Query 018505
Match_columns 355
No_of_seqs 235 out of 1105
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 09:34:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018505.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018505hhsearch_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 3.7E-98 8E-103 726.3 24.3 339 1-348 1-348 (395)
2 KOG0706 Predicted GTPase-activ 100.0 1.4E-79 3.1E-84 608.4 20.2 341 1-348 2-404 (454)
3 KOG0704 ADP-ribosylation facto 100.0 2.7E-37 5.9E-42 299.5 8.7 117 8-124 5-122 (386)
4 COG5347 GTPase-activating prot 100.0 3.6E-35 7.9E-40 286.4 10.0 117 9-125 7-124 (319)
5 KOG0703 Predicted GTPase-activ 100.0 1.5E-34 3.2E-39 276.7 4.5 104 7-110 10-123 (287)
6 PF01412 ArfGap: Putative GTPa 100.0 5.7E-34 1.2E-38 241.4 4.7 83 11-93 2-84 (116)
7 smart00105 ArfGap Putative GTP 100.0 2E-31 4.4E-36 224.6 7.2 77 20-96 1-77 (112)
8 PLN03131 hypothetical protein; 99.9 7E-28 1.5E-32 247.6 11.0 90 1-93 1-91 (705)
9 PLN03119 putative ADP-ribosyla 99.9 7.7E-28 1.7E-32 245.6 11.1 90 1-93 1-91 (648)
10 KOG0705 GTPase-activating prot 99.9 7.8E-23 1.7E-27 208.9 4.4 97 12-108 503-611 (749)
11 KOG0521 Putative GTPase activa 99.8 1.4E-20 3E-25 202.4 2.0 97 12-108 416-526 (785)
12 KOG0818 GTPase-activating prot 99.7 3.3E-18 7.2E-23 173.0 0.1 92 17-108 3-114 (669)
13 KOG1117 Rho- and Arf-GTPase ac 99.6 6.3E-16 1.4E-20 163.9 2.8 99 11-109 287-399 (1186)
14 KOG0702 Predicted GTPase-activ 99.2 2.1E-11 4.6E-16 124.0 4.5 83 9-92 12-95 (524)
15 KOG0521 Putative GTPase activa 93.6 0.017 3.8E-07 63.6 -0.4 73 17-91 625-698 (785)
16 PRK00085 recO DNA repair prote 83.8 0.64 1.4E-05 43.5 1.9 35 18-52 145-180 (247)
17 TIGR00613 reco DNA repair prot 74.4 2.1 4.6E-05 39.9 2.2 35 17-51 142-177 (241)
18 PF00643 zf-B_box: B-box zinc 72.0 2.8 6.1E-05 28.7 1.8 34 21-54 2-36 (42)
19 PF00320 GATA: GATA zinc finge 64.8 3.6 7.8E-05 28.0 1.1 32 25-56 1-34 (36)
20 smart00401 ZnF_GATA zinc finge 64.3 5.2 0.00011 29.4 2.0 37 21-57 2-40 (52)
21 PLN03114 ADP-ribosylation fact 61.8 3.5 7.5E-05 42.1 0.9 45 296-340 325-374 (395)
22 PF08271 TF_Zn_Ribbon: TFIIB z 59.9 4.1 8.8E-05 28.6 0.7 27 24-51 2-28 (43)
23 PRK11019 hypothetical protein; 57.4 5.1 0.00011 33.0 1.0 37 21-58 35-73 (88)
24 KOG0706 Predicted GTPase-activ 57.3 6.8 0.00015 40.9 2.1 27 294-320 379-405 (454)
25 PF01286 XPA_N: XPA protein N- 56.2 4.1 8.9E-05 27.9 0.2 27 23-49 4-31 (34)
26 PRK12495 hypothetical protein; 55.3 8.3 0.00018 36.8 2.1 30 19-52 39-68 (226)
27 COG1381 RecO Recombinational D 52.1 8 0.00017 37.1 1.5 32 18-49 150-182 (251)
28 PF11781 RRN7: RNA polymerase 50.8 11 0.00023 25.9 1.6 27 20-49 6-32 (36)
29 COG1997 RPL43A Ribosomal prote 49.6 20 0.00043 29.7 3.2 34 17-52 30-63 (89)
30 PF10764 Gin: Inhibitor of sig 49.2 9.5 0.00021 27.7 1.2 26 24-50 1-26 (46)
31 TIGR02419 C4_traR_proteo phage 44.4 14 0.00031 28.3 1.6 34 18-52 27-62 (63)
32 cd07173 NR_DBD_AR DNA-binding 42.4 15 0.00034 29.5 1.6 32 20-54 1-32 (82)
33 cd07171 NR_DBD_ER DNA-binding 41.1 16 0.00035 29.3 1.5 31 21-54 2-32 (82)
34 cd00202 ZnF_GATA Zinc finger D 41.0 17 0.00037 27.0 1.5 34 24-57 1-36 (54)
35 cd06968 NR_DBD_ROR DNA-binding 38.3 19 0.00042 29.7 1.6 31 21-54 4-34 (95)
36 PF14803 Nudix_N_2: Nudix N-te 37.2 12 0.00026 25.5 0.2 30 23-53 1-33 (34)
37 cd07160 NR_DBD_LXR DNA-binding 36.6 21 0.00046 29.9 1.6 31 21-54 17-47 (101)
38 cd07170 NR_DBD_ERR DNA-binding 36.3 20 0.00043 29.8 1.3 30 22-54 4-33 (97)
39 TIGR02890 spore_yteA sporulati 35.4 21 0.00045 32.3 1.4 42 11-54 76-119 (159)
40 PF07282 OrfB_Zn_ribbon: Putat 34.9 19 0.00041 27.2 0.9 28 21-50 27-54 (69)
41 PF01258 zf-dskA_traR: Prokary 34.3 6.3 0.00014 26.6 -1.6 29 24-52 5-34 (36)
42 PF12760 Zn_Tnp_IS1595: Transp 32.3 51 0.0011 23.3 2.8 39 9-49 6-44 (46)
43 cd06966 NR_DBD_CAR DNA-binding 32.1 22 0.00047 29.3 0.9 29 23-54 1-29 (94)
44 COG2174 RPL34A Ribosomal prote 30.3 29 0.00062 28.9 1.3 35 16-50 28-79 (93)
45 PTZ00255 60S ribosomal protein 30.1 52 0.0011 27.3 2.8 38 12-51 26-63 (90)
46 cd07169 NR_DBD_GCNF_like DNA-b 29.5 31 0.00067 28.2 1.4 32 20-54 4-35 (90)
47 PRK00423 tfb transcription ini 29.3 32 0.0007 33.9 1.7 33 20-53 9-41 (310)
48 PHA00080 DksA-like zinc finger 28.2 26 0.00055 27.6 0.7 34 19-53 28-63 (72)
49 cd07163 NR_DBD_TLX DNA-binding 28.0 27 0.0006 28.6 0.9 31 21-54 5-35 (92)
50 cd07166 NR_DBD_REV_ERB DNA-bin 27.6 32 0.0007 28.0 1.2 30 22-54 3-32 (89)
51 smart00782 PhnA_Zn_Ribbon PhnA 27.2 39 0.00085 24.6 1.5 29 22-50 7-44 (47)
52 cd07161 NR_DBD_EcR DNA-binding 26.9 36 0.00079 27.9 1.4 29 23-54 2-30 (91)
53 cd07162 NR_DBD_PXR DNA-binding 26.8 37 0.0008 27.4 1.4 28 24-54 1-28 (87)
54 COG2158 Uncharacterized protei 26.6 35 0.00075 29.3 1.2 25 34-58 52-78 (112)
55 cd06965 NR_DBD_Ppar DNA-bindin 26.4 34 0.00073 27.5 1.1 27 25-54 2-28 (84)
56 smart00290 ZnF_UBP Ubiquitin C 26.2 46 0.00099 23.4 1.7 24 24-47 1-24 (50)
57 cd07172 NR_DBD_GR_PR DNA-bindi 25.9 38 0.00083 26.9 1.3 30 22-54 2-31 (78)
58 cd07165 NR_DBD_DmE78_like DNA- 25.8 36 0.00078 27.1 1.2 27 25-54 1-27 (81)
59 PRK13715 conjugal transfer pro 25.3 30 0.00066 27.3 0.6 33 22-54 34-67 (73)
60 PRK10778 dksA RNA polymerase-b 24.5 44 0.00094 30.0 1.5 38 18-55 107-145 (151)
61 KOG3362 Predicted BBOX Zn-fing 24.1 28 0.00061 31.4 0.2 34 20-54 116-150 (156)
62 cd07168 NR_DBD_DHR4_like DNA-b 23.9 51 0.0011 26.9 1.7 31 21-54 5-35 (90)
63 cd06955 NR_DBD_VDR DNA-binding 23.9 43 0.00094 28.4 1.3 30 22-54 6-35 (107)
64 cd07158 NR_DBD_Ppar_like The D 23.8 43 0.00094 26.0 1.2 27 25-54 1-27 (73)
65 cd06956 NR_DBD_RXR DNA-binding 23.7 45 0.00098 26.3 1.3 28 24-54 2-29 (77)
66 cd07156 NR_DBD_VDR_like The DN 23.5 44 0.00095 25.9 1.2 27 25-54 1-27 (72)
67 cd07157 2DBD_NR_DBD1 The first 23.3 34 0.00074 27.6 0.6 28 24-54 2-29 (86)
68 TIGR00373 conserved hypothetic 23.1 35 0.00075 30.6 0.6 37 15-52 100-138 (158)
69 PF13462 Thioredoxin_4: Thiore 23.1 36 0.00077 28.8 0.7 28 29-56 8-35 (162)
70 cd03031 GRX_GRX_like Glutaredo 22.9 53 0.0012 29.2 1.8 35 12-55 89-123 (147)
71 PF06689 zf-C4_ClpX: ClpX C4-t 22.2 55 0.0012 22.9 1.4 29 23-51 2-33 (41)
72 cd07155 NR_DBD_ER_like DNA-bin 22.0 46 0.001 26.0 1.1 27 25-54 1-27 (75)
73 COG0675 Transposase and inacti 22.0 36 0.00077 32.2 0.5 23 22-51 309-331 (364)
74 cd07179 2DBD_NR_DBD2 The secon 21.8 49 0.0011 25.9 1.2 27 25-54 1-27 (74)
75 PF01780 Ribosomal_L37ae: Ribo 21.8 56 0.0012 27.1 1.5 39 11-51 24-62 (90)
76 COG1734 DksA DnaK suppressor p 21.6 40 0.00087 29.2 0.7 31 23-53 81-112 (120)
77 cd06958 NR_DBD_COUP_TF DNA-bin 21.4 52 0.0011 25.6 1.2 27 25-54 1-27 (73)
78 PF13119 DUF3973: Domain of un 21.1 30 0.00064 24.6 -0.2 14 43-56 2-15 (41)
79 TIGR02420 dksA RNA polymerase- 20.9 54 0.0012 27.4 1.3 30 20-49 78-108 (110)
80 PF12156 ATPase-cat_bd: Putati 20.8 60 0.0013 26.3 1.5 31 24-54 2-38 (88)
81 cd06970 NR_DBD_PNR DNA-binding 20.8 48 0.001 27.2 1.0 32 20-54 4-35 (92)
82 cd07164 NR_DBD_PNR_like_1 DNA- 20.4 55 0.0012 25.8 1.2 27 25-54 1-27 (78)
83 cd06967 NR_DBD_TR2_like DNA-bi 20.3 46 0.00099 27.0 0.8 30 22-54 3-32 (87)
84 PF08792 A2L_zn_ribbon: A2L zi 20.3 44 0.00095 22.5 0.5 29 22-52 3-31 (33)
85 TIGR00100 hypA hydrogenase nic 20.3 55 0.0012 27.8 1.3 45 18-67 66-112 (115)
86 PRK06266 transcription initiat 20.1 42 0.00091 30.7 0.6 29 24-53 119-147 (178)
87 PTZ00218 40S ribosomal protein 20.1 48 0.0011 25.0 0.8 32 19-52 13-44 (54)
No 1
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=100.00 E-value=3.7e-98 Score=726.31 Aligned_cols=339 Identities=67% Similarity=1.009 Sum_probs=311.1
Q ss_pred CCCcchhhHHHHHHHHHcCCCCCCCcCCCCCCCCeeEeccccccchhchhhhccCCCccceeeeccCCCCCHHHHHHHhc
Q 018505 1 MASDNLTDKNLVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVY 80 (355)
Q Consensus 1 M~~~~~~~~~~i~~~L~~~p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~LG~hiS~VkS~~lD~W~~~~l~~m~~ 80 (355)
|+....+|+.++|++|+..|+|++|||||+++|+|+|+|||||||++|+||||.||+||++|||++||.|++++|++|+.
