Query 017907
Match_columns 364
No_of_seqs 197 out of 1154
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 04:28:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017907.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017907hhsearch_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 5.6E-77 1.2E-81 579.2 20.6 330 3-358 6-386 (386)
2 KOG0706 Predicted GTPase-activ 100.0 4.6E-36 9.9E-41 300.3 9.6 114 3-117 10-123 (454)
3 COG5347 GTPase-activating prot 100.0 7.7E-36 1.7E-40 292.1 10.2 121 3-123 7-128 (319)
4 PLN03114 ADP-ribosylation fact 100.0 3.5E-35 7.6E-40 288.5 10.7 115 4-118 10-124 (395)
5 KOG0703 Predicted GTPase-activ 100.0 8.3E-35 1.8E-39 280.0 7.9 116 3-124 12-127 (287)
6 PF01412 ArfGap: Putative GTPa 100.0 1.9E-34 4.1E-39 244.7 8.7 114 5-122 2-115 (116)
7 smart00105 ArfGap Putative GTP 100.0 1.2E-32 2.6E-37 232.6 9.6 107 14-123 1-107 (112)
8 PLN03131 hypothetical protein; 99.9 4.6E-28 9.9E-33 250.5 12.0 114 3-122 10-123 (705)
9 PLN03119 putative ADP-ribosyla 99.9 3.2E-28 7E-33 249.9 10.2 114 3-122 10-123 (648)
10 KOG0705 GTPase-activating prot 99.8 2.5E-21 5.3E-26 199.5 7.1 115 4-124 501-617 (749)
11 KOG0521 Putative GTPase activa 99.8 8.2E-20 1.8E-24 196.9 2.4 83 7-89 417-499 (785)
12 KOG0818 GTPase-activating prot 99.6 3.5E-16 7.6E-21 159.7 3.7 80 11-90 3-82 (669)
13 KOG1117 Rho- and Arf-GTPase ac 99.5 1.3E-15 2.9E-20 162.5 2.4 81 10-90 292-374 (1186)
14 KOG0702 Predicted GTPase-activ 99.4 3.3E-13 7.2E-18 137.9 6.9 118 4-125 13-131 (524)
15 KOG0521 Putative GTPase activa 89.2 0.087 1.9E-06 58.5 -0.9 70 11-82 625-695 (785)
16 PRK00085 recO DNA repair prote 82.9 0.82 1.8E-05 42.8 2.2 40 5-44 138-178 (247)
17 TIGR00613 reco DNA repair prot 76.9 2 4.3E-05 40.1 2.7 41 5-45 136-177 (241)
18 PF00643 zf-B_box: B-box zinc 76.6 2.5 5.5E-05 29.2 2.5 34 15-48 2-36 (42)
19 COG1997 RPL43A Ribosomal prote 73.3 3.5 7.6E-05 34.5 2.9 41 3-45 21-62 (89)
20 COG1381 RecO Recombinational D 70.2 2.5 5.4E-05 40.7 1.7 39 5-43 143-182 (251)
21 PRK12495 hypothetical protein; 62.6 6.3 0.00014 38.0 2.7 29 13-45 39-67 (226)
22 TIGR02419 C4_traR_proteo phage 61.3 3.2 6.8E-05 32.2 0.4 35 12-46 27-62 (63)
23 PF08271 TF_Zn_Ribbon: TFIIB z 58.2 5.7 0.00012 28.1 1.3 27 18-45 2-28 (43)
24 PRK11019 hypothetical protein; 55.3 5.3 0.00012 33.2 0.8 37 15-52 35-73 (88)
25 PF10764 Gin: Inhibitor of sig 52.8 8.6 0.00019 28.3 1.4 26 18-44 1-26 (46)
26 smart00401 ZnF_GATA zinc finge 52.4 13 0.00028 27.7 2.4 37 15-51 2-40 (52)
27 PRK13715 conjugal transfer pro 50.9 5.9 0.00013 31.7 0.4 33 16-48 34-67 (73)
28 PTZ00255 60S ribosomal protein 48.5 19 0.00041 30.3 3.0 40 3-44 22-62 (90)
29 PF00320 GATA: GATA zinc finge 48.3 13 0.00029 25.6 1.7 32 19-50 1-34 (36)
30 PF01286 XPA_N: XPA protein N- 48.2 6.3 0.00014 27.4 0.1 27 17-43 4-31 (34)
31 PF11781 RRN7: RNA polymerase 45.2 17 0.00037 25.3 1.9 27 14-43 6-32 (36)
32 COG1734 DksA DnaK suppressor p 45.2 4.7 0.0001 35.3 -1.1 30 18-47 82-112 (120)
33 PF10310 DUF2413: Protein of u 42.8 22 0.00047 37.6 3.1 51 162-214 118-171 (444)
34 PF01258 zf-dskA_traR: Prokary 40.3 4.8 0.0001 27.5 -1.4 30 17-46 4-34 (36)
35 PF12760 Zn_Tnp_IS1595: Transp 40.0 33 0.00072 24.6 2.8 39 3-43 6-44 (46)
36 PF01780 Ribosomal_L37ae: Ribo 39.8 18 0.0004 30.3 1.7 40 3-44 21-61 (90)
37 PF07282 OrfB_Zn_ribbon: Putat 39.2 17 0.00038 27.6 1.4 27 16-44 28-54 (69)
38 cd07171 NR_DBD_ER DNA-binding 38.7 22 0.00047 28.9 1.9 31 15-48 2-32 (82)
39 cd07173 NR_DBD_AR DNA-binding 37.7 20 0.00044 29.1 1.6 32 14-48 1-32 (82)
40 PHA00080 DksA-like zinc finger 36.1 20 0.00043 28.6 1.2 34 13-47 28-63 (72)
41 cd06968 NR_DBD_ROR DNA-binding 35.9 23 0.00051 29.5 1.7 31 15-48 4-34 (95)
42 PRK00423 tfb transcription ini 34.4 24 0.00053 34.9 1.9 34 12-46 7-40 (310)
43 cd07170 NR_DBD_ERR DNA-binding 32.6 26 0.00057 29.4 1.5 29 17-48 5-33 (97)
44 TIGR02890 spore_yteA sporulati 32.5 24 0.00051 32.2 1.3 35 14-48 84-119 (159)
45 PRK10778 dksA RNA polymerase-b 32.3 28 0.0006 31.5 1.7 38 12-49 107-145 (151)
46 KOG3362 Predicted BBOX Zn-fing 31.6 20 0.00043 32.7 0.6 34 14-48 116-150 (156)
47 KOG0457 Histone acetyltransfer 31.6 35 0.00076 36.0 2.5 39 36-74 38-86 (438)
48 cd07160 NR_DBD_LXR DNA-binding 30.9 34 0.00073 29.0 1.9 31 15-48 17-47 (101)
49 cd07169 NR_DBD_GCNF_like DNA-b 29.8 31 0.00068 28.4 1.5 32 14-48 4-35 (90)
50 COG0675 Transposase and inacti 29.2 24 0.00051 33.3 0.8 21 17-44 310-330 (364)
51 PF01387 Synuclein: Synuclein; 29.0 50 0.0011 29.6 2.6 79 166-248 1-86 (131)
52 cd06966 NR_DBD_CAR DNA-binding 28.9 27 0.00059 29.0 1.0 29 17-48 1-29 (94)
53 PF14803 Nudix_N_2: Nudix N-te 28.4 24 0.00053 24.4 0.5 30 17-47 1-33 (34)
54 KOG3507 DNA-directed RNA polym 28.3 28 0.00061 27.3 0.9 24 17-43 21-44 (62)
55 COG2174 RPL34A Ribosomal prote 28.1 38 0.00082 28.6 1.7 34 11-44 29-79 (93)
56 TIGR00280 L37a ribosomal prote 27.8 62 0.0013 27.3 2.9 40 3-44 21-61 (91)
57 PF02993 MCPVI: Minor capsid p 26.1 22 0.00048 34.6 0.0 70 162-247 32-101 (238)
58 PTZ00218 40S ribosomal protein 26.0 28 0.0006 26.7 0.5 39 14-57 14-52 (54)
59 PHA02942 putative transposase; 24.9 35 0.00076 35.0 1.1 25 17-44 326-350 (383)
60 cd07162 NR_DBD_PXR DNA-binding 24.4 48 0.001 27.0 1.7 28 18-48 1-28 (87)
61 cd07161 NR_DBD_EcR DNA-binding 24.4 48 0.001 27.4 1.7 29 17-48 2-30 (91)
62 cd07163 NR_DBD_TLX DNA-binding 23.4 37 0.00079 28.1 0.8 30 16-48 6-35 (92)
63 PF06827 zf-FPG_IleRS: Zinc fi 23.3 33 0.00071 22.4 0.4 28 17-44 2-29 (30)
64 PF14471 DUF4428: Domain of un 23.3 33 0.00071 25.6 0.4 43 18-61 1-45 (51)
65 COG2158 Uncharacterized protei 23.1 47 0.001 28.9 1.4 24 28-51 52-77 (112)
66 KOG0704 ADP-ribosylation facto 22.9 46 0.001 34.4 1.5 64 162-228 251-324 (386)
67 TIGR00382 clpX endopeptidase C 22.7 42 0.00091 35.0 1.2 29 16-44 7-37 (413)
68 PF14179 YppG: YppG-like prote 22.5 41 0.00088 29.3 0.9 35 202-240 76-111 (112)
69 cd06956 NR_DBD_RXR DNA-binding 22.3 60 0.0013 25.8 1.8 28 18-48 2-29 (77)
70 cd00202 ZnF_GATA Zinc finger D 22.2 53 0.0011 24.7 1.4 34 18-51 1-36 (54)
71 PRK03976 rpl37ae 50S ribosomal 21.8 81 0.0018 26.5 2.5 39 3-43 22-61 (90)
72 cd07156 NR_DBD_VDR_like The DN 21.7 58 0.0012 25.5 1.6 27 19-48 1-27 (72)
73 cd07172 NR_DBD_GR_PR DNA-bindi 21.4 60 0.0013 26.0 1.6 29 17-48 3-31 (78)
74 COG5145 RAD14 DNA excision rep 21.1 32 0.00068 33.7 -0.0 35 11-46 111-147 (292)
75 cd07158 NR_DBD_Ppar_like The D 21.1 55 0.0012 25.6 1.4 27 19-48 1-27 (73)
76 cd06955 NR_DBD_VDR DNA-binding 21.0 44 0.00096 28.6 0.9 30 16-48 6-35 (107)
77 PRK06266 transcription initiat 20.7 36 0.00077 31.4 0.2 28 18-46 119-146 (178)
78 cd07165 NR_DBD_DmE78_like DNA- 20.3 52 0.0011 26.4 1.1 27 19-48 1-27 (81)
79 cd07166 NR_DBD_REV_ERB DNA-bin 20.3 48 0.001 27.3 0.9 30 16-48 3-32 (89)
80 cd07168 NR_DBD_DHR4_like DNA-b 20.1 73 0.0016 26.2 1.9 31 15-48 5-35 (90)
No 1
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=100.00 E-value=5.6e-77 Score=579.18 Aligned_cols=330 Identities=48% Similarity=0.827 Sum_probs=271.5
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHhhccChHHHHH
Q 017907 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (364)
Q Consensus 3 a~r~LreL~~~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~LG~hiS~VKSvtmD~Ws~~eL~~Mk~gGN~~an~ 82 (364)
++|+|.+|+...+|++||||+++|||||||+||||||++|+|+||+||||||||||||||+|+++||++|++|||.++++
T Consensus 6 trr~L~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~~~e 85 (386)
T KOG0704|consen 6 TRRVLLELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNERFRE 85 (386)
T ss_pred HHHHHHhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchhHHH
Confidence 67777777777799999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcCCCCCC-CccccccchhHHHHHHHHHHHHcCCCCCCCCcchhcccCCCCCCCC-C-CCCC-----------C---
Q 017907 83 FLSQYGIPKET-DIVTKYNTNAASIYRDRIQAIAEGRPWRDPPVVKETLNAGKSSSRP-P-LAQS-----------A--- 145 (364)
Q Consensus 83 f~e~~~~~~e~-~I~~KY~s~aa~~yreki~a~~egr~w~~pp~~kE~~~~~~~~~~p-~-~~~~-----------~--- 145 (364)
||+.+.+.++. +|++||++++|++||+||++++|||+|.+||+++|..++ ...+| + +... .
