Query 016929
Match_columns 380
No_of_seqs 230 out of 1151
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 04:05:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016929.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016929hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03114 ADP-ribosylation fact 100.0 6E-94 1.3E-98 700.5 28.3 363 1-372 24-394 (395)
2 KOG0706 Predicted GTPase-activ 100.0 1.5E-82 3.2E-87 633.5 24.3 370 1-380 25-454 (454)
3 KOG0704 ADP-ribosylation facto 100.0 6.1E-36 1.3E-40 291.5 7.6 100 1-100 21-121 (386)
4 COG5347 GTPase-activating prot 100.0 1.2E-33 2.7E-38 277.9 8.8 102 1-102 22-124 (319)
5 KOG0703 Predicted GTPase-activ 100.0 4E-31 8.7E-36 254.7 3.5 88 1-88 27-124 (287)
6 smart00105 ArfGap Putative GTP 100.0 4E-30 8.7E-35 218.6 8.0 93 1-93 5-102 (112)
7 PF01412 ArfGap: Putative GTPa 100.0 4.5E-30 9.8E-35 219.4 4.3 70 1-70 15-84 (116)
8 PLN03131 hypothetical protein; 99.9 8.3E-24 1.8E-28 218.9 6.3 82 1-86 25-120 (705)
9 PLN03119 putative ADP-ribosyla 99.9 7.7E-24 1.7E-28 217.7 5.9 83 1-86 25-120 (648)
10 KOG0705 GTPase-activating prot 99.8 1.2E-20 2.6E-25 194.0 6.7 86 1-86 515-612 (749)
11 KOG0521 Putative GTPase activa 99.7 7.5E-19 1.6E-23 190.8 1.0 85 1-85 428-526 (785)
12 KOG0818 GTPase-activating prot 99.7 2.2E-17 4.9E-22 167.8 2.2 86 1-86 10-115 (669)
13 KOG1117 Rho- and Arf-GTPase ac 99.5 9.9E-15 2.2E-19 155.7 1.5 86 1-86 300-399 (1186)
14 KOG0702 Predicted GTPase-activ 98.4 9.9E-08 2.1E-12 98.2 3.1 68 1-69 27-95 (524)
15 KOG0521 Putative GTPase activa 92.9 0.023 4.9E-07 63.3 -0.8 65 1-67 632-697 (785)
16 PLN03114 ADP-ribosylation fact 87.8 0.89 1.9E-05 46.4 5.2 20 308-327 300-319 (395)
17 KOG0706 Predicted GTPase-activ 86.9 1.6 3.4E-05 45.6 6.5 75 270-371 378-452 (454)
18 PRK00085 recO DNA repair prote 79.0 1.3 2.8E-05 41.9 2.2 28 1-28 151-179 (247)
19 TIGR00613 reco DNA repair prot 66.1 3.6 7.8E-05 38.8 1.8 28 1-28 149-177 (241)
20 PF00320 GATA: GATA zinc finge 62.4 5.7 0.00012 27.1 1.8 32 2-33 1-34 (36)
21 PF10764 Gin: Inhibitor of sig 56.4 6.2 0.00013 28.7 1.2 26 1-27 1-26 (46)
22 PF00643 zf-B_box: B-box zinc 56.0 6.6 0.00014 27.0 1.2 31 1-31 5-36 (42)
23 PF08271 TF_Zn_Ribbon: TFIIB z 51.1 9.3 0.0002 26.8 1.4 25 1-26 2-26 (43)
24 smart00401 ZnF_GATA zinc finge 48.2 15 0.00033 27.1 2.1 35 1-35 5-41 (52)
25 COG1381 RecO Recombinational D 44.2 11 0.00024 36.5 1.1 26 1-26 156-182 (251)
26 PRK12495 hypothetical protein; 41.8 13 0.00029 35.7 1.2 23 1-27 44-66 (226)
27 COG1997 RPL43A Ribosomal prote 39.7 22 0.00047 29.5 2.0 25 1-27 37-61 (89)
28 cd00202 ZnF_GATA Zinc finger D 38.6 18 0.0004 27.0 1.3 34 1-34 1-36 (54)
29 smart00659 RPOLCX RNA polymera 37.6 13 0.00029 26.6 0.5 27 1-32 4-30 (44)
30 PRK11019 hypothetical protein; 36.1 6 0.00013 32.7 -1.7 35 1-36 38-74 (88)
