Query 015634
Match_columns 403
No_of_seqs 249 out of 1183
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 08:08:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015634.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015634hhsearch_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 6E-100 1E-104 748.1 30.4 386 1-395 1-394 (395)
2 KOG0706 Predicted GTPase-activ 100.0 1E-87 2.2E-92 675.5 26.3 393 1-403 2-454 (454)
3 KOG0704 ADP-ribosylation facto 100.0 5.2E-38 1.1E-42 308.3 8.5 116 8-123 5-121 (386)
4 COG5347 GTPase-activating prot 100.0 2.8E-36 6.1E-41 298.9 10.0 118 8-125 6-124 (319)
5 KOG0703 Predicted GTPase-activ 100.0 4.3E-34 9.4E-39 277.4 4.5 103 7-109 10-122 (287)
6 PF01412 ArfGap: Putative GTPa 100.0 1.9E-33 4.2E-38 242.2 5.7 83 11-93 2-84 (116)
7 smart00105 ArfGap Putative GTP 100.0 1.1E-31 2.4E-36 230.0 7.9 97 20-116 1-102 (112)
8 PLN03119 putative ADP-ribosyla 99.9 2.6E-28 5.6E-33 252.3 7.5 90 1-93 1-91 (648)
9 PLN03131 hypothetical protein; 99.9 4.5E-27 9.8E-32 244.8 11.2 90 1-93 1-91 (705)
10 KOG0705 GTPase-activating prot 99.9 4.9E-22 1.1E-26 205.6 6.4 97 12-108 503-611 (749)
11 KOG0521 Putative GTPase activa 99.8 5.3E-20 1.1E-24 201.3 2.3 97 12-108 416-526 (785)
12 KOG0818 GTPase-activating prot 99.7 8.5E-18 1.8E-22 172.1 0.6 93 17-109 3-115 (669)
13 KOG1117 Rho- and Arf-GTPase ac 99.6 8.5E-16 1.8E-20 164.9 3.0 98 11-108 287-398 (1186)
14 KOG0702 Predicted GTPase-activ 99.1 4.2E-11 9.1E-16 123.5 5.0 84 8-92 11-95 (524)
15 KOG0521 Putative GTPase activa 93.1 0.025 5.3E-07 63.5 -0.2 73 17-91 625-698 (785)
16 KOG0706 Predicted GTPase-activ 88.0 1 2.2E-05 47.3 6.0 76 293-395 378-453 (454)
17 PLN03114 ADP-ribosylation fact 84.2 1.3 2.9E-05 45.5 4.5 20 331-350 300-319 (395)
18 PRK00085 recO DNA repair prote 82.6 0.75 1.6E-05 44.0 1.9 35 18-52 145-180 (247)
19 TIGR00613 reco DNA repair prot 72.2 2.5 5.3E-05 40.3 2.1 35 17-51 142-177 (241)
20 PF00320 GATA: GATA zinc finge 70.9 2.4 5.2E-05 29.3 1.2 32 25-56 1-34 (36)
21 smart00401 ZnF_GATA zinc finge 67.5 4.2 9.2E-05 30.3 2.1 38 21-58 2-41 (52)
22 PRK12495 hypothetical protein; 65.3 5 0.00011 38.8 2.6 29 19-51 39-67 (226)
23 PF00643 zf-B_box: B-box zinc 64.2 4.9 0.00011 27.9 1.8 34 21-54 2-36 (42)
24 PRK11019 hypothetical protein; 60.7 4.9 0.00011 33.5 1.4 37 21-58 35-73 (88)
25 PF08271 TF_Zn_Ribbon: TFIIB z 50.8 6.8 0.00015 27.8 0.6 27 24-51 2-28 (43)
26 PF10764 Gin: Inhibitor of sig 50.1 9 0.00019 28.1 1.2 27 24-51 1-27 (46)
27 COG1381 RecO Recombinational D 50.1 8.8 0.00019 37.4 1.5 32 18-49 150-182 (251)
28 COG1997 RPL43A Ribosomal prote 48.9 19 0.00041 30.1 3.0 40 11-52 24-63 (89)
29 TIGR02419 C4_traR_proteo phage 47.5 9.6 0.00021 29.6 1.1 34 18-52 27-62 (63)
30 cd00202 ZnF_GATA Zinc finger D 46.5 13 0.00028 28.0 1.6 34 24-57 1-36 (54)
31 PF01286 XPA_N: XPA protein N- 44.5 7.4 0.00016 26.9 -0.0 27 23-49 4-31 (34)
32 cd07171 NR_DBD_ER DNA-binding 40.8 16 0.00035 29.7 1.5 31 21-54 2-32 (82)
33 PF11781 RRN7: RNA polymerase 39.7 19 0.00041 25.0 1.4 28 20-50 6-33 (36)
34 COG2174 RPL34A Ribosomal prote 38.9 18 0.00039 30.4 1.5 34 17-50 29-79 (93)
35 cd06968 NR_DBD_ROR DNA-binding 38.5 18 0.00039 30.4 1.4 32 20-54 3-34 (95)
36 PF14471 DUF4428: Domain of un 37.2 15 0.00032 27.4 0.7 30 24-54 1-32 (51)
37 cd07170 NR_DBD_ERR DNA-binding 36.1 19 0.00042 30.4 1.2 30 22-54 4-33 (97)
38 cd07173 NR_DBD_AR DNA-binding 35.2 23 0.0005 28.9 1.6 32 20-54 1-32 (82)
39 PHA00080 DksA-like zinc finger 34.7 19 0.00042 28.7 1.0 33 19-52 28-62 (72)
40 PF07282 OrfB_Zn_ribbon: Putat 33.1 21 0.00045 27.4 0.9 28 21-50 27-54 (69)
41 cd07160 NR_DBD_LXR DNA-binding 32.6 27 0.00059 29.7 1.6 31 21-54 17-47 (101)
42 cd07169 NR_DBD_GCNF_like DNA-b 31.4 26 0.00056 29.1 1.3 32 20-54 4-35 (90)
43 cd06966 NR_DBD_CAR DNA-binding 28.9 25 0.00054 29.4 0.8 29 23-54 1-29 (94)
44 PTZ00255 60S ribosomal protein 28.7 53 0.0011 27.6 2.6 39 11-51 25-63 (90)
45 PRK00423 tfb transcription ini 28.0 34 0.00073 34.4 1.7 33 20-53 9-41 (310)
46 PF01258 zf-dskA_traR: Prokary 27.6 12 0.00026 25.5 -1.1 29 24-52 5-34 (36)
47 TIGR02890 spore_yteA sporulati 26.2 55 0.0012 30.0 2.6 42 10-53 75-118 (159)
48 PF14803 Nudix_N_2: Nudix N-te 25.1 25 0.00053 24.2 0.1 29 23-52 1-32 (34)
49 PRK13715 conjugal transfer pro 25.0 24 0.00053 28.3 0.0 33 22-54 34-67 (73)
50 PF14376 Haem_bd: Haem-binding 24.9 35 0.00077 30.3 1.0 15 22-36 41-55 (137)
51 cd07162 NR_DBD_PXR DNA-binding 23.4 46 0.001 27.3 1.4 28 24-54 1-28 (87)
52 PF13462 Thioredoxin_4: Thiore 23.4 37 0.0008 29.4 0.9 28 29-56 8-35 (162)
53 COG0675 Transposase and inacti 23.4 32 0.00069 33.3 0.5 24 21-51 308-331 (364)
54 cd07163 NR_DBD_TLX DNA-binding 23.3 36 0.00078 28.3 0.7 31 21-54 5-35 (92)
55 PF06689 zf-C4_ClpX: ClpX C4-t 23.2 51 0.0011 23.4 1.4 29 23-51 2-33 (41)
56 PHA02942 putative transposase; 23.2 36 0.00078 35.4 0.9 28 22-52 325-352 (383)
57 PTZ00074 60S ribosomal protein 23.1 50 0.0011 29.8 1.6 34 17-50 36-86 (135)
58 PF08792 A2L_zn_ribbon: A2L zi 22.9 33 0.0007 23.4 0.3 29 22-52 3-31 (33)
59 cd07166 NR_DBD_REV_ERB DNA-bin 22.8 43 0.00093 27.7 1.1 30 22-54 3-32 (89)
60 COG5145 RAD14 DNA excision rep 22.7 26 0.00056 34.2 -0.3 33 19-52 113-147 (292)
61 cd07161 NR_DBD_EcR DNA-binding 22.6 48 0.001 27.5 1.4 29 23-54 2-30 (91)
62 smart00782 PhnA_Zn_Ribbon PhnA 22.2 61 0.0013 23.9 1.7 30 21-50 6-44 (47)
63 cd06965 NR_DBD_Ppar DNA-bindin 22.2 44 0.00095 27.3 1.0 27 25-54 2-28 (84)
64 cd07165 NR_DBD_DmE78_like DNA- 22.1 46 0.001 26.9 1.1 27 25-54 1-27 (81)
65 KOG3362 Predicted BBOX Zn-fing 21.8 36 0.00078 31.0 0.5 34 19-53 115-149 (156)
66 cd03031 GRX_GRX_like Glutaredo 21.6 57 0.0012 29.5 1.7 36 11-55 88-123 (147)
67 smart00290 ZnF_UBP Ubiquitin C 21.5 58 0.0013 23.2 1.5 22 24-45 1-22 (50)
68 PF13119 DUF3973: Domain of un 21.0 31 0.00068 24.7 -0.1 14 43-56 2-15 (41)
69 PF12760 Zn_Tnp_IS1595: Transp 21.0 1E+02 0.0023 22.0 2.7 38 10-49 7-44 (46)
70 cd06955 NR_DBD_VDR DNA-binding 20.9 44 0.00096 28.7 0.8 30 22-54 6-35 (107)
71 cd07172 NR_DBD_GR_PR DNA-bindi 20.8 54 0.0012 26.4 1.3 29 23-54 3-31 (78)
72 PRK10778 dksA RNA polymerase-b 20.8 1.1E+02 0.0023 27.9 3.4 38 18-55 107-145 (151)
73 cd07168 NR_DBD_DHR4_like DNA-b 20.8 63 0.0014 26.8 1.7 31 21-54 5-35 (90)
74 PTZ00218 40S ribosomal protein 20.8 49 0.0011 25.3 0.9 40 19-63 13-52 (54)
75 cd07157 2DBD_NR_DBD1 The first 20.7 37 0.00079 27.9 0.3 28 24-54 2-29 (86)
76 cd07158 NR_DBD_Ppar_like The D 20.5 56 0.0012 25.7 1.3 27 25-54 1-27 (73)
77 cd06956 NR_DBD_RXR DNA-binding 20.3 59 0.0013 26.0 1.4 28 24-54 2-29 (77)
No 1
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=100.00 E-value=6.1e-100 Score=748.08 Aligned_cols=386 Identities=70% Similarity=1.027 Sum_probs=343.8
Q ss_pred CCCcchhHHHHHHHHHHcCCCCCCccCCCCCCCCceeeccccccchhhhhhhccCCCcccceeecCCCCCCHHHHHHHhc
Q 015634 1 MASDNLTDKNLVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVY 80 (403)
Q Consensus 1 m~~~~~~~~~~i~~~L~~~p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~LG~hiS~VkSi~lD~W~~~ql~~m~~ 80 (403)
|+.+.++|+.+||++|+..|+|++||||++++|+|+|++||||||++|+|+||.||+|||+|||++||.|+++||++|+.
