0014 25.8 2.4 39 3-43 21-60 (91)
78 cd07157 2DBD_NR_DBD1 The first 25.1 31 0.00066 26.8 0.6 28 18-48 2-29 (86)
79 smart00399 ZnF_C4 c4 zinc fing 24.9 39 0.00084 24.9 1.1 27 19-48 2-28 (70)
80 cd06962 NR_DBD_FXR DNA-binding 24.2 35 0.00075 26.4 0.8 29 17-48 2-30 (84)
81 KOG1560 Translation initiation 24.2 71 0.0015 30.8 2.9 25 215-239 257-282 (339)
82 cd06967 NR_DBD_TR2_like DNA-bi 23.7 36 0.00079 26.5 0.8 30 16-48 3-32 (87)
83 PRK03976 rpl37ae 50S ribosomal 23.7 61 0.0013 25.9 2.0 39 3-43 22-61 (90)
84 PF00105 zf-C4: Zinc finger, C 23.6 51 0.0011 24.1 1.5 26 17-45 1-26 (70)
85 cd07155 NR_DBD_ER_like DNA-bin 23.4 43 0.00092 25.2 1.1 27 19-48 1-27 (75)
86 cd06958 NR_DBD_COUP_TF DNA-bin 23.0 45 0.00098 24.9 1.2 27 19-48 1-27 (73)
87 PF06827 zf-FPG_IleRS: Zinc fi 22.9 30 0.00064 21.3 0.1 28 17-44 2-29 (30)
88 smart00659 RPOLCX RNA polymera 22.8 38 0.00082 23.3 0.6 23 18-43 4-26 (44)
89 cd06960 NR_DBD_HNF4A DNA-bindi 22.7 44 0.00095 25.1 1.1 27 19-48 1-27 (76)
90 PF13119 DUF3973: Domain of un 22.4 37 0.0008 23.2 0.5 13 37-49 2-14 (41)
91 PRK05766 rps14P 30S ribosomal 22.3 24 0.00051 25.3 -0.5 38 15-57 13-50 (52)
92 cd07164 NR_DBD_PNR_like_1 DNA- 22.1 49 0.0011 25.1 1.2 27 19-48 1-27 (78)
93 cd06959 NR_DBD_EcR_like The DN 21.8 56 0.0012 24.4 1.5 27 19-48 2-28 (73)
94 PHA02942 putative transposase; 21.8 41 0.00089 33.0 0.9 26 16-44 325-350 (383)
95 cd06963 NR_DBD_GR_like The DNA 21.7 56 0.0012 24.5 1.4 27 19-48 1-27 (73)
96 PRK03681 hypA hydrogenase nick 21.7 28 0.00062 28.4 -0.2 33 11-46 65-97 (114)
97 KOG1597 Transcription initiati 21.0 61 0.0013 31.2 1.9 28 17-44 1-29 (308)
98 cd06961 NR_DBD_TR DNA-binding 20.4 50 0.0011 25.5 0.9 27 19-48 2-28 (85)
99 PHA02540 61 DNA primase; Provi 20.2 62 0.0013 31.5 1.7 58 15-76 26-91 (337)
No 1
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=100.00 E-value=4.6e-71 Score=516.67 Aligned_cols=215 Identities=58% Similarity=0.975 Sum_probs=183.0
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccccceehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 023884 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (276)
Q Consensus 3 a~~~L~~L~~~p~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~LGvhiS~VrSvtmD~Ws~~el~~m~~gGN~~~n~ 82 (276)
+|+.|++|+...+|++||||+++||||||++|||||||+|+|+||+||||||||||||||+|++.||++|++|||.++++
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 77888888888899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcCCCCCC-ChhhhccchHHHHHHHHHHHHHcCCCCCCCCchhhhhccCCCCCCCCCcCCCCCCCCCCCCCCCCCCC
Q 023884 83 FLSQYGIPKET-DIVTKYNTNAASIYRDRIQAIAEGRPWRDPPVVKETLNAGKSSSRPPLAQSASVGGVGRNGNYGNHGG 161 (276)
Q Consensus 83 ~~e~~~~~~~~-~i~~KY~s~aa~~yr~kl~~~~egr~~~~~p~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 161 (276)
||+.+++-++. +|++||++++|++||+||++++|||+|.+||.++|..++ +..++. +.
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------AQ------------- 144 (386)
T ss_pred HHhhCccccccccHHHhhccHHHHHHHHHHHHHhcCCcccccccccccCcc--cccccC------CC-------------
Confidence 99999876665 999999999999999999999999999999999887531 111110 00
Q ss_pred CCCCCCCCCCCcccccccCCcCCCCCCCCCCCCCCCCCCCchhhhhhHHHHHHHhhhhhhhhHHHhhhhhcCCCCCCCCC
Q 023884 162 WDSWDNDDFRSSNDMRRNQSVSDFRGGSGGMGGMPASRSKSTEDIYTRAELEASAANKEGFFSRKIAENEARPEGLPPSQ 241 (276)
Q Consensus 162 ~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~yFa~~~~~Na~rp~~lppsQ 241 (276)
..+.++..+|+..|.+++++.+|.||++++.+|++|||+|||||
T Consensus 145 ------------------------------------~~~~ss~~~~~~sq~~~~~~~ke~~fa~~~~~n~srpd~lppsQ 188 (386)
T KOG0704|consen 145 ------------------------------------LGSKSSETIYTISQLSNSAAGKESYFAKRLSENQSRPDGLPPSQ 188 (386)
T ss_pred ------------------------------------cCCCcCCcccccccchhhhcchhHHHHHhcccccCCCCCCCccc
Confidence 00011112234445566778999999999999999999999999
Q ss_pred CCcccccCCCCCCCCCCCCcccChhhhhhhcccC
Q 023884 242 GGKYVGFGSTPPPTQRNTNSQGDVLSAVSQVIDG 275 (276)
Q Consensus 242 ggkY~GFG~~p~~~~~~~~~~~d~~~~l~~g~~~ 275 (276)
||||+|||+|+.|||+.+. ++|+|++|++||++
T Consensus 189 ggkY~GFGst~~~ppqs~~-~~~~~s~ls~Gws~ 221 (386)
T KOG0704|consen 189 GGKYQGFGSTNAPPPQSNS-QDDAMSVLSSGWSR 221 (386)
T ss_pred CCcccccCCCCCCCCcccc-ccchhhhhcccccc
Confidence 9999999999877776432 33899999999986
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=1.2e-38 Score=299.82 Aligned_cols=118 Identities=39% Similarity=0.727 Sum_probs=111.3
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccccceehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 023884 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (276)
Q Consensus 3 a~~~L~~L~~~p~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~LGvhiS~VrSvtmD~Ws~~el~~m~~gGN~~~n~ 82 (276)
.+++|..|++.++|++|||||+++|+|||++||||||++||||||+|||||||||||+||.|+++||++|+.+||.++++
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 023884 83 FLSQYGIPK-ETDIVTKYNTNAASIYRDRIQAIAEGRPW 120 (276)
Q Consensus 83 ~~e~~~~~~-~~~i~~KY~s~aa~~yr~kl~~~~egr~~ 120 (276)
||+.+++.. ..+|++||++.+++.|++++..+.....|
T Consensus 87 ~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~ 125 (319)
T COG5347 87 FYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDD 125 (319)
T ss_pred HhccCCCcccccccccccCHHHHHHHHHHHHHhhhcccc
Confidence 999998874 47899999999999999998888877766
No 3
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=6.3e-38 Score=301.38 Aligned_cols=113 Identities=47% Similarity=0.938 Sum_probs=107.1
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccccceehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 023884 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (276)
Q Consensus 3 a~~~L~~L~~~p~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~LGvhiS~VrSvtmD~Ws~~el~~m~~gGN~~~n~ 82 (276)
...+++.|+..+.||+||||+++||.|+||+||||||++|+++||.||||||||||+.||.|+.+||++|+.|||.+++.
T Consensus 10 ~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~~ 89 (454)
T KOG0706|consen 10 IQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANARV 89 (454)
T ss_pred HHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHHH
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcCCCCCCChhhhccchHHHHHHHHHHHHHc
Q 023884 83 FLSQYGIPKETDIVTKYNTNAASIYRDRIQAIAE 116 (276)
Q Consensus 83 ~~e~~~~~~~~~i~~KY~s~aa~~yr~kl~~~~e 116 (276)
||.+|+... .+++.||++++|..||++|..++.
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=1.5e-37 Score=293.07 Aligned_cols=114 Identities=46% Similarity=0.885 Sum_probs=109.5
Q ss_pred HHHHHHHhcCCCCCCccCCCCCCCCceEeccccceehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHHH
Q 023884 4 TRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTF 83 (276)
Q Consensus 4 ~~~L~~L~~~p~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~LGvhiS~VrSvtmD~Ws~~el~~m~~gGN~~~n~~ 83 (276)
.++|++|+..|+|++|+||++++|+|||++||||||++|+|+||.||+||||||||+||.|+++||++|+.+||.++++|
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 45699999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcCCCCCCChhhhccchHHHHHHHHHHHHHcC
Q 023884 84 LSQYGIPKETDIVTKYNTNAASIYRDRIQAIAEG 117 (276)
Q Consensus 84 ~e~~~~~~~~~i~~KY~s~aa~~yr~kl~~~~eg 117 (276)
|++|++.....|++||++++|+.||++|.+++++
T Consensus 90 F~qhG~~~~~~~~~KY~S~aA~~Yre~L~keVa~ 123 (395)
T PLN03114 90 FKQYGWSDGGKTEAKYTSRAADLYKQILAKEVAK 123 (395)
T ss_pred HHHcCCCCCCCcccccCCHHHHHHHHHHHHHHHH
Confidence 9999998778899999999999999999988765
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=2.1e-36 Score=247.15 Aligned_cols=114 Identities=41% Similarity=0.810 Sum_probs=90.2
Q ss_pred HHHHHHhcCCCCCCccCCCCCCCCceEeccccceehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHHHH
Q 023884 5 RRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTFL 84 (276)
Q Consensus 5 ~~L~~L~~~p~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~LGvhiS~VrSvtmD~Ws~~el~~m~~gGN~~~n~~~ 84 (276)
++|+.|++.|+|++|+|||+++|+|||++||||||++|+++||.||+|||+||||+||.|+++||++|+.+||..+|++|
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 023884 85 SQYGIPKETDIVTKYNTNAASIYRDRIQAIAEGRPWRD 122 (276)
Q Consensus 85 e~~~~~~~~~i~~KY~s~aa~~yr~kl~~~~egr~~~~ 122 (276)
+++. +.. ...-.......|+++|+++|+.+.|..