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 CChHHHHHHHhhcCCCCCCccccccccHHHHHHHHHHHHHHHHHhhhcc-CCCCCCCCCCCcccCCCCCCccCCCCCCC-
Q 018505 81 GGNNRAQVFFKQHGWTDGGKIEAKYTSRAAELYKQILAKEVAKNMAEEA-GLPSSPVASQPAQAANALPDVKIQDAPKE- 158 (355)
Q Consensus 81 gGN~~an~~~e~~g~~~~~~i~~KY~~raa~~Yr~~l~~~v~k~~~~~~-~~~~~~~~~~~~~~~d~f~~~~~~~~~~~- 158 (355)
+||.++|.||++||+.....|+.||.++++.+||++|.++|++.++++. .+|++++++.. ..|+|++.+..+.|.+
T Consensus 81 GGN~rA~~fF~qhG~~~~~~~~~KY~S~aA~~Yre~L~keVa~~~a~~~~~~p~~~~~~~~--~~~~~~~~~~~e~~~~~ 158 (395)
T PLN03114 81 GGNNRAQVFFKQYGWSDGGKTEAKYTSRAADLYKQILAKEVAKSKAEEELDLPPSPPDSTQ--VPNGLSSIKTSEALKES 158 (395)
T ss_pred hcCHHHHHHHHHcCCCCCCCcccccCCHHHHHHHHHHHHHHHHhhhccccCCCCCCCCccc--cccCccccccccccccc
Confidence 9999999999999998877899999999999999999999999998765 56677766433 8899999999888865
Q ss_pred -CcCCCCCCCCCCCCCcccccccccccccCcccccCCCCCCcCceeccCCCCccccccCCCCCCCCCCCCCCC-CCCCCC
Q 018505 159 -NYQGRQETQDAPGSPKVSRTVLTSTVKKPLGAKKSGKTGGLGARKLTSKPSESLYEQKPEEPSVPISSSTSN-TSSVSL 236 (355)
Q Consensus 159 -~~~~~~~~~~~~~~p~~~~~~~s~~~KKp~~aKklGKkggLGAqKv~t~~~e~l~eQk~~E~~~~~~~~~~~-~~~~~~ 236 (355)
+...+++|....++|+++ +..|||||+||.||+|||||+||+|+++|+||||||+| .++.|++++. .+..++
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 334455665666677765 57899999999999999999999999999999999999 7788877765 367788
Q ss_pred CcccchhhhccccccCCCCCCCCcccccCCCCCCccc-cccCCCCC-cccCCC--CCcccccccHHHHHhcccccccccc
Q 018505 237 PFASRFEYVDNVQSSELSSGGPQVLSHVAPPKSSSFF-ADYGMDNG-FQKKSG--SSKVQIQETDEARKKFSNAKSISSS 312 (355)
Q Consensus 237 ~~ssRlaY~d~~~~~~~~~~~~~~~shs~~p~~~~ff-~~~gm~~~-~~~~~~--~~k~~~~~t~ea~kKF~naKaISSd 312 (355)
+.++||.|.|++|. ++..+++++++|++||++++|| ++|||+.| +++++. +.|+|++++|||||||+|||+||||
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 89999999999998 8888889999999999999999 89999999 888887 7899999999999999999999999
Q ss_pred cccCCCCCCcccchhhcccccccCC-CCCccccCccc
Q 018505 313 QFFGDQNNSIDMDTQVSLQKFSVCP-LPYAGLLGKFC 348 (355)
Q Consensus 313 ~~FG~~~~~~~~e~~~rL~~f~gs~-iss~~~fg~~~ 348 (355)
||||+++++.|+|++++|+||+|++ |||+||||++.
T Consensus 312 qfFg~~~~~~d~~~~~~l~kf~gs~~ISsad~fg~~~ 348 (395)
T PLN03114 312 QYFGNDNNSADLEAKSSLKKFSGSSAISSADLFGDSD 348 (395)
T ss_pred hhccccccccchhhHHHHHhhccccccchHHhcCCCC
Confidence 9999999888999999999999999 99999999983
No 2
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=1.4e-79 Score=608.45 Aligned_cols=341 Identities=46% Similarity=0.676 Sum_probs=265.7
Q ss_pred CCCcchhhHHHHHHHHHcCCCCCCCcCCCCCCCCeeEeccccccchhchhhhccCCCccceeeeccCCCCCHHHHHHHhc
Q 018505 1 MASDNLTDKNLVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVY 80 (355)
Q Consensus 1 M~~~~~~~~~~i~~~L~~~p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~LG~hiS~VkS~~lD~W~~~~l~~m~~ 80 (355)
|+.+...+.+.+|++|+.+++||+|||||++||+|+||+||||||++|+++||+|||||+||||++||+|++.||++|+.
T Consensus 2 ~~~~~k~d~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~ 81 (454)
T KOG0706|consen 2 MATPNKQDIQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQV 81 (454)
T ss_pred CCccchhhHHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhh
Confidence 78899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CChHHHHHHHhhcCCCCCCccccccccHHHHHHHHHHHHHHHHHhhhcc-C--CCC-CCCCCCCcccCCCCCCccCCCC-
Q 018505 81 GGNNRAQVFFKQHGWTDGGKIEAKYTSRAAELYKQILAKEVAKNMAEEA-G--LPS-SPVASQPAQAANALPDVKIQDA- 155 (355)
Q Consensus 81 gGN~~an~~~e~~g~~~~~~i~~KY~~raa~~Yr~~l~~~v~k~~~~~~-~--~~~-~~~~~~~~~~~d~f~~~~~~~~- 155 (355)
|||.+|+.||++|||.. .++++||.+|++++||+.|..+|.+.+.+.+ . +.. .++..++..+.|||+.+.....
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 99999999999999988 5999999999999999999999999998764 2 222 2333456667899998765431
Q ss_pred CCCCcCCCCCCCCCCCCCcccccccccccccCcccccCC-CCC-CcCceeccCCCCccccccCCCCCCCCCCCCCCCCC-
Q 018505 156 PKENYQGRQETQDAPGSPKVSRTVLTSTVKKPLGAKKSG-KTG-GLGARKLTSKPSESLYEQKPEEPSVPISSSTSNTS- 232 (355)
Q Consensus 156 ~~~~~~~~~~~~~~~~~p~~~~~~~s~~~KKp~~aKklG-Kkg-gLGAqKv~t~~~e~l~eQk~~E~~~~~~~~~~~~~- 232 (355)
-..+.... ..+++|+++.+++++.+|+|+.++++| ++| +||||||+++.+.++++|.+++......+++.+..
T Consensus 161 ~~~s~~~l----~~~~s~~~S~~v~sg~~k~p~~~k~~g~~k~~~lgarkv~t~s~~~~~~~~~~~~~~~i~a~s~~~~s 236 (454)
T KOG0706|consen 161 HEPSTDAL----KSLSSPSASNTVVSGKKKPPVTKKGLGAKKGVTLGARKVNTKSFKSIESQAQEAEKNKIKAASPKPSS 236 (454)
T ss_pred cCCccccc----ccccCCccccccccccccCCccccccccccccccCceecccccccchhhccchhhhccccccCCCcch
Confidence 11111111 123467777777777788888888899 554 49999999987767888877664444443333321
Q ss_pred CCCCCcccchhhhccccc-------------------cCCCCCCCCccccc-----------CCCCCCccccccCCCCC-
Q 018505 233 SVSLPFASRFEYVDNVQS-------------------SELSSGGPQVLSHV-----------APPKSSSFFADYGMDNG- 281 (355)
Q Consensus 233 ~~~~~~ssRlaY~d~~~~-------------------~~~~~~~~~~~shs-----------~~p~~~~ff~~~gm~~~- 281 (355)
+.....+.+++|+|...+ .||| +.++..+|| +||+...+|...+|...
T Consensus 237 ~~~~~~s~~~~~~e~~dd~~~~E~k~~d~~k~~~~~rlgmg-~~~s~~~hs~~~~~~~i~~~t~~~~k~~~~~~~~~~~~ 315 (454)
T KOG0706|consen 237 EESSARSSRLARQELQDDRKKEEAKAKDGKKASSSERLGMG-GYRSVMSHSVLGGMQVIEQVTPPKAKPSFLELDMFSDT 315 (454)
T ss_pred hhhcccchhhhhhHHHHHHHhhhhhhcCcccccchhhhccc-cccchhhhcccCCceeeecccCccccccccccccccch
Confidence 234445677777663322 1566 335555555 57776555555544332
Q ss_pred ------------cccCCC--CCc--------ccccccHHHHHhcccccccccccccCCCCCCcccchhhcccccccCC-C
Q 018505 282 ------------FQKKSG--SSK--------VQIQETDEARKKFSNAKSISSSQFFGDQNNSIDMDTQVSLQKFSVCP-L 338 (355)
Q Consensus 282 ------------~~~~~~--~~k--------~~~~~t~ea~kKF~naKaISSd~~FG~~~~~~~~e~~~rL~~f~gs~-i 338 (355)
+.++.+ .++ .+|+++|||||||||||||||||||||+.. +++|+++||++|+|++ |
T Consensus 316 ~~~~~s~~~~~~~~~~~ss~ss~~a~~~~~~~~v~~td~~rkkF~naKaISSdqyFG~~~~-ad~Ea~~~L~~f~gstaI 394 (454)
T KOG0706|consen 316 TKQSSSNYKDAPFGKGSSSSSSKDAKRAKESRPVEETDEARKKFGNAKAISSDQYFGRGSE-ADLEARARLQKFSGSTAI 394 (454)
T ss_pred hccccCCcccCccccCcccccchhhhccccccccccccHHHHhhccccccchhhhcCCcch-hhhHHHHHHHhccCcccc
Confidence 122221 222 478999999999999999999999999984 5999999999999999 9
Q ss_pred CCccccCccc
Q 018505 339 PYAGLLGKFC 348 (355)
Q Consensus 339 ss~~~fg~~~ 348 (355)
||+||||+..