T Consensus 1 m~~e~~~d~~~vfrkL~~kPgNk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~Ws~eqL~~Mk~ 80 (395)
T PLN03114 1 MASENLNDKISVFKKLKAKSDNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSSEQLKMMIY 80 (395)
T ss_pred CcchhhccHHHHHHHHHhCcCCCcCccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCCCCHHHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcHHHHHHHHhcCCCCCCchhhhcccHHHHHHHHHHHHHHHHHHhhcc-CCCCCCCCCCCCCCCCCCCCCCCCCCCCC-
Q 015634 81 GGNNRAQVFFKQHGWTDGGKIEAKYTSRAAELYKQILAKEVAKNMAEEA-GLPSSPVASQPAQAANALPDVKIQDAPKE- 158 (403)
Q Consensus 81 gGN~~a~~~~~~~~~~~~~~i~~KY~~~~a~~Yr~~l~~~v~k~~~~~~-~~~~~~~~~~~~~~~dff~~~~~~~~p~~- 158 (403)
|||.++++||++||+.....++.||++++|.+||++|+++|++.++++. .+|+.++++ ...+|+|++.+..+.|..
T Consensus 81 GGN~rA~~fF~qhG~~~~~~~~~KY~S~aA~~Yre~L~keVa~~~a~~~~~~p~~~~~~--~~~~~~~~~~~~~e~~~~~ 158 (395)
T PLN03114 81 GGNNRAQVFFKQYGWSDGGKTEAKYTSRAADLYKQILAKEVAKSKAEEELDLPPSPPDS--TQVPNGLSSIKTSEALKES 158 (395)
T ss_pred hcCHHHHHHHHHcCCCCCCCcccccCCHHHHHHHHHHHHHHHHhhhccccCCCCCCCCc--cccccCccccccccccccc
Confidence 9999999999999998767899999999999999999999999998765 445555543 237899999888876643
Q ss_pred CcCCCCCCCC-CCCCCCcccccccccccCCCccccCCCCCCccccccCCCCCccccCCCCCCCCCCCCCCCCCC-CCCCC
Q 015634 159 NYQGRQETQD-APGSPKVSRTVLTSTVKKPLGAKKSGKTGGLGARKLTSKPSESLYEQKPEEPSVPISSSTSNT-SSVSL 236 (403)
Q Consensus 159 ~~~~~~~~~~-~~~~p~~~~~~~s~~~kk~~~aKk~~K~~~LgAkKv~~~~~e~~~d~~~ee~~~~~~~~~~~~-~~~~~ 236 (403)
+++...+.+. +..+|+++ ++.|||+|+||.||+|||||+|++++..|.||||+||| .++.+++++.. +...+
T Consensus 159 ~~~~~~~~~~~~~~s~~~~-----~~~kk~~gak~~gktgglg~~klttk~~~~ly~qkp~e-~~~~~~~~~~~~~~~~~ 232 (395)
T PLN03114 159 NTLKQQEKPDVVPVSPRIS-----RSVKKPLGAKKTGKTGGLGARKLTTKSSGTLYDQKPEE-SVIIQATSPVSAKSARS 232 (395)
T ss_pred CCcccccCCcccCCCCCCc-----cccccccccccccccCCccccccccCCchhhhhcCccc-cCCCCCCCccccccCCC
Confidence 2334433332 23355443 56899999999999999999999999999999999999 56555555443 44556
Q ss_pred CcccchhchhhhcccccCCCCCCcccccCCCCCCccc-ccCCCCCC-CCCCCC--CcccchhhhHHHHHHhccCCcCccc
Q 015634 237 PFASRFEYVDNVQSSELSSGGPQVLSHVAPPKSSSFF-ADYGMDNG-FQKKSG--SSKVQIQETDEARKKFSNAKSISSS 312 (403)
Q Consensus 237 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~gm~~~-~~~~~~--~~~~~~~~t~~a~~KFgnaKaISSd 312 (403)
+..+||.|.|++|. +...++.+..+||+||+++.|| ..|||+.+ +++++. +.+.+++++++||+||+|||+||||
T Consensus 233 ~~~srf~y~d~~~~-~~~~~~~~~~~hvapp~ss~ff~~e~g~~~~~~~k~~~~~~~k~q~~e~~~a~kKF~naKsisS~ 311 (395)
T PLN03114 233 SFSSRFDYADNVQN-REDYMSPQVVSHVAPPKSSGFFEEELEMNGGRFQKKPITSSSKLQIQETDEARKKFTNAKSISSA 311 (395)
T ss_pred Ccchhhhhcccccc-ccccCCcccccccCCCccchhhHHhhcCCcccccCCCCCccccccccchHHHHHHhcccccccHH
Confidence 77899999999998 6667788999999999999999 67999998 888876 6778999999999999999999999
Q ss_pred cccCCCCCccchhHHHHhhhccCCcccccccccCCCCCCcccccchHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 015634 313 QFFGDQNNSIDMDTQVSLQKFSGSASISSADLFGHDSDNASLDLAASDLINRLSFQAQQDISSLKNIAGETGKKLSSLAS 392 (403)
Q Consensus 313 ~yFG~~~~~a~~ea~~rL~~F~gatsISS~~yFg~~~~~~~~~~sa~d~~~~~~~~a~~Dl~~lk~~v~~~A~KLs~~a~ 392 (403)
||||+++..+++|++.||++|+|+++|||+||||+++++.+++++|.||++||++||.+||+.||+++++++.||++||+
T Consensus 312 qfFg~~~~~~d~~~~~~l~kf~gs~~ISsad~fg~~~~d~~id~ta~dli~r~s~qa~qd~sslkn~aget~~kl~s~as 391 (395)
T PLN03114 312 QYFGNDNNSADLEAKSSLKKFSGSSAISSADLFGDSDGDFTLDLTAGDLLNRLSLQAQQDISSLKNMAEETKKKLGSVAS 391 (395)
T ss_pred hhccccccccchhhHHHHHhhccccccchHHhcCCCCccccccccHHHHHHHhhhhhHhHHHHHHHHHHHHHHHHHHHHH
Confidence 99999998889999999999999999999999999988889999999999999999999999999999999999999999
Q ss_pred HHH
Q 015634 393 SLI 395 (403)
Q Consensus 393 ~~~ 395 (403)
+++
T Consensus 392 ~~~ 394 (395)
T PLN03114 392 SLW 394 (395)
T ss_pred hhc
Confidence 985
No 2
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=1e-87 Score=675.48 Aligned_cols=393 Identities=48% Similarity=0.677 Sum_probs=298.5
Q ss_pred CCCcchhHHHHHHHHHHcCCCCCCccCCCCCCCCceeeccccccchhhhhhhccCCCcccceeecCCCCCCHHHHHHHhc
Q 015634 1 MASDNLTDKNLVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVY 80 (403)
Q Consensus 1 m~~~~~~~~~~i~~~L~~~p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~LG~hiS~VkSi~lD~W~~~ql~~m~~ 80 (403)
|+.++..+.+.+|++|+..++||+|||||++||+|+||+||||||++|+++||+||||||||||++||.|++.|||+|++
T Consensus 2 ~~~~~k~d~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~ 81 (454)
T KOG0706|consen 2 MATPNKQDIQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQV 81 (454)
T ss_pred CCccchhhHHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhh
Confidence 77889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcHHHHHHHHhcCCCCCCchhhhcccHHHHHHHHHHHHHHHHHHhhcc---CCCC-CCCCCCCCCCCCCCCCCCCCCCC
Q 015634 81 GGNNRAQVFFKQHGWTDGGKIEAKYTSRAAELYKQILAKEVAKNMAEEA---GLPS-SPVASQPAQAANALPDVKIQDAP 156 (403)
Q Consensus 81 gGN~~a~~~~~~~~~~~~~~i~~KY~~~~a~~Yr~~l~~~v~k~~~~~~---~~~~-~~~~~~~~~~~dff~~~~~~~~p 156 (403)
|||.+|+.||++|||.. .++++||++|++++|+++|+.+|.+.+.+++ .++. .++..++..+.|||+.+....+.
T Consensus 82 GGN~nA~~FFkqhg~~t-~d~~aKY~SraA~~Yr~kl~~lv~kam~~~~~~l~l~~~~~~~~~~~~~~dffs~~~k~~~~ 160 (454)
T KOG0706|consen 82 GGNANARVFFKQHGCVT-LDANAKYNSRAAKLYREKLKKLVQKAMAEHGTSLLLDSAVSSGSPESEDSDFFSESDKESSK 160 (454)
T ss_pred cCchhHHHHHHHcCCcc-hhhhhhhccHHHHHHHHHHHHHHHHHHHhcCccccccCCCCCCCCccccccchhhccccccc
Confidence 99999999999999987 5999999999999999999999999999886 2333 23333556678999887654311
Q ss_pred CCCcCCCCCCCCCCCCCCcccccccccccCCCccccCCCCCC--ccccccCCCCCccccCCCCCCCCCCCCCCCCCCCC-
Q 015634 157 KENYQGRQETQDAPGSPKVSRTVLTSTVKKPLGAKKSGKTGG--LGARKLTSKPSESLYEQKPEEPSVPISSSTSNTSS- 233 (403)
Q Consensus 157 ~~~~~~~~~~~~~~~~p~~~~~~~s~~~kk~~~aKk~~K~~~--LgAkKv~~~~~e~~~d~~~ee~~~~~~~~~~~~~~- 233 (403)
........ ....+|+++.+..+...++|.++|++|++++ |||+||.++.+..++.+..+++.....+.++....
T Consensus 161 ~~~s~~~l---~~~~s~~~S~~v~sg~~k~p~~~k~~g~~k~~~lgarkv~t~s~~~~~~~~~~~~~~~i~a~s~~~~s~ 237 (454)
T KOG0706|consen 161 HEPSTDAL---KSLSSPSASNTVVSGKKKPPVTKKGLGAKKGVTLGARKVNTKSFKSIESQAQEAEKNKIKAASPKPSSE 237 (454)
T ss_pred cCCccccc---ccccCCccccccccccccCCccccccccccccccCceecccccccchhhccchhhhccccccCCCcchh
Confidence 00000000 1122444455545556677777777884444 99999999877778887776654333322222111
Q ss_pred CCCCcccchhc---hhhhc----------------ccccCCCCCCccccc-----------CCCCCCcccccCCCCCC--
Q 015634 234 VSLPFASRFEY---VDNVQ----------------SSELSSGGPQVLSHV-----------APPKSSSFFADYGMDNG-- 281 (403)
Q Consensus 234 ~~~~~~~~~~~---~~~~~----------------~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~gm~~~-- 281 (403)
.....+.++.| .++.+ ..+|| +.|+...|+ ++|+..++|..++|...