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 111123345678889999999999975
No 6
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=7.3e-36 Score=275.91 Aligned_cols=115 Identities=41% Similarity=0.815 Sum_probs=100.0
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccccceehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 023884 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (276)
Q Consensus 3 a~~~L~~L~~~p~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~LGvhiS~VrSvtmD~Ws~~el~~m~~gGN~~~n~ 82 (276)
.+++|++|++.|+|+.|+||+++.|.|||+++|||||+.|+||||.||||||+||||+||.|++|||+.|+..||.++|+
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 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcCCCCCCChhhhccchHHH-HHHHHHHHHHcCCCCCCCC
Q 023884 83 FLSQYGIPKETDIVTKYNTNAAS-IYRDRIQAIAEGRPWRDPP 124 (276)
Q Consensus 83 ~~e~~~~~~~~~i~~KY~s~aa~-~yr~kl~~~~egr~~~~~p 124 (276)
|||+. ++.. |...-.. ..-.+|+++||-++|+++.
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 1111111 3455788999999999864
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=1.1e-34 Score=235.88 Aligned_cols=107 Identities=43% Similarity=0.783 Sum_probs=93.7
Q ss_pred CCCCCccCCCCCCCCceEeccccceehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHHHHhhcCCCCCC
Q 023884 14 PGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTFLSQYGIPKET 93 (276)
Q Consensus 14 p~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~LGvhiS~VrSvtmD~Ws~~el~~m~~gGN~~~n~~~e~~~~~~~~ 93 (276)
|+|++|+||++++|+|||++||||||++|+|+||.||+|||+||||+||+|++++|++|+.+||.++|+||+++..+...
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 58999999999999999999999999999999999999999999999999999999999999999999999987654321
Q ss_pred ChhhhccchHHHHHHHHHHHHHcCCCCCCC
Q 023884 94 DIVTKYNTNAASIYRDRIQAIAEGRPWRDP 123 (276)
Q Consensus 94 ~i~~KY~s~aa~~yr~kl~~~~egr~~~~~ 123 (276)
.. . .......|+++|+.+|+.+.|.++
T Consensus 81 ~~--~-~~~~~~~~~~fI~~KY~~k~f~~~ 107 (112)
T smart00105 81 KP--P-DSDDQQKYESFIAAKYEEKLFVPP 107 (112)
T ss_pred CC--C-CCchHHHHHHHHHHHHHhhhcccc
Confidence 11 1 122345788999999999999874
No 8
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=99.96 E-value=2e-29 Score=248.66 Aligned_cols=115 Identities=23% Similarity=0.493 Sum_probs=97.3
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccccceehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 023884 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (276)
Q Consensus 3 a~~~L~~L~~~p~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~LGvhiS~VrSvtmD~Ws~~el~~m~~gGN~~~n~ 82 (276)
.+++|++|++.|+|++|+||++.+|+|||++||||||++|+||||.|| ++||||+||+|+++||++|+.+||+++|+
T Consensus 10 nekILreLlklPgNk~CADCgs~~P~WASiNlGIFICi~CSGIHRsLG---hRVKSLSLDkWT~EEVe~Mk~gGN~~AN~ 86 (648)
T PLN03119 10 NEKIIRGLMKLPPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREFT---HRVKSVSMSKFTSKEVEVLQNGGNQRARE 86 (648)
T ss_pred HHHHHHHHhhCcCCCccccCCCCCCCceeeccceEEeccchhhhccCC---ceeeccccCCCCHHHHHHHHHhchHHHHH
Confidence 467899999999999999999999999999999999999999999998 38999999999999999999999999999
Q ss_pred HHhhcCCCCCCChhhhccchHHHHHHHHHHHHHcCCCCCCC
Q 023884 83 FLSQYGIPKETDIVTKYNTNAASIYRDRIQAIAEGRPWRDP 123 (276)
Q Consensus 83 ~~e~~~~~~~~~i~~KY~s~aa~~yr~kl~~~~egr~~~~~ 123 (276)
||+++.......+.. ....+..+++|+.+|+.|.|...
T Consensus 87 iyeanw~~~~~~~P~---~sD~e~lr~FIR~KYVeKRF~~~ 124 (648)
T PLN03119 87 IYLKNWDHQRQRLPE---NSNAERVREFIKNVYVQKKYAGA 124 (648)
T ss_pred HHHhhcccccCCCCC---CccHHHHHHHHHHHHhhhhccCc
Confidence 999754322111111 11224567899999999999853
No 9
>PLN03131 hypothetical protein; Provisional
Probab=99.96 E-value=2.2e-29 Score=250.12 Aligned_cols=114 Identities=24% Similarity=0.516 Sum_probs=96.5
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccccceehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 023884 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (276)
Q Consensus 3 a~~~L~~L~~~p~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~LGvhiS~VrSvtmD~Ws~~el~~m~~gGN~~~n~ 82 (276)
.+++|++|++.|+|++|+||++++|+|||++||||||++|+||||.|| | +||||+||+|+++||++|+.+||+++|+
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 3 8999999999999999999999999999
Q ss_pred HHhhcCCCCCCChhhhccchHHHHHHHHHHHHHcCCCCCC
Q 023884 83 FLSQYGIPKETDIVTKYNTNAASIYRDRIQAIAEGRPWRD 122 (276)
Q Consensus 83 ~~e~~~~~~~~~i~~KY~s~aa~~yr~kl~~~~egr~~~~ 122 (276)
||+++.......+.. ....+..+++|+.+|+.|+|..
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 999653222111111 1223456789999999999975
No 10
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.86 E-value=3.6e-22 Score=197.53 Aligned_cols=113 Identities=38% Similarity=0.689 Sum_probs=92.6
Q ss_pred HHHHHHHhcCCCCCCccCCCCCCCCceEeccccceehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHHH
Q 023884 4 TRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTF 83 (276)
Q Consensus 4 ~~~L~~L~~~p~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~LGvhiS~VrSvtmD~Ws~~el~~m~~gGN~~~n~~ 83 (276)
+-.|+.|+..+||..|+||+.++|.|||+++||.||++|+||||.||.|+|+||+|.||.|..|.+..|..+||+.+|.+
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 44688899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Hhh--cCCCCCCChhhhccchHHHHHH-HHHHHHHcCCCCCCC
Q 023884 84 LSQ--YGIPKETDIVTKYNTNAASIYR-DRIQAIAEGRPWRDP 123 (276)
Q Consensus 84 ~e~--~~~~~~~~i~~KY~s~aa~~yr-~kl~~~~egr~~~~~ 123 (276)
||. .|..++. -+..+.-| .+|.++||.+.|..|
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 984 2322221 11111122 256777777766654
No 11
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.80 E-value=1.2e-20 Score=195.54 Aligned_cols=81 Identities=44% Similarity=0.882 Sum_probs=78.9
Q ss_pred HHHHhcCCCCCCccCCCCCCCCceEeccccceehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHHHHhh
Q 023884 7 LRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTFLSQ 86 (276)
Q Consensus 7 L~~L~~~p~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~LGvhiS~VrSvtmD~Ws~~el~~m~~gGN~~~n~~~e~ 86 (276)
+..+++.|+|.+|+|||++.|.|+|+++||.+|++|+|+||.||||||+||||+||.|..+.+..|+..||..+|.+|++
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 67889999999999999999999999999999999999999999999999999999999999999999999999999986
Q ss_pred c
Q 023884 87 Y 87 (276)
Q Consensus 87 ~ 87 (276)
.
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=99.68 E-value=1.2e-17 Score=163.60 Aligned_cols=108 Identities=29% Similarity=0.504 Sum_probs=86.7
Q ss_pred cCCCCCCccCCCCCCCCceEeccccceehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHHHHhhcCCCC
Q 023884 12 SQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTFLSQYGIPK 91 (276)
Q Consensus 12 ~~p~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~LGvhiS~VrSvtmD~Ws~~el~~m~~gGN~~~n~~~e~~~~~~ 91 (276)
+...-++|+||++++|.||||+-|||||.+|..+||.||.|||.||+|....|.++.|+++....|..+|.+||.+.++.
T Consensus 4 ~~l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaNsIWEh~Lld~ 83 (669)
T KOG0818|consen 4 RLLSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGANSIWEHSLLDP 83 (669)
T ss_pred cchhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcchhhhhhccCc
Confidence 44567899999999999999999999999999999999999999999999999999999999999999999999765542
Q ss_pred C--------CChhhhccchHHHHHHHHHHHHHcCCCCCCC
Q 023884 92 E--------TDIVTKYNTNAASIYRDRIQAIAEGRPWRDP 123 (276)
Q Consensus 92 ~--------~~i~~KY~s~aa~~yr~kl~~~~egr~~~~~ 123 (276)
. ...++|.+...++ +|+++|+-..|+..
T Consensus 84 st~~sg~rk~~pqD~~Hp~K~e----FIkaKy~~LtFv~~ 119 (669)
T KOG0818|consen 84 ATIMSGRRKANPQDKVHPNKAE----FIRAKYQMLAFVHR 119 (669)
T ss_pred hhhhcccCCCCCcCCCCccHHH----HHHHHHHheeeecc
Confidence 1 1234444433333 44455555566653
No 13
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.58 E-value=4.8e-16 Score=159.44 Aligned_cols=94 Identities=36% Similarity=0.616 Sum_probs=81.6
Q ss_pred HHhcCCCCCCccCCCCCCCCceEeccccceehhhhhhhccCCCcccceeecccC--CCCHHHHHHHHhcChHHHHHHHhh
Q 023884 9 DLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMD--SWSEIQIKKMEAGGNERLNTFLSQ 86 (276)
Q Consensus 9 ~L~~~p~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~LGvhiS~VrSvtmD--~Ws~~el~~m~~gGN~~~n~~~e~ 86 (276)
.+=....|+.|+||+++.|.|||+|++|.||-.|+|-||+||..+|+|+|++|| .|+.+-|+++...||.++|+||..