T Consensus 395 SSsd~fG~~~ 404 (454)
T KOG0706|consen 395 SSSDLFGEGD 404 (454)
T ss_pred chHhhcCCCC
Confidence 9999999975
No 3
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=100.00 E-value=2.7e-37 Score=299.51 Aligned_cols=117 Identities=47% Similarity=0.851 Sum_probs=106.6
Q ss_pred hHHHHHHHHHcCCCCCCCcCCCCCCCCeeEeccccccchhchhhhccCCCccceeeeccCCCCCHHHHHHHhcCChHHHH
Q 018505 8 DKNLVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQ 87 (355)
Q Consensus 8 ~~~~i~~~L~~~p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~an 87 (355)
++.++|.+|+...+|++||||+++||+||||+||||||++|+|+||.|||||||||||+||.|.+.||+.|+.|||.+++
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 34556777776779999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcCCCCC-CccccccccHHHHHHHHHHHHHHHHH
Q 018505 88 VFFKQHGWTDG-GKIEAKYTSRAAELYKQILAKEVAKN 124 (355)
Q Consensus 88 ~~~e~~g~~~~-~~i~~KY~~raa~~Yr~~l~~~v~k~ 124 (355)
+||+.++.... ..|++||.+++|.+||++|..+++..
T Consensus 85 eFL~s~~~~~e~~~i~eKYns~aAa~yRdki~~laegr 122 (386)
T KOG0704|consen 85 EFLSSQGIYKETWPIREKYNSRAAALYRDKIAALAEGR 122 (386)
T ss_pred HHHhhCccccccccHHHhhccHHHHHHHHHHHHHhcCC
Confidence 99999985544 58999999999999999998866543
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=3.6e-35 Score=286.43 Aligned_cols=117 Identities=45% Similarity=0.723 Sum_probs=107.6
Q ss_pred HHHHHHHHHcCCCCCCCcCCCCCCCCeeEeccccccchhchhhhccCCCccceeeeccCCCCCHHHHHHHhcCChHHHHH
Q 018505 9 KNLVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQV 88 (355)
Q Consensus 9 ~~~i~~~L~~~p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~an~ 88 (355)
-+.++..|+..++|+.|||||+++|+|+|||||||||++||||||+||+|||+||||+||.|+.+||++|..+||.+||.
T Consensus 7 ~~~~l~~l~~~~~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~wt~~~l~~m~~gGN~~a~~ 86 (319)
T COG5347 7 DRKLLKLLKSDSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWTEEELRRMEVGGNSNANR 86 (319)
T ss_pred HHHHHHHHhhccccCccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeecccCCHHHHHHHHHhcchhhhh
Confidence 35678899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcCCCC-CCccccccccHHHHHHHHHHHHHHHHHh
Q 018505 89 FFKQHGWTD-GGKIEAKYTSRAAELYKQILAKEVAKNM 125 (355)
Q Consensus 89 ~~e~~g~~~-~~~i~~KY~~raa~~Yr~~l~~~v~k~~ 125 (355)
||+.++... ...|+.||.+..++-|.+.+..++...+
T Consensus 87 ~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~ 124 (319)
T COG5347 87 FYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFID 124 (319)
T ss_pred HhccCCCcccccccccccCHHHHHHHHHHHHHhhhccc
Confidence 999998874 3689999999999999988876555444
No 5
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=1.5e-34 Score=276.70 Aligned_cols=104 Identities=38% Similarity=0.744 Sum_probs=94.0
Q ss_pred hhHHHHHHHHHcCCCCCCCcCCCCCCCCeeEeccccccchhchhhhccCCCccceeeeccCCCCCHHHHHHHhcCChHHH
Q 018505 7 TDKNLVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRA 86 (355)
Q Consensus 7 ~~~~~i~~~L~~~p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~a 86 (355)
...+.+|++|++.|+|++|+|||++.|.|||+|+|||||+.|+||||+||+|||+||||+||.|++|||+.|+..||.+|
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 34477999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhcCCCC----------CCccccccccHHH
Q 018505 87 QVFFKQHGWTD----------GGKIEAKYTSRAA 110 (355)
Q Consensus 87 n~~~e~~g~~~----------~~~i~~KY~~raa 110 (355)
|+|||+..... ..|||+||+.+..
T Consensus 90 n~~~ea~~p~~~~~p~~d~~~e~FIR~KYE~kkf 123 (287)
T KOG0703|consen 90 NSYYEAKLPDPFRRPGPDDLVEQFIRDKYERKKF 123 (287)
T ss_pred hhhccccCCccccCCChHHHHHHHHHHHHhhhhh
Confidence 99999872211 2588999887643
No 6
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=100.00 E-value=5.7e-34 Score=241.35 Aligned_cols=83 Identities=52% Similarity=1.020 Sum_probs=71.7
Q ss_pred HHHHHHHcCCCCCCCcCCCCCCCCeeEeccccccchhchhhhccCCCccceeeeccCCCCCHHHHHHHhcCChHHHHHHH
Q 018505 11 LVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFF 90 (355)
Q Consensus 11 ~i~~~L~~~p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~an~~~ 90 (355)
++|+.|++.|+|++|+|||+++|+|||++||||||+.|+|+||.||+|||+||||+||.|++++|++|+.+||..+|++|
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 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhc
Q 018505 91 KQH 93 (355)
Q Consensus 91 e~~ 93 (355)
+++
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=2e-31 Score=224.58 Aligned_cols=77 Identities=55% Similarity=1.029 Sum_probs=74.5
Q ss_pred CCCCCCcCCCCCCCCeeEeccccccchhchhhhccCCCccceeeeccCCCCCHHHHHHHhcCChHHHHHHHhhcCCC
Q 018505 20 SENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWT 96 (355)
Q Consensus 20 p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~an~~~e~~g~~ 96 (355)
|+|++||||++++|+|+|++||||||+.|+|+||.||+|||+||||+||+|++++|++|+.+||.++|+||+++...
T Consensus 1 ~~N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~VkSl~md~w~~~~i~~~~~~GN~~~n~~~e~~~~~ 77 (112)
T smart00105 1 PGNKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTLDTWTEEELRLLQKGGNENANSIWESNLDD 77 (112)
T ss_pred CCCCcccCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCeeeecccCCCCHHHHHHHHHhhhHHHHHHHHhhCCc
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999988643
No 8
>PLN03131 hypothetical protein; Provisional
Probab=99.95 E-value=7e-28 Score=247.58 Aligned_cols=90 Identities=27% Similarity=0.651 Sum_probs=85.2
Q ss_pred CCCcchhhHH-HHHHHHHcCCCCCCCcCCCCCCCCeeEeccccccchhchhhhccCCCccceeeeccCCCCCHHHHHHHh
Q 018505 1 MASDNLTDKN-LVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMV 79 (355)
Q Consensus 1 M~~~~~~~~~-~i~~~L~~~p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~LG~hiS~VkS~~lD~W~~~~l~~m~ 79 (355)
|.++..++++ ++|++|++.|+|++|+||++++|+|||+|||||||+.|+||||.|| | +||||+||.|+++||++|+
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 8888877774 6999999999999999999999999999999999999999999998 3 8999999999999999999
Q ss_pred cCChHHHHHHHhhc
Q 018505 80 YGGNNRAQVFFKQH 93 (355)
Q Consensus 80 ~gGN~~an~~~e~~ 93 (355)
.+||.++|+||+++
T Consensus 78 ~gGN~~AN~iyean 91 (705)
T PLN03131 78 NGGNQRAREIYLKD 91 (705)
T ss_pred HhccHHHHHHHHhh
Confidence 99999999999964
No 9
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=99.95 E-value=7.7e-28 Score=245.60 Aligned_cols=90 Identities=27% Similarity=0.646 Sum_probs=85.8
Q ss_pred CCCcchhhHH-HHHHHHHcCCCCCCCcCCCCCCCCeeEeccccccchhchhhhccCCCccceeeeccCCCCCHHHHHHHh
Q 018505 1 MASDNLTDKN-LVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMV 79 (355)
Q Consensus 1 M~~~~~~~~~-~i~~~L~~~p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~LG~hiS~VkS~~lD~W~~~~l~~m~ 79 (355)
|+++...+|+ +||++|++.|+|++|+||++++|+|||+|||||||+.|+||||.|| ++||||+||.|+++||++|+
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 8888888885 6999999999999999999999999999999999999999999998 38999999999999999999
Q ss_pred cCChHHHHHHHhhc
Q 018505 80 YGGNNRAQVFFKQH 93 (355)
Q Consensus 80 ~gGN~~an~~~e~~ 93 (355)
.+||.++|+||+++
T Consensus 78 ~gGN~~AN~iyean 91 (648)
T PLN03119 78 NGGNQRAREIYLKN 91 (648)
T ss_pred HhchHHHHHHHHhh
Confidence 99999999999975
No 10
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.86 E-value=7.8e-23 Score=208.94 Aligned_cols=97 Identities=40% Similarity=0.787 Sum_probs=88.2
Q ss_pred HHHHHHcCCCCCCCcCCCCCCCCeeEeccccccchhchhhhccCCCccceeeeccCCCCCHHHHHHHhcCChHHHHHHHh
Q 018505 12 VFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFK 91 (355)
Q Consensus 12 i~~~L~~~p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~an~~~e 91 (355)
.++.|++.+||..|+||+.++|.|||+|+|+++|++|+||||.||.|+|+||||.||.|-.|.+..|..+||+.||.+||
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 57889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hc--CCCC----------CCccccccccH
Q 018505 92 QH--GWTD----------GGKIEAKYTSR 108 (355)
Q Consensus 92 ~~--g~~~----------~~~i~~KY~~r 108 (355)
.. |... +.||++||..+
T Consensus 583 ~~~~G~~KPs~~s~REEkErwIr~KYeqk 611 (749)
T KOG0705|consen 583 GSSQGQTKPSPDSSREEKERWIRAKYEQK 611 (749)
T ss_pred hhccCCcCCCccccHHHHHHHHHHHHHHH
Confidence 53 2111 25888888876
No 11
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.79 E-value=1.4e-20 Score=202.41 Aligned_cols=97 Identities=43% Similarity=0.741 Sum_probs=89.0
Q ss_pred HHHHHHcCCCCCCCcCCCCCCCCeeEeccccccchhchhhhccCCCccceeeeccCCCCCHHHHHHHhcCChHHHHHHHh
Q 018505 12 VFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFK 91 (355)
Q Consensus 12 i~~~L~~~p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~an~~~e 91 (355)
++..++..|+|..|+|||++.|+|+|+|+||.+|++|+|+||+||+|+|+|+|++||.|..+.+.+|+.+||..+|.+|+
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--------------CCccccccccH
Q 018505 92 QHGWTD--------------GGKIEAKYTSR 108 (355)
Q Consensus 92 ~~g~~~--------------~~~i~~KY~~r 108 (355)
+..+.. ..+|++||..+
T Consensus 496 ~~l~~~~~~~~~~~~~~~~r~~~i~~kyve~ 526 (785)
T KOG0521|consen 496 ALLPSYDSSKPTASSSRQAREAWIKAKYVER 526 (785)
T ss_pred cccccccccCCCCccchhhhhHhhhccccee
Confidence 875432 14688888765
No 12
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.69 E-value=3.3e-18 Score=172.98 Aligned_cols=92 Identities=38% Similarity=0.645 Sum_probs=82.6
Q ss_pred HcCCCCCCCcCCCCCCCCeeEeccccccchhchhhhccCCCccceeeeccCCCCCHHHHHHHhcCChHHHHHHHhhcCCC
Q 018505 17 KAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWT 96 (355)
Q Consensus 17 ~~~p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~an~~~e~~g~~ 96 (355)
++...-++|+|||+++|.||||+-|+|||.+|..+||+||.|||.||+|....|.+..|++.....|..+|.+||.+.++
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 34566789999999999999999999999999999999999999999999999999999999999999999999976332
Q ss_pred C--------------------CCccccccccH
Q 018505 97 D--------------------GGKIEAKYTSR 108 (355)
Q Consensus 97 ~--------------------~~~i~~KY~~r 108 (355)
. ..||++||..-
T Consensus 83 ~st~~sg~rk~~pqD~~Hp~K~eFIkaKy~~L 114 (669)
T KOG0818|consen 83 PATIMSGRRKANPQDKVHPNKAEFIRAKYQML 114 (669)
T ss_pred chhhhcccCCCCCcCCCCccHHHHHHHHHHhe
Confidence 1 25899999754
No 13
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.57 E-value=6.3e-16 Score=163.86 Aligned_cols=99 Identities=33% Similarity=0.595 Sum_probs=88.3
Q ss_pred HHHHHHHcCCCCCCCcCCCCCCCCeeEeccccccchhchhhhccCCCccceeeeccCCC--CCHHHHHHHhcCChHHHHH
Q 018505 11 LVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDS--WSAEQLKMMVYGGNNRAQV 88 (355)
Q Consensus 11 ~i~~~L~~~p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~LG~hiS~VkS~~lD~--W~~~~l~~m~~gGN~~an~ 88 (355)
++..++-....|+.|+||+++.|.|||+|++|.||-.|+|-||+||..+|+|+|+.||. |+.+-++++...||.++|.