T Consensus 86 FL~s~~~~~e~~~i~eKYns~aAa~yRdki~~laegr~w~d~~~~k~~~p~--~syt~a~~~~~~ss~~~~~~sq~~~~~ 163 (386)
T KOG0704|consen 86 FLSSQGIYKETWPIREKYNSRAAALYRDKIAALAEGREWNDPPYLKEDNPA--QSYTSAAQLGSKSSETIYTISQLSNSA 163 (386)
T ss_pred HHhhCccccccccHHHhhccHHHHHHHHHHHHHhcCCcccccccccccCcc--cccccCCCcCCCcCCcccccccchhhh
Confidence 99998866665 999999999999999999999999999999999999863 22333 1 1100 0
Q ss_pred ----------------CCCC--CCCCCCCCCCCC----------cccchhhhhccchhhHHHHHHHHHHHHHHHhhhhhh
Q 017907 146 ----------------SVGG--VGRNGNYGNHGG----------WDNVLSAVSQGFGRISLVAASAAQSAATVVQAGTRE 197 (364)
Q Consensus 146 ----------------~~~g--~~~ng~y~sqgg----------~~d~~ssLssG~g~fS~~A~~~A~~A~~~~~~~~k~ 197 (364)
++.+ +.|.|+|.++|. ++|+||.|++||++||++|+.+|+ |++++++.
T Consensus 164 ~~ke~~fa~~~~~n~srpd~lppsQggkY~GFGst~~~ppqs~~~~~~~s~ls~Gws~~s~~as~~a~----~~~~~~~~ 239 (386)
T KOG0704|consen 164 AGKESYFAKRLSENQSRPDGLPPSQGGKYQGFGSTNAPPPQSNSQDDAMSVLSSGWSRLSTGASSAAS----VGQTATQK 239 (386)
T ss_pred cchhHHHHHhcccccCCCCCCCcccCCcccccCCCCCCCCccccccchhhhhccccccccchhhhhhh----hhhhhhhh
Confidence 1111 222355655544 778999999999999999988766 66677666
Q ss_pred hhcccccccccchhchhhhhhhhhccccccchhhhhhhHHHHhhhhhhhhhhcCCCCccccccCCCCCccccccCCCCCC
Q 017907 198 FTSKVREGGYDHKVNETVNVVTAKTSEIGQRTWGIMKGVMAMASQKVEEYTKEGWNNDNWQRNESESNGYYQEFNHGNKG 277 (364)
Q Consensus 198 ~~~kvkeg~l~~~v~~~v~~va~Kv~e~g~~gw~~~~gv~~~~s~kvE~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~ 277 (364)
++ ||||| |++.|+..|++||.||+|||+|||++|+ .+++|++|+. |+++...+.+||.+.++|..
T Consensus 240 ~s-kvkeg-l~~~~s~~v~~va~k~t~vG~r~W~~ls---~~~sq~~e~f----------q~~~s~g~~~~qn~~~~n~~ 304 (386)
T KOG0704|consen 240 AS-KVKEG-LDDFVSDPVGTVASKVTEVGTRGWGLLS---AAVSQSVEDF----------QDSESVGGPYYQNSGQGNFS 304 (386)
T ss_pred hh-hhhhh-hhhhcccchhhhhhhcccccccchhhhH---Hhhccccccc----------cccCccCCcccccccccccc
Confidence 65 99999 9999999999999999999999998888 8899999977 78888999999999998876
Q ss_pred CCCCCCCCC-CCCCCCCCC-CCCCCCcCCCCCCC--CCCCCCCCCCCCCCCcCcc--CCCCCCccccccccccccccCCC
Q 017907 278 QDSPAGGGQ-YSAGHHNSY-GSSSWDDWDQKDKK--EDTPKGTGSGNNDAWAGWD--DAKDDGYDNFYQSASDKKALGHN 351 (364)
Q Consensus 278 ~~~~~~~~~-~~~~~~~~~-~~~~w~~w~~~~~~--~~~~~~~~~~~~~~w~g~~--~~~~~~~~~~~~~~~~~~~~~~~ 351 (364)
=|++.++.+ ++-+|.+++ ++++|+.|...+.. +........+++.+|+||| +++++ +.+|+.++++ .|+
T Consensus 305 sn~~~g~~q~~~~~~~~s~~~s~s~s~~~~n~~~~~s~~~gta~~~~ds~~~g~e~~~~k~~--~~~~~~a~dk---s~~ 379 (386)
T KOG0704|consen 305 SNSKRGGWQFSSKGHEKSSLPSNSFSCFTENDQNSSSDSKGTASADDDSGWSGFEASDAKDD--ETSYQNAPDK---SHD 379 (386)
T ss_pred ccccccccccccccccccCCCCccccccccCcccCcccccCccccCCCCcccccccCCCCcc--cccccccccc---ccC
Confidence 566666555 335555544 89999999987533 3333333445566899999 67777 4588888877 399
Q ss_pred CCCCCcc
Q 017907 352 GKSDATW 358 (364)
Q Consensus 352 ~~~~~~~ 358 (364)
|++|.+|
T Consensus 380 g~~d~aw 386 (386)
T KOG0704|consen 380 GWDDDAW 386 (386)
T ss_pred CccccCC
Confidence 9999998
No 2
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=4.6e-36 Score=300.35 Aligned_cols=114 Identities=46% Similarity=0.927 Sum_probs=108.0
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHhhccChHHHHH
Q 017907 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (364)
Q Consensus 3 a~r~LreL~~~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~LG~hiS~VKSvtmD~Ws~~eL~~Mk~gGN~~an~ 82 (364)
..++|+.|+.+|+||+||||++++|.|+||+||||||++|+++||+||||||||||+.||+|+..||++|+.|||.+|+.
T Consensus 10 ~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~~ 89 (454)
T KOG0706|consen 10 IQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANARV 89 (454)
T ss_pred HHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHHH
Confidence 56789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcCCCCCCCccccccchhHHHHHHHHHHHHcC
Q 017907 83 FLSQYGIPKETDIVTKYNTNAASIYRDRIQAIAEG 117 (364)
Q Consensus 83 f~e~~~~~~e~~I~~KY~s~aa~~yreki~a~~eg 117 (364)
||++|+... .++..||+++++..||++|..++..
T Consensus 90 FFkqhg~~t-~d~~aKY~SraA~~Yr~kl~~lv~k 123 (454)
T KOG0706|consen 90 FFKQHGCVT-LDANAKYNSRAAKLYREKLKKLVQK 123 (454)
T ss_pred HHHHcCCcc-hhhhhhhccHHHHHHHHHHHHHHHH
Confidence 999998763 4899999999999999999887743
No 3
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=100.00 E-value=7.7e-36 Score=292.14 Aligned_cols=121 Identities=38% Similarity=0.711 Sum_probs=111.7
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHhhccChHHHHH
Q 017907 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (364)
Q Consensus 3 a~r~LreL~~~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~LG~hiS~VKSvtmD~Ws~~eL~~Mk~gGN~~an~ 82 (364)
.+++|..|++.++|++|||||+++|+|||++||||||++||||||+||+||||||||+||.|+++||++|+.+||.++|+
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-CCCccccccchhHHHHHHHHHHHHcCCCCCCC
Q 017907 83 FLSQYGIPK-ETDIVTKYNTNAASIYRDRIQAIAEGRPWRDP 123 (364)
Q Consensus 83 f~e~~~~~~-e~~I~~KY~s~aa~~yreki~a~~egr~w~~p 123 (364)
||++++... ..+|+.||++..+..|++++..+.....+...
T Consensus 87 ~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~~~~ 128 (319)
T COG5347 87 FYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDDSSS 128 (319)
T ss_pred HhccCCCcccccccccccCHHHHHHHHHHHHHhhhccccccC
Confidence 999887763 47899999999999999998877777766433
No 4
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=100.00 E-value=3.5e-35 Score=288.46 Aligned_cols=115 Identities=45% Similarity=0.877 Sum_probs=109.9
Q ss_pred HHHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHhhccChHHHHHH
Q 017907 4 TRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTF 83 (364)
Q Consensus 4 ~r~LreL~~~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~LG~hiS~VKSvtmD~Ws~~eL~~Mk~gGN~~an~f 83 (364)
.++|++|+..|+|++||||++++|+|||++||||||++|+||||.||+|||+||||+||.|++++|++|+.+||.++|+|
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 46799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcCCCCCCCccccccchhHHHHHHHHHHHHcCC
Q 017907 84 LSQYGIPKETDIVTKYNTNAASIYRDRIQAIAEGR 118 (364)
Q Consensus 84 ~e~~~~~~e~~I~~KY~s~aa~~yreki~a~~egr 118 (364)
|+.|+......|+.||++++|.+||++|.++++..