T Consensus 291 riW~ne~nr~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~Fwa~ 370 (1186)
T KOG1117|consen 291 RIWLNEENRECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANRFWAG 370 (1186)
T ss_pred HHHhccccccccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCccccccccc
Confidence 344567899999999999999999999999999999999999999999999999 899999999999999999999975
Q ss_pred cCCCC------------CCChhhhccch
Q 023884 87 YGIPK------------ETDIVTKYNTN 102 (276)
Q Consensus 87 ~~~~~------------~~~i~~KY~s~ 102 (276)
+-.+. ..+|++||.+-
T Consensus 371 nl~~~e~lh~dssp~~r~~fi~~Kykeg 398 (1186)
T KOG1117|consen 371 NLPPNEHLHPDSSPSTRRQFIKEKYKEG 398 (1186)
T ss_pred CCCCccccCCCCCcchhhhHHHHHhhcc
Confidence 43221 13667777654
No 14
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.40 E-value=3.2e-13 Score=132.50 Aligned_cols=117 Identities=18% Similarity=0.371 Sum_probs=96.0
Q ss_pred HHHHHHHhcCCCCCCccCCCCCCC-CceEeccccceehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 023884 4 TRRLRDLQSQPGNKICVDCAQKNP-QWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (276)
Q Consensus 4 ~~~L~~L~~~p~Nk~C~DCga~~P-~WaS~~~GiFICl~CsgiHR~LGvhiS~VrSvtmD~Ws~~el~~m~~gGN~~~n~ 82 (276)
+.+||.|+++|+|++|++|....+ .|+.++-|-|+|+.|+|.-|+|-. -.+||||.|..|++.|+..++.+||+.+++
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 678999999999999999999887 999999999999999999999843 358999999999999999999999999999
Q ss_pred HHhhcCCCCCCChhhhccchHHHHHHHHHHHHHcCCCCCCCC
Q 023884 83 FLSQYGIPKETDIVTKYNTNAASIYRDRIQAIAEGRPWRDPP 124 (276)
Q Consensus 83 ~~e~~~~~~~~~i~~KY~s~aa~~yr~kl~~~~egr~~~~~p 124 (276)
+|-+--......+. +.+.....|++|+.+|+++.|+.++
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 88532111111111 1222345788999999999999875
No 15
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=91.91 E-value=0.042 Score=58.43 Aligned_cols=69 Identities=14% Similarity=0.289 Sum_probs=56.5
Q ss_pred cCCCCCCccCCCC-CCCCceEeccccceehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 023884 12 SQPGNKICVDCAQ-KNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (276)
Q Consensus 12 ~~p~Nk~C~DCga-~~P~WaS~~~GiFICl~CsgiHR~LGvhiS~VrSvtmD~Ws~~el~~m~~gGN~~~n~ 82 (276)
....+-.|++|.+ ..-.|+++++.+-+|..|+++|+.++.|++.++++.++...+ |.....-|+..++.
T Consensus 626 ~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~ 695 (785)
T KOG0521|consen 626 KASSDGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHH 695 (785)
T ss_pred HhccCccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchh
Confidence 3445778999998 688899999999999999999999999999999999998888 44444445555544
No 16
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=85.03 E-value=0.61 Score=41.96 Aligned_cols=39 Identities=23% Similarity=0.389 Sum_probs=30.6
Q ss_pred HHHHHhcCCCCCCccCCCCCCC-CceEeccccceehhhhh
Q 023884 6 RLRDLQSQPGNKICVDCAQKNP-QWASVSYGVFMCLECSG 44 (276)
Q Consensus 6 ~L~~L~~~p~Nk~C~DCga~~P-~WaS~~~GiFICl~Csg 44 (276)
.|..+--.|.-..|+-||.+.. .|.++..|.++|..|..
T Consensus 139 lL~~~G~~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~ 178 (247)
T PRK00085 139 LLAELGYGLDLDHCAVCGAPGDHRYFSPKEGGAVCSECGD 178 (247)
T ss_pred HHHHcCCccchhhHhcCCCCCCceEEecccCCcccccccC
Confidence 3444445666779999999755 78899999999999973
No 17
>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=78.28 E-value=1.6 Score=39.02 Aligned_cols=40 Identities=28% Similarity=0.501 Sum_probs=30.6
Q ss_pred HHHHHhcCCCCCCccCCCCCCC-CceEeccccceehhhhhh
Q 023884 6 RLRDLQSQPGNKICVDCAQKNP-QWASVSYGVFMCLECSGK 45 (276)
Q Consensus 6 ~L~~L~~~p~Nk~C~DCga~~P-~WaS~~~GiFICl~Csgi 45 (276)
.|..+--.|.-..|+.||...+ .+.++..|.|+|.+|...
T Consensus 137 lL~~~G~~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 137 LLQILGYALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred HHHHcCCCcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 3444455667789999998544 688999999999999764
No 18
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=75.36 E-value=2.7 Score=27.68 Aligned_cols=34 Identities=18% Similarity=0.387 Sum_probs=28.9
Q ss_pred CCCCccCCCCCCCCceEeccccceehhhhhh-hcc
Q 023884 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGK-HRG 48 (276)
Q Consensus 15 ~Nk~C~DCga~~P~WaS~~~GiFICl~Csgi-HR~ 48 (276)
.+..|..|......+-..+-.++||..|... |++
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 3568999998878899999999999999987 887
No 19
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=73.52 E-value=3.2 Score=32.94 Aligned_cols=41 Identities=22% Similarity=0.656 Sum_probs=29.6
Q ss_pred HHHHHHHH-hcCCCCCCccCCCCCCCCceEeccccceehhhhhh
Q 023884 3 ATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGK 45 (276)
Q Consensus 3 a~~~L~~L-~~~p~Nk~C~DCga~~P~WaS~~~GiFICl~Csgi 45 (276)
.|+...+| .....-..|-.|+.+ .---+..||+.|..|-..
T Consensus 21 ~Rrrv~~ie~~~~~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~~ 62 (89)
T COG1997 21 LRRRVKEIEAQQRAKHVCPFCGRT--TVKRIATGIWKCRKCGAK 62 (89)
T ss_pred HHHHHHHHHHHHhcCCcCCCCCCc--ceeeeccCeEEcCCCCCe
Confidence 45555555 344456789999998 455778999999999543
No 20
>PRK12495 hypothetical protein; Provisional
Probab=73.50 E-value=2.5 Score=38.76 Aligned_cols=29 Identities=21% Similarity=0.399 Sum_probs=23.5
Q ss_pred CCCCCCccCCCCCCCCceEeccccceehhhhhh
Q 023884 13 QPGNKICVDCAQKNPQWASVSYGVFMCLECSGK 45 (276)
Q Consensus 13 ~p~Nk~C~DCga~~P~WaS~~~GiFICl~Csgi 45 (276)
...+..|-+||.|-|.. -|+.+|..|..+
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 34689999999999932 699999999744
No 21
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=70.44 E-value=2.5 Score=38.93 Aligned_cols=37 Identities=27% Similarity=0.579 Sum_probs=29.4
Q ss_pred HHHHhcCCCCCCccCCCCCCC-CceEeccccceehhhh
Q 023884 7 LRDLQSQPGNKICVDCAQKNP-QWASVSYGVFMCLECS 43 (276)
Q Consensus 7 L~~L~~~p~Nk~C~DCga~~P-~WaS~~~GiFICl~Cs 43 (276)
|..+--.+.=..|+.||.+.+ ...|+..|-+||.+|+
T Consensus 145 L~~~G~~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 145 LGELGIGPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred HHHcCCccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 333444556678999999755 6999999999999998
No 22
>PRK11019 hypothetical protein; Provisional
Probab=66.30 E-value=2 Score=34.02 Aligned_cols=37 Identities=19% Similarity=0.510 Sum_probs=25.5
Q ss_pred CCCCccCCCCCCC--CceEeccccceehhhhhhhccCCCc
Q 023884 15 GNKICVDCAQKNP--QWASVSYGVFMCLECSGKHRGLGVH 52 (276)
Q Consensus 15 ~Nk~C~DCga~~P--~WaS~~~GiFICl~CsgiHR~LGvh 52 (276)
.-..|.|||.+=| .+.-+. ++-.|++|...+-..+.|
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 4579999999655 333333 678899999876554444
No 23
>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=63.45 E-value=4 Score=27.45 Aligned_cols=26 Identities=23% Similarity=0.543 Sum_probs=20.7
Q ss_pred CccCCCCCCCCceEeccccceehhhhh
Q 023884 18 ICVDCAQKNPQWASVSYGVFMCLECSG 44 (276)
Q Consensus 18 ~C~DCga~~P~WaS~~~GiFICl~Csg 44 (276)
+|-.||+.. .-....-|-+||..|--
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-B
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCCC
Confidence 699999977 45567789999999943
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=63.36 E-value=4.8 Score=26.30 Aligned_cols=32 Identities=28% Similarity=0.726 Sum_probs=23.0
Q ss_pred ccCCCC-CCCCceEeccccc-eehhhhhhhccCC
Q 023884 19 CVDCAQ-KNPQWASVSYGVF-MCLECSGKHRGLG 50 (276)
Q Consensus 19 C~DCga-~~P~WaS~~~GiF-ICl~CsgiHR~LG 50 (276)
|..|+. ..|+|=....|-. ||-.|--.+|..+
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 5899998888887 9999987766543
No 25
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=61.96 E-value=7.6 Score=27.47 Aligned_cols=38 Identities=21% Similarity=0.531 Sum_probs=30.6
Q ss_pred CCCCccCCCC-CCCCceEecccc-ceehhhhhhhccCCCc
Q 023884 15 GNKICVDCAQ-KNPQWASVSYGV-FMCLECSGKHRGLGVH 52 (276)
Q Consensus 15 ~Nk~C~DCga-~~P~WaS~~~Gi-FICl~CsgiHR~LGvh 52 (276)
....|..|+. ..|+|=.-..|. +||-.|.-..+..+..
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC
Confidence 3578999999 689998888886 9999998777765543
No 26
>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=59.10 E-value=5.5 Score=27.77 Aligned_cols=26 Identities=27% Similarity=0.836 Sum_probs=20.0
Q ss_pred CccCCCCCCCCceEeccccceehhhhh
Q 023884 18 ICVDCAQKNPQWASVSYGVFMCLECSG 44 (276)
Q Consensus 18 ~C~DCga~~P~WaS~~~GiFICl~Csg 44 (276)
+|+=|+.+.+. -=.=+|-|||.+|-.
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHH
Confidence 48889987776 344589999999954
No 27
>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=55.51 E-value=4.4 Score=26.69 Aligned_cols=27 Identities=15% Similarity=0.533 Sum_probs=16.3
Q ss_pred CCccCCCCC-CCCceEeccccceehhhh
Q 023884 17 KICVDCAQK-NPQWASVSYGVFMCLECS 43 (276)
Q Consensus 17 k~C~DCga~-~P~WaS~~~GiFICl~Cs 43 (276)
..|.+|+.+ .-.|..-+|+.-||..|.