T Consensus 238 ~~~~~s~~~~~~e~~dd~~~~E~k~~d~~k~~~~~rlgmg-~~~s~~~hs~~~~~~~i~~~t~~~~k~~~~~~~~~~~~~ 316 (454)
T KOG0706|consen 238 ESSARSSRLARQELQDDRKKEEAKAKDGKKASSSERLGMG-GYRSVMSHSVLGGMQVIEQVTPPKAKPSFLELDMFSDTT 316 (454)
T ss_pred hhcccchhhhhhHHHHHHHhhhhhhcCcccccchhhhccc-cccchhhhcccCCceeeecccCccccccccccccccchh
Confidence 01111223333 22211 13455 334544444 45655555444443221
Q ss_pred -----------CCCCCC----------CcccchhhhHHHHHHhccCCcCccccccCCCCCccchhHHHHhhhccCCcccc
Q 015634 282 -----------FQKKSG----------SSKVQIQETDEARKKFSNAKSISSSQFFGDQNNSIDMDTQVSLQKFSGSASIS 340 (403)
Q Consensus 282 -----------~~~~~~----------~~~~~~~~t~~a~~KFgnaKaISSd~yFG~~~~~a~~ea~~rL~~F~gatsIS 340 (403)
+.+... ..+.++++|++||+||||||+|||||||||+. ++++|+|+||++|+|+++||
T Consensus 317 ~~~~s~~~~~~~~~~~ss~ss~~a~~~~~~~~v~~td~~rkkF~naKaISSdqyFG~~~-~ad~Ea~~~L~~f~gstaIS 395 (454)
T KOG0706|consen 317 KQSSSNYKDAPFGKGSSSSSSKDAKRAKESRPVEETDEARKKFGNAKAISSDQYFGRGS-EADLEARARLQKFSGSTAIS 395 (454)
T ss_pred ccccCCcccCccccCcccccchhhhccccccccccccHHHHhhccccccchhhhcCCcc-hhhhHHHHHHHhccCccccc
Confidence 111111 12246788999999999999999999999998 67999999999999999999
Q ss_pred cccccCCCCCCcccccchHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhC
Q 015634 341 SADLFGHDSDNASLDLAASDLINRLSFQAQQDISSLKNIAGETGKKLSSLASSLITDIQDRIL 403 (403)
Q Consensus 341 S~~yFg~~~~~~~~~~sa~d~~~~~~~~a~~Dl~~lk~~v~~~A~KLs~~a~~~~~~lQ~ry~ 403 (403)
|+||||++++ ..++.+++.++.+++.+||.++|++|+++|+||+++|++|+++|||||+
T Consensus 396 Ssd~fG~~~~----~~~~g~~~~~~~~~a~~di~~~k~~~~~~a~kls~~a~~v~~~~qd~~~ 454 (454)
T KOG0706|consen 396 SSDLFGEGDD----DHTAGSLALRDSFRAAQDIASFKNSARSVAGKLSVLASKVGSSLQDRYG 454 (454)
T ss_pred hHhhcCCCCC----CCCccchhhcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 9999999876 3567778888899999999999999999999999999999999999995
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-38 Score=308.27 Aligned_cols=116 Identities=47% Similarity=0.858 Sum_probs=105.7
Q ss_pred HHHHHHHHHHcCCCCCCccCCCCCCCCceeeccccccchhhhhhhccCCCcccceeecCCCCCCHHHHHHHhcCCcHHHH
Q 015634 8 DKNLVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQ 87 (403)
Q Consensus 8 ~~~~i~~~L~~~p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~LG~hiS~VkSi~lD~W~~~ql~~m~~gGN~~a~ 87 (403)
++...|..|+-..+|++||||+++||+|+||+||||||++|+|+||.||||||||||||||+|.+.||+.|+.|||.+++
T Consensus 5 rtrr~L~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~~~ 84 (386)
T KOG0704|consen 5 RTRRVLLELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNERFR 84 (386)
T ss_pred HHHHHHHhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchhHH
Confidence 34455666666669999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcCCCCC-CchhhhcccHHHHHHHHHHHHHHHH
Q 015634 88 VFFKQHGWTDG-GKIEAKYTSRAAELYKQILAKEVAK 123 (403)
Q Consensus 88 ~~~~~~~~~~~-~~i~~KY~~~~a~~Yr~~l~~~v~k 123 (403)
+||+.++.... ..|++||.+++|.+||++|..+++-
T Consensus 85 eFL~s~~~~~e~~~i~eKYns~aAa~yRdki~~laeg 121 (386)
T KOG0704|consen 85 EFLSSQGIYKETWPIREKYNSRAAALYRDKIAALAEG 121 (386)
T ss_pred HHHhhCccccccccHHHhhccHHHHHHHHHHHHHhcC
Confidence 99999985544 4899999999999999999986653
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=2.8e-36 Score=298.94 Aligned_cols=118 Identities=45% Similarity=0.724 Sum_probs=109.2
Q ss_pred HHHHHHHHHHcCCCCCCccCCCCCCCCceeeccccccchhhhhhhccCCCcccceeecCCCCCCHHHHHHHhcCCcHHHH
Q 015634 8 DKNLVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQ 87 (403)
Q Consensus 8 ~~~~i~~~L~~~p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~LG~hiS~VkSi~lD~W~~~ql~~m~~gGN~~a~ 87 (403)
+-+.++..|+..++|++|||||+++|+|+||+||||||++||||||+|||||||||||+||+|+++||++|..|||.+|+
T Consensus 6 ~~~~~l~~l~~~~~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~wt~~~l~~m~~gGN~~a~ 85 (319)
T COG5347 6 EDRKLLKLLKSDSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWTEEELRRMEVGGNSNAN 85 (319)
T ss_pred HHHHHHHHHhhccccCccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeecccCCHHHHHHHHHhcchhhh
Confidence 34678889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcCCCC-CCchhhhcccHHHHHHHHHHHHHHHHHH
Q 015634 88 VFFKQHGWTD-GGKIEAKYTSRAAELYKQILAKEVAKNM 125 (403)
Q Consensus 88 ~~~~~~~~~~-~~~i~~KY~~~~a~~Yr~~l~~~v~k~~ 125 (403)
.||+.|++.. ...++.||.+.+++.|.+.+..++....
T Consensus 86 ~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~ 124 (319)
T COG5347 86 RFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFID 124 (319)
T ss_pred hHhccCCCcccccccccccCHHHHHHHHHHHHHhhhccc
Confidence 9999998874 3689999999999999998887665554
No 5
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=4.3e-34 Score=277.35 Aligned_cols=103 Identities=39% Similarity=0.759 Sum_probs=93.2
Q ss_pred hHHHHHHHHHHcCCCCCCccCCCCCCCCceeeccccccchhhhhhhccCCCcccceeecCCCCCCHHHHHHHhcCCcHHH
Q 015634 7 TDKNLVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRA 86 (403)
Q Consensus 7 ~~~~~i~~~L~~~p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~LG~hiS~VkSi~lD~W~~~ql~~m~~gGN~~a 86 (403)
..-+.+++.|++.|+|++|+|||++.|.|||+++|||||+.|+||||+||||||+||||+||.|+++||..|+..||.+|
T Consensus 10 ~~~~~~l~~Ll~~~~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~~GN~~a 89 (287)
T KOG0703|consen 10 ERNKRRLRELLREPDNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMISMGNAKA 89 (287)
T ss_pred chHHHHHHHHHcCcccCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHHHcchhh
Confidence 34478999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCCCC----------CCchhhhcccHH
Q 015634 87 QVFFKQHGWTD----------GGKIEAKYTSRA 109 (403)
Q Consensus 87 ~~~~~~~~~~~----------~~~i~~KY~~~~ 109 (403)
|.|||+.-... ..|||.||+.+.
T Consensus 90 n~~~ea~~p~~~~~p~~d~~~e~FIR~KYE~kk 122 (287)
T KOG0703|consen 90 NSYYEAKLPDPFRRPGPDDLVEQFIRDKYERKK 122 (287)
T ss_pred hhhccccCCccccCCChHHHHHHHHHHHHhhhh
Confidence 99999872111 258889888764
No 6
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=99.98 E-value=1.9e-33 Score=242.19 Aligned_cols=83 Identities=52% Similarity=1.020 Sum_probs=71.7
Q ss_pred HHHHHHHcCCCCCCccCCCCCCCCceeeccccccchhhhhhhccCCCcccceeecCCCCCCHHHHHHHhcCCcHHHHHHH
Q 015634 11 LVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFF 90 (403)
Q Consensus 11 ~i~~~L~~~p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~LG~hiS~VkSi~lD~W~~~ql~~m~~gGN~~a~~~~ 90 (403)
++|+.|++.|+|++|+|||+++|+|+|++||||||+.|+|+||.||+|||+||||+||.|++++|++|+.+||..+|+||
T Consensus 2 ~~l~~l~~~~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~VkSi~~d~w~~~ev~~~~~~GN~~~n~~~ 81 (116)
T PF01412_consen 2 KILRELLKKPGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRVKSITMDNWSPEEVQRMREGGNKRANSIW 81 (116)
T ss_dssp HHHHHHHCSTTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--EEETTTS---HHHHHHHHHSHHHHHHHHH
T ss_pred HHHHHHHcCcCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhccccccCCCCHHHHHHHHHHChHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Hhc
Q 015634 91 KQH 93 (403)
Q Consensus 91 ~~~ 93 (403)
+.+
T Consensus 82 e~~ 84 (116)
T PF01412_consen 82 EAN 84 (116)
T ss_dssp TTT
T ss_pred HcC
Confidence 988
No 7
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=99.97 E-value=1.1e-31 Score=229.95 Aligned_cols=97 Identities=48% Similarity=0.860 Sum_probs=82.8
Q ss_pred CCCCCccCCCCCCCCceeeccccccchhhhhhhccCCCcccceeecCCCCCCHHHHHHHhcCCcHHHHHHHHhcCCCCC-
Q 015634 20 SENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTDG- 98 (403)
Q Consensus 20 p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~LG~hiS~VkSi~lD~W~~~ql~~m~~gGN~~a~~~~~~~~~~~~- 98 (403)
|+|++||||++++|+|+|++||||||++|+|+||.||+|||+||||+||+|++++|++|+.+||.++|+||+.+.....
