Query 016665
Match_columns 385
No_of_seqs 239 out of 1156
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 08:53:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016665.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016665hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03114 ADP-ribosylation fact 100.0 2.6E-96 6E-101 718.3 28.7 368 1-377 19-394 (395)
2 KOG0706 Predicted GTPase-activ 100.0 1.4E-84 3E-89 649.2 24.5 374 1-385 20-454 (454)
3 KOG0704 ADP-ribosylation facto 100.0 5.2E-37 1.1E-41 299.5 7.4 104 3-106 18-122 (386)
4 COG5347 GTPase-activating prot 100.0 4.6E-35 1E-39 288.5 7.5 107 1-107 17-124 (319)
5 smart00105 ArfGap Putative GTP 100.0 9E-32 2E-36 229.1 8.7 98 2-99 1-103 (112)
6 KOG0703 Predicted GTPase-activ 100.0 3.4E-32 7.3E-37 262.6 3.3 92 2-93 23-124 (287)
7 PF01412 ArfGap: Putative GTPa 100.0 3.9E-31 8.5E-36 226.4 5.2 75 1-75 10-84 (116)
8 PLN03119 putative ADP-ribosyla 99.9 8.7E-26 1.9E-30 232.4 5.6 87 1-91 20-120 (648)
9 PLN03131 hypothetical protein; 99.9 1E-25 2.2E-30 233.5 6.0 87 1-91 20-120 (705)
10 KOG0705 GTPase-activating prot 99.8 2E-21 4.3E-26 200.0 6.2 91 1-91 510-612 (749)
11 KOG0521 Putative GTPase activa 99.7 3.3E-19 7.2E-24 193.9 2.4 90 1-90 423-526 (785)
12 KOG0818 GTPase-activating prot 99.6 3.2E-17 7E-22 167.0 1.5 91 2-92 6-116 (669)
13 KOG1117 Rho- and Arf-GTPase ac 99.5 4.6E-15 1E-19 158.5 1.1 92 2-93 296-401 (1186)
14 KOG0702 Predicted GTPase-activ 98.9 4.6E-10 9.9E-15 115.3 3.2 74 1-75 22-96 (524)
15 KOG0521 Putative GTPase activa 91.6 0.044 9.6E-07 61.1 -0.6 68 4-73 630-698 (785)
16 KOG0706 Predicted GTPase-activ 88.9 0.8 1.7E-05 47.8 5.8 75 275-376 378-452 (454)
17 PLN03114 ADP-ribosylation fact 85.6 1.1 2.3E-05 45.9 4.5 20 313-332 300-319 (395)
18 PRK00085 recO DNA repair prote 80.9 1 2.2E-05 42.8 2.1 31 2-32 147-178 (247)
19 PF00320 GATA: GATA zinc finge 69.4 3.4 7.5E-05 28.3 1.8 32 7-38 1-34 (36)
20 PF00643 zf-B_box: B-box zinc 68.8 3.5 7.6E-05 28.4 1.8 34 3-36 2-36 (42)
21 smart00401 ZnF_GATA zinc finge 67.2 5 0.00011 29.8 2.4 38 3-40 2-41 (52)
22 TIGR00613 reco DNA repair prot 63.6 4.1 8.9E-05 38.5 1.7 32 2-33 145-177 (241)
23 PF10764 Gin: Inhibitor of sig 52.8 7.5 0.00016 28.3 1.1 26 6-32 1-26 (46)
24 PF08271 TF_Zn_Ribbon: TFIIB z 51.4 6.5 0.00014 27.7 0.6 26 6-32 2-27 (43)
25 cd07171 NR_DBD_ER DNA-binding 49.6 10 0.00022 30.7 1.6 31 3-36 2-32 (82)
26 PF01286 XPA_N: XPA protein N- 49.4 6.5 0.00014 27.0 0.3 27 5-31 4-31 (34)
27 cd07173 NR_DBD_AR DNA-binding 48.0 12 0.00026 30.4 1.7 32 2-36 1-32 (82)
28 cd00202 ZnF_GATA Zinc finger D 47.8 14 0.0003 27.7 1.9 34 6-39 1-36 (54)
29 cd07170 NR_DBD_ERR DNA-binding 44.7 13 0.00027 31.2 1.4 30 4-36 4-33 (97)
30 PRK12495 hypothetical protein; 44.6 9.7 0.00021 36.6 0.8 27 2-32 40-66 (226)
31 cd06968 NR_DBD_ROR DNA-binding 44.0 14 0.00031 30.8 1.6 31 3-36 4-34 (95)
32 cd07160 NR_DBD_LXR DNA-binding 43.0 16 0.00034 30.9 1.8 31 3-36 17-47 (101)
33 COG1381 RecO Recombinational D 42.9 12 0.00027 36.2 1.3 27 5-31 155-182 (251)
34 PTZ00218 40S ribosomal protein 42.8 13 0.00028 28.2 1.0 39 2-45 14-52 (54)
35 TIGR02419 C4_traR_proteo phage 39.3 14 0.00031 28.5 0.9 32 2-34 29-62 (63)
36 cd07169 NR_DBD_GCNF_like DNA-b 38.8 18 0.00039 29.8 1.4 32 2-36 4-35 (90)
37 PF11781 RRN7: RNA polymerase 38.8 19 0.00041 24.8 1.3 25 4-31 8-32 (36)
38 PF14471 DUF4428: Domain of un 37.2 16 0.00034 27.1 0.8 30 6-36 1-32 (51)
39 COG1997 RPL43A Ribosomal prote 35.0 23 0.00049 29.5 1.4 26 5-32 36-61 (89)
40 cd06966 NR_DBD_CAR DNA-binding 34.7 17 0.00037 30.2 0.7 29 5-36 1-29 (94)
41 PHA00080 DksA-like zinc finger 33.6 21 0.00045 28.3 1.0 32 3-35 30-63 (72)
42 PF07282 OrfB_Zn_ribbon: Putat 32.3 22 0.00047 27.1 0.9 25 5-31 29-53 (69)
43 PF03604 DNA_RNApol_7kD: DNA d 31.7 17 0.00037 24.5 0.2 23 6-31 2-24 (32)
44 cd07162 NR_DBD_PXR DNA-binding 29.9 34 0.00074 27.9 1.7 28 6-36 1-28 (87)
45 PF04770 ZF-HD_dimer: ZF-HD pr 29.9 21 0.00045 27.7 0.4 30 7-37 21-52 (60)
46 cd07168 NR_DBD_DHR4_like DNA-b 28.9 33 0.00071 28.2 1.5 30 4-36 6-35 (90)
47 COG2174 RPL34A Ribosomal prote 28.8 35 0.00076 28.5 1.6 31 2-32 32-79 (93)
48 PRK00423 tfb transcription ini 28.8 32 0.0007 34.3 1.7 31 3-34 10-40 (310)
49 PF14376 Haem_bd: Haem-binding 28.7 27 0.00059 30.8 1.0 15 4-18 41-55 (137)
50 cd07165 NR_DBD_DmE78_like DNA- 27.4 37 0.00079 27.3 1.5 27 7-36 1-27 (81)
51 PF01258 zf-dskA_traR: Prokary 26.5 12 0.00027 25.3 -1.2 30 5-34 4-34 (36)
52 smart00290 ZnF_UBP Ubiquitin C 26.2 43 0.00093 23.7 1.5 24 6-29 1-24 (50)
53 cd06970 NR_DBD_PNR DNA-binding 26.2 28 0.0006 28.9 0.6 32 2-36 4-35 (92)
54 cd07161 NR_DBD_EcR DNA-binding 26.1 43 0.00093 27.7 1.7 29 5-36 2-30 (91)
55 cd07172 NR_DBD_GR_PR DNA-bindi 25.4 44 0.00096 26.7 1.6 30 4-36 2-31 (78)
56 cd06965 NR_DBD_Ppar DNA-bindin 25.3 32 0.00069 27.9 0.8 27 7-36 2-28 (84)
57 cd06956 NR_DBD_RXR DNA-binding 25.3 47 0.001 26.4 1.7 29 5-36 1-29 (77)
58 PRK11019 hypothetical protein; 25.2 27 0.00059 28.9 0.3 36 4-40 36-73 (88)
59 PTZ00074 60S ribosomal protein 25.0 39 0.00084 30.2 1.3 27 6-32 43-86 (135)
60 PF13462 Thioredoxin_4: Thiore 24.2 42 0.0009 28.8 1.3 28 11-38 8-35 (162)
61 cd07158 NR_DBD_Ppar_like The D 24.1 46 0.001 26.0 1.5 27 7-36 1-27 (73)
62 PRK13715 conjugal transfer pro 23.5 27 0.00059 27.8 0.0 32 5-36 35-67 (73)
63 cd07166 NR_DBD_REV_ERB DNA-bin 22.9 45 0.00098 27.3 1.2 30 4-36 3-32 (89)
64 cd07163 NR_DBD_TLX DNA-binding 22.9 32 0.0007 28.4 0.4 30 4-36 6-35 (92)
65 cd07156 NR_DBD_VDR_like The DN 22.7 48 0.001 26.0 1.3 27 7-36 1-27 (72)
66 cd06955 NR_DBD_VDR DNA-binding 22.5 36 0.00078 29.1 0.6 30 4-36 6-35 (107)
67 cd07157 2DBD_NR_DBD1 The first 22.2 28 0.00062 28.3 -0.1 28 6-36 2-29 (86)
68 PF08792 A2L_zn_ribbon: A2L zi 21.9 34 0.00074 23.2 0.3 29 4-34 3-31 (33)
69 KOG3507 DNA-directed RNA polym 21.7 37 0.00079 26.3 0.4 27 6-37 22-48 (62)
70 PF13119 DUF3973: Domain of un 21.0 34 0.00074 24.3 0.1 14 25-38 2-15 (41)
71 cd07164 NR_DBD_PNR_like_1 DNA- 20.7 57 0.0012 25.9 1.4 27 7-36 1-27 (78)
No 1
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=100.00 E-value=2.6e-96 Score=718.30 Aligned_cols=368 Identities=69% Similarity=1.015 Sum_probs=326.9
Q ss_pred CCCCCcccCCCCCCCCeeEeccccccchhhhhhhhcCCCcccceeccCCCCCCHHHHHHHhcCChHHHHHHHHhcCCCCC
Q 016665 1 MTPRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTDG 80 (385)
Q Consensus 1 ~p~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~lG~hiS~VkSi~lD~W~~~~l~~m~~gGN~~a~~f~~~~g~~~~ 80 (385)
.|+|++||||++++|+|+|++||||||++|+|+||.||+||++|||++||.|+++||++|+.|||.+++.||++||+...