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 667999999999999994
No 28
>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=54.83 E-value=5.3 Score=29.46 Aligned_cols=35 Identities=26% Similarity=0.510 Sum_probs=23.2
Q ss_pred cCCCCCCccCCCCCCCCce-Eeccccceehhhhhhh
Q 023884 12 SQPGNKICVDCAQKNPQWA-SVSYGVFMCLECSGKH 46 (276)
Q Consensus 12 ~~p~Nk~C~DCga~~P~Wa-S~~~GiFICl~CsgiH 46 (276)
..++...|.|||.+=|.=- -.--++..|..|...|
T Consensus 27 ~~~s~g~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 27 IGPSLRECEDCGEPIPEARREALPGVTRCVSCQEIL 62 (63)
T ss_pred cCCCCCeeccCCCcChHHHHhhcCCcCCcHHHHhhc
Confidence 3456779999999655211 1223678899998654
No 29
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=54.17 E-value=9.3 Score=25.22 Aligned_cols=27 Identities=26% Similarity=0.728 Sum_probs=22.8
Q ss_pred CCCCCccCCCCCCCCceEeccccceehhhh
Q 023884 14 PGNKICVDCAQKNPQWASVSYGVFMCLECS 43 (276)
Q Consensus 14 p~Nk~C~DCga~~P~WaS~~~GiFICl~Cs 43 (276)
..|..|..|++. |....=|-++|..|-
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCc
Confidence 346679999998 888899999999983
No 30
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=50.96 E-value=15 Score=29.26 Aligned_cols=39 Identities=21% Similarity=0.572 Sum_probs=29.1
Q ss_pred HHHHHHHH-hcCCCCCCccCCCCCCCCceEeccccceehhhh
Q 023884 3 ATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECS 43 (276)
Q Consensus 3 a~~~L~~L-~~~p~Nk~C~DCga~~P~WaS~~~GiFICl~Cs 43 (276)
.|+.+.+| .....--.|.-|+........+ ||+-|..|.
T Consensus 22 lRK~v~kie~~q~a~y~CpfCgk~~vkR~a~--GIW~C~~C~ 61 (90)
T PTZ00255 22 LRKQIKKIEISQHAKYFCPFCGKHAVKRQAV--GIWRCKGCK 61 (90)
T ss_pred HHHHHHHHHHHHhCCccCCCCCCCceeeeee--EEEEcCCCC
Confidence 45666665 4555677999999877766554 999999994
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=50.54 E-value=11 Score=29.18 Aligned_cols=31 Identities=23% Similarity=0.643 Sum_probs=25.7
Q ss_pred CCCCccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 15 ~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
.|..|.-|+.+.- ...||++.|..|.+..|-
T Consensus 2 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 2 DTHFCAVCSDYAS---GYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 4678999997554 579999999999998864
No 32
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=46.02 E-value=8.6 Score=29.25 Aligned_cols=33 Identities=24% Similarity=0.583 Sum_probs=22.2
Q ss_pred CCCccCCCCCCCCc-eEeccccceehhhhhhhcc
Q 023884 16 NKICVDCAQKNPQW-ASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 16 Nk~C~DCga~~P~W-aS~~~GiFICl~CsgiHR~ 48 (276)
...|.|||.+=|.= .-.--|+..|++|...+-.
T Consensus 34 ~~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~E~ 67 (73)
T PRK13715 34 VYLCEACGNPIPEARRKIFPGVTLCVECQAYQER 67 (73)
T ss_pred cccHhhcCCcCCHHHHhcCCCcCCCHHHHHHHHH
Confidence 45899999975521 1122378899999876543
No 33
>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=45.15 E-value=3.5 Score=26.75 Aligned_cols=29 Identities=31% Similarity=0.787 Sum_probs=16.4
Q ss_pred CccCCCCCCCC-ceEeccccceehhhhhhh
Q 023884 18 ICVDCAQKNPQ-WASVSYGVFMCLECSGKH 46 (276)
Q Consensus 18 ~C~DCga~~P~-WaS~~~GiFICl~CsgiH 46 (276)
.|.+||.+=|. =.-+--+..+|..|+..|
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 111223678899998765
No 34
>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=44.23 E-value=15 Score=29.23 Aligned_cols=31 Identities=32% Similarity=0.684 Sum_probs=25.6
Q ss_pred CCCCccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 15 ~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
.+..|.-||.+.- ...||++.|..|.+..|-
T Consensus 4 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 4 EVIPCKICGDKSS---GIHYGVITCEGCKGFFRR 34 (95)
T ss_pred cccCCcccCCcCc---ceEECceeehhhHHhhHH
Confidence 4668999998664 458999999999998873
No 35
>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=43.78 E-value=14 Score=29.56 Aligned_cols=30 Identities=23% Similarity=0.666 Sum_probs=24.6
Q ss_pred CCCccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 16 NKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 16 Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
+..|.-|+.+.- ...||++.|..|.+..|-
T Consensus 4 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 33 (97)
T cd07170 4 KRLCLVCGDIAS---GYHYGVASCEACKAFFKR 33 (97)
T ss_pred CCCCeecCCcCc---ceEECceeehhhhHHHHH
Confidence 357999998664 458999999999998874
No 36
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=42.81 E-value=10 Score=27.49 Aligned_cols=39 Identities=26% Similarity=0.571 Sum_probs=27.9
Q ss_pred CCCCCccCCCCCCCCceEeccccceehhhhhhhccCCCccccee
Q 023884 14 PGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVR 57 (276)
Q Consensus 14 p~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~LGvhiS~Vr 57 (276)
++-+.|.-||.+. =+--.||+.||..|- |.+-..|.|||
T Consensus 14 kGsr~C~vCg~~~--gliRkygL~~CRqCF---Re~A~~iGF~K 52 (54)
T PTZ00218 14 KGSRQCRVCSNRH--GLIRKYGLNVCRQCF---RENAELIGFHK 52 (54)
T ss_pred CCCCeeecCCCcc--hhhhhcCcchhhHHH---HHhhHhcCeee
Confidence 4678999999854 234489999999995 34445566655
No 37
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=42.16 E-value=22 Score=35.76 Aligned_cols=63 Identities=24% Similarity=0.400 Sum_probs=32.0
Q ss_pred cCCCCCCccC-CCC--CCCCceEeccc--cceehhhhhhhccCCCcc-----cceeecc----cCCCCH-HHHHHHHh
Q 023884 12 SQPGNKICVD-CAQ--KNPQWASVSYG--VFMCLECSGKHRGLGVHI-----SFVRSVT----MDSWSE-IQIKKMEA 74 (276)
Q Consensus 12 ~~p~Nk~C~D-Cga--~~P~WaS~~~G--iFICl~CsgiHR~LGvhi-----S~VrSvt----mD~Ws~-~el~~m~~ 74 (276)
..++++.||| |.. ..+..+...-. .+||+.|-.+--.+|+|- -.|...+ --.|+. |||++++.
T Consensus 9 ~~~g~ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLea 86 (438)
T KOG0457|consen 9 DDPGGKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSVGAETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLEA 86 (438)
T ss_pred hcCCCCCCCccHhHHhccceEEEeecCCCcchhHHHHhcccccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHHH
Confidence 3455555444 655 23332222111 479999986444444442 2233322 137886 67777764
No 38
>PHA00080 DksA-like zinc finger domain containing protein
Probab=41.01 E-value=15 Score=27.85 Aligned_cols=34 Identities=24% Similarity=0.620 Sum_probs=22.5
Q ss_pred CCCCCCccCCCCCCC--CceEeccccceehhhhhhhc
Q 023884 13 QPGNKICVDCAQKNP--QWASVSYGVFMCLECSGKHR 47 (276)
Q Consensus 13 ~p~Nk~C~DCga~~P--~WaS~~~GiFICl~CsgiHR 47 (276)
......|.|||.+=| .+.-+. ++..|++|...+-
T Consensus 28 ~~~~~~C~~Cg~~Ip~~Rl~a~P-~~~~Cv~Cq~~~E 63 (72)
T PHA00080 28 APSATHCEECGDPIPEARREAVP-GCRTCVSCQEILE 63 (72)
T ss_pred CCCCCEecCCCCcCcHHHHHhCC-CccCcHHHHHHHH
Confidence 344568999999543 333333 5667999988654
No 39
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=40.87 E-value=9.4 Score=31.82 Aligned_cols=30 Identities=23% Similarity=0.665 Sum_probs=20.0
Q ss_pred CccCCCCCCCC-ceEeccccceehhhhhhhc
Q 023884 18 ICVDCAQKNPQ-WASVSYGVFMCLECSGKHR 47 (276)
Q Consensus 18 ~C~DCga~~P~-WaS~~~GiFICl~CsgiHR 47 (276)
+|.+||.+=|. =.-.--+..+|++|.-.|-
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 89999996441 1122235788999987663
No 40
>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=40.80 E-value=18 Score=27.98 Aligned_cols=31 Identities=23% Similarity=0.596 Sum_probs=25.4
Q ss_pred CCCCccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 15 ~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
..+.|.-|+.+.- ...||++-|..|.+..|-
T Consensus 2 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 32 (82)
T cd07173 2 PQKTCLICGDEAS---GCHYGALTCGSCKVFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECcchhhhHHHHHHH
Confidence 4567999998654 568999999999998874
No 41
>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=40.75 E-value=15 Score=26.66 Aligned_cols=27 Identities=30% Similarity=0.710 Sum_probs=22.7
Q ss_pred CCCCccCCCCCCCCceEeccccceehhhh
Q 023884 15 GNKICVDCAQKNPQWASVSYGVFMCLECS 43 (276)
Q Consensus 15 ~Nk~C~DCga~~P~WaS~~~GiFICl~Cs 43 (276)
--+.|..||..... ..+--+|.|..|-
T Consensus 27 TSq~C~~CG~~~~~--~~~~r~~~C~~Cg 53 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK--RRSGRVFTCPNCG 53 (69)
T ss_pred CccCccCccccccc--ccccceEEcCCCC
Confidence 45789999998887 7788899999984
No 42
>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=40.70 E-value=30 Score=23.50 Aligned_cols=39 Identities=15% Similarity=0.456 Sum_probs=26.3
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccccceehhhh
Q 023884 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECS 43 (276)
Q Consensus 3 a~~~L~~L~~~p~Nk~C~DCga~~P~WaS~~~GiFICl~Cs 43 (276)
+++.|.+|+=. ..-+|.-||....-+.. +.+.|-|-.|.