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 5899999999999999999999999999999999999999999999999999999999999999999999999864321
Q ss_pred ----CchhhhcccHHHHHHHHH
Q 015634 99 ----GKIEAKYTSRAAELYKQI 116 (403)
Q Consensus 99 ----~~i~~KY~~~~a~~Yr~~ 116 (403)
.....+|+..+...|+++
T Consensus 81 ~~~~~~~~~~~~~fI~~KY~~k 102 (112)
T smart00105 81 KPPDSDDQQKYESFIAAKYEEK 102 (112)
T ss_pred CCCCCchHHHHHHHHHHHHHhh
Confidence 123344555555555443
No 8
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=99.95 E-value=2.6e-28 Score=252.31 Aligned_cols=90 Identities=26% Similarity=0.635 Sum_probs=85.4
Q ss_pred CCCcchhHH-HHHHHHHHcCCCCCCccCCCCCCCCceeeccccccchhhhhhhccCCCcccceeecCCCCCCHHHHHHHh
Q 015634 1 MASDNLTDK-NLVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMV 79 (403)
Q Consensus 1 m~~~~~~~~-~~i~~~L~~~p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~LG~hiS~VkSi~lD~W~~~ql~~m~ 79 (403)
|+++...+| ++||++|++.|+|++|+||+.++|+|||++||||||+.|+||||.|| ++||||+||+|+++||++|+
T Consensus 1 M~SKR~qERnekILreLlklPgNk~CADCgs~~P~WASiNlGIFICi~CSGIHRsLG---hRVKSLSLDkWT~EEVe~Mk 77 (648)
T PLN03119 1 MGSKREEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREFT---HRVKSVSMSKFTSKEVEVLQ 77 (648)
T ss_pred CcchHHHHHHHHHHHHHhhCcCCCccccCCCCCCCceeeccceEEeccchhhhccCC---ceeeccccCCCCHHHHHHHH
Confidence 888877777 56999999999999999999999999999999999999999999998 38999999999999999999
Q ss_pred cCCcHHHHHHHHhc
Q 015634 80 YGGNNRAQVFFKQH 93 (403)
Q Consensus 80 ~gGN~~a~~~~~~~ 93 (403)
.+||.++|+||+++
T Consensus 78 ~gGN~~AN~iyean 91 (648)
T PLN03119 78 NGGNQRAREIYLKN 91 (648)
T ss_pred HhchHHHHHHHHhh
Confidence 99999999999986
No 9
>PLN03131 hypothetical protein; Provisional
Probab=99.94 E-value=4.5e-27 Score=244.81 Aligned_cols=90 Identities=26% Similarity=0.640 Sum_probs=84.3
Q ss_pred CCCcchhHH-HHHHHHHHcCCCCCCccCCCCCCCCceeeccccccchhhhhhhccCCCcccceeecCCCCCCHHHHHHHh
Q 015634 1 MASDNLTDK-NLVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMV 79 (403)
Q Consensus 1 m~~~~~~~~-~~i~~~L~~~p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~LG~hiS~VkSi~lD~W~~~ql~~m~ 79 (403)
|.+....++ +++|++|++.|+|++|+||++++|+|||++||||||+.|+||||.|| | +||||+||.|+++||++|+
T Consensus 1 m~SkkqqErnekiLreLlk~PgNk~CADCga~~P~WASiNlGIFICi~CSGIHRsLg-h--RVKSVTLD~WtdeEV~~Mk 77 (705)
T PLN03131 1 MGSRKEEERNEKIIRGLMKLPPNRRCINCNSLGPQFVCTNFWTFICMTCSGIHREFT-H--RVKSVSMSKFTSQDVEALQ 77 (705)
T ss_pred CcchHHHHHHHHHHHHHhhCcCCCccccCCCCCCCeeEeccceEEchhchhhhcccC-c--ccccccCCCCCHHHHHHHH
Confidence 777765666 57999999999999999999999999999999999999999999998 3 8999999999999999999
Q ss_pred cCCcHHHHHHHHhc
Q 015634 80 YGGNNRAQVFFKQH 93 (403)
Q Consensus 80 ~gGN~~a~~~~~~~ 93 (403)
.+||.++|+||+++
T Consensus 78 ~gGN~~AN~iyean 91 (705)
T PLN03131 78 NGGNQRAREIYLKD 91 (705)
T ss_pred HhccHHHHHHHHhh
Confidence 99999999999975
No 10
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.85 E-value=4.9e-22 Score=205.62 Aligned_cols=97 Identities=40% Similarity=0.787 Sum_probs=88.4
Q ss_pred HHHHHHcCCCCCCccCCCCCCCCceeeccccccchhhhhhhccCCCcccceeecCCCCCCHHHHHHHhcCCcHHHHHHHH
Q 015634 12 VFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFK 91 (403)
Q Consensus 12 i~~~L~~~p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~LG~hiS~VkSi~lD~W~~~ql~~m~~gGN~~a~~~~~ 91 (403)
.++.|+..++|..|+||+++||.|||+|+|+.+|++|+||||+||.|+|+|||+.||.|..+-+..|...||..||.+|+
T Consensus 503 a~qairn~rgn~~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl~~Vm~aiGN~~AN~vWE 582 (749)
T KOG0705|consen 503 ALQAIRNMRGNSHCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVELLKVMSAIGNDLANSVWE 582 (749)
T ss_pred HHHHHhcCcCCceeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHHHHHHHHhhhhHHHHHhh
Confidence 56788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hc--CCCC----------CCchhhhcccH
Q 015634 92 QH--GWTD----------GGKIEAKYTSR 108 (403)
Q Consensus 92 ~~--~~~~----------~~~i~~KY~~~ 108 (403)
.. |... +.||+.||+.+
T Consensus 583 ~~~~G~~KPs~~s~REEkErwIr~KYeqk 611 (749)
T KOG0705|consen 583 GSSQGQTKPSPDSSREEKERWIRAKYEQK 611 (749)
T ss_pred hhccCCcCCCccccHHHHHHHHHHHHHHH
Confidence 53 2110 24899999887
No 11
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.77 E-value=5.3e-20 Score=201.35 Aligned_cols=97 Identities=43% Similarity=0.741 Sum_probs=88.6
Q ss_pred HHHHHHcCCCCCCccCCCCCCCCceeeccccccchhhhhhhccCCCcccceeecCCCCCCHHHHHHHhcCCcHHHHHHHH
Q 015634 12 VFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFK 91 (403)
Q Consensus 12 i~~~L~~~p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~LG~hiS~VkSi~lD~W~~~ql~~m~~gGN~~a~~~~~ 91 (403)
.+..++..|+|..|+|||++.|+|+|+|+||.+|++|+|+||+||||||+|+|++||.|..+.+.+|+.+||..+|.+|+
T Consensus 416 ~~~~vq~~pgN~~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~~~~l~~l~~~lgn~~~N~i~e 495 (785)
T KOG0521|consen 416 VIEEVQSVPGNAQCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVWEPELLLLFKNLGNKYVNEIYE 495 (785)
T ss_pred hhhhhhcCCchhhhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhccCcHHHHHHHHhCcchhhhhhh
Confidence 47888999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCC--------------CCchhhhcccH
Q 015634 92 QHGWTD--------------GGKIEAKYTSR 108 (403)
Q Consensus 92 ~~~~~~--------------~~~i~~KY~~~ 108 (403)
.+-+.. ..+|++||..+
T Consensus 496 ~~l~~~~~~~~~~~~~~~~r~~~i~~kyve~ 526 (785)
T KOG0521|consen 496 ALLPSYDSSKPTASSSRQAREAWIKAKYVER 526 (785)
T ss_pred cccccccccCCCCccchhhhhHhhhccccee
Confidence 875422 13578888765
No 12
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.67 E-value=8.5e-18 Score=172.07 Aligned_cols=93 Identities=39% Similarity=0.646 Sum_probs=83.1
Q ss_pred HcCCCCCCccCCCCCCCCceeeccccccchhhhhhhccCCCcccceeecCCCCCCHHHHHHHhcCCcHHHHHHHHhcCCC
Q 015634 17 KAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWT 96 (403)
Q Consensus 17 ~~~p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~LG~hiS~VkSi~lD~W~~~ql~~m~~gGN~~a~~~~~~~~~~ 96 (403)
+....-++|+|||+++|.||||+-|+|||.+|..+||+||.|||.||++-...|.+..|++.....|..+|.+||.+.++
T Consensus 3 k~~l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaNsIWEh~Lld 82 (669)
T KOG0818|consen 3 KRLLSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGANSIWEHSLLD 82 (669)
T ss_pred ccchhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcchhhhhhccC
Confidence 34566789999999999999999999999999999999999999999999999999999999999999999999977332
Q ss_pred C--------------------CCchhhhcccHH
Q 015634 97 D--------------------GGKIEAKYTSRA 109 (403)
Q Consensus 97 ~--------------------~~~i~~KY~~~~ 109 (403)
. ..||++||...+
T Consensus 83 ~st~~sg~rk~~pqD~~Hp~K~eFIkaKy~~Lt 115 (669)
T KOG0818|consen 83 PATIMSGRRKANPQDKVHPNKAEFIRAKYQMLA 115 (669)
T ss_pred chhhhcccCCCCCcCCCCccHHHHHHHHHHhee
Confidence 1 258999998653
No 13
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.56 E-value=8.5e-16 Score=164.91 Aligned_cols=98 Identities=34% Similarity=0.594 Sum_probs=87.8
Q ss_pred HHHHHHHcCCCCCCccCCCCCCCCceeeccccccchhhhhhhccCCCcccceeecCCCC--CCHHHHHHHhcCCcHHHHH
Q 015634 11 LVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDS--WSAEQLKMMVYGGNNRAQV 88 (403)
Q Consensus 11 ~i~~~L~~~p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~LG~hiS~VkSi~lD~--W~~~ql~~m~~gGN~~a~~ 88 (403)
.+-.++-....|+.|+||+++.|.|||+|++|.||-.|+|-||+||..+|+|+|++||. |+.+-++++.+.||.++|.
T Consensus 287 evaeriW~ne~nr~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~ 366 (1186)
T KOG1117|consen 287 EVAERIWLNEENRECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANR 366 (1186)
T ss_pred HHHHHHHhccccccccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCccccc
Confidence 45667778899999999999999999999999999999999999999999999999996 9999999999999999999
Q ss_pred HHHhcCCC------------CCCchhhhcccH
Q 015634 89 FFKQHGWT------------DGGKIEAKYTSR 108 (403)
Q Consensus 89 ~~~~~~~~------------~~~~i~~KY~~~ 108 (403)
||..+--. ...||.+||++-
T Consensus 367 Fwa~nl~~~e~lh~dssp~~r~~fi~~Kykeg 398 (1186)
T KOG1117|consen 367 FWAGNLPPNEHLHPDSSPSTRRQFIKEKYKEG 398 (1186)
T ss_pred ccccCCCCccccCCCCCcchhhhHHHHHhhcc
Confidence 99865211 126899998876
No 14
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.12 E-value=4.2e-11 Score=123.47 Aligned_cols=84 Identities=24% Similarity=0.469 Sum_probs=78.1
Q ss_pred HHHHHHHHHHcCCCCCCccCCCCCCC-CceeeccccccchhhhhhhccCCCcccceeecCCCCCCHHHHHHHhcCCcHHH
Q 015634 8 DKNLVFRKLKAKSENKMCFDCNAKNP-TWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRA 86 (403)
Q Consensus 8 ~~~~i~~~L~~~p~Nk~C~DCga~nP-~WaSv~~GiflC~~CsgiHR~LG~hiS~VkSi~lD~W~~~ql~~m~~gGN~~a 86 (403)
+.+.++|.|+..|+|++|++|....+ +|++++-|-|+|+.|+|.-|.|.. -++||||.|-.++..++..++.+||..+
T Consensus 11 ~~ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~~-ahRvksiSmttft~qevs~lQshgNq~~ 89 (524)
T KOG0702|consen 11 DYEKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLNP-AHRVKSISMTTFTDQEVSFLQSHGNQVC 89 (524)
T ss_pred HHHHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccCCC-ccccceeeeeeccccchHHHhhcchhhh
Confidence 34789999999999999999999988 999999999999999999999863 3589999999999999999999999999
Q ss_pred HHHHHh
Q 015634 87 QVFFKQ 92 (403)
Q Consensus 87 ~~~~~~ 92 (403)
+++|-+
T Consensus 90 k~i~fk 95 (524)
T KOG0702|consen 90 KEIWFK 95 (524)
T ss_pred hhhhhc
Confidence 999975
No 15
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=93.15 E-value=0.025 Score=63.54 Aligned_cols=73 Identities=18% Similarity=0.189 Sum_probs=58.2
Q ss_pred HcCCCCCCccCCCC-CCCCceeeccccccchhhhhhhccCCCcccceeecCCCCCCHHHHHHHhcCCcHHHHHHHH
Q 015634 17 KAKSENKMCFDCNA-KNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFK 91 (403)
Q Consensus 17 ~~~p~Nk~C~DCga-~nP~WaSv~~GiflC~~CsgiHR~LG~hiS~VkSi~lD~W~~~ql~~m~~gGN~~a~~~~~ 91 (403)
.....+-.|++|++ ..-.|+++++.+-+|+.|+++|+.++.|++.++++.||+-.+ +.....-||...+.-+.