T Consensus 90 F~qhG~~~~~~~~~KY~S~aA~~Yre~L~keVa~~ 124 (395)
T PLN03114 90 FKQYGWSDGGKTEAKYTSRAADLYKQILAKEVAKS 124 (395)
T ss_pred HHHcCCCCCCCcccccCCHHHHHHHHHHHHHHHHh
Confidence 99999877778999999999999999999888664
No 5
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=8.3e-35 Score=279.95 Aligned_cols=116 Identities=40% Similarity=0.718 Sum_probs=99.8
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHhhccChHHHHH
Q 017907 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (364)
Q Consensus 3 a~r~LreL~~~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~LG~hiS~VKSvtmD~Ws~~eL~~Mk~gGN~~an~ 82 (364)
.+++|++|++.|+|+.|||||++.|+|||+++|||||+.|+||||.||+|||+||||+||.|+++||+.|+..||.++|.
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 HHhhcCCCCCCCccccccchhHHHHHHHHHHHHcCCCCCCCC
Q 017907 83 FLSQYGIPKETDIVTKYNTNAASIYRDRIQAIAEGRPWRDPP 124 (364)
Q Consensus 83 f~e~~~~~~e~~I~~KY~s~aa~~yreki~a~~egr~w~~pp 124 (364)
|||+..+. ....+ . .-.....+|+++||-+.|.+++
T Consensus 92 ~~ea~~p~-~~~~p-~----~d~~~e~FIR~KYE~kkf~~~~ 127 (287)
T KOG0703|consen 92 YYEAKLPD-PFRRP-G----PDDLVEQFIRDKYERKKFLDPE 127 (287)
T ss_pred hccccCCc-cccCC-C----hHHHHHHHHHHHHhhhhhccch
Confidence 99987332 11111 0 0113556788888888888765
No 6
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=100.00 E-value=1.9e-34 Score=244.71 Aligned_cols=114 Identities=41% Similarity=0.811 Sum_probs=89.8
Q ss_pred HHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHhhccChHHHHHHH
Q 017907 5 RRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTFL 84 (364)
Q Consensus 5 r~LreL~~~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~LG~hiS~VKSvtmD~Ws~~eL~~Mk~gGN~~an~f~ 84 (364)
++|++|++.|+|++|||||+++|+|||++||||||+.|+++||.||+|||+||||+||.|+++||++|+.+||.++|++|
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 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCCCCCCCccccccchhHHHHHHHHHHHHcCCCCCC
Q 017907 85 SQYGIPKETDIVTKYNTNAASIYRDRIQAIAEGRPWRD 122 (364)
Q Consensus 85 e~~~~~~e~~I~~KY~s~aa~~yreki~a~~egr~w~~ 122 (364)
+++. +....+ -.......|+++|+++|+.+.|..
T Consensus 82 e~~~-~~~~~~---~~~~~~~~~~~fI~~KY~~k~f~~ 115 (116)
T PF01412_consen 82 EANS-PPPKKP---PPSSDQEKREQFIRAKYVEKAFIS 115 (116)
T ss_dssp TTTS-TTTTTH---CTTSHHHHHHHHHHHHHTTHTTS-
T ss_pred HcCC-CCCCCC---CCCCcHHHHHHHHHHHHHhhhhcc
Confidence 9872 111111 123344578889999999998864
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=99.98 E-value=1.2e-32 Score=232.57 Aligned_cols=107 Identities=43% Similarity=0.783 Sum_probs=93.4
Q ss_pred CCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHhhccChHHHHHHHhhcCCCCCC
Q 017907 14 PGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTFLSQYGIPKET 93 (364)
Q Consensus 14 p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~LG~hiS~VKSvtmD~Ws~~eL~~Mk~gGN~~an~f~e~~~~~~e~ 93 (364)
|+|++||||++++|+|||++||||||++|+|+||.||+|||+||||+||+|++++|++|+.+||.++|+||+++.++...
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 68999999999999999999999999999999999999999999999999999999999999999999999987654322
Q ss_pred CccccccchhHHHHHHHHHHHHcCCCCCCC
Q 017907 94 DIVTKYNTNAASIYRDRIQAIAEGRPWRDP 123 (364)
Q Consensus 94 ~I~~KY~s~aa~~yreki~a~~egr~w~~p 123 (364)
.. . .......|+.+|+.+|+.+.|.++
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 122345788899999999999753
No 8
>PLN03131 hypothetical protein; Provisional
Probab=99.95 E-value=4.6e-28 Score=250.48 Aligned_cols=114 Identities=24% Similarity=0.509 Sum_probs=96.6
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHhhccChHHHHH
Q 017907 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (364)
Q Consensus 3 a~r~LreL~~~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~LG~hiS~VKSvtmD~Ws~~eL~~Mk~gGN~~an~ 82 (364)
.+++|++|++.|+|++|+||++++|+|||++||||||++|+||||.|| | |||||+||.|+++||++|+.+||.++|+
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 9999999999999999999999999999
Q ss_pred HHhhcCCCCCCCccccccchhHHHHHHHHHHHHcCCCCCC
Q 017907 83 FLSQYGIPKETDIVTKYNTNAASIYRDRIQAIAEGRPWRD 122 (364)
Q Consensus 83 f~e~~~~~~e~~I~~KY~s~aa~~yreki~a~~egr~w~~ 122 (364)
||+++..+....+.... .....+++|+.+|+.|.|..
T Consensus 87 iyeanwd~~r~~lP~~s---d~ekrr~FIR~KYVeKRFa~ 123 (705)
T PLN03131 87 IYLKDWDQQRQRLPDNS---KVDKIREFIKDIYVDKKYAG 123 (705)
T ss_pred HHHhhcccccCCCCCCc---cHHHHHHHHHHHHhhhhhhc
Confidence 99976543322222221 22356788899998888754
No 9
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=99.95 E-value=3.2e-28 Score=249.94 Aligned_cols=114 Identities=23% Similarity=0.489 Sum_probs=97.4
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHhhccChHHHHH
Q 017907 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (364)
Q Consensus 3 a~r~LreL~~~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~LG~hiS~VKSvtmD~Ws~~eL~~Mk~gGN~~an~ 82 (364)
.+++|++|++.|+|++|+||++++|+|||++||||||++|+||||.|| ++||||+||+|+++||++|+.+||.++|+
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 39999999999999999999999999999
Q ss_pred HHhhcCCCCCCCccccccchhHHHHHHHHHHHHcCCCCCC
Q 017907 83 FLSQYGIPKETDIVTKYNTNAASIYRDRIQAIAEGRPWRD 122 (364)
Q Consensus 83 f~e~~~~~~e~~I~~KY~s~aa~~yreki~a~~egr~w~~ 122 (364)
||+++..+....+.... .....+++|+.+|+.|.|..
T Consensus 87 iyeanw~~~~~~~P~~s---D~e~lr~FIR~KYVeKRF~~ 123 (648)
T PLN03119 87 IYLKNWDHQRQRLPENS---NAERVREFIKNVYVQKKYAG 123 (648)
T ss_pred HHHhhcccccCCCCCCc---cHHHHHHHHHHHHhhhhccC
Confidence 99986543222222211 12356789999999999875
No 10
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.84 E-value=2.5e-21 Score=199.46 Aligned_cols=115 Identities=37% Similarity=0.643 Sum_probs=94.5
Q ss_pred HHHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHhhccChHHHHHH
Q 017907 4 TRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTF 83 (364)
Q Consensus 4 ~r~LreL~~~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~LG~hiS~VKSvtmD~Ws~~eL~~Mk~gGN~~an~f 83 (364)
+-+|..|+..++|..|+||+.++|.|||+|+|+.||++|+||||.||.|+|+||+|.||.|..|.+..|..+||+.||.+
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 44677899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Hhh--cCCCCCCCccccccchhHHHHHHHHHHHHcCCCCCCCC
Q 017907 84 LSQ--YGIPKETDIVTKYNTNAASIYRDRIQAIAEGRPWRDPP 124 (364)
Q Consensus 84 ~e~--~~~~~e~~I~~KY~s~aa~~yreki~a~~egr~w~~pp 124 (364)
||. .+..+..+-. ++ .....+|+++||.+-|-.|-
T Consensus 581 WE~~~~G~~KPs~~s----~R--EEkErwIr~KYeqklFLaPl 617 (749)
T KOG0705|consen 581 WEGSSQGQTKPSPDS----SR--EEKERWIRAKYEQKLFLAPL 617 (749)
T ss_pred hhhhccCCcCCCccc----cH--HHHHHHHHHHHHHHhhcCCC
Confidence 995 2222211100 11 12233588888888886653
No 11
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.77 E-value=8.2e-20 Score=196.87 Aligned_cols=83 Identities=43% Similarity=0.833 Sum_probs=79.8
Q ss_pred HHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHhhccChHHHHHHHhh
Q 017907 7 LRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTFLSQ 86 (364)
Q Consensus 7 LreL~~~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~LG~hiS~VKSvtmD~Ws~~eL~~Mk~gGN~~an~f~e~ 86 (364)
+.++++.|+|..|+|||++.|+|+|+|+||.+|++|+|+||.||+|||+||||+||.|.++.+.+|+.+||..+|.+|++
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 67889999999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred cCC
Q 017907 87 YGI 89 (364)
Q Consensus 87 ~~~ 89 (364)
...