T Consensus 6 c~~~l~~~RW~-~g~~CP~Cg~~~~~~~~-~~~~~~C~~C~ 44 (46)
T PF12760_consen 6 CREYLEEIRWP-DGFVCPHCGSTKHYRLK-TRGRYRCKACR 44 (46)
T ss_pred HHHHHHHhcCC-CCCCCCCCCCeeeEEeC-CCCeEECCCCC
Confidence 55566666544 44779999998554433 26889998884
No 43
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=40.28 E-value=11 Score=31.10 Aligned_cols=25 Identities=40% Similarity=0.781 Sum_probs=21.8
Q ss_pred CceEeccc--cceehhhhhhhccCCCc
Q 023884 28 QWASVSYG--VFMCLECSGKHRGLGVH 52 (276)
Q Consensus 28 ~WaS~~~G--iFICl~CsgiHR~LGvh 52 (276)
.|++-.-| |+-|.+|--|||.-++.
T Consensus 52 ewi~~~~G~~VwSC~dC~~iH~ke~~~ 78 (112)
T COG2158 52 EWISDSNGRKVWSCSDCHWIHRKEGAE 78 (112)
T ss_pred ceeEcCCCCEEeeccccceecccchHH
Confidence 89999989 99999999999975543
No 44
>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=39.85 E-value=20 Score=28.84 Aligned_cols=31 Identities=35% Similarity=0.832 Sum_probs=25.7
Q ss_pred CCCCccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 15 ~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
.+..|.-|+.+.- ...||+..|..|.+..|-
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 4678999998654 569999999999998874
No 45
>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=38.89 E-value=21 Score=28.06 Aligned_cols=32 Identities=22% Similarity=0.736 Sum_probs=26.2
Q ss_pred CCCCCccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 14 PGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 14 p~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
..++.|.-|+.+.- ...||+..|..|....|-
T Consensus 4 ~~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (90)
T cd07169 4 AEQRTCLICGDRAT---GLHYGIISCEGCKGFFKR 35 (90)
T ss_pred ccCCCCeecCCcCc---ceEECcceehhhHHHHHH
Confidence 45778999998653 568999999999998864
No 46
>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=38.49 E-value=15 Score=29.03 Aligned_cols=29 Identities=28% Similarity=0.615 Sum_probs=23.4
Q ss_pred CCccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 17 KICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 17 k~C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
+.|.-|+.+.- ...||++.|..|.+..|-
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 46888987544 458999999999998874
No 47
>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=38.16 E-value=17 Score=28.98 Aligned_cols=39 Identities=23% Similarity=0.587 Sum_probs=28.1
Q ss_pred HHHHHHHH-hcCCCCCCccCCCCCCCCceEeccccceehhhh
Q 023884 3 ATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECS 43 (276)
Q Consensus 3 a~~~L~~L-~~~p~Nk~C~DCga~~P~WaS~~~GiFICl~Cs 43 (276)
.|+.+.+| ......-.|.-||.... --+..|||-|..|-
T Consensus 21 lRK~vkkie~~q~~ky~Cp~Cgk~~v--kR~a~GIW~C~~C~ 60 (90)
T PF01780_consen 21 LRKRVKKIEISQHAKYTCPFCGKTSV--KRVATGIWKCKKCG 60 (90)
T ss_dssp HHHHHHHHHHHHHS-BEESSSSSSEE--EEEETTEEEETTTT
T ss_pred HHHHHHHHHHHHhCCCcCCCCCCcee--EEeeeEEeecCCCC
Confidence 35555555 44556789999999874 45678999999995
No 48
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=37.25 E-value=13 Score=24.39 Aligned_cols=30 Identities=20% Similarity=0.397 Sum_probs=15.2
Q ss_pred CCccCCCCCCCCceEe---ccccceehhhhhhhc
Q 023884 17 KICVDCAQKNPQWASV---SYGVFMCLECSGKHR 47 (276)
Q Consensus 17 k~C~DCga~~P~WaS~---~~GiFICl~CsgiHR 47 (276)
|.|-.||.+- ++..+ +.--++|..|.-||-
T Consensus 1 kfC~~CG~~l-~~~ip~gd~r~R~vC~~Cg~IhY 33 (34)
T PF14803_consen 1 KFCPQCGGPL-ERRIPEGDDRERLVCPACGFIHY 33 (34)
T ss_dssp -B-TTT--B--EEE--TT-SS-EEEETTTTEEE-
T ss_pred CccccccChh-hhhcCCCCCccceECCCCCCEEe
Confidence 5788899862 23322 344578999988883
No 49
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=35.84 E-value=16 Score=31.67 Aligned_cols=34 Identities=26% Similarity=0.654 Sum_probs=26.4
Q ss_pred CCCCCccCCCCCCCCceEeccccceeh-hhhhhhcc
Q 023884 14 PGNKICVDCAQKNPQWASVSYGVFMCL-ECSGKHRG 48 (276)
Q Consensus 14 p~Nk~C~DCga~~P~WaS~~~GiFICl-~CsgiHR~ 48 (276)
|--+.|+-||- ...|.+++.|.-+|. .|-.+|..
T Consensus 116 P~r~fCaVCG~-~S~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 116 PLRKFCAVCGY-DSKYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred CcchhhhhcCC-CchhHHHhcCCceeechhhhhccc
Confidence 45678999994 444899999999885 67777754
No 50
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=35.44 E-value=23 Score=33.54 Aligned_cols=33 Identities=15% Similarity=0.440 Sum_probs=23.5
Q ss_pred CCCCCCccCCCCCCCCceEeccccceehhhhhhh
Q 023884 13 QPGNKICVDCAQKNPQWASVSYGVFMCLECSGKH 46 (276)
Q Consensus 13 ~p~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiH 46 (276)
.....+|.+||..+. =....-|-.||.+|--|.
T Consensus 8 ~~~~~~Cp~Cg~~~i-v~d~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 8 EEEKLVCPECGSDKL-IYDYERGEIVCADCGLVI 40 (310)
T ss_pred cccCCcCcCCCCCCe-eEECCCCeEeecccCCcc
Confidence 345568999997432 234578999999997643
No 51
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=34.63 E-value=19 Score=26.76 Aligned_cols=22 Identities=45% Similarity=0.854 Sum_probs=14.4
Q ss_pred CccCCCCCCCCceEeccccceehhh
Q 023884 18 ICVDCAQKNPQWASVSYGVFMCLEC 42 (276)
Q Consensus 18 ~C~DCga~~P~WaS~~~GiFICl~C 42 (276)
+|.|||+.|.- -.--++-|-+|
T Consensus 22 iCgdC~~en~l---k~~D~irCReC 43 (62)
T KOG3507|consen 22 ICGDCGQENTL---KRGDVIRCREC 43 (62)
T ss_pred Eeccccccccc---cCCCcEehhhc
Confidence 68888887642 12336778888
No 52
>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=33.96 E-value=26 Score=24.97 Aligned_cols=34 Identities=26% Similarity=0.647 Sum_probs=27.3
Q ss_pred CccCCCC-CCCCceEec-cccceehhhhhhhccCCC
Q 023884 18 ICVDCAQ-KNPQWASVS-YGVFMCLECSGKHRGLGV 51 (276)
Q Consensus 18 ~C~DCga-~~P~WaS~~-~GiFICl~CsgiHR~LGv 51 (276)
+|..|+. .-|+|=... -+..||-.|--..+..|.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~ 36 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGV 36 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCC
Confidence 5999998 678898765 788999999877776653
No 53
>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=32.66 E-value=23 Score=35.34 Aligned_cols=30 Identities=23% Similarity=0.562 Sum_probs=21.5
Q ss_pred CCCCccCCCCCCCCceEecc--ccceehhhhh
Q 023884 15 GNKICVDCAQKNPQWASVSY--GVFMCLECSG 44 (276)
Q Consensus 15 ~Nk~C~DCga~~P~WaS~~~--GiFICl~Csg 44 (276)
++..|--||.+..+--.+-. ++|||.+|..
T Consensus 6 ~~~~c~fc~~~~~~~~~~~~~~~~~ic~~c~~ 37 (413)
T TIGR00382 6 ETLYCSFCGKSQDEVRKLIAGPGVYICDECIE 37 (413)
T ss_pred CCeecCCCCCChhhcccccCCCCCcCCCchHH
Confidence 34589999997665444433 4899999975
No 54
>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=32.21 E-value=29 Score=27.29 Aligned_cols=29 Identities=24% Similarity=0.750 Sum_probs=23.3
Q ss_pred CCccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 17 KICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 17 k~C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
..|.-|+.+.- ...||++.|..|.+..|-
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 35888997655 458999999999998863
No 55
>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=31.88 E-value=31 Score=26.79 Aligned_cols=28 Identities=25% Similarity=0.675 Sum_probs=22.4
Q ss_pred CccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 18 ICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 18 ~C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
+|.-|+.+.-. ..||++.|..|++..|-
T Consensus 1 ~C~VCg~~~~g---~hygv~sC~aC~~FFRR 28 (87)
T cd07162 1 ICRVCGDRATG---YHFNAMTCEGCKGFFRR 28 (87)
T ss_pred CCcccCCcCcc---eEECcceehhhHHHHHh
Confidence 47788876553 58999999999998764
No 56
>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=31.64 E-value=33 Score=26.01 Aligned_cols=28 Identities=32% Similarity=0.856 Sum_probs=22.9
Q ss_pred CccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 18 ICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 18 ~C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
.|.-|+.+.- ...||++.|..|.+..|-
T Consensus 2 ~C~VC~~~~~---g~hygv~sC~aC~~FFRR 29 (77)
T cd06956 2 ICAICGDRAS---GKHYGVYSCEGCKGFFKR 29 (77)
T ss_pred CCcccCCcCc---ceEECceeehhHHHHHHH
Confidence 5888887654 468999999999998863
No 57
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=30.99 E-value=38 Score=22.85 Aligned_cols=22 Identities=23% Similarity=0.646 Sum_probs=13.8
Q ss_pred CccCCCCCCCCceEecccccee
Q 023884 18 ICVDCAQKNPQWASVSYGVFMC 39 (276)
Q Consensus 18 ~C~DCga~~P~WaS~~~GiFIC 39 (276)
+|.+|+..+.-|+++.-+-..|
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c 22 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGC 22 (50)
T ss_pred CcccCCCcCCeEEecCCCCccc
Confidence 5999998776555444443333
No 58
>cd07166 NR_DBD_REV_ERB DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers. DNA-binding domain of REV-ERB receptor- like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. REV-ERB receptors are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. REV-ERB receptors bind as a monomer to a (A/G)GGTCA half-site with a 5' AT-rich extension or as a homodimer to a direct repeat 2 element (AGGTCA sequence with a 2-bp spacer), indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target genes. The porphyr
Probab=30.95 E-value=25 Score=27.52 Aligned_cols=30 Identities=33% Similarity=0.730 Sum_probs=24.3
Q ss_pred CCCccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 16 NKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 16 Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
+..|.-||.+.- ...||++.|..|....|-
T Consensus 3 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 32 (89)
T cd07166 3 VVLCKVCGDKAS---GFHYGVHACEGCKGFFRR 32 (89)
T ss_pred CCCCcccCccCc---ceEEChhhhhhHhhEecc
Confidence 456999998665 457999999999998774
No 59
>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=30.82 E-value=23 Score=27.88 Aligned_cols=30 Identities=27% Similarity=0.744 Sum_probs=24.9
Q ss_pred CCCccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 16 NKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 16 Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
+..|.-|+.+.- ...||+..|..|++..|-
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 678999998654 469999999999998764
No 60
>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=30.52 E-value=23 Score=30.73 Aligned_cols=41 Identities=20% Similarity=0.528 Sum_probs=24.0
Q ss_pred HHHHHhcCCCCCCccCCCCCCC--CceEeccccceehhhhhhhcc
Q 023884 6 RLRDLQSQPGNKICVDCAQKNP--QWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 6 ~L~~L~~~p~Nk~C~DCga~~P--~WaS~~~GiFICl~CsgiHR~ 48 (276)
+|..|. ...=-+|.+||.+=| ..--+. .+-.|+.|...+-.