T Consensus 625 ~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~~~~ 698 (785)
T KOG0521|consen 625 VKASSDGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHHATA 698 (785)
T ss_pred HHhccCccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchhhhh
Confidence 34456889999997 468999999999999999999999999999999999988766 55555555555544443
No 16
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=88.04 E-value=1 Score=47.30 Aligned_cols=76 Identities=24% Similarity=0.288 Sum_probs=51.6
Q ss_pred hhhhHHHHHHhccCCcCccccccCCCCCccchhHHHHhhhccCCcccccccccCCCCCCcccccchHHHHHHhhhhhHHH
Q 015634 293 IQETDEARKKFSNAKSISSSQFFGDQNNSIDMDTQVSLQKFSGSASISSADLFGHDSDNASLDLAASDLINRLSFQAQQD 372 (403)
Q Consensus 293 ~~~t~~a~~KFgnaKaISSd~yFG~~~~~a~~ea~~rL~~F~gatsISS~~yFg~~~~~~~~~~sa~d~~~~~~~~a~~D 372 (403)
.-++....+||.++-||||.-|||.+++ .+...++.++.- +.... ||+. |. .=
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 3466777999999999999999999974 334444554431 12222 6655 22 22
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 015634 373 ISSLKNIAGETGKKLSSLASSLI 395 (403)
Q Consensus 373 l~~lk~~v~~~A~KLs~~a~~~~ 395 (403)
+.+++.-+..+|.||.......|
T Consensus 431 ~~~~a~kls~~a~~v~~~~qd~~ 453 (454)
T KOG0706|consen 431 ARSVAGKLSVLASKVGSSLQDRY 453 (454)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 44589999999999888766543
No 17
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=84.21 E-value=1.3 Score=45.51 Aligned_cols=20 Identities=50% Similarity=0.846 Sum_probs=17.5
Q ss_pred hhccCCcccccccccCCCCC
Q 015634 331 QKFSGSASISSADLFGHDSD 350 (403)
Q Consensus 331 ~~F~gatsISS~~yFg~~~~ 350 (403)
++|.|+.+|||++|||+...
T Consensus 300 kKF~naKsisS~qfFg~~~~ 319 (395)
T PLN03114 300 KKFTNAKSISSAQYFGNDNN 319 (395)
T ss_pred HHhcccccccHHhhcccccc
Confidence 56999999999999998743
No 18
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=82.59 E-value=0.75 Score=43.96 Aligned_cols=35 Identities=20% Similarity=0.327 Sum_probs=28.8
Q ss_pred cCCCCCCccCCCCCCC-Cceeeccccccchhhhhhh
Q 015634 18 AKSENKMCFDCNAKNP-TWASVTYGIFLCIDCSAVH 52 (403)
Q Consensus 18 ~~p~Nk~C~DCga~nP-~WaSv~~GiflC~~CsgiH 52 (403)
-.|.-..|+-||.+.. .|.++..|.++|..|...|
T Consensus 145 ~~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~~~ 180 (247)
T PRK00085 145 YGLDLDHCAVCGAPGDHRYFSPKEGGAVCSECGDPY 180 (247)
T ss_pred CccchhhHhcCCCCCCceEEecccCCcccccccCcc
Confidence 4567789999998765 7889999999999997433
No 19
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=72.19 E-value=2.5 Score=40.26 Aligned_cols=35 Identities=29% Similarity=0.524 Sum_probs=28.6
Q ss_pred HcCCCCCCccCCCCCCC-Cceeeccccccchhhhhh
Q 015634 17 KAKSENKMCFDCNAKNP-TWASVTYGIFLCIDCSAV 51 (403)
Q Consensus 17 ~~~p~Nk~C~DCga~nP-~WaSv~~GiflC~~Csgi 51 (403)
--.|.-..|..||..++ .|.++..|.++|.+|...
T Consensus 142 G~~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 142 GYALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred CCCcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 34577789999998655 677999999999999764
No 20
>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=70.93 E-value=2.4 Score=29.27 Aligned_cols=32 Identities=28% Similarity=0.731 Sum_probs=24.4
Q ss_pred ccCCCCC-CCCceeeccccc-cchhhhhhhccCC
Q 015634 25 CFDCNAK-NPTWASVTYGIF-LCIDCSAVHRSLG 56 (403)
Q Consensus 25 C~DCga~-nP~WaSv~~Gif-lC~~CsgiHR~LG 56 (403)
|..|+.. -|.|-..+.|-. ||-.|.-.+|..|
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 8899986 599999999988 9999998887655
No 21
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=67.53 E-value=4.2 Score=30.34 Aligned_cols=38 Identities=24% Similarity=0.567 Sum_probs=31.4
Q ss_pred CCCCccCCCCCC-CCceeecccc-ccchhhhhhhccCCCc
Q 015634 21 ENKMCFDCNAKN-PTWASVTYGI-FLCIDCSAVHRSLGVH 58 (403)
Q Consensus 21 ~Nk~C~DCga~n-P~WaSv~~Gi-flC~~CsgiHR~LG~h 58 (403)
....|..|+... |.|=..+.|- +||-.|.-..+..|..
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC
Confidence 467899999864 8999888996 9999999888776653
No 22
>PRK12495 hypothetical protein; Provisional
Probab=65.32 E-value=5 Score=38.81 Aligned_cols=29 Identities=21% Similarity=0.374 Sum_probs=24.3
Q ss_pred CCCCCCccCCCCCCCCceeeccccccchhhhhh
Q 015634 19 KSENKMCFDCNAKNPTWASVTYGIFLCIDCSAV 51 (403)
Q Consensus 19 ~p~Nk~C~DCga~nP~WaSv~~GiflC~~Csgi 51 (403)
...+..|-+||.+-|.. -|+.+|..|..+
T Consensus 39 tmsa~hC~~CG~PIpa~----pG~~~Cp~CQ~~ 67 (226)
T PRK12495 39 TMTNAHCDECGDPIFRH----DGQEFCPTCQQP 67 (226)
T ss_pred ccchhhcccccCcccCC----CCeeECCCCCCc
Confidence 46899999999999932 599999999854
No 23
>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=64.21 E-value=4.9 Score=27.91 Aligned_cols=34 Identities=15% Similarity=0.340 Sum_probs=29.0
Q ss_pred CCCCccCCCCCCCCceeeccccccchhhhhh-hcc
Q 015634 21 ENKMCFDCNAKNPTWASVTYGIFLCIDCSAV-HRS 54 (403)
Q Consensus 21 ~Nk~C~DCga~nP~WaSv~~GiflC~~Csgi-HR~ 54 (403)
.+..|..|......|-..+=+++||..|... |+.
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 3578999998878999999999999999987 886
No 24
>PRK11019 hypothetical protein; Provisional
Probab=60.68 E-value=4.9 Score=33.53 Aligned_cols=37 Identities=19% Similarity=0.479 Sum_probs=27.3
Q ss_pred CCCCccCCCCCCC--CceeeccccccchhhhhhhccCCCc
Q 015634 21 ENKMCFDCNAKNP--TWASVTYGIFLCIDCSAVHRSLGVH 58 (403)
Q Consensus 21 ~Nk~C~DCga~nP--~WaSv~~GiflC~~CsgiHR~LG~h 58 (403)
.-.+|.|||.+=| .|.-++ ++-.|++|...+-..+.|
T Consensus 35 syg~C~~CG~~Ip~~Rl~A~P-~a~~Cv~Cq~~~E~~~k~ 73 (88)
T PRK11019 35 SLTECEECGEPIPEARRKAIP-GVRLCVACQQEKDLQQAA 73 (88)
T ss_pred cCCeeCcCCCcCcHHHHhhcC-CccccHHHHHHHHHHHhH
Confidence 4579999999765 565555 788999999977554444
No 25
>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=50.76 E-value=6.8 Score=27.79 Aligned_cols=27 Identities=26% Similarity=0.615 Sum_probs=20.6
Q ss_pred CccCCCCCCCCceeeccccccchhhhhh
Q 015634 24 MCFDCNAKNPTWASVTYGIFLCIDCSAV 51 (403)
Q Consensus 24 ~C~DCga~nP~WaSv~~GiflC~~Csgi 51 (403)
+|-.||+.. .-..-.-|-++|..|..|
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-BB
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCCCE
Confidence 689999977 444566899999999654
No 26
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=50.14 E-value=9 Score=28.13 Aligned_cols=27 Identities=30% Similarity=0.768 Sum_probs=20.6
Q ss_pred CccCCCCCCCCceeeccccccchhhhhh
Q 015634 24 MCFDCNAKNPTWASVTYGIFLCIDCSAV 51 (403)
Q Consensus 24 ~C~DCga~nP~WaSv~~GiflC~~Csgi 51 (403)
+|+=|+...+. -=.=+|-|||.+|-.-
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~~ 27 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEKE 27 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHHH
Confidence 48889988776 3334799999999763
No 27
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=50.11 E-value=8.8 Score=37.45 Aligned_cols=32 Identities=28% Similarity=0.600 Sum_probs=27.7
Q ss_pred cCCCCCCccCCCCCC-CCceeeccccccchhhh
Q 015634 18 AKSENKMCFDCNAKN-PTWASVTYGIFLCIDCS 49 (403)
Q Consensus 18 ~~p~Nk~C~DCga~n-P~WaSv~~GiflC~~Cs 49 (403)
-.|.=..|+.||.+. |...++-.|-++|..|.
T Consensus 150 ~~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 150 IGPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred CccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 346677999999986 57999999999999998
No 28
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=48.92 E-value=19 Score=30.11 Aligned_cols=40 Identities=23% Similarity=0.393 Sum_probs=29.0
Q ss_pred HHHHHHHcCCCCCCccCCCCCCCCceeeccccccchhhhhhh
Q 015634 11 LVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVH 52 (403)
Q Consensus 11 ~i~~~L~~~p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiH 52 (403)
.+-+-......-..|-.|+.+ +---+..||+.|..|-..-
T Consensus 24 rv~~ie~~~~~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 24 RVKEIEAQQRAKHVCPFCGRT--TVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred HHHHHHHHHhcCCcCCCCCCc--ceeeeccCeEEcCCCCCee
Confidence 333333445566799999998 5667889999999997643
No 29
>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=47.52 E-value=9.6 Score=29.64 Aligned_cols=34 Identities=21% Similarity=0.582 Sum_probs=24.6
Q ss_pred cCCCCCCccCCCCCCC--Cceeeccccccchhhhhhh
Q 015634 18 AKSENKMCFDCNAKNP--TWASVTYGIFLCIDCSAVH 52 (403)
Q Consensus 18 ~~p~Nk~C~DCga~nP--~WaSv~~GiflC~~CsgiH 52 (403)
..++...|.|||.+=| .|.-++ |+..|++|...|
T Consensus 27 ~~~s~g~C~~Cg~~Ip~~Rl~a~p-~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 27 IGPSLRECEDCGEPIPEARREALP-GVTRCVSCQEIL 62 (63)
T ss_pred cCCCCCeeccCCCcChHHHHhhcC-CcCCcHHHHhhc
Confidence 3466789999998755 444443 788999998754
No 30
>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=46.47 E-value=13 Score=28.04 Aligned_cols=34 Identities=29% Similarity=0.691 Sum_probs=28.2
Q ss_pred CccCCCCCC-CCceeec-cccccchhhhhhhccCCC
Q 015634 24 MCFDCNAKN-PTWASVT-YGIFLCIDCSAVHRSLGV 57 (403)
Q Consensus 24 ~C~DCga~n-P~WaSv~-~GiflC~~CsgiHR~LG~ 57 (403)
+|..|+... |.|-..+ -+..||-.|.-..+..|.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~ 36 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGV 36 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCC
Confidence 599999865 8898776 788999999988887764
No 31
>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=44.46 E-value=7.4 Score=26.93 Aligned_cols=27 Identities=15% Similarity=0.506 Sum_probs=16.7
Q ss_pred CCccCCCCCC-CCceeeccccccchhhh
Q 015634 23 KMCFDCNAKN-PTWASVTYGIFLCIDCS 49 (403)
Q Consensus 23 k~C~DCga~n-P~WaSv~~GiflC~~Cs 49 (403)
..|.+|+.+- -+|..-+|+.-+|..|.