T Consensus 19 kPgNk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~Ws~eqL~~Mk~GGN~rA~~fF~qhG~~~~ 98 (395)
T PLN03114 19 KSDNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSSEQLKMMIYGGNNRAQVFFKQYGWSDG 98 (395)
T ss_pred CcCCCcCccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCCCCHHHHHHHHHhcCHHHHHHHHHcCCCCC
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999876
Q ss_pred CchhhhhchHHHHHHHHHHHHHHHHHhhhhC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CcCCCCCCCCCCC-CCCc
Q 016665 81 GKIEAKYTSRAAELYKQILAKEVAKNMAEEA-GLPSSPVASQPAQAANALPDVKIQDAPKE-NYQGRQETQDAPG-SPKV 157 (385)
Q Consensus 81 ~~i~~KY~s~~a~~Yr~~l~~~v~~~~~~~~-~~~~~~~~~~~~~~~d~f~~~~~~~~p~~-~~~~~~~~~~~~~-~p~~ 157 (385)
..+++||+++++.+||++|+++|++.+.++. .+|+.++++. +.+|+|++.+..+.|.. +++...+.|...+ +|++
T Consensus 99 ~~~~~KY~S~aA~~Yre~L~keVa~~~a~~~~~~p~~~~~~~--~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~s~~~ 176 (395)
T PLN03114 99 GKTEAKYTSRAADLYKQILAKEVAKSKAEEELDLPPSPPDST--QVPNGLSSIKTSEALKESNTLKQQEKPDVVPVSPRI 176 (395)
T ss_pred CCcccccCCHHHHHHHHHHHHHHHHhhhccccCCCCCCCCcc--ccccCcccccccccccccCCcccccCCcccCCCCCC
Confidence 7899999999999999999999999998766 4566666543 38899999888776643 2333333333322 4544
Q ss_pred ccccccccccCCCccccCCCCCCccccccCCCCCccccCCCCCCCCCCCCCCCCCC-CCCCCCcccchhhhhhhcccccC
Q 016665 158 SRTVLTSTVKKPLGAKKSGKTGGLGARKLTSKPSESLYEQKPEEPSVPISSSTSNT-SSVSLPFASRFEYVDNVQSSELS 236 (385)
Q Consensus 158 ~~~~~s~~~kk~~~aKk~~K~~~LgAkKv~~~~~e~~~d~~~ee~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 236 (385)
+ ++.|||+|+||.||+|||||+|++++..|.||||++|| .++.++++++. +...+++.+||.|.|+++. +..
T Consensus 177 ~-----~~~kk~~gak~~gktgglg~~klttk~~~~ly~qkp~e-~~~~~~~~~~~~~~~~~~~~srf~y~d~~~~-~~~ 249 (395)
T PLN03114 177 S-----RSVKKPLGAKKTGKTGGLGARKLTTKSSGTLYDQKPEE-SVIIQATSPVSAKSARSSFSSRFDYADNVQN-RED 249 (395)
T ss_pred c-----cccccccccccccccCCccccccccCCchhhhhcCccc-cCCCCCCCccccccCCCCcchhhhhcccccc-ccc
Confidence 3 56899999999999999999999999999999999999 56666555543 4456777899999999998 776
Q ss_pred CCCCCcccccCCCCCCccc-ccCCCCcC-CcCCCC--CcccchhhhHHHHHHhccCCcCccccccCCCCCccchhHHHHh
Q 016665 237 SGGPQVLSHVAPPKSSSFF-ADYGMDNG-FQKKSG--SSKVQIQETDEARKKFSNAKSISSSQFFGDQNNSIDMDTQVSL 312 (385)
Q Consensus 237 ~~~~~~~~~~~~~~~~~~f-~~~gm~~~-~~~~~~--~~~~~~~~t~~a~~KFgnaKaISSd~yFGr~~~~a~~ea~~rL 312 (385)
.++.+..+||+||++..|| .+|||+.+ +++++. +.+.+++++++||+||+|||+||||||||+++..+++|++.||
T Consensus 250 ~~~~~~~~hvapp~ss~ff~~e~g~~~~~~~k~~~~~~~k~q~~e~~~a~kKF~naKsisS~qfFg~~~~~~d~~~~~~l 329 (395)
T PLN03114 250 YMSPQVVSHVAPPKSSGFFEEELEMNGGRFQKKPITSSSKLQIQETDEARKKFTNAKSISSAQYFGNDNNSADLEAKSSL 329 (395)
T ss_pred cCCcccccccCCCccchhhHHhhcCCcccccCCCCCccccccccchHHHHHHhcccccccHHhhccccccccchhhHHHH
Confidence 7788999999999999999 67999998 888876 7788999999999999999999999999999988899999999
Q ss_pred hhccCCcccccccccCCCCCCcccchhhHHHHHHhhhchHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016665 313 QKFSGSASISSADLFGHDSDNASLDLAASDLINRLSFQAQQDISSLKNIAGETGKKLSSLASSLI 377 (385)
Q Consensus 313 ~~F~gatsISS~~yFg~~~~~~~~~~sa~d~~~~~~~~a~~Dl~~lk~~v~~~A~KLs~~a~~~~ 377 (385)
++|+|+++|||+|||||++++.+++++|.||++||++||.+||+.||+++++++.||++||++++
T Consensus 330 ~kf~gs~~ISsad~fg~~~~d~~id~ta~dli~r~s~qa~qd~sslkn~aget~~kl~s~as~~~ 394 (395)
T PLN03114 330 KKFSGSSAISSADLFGDSDGDFTLDLTAGDLLNRLSLQAQQDISSLKNMAEETKKKLGSVASSLW 394 (395)
T ss_pred HhhccccccchHHhcCCCCccccccccHHHHHHHhhhhhHhHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 99999999999999999988889999999999999999999999999999999999999999985
No 2
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=1.4e-84 Score=649.20 Aligned_cols=374 Identities=47% Similarity=0.676 Sum_probs=281.9
Q ss_pred CCCCCcccCCCCCCCCeeEeccccccchhhhhhhhcCCCcccceeccCCCCCCHHHHHHHhcCChHHHHHHHHhcCCCCC
Q 016665 1 MTPRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTDG 80 (385)
Q Consensus 1 ~p~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~lG~hiS~VkSi~lD~W~~~~l~~m~~gGN~~a~~f~~~~g~~~~ 80 (385)
+++||+|||||++||+|+||+||||||++|+++||+|||||+||||++||.|+|.|||+|++|||.+|+.||.+|||..
T Consensus 20 ~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~~FFkqhg~~t- 98 (454)
T KOG0706|consen 20 QSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANARVFFKQHGCVT- 98 (454)
T ss_pred CCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHHHHHHHcCCcc-
Confidence 4799999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred CchhhhhchHHHHHHHHHHHHHHHHHhhhhC---CCCCC-CCCCCCCCCCCCCCCCCCCCCC-CCCcCCCCCCCCCCCCC
Q 016665 81 GKIEAKYTSRAAELYKQILAKEVAKNMAEEA---GLPSS-PVASQPAQAANALPDVKIQDAP-KENYQGRQETQDAPGSP 155 (385)
Q Consensus 81 ~~i~~KY~s~~a~~Yr~~l~~~v~~~~~~~~---~~~~~-~~~~~~~~~~d~f~~~~~~~~p-~~~~~~~~~~~~~~~~p 155 (385)
.++++||++|++++||++|+.+|.+.+.+++ .++.. ++..+...+.|||+.|.++..- ..++.. .....+|
T Consensus 99 ~d~~aKY~SraA~~Yr~kl~~lv~kam~~~~~~l~l~~~~~~~~~~~~~~dffs~~~k~~~~~~~s~~~----l~~~~s~ 174 (454)
T KOG0706|consen 99 LDANAKYNSRAAKLYREKLKKLVQKAMAEHGTSLLLDSAVSSGSPESEDSDFFSESDKESSKHEPSTDA----LKSLSSP 174 (454)
T ss_pred hhhhhhhccHHHHHHHHHHHHHHHHHHHhcCccccccCCCCCCCCccccccchhhccccccccCCcccc----cccccCC
Confidence 5999999999999999999999999999886 33333 3333555678999888665321 001110 0122345
Q ss_pred CcccccccccccCCCccccCCCCCC--ccccccCCCCCccccCCCCCCCCCCCCCCCCCCCC-CCCCcccchhh---hhh
Q 016665 156 KVSRTVLTSTVKKPLGAKKSGKTGG--LGARKLTSKPSESLYEQKPEEPSVPISSSTSNTSS-VSLPFASRFEY---VDN 229 (385)
Q Consensus 156 ~~~~~~~s~~~kk~~~aKk~~K~~~--LgAkKv~~~~~e~~~d~~~ee~~~~~~~~~~~~~~-~~~~~~~~~~~---~~~ 229 (385)
+++.++.+...++|.++|++|++++ |||+||.++.+..++.+..+++.....+.++.... .....+.++.| .++
T Consensus 175 ~~S~~v~sg~~k~p~~~k~~g~~k~~~lgarkv~t~s~~~~~~~~~~~~~~~i~a~s~~~~s~~~~~~s~~~~~~e~~dd 254 (454)
T KOG0706|consen 175 SASNTVVSGKKKPPVTKKGLGAKKGVTLGARKVNTKSFKSIESQAQEAEKNKIKAASPKPSSEESSARSSRLARQELQDD 254 (454)
T ss_pred ccccccccccccCCccccccccccccccCceecccccccchhhccchhhhccccccCCCcchhhhcccchhhhhhHHHHH
Confidence 5555555566677777777884444 99999998877778887766544333322222100 01111223333 222
Q ss_pred hc----------------ccccCCCCCCcccc-----------cCCCCCCcccccCCCCcC-------------CcCCCC
Q 016665 230 VQ----------------SSELSSGGPQVLSH-----------VAPPKSSSFFADYGMDNG-------------FQKKSG 269 (385)
Q Consensus 230 ~~----------------~~~~~~~~~~~~~~-----------~~~~~~~~~f~~~gm~~~-------------~~~~~~ 269 (385)
.+ +++|| +.++...| +++|+..++|..++|... +.+...