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 45567778899999999999999999999999999999999999999999999999997 9999999999999999999
Q ss_pred HHhhcCCCC------------CCccccccccHH
Q 018505 89 FFKQHGWTD------------GGKIEAKYTSRA 109 (355)
Q Consensus 89 ~~e~~g~~~------------~~~i~~KY~~ra 109 (355)
||-.+...+ ..||.+||++-.
T Consensus 367 Fwa~nl~~~e~lh~dssp~~r~~fi~~Kykeg~ 399 (1186)
T KOG1117|consen 367 FWAGNLPPNEHLHPDSSPSTRRQFIKEKYKEGK 399 (1186)
T ss_pred ccccCCCCccccCCCCCcchhhhHHHHHhhccc
Confidence 997542211 268999998763
No 14
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.16 E-value=2.1e-11 Score=123.97 Aligned_cols=83 Identities=23% Similarity=0.456 Sum_probs=77.5
Q ss_pred HHHHHHHHHcCCCCCCCcCCCCCCC-CeeEeccccccchhchhhhccCCCccceeeeccCCCCCHHHHHHHhcCChHHHH
Q 018505 9 KNLVFRKLKAKSENKMCFDCNAKNP-TWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQ 87 (355)
Q Consensus 9 ~~~i~~~L~~~p~Nk~C~DCga~~P-~WaSv~~GiflC~~CsgiHR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~an 87 (355)
.+.++|+|+.+|+|++|++|....+ +|++++-|-|+|..|+|+-|.|.. -++||||.|.++++.++..++.+||....
T Consensus 12 ~ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~~-ahRvksiSmttft~qevs~lQshgNq~~k 90 (524)
T KOG0702|consen 12 YEKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLNP-AHRVKSISMTTFTDQEVSFLQSHGNQVCK 90 (524)
T ss_pred HHHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccCCC-ccccceeeeeeccccchHHHhhcchhhhh
Confidence 3679999999999999999999988 999999999999999999999864 35999999999999999999999999999
Q ss_pred HHHhh
Q 018505 88 VFFKQ 92 (355)
Q Consensus 88 ~~~e~ 92 (355)
++|-.
T Consensus 91 ~i~fk 95 (524)
T KOG0702|consen 91 EIWFK 95 (524)
T ss_pred hhhhc
Confidence 99964
No 15
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=93.64 E-value=0.017 Score=63.64 Aligned_cols=73 Identities=18% Similarity=0.191 Sum_probs=60.0
Q ss_pred HcCCCCCCCcCCCCC-CCCeeEeccccccchhchhhhccCCCccceeeeccCCCCCHHHHHHHhcCChHHHHHHHh
Q 018505 17 KAKSENKMCFDCNAK-NPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFK 91 (355)
Q Consensus 17 ~~~p~Nk~C~DCga~-~P~WaSv~~GiflC~~CsgiHR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~an~~~e 91 (355)
.....+..|++|++. .-.|+++++.+-+|++|+++|+.++.|++...++.|++-.+ +.....-||..++.-+.
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 345568899999985 58999999999999999999999999999999998888776 66666666666655554
No 16
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=83.81 E-value=0.64 Score=43.53 Aligned_cols=35 Identities=20% Similarity=0.327 Sum_probs=28.9
Q ss_pred cCCCCCCCcCCCCCCC-CeeEeccccccchhchhhh
Q 018505 18 AKSENKMCFDCNAKNP-TWASVTYGIFLCIDCSAVH 52 (355)
Q Consensus 18 ~~p~Nk~C~DCga~~P-~WaSv~~GiflC~~CsgiH 52 (355)
-.|.-..|+-||.+.. .|.++..|.++|..|...|
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 8899999999999997433
No 17
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=74.37 E-value=2.1 Score=39.88 Aligned_cols=35 Identities=29% Similarity=0.524 Sum_probs=28.9
Q ss_pred HcCCCCCCCcCCCCCCC-CeeEeccccccchhchhh
Q 018505 17 KAKSENKMCFDCNAKNP-TWASVTYGIFLCIDCSAV 51 (355)
Q Consensus 17 ~~~p~Nk~C~DCga~~P-~WaSv~~GiflC~~Csgi 51 (355)
--.|.-..|..||..++ .|.++..|.++|.+|...
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 34577789999998654 788999999999999864
No 18
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=72.00 E-value=2.8 Score=28.68 Aligned_cols=34 Identities=15% Similarity=0.340 Sum_probs=29.4
Q ss_pred CCCCCcCCCCCCCCeeEeccccccchhchhh-hcc
Q 018505 21 ENKMCFDCNAKNPTWASVTYGIFLCIDCSAV-HRS 54 (355)
Q Consensus 21 ~Nk~C~DCga~~P~WaSv~~GiflC~~Csgi-HR~ 54 (355)
.+..|..|......|...+-+++||..|... |+.
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 3678999999889999999999999999987 886
No 19
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=64.77 E-value=3.6 Score=28.02 Aligned_cols=32 Identities=28% Similarity=0.731 Sum_probs=24.0
Q ss_pred CcCCCCC-CCCeeEeccccc-cchhchhhhccCC
Q 018505 25 CFDCNAK-NPTWASVTYGIF-LCIDCSAVHRSLG 56 (355)
Q Consensus 25 C~DCga~-~P~WaSv~~Gif-lC~~CsgiHR~LG 56 (355)
|..|+.. -|.|=....|-. ||-.|.-.+|..|
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 499999998988 9999988777644
No 20
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=64.30 E-value=5.2 Score=29.45 Aligned_cols=37 Identities=24% Similarity=0.600 Sum_probs=30.6
Q ss_pred CCCCCcCCCCCC-CCeeEecccc-ccchhchhhhccCCC
Q 018505 21 ENKMCFDCNAKN-PTWASVTYGI-FLCIDCSAVHRSLGV 57 (355)
Q Consensus 21 ~Nk~C~DCga~~-P~WaSv~~Gi-flC~~CsgiHR~LG~ 57 (355)
....|..|+... |.|=.-..|- +||-.|.-..+..|.