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 4799999864 68999999999999995
No 32
>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=40.78 E-value=16 Score=29.75 Aligned_cols=31 Identities=23% Similarity=0.701 Sum_probs=25.5
Q ss_pred CCCCccCCCCCCCCceeeccccccchhhhhhhcc
Q 015634 21 ENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 21 ~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~ 54 (403)
.|..|.=||.+.- ...||++.|..|.++.|-
T Consensus 2 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 2 DTHFCAVCSDYAS---GYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 4678999997553 578999999999998874
No 33
>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=39.68 E-value=19 Score=25.04 Aligned_cols=28 Identities=25% Similarity=0.719 Sum_probs=23.1
Q ss_pred CCCCCccCCCCCCCCceeeccccccchhhhh
Q 015634 20 SENKMCFDCNAKNPTWASVTYGIFLCIDCSA 50 (403)
Q Consensus 20 p~Nk~C~DCga~nP~WaSv~~GiflC~~Csg 50 (403)
..|..|..|++. |....=|-++|..|-.
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCce
Confidence 346679999998 8888889999999854
No 34
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=38.95 E-value=18 Score=30.41 Aligned_cols=34 Identities=26% Similarity=0.565 Sum_probs=24.2
Q ss_pred HcCCCCCCccCCCCCC--------CCc---------eeeccccccchhhhh
Q 015634 17 KAKSENKMCFDCNAKN--------PTW---------ASVTYGIFLCIDCSA 50 (403)
Q Consensus 17 ~~~p~Nk~C~DCga~n--------P~W---------aSv~~GiflC~~Csg 50 (403)
+..+.--.|++||.+- +.+ .+=+||-.+|..|..
T Consensus 29 kK~~~~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~ 79 (93)
T COG2174 29 KKKPTIPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVR 79 (93)
T ss_pred eccCCCCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHHH
Confidence 4567778999999641 111 244699999999975
No 35
>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=38.52 E-value=18 Score=30.35 Aligned_cols=32 Identities=28% Similarity=0.641 Sum_probs=26.1
Q ss_pred CCCCCccCCCCCCCCceeeccccccchhhhhhhcc
Q 015634 20 SENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 20 p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~ 54 (403)
-++..|.=||.+.- ...||++.|..|.++.|-
T Consensus 3 ~~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 3 IEVIPCKICGDKSS---GIHYGVITCEGCKGFFRR 34 (95)
T ss_pred ccccCCcccCCcCc---ceEECceeehhhHHhhHH
Confidence 35678999998653 468999999999998874
No 36
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=37.17 E-value=15 Score=27.44 Aligned_cols=30 Identities=23% Similarity=0.563 Sum_probs=20.4
Q ss_pred CccCCCCCCCCcee--eccccccchhhhhhhcc
Q 015634 24 MCFDCNAKNPTWAS--VTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 24 ~C~DCga~nP~WaS--v~~GiflC~~CsgiHR~ 54 (403)
.|+=||.+-.-... +.=| +||-+|..--..
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 48888887655443 4447 899999975433
No 37
>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=36.06 E-value=19 Score=30.36 Aligned_cols=30 Identities=23% Similarity=0.707 Sum_probs=24.5
Q ss_pred CCCccCCCCCCCCceeeccccccchhhhhhhcc
Q 015634 22 NKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 22 Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~ 54 (403)
+..|.=|+.+.- ...||++.|..|.++.|-
T Consensus 4 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 33 (97)
T cd07170 4 KRLCLVCGDIAS---GYHYGVASCEACKAFFKR 33 (97)
T ss_pred CCCCeecCCcCc---ceEECceeehhhhHHHHH
Confidence 457999997653 468999999999998874
No 38
>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=35.20 E-value=23 Score=28.88 Aligned_cols=32 Identities=22% Similarity=0.645 Sum_probs=25.8
Q ss_pred CCCCCccCCCCCCCCceeeccccccchhhhhhhcc
Q 015634 20 SENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 20 p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~ 54 (403)
|..+.|.=|+.+.- ...||++.|..|.++.|-
T Consensus 1 ~~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 32 (82)
T cd07173 1 PPQKTCLICGDEAS---GCHYGALTCGSCKVFFKR 32 (82)
T ss_pred CCCCCCeecCCcCc---ceEECcchhhhHHHHHHH
Confidence 34677999997554 568999999999998874
No 39
>PHA00080 DksA-like zinc finger domain containing protein
Probab=34.71 E-value=19 Score=28.73 Aligned_cols=33 Identities=21% Similarity=0.572 Sum_probs=23.8
Q ss_pred CCCCCCccCCCCCCC--Cceeeccccccchhhhhhh
Q 015634 19 KSENKMCFDCNAKNP--TWASVTYGIFLCIDCSAVH 52 (403)
Q Consensus 19 ~p~Nk~C~DCga~nP--~WaSv~~GiflC~~CsgiH 52 (403)
.+....|.|||.+=| .|.-++ |+-.|++|...+
T Consensus 28 ~~~~~~C~~Cg~~Ip~~Rl~a~P-~~~~Cv~Cq~~~ 62 (72)
T PHA00080 28 APSATHCEECGDPIPEARREAVP-GCRTCVSCQEIL 62 (72)
T ss_pred CCCCCEecCCCCcCcHHHHHhCC-CccCcHHHHHHH
Confidence 345568999998654 555555 566799999865
No 40
>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=33.11 E-value=21 Score=27.44 Aligned_cols=28 Identities=21% Similarity=0.596 Sum_probs=23.5
Q ss_pred CCCCccCCCCCCCCceeeccccccchhhhh
Q 015634 21 ENKMCFDCNAKNPTWASVTYGIFLCIDCSA 50 (403)
Q Consensus 21 ~Nk~C~DCga~nP~WaSv~~GiflC~~Csg 50 (403)
.-+.|..||..... ..+..+|.|..|.-
T Consensus 27 TSq~C~~CG~~~~~--~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK--RRSGRVFTCPNCGF 54 (69)
T ss_pred CccCccCccccccc--ccccceEEcCCCCC
Confidence 45789999998887 77788999999865
No 41
>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=32.60 E-value=27 Score=29.67 Aligned_cols=31 Identities=26% Similarity=0.682 Sum_probs=25.6
Q ss_pred CCCCccCCCCCCCCceeeccccccchhhhhhhcc
Q 015634 21 ENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 21 ~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~ 54 (403)
.+..|.=|+.+.- ...||+..|..|.++.|-
T Consensus 17 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 47 (101)
T cd07160 17 GNEVCSVCGDKAS---GFHYNVLSCEGCKGFFRR 47 (101)
T ss_pred CCCCCeecCCcCc---ceEECcceehhhhhhhhh
Confidence 4678999997554 568999999999998874
No 42
>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=31.41 E-value=26 Score=29.08 Aligned_cols=32 Identities=25% Similarity=0.776 Sum_probs=26.1
Q ss_pred CCCCCccCCCCCCCCceeeccccccchhhhhhhcc
Q 015634 20 SENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 20 p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~ 54 (403)
.+++.|.=|+.+. ....||+..|..|.++.|-
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 4677899999755 3568999999999998864
No 43
>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian
Probab=28.92 E-value=25 Score=29.39 Aligned_cols=29 Identities=28% Similarity=0.613 Sum_probs=23.2
Q ss_pred CCccCCCCCCCCceeeccccccchhhhhhhcc
Q 015634 23 KMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 23 k~C~DCga~nP~WaSv~~GiflC~~CsgiHR~ 54 (403)
+.|.=||.+.- ...||++.|..|.++.|-
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 46888887544 458999999999998875
No 44
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=28.70 E-value=53 Score=27.61 Aligned_cols=39 Identities=18% Similarity=0.388 Sum_probs=28.5
Q ss_pred HHHHHHHcCCCCCCccCCCCCCCCceeeccccccchhhhhh
Q 015634 11 LVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAV 51 (403)
Q Consensus 11 ~i~~~L~~~p~Nk~C~DCga~nP~WaSv~~GiflC~~Csgi 51 (403)
.+-+-..+...-..|--||........+ ||+-|..|.-.
T Consensus 25 ~v~kie~~q~a~y~CpfCgk~~vkR~a~--GIW~C~~C~~~ 63 (90)
T PTZ00255 25 QIKKIEISQHAKYFCPFCGKHAVKRQAV--GIWRCKGCKKT 63 (90)
T ss_pred HHHHHHHHHhCCccCCCCCCCceeeeee--EEEEcCCCCCE
Confidence 3333335567778999999877766655 99999999753
No 45
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=27.96 E-value=34 Score=34.43 Aligned_cols=33 Identities=24% Similarity=0.562 Sum_probs=23.4
Q ss_pred CCCCCccCCCCCCCCceeeccccccchhhhhhhc
Q 015634 20 SENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHR 53 (403)
Q Consensus 20 p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR 53 (403)
.....|.+||..+.- ....-|-.+|.+|.-|..
T Consensus 9 ~~~~~Cp~Cg~~~iv-~d~~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 9 EEKLVCPECGSDKLI-YDYERGEIVCADCGLVIE 41 (310)
T ss_pred ccCCcCcCCCCCCee-EECCCCeEeecccCCccc
Confidence 445689999974322 234579999999998653
No 46
>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=27.60 E-value=12 Score=25.55 Aligned_cols=29 Identities=28% Similarity=0.681 Sum_probs=16.3
Q ss_pred CccCCCCCCCC-ceeeccccccchhhhhhh
Q 015634 24 MCFDCNAKNPT-WASVTYGIFLCIDCSAVH 52 (403)
Q Consensus 24 ~C~DCga~nP~-WaSv~~GiflC~~CsgiH 52 (403)
.|.+||..=|. -.-+-=|..+|+.|...|
T Consensus 5 ~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~~ 34 (36)
T PF01258_consen 5 ICEDCGEPIPEERLVAVPGATLCVECQERR 34 (36)
T ss_dssp B-TTTSSBEEHHHHHHCTTECS-HHHHHHH
T ss_pred CccccCChHHHHHHHhCCCcEECHHHhCcc
Confidence 49999975331 111122778999998765
No 47
>TIGR02890 spore_yteA sporulation protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to PFAM family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. The function of proteins in this family is unknown. YteA was detected in mature spores of Bacillus subtilis by Kuwana, et al., and appears to be expressed under control of sigma-K.