T Consensus 255 ~~~~E~k~~d~~k~~~~~rlgmg-~~~s~~~hs~~~~~~~i~~~t~~~~k~~~~~~~~~~~~~~~~~s~~~~~~~~~~~s 333 (454)
T KOG0706|consen 255 RKKEEAKAKDGKKASSSERLGMG-GYRSVMSHSVLGGMQVIEQVTPPKAKPSFLELDMFSDTTKQSSSNYKDAPFGKGSS 333 (454)
T ss_pred HHhhhhhhcCcccccchhhhccc-cccchhhhcccCCceeeecccCccccccccccccccchhccccCCcccCccccCcc
Confidence 11 13555 33444444 446665555544444222 111111
Q ss_pred ----------CcccchhhhHHHHHHhccCCcCccccccCCCCCccchhHHHHhhhccCCcccccccccCCCCCCcccchh
Q 016665 270 ----------SSKVQIQETDEARKKFSNAKSISSSQFFGDQNNSIDMDTQVSLQKFSGSASISSADLFGHDSDNASLDLA 339 (385)
Q Consensus 270 ----------~~~~~~~~t~~a~~KFgnaKaISSd~yFGr~~~~a~~ea~~rL~~F~gatsISS~~yFg~~~~~~~~~~s 339 (385)
..+.++++|++||+||||||+|||||||||+. +|++|+|+||++|+|+++|||+||||++++ ..+
T Consensus 334 s~ss~~a~~~~~~~~v~~td~~rkkF~naKaISSdqyFG~~~-~ad~Ea~~~L~~f~gstaISSsd~fG~~~~----~~~ 408 (454)
T KOG0706|consen 334 SSSSKDAKRAKESRPVEETDEARKKFGNAKAISSDQYFGRGS-EADLEARARLQKFSGSTAISSSDLFGEGDD----DHT 408 (454)
T ss_pred cccchhhhccccccccccccHHHHhhccccccchhhhcCCcc-hhhhHHHHHHHhccCccccchHhhcCCCCC----CCC
Confidence 12246788999999999999999999999998 679999999999999999999999999876 356
Q ss_pred hHHHHHHhhhchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 016665 340 ASDLINRLSFQAQQDISSLKNIAGETGKKLSSLASSLITDIQDRIL 385 (385)
Q Consensus 340 a~d~~~~~~~~a~~Dl~~lk~~v~~~A~KLs~~a~~~~~~lQdry~ 385 (385)
+.+++.++.+++.+||.+++++|+++|+||+++|++|+++|||||+
T Consensus 409 ~g~~~~~~~~~a~~di~~~k~~~~~~a~kls~~a~~v~~~~qd~~~ 454 (454)
T KOG0706|consen 409 AGSLALRDSFRAAQDIASFKNSARSVAGKLSVLASKVGSSLQDRYG 454 (454)
T ss_pred ccchhhcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 7778888999999999999999999999999999999999999995
No 3
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=100.00 E-value=5.2e-37 Score=299.53 Aligned_cols=104 Identities=48% Similarity=0.896 Sum_probs=98.5
Q ss_pred CCCcccCCCCCCCCeeEeccccccchhhhhhhhcCCCcccceeccCCCCCCHHHHHHHhcCChHHHHHHHHhcCCCCC-C
Q 016665 3 PRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTDG-G 81 (385)
Q Consensus 3 ~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~lG~hiS~VkSi~lD~W~~~~l~~m~~gGN~~a~~f~~~~g~~~~-~ 81 (385)
+|++||||+++||+||||+||||||++|+|+||.|||||||||||+||+|.+.||+.|+.|||.++++||..++.-.+ -
T Consensus 18 eNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~~~eFL~s~~~~~e~~ 97 (386)
T KOG0704|consen 18 ENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNERFREFLSSQGIYKETW 97 (386)
T ss_pred cCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchhHHHHHhhCccccccc
Confidence 899999999999999999999999999999999999999999999999999999999999999999999999986554 4
Q ss_pred chhhhhchHHHHHHHHHHHHHHHHH
Q 016665 82 KIEAKYTSRAAELYKQILAKEVAKN 106 (385)
Q Consensus 82 ~i~~KY~s~~a~~Yr~~l~~~v~~~ 106 (385)
.|++||.+++|.+||++|..+++..
T Consensus 98 ~i~eKYns~aAa~yRdki~~laegr 122 (386)
T KOG0704|consen 98 PIREKYNSRAAALYRDKIAALAEGR 122 (386)
T ss_pred cHHHhhccHHHHHHHHHHHHHhcCC
Confidence 8999999999999999999877543
No 4
>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=4.6e-35 Score=288.48 Aligned_cols=107 Identities=46% Similarity=0.731 Sum_probs=100.0
Q ss_pred CCCCCcccCCCCCCCCeeEeccccccchhhhhhhhcCCCcccceeccCCCCCCHHHHHHHhcCChHHHHHHHHhcCCCC-
Q 016665 1 MTPRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTD- 79 (385)
Q Consensus 1 ~p~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~lG~hiS~VkSi~lD~W~~~~l~~m~~gGN~~a~~f~~~~g~~~- 79 (385)
.++|++|||||+++|+|+||+||||||++|+||||+||+||+|||||+||.|+++||++|++|||.+|++||+.|++..
T Consensus 17 ~~~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~wt~~~l~~m~~gGN~~a~~~~e~~~~~~~ 96 (319)
T COG5347 17 DSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWTEEELRRMEVGGNSNANRFYEKNLLDQL 96 (319)
T ss_pred ccccCccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeecccCCHHHHHHHHHhcchhhhhHhccCCCccc
Confidence 4789999999999999999999999999999999999999999999999999999999999999999999999998874
Q ss_pred CCchhhhhchHHHHHHHHHHHHHHHHHh
Q 016665 80 GGKIEAKYTSRAAELYKQILAKEVAKNM 107 (385)
Q Consensus 80 ~~~i~~KY~s~~a~~Yr~~l~~~v~~~~ 107 (385)
...++.||.+.+++.|.+.+..++....
T Consensus 97 ~~~~k~~yd~~v~~~y~~~ky~~~~~~~ 124 (319)
T COG5347 97 LLPIKAKYDSSVAKKYIRKKYELKKFID 124 (319)
T ss_pred ccccccccCHHHHHHHHHHHHHhhhccc
Confidence 3689999999999999999877665554
No 5
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=99.97 E-value=9e-32 Score=229.12 Aligned_cols=98 Identities=48% Similarity=0.850 Sum_probs=86.2
Q ss_pred CCCCcccCCCCCCCCeeEeccccccchhhhhhhhcCCCcccceeccCCCCCCHHHHHHHhcCChHHHHHHHHhcCCCCC-
Q 016665 2 TPRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTDG- 80 (385)
Q Consensus 2 p~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~lG~hiS~VkSi~lD~W~~~~l~~m~~gGN~~a~~f~~~~g~~~~- 80 (385)
|+|++||||++++|+|+|++||||||+.|+|+||.||+|||+||||+||+|++++|++|+.+||.++|+||+++.....
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 6899999999999999999999999999999999999999999999999999999999999999999999999864321
Q ss_pred ----CchhhhhchHHHHHHHHHH
Q 016665 81 ----GKIEAKYTSRAAELYKQIL 99 (385)
Q Consensus 81 ----~~i~~KY~s~~a~~Yr~~l 99 (385)
.....+|+..+...|++++
T Consensus 81 ~~~~~~~~~~~~~fI~~KY~~k~ 103 (112)
T smart00105 81 KPPDSDDQQKYESFIAAKYEEKL 103 (112)
T ss_pred CCCCCchHHHHHHHHHHHHHhhh
Confidence 1245666666666666554
No 6
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.97 E-value=3.4e-32 Score=262.62 Aligned_cols=92 Identities=40% Similarity=0.778 Sum_probs=83.8
Q ss_pred CCCCcccCCCCCCCCeeEeccccccchhhhhhhhcCCCcccceeccCCCCCCHHHHHHHhcCChHHHHHHHHhcCCCC--
Q 016665 2 TPRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTD-- 79 (385)
Q Consensus 2 p~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~lG~hiS~VkSi~lD~W~~~~l~~m~~gGN~~a~~f~~~~g~~~-- 79 (385)
|+|++|+|||++.|.|||+++|||||+.|+||||+||+|||+||||+||.|+++||..|+..||.+||+||++.-...
T Consensus 23 ~~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~~GN~~an~~~ea~~p~~~~ 102 (287)
T KOG0703|consen 23 PDNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMISMGNAKANSYYEAKLPDPFR 102 (287)
T ss_pred cccCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHHHcchhhhhhccccCCcccc
Confidence 789999999999999999999999999999999999999999999999999999999999999999999999882211
Q ss_pred --------CCchhhhhchHHHH
Q 016665 80 --------GGKIEAKYTSRAAE 93 (385)
Q Consensus 80 --------~~~i~~KY~s~~a~ 93 (385)
+.|||.||+.+...