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~ 40 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCC
Confidence 467899999865 8998888886 999999988777554
No 21
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=61.83 E-value=3.5 Score=42.07 Aligned_cols=45 Identities=27% Similarity=0.470 Sum_probs=30.4
Q ss_pred cHHHHHhcccccccccccccCCCC--CCcccchhhcccc--cccCC-CCC
Q 018505 296 TDEARKKFSNAKSISSSQFFGDQN--NSIDMDTQVSLQK--FSVCP-LPY 340 (355)
Q Consensus 296 t~ea~kKF~naKaISSd~~FG~~~--~~~~~e~~~rL~~--f~gs~-iss 340 (355)
..--.+||.+.-+|||+.|||+.+ .+.|..+..-+.| |+.++ |||
T Consensus 325 ~~~~l~kf~gs~~ISsad~fg~~~~d~~id~ta~dli~r~s~qa~qd~ss 374 (395)
T PLN03114 325 AKSSLKKFSGSSAISSADLFGDSDGDFTLDLTAGDLLNRLSLQAQQDISS 374 (395)
T ss_pred hHHHHHhhccccccchHHhcCCCCccccccccHHHHHHHhhhhhHhHHHH
Confidence 333478999999999999999994 3444444443333 45555 665
No 22
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=59.89 E-value=4.1 Score=28.56 Aligned_cols=27 Identities=26% Similarity=0.615 Sum_probs=20.8
Q ss_pred CCcCCCCCCCCeeEeccccccchhchhh
Q 018505 24 MCFDCNAKNPTWASVTYGIFLCIDCSAV 51 (355)
Q Consensus 24 ~C~DCga~~P~WaSv~~GiflC~~Csgi 51 (355)
+|..||+.. .-..-..|-++|..|..|
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-BB
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCCCE
Confidence 699999977 445567899999999554
No 23
>PRK11019 hypothetical protein; Provisional
Probab=57.43 E-value=5.1 Score=32.99 Aligned_cols=37 Identities=19% Similarity=0.479 Sum_probs=26.5
Q ss_pred CCCCCcCCCCCCC--CeeEeccccccchhchhhhccCCCc
Q 018505 21 ENKMCFDCNAKNP--TWASVTYGIFLCIDCSAVHRSLGVH 58 (355)
Q Consensus 21 ~Nk~C~DCga~~P--~WaSv~~GiflC~~CsgiHR~LG~h 58 (355)
.-.+|.|||.+=| .|.-+. ++-.|++|...+-..+.|
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 344333 788999999987654444
No 24
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=57.34 E-value=6.8 Score=40.86 Aligned_cols=27 Identities=37% Similarity=0.609 Sum_probs=23.7
Q ss_pred cccHHHHHhcccccccccccccCCCCC
Q 018505 294 QETDEARKKFSNAKSISSSQFFGDQNN 320 (355)
Q Consensus 294 ~~t~ea~kKF~naKaISSd~~FG~~~~ 320 (355)
-|+-+..+||.++.||||.-|||.+++
T Consensus 379 ~Ea~~~L~~f~gstaISSsd~fG~~~~ 405 (454)
T KOG0706|consen 379 LEARARLQKFSGSTAISSSDLFGEGDD 405 (454)
T ss_pred hHHHHHHHhccCccccchHhhcCCCCC
Confidence 366677899999999999999999984
No 25
>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=56.20 E-value=4.1 Score=27.89 Aligned_cols=27 Identities=15% Similarity=0.506 Sum_probs=16.8
Q ss_pred CCCcCCCCCC-CCeeEeccccccchhch
Q 018505 23 KMCFDCNAKN-PTWASVTYGIFLCIDCS 49 (355)
Q Consensus 23 k~C~DCga~~-P~WaSv~~GiflC~~Cs 49 (355)
..|.+|+.+- -+|..-+|+.-||..|.
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 4799999874 68999999999999995
No 26
>PRK12495 hypothetical protein; Provisional
Probab=55.27 E-value=8.3 Score=36.85 Aligned_cols=30 Identities=20% Similarity=0.339 Sum_probs=24.7
Q ss_pred CCCCCCCcCCCCCCCCeeEeccccccchhchhhh
Q 018505 19 KSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVH 52 (355)
Q Consensus 19 ~p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiH 52 (355)
...+..|-+||.+=|.. -|+.+|..|-.+-
T Consensus 39 tmsa~hC~~CG~PIpa~----pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 39 TMTNAHCDECGDPIFRH----DGQEFCPTCQQPV 68 (226)
T ss_pred ccchhhcccccCcccCC----CCeeECCCCCCcc
Confidence 46899999999999932 5999999998553
No 27
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=52.05 E-value=8 Score=37.06 Aligned_cols=32 Identities=28% Similarity=0.600 Sum_probs=27.8
Q ss_pred cCCCCCCCcCCCCCC-CCeeEeccccccchhch
Q 018505 18 AKSENKMCFDCNAKN-PTWASVTYGIFLCIDCS 49 (355)
Q Consensus 18 ~~p~Nk~C~DCga~~-P~WaSv~~GiflC~~Cs 49 (355)
-.|.=..|+.||.+. |...++-.|-++|..|.
T Consensus 150 ~~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 150 IGPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred CccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 346667999999986 57999999999999998
No 28
>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=50.77 E-value=11 Score=25.93 Aligned_cols=27 Identities=26% Similarity=0.755 Sum_probs=22.8
Q ss_pred CCCCCCcCCCCCCCCeeEeccccccchhch
Q 018505 20 SENKMCFDCNAKNPTWASVTYGIFLCIDCS 49 (355)
Q Consensus 20 p~Nk~C~DCga~~P~WaSv~~GiflC~~Cs 49 (355)
..|..|..|++. |....=|-+.|..|-
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCc
Confidence 346679999998 888899999999885
No 29
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=49.65 E-value=20 Score=29.67 Aligned_cols=34 Identities=24% Similarity=0.526 Sum_probs=26.3
Q ss_pred HcCCCCCCCcCCCCCCCCeeEeccccccchhchhhh
Q 018505 17 KAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVH 52 (355)
Q Consensus 17 ~~~p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiH 52 (355)
...-.-..|..|+.+ .---+..||+.|..|-..-
T Consensus 30 ~~~~~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 30 AQQRAKHVCPFCGRT--TVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred HHHhcCCcCCCCCCc--ceeeeccCeEEcCCCCCee
Confidence 344566799999998 4556789999999997654
No 30
>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=49.15 E-value=9.5 Score=27.67 Aligned_cols=26 Identities=31% Similarity=0.821 Sum_probs=20.1
Q ss_pred CCcCCCCCCCCeeEeccccccchhchh
Q 018505 24 MCFDCNAKNPTWASVTYGIFLCIDCSA 50 (355)
Q Consensus 24 ~C~DCga~~P~WaSv~~GiflC~~Csg 50 (355)
.|.=|+...+. --.=+|-|||.+|=.
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHH
Confidence 48889988776 334489999999965
No 31
>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=44.39 E-value=14 Score=28.27 Aligned_cols=34 Identities=21% Similarity=0.520 Sum_probs=23.9
Q ss_pred cCCCCCCCcCCCCCCC--CeeEeccccccchhchhhh
Q 018505 18 AKSENKMCFDCNAKNP--TWASVTYGIFLCIDCSAVH 52 (355)
Q Consensus 18 ~~p~Nk~C~DCga~~P--~WaSv~~GiflC~~CsgiH 52 (355)
..++...|.|||.+=| .|.- .-|+..|+.|...+
T Consensus 27 ~~~s~g~C~~Cg~~Ip~~Rl~a-~p~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 27 IGPSLRECEDCGEPIPEARREA-LPGVTRCVSCQEIL 62 (63)
T ss_pred cCCCCCeeccCCCcChHHHHhh-cCCcCCcHHHHhhc
Confidence 3466789999998755 3322 23788999998654
No 32
>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=42.41 E-value=15 Score=29.47 Aligned_cols=32 Identities=22% Similarity=0.645 Sum_probs=26.0
Q ss_pred CCCCCCcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 20 SENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 20 p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
|.++.|.-||.+.- ...||++.|..|.+..|-
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 35677999997654 458999999999998874
No 33
>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=41.11 E-value=16 Score=29.31 Aligned_cols=31 Identities=23% Similarity=0.701 Sum_probs=25.7
Q ss_pred CCCCCcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 21 ENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 21 ~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
.|..|.-||.+.- ...||++.|..|.+..|-
T Consensus 2 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 2 DTHFCAVCSDYAS---GYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 4678999997554 468999999999998874
No 34
>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=40.98 E-value=17 Score=27.00 Aligned_cols=34 Identities=29% Similarity=0.691 Sum_probs=27.7
Q ss_pred CCcCCCCCC-CCeeEec-cccccchhchhhhccCCC
Q 018505 24 MCFDCNAKN-PTWASVT-YGIFLCIDCSAVHRSLGV 57 (355)
Q Consensus 24 ~C~DCga~~-P~WaSv~-~GiflC~~CsgiHR~LG~ 57 (355)
+|..|+... |.|=... -+..||-.|.--.+..|.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~ 36 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGV 36 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCC
Confidence 599999865 8898765 788999999987777663
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=38.28 E-value=19 Score=29.71 Aligned_cols=31 Identities=29% Similarity=0.665 Sum_probs=25.8
Q ss_pred CCCCCcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 21 ENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 21 ~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
++..|.-||.+.-. ..||++.|..|.++.|-
T Consensus 4 ~~~~C~VCg~~~~g---~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 4 EVIPCKICGDKSSG---IHYGVITCEGCKGFFRR 34 (95)
T ss_pred cccCCcccCCcCcc---eEECceeehhhHHhhHH
Confidence 56789999986644 57999999999998874
No 36
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=37.20 E-value=12 Score=25.46 Aligned_cols=30 Identities=20% Similarity=0.460 Sum_probs=15.0
Q ss_pred CCCcCCCCCCCCeeEe---ccccccchhchhhhc
Q 018505 23 KMCFDCNAKNPTWASV---TYGIFLCIDCSAVHR 53 (355)
Q Consensus 23 k~C~DCga~~P~WaSv---~~GiflC~~CsgiHR 53 (355)
+.|..||.+ -.+..+ +.-=++|..|.-||-
T Consensus 1 kfC~~CG~~-l~~~ip~gd~r~R~vC~~Cg~IhY 33 (34)
T PF14803_consen 1 KFCPQCGGP-LERRIPEGDDRERLVCPACGFIHY 33 (34)
T ss_dssp -B-TTT--B--EEE--TT-SS-EEEETTTTEEE-
T ss_pred CccccccCh-hhhhcCCCCCccceECCCCCCEEe
Confidence 578899986 233222 333468999999883
No 37
>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=36.56 E-value=21 Score=29.90 Aligned_cols=31 Identities=26% Similarity=0.682 Sum_probs=25.7
Q ss_pred CCCCCcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 21 ENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 21 ~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
.+..|.-|+.+.- ...||+..|..|.++.|-
T Consensus 17 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 47 (101)
T cd07160 17 GNEVCSVCGDKAS---GFHYNVLSCEGCKGFFRR 47 (101)
T ss_pred CCCCCeecCCcCc---ceEECcceehhhhhhhhh
Confidence 4678999998654 458999999999999874
No 38
>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=36.25 E-value=20 Score=29.82 Aligned_cols=30 Identities=23% Similarity=0.707 Sum_probs=24.5
Q ss_pred CCCCcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 22 NKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 22 Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
+..|.-||.+.- ...||++.|..|.++.|-
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 357999997664 358999999999999874
No 39
>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=35.37 E-value=21 Score=32.30 Aligned_cols=42 Identities=14% Similarity=0.438 Sum_probs=25.4
Q ss_pred HHHHHHHcCCCCCCCcCCCCCCC--CeeEeccccccchhchhhhcc
Q 018505 11 LVFRKLKAKSENKMCFDCNAKNP--TWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 11 ~i~~~L~~~p~Nk~C~DCga~~P--~WaSv~~GiflC~~CsgiHR~ 54 (355)
+.+.+|. ...=.+|.+||.+=| .+-.++ ++-+|+.|...+-.