T Consensus 497 ~l~ 499 (785)
T KOG0521|consen 497 LLP 499 (785)
T ss_pred ccc
Confidence 543
No 12
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.60 E-value=3.5e-16 Score=159.67 Aligned_cols=80 Identities=33% Similarity=0.664 Sum_probs=74.4
Q ss_pred hcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHhhccChHHHHHHHhhcCCC
Q 017907 11 QSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTFLSQYGIP 90 (364)
Q Consensus 11 ~~~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~LG~hiS~VKSvtmD~Ws~~eL~~Mk~gGN~~an~f~e~~~~~ 90 (364)
++.+.-++|+||++++|.||||+-|+|||.+|+.+||.||.|||.||+|....|.++.|++.....|..+|.+||...++
T Consensus 3 k~~l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaNsIWEh~Lld 82 (669)
T KOG0818|consen 3 KRLLSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGANSIWEHSLLD 82 (669)
T ss_pred ccchhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcchhhhhhccC
Confidence 45567789999999999999999999999999999999999999999999999999999999999999999999975443
No 13
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.55 E-value=1.3e-15 Score=162.47 Aligned_cols=81 Identities=38% Similarity=0.671 Sum_probs=75.4
Q ss_pred HhcCCCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCcccceeecccC--CCCHHHHHHhhccChHHHHHHHhhc
Q 017907 10 LQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMD--SWSEIQIKKMEAGGNERLNTFLSQY 87 (364)
Q Consensus 10 L~~~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~LG~hiS~VKSvtmD--~Ws~~eL~~Mk~gGN~~an~f~e~~ 87 (364)
+=....|+.|+||+++.|.||++|++|.||-.|+|-||+||..+|+|||++|| .|+.+-|+++...||.++|.||..+
T Consensus 292 iW~ne~nr~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~Fwa~n 371 (1186)
T KOG1117|consen 292 IWLNEENRECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANRFWAGN 371 (1186)
T ss_pred HHhccccccccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCcccccccccC
Confidence 34567899999999999999999999999999999999999999999999999 6999999999999999999999865
Q ss_pred CCC
Q 017907 88 GIP 90 (364)
Q Consensus 88 ~~~ 90 (364)
..+
T Consensus 372 l~~ 374 (1186)
T KOG1117|consen 372 LPP 374 (1186)
T ss_pred CCC
Confidence 544
No 14
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.40 E-value=3.3e-13 Score=137.87 Aligned_cols=118 Identities=18% Similarity=0.356 Sum_probs=97.5
Q ss_pred HHHHHHHhcCCCCCCccCCCCCCC-CceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHhhccChHHHHH
Q 017907 4 TRRLRDLQSQPGNKICVDCAQKNP-QWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (364)
Q Consensus 4 ~r~LreL~~~p~Nk~CaDCGa~nP-~WaSvn~GIFIC~~CSGiHR~LG~hiS~VKSvtmD~Ws~~eL~~Mk~gGN~~an~ 82 (364)
+++||.|+++|+|++|++|....+ .|++++-|-|+|+.|+|.-|.|-. -.+||+|.|-.+++.|+..++.+||..+++
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 789999999999999999999888 999999999999999999999853 349999999999999999999999999999
Q ss_pred HHhhcCCCCCCCccccccchhHHHHHHHHHHHHcCCCCCCCCc
Q 017907 83 FLSQYGIPKETDIVTKYNTNAASIYRDRIQAIAEGRPWRDPPV 125 (364)
Q Consensus 83 f~e~~~~~~e~~I~~KY~s~aa~~yreki~a~~egr~w~~pp~ 125 (364)
+|-+-......-+.+ .+-...-|+.|+.+|+++.|+.|+.
T Consensus 92 i~fkl~D~q~S~vPD---~rn~~~~kef~q~~y~~kr~~v~~n 131 (524)
T KOG0702|consen 92 IWFKLFDFQRSNVPD---SRNPQKVKEFQQEKYVKKRYYVPKN 131 (524)
T ss_pred hhhcchhhhhccCCC---cccchhhHHHHhhhhccceeecCcc
Confidence 886421111122222 2223457889999999999998764
No 15
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=89.20 E-value=0.087 Score=58.49 Aligned_cols=70 Identities=14% Similarity=0.277 Sum_probs=55.8
Q ss_pred hcCCCCCCccCCCC-CCCCceEeccceeeehhhhhhhccCCCcccceeecccCCCCHHHHHHhhccChHHHHH
Q 017907 11 QSQPGNKICVDCAQ-KNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (364)
Q Consensus 11 ~~~p~Nk~CaDCGa-~nP~WaSvn~GIFIC~~CSGiHR~LG~hiS~VKSvtmD~Ws~~eL~~Mk~gGN~~an~ 82 (364)
.....+-.|++|.+ +...|+++++.+-+|..|+++|+.++.|++..+++.++...+ |.....-|+..++.
T Consensus 625 ~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~ 695 (785)
T KOG0521|consen 625 VKASSDGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHH 695 (785)
T ss_pred HHhccCccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchh
Confidence 44445788999976 578899999999999999999999999999999999988877 44444445444443
No 16
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=82.94 E-value=0.82 Score=42.83 Aligned_cols=40 Identities=25% Similarity=0.419 Sum_probs=32.2
Q ss_pred HHHHHHhcCCCCCCccCCCCCCC-CceEeccceeeehhhhh
Q 017907 5 RRLRDLQSQPGNKICVDCAQKNP-QWASVSYGVFMCLECSG 44 (364)
Q Consensus 5 r~LreL~~~p~Nk~CaDCGa~nP-~WaSvn~GIFIC~~CSG 44 (364)
+.|+.+--.|.-..|+-||.+.. .+.++..|.++|..|..
T Consensus 138 ~lL~~~G~~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~ 178 (247)
T PRK00085 138 RLLAELGYGLDLDHCAVCGAPGDHRYFSPKEGGAVCSECGD 178 (247)
T ss_pred HHHHHcCCccchhhHhcCCCCCCceEEecccCCcccccccC
Confidence 45555566777789999998754 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=76.92 E-value=2 Score=40.11 Aligned_cols=41 Identities=27% Similarity=0.510 Sum_probs=32.2
Q ss_pred HHHHHHhcCCCCCCccCCCCCCC-CceEeccceeeehhhhhh
Q 017907 5 RRLRDLQSQPGNKICVDCAQKNP-QWASVSYGVFMCLECSGK 45 (364)
Q Consensus 5 r~LreL~~~p~Nk~CaDCGa~nP-~WaSvn~GIFIC~~CSGi 45 (364)
+.|..+--.|.-..|+.||..++ .+.++..|.++|.+|...
T Consensus 136 ~lL~~~G~~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 136 KLLQILGYALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred HHHHHcCCCcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 34555566777789999998544 678899999999999764
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=76.57 E-value=2.5 Score=29.17 Aligned_cols=34 Identities=18% Similarity=0.387 Sum_probs=29.2
Q ss_pred CCCCccCCCCCCCCceEeccceeeehhhhhh-hcc
Q 017907 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGK-HRG 48 (364)
Q Consensus 15 ~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGi-HR~ 48 (364)
.+..|..|......+-+.+-.++||..|... |+.
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 3578999998888899999999999999987 887
No 19
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=73.32 E-value=3.5 Score=34.45 Aligned_cols=41 Identities=22% Similarity=0.656 Sum_probs=30.0
Q ss_pred HHHHHHHH-hcCCCCCCccCCCCCCCCceEeccceeeehhhhhh
Q 017907 3 ATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGK 45 (364)
Q Consensus 3 a~r~LreL-~~~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGi 45 (364)
.++..++| .....-..|-.|+.+ .---+..|||.|..|-..
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 45555554 445566799999998 555788999999999543
No 20
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=70.20 E-value=2.5 Score=40.67 Aligned_cols=39 Identities=28% Similarity=0.624 Sum_probs=31.2
Q ss_pred HHHHHHhcCCCCCCccCCCCCC-CCceEeccceeeehhhh
Q 017907 5 RRLRDLQSQPGNKICVDCAQKN-PQWASVSYGVFMCLECS 43 (364)
Q Consensus 5 r~LreL~~~p~Nk~CaDCGa~n-P~WaSvn~GIFIC~~CS 43 (364)
++|..+--.|.=..|+.||.+. |...++-.|-++|.+|.
T Consensus 143 ~lL~~~G~~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 143 KLLGELGIGPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred HHHHHcCCccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 3444455556668999999984 57999999999999998
No 21
>PRK12495 hypothetical protein; Provisional
Probab=62.62 E-value=6.3 Score=38.03 Aligned_cols=29 Identities=21% Similarity=0.385 Sum_probs=23.6
Q ss_pred CCCCCCccCCCCCCCCceEeccceeeehhhhhh
Q 017907 13 QPGNKICVDCAQKNPQWASVSYGVFMCLECSGK 45 (364)
Q Consensus 13 ~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGi 45 (364)
.+.+..|-+||.+-|. + -|+.+|..|..+
T Consensus 39 tmsa~hC~~CG~PIpa---~-pG~~~Cp~CQ~~ 67 (226)
T PRK12495 39 TMTNAHCDECGDPIFR---H-DGQEFCPTCQQP 67 (226)
T ss_pred ccchhhcccccCcccC---C-CCeeECCCCCCc
Confidence 4567899999999993 2 699999999754
No 22
>TIGR02419 C4_traR_proteo phage/conjugal plasmid C-4 type zinc finger protein, TraR family. Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA.
Probab=61.34 E-value=3.2 Score=32.23 Aligned_cols=35 Identities=26% Similarity=0.510 Sum_probs=23.4
Q ss_pred cCCCCCCccCCCCCCCCc-eEeccceeeehhhhhhh
Q 017907 12 SQPGNKICVDCAQKNPQW-ASVSYGVFMCLECSGKH 46 (364)
Q Consensus 12 ~~p~Nk~CaDCGa~nP~W-aSvn~GIFIC~~CSGiH 46 (364)
..++...|.+||.+=|.= .-.--|+..|+.|...+
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 456678999999974421 11223788899997654
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=58.25 E-value=5.7 Score=28.09 Aligned_cols=27 Identities=22% Similarity=0.502 Sum_probs=20.8
Q ss_pred CccCCCCCCCCceEeccceeeehhhhhh
Q 017907 18 ICVDCAQKNPQWASVSYGVFMCLECSGK 45 (364)
Q Consensus 18 ~CaDCGa~nP~WaSvn~GIFIC~~CSGi 45 (364)
+|..||+.. .-..-..|-++|..|.-|
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-BB
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCCCE
Confidence 699999976 455667899999999543
No 24
>PRK11019 hypothetical protein; Provisional
Probab=55.29 E-value=5.3 Score=33.25 Aligned_cols=37 Identities=19% Similarity=0.510 Sum_probs=25.5
Q ss_pred CCCCccCCCCCCC--CceEeccceeeehhhhhhhccCCCc
Q 017907 15 GNKICVDCAQKNP--QWASVSYGVFMCLECSGKHRGLGVH 52 (364)
Q Consensus 15 ~Nk~CaDCGa~nP--~WaSvn~GIFIC~~CSGiHR~LG~h 52 (364)
.-..|.+||.+=| .+.-+. ++-.|++|...+-..+.|
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 4579999999744 233333 788899999877654444
No 25
>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=52.79 E-value=8.6 Score=28.29 Aligned_cols=26 Identities=27% Similarity=0.836 Sum_probs=20.3
Q ss_pred CccCCCCCCCCceEeccceeeehhhhh
Q 017907 18 ICVDCAQKNPQWASVSYGVFMCLECSG 44 (364)
Q Consensus 18 ~CaDCGa~nP~WaSvn~GIFIC~~CSG 44 (364)
+|+=|+...+. --.=+|.|||.+|-.