T Consensus 77 AL~Ri~-~G~YG~Ce~CGe~I~~~RL~a~P-~a~~Ci~Cq~~~E~ 119 (159)
T TIGR02890 77 ALQKIE-NGTYGICEVCGKPIPYERLEAIP-TATTCVECQNRKEV 119 (159)
T ss_pred HHHHHh-CCCCCeecccCCcccHHHHhhCC-CcchhHHHHHHhhh
Confidence 344442 234458999999522 222222 35679999987643
No 61
>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=30.23 E-value=33 Score=26.15 Aligned_cols=29 Identities=31% Similarity=0.755 Sum_probs=23.6
Q ss_pred CCccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 17 KICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 17 k~C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
+.|.-|+.+.- ...||++-|..|.+..|-
T Consensus 3 ~~C~VCg~~a~---g~hyGv~sC~aC~~FFRR 31 (78)
T cd07172 3 KICLVCSDEAS---GCHYGVLTCGSCKVFFKR 31 (78)
T ss_pred CCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 56888997654 469999999999998863
No 62
>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=29.96 E-value=65 Score=20.98 Aligned_cols=21 Identities=38% Similarity=0.830 Sum_probs=14.8
Q ss_pred CCCCHHHHHHHHhcChHHHHHHHhhcCCCCCC
Q 023884 62 DSWSEIQIKKMEAGGNERLNTFLSQYGIPKET 93 (276)
Q Consensus 62 D~Ws~~el~~m~~gGN~~~n~~~e~~~~~~~~ 93 (276)
|+|++++|+. ||+.|++..+.
T Consensus 2 dtWs~~~L~~-----------wL~~~gi~~~~ 22 (38)
T PF10281_consen 2 DTWSDSDLKS-----------WLKSHGIPVPK 22 (38)
T ss_pred CCCCHHHHHH-----------HHHHcCCCCCC
Confidence 6788877654 78888876543
No 63
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=29.68 E-value=37 Score=27.22 Aligned_cols=34 Identities=21% Similarity=0.636 Sum_probs=23.6
Q ss_pred hcCCCCCCccCCCCCC--------CCc---------eEeccccceehhhhh
Q 023884 11 QSQPGNKICVDCAQKN--------PQW---------ASVSYGVFMCLECSG 44 (276)
Q Consensus 11 ~~~p~Nk~C~DCga~~--------P~W---------aS~~~GiFICl~Csg 44 (276)
++.++--+|+|||.+- .+. .+=.||-.+|..|..
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 4566777999999851 111 134599999999964
No 64
>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=29.49 E-value=35 Score=25.46 Aligned_cols=27 Identities=22% Similarity=0.635 Sum_probs=20.8
Q ss_pred ccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 19 C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
|.-|+.+.-. ..||++.|..|.+..|-
T Consensus 1 C~VC~~~~~g---~hygv~sC~aC~~FFRR 27 (72)
T cd07156 1 CGVCGDRATG---YHFNAMTCEGCKGFFRR 27 (72)
T ss_pred CCccCccCcc---cEECcceehhhhhhhch
Confidence 5567765543 48999999999998774
No 65
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=29.34 E-value=20 Score=25.35 Aligned_cols=43 Identities=21% Similarity=0.557 Sum_probs=25.5
Q ss_pred CccCCCCCCCCce--EeccccceehhhhhhhccCCCcccceeeccc
Q 023884 18 ICVDCAQKNPQWA--SVSYGVFMCLECSGKHRGLGVHISFVRSVTM 61 (276)
Q Consensus 18 ~C~DCga~~P~Wa--S~~~GiFICl~CsgiHR~LGvhiS~VrSvtm 61 (276)
.|+=||..-.-.- -+.=| +||-.|...-..+-..+..++++|+
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 4788888654443 34556 8999999765444333333444544
No 66
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=29.13 E-value=35 Score=29.40 Aligned_cols=38 Identities=11% Similarity=0.187 Sum_probs=23.6
Q ss_pred cCCCCCCccCCCCCCCC-ceEeccccceehhhhhhhccC
Q 023884 12 SQPGNKICVDCAQKNPQ-WASVSYGVFMCLECSGKHRGL 49 (276)
Q Consensus 12 ~~p~Nk~C~DCga~~P~-WaS~~~GiFICl~CsgiHR~L 49 (276)
..+.--+|-+||.+=|. =.-+--++..|+.|...|-..
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 44567799999995221 111112357899999877543
No 67
>PF14376 Haem_bd: Haem-binding domain
Probab=29.05 E-value=28 Score=29.29 Aligned_cols=14 Identities=29% Similarity=0.847 Sum_probs=11.6
Q ss_pred CCccCCCCCCCCce
Q 023884 17 KICVDCAQKNPQWA 30 (276)
Q Consensus 17 k~C~DCga~~P~Wa 30 (276)
+-|.||++.+..|.
T Consensus 42 ~~CydCHSn~T~~P 55 (137)
T PF14376_consen 42 NSCYDCHSNNTRYP 55 (137)
T ss_pred ccccccCCCCCCCc
Confidence 46999999887775
No 68
>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=28.70 E-value=34 Score=23.96 Aligned_cols=34 Identities=21% Similarity=0.563 Sum_probs=22.2
Q ss_pred HhcCCCCCCccCCCCCCC--Cc-------eEeccccceehhhhh
Q 023884 10 LQSQPGNKICVDCAQKNP--QW-------ASVSYGVFMCLECSG 44 (276)
Q Consensus 10 L~~~p~Nk~C~DCga~~P--~W-------aS~~~GiFICl~Csg 44 (276)
|+++.+| +|-=|++..+ .| .+..-.|+||..|..
T Consensus 2 L~~Rs~~-kCELC~a~~~L~vy~Vpp~~~~~~d~~iliC~tC~~ 44 (47)
T smart00782 2 LLARCES-KCELCGSDSPLVVYAVPPSSDVTADNSVMLCDTCHS 44 (47)
T ss_pred hhHHcCC-cccCcCCCCCceEEecCCCCCCCccceeeechHHHH
Confidence 3444444 4999998543 12 245678999999975
No 69
>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=28.61 E-value=28 Score=28.37 Aligned_cols=31 Identities=23% Similarity=0.608 Sum_probs=25.1
Q ss_pred CCCCccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 15 ~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
..+.|.-|+.+.- ...||++.|..|.+..|-
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 3467999998655 459999999999998774
No 70
>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=28.37 E-value=31 Score=26.37 Aligned_cols=27 Identities=37% Similarity=0.775 Sum_probs=21.1
Q ss_pred ccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 19 C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
|.-||.+.- ...||++.|..|....|-
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 556776554 459999999999998874
No 71
>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=27.91 E-value=35 Score=25.44 Aligned_cols=27 Identities=37% Similarity=0.816 Sum_probs=20.8
Q ss_pred ccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 19 C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
|.-|+.+.- ...||++.|..|....|-
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 555776544 358999999999998874
No 72
>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=27.81 E-value=30 Score=26.73 Aligned_cols=27 Identities=37% Similarity=0.821 Sum_probs=21.8
Q ss_pred ccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 19 C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
|.-||.+.- ...||++.|..|.+.+|-
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 777887554 457999999999999874
No 73
>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=27.02 E-value=46 Score=26.04 Aligned_cols=31 Identities=29% Similarity=0.773 Sum_probs=25.2
Q ss_pred CCCCccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 15 ~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
..+.|.-|+.+.- ...||+..|..|....|-
T Consensus 5 ~~~~C~VCg~~~~---g~hyGv~sC~aCk~FFRR 35 (90)
T cd07168 5 SPKLCSICEDKAT---GLHYGIITCEGCKGFFKR 35 (90)
T ss_pred cCCCCcccCCcCc---ceEECceehhhhhHhhhh
Confidence 4567999998654 569999999999998864
No 74
>cd07179 2DBD_NR_DBD2 The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type zinc fingers. The second DNA-binding domain (DBD) of the 2DBD nuclear receptor (NR) 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. The proteins contain two DBDs in tandem, probably resulting from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=26.84 E-value=40 Score=25.31 Aligned_cols=27 Identities=30% Similarity=0.765 Sum_probs=20.8
Q ss_pred ccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 19 C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
|.-|+.+.- ...||++.|..|.+..|-
T Consensus 1 C~VCg~~~~---g~hygv~sC~aC~~FFRR 27 (74)
T cd07179 1 CRVCGGKSS---GFHFGALTCEGCKGFFRR 27 (74)
T ss_pred CcccCccCc---ceEECceeehhHHHHHHH
Confidence 556776554 458999999999998763
No 75
>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=26.59 E-value=53 Score=22.02 Aligned_cols=28 Identities=29% Similarity=0.646 Sum_probs=16.3
Q ss_pred CCccCCCCCCCC---ceEeccccceehhhhh
Q 023884 17 KICVDCAQKNPQ---WASVSYGVFMCLECSG 44 (276)
Q Consensus 17 k~C~DCga~~P~---WaS~~~GiFICl~Csg 44 (276)
++|.=||.+..+ -++-.-+++||.+|.-
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~ 32 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNGAYICDECVE 32 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-SEEEEHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCCcEECHHHHH
Confidence 468889886543 3344557999999975
No 76
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.68 E-value=28 Score=31.60 Aligned_cols=22 Identities=32% Similarity=0.695 Sum_probs=18.8
Q ss_pred CCCccCCCCCCCCceEeccccceehhhhh
Q 023884 16 NKICVDCAQKNPQWASVSYGVFMCLECSG 44 (276)
Q Consensus 16 Nk~C~DCga~~P~WaS~~~GiFICl~Csg 44 (276)
-+.|.-||. +.-..|.|..|..