T Consensus 76 ~AL~Ri~-~G~YG~Ce~CGe~I~~~RL~a~P-~a~~Ci~Cq~~~E~ 119 (159)
T TIGR02890 76 HALQKIE-NGTYGICEVCGKPIPYERLEAIP-TATTCVECQNRKEV 119 (159)
T ss_pred HHHHHHh-CCCCCeecccCCcccHHHHhhCC-CcchhHHHHHHhhh
Confidence 3444453 344457999998633 222222 45789999987643
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=34.90 E-value=19 Score=27.22 Aligned_cols=28 Identities=21% Similarity=0.596 Sum_probs=23.3
Q ss_pred CCCCCcCCCCCCCCeeEeccccccchhchh
Q 018505 21 ENKMCFDCNAKNPTWASVTYGIFLCIDCSA 50 (355)
Q Consensus 21 ~Nk~C~DCga~~P~WaSv~~GiflC~~Csg 50 (355)
.-+.|..||..... ..+.-+|.|..|--
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 45689999998887 77888999999854
No 41
>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=34.32 E-value=6.3 Score=26.61 Aligned_cols=29 Identities=28% Similarity=0.681 Sum_probs=16.6
Q ss_pred CCcCCCCCCC-CeeEeccccccchhchhhh
Q 018505 24 MCFDCNAKNP-TWASVTYGIFLCIDCSAVH 52 (355)
Q Consensus 24 ~C~DCga~~P-~WaSv~~GiflC~~CsgiH 52 (355)
.|.+||..=| .-.-+-=|..+|+.|...|
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 4899997533 1122223778899998765
No 42
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=32.34 E-value=51 Score=23.29 Aligned_cols=39 Identities=13% Similarity=0.369 Sum_probs=26.8
Q ss_pred HHHHHHHHHcCCCCCCCcCCCCCCCCeeEeccccccchhch
Q 018505 9 KNLVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCS 49 (355)
Q Consensus 9 ~~~i~~~L~~~p~Nk~C~DCga~~P~WaSv~~GiflC~~Cs 49 (355)
-.+.|..++ =|..-+|.-||.....|..- .+.|-|-.|.
T Consensus 6 c~~~l~~~R-W~~g~~CP~Cg~~~~~~~~~-~~~~~C~~C~ 44 (46)
T PF12760_consen 6 CREYLEEIR-WPDGFVCPHCGSTKHYRLKT-RGRYRCKACR 44 (46)
T ss_pred HHHHHHHhc-CCCCCCCCCCCCeeeEEeCC-CCeEECCCCC
Confidence 345566664 45557899999985555433 6889998885
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=32.07 E-value=22 Score=29.30 Aligned_cols=29 Identities=28% Similarity=0.596 Sum_probs=23.4
Q ss_pred CCCcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 23 KMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 23 k~C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
+.|.-||.+.-. ..||++.|..|.++.|-
T Consensus 1 ~~C~VCg~~a~g---~hyGv~sC~aC~~FFRR 29 (94)
T cd06966 1 KICGVCGDKALG---YNFNAITCESCKAFFRR 29 (94)
T ss_pred CCCeeCCCcCcc---eEECcceeeeehheehh
Confidence 468889875543 48999999999998875
No 44
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=30.29 E-value=29 Score=28.93 Aligned_cols=35 Identities=29% Similarity=0.556 Sum_probs=24.9
Q ss_pred HHcCCCCCCCcCCCCCC-------C----------CeeEeccccccchhchh
Q 018505 16 LKAKSENKMCFDCNAKN-------P----------TWASVTYGIFLCIDCSA 50 (355)
Q Consensus 16 L~~~p~Nk~C~DCga~~-------P----------~WaSv~~GiflC~~Csg 50 (355)
.+..++--.|++||.+- | .-.+=.||-.+|..|..
T Consensus 28 ~kK~~~~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~ 79 (93)
T COG2174 28 EKKKPTIPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVR 79 (93)
T ss_pred eeccCCCCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHHH
Confidence 35667778999999741 1 11245799999999975
No 45
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=30.10 E-value=52 Score=27.32 Aligned_cols=38 Identities=18% Similarity=0.413 Sum_probs=27.7
Q ss_pred HHHHHHcCCCCCCCcCCCCCCCCeeEeccccccchhchhh
Q 018505 12 VFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAV 51 (355)
Q Consensus 12 i~~~L~~~p~Nk~C~DCga~~P~WaSv~~GiflC~~Csgi 51 (355)
+-+-..+.-.-..|.-||........+ ||+-|..|.-.
T Consensus 26 v~kie~~q~a~y~CpfCgk~~vkR~a~--GIW~C~~C~~~ 63 (90)
T PTZ00255 26 IKKIEISQHAKYFCPFCGKHAVKRQAV--GIWRCKGCKKT 63 (90)
T ss_pred HHHHHHHHhCCccCCCCCCCceeeeee--EEEEcCCCCCE
Confidence 333334566778999999877766654 99999999654
No 46
>cd07169 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=29.46 E-value=31 Score=28.18 Aligned_cols=32 Identities=25% Similarity=0.771 Sum_probs=26.2
Q ss_pred CCCCCCcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 20 SENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 20 p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
.++..|.-|+.+.- ...||+..|..|.++.|-
T Consensus 4 ~~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (90)
T cd07169 4 AEQRTCLICGDRAT---GLHYGIISCEGCKGFFKR 35 (90)
T ss_pred ccCCCCeecCCcCc---ceEECcceehhhHHHHHH
Confidence 46778999997654 458999999999998874
No 47
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=29.28 E-value=32 Score=33.94 Aligned_cols=33 Identities=24% Similarity=0.562 Sum_probs=23.2
Q ss_pred CCCCCCcCCCCCCCCeeEeccccccchhchhhhc
Q 018505 20 SENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHR 53 (355)
Q Consensus 20 p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR 53 (355)
.....|.+||..+.- ..-.-|-.+|.+|--|..
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 345689999974321 234679999999988654
No 48
>PHA00080 DksA-like zinc finger domain containing protein
Probab=28.15 E-value=26 Score=27.65 Aligned_cols=34 Identities=21% Similarity=0.559 Sum_probs=23.5
Q ss_pred CCCCCCCcCCCCCCC--CeeEeccccccchhchhhhc
Q 018505 19 KSENKMCFDCNAKNP--TWASVTYGIFLCIDCSAVHR 53 (355)
Q Consensus 19 ~p~Nk~C~DCga~~P--~WaSv~~GiflC~~CsgiHR 53 (355)
.++...|.|||.+=| .|.-++ |+-.|++|...+-
T Consensus 28 ~~~~~~C~~Cg~~Ip~~Rl~a~P-~~~~Cv~Cq~~~E 63 (72)
T PHA00080 28 APSATHCEECGDPIPEARREAVP-GCRTCVSCQEILE 63 (72)
T ss_pred CCCCCEecCCCCcCcHHHHHhCC-CccCcHHHHHHHH
Confidence 345568999998754 443333 6778999988653
No 49
>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=27.99 E-value=27 Score=28.56 Aligned_cols=31 Identities=26% Similarity=0.640 Sum_probs=25.5
Q ss_pred CCCCCcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 21 ENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 21 ~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
-|..|.-||.+.-. ..||+..|..|.+..|-
T Consensus 5 ~~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 35 (92)
T cd07163 5 LDIPCKVCGDRSSG---KHYGIYACDGCSGFFKR 35 (92)
T ss_pred cCCCCcccCCcCcc---cEECceeeeeeeeEEee
Confidence 37789999976544 58999999999998874
No 50
>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=27.61 E-value=32 Score=27.97 Aligned_cols=30 Identities=27% Similarity=0.661 Sum_probs=24.4
Q ss_pred CCCCcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 22 NKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 22 Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
+..|.-||.+.-. ..||++.|..|.++.|-
T Consensus 3 ~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 32 (89)
T cd07166 3 VVLCKVCGDKASG---FHYGVHACEGCKGFFRR 32 (89)
T ss_pred CCCCcccCccCcc---eEEChhhhhhHhhEecc
Confidence 4569999986654 47999999999998875
No 51
>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=27.24 E-value=39 Score=24.63 Aligned_cols=29 Identities=24% Similarity=0.702 Sum_probs=20.6
Q ss_pred CCCCcCCCCCCC--Cee-------Eeccccccchhchh
Q 018505 22 NKMCFDCNAKNP--TWA-------SVTYGIFLCIDCSA 50 (355)
Q Consensus 22 Nk~C~DCga~~P--~Wa-------Sv~~GiflC~~Csg 50 (355)
+..|-=|++..+ .|. ++...|+||..|..
T Consensus 7 ~~kCELC~a~~~L~vy~Vpp~~~~~~d~~iliC~tC~~ 44 (47)
T smart00782 7 ESKCELCGSDSPLVVYAVPPSSDVTADNSVMLCDTCHS 44 (47)
T ss_pred CCcccCcCCCCCceEEecCCCCCCCccceeeechHHHH
Confidence 445999998654 222 45678999999975
No 52
>cd07161 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers. DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs h
Probab=26.87 E-value=36 Score=27.86 Aligned_cols=29 Identities=21% Similarity=0.691 Sum_probs=23.3
Q ss_pred CCCcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 23 KMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 23 k~C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
..|.-||.+.-. ..||++.|..|.++.|-
T Consensus 2 ~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 30 (91)
T cd07161 2 ELCLVCGDRASG---YHYNALTCEGCKGFFRR 30 (91)
T ss_pred CCCeeCCCcCcc---eEECceeehhhHHHHHH
Confidence 358889876553 58999999999998874
No 53
>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=26.76 E-value=37 Score=27.44 Aligned_cols=28 Identities=18% Similarity=0.596 Sum_probs=22.5
Q ss_pred CCcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 24 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 24 ~C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
.|.-||.+.-. ..||++.|..|.+..|-
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 47788876554 48999999999998874
No 54
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=26.57 E-value=35 Score=29.25 Aligned_cols=25 Identities=36% Similarity=0.856 Sum_probs=22.0
Q ss_pred CeeEeccc--cccchhchhhhccCCCc
Q 018505 34 TWASVTYG--IFLCIDCSAVHRSLGVH 58 (355)
Q Consensus 34 ~WaSv~~G--iflC~~CsgiHR~LG~h 58 (355)
.|++-.-| |+-|.+|-=|||.-++.
T Consensus 52 ewi~~~~G~~VwSC~dC~~iH~ke~~~ 78 (112)
T COG2158 52 EWISDSNGRKVWSCSDCHWIHRKEGAE 78 (112)
T ss_pred ceeEcCCCCEEeeccccceecccchHH
Confidence 89999999 99999999999976553
No 55
>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=26.39 E-value=34 Score=27.54 Aligned_cols=27 Identities=30% Similarity=0.749 Sum_probs=21.8
Q ss_pred CcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 25 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 25 C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
|.-||.+.-. ..||++.|..|.+.+|-
T Consensus 2 C~VCg~~~~g---~hyGv~sC~aCk~FFRR 28 (84)
T cd06965 2 CRVCGDKASG---FHYGVHACEGCKGFFRR 28 (84)
T ss_pred CcccCccCcc---eEEChhhhhhhhhheee
Confidence 7778875543 47999999999999885
No 56
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=26.23 E-value=46 Score=23.39 Aligned_cols=24 Identities=25% Similarity=0.517 Sum_probs=18.0
Q ss_pred CCcCCCCCCCCeeEeccccccchh
Q 018505 24 MCFDCNAKNPTWASVTYGIFLCID 47 (355)
Q Consensus 24 ~C~DCga~~P~WaSv~~GiflC~~ 47 (355)
.|.+|+..+.-|+++.-|-..|..