T Consensus 103 ~p~~d~~~e~FIR~KYE~kkf~ 124 (287)
T KOG0703|consen 103 RPGPDDLVEQFIRDKYERKKFL 124 (287)
T ss_pred CCChHHHHHHHHHHHHhhhhhc
Confidence 36899999877543
No 7
>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=99.97 E-value=3.9e-31 Score=226.40 Aligned_cols=75 Identities=52% Similarity=1.041 Sum_probs=63.9
Q ss_pred CCCCCcccCCCCCCCCeeEeccccccchhhhhhhhcCCCcccceeccCCCCCCHHHHHHHhcCChHHHHHHHHhc
Q 016665 1 MTPRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQH 75 (385)
Q Consensus 1 ~p~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~lG~hiS~VkSi~lD~W~~~~l~~m~~gGN~~a~~f~~~~ 75 (385)
.|+|++|+|||+++|+|+|++||||||+.|+|+||.||+|||+||||+||.|++++|+.|+.+||..+|+||+++
T Consensus 10 ~~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~VkSi~~d~w~~~ev~~~~~~GN~~~n~~~e~~ 84 (116)
T PF01412_consen 10 KPGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRVKSITMDNWSPEEVQRMREGGNKRANSIWEAN 84 (116)
T ss_dssp STTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--EEETTTS---HHHHHHHHHSHHHHHHHHHTTT
T ss_pred CcCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhccccccCCCCHHHHHHHHHHChHHHHHHHHcC
Confidence 489999999999999999999999999999999999999999999999999999999999999999999999998
No 8
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=99.92 E-value=8.7e-26 Score=232.37 Aligned_cols=87 Identities=25% Similarity=0.707 Sum_probs=78.8
Q ss_pred CCCCCcccCCCCCCCCeeEeccccccchhhhhhhhcCCCcccceeccCCCCCCHHHHHHHhcCChHHHHHHHHhcCCCC-
Q 016665 1 MTPRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTD- 79 (385)
Q Consensus 1 ~p~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~lG~hiS~VkSi~lD~W~~~~l~~m~~gGN~~a~~f~~~~g~~~- 79 (385)
+|+|++|+||++++|+|||++||||||+.|+||||.|| ++||||+||+|+++||++|+.+||.++|+||+++ |..
T Consensus 20 lPgNk~CADCgs~~P~WASiNlGIFICi~CSGIHRsLG---hRVKSLSLDkWT~EEVe~Mk~gGN~~AN~iyean-w~~~ 95 (648)
T PLN03119 20 LPPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREFT---HRVKSVSMSKFTSKEVEVLQNGGNQRAREIYLKN-WDHQ 95 (648)
T ss_pred CcCCCccccCCCCCCCceeeccceEEeccchhhhccCC---ceeeccccCCCCHHHHHHHHHhchHHHHHHHHhh-cccc
Confidence 58999999999999999999999999999999999998 3999999999999999999999999999999986 321
Q ss_pred -------------CCchhhhhchHH
Q 016665 80 -------------GGKIEAKYTSRA 91 (385)
Q Consensus 80 -------------~~~i~~KY~s~~ 91 (385)
..||+.||..+.
T Consensus 96 ~~~~P~~sD~e~lr~FIR~KYVeKR 120 (648)
T PLN03119 96 RQRLPENSNAERVREFIKNVYVQKK 120 (648)
T ss_pred cCCCCCCccHHHHHHHHHHHHhhhh
Confidence 147888887774
No 9
>PLN03131 hypothetical protein; Provisional
Probab=99.92 E-value=1e-25 Score=233.46 Aligned_cols=87 Identities=25% Similarity=0.715 Sum_probs=78.9
Q ss_pred CCCCCcccCCCCCCCCeeEeccccccchhhhhhhhcCCCcccceeccCCCCCCHHHHHHHhcCChHHHHHHHHhcCCCC-
Q 016665 1 MTPRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTD- 79 (385)
Q Consensus 1 ~p~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~lG~hiS~VkSi~lD~W~~~~l~~m~~gGN~~a~~f~~~~g~~~- 79 (385)
+|+|++|+||++++|+|+|++||||||+.|+||||.|| | +||||+||.|+++||++|+.+||.++|+||+++ |..
T Consensus 20 ~PgNk~CADCga~~P~WASiNlGIFICi~CSGIHRsLg-h--RVKSVTLD~WtdeEV~~Mk~gGN~~AN~iyean-wd~~ 95 (705)
T PLN03131 20 LPPNRRCINCNSLGPQFVCTNFWTFICMTCSGIHREFT-H--RVKSVSMSKFTSQDVEALQNGGNQRAREIYLKD-WDQQ 95 (705)
T ss_pred CcCCCccccCCCCCCCeeEeccceEEchhchhhhcccC-c--ccccccCCCCCHHHHHHHHHhccHHHHHHHHhh-cccc
Confidence 58999999999999999999999999999999999998 3 999999999999999999999999999999975 321
Q ss_pred -------------CCchhhhhchHH
Q 016665 80 -------------GGKIEAKYTSRA 91 (385)
Q Consensus 80 -------------~~~i~~KY~s~~ 91 (385)
..||+.||..+.
T Consensus 96 r~~lP~~sd~ekrr~FIR~KYVeKR 120 (705)
T PLN03131 96 RQRLPDNSKVDKIREFIKDIYVDKK 120 (705)
T ss_pred cCCCCCCccHHHHHHHHHHHHhhhh
Confidence 257888888774
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=2e-21 Score=200.05 Aligned_cols=91 Identities=43% Similarity=0.804 Sum_probs=83.5
Q ss_pred CCCCCcccCCCCCCCCeeEeccccccchhhhhhhhcCCCcccceeccCCCCCCHHHHHHHhcCChHHHHHHHHhc--CCC
Q 016665 1 MTPRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQH--GWT 78 (385)
Q Consensus 1 ~p~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~lG~hiS~VkSi~lD~W~~~~l~~m~~gGN~~a~~f~~~~--g~~ 78 (385)
|++|..|+||+++||.|||++.|+.+|++|+||||+||.|+|+||++.||.|..+.+..|...||+.||.+|+.. |-.
T Consensus 510 ~rgn~~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl~~Vm~aiGN~~AN~vWE~~~~G~~ 589 (749)
T KOG0705|consen 510 MRGNSHCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVELLKVMSAIGNDLANSVWEGSSQGQT 589 (749)
T ss_pred CcCCceeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHHHHHHHHhhhhHHHHHhhhhccCCc
Confidence 689999999999999999999999999999999999999999999999999999999999999999999999964 211
Q ss_pred ---C-------CCchhhhhchHH
Q 016665 79 ---D-------GGKIEAKYTSRA 91 (385)
Q Consensus 79 ---~-------~~~i~~KY~s~~ 91 (385)
. +.||+.||..+.
T Consensus 590 KPs~~s~REEkErwIr~KYeqkl 612 (749)
T KOG0705|consen 590 KPSPDSSREEKERWIRAKYEQKL 612 (749)
T ss_pred CCCccccHHHHHHHHHHHHHHHh
Confidence 1 368999999884
No 11
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.74 E-value=3.3e-19 Score=193.91 Aligned_cols=90 Identities=44% Similarity=0.756 Sum_probs=83.0
Q ss_pred CCCCCcccCCCCCCCCeeEeccccccchhhhhhhhcCCCcccceeccCCCCCCHHHHHHHhcCChHHHHHHHHhcCCCC-
Q 016665 1 MTPRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTD- 79 (385)
Q Consensus 1 ~p~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~lG~hiS~VkSi~lD~W~~~~l~~m~~gGN~~a~~f~~~~g~~~- 79 (385)
+|+|..|+|||++.|+|+|+++||.+|++|+|+||+||||||+|+|++||.|..+.+.+|+.+||..+|.+|+.+.+..
T Consensus 423 ~pgN~~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~~~~l~~l~~~lgn~~~N~i~e~~l~~~~ 502 (785)
T KOG0521|consen 423 VPGNAQCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVWEPELLLLFKNLGNKYVNEIYEALLPSYD 502 (785)
T ss_pred CCchhhhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhccCcHHHHHHHHhCcchhhhhhhccccccc
Confidence 5899999999999999999999999999999999999999999999999999999999999999999999999885422
Q ss_pred -------------CCchhhhhchH
Q 016665 80 -------------GGKIEAKYTSR 90 (385)
Q Consensus 80 -------------~~~i~~KY~s~ 90 (385)
..+|++||..+
T Consensus 503 ~~~~~~~~~~~~r~~~i~~kyve~ 526 (785)
T KOG0521|consen 503 SSKPTASSSRQAREAWIKAKYVER 526 (785)
T ss_pred ccCCCCccchhhhhHhhhccccee
Confidence 14688888776
No 12
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.64 E-value=3.2e-17 Score=166.97 Aligned_cols=91 Identities=38% Similarity=0.650 Sum_probs=81.6
Q ss_pred CCCCcccCCCCCCCCeeEeccccccchhhhhhhhcCCCcccceeccCCCCCCHHHHHHHhcCChHHHHHHHHhcCCCC--
Q 016665 2 TPRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTD-- 79 (385)
Q Consensus 2 p~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~lG~hiS~VkSi~lD~W~~~~l~~m~~gGN~~a~~f~~~~g~~~-- 79 (385)
..-++|.|||++.|.||||+-|+|||.+|..+||.||.|||.||++-...|.+.-|++...+.|..+|.+|+.+.+++
T Consensus 6 l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaNsIWEh~Lld~st 85 (669)
T KOG0818|consen 6 LSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGANSIWEHSLLDPAT 85 (669)
T ss_pred hhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcchhhhhhccCchh
Confidence 345799999999999999999999999999999999999999999999999999999999999999999999873321
Q ss_pred ------------------CCchhhhhchHHH
Q 016665 80 ------------------GGKIEAKYTSRAA 92 (385)
Q Consensus 80 ------------------~~~i~~KY~s~~a 92 (385)
..||++||....-
T Consensus 86 ~~sg~rk~~pqD~~Hp~K~eFIkaKy~~LtF 116 (669)
T KOG0818|consen 86 IMSGRRKANPQDKVHPNKAEFIRAKYQMLAF 116 (669)
T ss_pred hhcccCCCCCcCCCCccHHHHHHHHHHheee
Confidence 2578999987643
No 13
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.49 E-value=4.6e-15 Score=158.46 Aligned_cols=92 Identities=33% Similarity=0.604 Sum_probs=82.3
Q ss_pred CCCCcccCCCCCCCCeeEeccccccchhhhhhhhcCCCcccceeccCCCC--CCHHHHHHHhcCChHHHHHHHHhcCCCC
Q 016665 2 TPRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDS--WSAEQLKMMVYGGNNRAQVFFKQHGWTD 79 (385)
Q Consensus 2 p~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~lG~hiS~VkSi~lD~--W~~~~l~~m~~gGN~~a~~f~~~~g~~~ 79 (385)
..|+.|+||+++.|.||++|.+|.||-.|+|-||+||..+|+|+|+.||. |+.+-|+++.+.||.++|+||..+-...