T Consensus 309 S~~C~~cg~-------~~~r~~~C~~cg~ 330 (364)
T COG0675 309 SKTCPCCGH-------LSGRLFKCPRCGF 330 (364)
T ss_pred cccccccCC-------ccceeEECCCCCC
Confidence 479999999 6678999999965
No 77
>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=25.33 E-value=64 Score=25.81 Aligned_cols=39 Identities=23% Similarity=0.593 Sum_probs=28.5
Q ss_pred HHHHHHHH-hcCCCCCCccCCCCCCCCceEeccccceehhhh
Q 023884 3 ATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECS 43 (276)
Q Consensus 3 a~~~L~~L-~~~p~Nk~C~DCga~~P~WaS~~~GiFICl~Cs 43 (276)
.|+.+.+| .....--.|.-|+..... -+..||+-|..|-
T Consensus 21 lRK~v~kie~~q~a~y~CpfCgk~~vk--R~a~GIW~C~~C~ 60 (91)
T TIGR00280 21 LRRQVKKIEIQQKAKYVCPFCGKKTVK--RGSTGIWTCRKCG 60 (91)
T ss_pred HHHHHHHHHHHHhcCccCCCCCCCceE--EEeeEEEEcCCCC
Confidence 45566665 455567799999976654 4578999999994
No 78
>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=25.10 E-value=31 Score=26.82 Aligned_cols=28 Identities=18% Similarity=0.527 Sum_probs=22.8
Q ss_pred CccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 18 ICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 18 ~C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
.|.-|+.+.- ...||++.|..|.+..|-
T Consensus 2 ~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 29 (86)
T cd07157 2 TCQVCGEPAA---GFHHGAYVCEACKKFFMR 29 (86)
T ss_pred CCcccCCcCc---ccEECcceeeEeeeEEec
Confidence 4888987654 469999999999998764
No 79
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=24.90 E-value=39 Score=24.89 Aligned_cols=27 Identities=26% Similarity=0.705 Sum_probs=21.3
Q ss_pred ccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 19 C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
|.-|+.+.- ...||++.|..|.+..|-
T Consensus 2 C~vC~~~~~---~~hygv~~C~aC~~FFRR 28 (70)
T smart00399 2 CCVCGDHAS---GFHFGVCSCRACKAFFRR 28 (70)
T ss_pred CeEeCCcCc---ccEeCCcEechhhhhhhh
Confidence 677877654 348999999999998773
No 80
>cd06962 NR_DBD_FXR DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. DNA-binding domain of Farnesoid X receptor (FXR) 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. FXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. FXR is a member of the nuclear receptor family of ligand activated transcription factors. Bile acids are endogenous ligands for FXRs. Upon binding of a ligand, FXR binds to FXR response element (FXRE), which is an inverted repeat of TGACCT spaced by one nucleotide, either as a monomer or as a heterodimer with retinoid X receptor (RXR), to regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, FXR has a central well conserved
Probab=24.20 E-value=35 Score=26.43 Aligned_cols=29 Identities=31% Similarity=0.775 Sum_probs=23.1
Q ss_pred CCccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 17 KICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 17 k~C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
..|.-|+.+.- ...||++.|..|.+..|-
T Consensus 2 ~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 30 (84)
T cd06962 2 ELCVVCGDKAS---GYHYNALTCEGCKGFFRR 30 (84)
T ss_pred CCCeecCCcCc---ceEECcceeecceeeeee
Confidence 35888887655 458999999999998763
No 81
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=24.20 E-value=71 Score=30.77 Aligned_cols=25 Identities=36% Similarity=0.652 Sum_probs=19.4
Q ss_pred HhhhhhhhhHHHhhhhhcC-CCCCCC
Q 023884 215 SAANKEGFFSRKIAENEAR-PEGLPP 239 (276)
Q Consensus 215 ~~~~~e~yFa~~~~~Na~r-p~~lpp 239 (276)
...++-.|-+++++||++| ..+.||
T Consensus 257 qq~~~~q~~aKrqaENa~R~argep~ 282 (339)
T KOG1560|consen 257 QQAKKHQWIAKRQAENANRAARGEPP 282 (339)
T ss_pred HHHHHHHHHHHHHHHhhhhhhcCCCC
Confidence 3456778999999999999 455555
No 82
>cd06967 NR_DBD_TR2_like DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. It has been shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or
Probab=23.75 E-value=36 Score=26.47 Aligned_cols=30 Identities=30% Similarity=0.716 Sum_probs=23.9
Q ss_pred CCCccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 16 NKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 16 Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
.+.|.-|+.+.-. ..||++.|..|.+..|-
T Consensus 3 ~~~C~VCg~~~~g---~hyGv~sC~aC~~FFRR 32 (87)
T cd06967 3 VELCVVCGDKASG---RHYGAVSCEGCKGFFKR 32 (87)
T ss_pred CCCCeecCCcCCc---CEeCcceEeeeeeEeee
Confidence 3568999986654 58999999999998763
No 83
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=23.67 E-value=61 Score=25.86 Aligned_cols=39 Identities=21% Similarity=0.635 Sum_probs=28.4
Q ss_pred HHHHHHHH-hcCCCCCCccCCCCCCCCceEeccccceehhhh
Q 023884 3 ATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECS 43 (276)
Q Consensus 3 a~~~L~~L-~~~p~Nk~C~DCga~~P~WaS~~~GiFICl~Cs 43 (276)
.|+.+.+| .....--.|.-|+...... +..||+-|..|-
T Consensus 22 lRK~v~kie~~q~a~y~CpfCgk~~vkR--~a~GIW~C~~C~ 61 (90)
T PRK03976 22 IRKRVADIEEKMRAKHVCPVCGRPKVKR--VGTGIWECRKCG 61 (90)
T ss_pred HHHHHHHHHHHHhcCccCCCCCCCceEE--EEEEEEEcCCCC
Confidence 35566665 4555677999998766654 567999999994
No 84
>PF00105 zf-C4: Zinc finger, C4 type (two domains); InterPro: IPR001628 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences, connected via a linker region to a C-terminal ligand-binding domain (IPR000536 from INTERPRO). In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The DNA-binding domain can elicit either an activating or repressing effect by binding to specific regions of the DNA known as hormone-response elements [, ]. These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension, where residues in the first zinc module determine the specificity of the DNA recognition and residues in the second zinc module are involved in dimerisation. The DNA-binding domain is furthermore involved in several other functions including nuclear localisation, and interaction with transcription factors and co-activators []. 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 the two C4-type zinc finger modules involved in DNA-binding. 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, 0005634 nucleus; PDB: 1DSZ_A 1LO1_A 3M9E_F 2EBL_A 1GA5_B 1A6Y_B 1HLZ_B 1HRA_A 1KB6_B 1KB4_B ....
Probab=23.61 E-value=51 Score=24.06 Aligned_cols=26 Identities=31% Similarity=0.657 Sum_probs=20.4
Q ss_pred CCccCCCCCCCCceEeccccceehhhhhh
Q 023884 17 KICVDCAQKNPQWASVSYGVFMCLECSGK 45 (276)
Q Consensus 17 k~C~DCga~~P~WaS~~~GiFICl~Csgi 45 (276)
+.|.-|+.+.. ...||++.|..|...
T Consensus 1 ~~C~VCg~~~~---~~~ygv~sC~~C~~F 26 (70)
T PF00105_consen 1 KKCKVCGDPAS---GYHYGVLSCNACKMF 26 (70)
T ss_dssp -BSTTTSSBES---EEETTEEEEHHHHHH
T ss_pred CCCeECCCccC---cccccccccccceee
Confidence 46888997543 568999999999984
No 85
>cd07155 NR_DBD_ER_like DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. E
Probab=23.43 E-value=43 Score=25.19 Aligned_cols=27 Identities=26% Similarity=0.662 Sum_probs=20.8
Q ss_pred ccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 19 C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
|.-|+.+.- ...||++.|..|.+..|-
T Consensus 1 C~VC~~~~~---g~hygv~sC~aCk~FFRR 27 (75)
T cd07155 1 CLVCGDIAS---GYHYGVASCEACKAFFKR 27 (75)
T ss_pred CcccCccCc---ceEEChhhhhhhHHHHHH
Confidence 556776543 468999999999998763
No 86
>cd06958 NR_DBD_COUP_TF DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. COUP-TFs homodimerize or heterodimerize with retinoid X receptor (RXR) and a few other nuclear receptors and bind to a variety of response elements that are composed of imperfect AGGTCA direct or inverted repeats with various spacings. COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone recept
Probab=23.00 E-value=45 Score=24.90 Aligned_cols=27 Identities=33% Similarity=0.807 Sum_probs=20.6
Q ss_pred ccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 19 C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
|.-|+.+.- ...||+..|..|.+..|-
T Consensus 1 C~VCg~~~~---g~hygv~sC~aC~~FFRR 27 (73)
T cd06958 1 CVVCGDKSS---GKHYGQFTCEGCKSFFKR 27 (73)
T ss_pred CCccCccCc---ceEEChhhhhhhhhhhhh
Confidence 556776544 458999999999998864
No 87
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=22.88 E-value=30 Score=21.34 Aligned_cols=28 Identities=14% Similarity=0.411 Sum_probs=16.3
Q ss_pred CCccCCCCCCCCceEeccccceehhhhh
Q 023884 17 KICVDCAQKNPQWASVSYGVFMCLECSG 44 (276)
Q Consensus 17 k~C~DCga~~P~WaS~~~GiFICl~Csg 44 (276)
+.|--|+..-+.=.--....++|..|..