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHH
Confidence 48889998887 444579999999954
No 26
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=52.40 E-value=13 Score=27.69 Aligned_cols=37 Identities=22% Similarity=0.553 Sum_probs=30.2
Q ss_pred CCCCccCCCCC-CCCceEeccce-eeehhhhhhhccCCC
Q 017907 15 GNKICVDCAQK-NPQWASVSYGV-FMCLECSGKHRGLGV 51 (364)
Q Consensus 15 ~Nk~CaDCGa~-nP~WaSvn~GI-FIC~~CSGiHR~LG~ 51 (364)
....|..|+.. -|+|=.-..|- +||-.|.-..+..+.
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~ 40 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCC
Confidence 45789999874 78998888886 999999887776554
No 27
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=50.88 E-value=5.9 Score=31.71 Aligned_cols=33 Identities=24% Similarity=0.583 Sum_probs=22.2
Q ss_pred CCCccCCCCCCCCc-eEeccceeeehhhhhhhcc
Q 017907 16 NKICVDCAQKNPQW-ASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 16 Nk~CaDCGa~nP~W-aSvn~GIFIC~~CSGiHR~ 48 (364)
...|.|||.+=|.= .-.--|+..|++|...+-.
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 45899999974421 1122378899999876543
No 28
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=48.46 E-value=19 Score=30.26 Aligned_cols=40 Identities=18% Similarity=0.512 Sum_probs=29.3
Q ss_pred HHHHHHHH-hcCCCCCCccCCCCCCCCceEeccceeeehhhhh
Q 017907 3 ATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECSG 44 (364)
Q Consensus 3 a~r~LreL-~~~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSG 44 (364)
.++.+++| .....--.|.-||....... ..||+-|..|.-
T Consensus 22 lRK~v~kie~~q~a~y~CpfCgk~~vkR~--a~GIW~C~~C~~ 62 (90)
T PTZ00255 22 LRKQIKKIEISQHAKYFCPFCGKHAVKRQ--AVGIWRCKGCKK 62 (90)
T ss_pred HHHHHHHHHHHHhCCccCCCCCCCceeee--eeEEEEcCCCCC
Confidence 45666665 56666789999998766554 449999999943
No 29
>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=48.26 E-value=13 Score=25.56 Aligned_cols=32 Identities=28% Similarity=0.715 Sum_probs=23.1
Q ss_pred ccCCCCC-CCCceEecccee-eehhhhhhhccCC
Q 017907 19 CVDCAQK-NPQWASVSYGVF-MCLECSGKHRGLG 50 (364)
Q Consensus 19 CaDCGa~-nP~WaSvn~GIF-IC~~CSGiHR~LG 50 (364)
|..|+.. -|.|-....|-. ||-.|--.+|..+
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 8899875 899999988888 9999987776543
No 30
>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=48.20 E-value=6.3 Score=27.43 Aligned_cols=27 Identities=15% Similarity=0.533 Sum_probs=16.5
Q ss_pred CCccCCCCC-CCCceEeccceeeehhhh
Q 017907 17 KICVDCAQK-NPQWASVSYGVFMCLECS 43 (364)
Q Consensus 17 k~CaDCGa~-nP~WaSvn~GIFIC~~CS 43 (364)
..|.+|+.+ .-+|..-+|+.-||..|.
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 479999985 667999999999999994
No 31
>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=45.20 E-value=17 Score=25.33 Aligned_cols=27 Identities=26% Similarity=0.728 Sum_probs=22.5
Q ss_pred CCCCCccCCCCCCCCceEeccceeeehhhh
Q 017907 14 PGNKICVDCAQKNPQWASVSYGVFMCLECS 43 (364)
Q Consensus 14 p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CS 43 (364)
..|..|..|++. |....=|-++|.+|-
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCc
Confidence 345679999998 778888999999984
No 32
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=45.18 E-value=4.7 Score=35.30 Aligned_cols=30 Identities=23% Similarity=0.644 Sum_probs=20.0
Q ss_pred CccCCCCCCC-CceEeccceeeehhhhhhhc
Q 017907 18 ICVDCAQKNP-QWASVSYGVFMCLECSGKHR 47 (364)
Q Consensus 18 ~CaDCGa~nP-~WaSvn~GIFIC~~CSGiHR 47 (364)
+|.+||.+=| .=.-.--+..+|++|.-.|-
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 8999999633 11122236789999988763
No 33
>PF10310 DUF2413: Protein of unknown function (DUF2413); InterPro: IPR018814 This entry represents a family of proteins conserved in fungi. Their function is not known.
Probab=42.83 E-value=22 Score=37.58 Aligned_cols=51 Identities=22% Similarity=0.228 Sum_probs=34.0
Q ss_pred cccchhhhhccc--hhhHHHHHHHHHHHHHHHhhhhhhhhcccccccc-cchhchh
Q 017907 162 WDNVLSAVSQGF--GRISLVAASAAQSAATVVQAGTREFTSKVREGGY-DHKVNET 214 (364)
Q Consensus 162 ~~d~~ssLssG~--g~fS~~A~~~A~~A~~~~~~~~k~~~~kvkeg~l-~~~v~~~ 214 (364)
..++..+++.+| |.+...|+++++.|.......++.+++ .+..+ .++|...
T Consensus 118 ~~~p~~s~ggwWsWGs~~stAss~~~~a~kqAe~~~k~i~q--eea~~w~eqv~~~ 171 (444)
T PF10310_consen 118 EPDPIASSGGWWSWGSIWSTASSAAEQAMKQAEAAVKEIQQ--EEAKKWAEQVRGN 171 (444)
T ss_pred CCCcccccCCcccccchhhHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHhhhh
Confidence 556777888877 688888888888887666666666666 33333 3444433
No 34
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=40.34 E-value=4.8 Score=27.50 Aligned_cols=30 Identities=30% Similarity=0.749 Sum_probs=16.9
Q ss_pred CCccCCCCCCCC-ceEeccceeeehhhhhhh
Q 017907 17 KICVDCAQKNPQ-WASVSYGVFMCLECSGKH 46 (364)
Q Consensus 17 k~CaDCGa~nP~-WaSvn~GIFIC~~CSGiH 46 (364)
..|.+||.+=|. =.-+--+..+|..|+..|
T Consensus 4 g~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~~ 34 (36)
T PF01258_consen 4 GICEDCGEPIPEERLVAVPGATLCVECQERR 34 (36)
T ss_dssp SB-TTTSSBEEHHHHHHCTTECS-HHHHHHH
T ss_pred CCccccCChHHHHHHHhCCCcEECHHHhCcc
Confidence 359999985221 112223788899998765
No 35
>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=39.98 E-value=33 Score=24.56 Aligned_cols=39 Identities=18% Similarity=0.513 Sum_probs=26.5
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeeehhhh
Q 017907 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECS 43 (364)
Q Consensus 3 a~r~LreL~~~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CS 43 (364)
+.+.|.+| +-|..-+|.-||...+-+.. +.+.|-|-.|.
T Consensus 6 c~~~l~~~-RW~~g~~CP~Cg~~~~~~~~-~~~~~~C~~C~ 44 (46)
T PF12760_consen 6 CREYLEEI-RWPDGFVCPHCGSTKHYRLK-TRGRYRCKACR 44 (46)
T ss_pred HHHHHHHh-cCCCCCCCCCCCCeeeEEeC-CCCeEECCCCC
Confidence 45555554 55566889999998543332 36899999884
No 36
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=39.80 E-value=18 Score=30.31 Aligned_cols=40 Identities=23% Similarity=0.563 Sum_probs=28.9
Q ss_pred HHHHHHHH-hcCCCCCCccCCCCCCCCceEeccceeeehhhhh
Q 017907 3 ATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECSG 44 (364)
Q Consensus 3 a~r~LreL-~~~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSG 44 (364)
.+++++++ ......-.|.-||.... --+..|||-|..|.-
T Consensus 21 lRK~vkkie~~q~~ky~Cp~Cgk~~v--kR~a~GIW~C~~C~~ 61 (90)
T PF01780_consen 21 LRKRVKKIEISQHAKYTCPFCGKTSV--KRVATGIWKCKKCGK 61 (90)
T ss_dssp HHHHHHHHHHHHHS-BEESSSSSSEE--EEEETTEEEETTTTE
T ss_pred HHHHHHHHHHHHhCCCcCCCCCCcee--EEeeeEEeecCCCCC
Confidence 35555554 55667789999999773 456889999999953
No 37
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=39.24 E-value=17 Score=27.60 Aligned_cols=27 Identities=30% Similarity=0.659 Sum_probs=22.7
Q ss_pred CCCccCCCCCCCCceEeccceeeehhhhh
Q 017907 16 NKICVDCAQKNPQWASVSYGVFMCLECSG 44 (364)
Q Consensus 16 Nk~CaDCGa~nP~WaSvn~GIFIC~~CSG 44 (364)
-+.|..||..... ..+.-+|.|..|--
T Consensus 28 Sq~C~~CG~~~~~--~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 28 SQTCPRCGHRNKK--RRSGRVFTCPNCGF 54 (69)
T ss_pred ccCccCccccccc--ccccceEEcCCCCC
Confidence 3789999998887 77888999999943
No 38
>cd07171 NR_DBD_ER DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ER interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Estrogen receptor is a transcription regulator that mediates the biological effects of hormone estrogen. The binding of estrogen to the receptor triggers the dimerization and the binding of the receptor dimer to estrogen response element, which is a palindromic inverted repeat: 5'GGTCAnnnTGACC-3', of target genes. Through ER, estrogen regulates development, reproduction and homeostasis. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well-conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserv
Probab=38.72 E-value=22 Score=28.86 Aligned_cols=31 Identities=23% Similarity=0.643 Sum_probs=25.4
Q ss_pred CCCCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 017907 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 15 ~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~ 48 (364)
.|..|.-|+.+.- ...||++.|..|.++.|-
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 4678999997553 579999999999998864
No 39
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=37.66 E-value=20 Score=29.07 Aligned_cols=32 Identities=25% Similarity=0.657 Sum_probs=25.9
Q ss_pred CCCCCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 017907 14 PGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 14 p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~ 48 (364)
|..+.|.-|+.+.- ...||++.|..|..+.|-
T Consensus 1 ~~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 32 (82)
T cd07173 1 PPQKTCLICGDEAS---GCHYGALTCGSCKVFFKR 32 (82)
T ss_pred CCCCCCeecCCcCc---ceEECcchhhhHHHHHHH
Confidence 45678999997654 568999999999998874
No 40