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c~~ 24 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGCGR 24 (50)
T ss_pred CcccCCCcCCeEEecCCCCcccCC
Confidence 599999888788777766666643
No 57
>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers. DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p
Probab=25.88 E-value=38 Score=26.87 Aligned_cols=30 Identities=23% Similarity=0.782 Sum_probs=23.9
Q ss_pred CCCCcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 22 NKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 22 Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
...|.-||.+.- ...||++-|..|.+..|-
T Consensus 2 ~~~C~VCg~~a~---g~hyGv~sC~aC~~FFRR 31 (78)
T cd07172 2 QKICLVCSDEAS---GCHYGVLTCGSCKVFFKR 31 (78)
T ss_pred CCCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 346888997654 358999999999998874
No 58
>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=25.82 E-value=36 Score=27.09 Aligned_cols=27 Identities=30% Similarity=0.715 Sum_probs=21.2
Q ss_pred CcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 25 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 25 C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
|.-||.+.- ...||++.|..|.+..|-
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 566776554 358999999999998885
No 59
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=25.33 E-value=30 Score=27.32 Aligned_cols=33 Identities=24% Similarity=0.610 Sum_probs=22.5
Q ss_pred CCCCcCCCCCCCC-eeEeccccccchhchhhhcc
Q 018505 22 NKMCFDCNAKNPT-WASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 22 Nk~C~DCga~~P~-WaSv~~GiflC~~CsgiHR~ 54 (355)
...|.|||.+=|. -.-.-=|+..|+.|...+-.
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 3589999987552 22222378899999876543
No 60
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=24.47 E-value=44 Score=29.98 Aligned_cols=38 Identities=18% Similarity=0.329 Sum_probs=23.9
Q ss_pred cCCCCCCCcCCCCCCC-CeeEeccccccchhchhhhccC
Q 018505 18 AKSENKMCFDCNAKNP-TWASVTYGIFLCIDCSAVHRSL 55 (355)
Q Consensus 18 ~~p~Nk~C~DCga~~P-~WaSv~~GiflC~~CsgiHR~L 55 (355)
..+.-.+|-+||.+=| .-.-+-=++.+|+.|...|-..
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 3467779999998633 1111111456899999877543
No 61
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=24.07 E-value=28 Score=31.36 Aligned_cols=34 Identities=24% Similarity=0.567 Sum_probs=26.3
Q ss_pred CCCCCCcCCCCCCCCeeEeccccccch-hchhhhcc
Q 018505 20 SENKMCFDCNAKNPTWASVTYGIFLCI-DCSAVHRS 54 (355)
Q Consensus 20 p~Nk~C~DCga~~P~WaSv~~GiflC~-~CsgiHR~ 54 (355)
|--+.|+-|| -.--|.+++.|.-.|. .|-.+|..
T Consensus 116 P~r~fCaVCG-~~S~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 116 PLRKFCAVCG-YDSKYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred CcchhhhhcC-CCchhHHHhcCCceeechhhhhccc
Confidence 5667999999 5566888899987774 67788854
No 62
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=23.91 E-value=51 Score=26.86 Aligned_cols=31 Identities=29% Similarity=0.740 Sum_probs=25.1
Q ss_pred CCCCCcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 21 ENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 21 ~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
....|.-||.+.- ...||+..|..|.+..|-
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 3557999997654 468999999999998874
No 63
>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=23.89 E-value=43 Score=28.35 Aligned_cols=30 Identities=17% Similarity=0.567 Sum_probs=24.6
Q ss_pred CCCCcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 22 NKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 22 Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
.+.|.-||...-. ..||++.|..|.++.|-
T Consensus 6 ~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 35 (107)
T cd06955 6 PRICGVCGDRATG---FHFNAMTCEGCKGFFRR 35 (107)
T ss_pred CCCCeecCCcCcc---cEECcceeeeecceecc
Confidence 4679999976554 58999999999998874
No 64
>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=23.76 E-value=43 Score=25.98 Aligned_cols=27 Identities=30% Similarity=0.737 Sum_probs=20.9
Q ss_pred CcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 25 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 25 C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
|.-||.+.-. ..||++.|..|.+..|-
T Consensus 1 C~VCg~~~~g---~hyGv~~C~aC~~FFRR 27 (73)
T cd07158 1 CKVCGDKASG---FHYGVHSCEGCKGFFRR 27 (73)
T ss_pred CcccCccCcc---eEECcchhhHHHHHHhh
Confidence 5567765443 58999999999999874
No 65
>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=23.71 E-value=45 Score=26.27 Aligned_cols=28 Identities=21% Similarity=0.752 Sum_probs=22.8
Q ss_pred CCcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 24 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 24 ~C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
.|.-||.+.-. ..||++.|..|.+..|-
T Consensus 2 ~C~VC~~~~~g---~hygv~sC~aC~~FFRR 29 (77)
T cd06956 2 ICAICGDRASG---KHYGVYSCEGCKGFFKR 29 (77)
T ss_pred CCcccCCcCcc---eEECceeehhHHHHHHH
Confidence 58888876543 58999999999998874
No 66
>cd07156 NR_DBD_VDR_like The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemi
Probab=23.51 E-value=44 Score=25.95 Aligned_cols=27 Identities=19% Similarity=0.562 Sum_probs=21.0
Q ss_pred CcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 25 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 25 C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
|.-|+.+.-. ..||++.|..|.+..|-
T Consensus 1 C~VC~~~~~g---~hygv~sC~aC~~FFRR 27 (72)
T cd07156 1 CGVCGDRATG---YHFNAMTCEGCKGFFRR 27 (72)
T ss_pred CCccCccCcc---cEECcceehhhhhhhch
Confidence 5567765544 48999999999998874
No 67
>cd07157 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers. The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=23.32 E-value=34 Score=27.64 Aligned_cols=28 Identities=18% Similarity=0.539 Sum_probs=22.8
Q ss_pred CCcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 24 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 24 ~C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
.|.-||.+.- ...||++.|..|.+..|-
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 4888887554 458999999999998875
No 68
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=23.09 E-value=35 Score=30.58 Aligned_cols=37 Identities=22% Similarity=0.397 Sum_probs=22.3
Q ss_pred HHHcCCCCC--CCcCCCCCCCCeeEeccccccchhchhhh
Q 018505 15 KLKAKSENK--MCFDCNAKNPTWASVTYGIFLCIDCSAVH 52 (355)
Q Consensus 15 ~L~~~p~Nk--~C~DCga~~P~WaSv~~GiflC~~CsgiH 52 (355)
+|....+|. +|..|+.+-..=--+++ -|.|..|.+.-
T Consensus 100 ~l~~e~~~~~Y~Cp~c~~r~tf~eA~~~-~F~Cp~Cg~~L 138 (158)
T TIGR00373 100 KLEFETNNMFFICPNMCVRFTFNEAMEL-NFTCPRCGAML 138 (158)
T ss_pred HHhhccCCCeEECCCCCcEeeHHHHHHc-CCcCCCCCCEe
Confidence 333334444 69999855332223344 49999999874
No 69
>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=23.08 E-value=36 Score=28.81 Aligned_cols=28 Identities=18% Similarity=0.391 Sum_probs=22.7
Q ss_pred CCCCCCeeEeccccccchhchhhhccCC
Q 018505 29 NAKNPTWASVTYGIFLCIDCSAVHRSLG 56 (355)
Q Consensus 29 ga~~P~WaSv~~GiflC~~CsgiHR~LG 56 (355)
|.++..+..+-|+-|.|.-|...|..++
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 5677888899999999999999998764
No 70
>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=22.88 E-value=53 Score=29.21 Aligned_cols=35 Identities=14% Similarity=0.568 Sum_probs=25.0
Q ss_pred HHHHHHcCCCCCCCcCCCCCCCCeeEeccccccchhchhhhccC
Q 018505 12 VFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRSL 55 (355)
Q Consensus 12 i~~~L~~~p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~L 55 (355)
+|+.+........|.-||- ++-.+|..|.|-|+.+
T Consensus 89 lL~~~~~~~~~~~C~~Cgg---------~rfv~C~~C~Gs~k~~ 123 (147)
T cd03031 89 LLKGIRARAGGGVCEGCGG---------ARFVPCSECNGSCKVF 123 (147)
T ss_pred HHhhcccccCCCCCCCCCC---------cCeEECCCCCCcceEE
Confidence 4444444456667999985 4567999999999874
No 71
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=22.20 E-value=55 Score=22.86 Aligned_cols=29 Identities=24% Similarity=0.538 Sum_probs=17.7
Q ss_pred CCCcCCCCCCC---CeeEeccccccchhchhh
Q 018505 23 KMCFDCNAKNP---TWASVTYGIFLCIDCSAV 51 (355)
Q Consensus 23 k~C~DCga~~P---~WaSv~~GiflC~~Csgi 51 (355)
++|.=||.+.. .-++-+.|++||.+|...
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 445556689999999753
No 72
>cd07155 NR_DBD_ER_like DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. E
Probab=22.04 E-value=46 Score=26.02 Aligned_cols=27 Identities=26% Similarity=0.707 Sum_probs=20.9
Q ss_pred CcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 25 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 25 C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
|.-||.+.- ...||++.|..|.+..|-
T Consensus 1 C~VC~~~~~---g~hygv~sC~aCk~FFRR 27 (75)
T cd07155 1 CLVCGDIAS---GYHYGVASCEACKAFFKR 27 (75)
T ss_pred CcccCccCc---ceEEChhhhhhhHHHHHH
Confidence 566776543 358999999999998874
No 73
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.01 E-value=36 Score=32.20 Aligned_cols=23 Identities=30% Similarity=0.677 Sum_probs=19.4
Q ss_pred CCCCcCCCCCCCCeeEeccccccchhchhh
Q 018505 22 NKMCFDCNAKNPTWASVTYGIFLCIDCSAV 51 (355)
Q Consensus 22 Nk~C~DCga~~P~WaSv~~GiflC~~Csgi 51 (355)
=+.|.-||. +.-+.|.|..|.-.
T Consensus 309 S~~C~~cg~-------~~~r~~~C~~cg~~ 331 (364)
T COG0675 309 SKTCPCCGH-------LSGRLFKCPRCGFV 331 (364)
T ss_pred cccccccCC-------ccceeEECCCCCCe
Confidence 379999999 56789999999874
No 74
>cd07179 2DBD_NR_DBD2 The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type zinc fingers. The second DNA-binding domain (DBD) of the 2DBD nuclear receptor (NR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. The proteins contain two DBDs in tandem, probably resulting from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=21.83 E-value=49 Score=25.86 Aligned_cols=27 Identities=26% Similarity=0.717 Sum_probs=20.9
Q ss_pred CcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 25 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 25 C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
|.-||.+.-. ..||++.|..|.+..|-
T Consensus 1 C~VCg~~~~g---~hygv~sC~aC~~FFRR 27 (74)
T cd07179 1 CRVCGGKSSG---FHFGALTCEGCKGFFRR 27 (74)
T ss_pred CcccCccCcc---eEECceeehhHHHHHHH
Confidence 5667765443 58999999999998874
No 75
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=21.80 E-value=56 Score=27.13 Aligned_cols=39 Identities=21% Similarity=0.347 Sum_probs=27.5
Q ss_pred HHHHHHHcCCCCCCCcCCCCCCCCeeEeccccccchhchhh
Q 018505 11 LVFRKLKAKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAV 51 (355)
Q Consensus 11 ~i~~~L~~~p~Nk~C~DCga~~P~WaSv~~GiflC~~Csgi 51 (355)
.+-+-..+.-..-.|..||...... +..||+-|..|.-.