Probab=26.17 E-value=55 Score=30.03 Aligned_cols=42 Identities=14% Similarity=0.453 Sum_probs=26.3
Q ss_pred HHHHHHHHcCCCCCCccCCCCCCC--Cceeeccccccchhhhhhhc
Q 015634 10 NLVFRKLKAKSENKMCFDCNAKNP--TWASVTYGIFLCIDCSAVHR 53 (403)
Q Consensus 10 ~~i~~~L~~~p~Nk~C~DCga~nP--~WaSv~~GiflC~~CsgiHR 53 (403)
++.+.+|. ...=.+|.+||.+=| .+.-++ ..-+|+.|...+-
T Consensus 75 e~AL~Ri~-~G~YG~Ce~CGe~I~~~RL~a~P-~a~~Ci~Cq~~~E 118 (159)
T TIGR02890 75 EHALQKIE-NGTYGICEVCGKPIPYERLEAIP-TATTCVECQNRKE 118 (159)
T ss_pred HHHHHHHh-CCCCCeecccCCcccHHHHhhCC-CcchhHHHHHHhh
Confidence 34444453 344568999998633 333444 4568999999763
No 48
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=25.06 E-value=25 Score=24.24 Aligned_cols=29 Identities=21% Similarity=0.496 Sum_probs=14.4
Q ss_pred CCccCCCCCCCCceee---ccccccchhhhhhh
Q 015634 23 KMCFDCNAKNPTWASV---TYGIFLCIDCSAVH 52 (403)
Q Consensus 23 k~C~DCga~nP~WaSv---~~GiflC~~CsgiH 52 (403)
|.|-.||.+ -.+.-+ +.==++|..|.-||
T Consensus 1 kfC~~CG~~-l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 1 KFCPQCGGP-LERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp -B-TTT--B--EEE--TT-SS-EEEETTTTEEE
T ss_pred CccccccCh-hhhhcCCCCCccceECCCCCCEE
Confidence 578889875 222211 23346899999888
No 49
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=25.00 E-value=24 Score=28.27 Aligned_cols=33 Identities=24% Similarity=0.590 Sum_probs=22.1
Q ss_pred CCCccCCCCCCCCce-eeccccccchhhhhhhcc
Q 015634 22 NKMCFDCNAKNPTWA-SVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 22 Nk~C~DCga~nP~Wa-Sv~~GiflC~~CsgiHR~ 54 (403)
...|.|||.+=|.== -.-=|+..|+.|...+-.
T Consensus 34 ~~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~E~ 67 (73)
T PRK13715 34 VYLCEACGNPIPEARRKIFPGVTLCVECQAYQER 67 (73)
T ss_pred cccHhhcCCcCCHHHHhcCCCcCCCHHHHHHHHH
Confidence 358999998755211 112278899999886543
No 50
>PF14376 Haem_bd: Haem-binding domain
Probab=24.88 E-value=35 Score=30.30 Aligned_cols=15 Identities=27% Similarity=0.981 Sum_probs=11.9
Q ss_pred CCCccCCCCCCCCce
Q 015634 22 NKMCFDCNAKNPTWA 36 (403)
Q Consensus 22 Nk~C~DCga~nP~Wa 36 (403)
.+-|.||++.+..|-
T Consensus 41 ~~~CydCHSn~T~~P 55 (137)
T PF14376_consen 41 KNSCYDCHSNNTRYP 55 (137)
T ss_pred HccccccCCCCCCCc
Confidence 367999999887664
No 51
>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=23.45 E-value=46 Score=27.30 Aligned_cols=28 Identities=18% Similarity=0.596 Sum_probs=22.2
Q ss_pred CccCCCCCCCCceeeccccccchhhhhhhcc
Q 015634 24 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 24 ~C~DCga~nP~WaSv~~GiflC~~CsgiHR~ 54 (403)
.|.=||.+.-. ..||++.|..|.++.|-
T Consensus 1 ~C~VCg~~~~g---~hygv~sC~aC~~FFRR 28 (87)
T cd07162 1 ICRVCGDRATG---YHFNAMTCEGCKGFFRR 28 (87)
T ss_pred CCcccCCcCcc---eEECcceehhhHHHHHh
Confidence 37778875543 58999999999998864
No 52
>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=23.43 E-value=37 Score=29.35 Aligned_cols=28 Identities=18% Similarity=0.391 Sum_probs=22.7
Q ss_pred CCCCCCceeeccccccchhhhhhhccCC
Q 015634 29 NAKNPTWASVTYGIFLCIDCSAVHRSLG 56 (403)
Q Consensus 29 ga~nP~WaSv~~GiflC~~CsgiHR~LG 56 (403)
|.++..+.-+-|.-|.|.-|...|..++
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 5677788889999999999999998764
No 53
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.37 E-value=32 Score=33.31 Aligned_cols=24 Identities=29% Similarity=0.647 Sum_probs=20.0
Q ss_pred CCCCccCCCCCCCCceeeccccccchhhhhh
Q 015634 21 ENKMCFDCNAKNPTWASVTYGIFLCIDCSAV 51 (403)
Q Consensus 21 ~Nk~C~DCga~nP~WaSv~~GiflC~~Csgi 51 (403)
.-+.|.-||. +.-+.|.|..|...
T Consensus 308 tS~~C~~cg~-------~~~r~~~C~~cg~~ 331 (364)
T COG0675 308 TSKTCPCCGH-------LSGRLFKCPRCGFV 331 (364)
T ss_pred CcccccccCC-------ccceeEECCCCCCe
Confidence 3489999999 56789999999874
No 54
>cd07163 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=23.25 E-value=36 Score=28.29 Aligned_cols=31 Identities=26% Similarity=0.656 Sum_probs=25.3
Q ss_pred CCCCccCCCCCCCCceeeccccccchhhhhhhcc
Q 015634 21 ENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 21 ~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~ 54 (403)
-|..|.=|+.+.- ...||+..|..|.++.|-
T Consensus 5 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (92)
T cd07163 5 LDIPCKVCGDRSS---GKHYGIYACDGCSGFFKR 35 (92)
T ss_pred cCCCCcccCCcCc---ccEECceeeeeeeeEEee
Confidence 3778999997544 358999999999998874
No 55
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=23.21 E-value=51 Score=23.36 Aligned_cols=29 Identities=24% Similarity=0.538 Sum_probs=17.5
Q ss_pred CCccCCCCCCC---Cceeeccccccchhhhhh
Q 015634 23 KMCFDCNAKNP---TWASVTYGIFLCIDCSAV 51 (403)
Q Consensus 23 k~C~DCga~nP---~WaSv~~GiflC~~Csgi 51 (403)
++|.=||.+.. .-++-+-|++||.+|...
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNGAYICDECVEQ 33 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-SEEEEHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCCcEECHHHHHH
Confidence 57888998654 444555689999999753
No 56
>PHA02942 putative transposase; Provisional
Probab=23.19 E-value=36 Score=35.41 Aligned_cols=28 Identities=21% Similarity=0.475 Sum_probs=21.4
Q ss_pred CCCccCCCCCCCCceeeccccccchhhhhhh
Q 015634 22 NKMCFDCNAKNPTWASVTYGIFLCIDCSAVH 52 (403)
Q Consensus 22 Nk~C~DCga~nP~WaSv~~GiflC~~CsgiH 52 (403)
-+.|..||...+ .+.-.+|.|..|.-.|
T Consensus 325 Sq~Cs~CG~~~~---~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 325 SVSCPKCGHKMV---EIAHRYFHCPSCGYEN 352 (383)
T ss_pred CccCCCCCCccC---cCCCCEEECCCCCCEe
Confidence 478999998775 3455689999998643
No 57
>PTZ00074 60S ribosomal protein L34; Provisional
Probab=23.09 E-value=50 Score=29.76 Aligned_cols=34 Identities=38% Similarity=0.619 Sum_probs=22.2
Q ss_pred HcCCCCCCccCCCCCC-------C----------Cceeeccccccchhhhh
Q 015634 17 KAKSENKMCFDCNAKN-------P----------TWASVTYGIFLCIDCSA 50 (403)
Q Consensus 17 ~~~p~Nk~C~DCga~n-------P----------~WaSv~~GiflC~~Csg 50 (403)
...+.--.|.|||.+- | .-++=.||-.+|..|..
T Consensus 36 KK~~~~pkC~~cg~~L~GI~~~Rp~e~~rlsK~~KtvsRaYGG~lC~~CVr 86 (135)
T PTZ00074 36 KKKSSGPKCGDCGKVLAGIKALRPTEYKQLSRRERTVSRAYGGVLCHKCVR 86 (135)
T ss_pred ccCCCCCCCCCCCCccCCccCCchHHHHHccccCCCccCCCccchhHHHHH
Confidence 3444555799999752 1 22345688888888865
No 58
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=22.93 E-value=33 Score=23.43 Aligned_cols=29 Identities=21% Similarity=0.358 Sum_probs=22.6
Q ss_pred CCCccCCCCCCCCceeeccccccchhhhhhh
Q 015634 22 NKMCFDCNAKNPTWASVTYGIFLCIDCSAVH 52 (403)
Q Consensus 22 Nk~C~DCga~nP~WaSv~~GiflC~~CsgiH 52 (403)
.+.|-.|+...--| -+-+..+|..|..++
T Consensus 3 ~~~C~~C~~~~i~~--~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVN--KEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEE--ecCCeEEcccCCcEe
Confidence 46788899887655 467899999998764
No 59
>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=22.85 E-value=43 Score=27.67 Aligned_cols=30 Identities=27% Similarity=0.678 Sum_probs=24.1
Q ss_pred CCCccCCCCCCCCceeeccccccchhhhhhhcc
Q 015634 22 NKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 22 Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~ 54 (403)
+..|.=||.+.- ...||++.|..|.++.|-
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 456999997554 457999999999998875
No 60
>COG5145 RAD14 DNA excision repair protein [DNA replication, recombination, and repair]
Probab=22.67 E-value=26 Score=34.19 Aligned_cols=33 Identities=21% Similarity=0.478 Sum_probs=25.3
Q ss_pred CCCCCCccCCCC--CCCCceeeccccccchhhhhhh
Q 015634 19 KSENKMCFDCNA--KNPTWASVTYGIFLCIDCSAVH 52 (403)
Q Consensus 19 ~p~Nk~C~DCga--~nP~WaSv~~GiflC~~CsgiH 52 (403)
..-|..|+.|.. .+|.+-+ .|||-+|..|+.-|
T Consensus 113 i~~apkC~eC~~IelD~~l~d-~F~~~VC~~Cr~~~ 147 (292)
T COG5145 113 IALAPKCKECLQIELDDELED-TFGISVCRSCRHSM 147 (292)
T ss_pred hhhCccceeeeeeecchHHHh-hhcchhHHhhhhhc
Confidence 346889999997 3444443 49999999999988
No 61
>cd07161 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers. DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs h
Probab=22.61 E-value=48 Score=27.55 Aligned_cols=29 Identities=21% Similarity=0.708 Sum_probs=23.0
Q ss_pred CCccCCCCCCCCceeeccccccchhhhhhhcc
Q 015634 23 KMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 23 k~C~DCga~nP~WaSv~~GiflC~~CsgiHR~ 54 (403)
..|.=||.+.- ...||++.|..|.++.|-
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 34888887544 458999999999998874
No 62
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=22.24 E-value=61 Score=23.94 Aligned_cols=30 Identities=20% Similarity=0.620 Sum_probs=20.9
Q ss_pred CCCCccCCCCCCC--Cc-------eeeccccccchhhhh
Q 015634 21 ENKMCFDCNAKNP--TW-------ASVTYGIFLCIDCSA 50 (403)
Q Consensus 21 ~Nk~C~DCga~nP--~W-------aSv~~GiflC~~Csg 50 (403)
.+..|-=|++..+ .| .++.-.|+||..|..