>PHA00080 DksA-like zinc finger domain containing protein
Probab=36.11 E-value=20 Score=28.60 Aligned_cols=34 Identities=24% Similarity=0.586 Sum_probs=22.4
Q ss_pred CCCCCCccCCCCCCC--CceEeccceeeehhhhhhhc
Q 017907 13 QPGNKICVDCAQKNP--QWASVSYGVFMCLECSGKHR 47 (364)
Q Consensus 13 ~p~Nk~CaDCGa~nP--~WaSvn~GIFIC~~CSGiHR 47 (364)
.+....|.+||.+=| .+.-+ -++..|+.|...+-
T Consensus 28 ~~~~~~C~~Cg~~Ip~~Rl~a~-P~~~~Cv~Cq~~~E 63 (72)
T PHA00080 28 APSATHCEECGDPIPEARREAV-PGCRTCVSCQEILE 63 (72)
T ss_pred CCCCCEecCCCCcCcHHHHHhC-CCccCcHHHHHHHH
Confidence 344568999999633 22222 26777999988654
No 41
>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=35.94 E-value=23 Score=29.51 Aligned_cols=31 Identities=32% Similarity=0.684 Sum_probs=25.4
Q ss_pred CCCCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 017907 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 15 ~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~ 48 (364)
++..|.=||.+.- ...||++.|..|.++.|-
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 5678999998654 468999999999998874
No 42
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=34.39 E-value=24 Score=34.92 Aligned_cols=34 Identities=15% Similarity=0.430 Sum_probs=23.9
Q ss_pred cCCCCCCccCCCCCCCCceEeccceeeehhhhhhh
Q 017907 12 SQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKH 46 (364)
Q Consensus 12 ~~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiH 46 (364)
.......|.+||..+. =....-|-.||.+|--|-
T Consensus 7 ~~~~~~~Cp~Cg~~~i-v~d~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 7 EEEEKLVCPECGSDKL-IYDYERGEIVCADCGLVI 40 (310)
T ss_pred hcccCCcCcCCCCCCe-eEECCCCeEeecccCCcc
Confidence 3345578999997432 224567999999998754
No 43
>cd07170 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription
Probab=32.55 E-value=26 Score=29.38 Aligned_cols=29 Identities=24% Similarity=0.679 Sum_probs=23.9
Q ss_pred CCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 017907 17 KICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 17 k~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~ 48 (364)
..|.-|+.+.- ...||++.|..|.++.|-
T Consensus 5 ~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 33 (97)
T cd07170 5 RLCLVCGDIAS---GYHYGVASCEACKAFFKR 33 (97)
T ss_pred CCCeecCCcCc---ceEECceeehhhhHHHHH
Confidence 56999997654 468999999999998874
No 44
>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=32.55 E-value=24 Score=32.22 Aligned_cols=35 Identities=20% Similarity=0.412 Sum_probs=21.4
Q ss_pred CCCCCccCCCCCCC-CceEeccceeeehhhhhhhcc
Q 017907 14 PGNKICVDCAQKNP-QWASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 14 p~Nk~CaDCGa~nP-~WaSvn~GIFIC~~CSGiHR~ 48 (364)
..=-.|.+||.+=| .=.-+--.+-.|+.|...+-.
T Consensus 84 G~YG~Ce~CGe~I~~~RL~a~P~a~~Ci~Cq~~~E~ 119 (159)
T TIGR02890 84 GTYGICEVCGKPIPYERLEAIPTATTCVECQNRKEV 119 (159)
T ss_pred CCCCeecccCCcccHHHHhhCCCcchhHHHHHHhhh
Confidence 34468999998511 111112246789999987644
No 45
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=32.29 E-value=28 Score=31.52 Aligned_cols=38 Identities=11% Similarity=0.217 Sum_probs=23.9
Q ss_pred cCCCCCCccCCCCCCC-CceEeccceeeehhhhhhhccC
Q 017907 12 SQPGNKICVDCAQKNP-QWASVSYGVFMCLECSGKHRGL 49 (364)
Q Consensus 12 ~~p~Nk~CaDCGa~nP-~WaSvn~GIFIC~~CSGiHR~L 49 (364)
..+.-..|-+||.+=| .=.-+--++..|+.|...|-..
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 4455689999998622 1111122467899999877643
No 46
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=31.65 E-value=20 Score=32.74 Aligned_cols=34 Identities=26% Similarity=0.650 Sum_probs=26.9
Q ss_pred CCCCCccCCCCCCCCceEeccceeeeh-hhhhhhcc
Q 017907 14 PGNKICVDCAQKNPQWASVSYGVFMCL-ECSGKHRG 48 (364)
Q Consensus 14 p~Nk~CaDCGa~nP~WaSvn~GIFIC~-~CSGiHR~ 48 (364)
|--+.|+-|| -...|.+++.|.-+|. .|-.+|..
T Consensus 116 P~r~fCaVCG-~~S~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 116 PLRKFCAVCG-YDSKYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred CcchhhhhcC-CCchhHHHhcCCceeechhhhhccc
Confidence 5557899999 5555999999998885 68888864
No 47
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=31.56 E-value=35 Score=35.96 Aligned_cols=39 Identities=26% Similarity=0.500 Sum_probs=22.0
Q ss_pred eeeehhhhhhhccCCCc-----ccceeeccc----CCCCH-HHHHHhhc
Q 017907 36 VFMCLECSGKHRGLGVH-----ISFVRSVTM----DSWSE-IQIKKMEA 74 (364)
Q Consensus 36 IFIC~~CSGiHR~LG~h-----iS~VKSvtm----D~Ws~-~eL~~Mk~ 74 (364)
..||+.|-.+--.+|+| +-.|...+. -.|+. +||+++++
T Consensus 38 fdLCl~CFs~GaE~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLea 86 (438)
T KOG0457|consen 38 FDLCLQCFSVGAETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLEA 86 (438)
T ss_pred cchhHHHHhcccccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHHH
Confidence 47899997644344443 222333222 26885 77887765
No 48
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=30.87 E-value=34 Score=28.98 Aligned_cols=31 Identities=35% Similarity=0.832 Sum_probs=25.3
Q ss_pred CCCCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 017907 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 15 ~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~ 48 (364)
.+..|.-|+.+.- ...||+..|..|.++.|-
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 4667999997554 568999999999998874
No 49
>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=29.78 E-value=31 Score=28.44 Aligned_cols=32 Identities=22% Similarity=0.736 Sum_probs=25.9
Q ss_pred CCCCCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 017907 14 PGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 14 p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~ 48 (364)
.+.+.|.-|+.+.- ...||+..|..|..+.|-
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 45678999997543 568999999999998864
No 50
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.24 E-value=24 Score=33.35 Aligned_cols=21 Identities=33% Similarity=0.714 Sum_probs=18.5
Q ss_pred CCccCCCCCCCCceEeccceeeehhhhh
Q 017907 17 KICVDCAQKNPQWASVSYGVFMCLECSG 44 (364)
Q Consensus 17 k~CaDCGa~nP~WaSvn~GIFIC~~CSG 44 (364)
+.|.-||. +.-..|.|..|..
T Consensus 310 ~~C~~cg~-------~~~r~~~C~~cg~ 330 (364)
T COG0675 310 KTCPCCGH-------LSGRLFKCPRCGF 330 (364)
T ss_pred ccccccCC-------ccceeEECCCCCC
Confidence 79999999 6678999999976
No 51
>PF01387 Synuclein: Synuclein; InterPro: IPR001058 Synucleins are small, soluble proteins expressed primarily in neural tissue and in certain tumors [, []. The family includes three known proteins: alpha-synuclein, beta-synuclein, and gamma-synuclein. All synucleins have in common a highly conserved alpha-helical lipid-binding motif with similarity to the class-A2 lipid-binding domains of the exchangeable apolipoproteins []. Synuclein family members are not found outside vertebrates, although they have some conserved structural similarity with plant 'late-embryo-abundant' proteins. The alpha- and beta-synuclein proteins are found primarily in brain tissue, where they are seen mainly in presynaptic terminals [, ]. The gamma-synuclein protein is found primarily in the peripheral nervous system and retina, but its expression in breast tumors is a marker for tumor progression []. Normal cellular functions have not been determined for any of the synuclein proteins, although some data suggest a role in the regulation of membrane stability and/or turnover. Mutations in alpha-synuclein are associated with rare familial cases of early-onset Parkinson's disease, and the protein accumulates abnormally in Parkinson's disease, Alzheimer's disease, and several other neurodegenerative illnesses []. ; PDB: 3Q27_A 3Q28_A 2KKW_A 3Q29_C 3Q25_A 2JN5_A 3Q26_A 1XQ8_A.
Probab=28.98 E-value=50 Score=29.58 Aligned_cols=79 Identities=25% Similarity=0.273 Sum_probs=49.3
Q ss_pred hhhhhccchhhHHHHHHHHHHHHHHHhhhhhhhhccccccccc------chhchhhhhhhhhccccccc-hhhhhhhHHH
Q 017907 166 LSAVSQGFGRISLVAASAAQSAATVVQAGTREFTSKVREGGYD------HKVNETVNVVTAKTSEIGQR-TWGIMKGVMA 238 (364)
Q Consensus 166 ~ssLssG~g~fS~~A~~~A~~A~~~~~~~~k~~~~kvkeg~l~------~~v~~~v~~va~Kv~e~g~~-gw~~~~gv~~ 238 (364)
|..|-+||+..-.+-..+|..-+..+. ++..|-|||-+- +.|-..|+.|+.|+-+-.+. |=.++.|+.+
T Consensus 1 mdvf~kgfs~akeGvv~aaeKTKqgv~----eaA~kTKegv~yvG~KTkegv~~~v~~va~kTkeqan~vg~avv~gvn~ 76 (131)
T PF01387_consen 1 MDVFMKGFSMAKEGVVAAAEKTKQGVT----EAAEKTKEGVMYVGSKTKEGVVQGVTSVAEKTKEQANNVGEAVVSGVNT 76 (131)
T ss_dssp HHHHHHHHHHHCHHHHHHHHHHHHHHH----HHHHHCCHHHCHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CcHHHhhhhhhhHHHHHHHHHHhcccc----hHHHHhcCCceeeehhhhhhhhhhhHHHHHHHHHHHHHhhhhhhcchhH
Confidence 445667777665555555554443322 334555555543 34556788888888776654 5556778888
Q ss_pred Hhhhhhhhhh
Q 017907 239 MASQKVEEYT 248 (364)
Q Consensus 239 ~~s~kvE~~~ 248 (364)
.+.+.||...