T Consensus 24 ~vkkie~~q~~ky~Cp~Cgk~~vkR--~a~GIW~C~~C~~~ 62 (90)
T PF01780_consen 24 RVKKIEISQHAKYTCPFCGKTSVKR--VATGIWKCKKCGKK 62 (90)
T ss_dssp HHHHHHHHHHS-BEESSSSSSEEEE--EETTEEEETTTTEE
T ss_pred HHHHHHHHHhCCCcCCCCCCceeEE--eeeEEeecCCCCCE
Confidence 3333334566788999999988554 56799999999743
No 76
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=21.56 E-value=40 Score=29.24 Aligned_cols=31 Identities=23% Similarity=0.528 Sum_probs=20.7
Q ss_pred CCCcCCCCCCC-CeeEeccccccchhchhhhc
Q 018505 23 KMCFDCNAKNP-TWASVTYGIFLCIDCSAVHR 53 (355)
Q Consensus 23 k~C~DCga~~P-~WaSv~~GiflC~~CsgiHR 53 (355)
.+|.+||.+=| .-.-.-=+..+|++|.-.|-
T Consensus 81 G~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~~E 112 (120)
T COG1734 81 GICEECGEPIPEARLEARPTARLCIECQERAE 112 (120)
T ss_pred cchhccCCcCCHHHHhhCcchHHHHHHHHHHH
Confidence 38999998743 11122235789999998764
No 77
>cd06958 NR_DBD_COUP_TF DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. COUP-TFs homodimerize or heterodimerize with retinoid X receptor (RXR) and a few other nuclear receptors and bind to a variety of response elements that are composed of imperfect AGGTCA direct or inverted repeats with various spacings. COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone recept
Probab=21.37 E-value=52 Score=25.61 Aligned_cols=27 Identities=30% Similarity=0.790 Sum_probs=20.8
Q ss_pred CcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 25 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 25 C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
|.-||.+.-. ..||+..|..|.+..|-
T Consensus 1 C~VCg~~~~g---~hygv~sC~aC~~FFRR 27 (73)
T cd06958 1 CVVCGDKSSG---KHYGQFTCEGCKSFFKR 27 (73)
T ss_pred CCccCccCcc---eEEChhhhhhhhhhhhh
Confidence 5567765443 58999999999998874
No 78
>PF13119 DUF3973: Domain of unknown function (DUF3973)
Probab=21.12 E-value=30 Score=24.60 Aligned_cols=14 Identities=43% Similarity=1.210 Sum_probs=11.2
Q ss_pred ccchhchhhhccCC
Q 018505 43 FLCIDCSAVHRSLG 56 (355)
Q Consensus 43 flC~~CsgiHR~LG 56 (355)
|-|+.||.+|-.-+
T Consensus 2 yYCi~Cs~~h~e~~ 15 (41)
T PF13119_consen 2 YYCINCSEIHHEKG 15 (41)
T ss_pred EEEEEhHHhHHhhc
Confidence 56999999997643
No 79
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=20.87 E-value=54 Score=27.43 Aligned_cols=30 Identities=27% Similarity=0.500 Sum_probs=17.5
Q ss_pred CCCCCCcCCCCCCCC-eeEeccccccchhch
Q 018505 20 SENKMCFDCNAKNPT-WASVTYGIFLCIDCS 49 (355)
Q Consensus 20 p~Nk~C~DCga~~P~-WaSv~~GiflC~~Cs 49 (355)
+.-.+|-|||.+=|. -.-+-=++..|+.|.
T Consensus 78 g~yG~C~~Cge~I~~~RL~a~P~a~~Cv~Cq 108 (110)
T TIGR02420 78 GEYGYCEECGEEIGLRRLEARPTATLCIDCK 108 (110)
T ss_pred CCCCchhccCCcccHHHHhhCCCccccHHhH
Confidence 455799999986331 111111346788885
No 80
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=20.84 E-value=60 Score=26.31 Aligned_cols=31 Identities=29% Similarity=0.612 Sum_probs=23.7
Q ss_pred CCcCCCCCCC---CeeEeccc---cccchhchhhhcc
Q 018505 24 MCFDCNAKNP---TWASVTYG---IFLCIDCSAVHRS 54 (355)
Q Consensus 24 ~C~DCga~~P---~WaSv~~G---iflC~~CsgiHR~ 54 (355)
.|+-||.+-| .|...--| .|-|..|.+|+..
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~~~ 38 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVYQL 38 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccccccHHHHHHHHH
Confidence 6999999876 34443344 8999999999865
No 81
>cd06970 NR_DBD_PNR DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of the nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hing
Probab=20.82 E-value=48 Score=27.22 Aligned_cols=32 Identities=25% Similarity=0.673 Sum_probs=25.7
Q ss_pred CCCCCCcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 20 SENKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 20 p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
+-...|.-||.+.-. ..||+..|..|.+..|-
T Consensus 4 ~p~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 35 (92)
T cd06970 4 NPGLLCRVCGDTSSG---KHYGIYACNGCSGFFKR 35 (92)
T ss_pred CCCCCCeecCCcCcc---cEECccEEeeeeeEeee
Confidence 445579999976554 48999999999998874
No 82
>cd07164 NR_DBD_PNR_like_1 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-t
Probab=20.39 E-value=55 Score=25.79 Aligned_cols=27 Identities=22% Similarity=0.623 Sum_probs=21.0
Q ss_pred CcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 25 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 25 C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
|.-||.+.-. ..||+..|..|.+..|-
T Consensus 1 C~VCg~~~~g---~hyG~~~C~~C~~FFRR 27 (78)
T cd07164 1 CRVCGDRASG---KHYGVPSCDGCRGFFKR 27 (78)
T ss_pred CcccCccCcc---eEECcchhhhhhhhhhh
Confidence 5667765543 48999999999998874
No 83
>cd06967 NR_DBD_TR2_like DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. It has been shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or
Probab=20.34 E-value=46 Score=26.97 Aligned_cols=30 Identities=23% Similarity=0.635 Sum_probs=24.1
Q ss_pred CCCCcCCCCCCCCeeEeccccccchhchhhhcc
Q 018505 22 NKMCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 54 (355)
Q Consensus 22 Nk~C~DCga~~P~WaSv~~GiflC~~CsgiHR~ 54 (355)
...|.-||.+.-. ..||++.|..|.+..|-
T Consensus 3 ~~~C~VCg~~~~g---~hyGv~sC~aC~~FFRR 32 (87)
T cd06967 3 VELCVVCGDKASG---RHYGAVSCEGCKGFFKR 32 (87)
T ss_pred CCCCeecCCcCCc---CEeCcceEeeeeeEeee
Confidence 3569999976554 47999999999998874
No 84
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=20.32 E-value=44 Score=22.54 Aligned_cols=29 Identities=21% Similarity=0.358 Sum_probs=22.6
Q ss_pred CCCCcCCCCCCCCeeEeccccccchhchhhh
Q 018505 22 NKMCFDCNAKNPTWASVTYGIFLCIDCSAVH 52 (355)
Q Consensus 22 Nk~C~DCga~~P~WaSv~~GiflC~~CsgiH 52 (355)
.+.|-.|+...--| -+-+..+|..|-.++
T Consensus 3 ~~~C~~C~~~~i~~--~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVN--KEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEE--ecCCeEEcccCCcEe
Confidence 46788899887554 578889999997765
No 85
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=20.28 E-value=55 Score=27.79 Aligned_cols=45 Identities=18% Similarity=0.431 Sum_probs=26.8
Q ss_pred cCCCCCCCcCCCCCCCCeeEeccccccchhchhhh-cc-CCCccceeeeccC
Q 018505 18 AKSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVH-RS-LGVHISFVRSTNL 67 (355)
Q Consensus 18 ~~p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiH-R~-LG~hiS~VkS~~l 67 (355)
..|..-+|.+||.. ..+..-.+.|..|.+.. +. -|.. -+|+++.+
T Consensus 66 ~~p~~~~C~~Cg~~----~~~~~~~~~CP~Cgs~~~~i~~G~E-l~I~~ie~ 112 (115)
T TIGR00100 66 DEPVECECEDCSEE----VSPEIDLYRCPKCHGIMLQVRAGKE-LNLKSIEV 112 (115)
T ss_pred eeCcEEEcccCCCE----EecCCcCccCcCCcCCCcEEecCCe-EEEEEEEE
Confidence 45777899999942 23332358899999854 22 2322 24555544
No 86
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=20.12 E-value=42 Score=30.73 Aligned_cols=29 Identities=21% Similarity=0.555 Sum_probs=19.1
Q ss_pred CCcCCCCCCCCeeEeccccccchhchhhhc
Q 018505 24 MCFDCNAKNPTWASVTYGIFLCIDCSAVHR 53 (355)
Q Consensus 24 ~C~DCga~~P~WaSv~~GiflC~~CsgiHR 53 (355)
+|..|+.+-..---+++ -|.|..|.+.-.
T Consensus 119 ~Cp~C~~rytf~eA~~~-~F~Cp~Cg~~L~ 147 (178)
T PRK06266 119 FCPNCHIRFTFDEAMEY-GFRCPQCGEMLE 147 (178)
T ss_pred ECCCCCcEEeHHHHhhc-CCcCCCCCCCCe
Confidence 69999865332223344 599999998654
No 87
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=20.12 E-value=48 Score=25.02 Aligned_cols=32 Identities=19% Similarity=0.486 Sum_probs=23.9
Q ss_pred CCCCCCCcCCCCCCCCeeEeccccccchhchhhh
Q 018505 19 KSENKMCFDCNAKNPTWASVTYGIFLCIDCSAVH 52 (355)
Q Consensus 19 ~p~Nk~C~DCga~~P~WaSv~~GiflC~~CsgiH 52 (355)
.+|-+.|.-||.+. =+--.||..||..|-.-+
T Consensus 13 GkGsr~C~vCg~~~--gliRkygL~~CRqCFRe~ 44 (54)
T PTZ00218 13 GKGSRQCRVCSNRH--GLIRKYGLNVCRQCFREN 44 (54)
T ss_pred CCCCCeeecCCCcc--hhhhhcCcchhhHHHHHh
Confidence 36778999999854 233489999999996433
Done!