T Consensus 296 e~nr~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~Fwa~nl~~~ 375 (1186)
T KOG1117|consen 296 EENRECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANRFWAGNLPPN 375 (1186)
T ss_pred cccccccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCcccccccccCCCCc
Confidence 36999999999999999999999999999999999999999999999995 9999999999999999999998763211
Q ss_pred ------------CCchhhhhchHHHH
Q 016665 80 ------------GGKIEAKYTSRAAE 93 (385)
Q Consensus 80 ------------~~~i~~KY~s~~a~ 93 (385)
..+|++||++..-.
T Consensus 376 e~lh~dssp~~r~~fi~~Kykeg~fR 401 (1186)
T KOG1117|consen 376 EHLHPDSSPSTRRQFIKEKYKEGKFR 401 (1186)
T ss_pred cccCCCCCcchhhhHHHHHhhccccc
Confidence 25899999887533
No 14
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=98.93 E-value=4.6e-10 Score=115.26 Aligned_cols=74 Identities=20% Similarity=0.471 Sum_probs=69.0
Q ss_pred CCCCCcccCCCCCCC-CeeEeccccccchhhhhhhhcCCCcccceeccCCCCCCHHHHHHHhcCChHHHHHHHHhc
Q 016665 1 MTPRKMCFDCNAKNP-TWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQH 75 (385)
Q Consensus 1 ~p~Nk~C~DCga~nP-~waSv~~GiflC~~Csg~HR~lG~hiS~VkSi~lD~W~~~~l~~m~~gGN~~a~~f~~~~ 75 (385)
||+|++|++|....+ +|++++-|-|+|+.|+|..|.|. --++||||.|-.++..++..++.+||+.++++|.+-
T Consensus 22 LP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~-~ahRvksiSmttft~qevs~lQshgNq~~k~i~fkl 96 (524)
T KOG0702|consen 22 LPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLN-PAHRVKSISMTTFTDQEVSFLQSHGNQVCKEIWFKL 96 (524)
T ss_pred CCCCCceeeccccccceEEEeeccceeeeccchhhccCC-CccccceeeeeeccccchHHHhhcchhhhhhhhhcc
Confidence 799999999999888 99999999999999999999984 356999999999999999999999999999999853
No 15
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=91.60 E-value=0.044 Score=61.14 Aligned_cols=68 Identities=18% Similarity=0.191 Sum_probs=54.4
Q ss_pred CCcccCCCC-CCCCeeEeccccccchhhhhhhhcCCCcccceeccCCCCCCHHHHHHHhcCChHHHHHHHH
Q 016665 4 RKMCFDCNA-KNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFK 73 (385)
Q Consensus 4 Nk~C~DCga-~nP~waSv~~GiflC~~Csg~HR~lG~hiS~VkSi~lD~W~~~~l~~m~~gGN~~a~~f~~ 73 (385)
+-.|++|++ ....|+++++.+-+|++|+++|+.++.|++..+++-|++-.+ +.....-||...+.-+.
T Consensus 630 ~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~~~~ 698 (785)
T KOG0521|consen 630 DGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHHATA 698 (785)
T ss_pred CccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchhhhh
Confidence 567999997 568999999999999999999999999999999998888776 55554445554444433
No 16
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=88.88 E-value=0.8 Score=47.80 Aligned_cols=75 Identities=24% Similarity=0.295 Sum_probs=50.8
Q ss_pred hhhhHHHHHHhccCCcCccccccCCCCCccchhHHHHhhhccCCcccccccccCCCCCCcccchhhHHHHHHhhhchHHH
Q 016665 275 IQETDEARKKFSNAKSISSSQFFGDQNNSIDMDTQVSLQKFSGSASISSADLFGHDSDNASLDLAASDLINRLSFQAQQD 354 (385)
Q Consensus 275 ~~~t~~a~~KFgnaKaISSd~yFGr~~~~a~~ea~~rL~~F~gatsISS~~yFg~~~~~~~~~~sa~d~~~~~~~~a~~D 354 (385)
.-++....+||.++-+|||.-|||.+++ .+...++.++.- +.... ||+. |. .=
T Consensus 378 d~Ea~~~L~~f~gstaISSsd~fG~~~~-----------------~~~~g~~~~~~~----~~a~~-di~~-~k----~~ 430 (454)
T KOG0706|consen 378 DLEARARLQKFSGSTAISSSDLFGEGDD-----------------DHTAGSLALRDS----FRAAQ-DIAS-FK----NS 430 (454)
T ss_pred hhHHHHHHHhccCccccchHhhcCCCCC-----------------CCCccchhhccc----ccccc-cHHH-HH----HH
Confidence 3466777999999999999999999984 334444444431 22222 5555 32 23
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 016665 355 ISSLKNIAGETGKKLSSLASSL 376 (385)
Q Consensus 355 l~~lk~~v~~~A~KLs~~a~~~ 376 (385)
+.+++.-+..+|.||.......
T Consensus 431 ~~~~a~kls~~a~~v~~~~qd~ 452 (454)
T KOG0706|consen 431 ARSVAGKLSVLASKVGSSLQDR 452 (454)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh
Confidence 3458999999999988876654
No 17
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=85.64 E-value=1.1 Score=45.92 Aligned_cols=20 Identities=50% Similarity=0.846 Sum_probs=17.6
Q ss_pred hhccCCcccccccccCCCCC
Q 016665 313 QKFSGSASISSADLFGHDSD 332 (385)
Q Consensus 313 ~~F~gatsISS~~yFg~~~~ 332 (385)
++|.|+.+|||++|||+...
T Consensus 300 kKF~naKsisS~qfFg~~~~ 319 (395)
T PLN03114 300 KKFTNAKSISSAQYFGNDNN 319 (395)
T ss_pred HHhcccccccHHhhcccccc
Confidence 56999999999999998753
No 18
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=80.94 E-value=1 Score=42.76 Aligned_cols=31 Identities=23% Similarity=0.428 Sum_probs=26.0
Q ss_pred CCCCcccCCCCCCC-CeeEeccccccchhhhh
Q 016665 2 TPRKMCFDCNAKNP-TWASVTYGIFLCIDCSA 32 (385)
Q Consensus 2 p~Nk~C~DCga~nP-~waSv~~GiflC~~Csg 32 (385)
|.-..|.-||.+.. .|.++..|.++|..|..
T Consensus 147 p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~ 178 (247)
T PRK00085 147 LDLDHCAVCGAPGDHRYFSPKEGGAVCSECGD 178 (247)
T ss_pred cchhhHhcCCCCCCceEEecccCCcccccccC
Confidence 45568999998755 78899999999999973
No 19
>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=69.42 E-value=3.4 Score=28.27 Aligned_cols=32 Identities=28% Similarity=0.731 Sum_probs=23.9
Q ss_pred ccCCCCC-CCCeeEeccccc-cchhhhhhhhcCC
Q 016665 7 CFDCNAK-NPTWASVTYGIF-LCIDCSAVHRSLG 38 (385)
Q Consensus 7 C~DCga~-nP~waSv~~Gif-lC~~Csg~HR~lG 38 (385)
|..|+.. -|.|-..+.|-. ||-.|.-.+|..|
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 8899985 699999999988 9999987777654
No 20
>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=68.84 E-value=3.5 Score=28.44 Aligned_cols=34 Identities=15% Similarity=0.316 Sum_probs=29.5
Q ss_pred CCCcccCCCCCCCCeeEeccccccchhhhhh-hhc
Q 016665 3 PRKMCFDCNAKNPTWASVTYGIFLCIDCSAV-HRS 36 (385)
Q Consensus 3 ~Nk~C~DCga~nP~waSv~~GiflC~~Csg~-HR~ 36 (385)
.+..|..|......|-..+-.++||..|... |+.
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 4678999999889999999999999999987 886
No 21
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=67.22 E-value=5 Score=29.77 Aligned_cols=38 Identities=24% Similarity=0.553 Sum_probs=31.0
Q ss_pred CCCcccCCCCC-CCCeeEecccc-ccchhhhhhhhcCCCc
Q 016665 3 PRKMCFDCNAK-NPTWASVTYGI-FLCIDCSAVHRSLGVH 40 (385)
Q Consensus 3 ~Nk~C~DCga~-nP~waSv~~Gi-flC~~Csg~HR~lG~h 40 (385)
....|..|+.. -|.|=.-+.|- +||-.|.-..+..+..
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC
Confidence 46799999975 58899989996 9999998777776553
No 22
>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=63.63 E-value=4.1 Score=38.45 Aligned_cols=32 Identities=31% Similarity=0.593 Sum_probs=25.9
Q ss_pred CCCCcccCCCCCCC-CeeEeccccccchhhhhh
Q 016665 2 TPRKMCFDCNAKNP-TWASVTYGIFLCIDCSAV 33 (385)
Q Consensus 2 p~Nk~C~DCga~nP-~waSv~~GiflC~~Csg~ 33 (385)
|.-..|..||..++ .|.++..|.++|.+|...
T Consensus 145 p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 145 LDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred cccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 44568999998655 678999999999999653
No 23
>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=7.5 Score=28.34 Aligned_cols=26 Identities=31% Similarity=0.821 Sum_probs=20.6
Q ss_pred cccCCCCCCCCeeEeccccccchhhhh
Q 016665 6 MCFDCNAKNPTWASVTYGIFLCIDCSA 32 (385)
Q Consensus 6 ~C~DCga~nP~waSv~~GiflC~~Csg 32 (385)
+|+=|+...+. .=.=+|.|||.+|-.
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHH
Confidence 58889988777 445589999999954
No 24
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=51.44 E-value=6.5 Score=27.69 Aligned_cols=26 Identities=23% Similarity=0.595 Sum_probs=20.5
Q ss_pred cccCCCCCCCCeeEeccccccchhhhh
Q 016665 6 MCFDCNAKNPTWASVTYGIFLCIDCSA 32 (385)
Q Consensus 6 ~C~DCga~nP~waSv~~GiflC~~Csg 32 (385)
+|-.||+.. .-..-.-|-++|..|..