T Consensus 77 Va~kTveg~e 86 (131)
T PF01387_consen 77 VAEKTVEGAE 86 (131)
T ss_dssp HHHHHHHHHH
T ss_pred HHHhhhcccc
Confidence 8888888765
No 52
>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=28.95 E-value=27 Score=29.02 Aligned_cols=29 Identities=28% Similarity=0.615 Sum_probs=23.2
Q ss_pred CCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 017907 17 KICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 17 k~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~ 48 (364)
+.|.-|+.+.- ...||++.|..|.++.|-
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 53
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=28.44 E-value=24 Score=24.37 Aligned_cols=30 Identities=20% Similarity=0.397 Sum_probs=14.9
Q ss_pred CCccCCCCCCCCceEe---ccceeeehhhhhhhc
Q 017907 17 KICVDCAQKNPQWASV---SYGVFMCLECSGKHR 47 (364)
Q Consensus 17 k~CaDCGa~nP~WaSv---n~GIFIC~~CSGiHR 47 (364)
|.|..||.+- ++..+ +.--++|..|.-||-
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 4688898862 22211 344578999988883
No 54
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=28.32 E-value=28 Score=27.27 Aligned_cols=24 Identities=42% Similarity=0.760 Sum_probs=15.5
Q ss_pred CCccCCCCCCCCceEeccceeeehhhh
Q 017907 17 KICVDCAQKNPQWASVSYGVFMCLECS 43 (364)
Q Consensus 17 k~CaDCGa~nP~WaSvn~GIFIC~~CS 43 (364)
-+|.|||+.|.- -.--++-|.+|.
T Consensus 21 YiCgdC~~en~l---k~~D~irCReCG 44 (62)
T KOG3507|consen 21 YICGDCGQENTL---KRGDVIRCRECG 44 (62)
T ss_pred EEeccccccccc---cCCCcEehhhcc
Confidence 378999887541 123467788883
No 55
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=28.13 E-value=38 Score=28.63 Aligned_cols=34 Identities=21% Similarity=0.656 Sum_probs=24.0
Q ss_pred hcCCCCCCccCCCCC--------CCCc---------eEeccceeeehhhhh
Q 017907 11 QSQPGNKICVDCAQK--------NPQW---------ASVSYGVFMCLECSG 44 (364)
Q Consensus 11 ~~~p~Nk~CaDCGa~--------nP~W---------aSvn~GIFIC~~CSG 44 (364)
++.|.--.|++||.+ .++. +.=.||-.+|..|..
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 556777899999975 1112 134599999999964
No 56
>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=27.85 E-value=62 Score=27.27 Aligned_cols=40 Identities=23% Similarity=0.566 Sum_probs=29.1
Q ss_pred HHHHHHHH-hcCCCCCCccCCCCCCCCceEeccceeeehhhhh
Q 017907 3 ATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECSG 44 (364)
Q Consensus 3 a~r~LreL-~~~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSG 44 (364)
.++++++| ..+..--.|.-|+.... --+..||+-|..|.-
T Consensus 21 lRK~v~kie~~q~a~y~CpfCgk~~v--kR~a~GIW~C~~C~~ 61 (91)
T TIGR00280 21 LRRQVKKIEIQQKAKYVCPFCGKKTV--KRGSTGIWTCRKCGA 61 (91)
T ss_pred HHHHHHHHHHHHhcCccCCCCCCCce--EEEeeEEEEcCCCCC
Confidence 45566665 55666789999997554 456789999999943
No 57
>PF02993 MCPVI: Minor capsid protein VI; InterPro: IPR004243 This minor capsid protein may act as a link between the external capsid and the internal DNA-protein core. Residues at the C-terminal end of the protein may act as a protease cofactor leading to activation of the adenovirus proteinase [].; GO: 0019028 viral capsid; PDB: 1AVP_B.
Probab=26.11 E-value=22 Score=34.65 Aligned_cols=70 Identities=19% Similarity=0.332 Sum_probs=0.0
Q ss_pred cccchhhhhccchhhHHHHHHHHHHHHHHHhhhhhhhhcccccccccchhchhhhhhhhhccccccchhhhhhhHHHHhh
Q 017907 162 WDNVLSAVSQGFGRISLVAASAAQSAATVVQAGTREFTSKVREGGYDHKVNETVNVVTAKTSEIGQRTWGIMKGVMAMAS 241 (364)
Q Consensus 162 ~~d~~ssLssG~g~fS~~A~~~A~~A~~~~~~~~k~~~~kvkeg~l~~~v~~~v~~va~Kv~e~g~~gw~~~~gv~~~~s 241 (364)
....-|+|++|+..|...-.+.++.|- +...-+.+-+++||-+|.++|-+.+.+-- .|+..+..
T Consensus 32 WgsLwS~is~glkn~Gs~l~n~g~k~w--nS~tgq~lrq~LkDsg~~~kVv~g~~~gi--------------~g~vDIgr 95 (238)
T PF02993_consen 32 WGSLWSSISSGLKNFGSFLKNYGSKAW--NSQTGQQLRQGLKDSGLQEKVVEGAGSGI--------------NGLVDIGR 95 (238)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cccchhhhhhhhhhHhHHHHHhhhhhh--hhhHHHHHHHHHhhhhHHHHHHHHHhhhh--------------hHHHHHHH
Confidence 445578888898888774333333332 22233456678888777776655444333 55566666
Q ss_pred hhhhhh
Q 017907 242 QKVEEY 247 (364)
Q Consensus 242 ~kvE~~ 247 (364)
|+||.-
T Consensus 96 q~vq~~ 101 (238)
T PF02993_consen 96 QKVQKD 101 (238)
T ss_dssp ------
T ss_pred HHHHHH
Confidence 666643
No 58
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=26.01 E-value=28 Score=26.72 Aligned_cols=39 Identities=23% Similarity=0.522 Sum_probs=26.6
Q ss_pred CCCCCccCCCCCCCCceEeccceeeehhhhhhhccCCCccccee
Q 017907 14 PGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVR 57 (364)
Q Consensus 14 p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~LG~hiS~VK 57 (364)
++-+.|.-||.+. =+--.||..||..|-. ++-..|-|||
T Consensus 14 kGsr~C~vCg~~~--gliRkygL~~CRqCFR---e~A~~iGF~K 52 (54)
T PTZ00218 14 KGSRQCRVCSNRH--GLIRKYGLNVCRQCFR---ENAELIGFHK 52 (54)
T ss_pred CCCCeeecCCCcc--hhhhhcCcchhhHHHH---HhhHhcCeee
Confidence 5668999999854 3344899999999954 3334444544
No 59
>PHA02942 putative transposase; Provisional
Probab=24.87 E-value=35 Score=35.05 Aligned_cols=25 Identities=24% Similarity=0.563 Sum_probs=19.8
Q ss_pred CCccCCCCCCCCceEeccceeeehhhhh
Q 017907 17 KICVDCAQKNPQWASVSYGVFMCLECSG 44 (364)
Q Consensus 17 k~CaDCGa~nP~WaSvn~GIFIC~~CSG 44 (364)
+.|..||...+ .++-.+|.|..|--
T Consensus 326 q~Cs~CG~~~~---~l~~r~f~C~~CG~ 350 (383)
T PHA02942 326 VSCPKCGHKMV---EIAHRYFHCPSCGY 350 (383)
T ss_pred ccCCCCCCccC---cCCCCEEECCCCCC
Confidence 78999998775 34566899999954
No 60
>cd07162 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers. DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding
Probab=24.42 E-value=48 Score=27.02 Aligned_cols=28 Identities=25% Similarity=0.675 Sum_probs=22.3
Q ss_pred CccCCCCCCCCceEeccceeeehhhhhhhcc
Q 017907 18 ICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 18 ~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~ 48 (364)
.|.-||.+... ..||++.|..|.++.|-
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 61
>cd07161 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers. DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs h
Probab=24.39 E-value=48 Score=27.44 Aligned_cols=29 Identities=24% Similarity=0.750 Sum_probs=23.1
Q ss_pred CCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 017907 17 KICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 17 k~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~ 48 (364)
..|.-|+.+.- ...||++.|..|.++.|-
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 35888987554 468999999999998863
No 62
>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=23.36 E-value=37 Score=28.09 Aligned_cols=30 Identities=27% Similarity=0.744 Sum_probs=24.7
Q ss_pred CCCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 017907 16 NKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 16 Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~ 48 (364)
+..|.-|+.+.- ...||+..|..|.++.|-
T Consensus 6 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (92)
T cd07163 6 DIPCKVCGDRSS---GKHYGIYACDGCSGFFKR 35 (92)
T ss_pred CCCCcccCCcCc---ccEECceeeeeeeeEEee
Confidence 678999997544 368999999999998774
No 63
>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=23.34 E-value=33 Score=22.35 Aligned_cols=28 Identities=14% Similarity=0.411 Sum_probs=17.0
Q ss_pred CCccCCCCCCCCceEeccceeeehhhhh
Q 017907 17 KICVDCAQKNPQWASVSYGVFMCLECSG 44 (364)
Q Consensus 17 k~CaDCGa~nP~WaSvn~GIFIC~~CSG 44 (364)
+.|.-|+..-+.=.--....++|..|..
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 4688888876655555677899999964
No 64
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=23.27 E-value=33 Score=25.60 Aligned_cols=43 Identities=21% Similarity=0.557 Sum_probs=26.3
Q ss_pred CccCCCCCCCCce--EeccceeeehhhhhhhccCCCcccceeeccc
Q 017907 18 ICVDCAQKNPQWA--SVSYGVFMCLECSGKHRGLGVHISFVRSVTM 61 (364)
Q Consensus 18 ~CaDCGa~nP~Wa--Svn~GIFIC~~CSGiHR~LG~hiS~VKSvtm 61 (364)
.|+=||..-.-.- -+.=| +||-.|...-..+-..+..++.+|+
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl~~~~~~~~~~~~~t~ 45 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKLSGFFSDVKIKKNLTL 45 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHhcCcccchhhhhhccH
Confidence 4888888644433 35567 8999999765544333334455555
No 65
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=23.12 E-value=47 Score=28.91 Aligned_cols=24 Identities=42% Similarity=0.808 Sum_probs=21.4
Q ss_pred CceEeccc--eeeehhhhhhhccCCC
Q 017907 28 QWASVSYG--VFMCLECSGKHRGLGV 51 (364)
Q Consensus 28 ~WaSvn~G--IFIC~~CSGiHR~LG~ 51 (364)
.|++-.-| |+-|.+|--|||.-++
T Consensus 52 ewi~~~~G~~VwSC~dC~~iH~ke~~ 77 (112)
T COG2158 52 EWISDSNGRKVWSCSDCHWIHRKEGA 77 (112)
T ss_pred ceeEcCCCCEEeeccccceecccchH
Confidence 89998889 9999999999997654
No 66
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=22.85 E-value=46 Score=34.39 Aligned_cols=64 Identities=13% Similarity=0.169 Sum_probs=38.3
Q ss_pred cccchhhhhcc--------chhhHHHHHHHHHHHHHH--Hhhhhhhhhcccccccccchhchhhhhhhhhccccccc
Q 017907 162 WDNVLSAVSQG--------FGRISLVAASAAQSAATV--VQAGTREFTSKVREGGYDHKVNETVNVVTAKTSEIGQR 228 (364)
Q Consensus 162 ~~d~~ssLssG--------~g~fS~~A~~~A~~A~~~--~~~~~k~~~~kvkeg~l~~~v~~~v~~va~Kv~e~g~~ 228 (364)
++++++.|++. |+.|+. .+.+++..+ ...+..+..+.+.-+.+...+.....+.+++..+-...