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCcC
Confidence 3577788876554444677899998864
No 88
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=22.77 E-value=38 Score=23.27 Aligned_cols=23 Identities=39% Similarity=0.787 Sum_probs=17.0
Q ss_pred CccCCCCCCCCceEeccccceehhhh
Q 023884 18 ICVDCAQKNPQWASVSYGVFMCLECS 43 (276)
Q Consensus 18 ~C~DCga~~P~WaS~~~GiFICl~Cs 43 (276)
+|.+||...... .....-|.+|.
T Consensus 4 ~C~~Cg~~~~~~---~~~~irC~~CG 26 (44)
T smart00659 4 ICGECGRENEIK---SKDVVRCRECG 26 (44)
T ss_pred ECCCCCCEeecC---CCCceECCCCC
Confidence 699999965433 46778899984
No 89
>cd06960 NR_DBD_HNF4A DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) 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. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is
Probab=22.72 E-value=44 Score=25.09 Aligned_cols=27 Identities=33% Similarity=0.829 Sum_probs=20.9
Q ss_pred ccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 19 C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
|.-||.+.- ...||++.|..|....|-
T Consensus 1 C~vCg~~~~---~~hygv~~C~aC~~FFrR 27 (76)
T cd06960 1 CAVCGDRAT---GKHYGVLSCNGCKGFFRR 27 (76)
T ss_pred CCccCccCc---ccEECcceeeeehheeCc
Confidence 556776544 458999999999998764
No 90
>PF13119 DUF3973: Domain of unknown function (DUF3973)
Probab=22.42 E-value=37 Score=23.22 Aligned_cols=13 Identities=31% Similarity=0.887 Sum_probs=10.7
Q ss_pred ceehhhhhhhccC
Q 023884 37 FMCLECSGKHRGL 49 (276)
Q Consensus 37 FICl~CsgiHR~L 49 (276)
|-|+.|+.+|-.-
T Consensus 2 yYCi~Cs~~h~e~ 14 (41)
T PF13119_consen 2 YYCINCSEIHHEK 14 (41)
T ss_pred EEEEEhHHhHHhh
Confidence 5799999999753
No 91
>PRK05766 rps14P 30S ribosomal protein S14P; Reviewed
Probab=22.32 E-value=24 Score=25.30 Aligned_cols=38 Identities=26% Similarity=0.741 Sum_probs=25.0
Q ss_pred CCCCccCCCCCCCCceEeccccceehhhhhhhccCCCccccee
Q 023884 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVR 57 (276)
Q Consensus 15 ~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiHR~LGvhiS~Vr 57 (276)
+-+.|.-||.+. =+--.||+.||-.|- |.+-.+|.|||
T Consensus 13 ~~nrC~~~Gr~r--gvirkf~l~lcR~~F---Re~A~~~gf~k 50 (52)
T PRK05766 13 GARECQRCGRKQ--GLIRKYGLYLCRQCF---REVAPKLGFKK 50 (52)
T ss_pred CCceeecCCCCc--eeHHhhCCcccHHHH---HHHHHHhCcee
Confidence 456899999843 334478999999886 44444455554
No 92
>cd07164 NR_DBD_PNR_like_1 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins 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. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-t
Probab=22.12 E-value=49 Score=25.06 Aligned_cols=27 Identities=30% Similarity=0.695 Sum_probs=20.7
Q ss_pred ccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 19 C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
|.-|+.+.- ...||+..|..|.+..|-
T Consensus 1 C~VCg~~~~---g~hyG~~~C~~C~~FFRR 27 (78)
T cd07164 1 CRVCGDRAS---GKHYGVPSCDGCRGFFKR 27 (78)
T ss_pred CcccCccCc---ceEECcchhhhhhhhhhh
Confidence 556776543 458999999999998864
No 93
>cd06959 NR_DBD_EcR_like The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of Ecdysone receptor (EcR) 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. EcR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: Ecdysone receptor (EcR), Liver X receptor (LXR) and Farnesoid X receptor (FXR). The DNA binding activity is regulated by their corresponding ligands. The ligands for EcR are ecdysteroids; LXR is regulated by oxidized cholesterol derivatives or oxysterols; and bile acids control FXR's activities. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcR-like receptors have a central well conserved DNA binding domai
Probab=21.85 E-value=56 Score=24.41 Aligned_cols=27 Identities=41% Similarity=0.904 Sum_probs=21.4
Q ss_pred ccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 19 C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
|.-|+.+.- ...||+..|..|.+..|-
T Consensus 2 C~vCg~~~~---~~hygv~sC~aC~~FFRR 28 (73)
T cd06959 2 CVVCGDKAS---GFHYGVLSCEGCKGFFRR 28 (73)
T ss_pred CceeCCcCc---ceEECceeehhhHHHHHH
Confidence 667776554 468999999999998874
No 94
>PHA02942 putative transposase; Provisional
Probab=21.76 E-value=41 Score=33.03 Aligned_cols=26 Identities=23% Similarity=0.553 Sum_probs=19.8
Q ss_pred CCCccCCCCCCCCceEeccccceehhhhh
Q 023884 16 NKICVDCAQKNPQWASVSYGVFMCLECSG 44 (276)
Q Consensus 16 Nk~C~DCga~~P~WaS~~~GiFICl~Csg 44 (276)
-+.|..||...+ .++-.+|.|..|--
T Consensus 325 Sq~Cs~CG~~~~---~l~~r~f~C~~CG~ 350 (383)
T PHA02942 325 SVSCPKCGHKMV---EIAHRYFHCPSCGY 350 (383)
T ss_pred CccCCCCCCccC---cCCCCEEECCCCCC
Confidence 468999998765 34556899999954
No 95
>cd06963 NR_DBD_GR_like The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. The DNA binding domain of GR_like nuclear receptors 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. It interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family of NRs includes four types of nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). The receptors bind to common DNA elements containing a partial palindrome of the core sequence 5'-TGTTCT-3' with a 3bp spacer. These four receptors regulate some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family have high sequence homology and sha
Probab=21.73 E-value=56 Score=24.50 Aligned_cols=27 Identities=26% Similarity=0.704 Sum_probs=20.6
Q ss_pred ccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 19 C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
|.-|+.+.- ...||++.|..|.+..|-
T Consensus 1 C~VCg~~a~---~~hygv~sC~aCk~FFRR 27 (73)
T cd06963 1 CLICGDEAS---GCHYGVLTCGSCKVFFKR 27 (73)
T ss_pred CcccCccCc---ceEECceeehhhhHhHHH
Confidence 555776443 568999999999998864
No 96
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=21.71 E-value=28 Score=28.36 Aligned_cols=33 Identities=24% Similarity=0.460 Sum_probs=23.1
Q ss_pred hcCCCCCCccCCCCCCCCceEeccccceehhhhhhh
Q 023884 11 QSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKH 46 (276)
Q Consensus 11 ~~~p~Nk~C~DCga~~P~WaS~~~GiFICl~CsgiH 46 (276)
...|..-+|-+||.. +....+..|.|..|-+..
T Consensus 65 ~~~p~~~~C~~Cg~~---~~~~~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 65 EEQEAECWCETCQQY---VTLLTQRVRRCPQCHGDM 97 (114)
T ss_pred EeeCcEEEcccCCCe---eecCCccCCcCcCcCCCC
Confidence 456777899999963 333345568899998654
No 97
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=21.01 E-value=61 Score=31.21 Aligned_cols=28 Identities=29% Similarity=0.502 Sum_probs=22.3
Q ss_pred CCccCCCCCCC-CceEeccccceehhhhh
Q 023884 17 KICVDCAQKNP-QWASVSYGVFMCLECSG 44 (276)
Q Consensus 17 k~C~DCga~~P-~WaS~~~GiFICl~Csg 44 (276)
..|.||..+-+ .-.+..-|..+|.+|--
T Consensus 1 ~~c~~C~~~~~~~V~d~~~gdtvC~~CGl 29 (308)
T KOG1597|consen 1 MTCPDCKRHPENLVEDHSAGDTVCSECGL 29 (308)
T ss_pred CCCCCCCCCCCCeeeeccCCceecccCCe
Confidence 36999999766 55566789999999954
No 98
>cd06961 NR_DBD_TR DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. DNA-binding domain of thyroid hormone receptors (TRs) 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. TR interacts with the thyroid response element, which is a DNA site with direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs, upstream of target genes and modulates the rate of transcriptional initiation. Thyroid hormone receptor (TR) mediates the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the he
Probab=20.36 E-value=50 Score=25.55 Aligned_cols=27 Identities=33% Similarity=0.748 Sum_probs=21.4
Q ss_pred ccCCCCCCCCceEeccccceehhhhhhhcc
Q 023884 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (276)
Q Consensus 19 C~DCga~~P~WaS~~~GiFICl~CsgiHR~ 48 (276)
|.-|+.+.- ...||++.|..|.+..|-
T Consensus 2 C~VCg~~~~---g~hygv~sC~aC~~FFRR 28 (85)
T cd06961 2 CVVCGDKAT---GYHYRCITCEGCKGFFRR 28 (85)
T ss_pred CceeCCcCc---ceEEChhhhhhhhHhhHh
Confidence 677887544 458999999999998873
No 99
>PHA02540 61 DNA primase; Provisional
Probab=20.17 E-value=62 Score=31.54 Aligned_cols=58 Identities=24% Similarity=0.492 Sum_probs=41.2
Q ss_pred CCCCccCCCCCCC------CceEeccc--cceehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcC
Q 023884 15 GNKICVDCAQKNP------QWASVSYG--VFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGG 76 (276)
Q Consensus 15 ~Nk~C~DCga~~P------~WaS~~~G--iFICl~CsgiHR~LGvhiS~VrSvtmD~Ws~~el~~m~~gG 76 (276)
-|-.|-=|+...+ =|++..-+ +|-|-.| |.| |--|.||....-..|.+.-.++.+..|
T Consensus 26 ~~~~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgC-Ga~---Gd~i~Flme~e~lsf~Eav~~la~~~g 91 (337)
T PHA02540 26 YNFRCPICGDSQKDKNKARGWIYEKKDGGVFKCHNC-GYH---RPFGNFLKDYEPDLYREYIMERFKERG 91 (337)
T ss_pred EEecCCCCCCccccCcCCcEEEeccCCceEEEecCC-CCC---CCHHHHHHHhcCCChHHHHHHHHHHhC
Confidence 3778999998554 48888888 9999999 555 345777777776677664444444445
Done!