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-B
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCCC
Confidence 699999977 55566789999999943
No 25
>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=49.56 E-value=10 Score=30.71 Aligned_cols=31 Identities=23% Similarity=0.665 Sum_probs=25.8
Q ss_pred CCCcccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 3 PRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 3 ~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
.|..|.-||.+. ....||++.|..|.++.|-
T Consensus 2 ~~~~C~VCg~~~---~g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 2 DTHFCAVCSDYA---SGYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CCCCCeecCCcC---cceEECceeehhhHHhHHH
Confidence 578899999744 4579999999999998874
No 26
>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=49.41 E-value=6.5 Score=27.03 Aligned_cols=27 Identities=15% Similarity=0.517 Sum_probs=16.7
Q ss_pred CcccCCCCC-CCCeeEeccccccchhhh
Q 016665 5 KMCFDCNAK-NPTWASVTYGIFLCIDCS 31 (385)
Q Consensus 5 k~C~DCga~-nP~waSv~~GiflC~~Cs 31 (385)
.+|.+|+.. .-+|..-+|+.-||..|.
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 479999986 568999999999999994
No 27
>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=48.03 E-value=12 Score=30.36 Aligned_cols=32 Identities=25% Similarity=0.742 Sum_probs=26.3
Q ss_pred CCCCcccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 2 TPRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 2 p~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
|..+.|.-||.+. ....||++.|..|.++.|-
T Consensus 1 ~~~~~C~VCg~~a---~g~hyGv~sC~aCk~FFRR 32 (82)
T cd07173 1 PPQKTCLICGDEA---SGCHYGALTCGSCKVFFKR 32 (82)
T ss_pred CCCCCCeecCCcC---cceEECcchhhhHHHHHHH
Confidence 4577899999754 3578999999999998875
No 28
>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=47.79 E-value=14 Score=27.68 Aligned_cols=34 Identities=29% Similarity=0.691 Sum_probs=27.4
Q ss_pred cccCCCCC-CCCeeEec-cccccchhhhhhhhcCCC
Q 016665 6 MCFDCNAK-NPTWASVT-YGIFLCIDCSAVHRSLGV 39 (385)
Q Consensus 6 ~C~DCga~-nP~waSv~-~GiflC~~Csg~HR~lG~ 39 (385)
+|..|+.. -|.|-..+ -+..||-.|.-..+..|.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~ 36 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGV 36 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCC
Confidence 59999985 48898776 788999999777777664
No 29
>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=44.70 E-value=13 Score=31.25 Aligned_cols=30 Identities=23% Similarity=0.735 Sum_probs=24.7
Q ss_pred CCcccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 4 RKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 4 Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
+..|.-||.+. ....||++.|..|.++.|-
T Consensus 4 ~~~C~VCg~~a---~g~hyGv~sC~aCk~FFRR 33 (97)
T cd07170 4 KRLCLVCGDIA---SGYHYGVASCEACKAFFKR 33 (97)
T ss_pred CCCCeecCCcC---cceEECceeehhhhHHHHH
Confidence 46799999755 3568999999999998874
No 30
>PRK12495 hypothetical protein; Provisional
Probab=44.58 E-value=9.7 Score=36.64 Aligned_cols=27 Identities=19% Similarity=0.376 Sum_probs=21.9
Q ss_pred CCCCcccCCCCCCCCeeEeccccccchhhhh
Q 016665 2 TPRKMCFDCNAKNPTWASVTYGIFLCIDCSA 32 (385)
Q Consensus 2 p~Nk~C~DCga~nP~waSv~~GiflC~~Csg 32 (385)
..++.|-+||.+-|. + -|+.+|..|..
T Consensus 40 msa~hC~~CG~PIpa---~-pG~~~Cp~CQ~ 66 (226)
T PRK12495 40 MTNAHCDECGDPIFR---H-DGQEFCPTCQQ 66 (226)
T ss_pred cchhhcccccCcccC---C-CCeeECCCCCC
Confidence 357899999999992 2 59999999963
No 31
>cd06968 NR_DBD_ROR DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RORS are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum particularly in the regulation of the maturation and survival of Purkinje cells. RORbe
Probab=44.04 E-value=14 Score=30.77 Aligned_cols=31 Identities=26% Similarity=0.646 Sum_probs=25.7
Q ss_pred CCCcccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 3 PRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 3 ~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
.+..|.-||.+. ....||++.|..|.++.|-
T Consensus 4 ~~~~C~VCg~~~---~g~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 4 EVIPCKICGDKS---SGIHYGVITCEGCKGFFRR 34 (95)
T ss_pred cccCCcccCCcC---cceEECceeehhhHHhhHH
Confidence 567899999755 4468999999999998874
No 32
>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=43.02 E-value=16 Score=30.92 Aligned_cols=31 Identities=23% Similarity=0.643 Sum_probs=25.6
Q ss_pred CCCcccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 3 PRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 3 ~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
.+..|.-|+.+. ....||+..|..|.++.|-
T Consensus 17 ~~~~C~VCg~~a---~g~hyGv~sC~aCk~FFRR 47 (101)
T cd07160 17 GNEVCSVCGDKA---SGFHYNVLSCEGCKGFFRR 47 (101)
T ss_pred CCCCCeecCCcC---cceEECcceehhhhhhhhh
Confidence 467899999754 3568999999999998874
No 33
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=42.87 E-value=12 Score=36.19 Aligned_cols=27 Identities=33% Similarity=0.755 Sum_probs=24.1
Q ss_pred CcccCCCCCC-CCeeEeccccccchhhh
Q 016665 5 KMCFDCNAKN-PTWASVTYGIFLCIDCS 31 (385)
Q Consensus 5 k~C~DCga~n-P~waSv~~GiflC~~Cs 31 (385)
..|+.||.+- |...++-.|-++|..|.
T Consensus 155 ~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 155 TSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred HHHhCcCCcCCCcceeeccCcccchhcc
Confidence 5799999975 57999999999999998
No 34
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=42.85 E-value=13 Score=28.22 Aligned_cols=39 Identities=21% Similarity=0.450 Sum_probs=27.2
Q ss_pred CCCCcccCCCCCCCCeeEeccccccchhhhhhhhcCCCccccee
Q 016665 2 TPRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVR 45 (385)
Q Consensus 2 p~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~lG~hiS~Vk 45 (385)
++-+.|.-||.+. =.--.||+.||..|-. .+-..|.|+|
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 4668899999853 3445799999999954 4445555554
No 35
>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=39.33 E-value=14 Score=28.49 Aligned_cols=32 Identities=22% Similarity=0.645 Sum_probs=21.9
Q ss_pred CCCCcccCCCCCCC--CeeEeccccccchhhhhhh
Q 016665 2 TPRKMCFDCNAKNP--TWASVTYGIFLCIDCSAVH 34 (385)
Q Consensus 2 p~Nk~C~DCga~nP--~waSv~~GiflC~~Csg~H 34 (385)
++...|.|||.+=| .|.-++ |+..|++|...|
T Consensus 29 ~s~g~C~~Cg~~Ip~~Rl~a~p-~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 29 PSLRECEDCGEPIPEARREALP-GVTRCVSCQEIL 62 (63)
T ss_pred CCCCeeccCCCcChHHHHhhcC-CcCCcHHHHhhc
Confidence 34568999998655 333333 677899997654
No 36
>cd07169 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=38.78 E-value=18 Score=29.82 Aligned_cols=32 Identities=22% Similarity=0.736 Sum_probs=26.0
Q ss_pred CCCCcccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 2 TPRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 2 p~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
.+++.|.-|+.+. ....||+..|..|.++.|-
T Consensus 4 ~~~~~C~VCg~~a---~g~hyGv~sC~aCk~FFRR 35 (90)
T cd07169 4 AEQRTCLICGDRA---TGLHYGIISCEGCKGFFKR 35 (90)
T ss_pred ccCCCCeecCCcC---cceEECcceehhhHHHHHH
Confidence 3567899999754 4568999999999998875
No 37
>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=38.77 E-value=19 Score=24.83 Aligned_cols=25 Identities=24% Similarity=0.770 Sum_probs=21.4
Q ss_pred CCcccCCCCCCCCeeEeccccccchhhh
Q 016665 4 RKMCFDCNAKNPTWASVTYGIFLCIDCS 31 (385)
Q Consensus 4 Nk~C~DCga~nP~waSv~~GiflC~~Cs 31 (385)
|..|..|++. |....=|-+.|..|-
T Consensus 8 ~~~C~~C~~~---~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 8 NEPCPVCGSR---WFYSDDGFYYCDRCG 32 (36)
T ss_pred CCcCCCCCCe---EeEccCCEEEhhhCc
Confidence 4459999998 889999999999983
No 38
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=37.25 E-value=16 Score=27.15 Aligned_cols=30 Identities=23% Similarity=0.563 Sum_probs=20.6
Q ss_pred cccCCCCCCCCeeE--eccccccchhhhhhhhc
Q 016665 6 MCFDCNAKNPTWAS--VTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 6 ~C~DCga~nP~waS--v~~GiflC~~Csg~HR~ 36 (385)
.|+=||.+-.-... +.=| +||-+|..--..
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl~~ 32 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKLSG 32 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHhcC
Confidence 48889987665543 4447 899999864433
No 39
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=35.01 E-value=23 Score=29.48 Aligned_cols=26 Identities=31% Similarity=0.691 Sum_probs=21.5
Q ss_pred CcccCCCCCCCCeeEeccccccchhhhh
Q 016665 5 KMCFDCNAKNPTWASVTYGIFLCIDCSA 32 (385)
Q Consensus 5 k~C~DCga~nP~waSv~~GiflC~~Csg 32 (385)
..|-.|+.+ +--=+..||+.|..|-.