T Consensus 6 s~~kCELC~a~~~L~vy~Vpp~~~~~~d~~iliC~tC~~ 44 (47)
T smart00782 6 CESKCELCGSDSPLVVYAVPPSSDVTADNSVMLCDTCHS 44 (47)
T ss_pred cCCcccCcCCCCCceEEecCCCCCCCccceeeechHHHH
Confidence 3445999998654 22 245678999999975
No 63
>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=22.17 E-value=44 Score=27.29 Aligned_cols=27 Identities=30% Similarity=0.768 Sum_probs=21.6
Q ss_pred ccCCCCCCCCceeeccccccchhhhhhhcc
Q 015634 25 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 25 C~DCga~nP~WaSv~~GiflC~~CsgiHR~ 54 (403)
|.=||.+.- ...||++.|..|.+.+|-
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 777876543 457999999999999875
No 64
>cd07165 NR_DBD_DmE78_like DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two C4-type zinc fingers. DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. The SmE78 may be involved in transduction of an ecdysone signal in S. mansoni,
Probab=22.12 E-value=46 Score=26.88 Aligned_cols=27 Identities=30% Similarity=0.715 Sum_probs=21.0
Q ss_pred ccCCCCCCCCceeeccccccchhhhhhhcc
Q 015634 25 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 25 C~DCga~nP~WaSv~~GiflC~~CsgiHR~ 54 (403)
|.=||.+.- ...||++.|..|.++.|-
T Consensus 1 C~VCg~~~~---g~hyG~~sC~aC~~FFRR 27 (81)
T cd07165 1 CKVCGDKAS---GYHYGVTSCEGCKGFFRR 27 (81)
T ss_pred CCccCccCc---ceEECchhhhhHHHHHHh
Confidence 556776443 458999999999998875
No 65
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=21.79 E-value=36 Score=31.03 Aligned_cols=34 Identities=26% Similarity=0.644 Sum_probs=24.4
Q ss_pred CCCCCCccCCCCCCCCceeeccccccc-hhhhhhhc
Q 015634 19 KSENKMCFDCNAKNPTWASVTYGIFLC-IDCSAVHR 53 (403)
Q Consensus 19 ~p~Nk~C~DCga~nP~WaSv~~GiflC-~~CsgiHR 53 (403)
+|--+.|+-|| -.--|++++-|.-+| ..|-.+|.
T Consensus 115 KP~r~fCaVCG-~~S~ysC~~CG~kyCsv~C~~~Hn 149 (156)
T KOG3362|consen 115 KPLRKFCAVCG-YDSKYSCVNCGTKYCSVRCLKTHN 149 (156)
T ss_pred CCcchhhhhcC-CCchhHHHhcCCceeechhhhhcc
Confidence 35667899999 555677888887666 46777774
No 66
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=21.56 E-value=57 Score=29.48 Aligned_cols=36 Identities=14% Similarity=0.533 Sum_probs=26.0
Q ss_pred HHHHHHHcCCCCCCccCCCCCCCCceeeccccccchhhhhhhccC
Q 015634 11 LVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSL 55 (403)
Q Consensus 11 ~i~~~L~~~p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~L 55 (403)
++++.+........|.-||. ++..+|..|.|-|+.+
T Consensus 88 ~lL~~~~~~~~~~~C~~Cgg---------~rfv~C~~C~Gs~k~~ 123 (147)
T cd03031 88 KLLKGIRARAGGGVCEGCGG---------ARFVPCSECNGSCKVF 123 (147)
T ss_pred HHHhhcccccCCCCCCCCCC---------cCeEECCCCCCcceEE
Confidence 34444444456667999985 5667999999999874
No 67
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=21.53 E-value=58 Score=23.22 Aligned_cols=22 Identities=27% Similarity=0.637 Sum_probs=15.7
Q ss_pred CccCCCCCCCCceeeccccccc
Q 015634 24 MCFDCNAKNPTWASVTYGIFLC 45 (403)
Q Consensus 24 ~C~DCga~nP~WaSv~~GiflC 45 (403)
.|.+|+..+.-|+++.-|-..|
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c 22 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGC 22 (50)
T ss_pred CcccCCCcCCeEEecCCCCccc
Confidence 5999998887776666555555
No 68
>PF13119 DUF3973: Domain of unknown function (DUF3973)
Probab=20.99 E-value=31 Score=24.70 Aligned_cols=14 Identities=43% Similarity=1.210 Sum_probs=11.1
Q ss_pred ccchhhhhhhccCC
Q 015634 43 FLCIDCSAVHRSLG 56 (403)
Q Consensus 43 flC~~CsgiHR~LG 56 (403)
|-|+.||.+|-.-+
T Consensus 2 yYCi~Cs~~h~e~~ 15 (41)
T PF13119_consen 2 YYCINCSEIHHEKG 15 (41)
T ss_pred EEEEEhHHhHHhhc
Confidence 57999999997543
No 69
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=20.98 E-value=1e+02 Score=22.00 Aligned_cols=38 Identities=13% Similarity=0.403 Sum_probs=26.0
Q ss_pred HHHHHHHHcCCCCCCccCCCCCCCCceeeccccccchhhh
Q 015634 10 NLVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCS 49 (403)
Q Consensus 10 ~~i~~~L~~~p~Nk~C~DCga~nP~WaSv~~GiflC~~Cs 49 (403)
.++|..++ =|..-+|--||...+.|..- .+.|-|-.|.
T Consensus 7 ~~~l~~~R-W~~g~~CP~Cg~~~~~~~~~-~~~~~C~~C~ 44 (46)
T PF12760_consen 7 REYLEEIR-WPDGFVCPHCGSTKHYRLKT-RGRYRCKACR 44 (46)
T ss_pred HHHHHHhc-CCCCCCCCCCCCeeeEEeCC-CCeEECCCCC
Confidence 45566654 34447899999985555433 5888898885
No 70
>cd06955 NR_DBD_VDR DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of core
Probab=20.85 E-value=44 Score=28.73 Aligned_cols=30 Identities=17% Similarity=0.584 Sum_probs=24.5
Q ss_pred CCCccCCCCCCCCceeeccccccchhhhhhhcc
Q 015634 22 NKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 22 Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~ 54 (403)
.+.|.=|+.+.- ...||++.|..|.++.|-
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 467999997554 458999999999998874
No 71
>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=20.85 E-value=54 Score=26.38 Aligned_cols=29 Identities=24% Similarity=0.801 Sum_probs=23.4
Q ss_pred CCccCCCCCCCCceeeccccccchhhhhhhcc
Q 015634 23 KMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 23 k~C~DCga~nP~WaSv~~GiflC~~CsgiHR~ 54 (403)
+.|.=|+.+.- ...||++.|..|.+..|-
T Consensus 3 ~~C~VCg~~a~---g~hyGv~sC~aC~~FFRR 31 (78)
T cd07172 3 KICLVCSDEAS---GCHYGVLTCGSCKVFFKR 31 (78)
T ss_pred CCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 46888987543 468999999999998864
No 72
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=20.82 E-value=1.1e+02 Score=27.91 Aligned_cols=38 Identities=18% Similarity=0.325 Sum_probs=23.5
Q ss_pred cCCCCCCccCCCCCCCC-ceeeccccccchhhhhhhccC
Q 015634 18 AKSENKMCFDCNAKNPT-WASVTYGIFLCIDCSAVHRSL 55 (403)
Q Consensus 18 ~~p~Nk~C~DCga~nP~-WaSv~~GiflC~~CsgiHR~L 55 (403)
..+.-.+|-+||.+=|. -.-+-=+..+|+.|...|-..
T Consensus 107 ~~gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~E~~ 145 (151)
T PRK10778 107 EDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIR 145 (151)
T ss_pred hCCCCceeccCCCcccHHHHhcCCCccccHHHHHHHHHH
Confidence 45677899999986331 000111346899999877543
No 73
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=20.79 E-value=63 Score=26.75 Aligned_cols=31 Identities=29% Similarity=0.740 Sum_probs=25.0
Q ss_pred CCCCccCCCCCCCCceeeccccccchhhhhhhcc
Q 015634 21 ENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 21 ~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~ 54 (403)
..+.|.=||.+.- ...||+..|..|.++.|-
T Consensus 5 ~~~~C~VCg~~~~---g~hyGv~sC~aCk~FFRR 35 (90)
T cd07168 5 SPKLCSICEDKAT---GLHYGIITCEGCKGFFKR 35 (90)
T ss_pred cCCCCcccCCcCc---ceEECceehhhhhHhhhh
Confidence 4567999997543 568999999999998874
No 74
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=20.76 E-value=49 Score=25.26 Aligned_cols=40 Identities=20% Similarity=0.463 Sum_probs=27.6
Q ss_pred CCCCCCccCCCCCCCCceeeccccccchhhhhhhccCCCccccee
Q 015634 19 KSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVR 63 (403)
Q Consensus 19 ~p~Nk~C~DCga~nP~WaSv~~GiflC~~CsgiHR~LG~hiS~Vk 63 (403)
.++-+.|.-||.+. =.--.||+.||..|-..+ -..|.|||
T Consensus 13 GkGsr~C~vCg~~~--gliRkygL~~CRqCFRe~---A~~iGF~K 52 (54)
T PTZ00218 13 GKGSRQCRVCSNRH--GLIRKYGLNVCRQCFREN---AELIGFHK 52 (54)
T ss_pred CCCCCeeecCCCcc--hhhhhcCcchhhHHHHHh---hHhcCeee
Confidence 36778999999854 233469999999997533 34455554
No 75
>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=20.70 E-value=37 Score=27.90 Aligned_cols=28 Identities=18% Similarity=0.539 Sum_probs=22.6
Q ss_pred CccCCCCCCCCceeeccccccchhhhhhhcc
Q 015634 24 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 24 ~C~DCga~nP~WaSv~~GiflC~~CsgiHR~ 54 (403)
.|.=||.+.- ...||++.|..|.+..|-
T Consensus 2 ~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 29 (86)
T cd07157 2 TCQVCGEPAA---GFHHGAYVCEACKKFFMR 29 (86)
T ss_pred CCcccCCcCc---ccEECcceeeEeeeEEec
Confidence 4888886543 568999999999998875
No 76
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=20.53 E-value=56 Score=25.74 Aligned_cols=27 Identities=30% Similarity=0.755 Sum_probs=20.5
Q ss_pred ccCCCCCCCCceeeccccccchhhhhhhcc
Q 015634 25 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 25 C~DCga~nP~WaSv~~GiflC~~CsgiHR~ 54 (403)
|.=|+.+.- ...||++.|..|.+..|-
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 455665444 358999999999998874
No 77
>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=20.25 E-value=59 Score=26.02 Aligned_cols=28 Identities=21% Similarity=0.770 Sum_probs=22.6
Q ss_pred CccCCCCCCCCceeeccccccchhhhhhhcc
Q 015634 24 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (403)
Q Consensus 24 ~C~DCga~nP~WaSv~~GiflC~~CsgiHR~ 54 (403)
.|.=|+.+.- ...||++.|..|.+..|-
T Consensus 2 ~C~VC~~~~~---g~hygv~sC~aC~~FFRR 29 (77)
T cd06956 2 ICAICGDRAS---GKHYGVYSCEGCKGFFKR 29 (77)
T ss_pred CCcccCCcCc---ceEECceeehhHHHHHHH
Confidence 5778887554 468999999999998874
Done!