T Consensus 251 ~s~~v~~va~k~t~vG~r~W~~ls~---~~sq~~e~fq~~~s~g~~~~qn~~~~n~~sn~~~g~~q~~~~~~~~s~~ 324 (386)
T KOG0704|consen 251 VSDPVGTVASKVTEVGTRGWGLLSA---AVSQSVEDFQDSESVGGPYYQNSGQGNFSSNSKRGGWQFSSKGHEKSSL 324 (386)
T ss_pred cccchhhhhhhcccccccchhhhHH---hhccccccccccCccCCccccccccccccccccccccccccccccccCC
Confidence 56788888843 999995 444555555 33444555555555555555555555555555555444
No 67
>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.
Probab=22.69 E-value=42 Score=35.00 Aligned_cols=29 Identities=24% Similarity=0.590 Sum_probs=20.9
Q ss_pred CCCccCCCCCCCCceEecc--ceeeehhhhh
Q 017907 16 NKICVDCAQKNPQWASVSY--GVFMCLECSG 44 (364)
Q Consensus 16 Nk~CaDCGa~nP~WaSvn~--GIFIC~~CSG 44 (364)
+..|--||....+--.+-. ++|||.+|..
T Consensus 7 ~~~c~fc~~~~~~~~~~~~~~~~~ic~~c~~ 37 (413)
T TIGR00382 7 TLYCSFCGKSQDEVRKLIAGPGVYICDECIE 37 (413)
T ss_pred CeecCCCCCChhhcccccCCCCCcCCCchHH
Confidence 4589999997555444333 4899999975
No 68
>PF14179 YppG: YppG-like protein
Probab=22.54 E-value=41 Score=29.28 Aligned_cols=35 Identities=20% Similarity=0.420 Sum_probs=27.8
Q ss_pred ccccccc-chhchhhhhhhhhccccccchhhhhhhHHHHh
Q 017907 202 VREGGYD-HKVNETVNVVTAKTSEIGQRTWGIMKGVMAMA 240 (364)
Q Consensus 202 vkeg~l~-~~v~~~v~~va~Kv~e~g~~gw~~~~gv~~~~ 240 (364)
=.||.|| .|+-.||.++...++-|+ +++|||+.+|
T Consensus 76 ~~dG~~D~nKmmnTaGQm~~avnQVs----~lVKg~~~~F 111 (112)
T PF14179_consen 76 NSDGNYDFNKMMNTAGQMMNAVNQVS----SLVKGFGSFF 111 (112)
T ss_pred cCCCcccHHHHHHHHHHHHHHHHHhH----HHHHHhhhcc
Confidence 3788886 788888888888888887 6788888776
No 69
>cd06956 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor, or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear rec
Probab=22.33 E-value=60 Score=25.82 Aligned_cols=28 Identities=32% Similarity=0.856 Sum_probs=22.7
Q ss_pred CccCCCCCCCCceEeccceeeehhhhhhhcc
Q 017907 18 ICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 18 ~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~ 48 (364)
.|.-|+.+.- ...||++.|..|.++.|-
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 5888887554 468999999999998864
No 70
>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=22.19 E-value=53 Score=24.70 Aligned_cols=34 Identities=26% Similarity=0.647 Sum_probs=27.0
Q ss_pred CccCCCCC-CCCceEec-cceeeehhhhhhhccCCC
Q 017907 18 ICVDCAQK-NPQWASVS-YGVFMCLECSGKHRGLGV 51 (364)
Q Consensus 18 ~CaDCGa~-nP~WaSvn-~GIFIC~~CSGiHR~LG~ 51 (364)
+|..|+.. -|+|=... -+..||-.|.-..+..+.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~ 36 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGV 36 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCC
Confidence 59999874 78888765 788999999877776653
No 71
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=21.79 E-value=81 Score=26.53 Aligned_cols=39 Identities=21% Similarity=0.646 Sum_probs=28.5
Q ss_pred HHHHHHHH-hcCCCCCCccCCCCCCCCceEeccceeeehhhh
Q 017907 3 ATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECS 43 (364)
Q Consensus 3 a~r~LreL-~~~p~Nk~CaDCGa~nP~WaSvn~GIFIC~~CS 43 (364)
.++.+++| .....--.|.-|+..... -+..||+-|..|.
T Consensus 22 lRK~v~kie~~q~a~y~CpfCgk~~vk--R~a~GIW~C~~C~ 61 (90)
T PRK03976 22 IRKRVADIEEKMRAKHVCPVCGRPKVK--RVGTGIWECRKCG 61 (90)
T ss_pred HHHHHHHHHHHHhcCccCCCCCCCceE--EEEEEEEEcCCCC
Confidence 35566665 556667899999866554 4577999999994
No 72
>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=21.73 E-value=58 Score=25.54 Aligned_cols=27 Identities=22% Similarity=0.635 Sum_probs=20.7
Q ss_pred ccCCCCCCCCceEeccceeeehhhhhhhcc
Q 017907 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 19 CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~ 48 (364)
|.-|+.+.-. ..||++.|..|.++.|-
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 5567765443 48999999999998774
No 73
>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=21.39 E-value=60 Score=26.02 Aligned_cols=29 Identities=31% Similarity=0.755 Sum_probs=23.4
Q ss_pred CCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 017907 17 KICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 17 k~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~ 48 (364)
+.|.-|+.+.- ...||++.|..|.++.|-
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 46888987544 469999999999998864
No 74
>COG5145 RAD14 DNA excision repair protein [DNA replication, recombination, and repair]
Probab=21.12 E-value=32 Score=33.67 Aligned_cols=35 Identities=17% Similarity=0.472 Sum_probs=25.8
Q ss_pred hcCCCCCCccCCCCC--CCCceEeccceeeehhhhhhh
Q 017907 11 QSQPGNKICVDCAQK--NPQWASVSYGVFMCLECSGKH 46 (364)
Q Consensus 11 ~~~p~Nk~CaDCGa~--nP~WaSvn~GIFIC~~CSGiH 46 (364)
+...-+.+|++|..- +|..-+ .||+-||..|+.-|
T Consensus 111 l~i~~apkC~eC~~IelD~~l~d-~F~~~VC~~Cr~~~ 147 (292)
T COG5145 111 LPIALAPKCKECLQIELDDELED-TFGISVCRSCRHSM 147 (292)
T ss_pred CChhhCccceeeeeeecchHHHh-hhcchhHHhhhhhc
Confidence 344457899999873 444433 58999999999887
No 75
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=21.08 E-value=55 Score=25.62 Aligned_cols=27 Identities=37% Similarity=0.816 Sum_probs=20.7
Q ss_pred ccCCCCCCCCceEeccceeeehhhhhhhcc
Q 017907 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 19 CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~ 48 (364)
|.-|+.+.- ...||++.|..|..+.|-
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 556776544 358999999999998874
No 76
>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=21.04 E-value=44 Score=28.57 Aligned_cols=30 Identities=23% Similarity=0.665 Sum_probs=24.5
Q ss_pred CCCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 017907 16 NKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 16 Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~ 48 (364)
.+.|.-|+.+.- ...||++.|..|.++.|-
T Consensus 6 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (107)
T cd06955 6 PRICGVCGDRAT---GFHFNAMTCEGCKGFFRR 35 (107)
T ss_pred CCCCeecCCcCc---ccEECcceeeeecceecc
Confidence 367999997654 459999999999998774
No 77
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=20.66 E-value=36 Score=31.43 Aligned_cols=28 Identities=21% Similarity=0.536 Sum_probs=18.1
Q ss_pred CccCCCCCCCCceEeccceeeehhhhhhh
Q 017907 18 ICVDCAQKNPQWASVSYGVFMCLECSGKH 46 (364)
Q Consensus 18 ~CaDCGa~nP~WaSvn~GIFIC~~CSGiH 46 (364)
.|..|+..-..=--+++ -|.|..|.+.-
T Consensus 119 ~Cp~C~~rytf~eA~~~-~F~Cp~Cg~~L 146 (178)
T PRK06266 119 FCPNCHIRFTFDEAMEY-GFRCPQCGEML 146 (178)
T ss_pred ECCCCCcEEeHHHHhhc-CCcCCCCCCCC
Confidence 69889865332223344 59999997654
No 78
>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=20.34 E-value=52 Score=26.41 Aligned_cols=27 Identities=37% Similarity=0.775 Sum_probs=21.0
Q ss_pred ccCCCCCCCCceEeccceeeehhhhhhhcc
Q 017907 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 19 CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~ 48 (364)
|.-||.+.- ...||++.|..|..+.|-
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 556776543 458999999999998874
No 79
>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=20.29 E-value=48 Score=27.26 Aligned_cols=30 Identities=33% Similarity=0.730 Sum_probs=23.9
Q ss_pred CCCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 017907 16 NKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 16 Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~ 48 (364)
+..|.-||.+.- ...||++.|..|..+.|-
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 356999997654 457999999999998774
No 80
>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=20.14 E-value=73 Score=26.20 Aligned_cols=31 Identities=29% Similarity=0.773 Sum_probs=24.8
Q ss_pred CCCCccCCCCCCCCceEeccceeeehhhhhhhcc
Q 017907 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (364)
Q Consensus 15 ~Nk~CaDCGa~nP~WaSvn~GIFIC~~CSGiHR~ 48 (364)
....|.-|+.+.- ...||+..|..|..+.|-
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 3457999997543 569999999999998874
Done!