T Consensus 36 ~~Cp~C~~~--~VkR~a~GIW~C~kCg~ 61 (89)
T COG1997 36 HVCPFCGRT--TVKRIATGIWKCRKCGA 61 (89)
T ss_pred CcCCCCCCc--ceeeeccCeEEcCCCCC
Confidence 579999988 55567899999999954
No 40
>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=34.72 E-value=17 Score=30.15 Aligned_cols=29 Identities=28% Similarity=0.613 Sum_probs=23.3
Q ss_pred CcccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 5 KMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 5 k~C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
|.|.-||.+.- ...||++.|..|.++.|-
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 56888987533 458999999999998875
No 41
>PHA00080 DksA-like zinc finger domain containing protein
Probab=33.65 E-value=21 Score=28.34 Aligned_cols=32 Identities=22% Similarity=0.593 Sum_probs=22.4
Q ss_pred CCCcccCCCCCCC--CeeEeccccccchhhhhhhh
Q 016665 3 PRKMCFDCNAKNP--TWASVTYGIFLCIDCSAVHR 35 (385)
Q Consensus 3 ~Nk~C~DCga~nP--~waSv~~GiflC~~Csg~HR 35 (385)
....|.+||..=| .|.-++ ++..|++|...+-
T Consensus 30 ~~~~C~~Cg~~Ip~~Rl~a~P-~~~~Cv~Cq~~~E 63 (72)
T PHA00080 30 SATHCEECGDPIPEARREAVP-GCRTCVSCQEILE 63 (72)
T ss_pred CCCEecCCCCcCcHHHHHhCC-CccCcHHHHHHHH
Confidence 3458999998654 555555 4556999988653
No 42
>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=32.26 E-value=22 Score=27.11 Aligned_cols=25 Identities=24% Similarity=0.687 Sum_probs=21.6
Q ss_pred CcccCCCCCCCCeeEeccccccchhhh
Q 016665 5 KMCFDCNAKNPTWASVTYGIFLCIDCS 31 (385)
Q Consensus 5 k~C~DCga~nP~waSv~~GiflC~~Cs 31 (385)
+.|..||..... ..+.-+|.|..|.
T Consensus 29 q~C~~CG~~~~~--~~~~r~~~C~~Cg 53 (69)
T PF07282_consen 29 QTCPRCGHRNKK--RRSGRVFTCPNCG 53 (69)
T ss_pred cCccCccccccc--ccccceEEcCCCC
Confidence 689999998887 7788899999994
No 43
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=31.69 E-value=17 Score=24.53 Aligned_cols=23 Identities=22% Similarity=0.541 Sum_probs=14.8
Q ss_pred cccCCCCCCCCeeEeccccccchhhh
Q 016665 6 MCFDCNAKNPTWASVTYGIFLCIDCS 31 (385)
Q Consensus 6 ~C~DCga~nP~waSv~~GiflC~~Cs 31 (385)
+|.+||+.+. . -.....-|..|.
T Consensus 2 ~C~~Cg~~~~--~-~~~~~irC~~CG 24 (32)
T PF03604_consen 2 ICGECGAEVE--L-KPGDPIRCPECG 24 (32)
T ss_dssp BESSSSSSE---B-STSSTSSBSSSS
T ss_pred CCCcCCCeeE--c-CCCCcEECCcCC
Confidence 6999998766 1 123445888883
No 44
>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=29.90 E-value=34 Score=27.87 Aligned_cols=28 Identities=18% Similarity=0.613 Sum_probs=22.2
Q ss_pred cccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 6 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 6 ~C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
+|.-||.+.- ...||++.|..|.++.|-
T Consensus 1 ~C~VCg~~~~---g~hygv~sC~aC~~FFRR 28 (87)
T cd07162 1 ICRVCGDRAT---GYHFNAMTCEGCKGFFRR 28 (87)
T ss_pred CCcccCCcCc---ceEECcceehhhHHHHHh
Confidence 4778887544 358999999999998875
No 45
>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors. HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.
Probab=29.88 E-value=21 Score=27.66 Aligned_cols=30 Identities=27% Similarity=0.527 Sum_probs=24.4
Q ss_pred ccC-CCCCCCC-eeEeccccccchhhhhhhhcC
Q 016665 7 CFD-CNAKNPT-WASVTYGIFLCIDCSAVHRSL 37 (385)
Q Consensus 7 C~D-Cga~nP~-waSv~~GiflC~~Csg~HR~l 37 (385)
+.| |+.-.|. |..-+-..+.|..| |.||++
T Consensus 21 a~DGCgEFm~~~g~eg~~~al~CaAC-gCHRnF 52 (60)
T PF04770_consen 21 AVDGCGEFMPSPGEEGTPEALKCAAC-GCHRNF 52 (60)
T ss_pred ccccccccccCCCCCCCcccceeccc-Ccchhc
Confidence 455 8888887 77677888999999 889986
No 46
>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=28.89 E-value=33 Score=28.23 Aligned_cols=30 Identities=30% Similarity=0.768 Sum_probs=24.5
Q ss_pred CCcccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 4 RKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 4 Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
.+.|.-||.+. ....||++.|..|.++.|-
T Consensus 6 ~~~C~VCg~~~---~g~hyGv~sC~aCk~FFRR 35 (90)
T cd07168 6 PKLCSICEDKA---TGLHYGIITCEGCKGFFKR 35 (90)
T ss_pred CCCCcccCCcC---cceEECceehhhhhHhhhh
Confidence 46799999754 3578999999999998874
No 47
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=28.81 E-value=35 Score=28.55 Aligned_cols=31 Identities=23% Similarity=0.546 Sum_probs=21.4
Q ss_pred CCCCcccCCCCC-----------------CCCeeEeccccccchhhhh
Q 016665 2 TPRKMCFDCNAK-----------------NPTWASVTYGIFLCIDCSA 32 (385)
Q Consensus 2 p~Nk~C~DCga~-----------------nP~waSv~~GiflC~~Csg 32 (385)
+.--.|++||.+ .-.-..=+||-.+|..|..
T Consensus 32 ~~~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~ 79 (93)
T COG2174 32 PTIPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVR 79 (93)
T ss_pred CCCCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHHH
Confidence 444589999964 1112245699999999965
No 48
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=28.77 E-value=32 Score=34.33 Aligned_cols=31 Identities=23% Similarity=0.555 Sum_probs=21.7
Q ss_pred CCCcccCCCCCCCCeeEeccccccchhhhhhh
Q 016665 3 PRKMCFDCNAKNPTWASVTYGIFLCIDCSAVH 34 (385)
Q Consensus 3 ~Nk~C~DCga~nP~waSv~~GiflC~~Csg~H 34 (385)
....|.+||..+. =....-|-.+|.+|.-|.
T Consensus 10 ~~~~Cp~Cg~~~i-v~d~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 10 EKLVCPECGSDKL-IYDYERGEIVCADCGLVI 40 (310)
T ss_pred cCCcCcCCCCCCe-eEECCCCeEeecccCCcc
Confidence 3467999997432 223467999999996644
No 49
>PF14376 Haem_bd: Haem-binding domain
Probab=28.72 E-value=27 Score=30.82 Aligned_cols=15 Identities=27% Similarity=1.023 Sum_probs=12.1
Q ss_pred CCcccCCCCCCCCee
Q 016665 4 RKMCFDCNAKNPTWA 18 (385)
Q Consensus 4 Nk~C~DCga~nP~wa 18 (385)
.+-|.||++.++.|-
T Consensus 41 ~~~CydCHSn~T~~P 55 (137)
T PF14376_consen 41 KNSCYDCHSNNTRYP 55 (137)
T ss_pred HccccccCCCCCCCc
Confidence 367999999887765
No 50
>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=27.43 E-value=37 Score=27.29 Aligned_cols=27 Identities=30% Similarity=0.715 Sum_probs=21.1
Q ss_pred ccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 7 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 7 C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
|.-||.+.- ...||++.|..|.++.|-
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 566776443 468999999999998885
No 51
>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=26.50 E-value=12 Score=25.29 Aligned_cols=30 Identities=27% Similarity=0.646 Sum_probs=16.6
Q ss_pred CcccCCCCCCCC-eeEeccccccchhhhhhh
Q 016665 5 KMCFDCNAKNPT-WASVTYGIFLCIDCSAVH 34 (385)
Q Consensus 5 k~C~DCga~nP~-waSv~~GiflC~~Csg~H 34 (385)
.+|.+||..=|. -.-+-=+..+|+.|...|
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 359999975321 111122678999998765
No 52
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=26.21 E-value=43 Score=23.74 Aligned_cols=24 Identities=25% Similarity=0.517 Sum_probs=18.0
Q ss_pred cccCCCCCCCCeeEeccccccchh
Q 016665 6 MCFDCNAKNPTWASVTYGIFLCID 29 (385)
Q Consensus 6 ~C~DCga~nP~waSv~~GiflC~~ 29 (385)
+|-+|+..+.-|+++.-+-..|..
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c~~ 24 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGCGR 24 (50)
T ss_pred CcccCCCcCCeEEecCCCCcccCC
Confidence 599999888788777766666643
No 53
>cd06970 NR_DBD_PNR DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of the nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hing
Probab=26.17 E-value=28 Score=28.87 Aligned_cols=32 Identities=28% Similarity=0.754 Sum_probs=25.5
Q ss_pred CCCCcccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 2 TPRKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 2 p~Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
+....|.-||.+.- ...||++.|..|.++.|-
T Consensus 4 ~p~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (92)
T cd06970 4 NPGLLCRVCGDTSS---GKHYGIYACNGCSGFFKR 35 (92)
T ss_pred CCCCCCeecCCcCc---ccEECccEEeeeeeEeee
Confidence 45667999997644 458999999999998864
No 54
>cd07161 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers. DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs h
Probab=26.11 E-value=43 Score=27.67 Aligned_cols=29 Identities=21% Similarity=0.708 Sum_probs=23.1
Q ss_pred CcccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 5 KMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 5 k~C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
..|.-||.+.- ...||++.|..|.++.|-
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 35888886543 468999999999998874
No 55
>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=25.35 E-value=44 Score=26.72 Aligned_cols=30 Identities=23% Similarity=0.799 Sum_probs=24.1
Q ss_pred CCcccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 4 RKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 4 Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
.+.|.-||.+. ....||++.|..|.++.|-
T Consensus 2 ~~~C~VCg~~a---~g~hyGv~sC~aC~~FFRR 31 (78)
T cd07172 2 QKICLVCSDEA---SGCHYGVLTCGSCKVFFKR 31 (78)
T ss_pred CCCCeecCCcC---cceEECceeehhhHHhHHH
Confidence 45788898754 3468999999999998874
No 56
>cd06965 NR_DBD_Ppar DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive gene
Probab=25.33 E-value=32 Score=27.89 Aligned_cols=27 Identities=30% Similarity=0.768 Sum_probs=21.5
Q ss_pred ccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 7 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 7 C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
|.-||.+.- ...||++.|..|.+++|-
T Consensus 2 C~VCg~~~~---g~hyGv~sC~aCk~FFRR 28 (84)
T cd06965 2 CRVCGDKAS---GFHYGVHACEGCKGFFRR 28 (84)
T ss_pred CcccCccCc---ceEEChhhhhhhhhheee
Confidence 777886443 457999999999998875
No 57
>cd06956 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor, or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear rec
Probab=25.25 E-value=47 Score=26.39 Aligned_cols=29 Identities=21% Similarity=0.750 Sum_probs=23.1
Q ss_pred CcccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 5 KMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 5 k~C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
+.|.-||.+.- ...||++.|..|.++.|-
T Consensus 1 ~~C~VC~~~~~---g~hygv~sC~aC~~FFRR 29 (77)
T cd06956 1 HICAICGDRAS---GKHYGVYSCEGCKGFFKR 29 (77)
T ss_pred CCCcccCCcCc---ceEECceeehhHHHHHHH
Confidence 35888886543 468999999999998875
No 58
>PRK11019 hypothetical protein; Provisional
Probab=25.17 E-value=27 Score=28.93 Aligned_cols=36 Identities=19% Similarity=0.498 Sum_probs=26.1
Q ss_pred CCcccCCCCCCC--CeeEeccccccchhhhhhhhcCCCc
Q 016665 4 RKMCFDCNAKNP--TWASVTYGIFLCIDCSAVHRSLGVH 40 (385)
Q Consensus 4 Nk~C~DCga~nP--~waSv~~GiflC~~Csg~HR~lG~h 40 (385)
-..|.|||.+=| .|.-++ ++-.|++|...+-..+.|
T Consensus 36 yg~C~~CG~~Ip~~Rl~A~P-~a~~Cv~Cq~~~E~~~k~ 73 (88)
T PRK11019 36 LTECEECGEPIPEARRKAIP-GVRLCVACQQEKDLQQAA 73 (88)
T ss_pred CCeeCcCCCcCcHHHHhhcC-CccccHHHHHHHHHHHhH
Confidence 468999999755 455555 677999999877654444
No 59
>PTZ00074 60S ribosomal protein L34; Provisional
Probab=24.96 E-value=39 Score=30.22 Aligned_cols=27 Identities=37% Similarity=0.678 Sum_probs=19.0
Q ss_pred cccCCCCCC-------C----------CeeEeccccccchhhhh
Q 016665 6 MCFDCNAKN-------P----------TWASVTYGIFLCIDCSA 32 (385)
Q Consensus 6 ~C~DCga~n-------P----------~waSv~~GiflC~~Csg 32 (385)
.|.|||.+= | .-++=.||-.+|..|..
T Consensus 43 kC~~cg~~L~GI~~~Rp~e~~rlsK~~KtvsRaYGG~lC~~CVr 86 (135)
T PTZ00074 43 KCGDCGKVLAGIKALRPTEYKQLSRRERTVSRAYGGVLCHKCVR 86 (135)
T ss_pred CCCCCCCccCCccCCchHHHHHccccCCCccCCCccchhHHHHH
Confidence 699999651 1 22355699999999944
No 60
>PF13462 Thioredoxin_4: Thioredoxin; PDB: 3FEU_A 3HZ8_A 3DVW_A 3A3T_E 3GMF_A 1Z6M_A 3GYK_C 3BCK_A 3BD2_A 3BCI_A ....
Probab=24.16 E-value=42 Score=28.79 Aligned_cols=28 Identities=18% Similarity=0.391 Sum_probs=22.8
Q ss_pred CCCCCCeeEeccccccchhhhhhhhcCC
Q 016665 11 NAKNPTWASVTYGIFLCIDCSAVHRSLG 38 (385)
Q Consensus 11 ga~nP~waSv~~GiflC~~Csg~HR~lG 38 (385)
|.++..+.-+=|.-|.|.-|...|..++
T Consensus 8 G~~~a~~~v~~f~d~~Cp~C~~~~~~~~ 35 (162)
T PF13462_consen 8 GNPDAPITVTEFFDFQCPHCAKFHEELE 35 (162)
T ss_dssp S-TTTSEEEEEEE-TTSHHHHHHHHHHH
T ss_pred cCCCCCeEEEEEECCCCHhHHHHHHHHh
Confidence 5678888899999999999999998764
No 61
>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=24.14 E-value=46 Score=26.03 Aligned_cols=27 Identities=30% Similarity=0.755 Sum_probs=20.5
Q ss_pred ccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 7 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 7 C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
|.-||.+.- ...||++.|..|.++.|-
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 555665433 368999999999998875
No 62
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=23.46 E-value=27 Score=27.81 Aligned_cols=32 Identities=25% Similarity=0.631 Sum_probs=21.0
Q ss_pred CcccCCCCCCCCee-Eeccccccchhhhhhhhc
Q 016665 5 KMCFDCNAKNPTWA-SVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 5 k~C~DCga~nP~wa-Sv~~GiflC~~Csg~HR~ 36 (385)
..|.|||.+=|.=- -.-=|+..|+.|...+-.
T Consensus 35 ~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~E~ 67 (73)
T PRK13715 35 YLCEACGNPIPEARRKIFPGVTLCVECQAYQER 67 (73)
T ss_pred ccHhhcCCcCCHHHHhcCCCcCCCHHHHHHHHH
Confidence 57999998755221 112277899999876543
No 63
>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=22.94 E-value=45 Score=27.34 Aligned_cols=30 Identities=27% Similarity=0.680 Sum_probs=24.1
Q ss_pred CCcccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 4 RKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 4 Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
+..|.-||.+.- ...||++.|..|.++.|-
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 457999997554 457999999999998775
No 64
>cd07163 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=22.86 E-value=32 Score=28.39 Aligned_cols=30 Identities=27% Similarity=0.681 Sum_probs=24.5
Q ss_pred CCcccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 4 RKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 4 Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
|..|.-||.+.- ...||+..|..|.++.|-
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 678999997543 468999999999998774
No 65
>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=22.65 E-value=48 Score=25.96 Aligned_cols=27 Identities=19% Similarity=0.581 Sum_probs=20.4
Q ss_pred ccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 7 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 7 C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
|.-|+.+.- ...||++.|..|.++.|-
T Consensus 1 C~VC~~~~~---g~hygv~sC~aC~~FFRR 27 (72)
T cd07156 1 CGVCGDRAT---GYHFNAMTCEGCKGFFRR 27 (72)
T ss_pred CCccCccCc---ccEECcceehhhhhhhch
Confidence 555665443 358999999999998874
No 66
>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=22.46 E-value=36 Score=29.05 Aligned_cols=30 Identities=17% Similarity=0.584 Sum_probs=24.2
Q ss_pred CCcccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 4 RKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 4 Nk~C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
.+.|.-||.+.- ...||++.|..|.++.|-
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 367999997543 468999999999998875
No 67
>cd07157 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers. The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=22.22 E-value=28 Score=28.35 Aligned_cols=28 Identities=21% Similarity=0.564 Sum_probs=22.6
Q ss_pred cccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 6 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 6 ~C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
.|.-||.+. ....||++.|..|.++.|-
T Consensus 2 ~C~VCg~~a---~g~hyGv~sC~aCk~FFRR 29 (86)
T cd07157 2 TCQVCGEPA---AGFHHGAYVCEACKKFFMR 29 (86)
T ss_pred CCcccCCcC---cccEECcceeeEeeeEEec
Confidence 488888654 4569999999999998775
No 68
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=21.89 E-value=34 Score=23.16 Aligned_cols=29 Identities=21% Similarity=0.367 Sum_probs=22.6
Q ss_pred CCcccCCCCCCCCeeEeccccccchhhhhhh
Q 016665 4 RKMCFDCNAKNPTWASVTYGIFLCIDCSAVH 34 (385)
Q Consensus 4 Nk~C~DCga~nP~waSv~~GiflC~~Csg~H 34 (385)
.++|-.|+...--| -.-+..+|..|..++
T Consensus 3 ~~~C~~C~~~~i~~--~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVN--KEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEE--ecCCeEEcccCCcEe
Confidence 57899999877555 578899999996654
No 69
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=21.67 E-value=37 Score=26.28 Aligned_cols=27 Identities=30% Similarity=0.615 Sum_probs=18.5
Q ss_pred cccCCCCCCCCeeEeccccccchhhhhhhhcC
Q 016665 6 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRSL 37 (385)
Q Consensus 6 ~C~DCga~nP~waSv~~GiflC~~Csg~HR~l 37 (385)
+|.|||+.|.- -.--++-|.+| -||.|
T Consensus 22 iCgdC~~en~l---k~~D~irCReC--G~RIl 48 (62)
T KOG3507|consen 22 ICGDCGQENTL---KRGDVIRCREC--GYRIL 48 (62)
T ss_pred Eeccccccccc---cCCCcEehhhc--chHHH
Confidence 79999998742 12346789999 35554
No 70
>PF13119 DUF3973: Domain of unknown function (DUF3973)
Probab=20.98 E-value=34 Score=24.34 Aligned_cols=14 Identities=43% Similarity=1.210 Sum_probs=11.1
Q ss_pred ccchhhhhhhhcCC
Q 016665 25 FLCIDCSAVHRSLG 38 (385)
Q Consensus 25 flC~~Csg~HR~lG 38 (385)
|-|+.||.+|-.-+
T Consensus 2 yYCi~Cs~~h~e~~ 15 (41)
T PF13119_consen 2 YYCINCSEIHHEKG 15 (41)
T ss_pred EEEEEhHHhHHhhc
Confidence 57999999997543
No 71
>cd07164 NR_DBD_PNR_like_1 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-t
Probab=20.74 E-value=57 Score=25.95 Aligned_cols=27 Identities=22% Similarity=0.650 Sum_probs=20.7
Q ss_pred ccCCCCCCCCeeEeccccccchhhhhhhhc
Q 016665 7 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 36 (385)
Q Consensus 7 C~DCga~nP~waSv~~GiflC~~Csg~HR~ 36 (385)
|.-||.+. ....||+..|..|.++.|-
T Consensus 1 C~VCg~~~---~g~hyG~~~C~~C~~FFRR 27 (78)
T cd07164 1 CRVCGDRA---SGKHYGVPSCDGCRGFFKR 27 (78)
T ss_pred CcccCccC---cceEECcchhhhhhhhhhh
Confidence 55677544 3458999999999998874
Done!