31 PF01286 XPA_N: XPA protein N- 32.7 14 0.0003 25.4 -0.1 26 1-26 5-31 (34)
32 PHA00080 DksA-like zinc finger 32.6 9.6 0.00021 30.2 -1.0 29 1-30 33-63 (72)
33 PF11781 RRN7: RNA polymerase 31.7 33 0.00071 23.6 1.6 21 2-25 11-31 (36)
34 cd07170 NR_DBD_ERR DNA-binding 30.1 26 0.00056 29.3 1.0 27 2-31 7-33 (97)
35 PF03604 DNA_RNApol_7kD: DNA d 30.1 13 0.00029 25.0 -0.6 22 1-25 2-23 (32)
36 cd07162 NR_DBD_PXR DNA-binding 28.6 36 0.00078 27.7 1.6 28 1-31 1-28 (87)
37 cd06968 NR_DBD_ROR DNA-binding 28.1 32 0.00068 28.6 1.2 27 2-31 8-34 (95)
38 PF07282 OrfB_Zn_ribbon: Putat 27.8 35 0.00077 25.9 1.4 24 1-26 30-53 (69)
39 PF14376 Haem_bd: Haem-binding 27.1 28 0.00062 30.6 0.9 13 1-13 43-55 (137)
40 COG2174 RPL34A Ribosomal prote 26.4 31 0.00068 28.8 0.9 14 14-27 66-79 (93)
41 PRK00423 tfb transcription ini 26.4 42 0.00092 33.4 2.0 28 1-29 13-40 (310)
42 cd07157 2DBD_NR_DBD1 The first 26.3 27 0.00059 28.4 0.5 27 2-31 3-29 (86)
43 PRK13715 conjugal transfer pro 25.2 14 0.00031 29.3 -1.3 31 1-31 36-67 (73)
44 TIGR02419 C4_traR_proteo phage 24.7 16 0.00036 28.1 -1.0 28 1-29 33-62 (63)
45 PF13119 DUF3973: Domain of un 24.6 32 0.00069 24.4 0.5 13 20-32 2-14 (41)
46 cd06965 NR_DBD_Ppar DNA-bindin 24.3 31 0.00067 27.9 0.5 27 2-31 2-28 (84)
47 cd07165 NR_DBD_DmE78_like DNA- 24.2 39 0.00084 27.1 1.1 27 2-31 1-27 (81)
48 smart00290 ZnF_UBP Ubiquitin C 23.7 54 0.0012 23.2 1.7 22 1-22 1-22 (50)
49 COG2158 Uncharacterized protei 23.3 52 0.0011 28.3 1.6 32 2-35 45-78 (112)
50 cd07160 NR_DBD_LXR DNA-binding 23.1 41 0.00089 28.3 1.0 27 2-31 21-47 (101)
51 cd06966 NR_DBD_CAR DNA-binding 23.0 42 0.00091 27.8 1.1 28 1-31 2-29 (94)
52 cd07171 NR_DBD_ER DNA-binding 22.7 43 0.00094 27.0 1.1 27 2-31 6-32 (82)
53 cd07168 NR_DBD_DHR4_like DNA-b 22.6 44 0.00096 27.4 1.1 27 2-31 9-35 (90)
54 PTZ00074 60S ribosomal protein 22.3 41 0.00089 30.0 0.9 25 1-25 43-84 (135)
55 cd07156 NR_DBD_VDR_like The DN 22.2 52 0.0011 25.7 1.4 27 2-31 1-27 (72)
56 PF04770 ZF-HD_dimer: ZF-HD pr 22.1 38 0.00083 26.1 0.6 29 3-32 22-52 (60)
57 cd07161 NR_DBD_EcR DNA-binding 21.7 51 0.0011 27.2 1.3 27 2-31 4-30 (91)
58 cd07158 NR_DBD_Ppar_like The D 21.6 49 0.0011 25.8 1.2 27 2-31 1-27 (73)
59 KOG3507 DNA-directed RNA polym 21.6 35 0.00076 26.3 0.3 27 1-32 22-48 (62)
60 cd07169 NR_DBD_GCNF_like DNA-b 20.9 46 0.001 27.3 0.9 27 2-31 9-35 (90)
61 cd07173 NR_DBD_AR DNA-binding 20.0 47 0.001 26.8 0.8 27 2-31 6-32 (82)
No 1
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=100.00 E-value=6e-94 Score=700.53 Aligned_cols=363 Identities=70% Similarity=1.024 Sum_probs=319.7
Q ss_pred CCCCCCCCCCCeeEeccceeecccchhhhhcCCCccccccccCCCCCCHHHHHHHhcCChHHHHHHHhhcCCCCCCchhh
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTDGGKIEA 80 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg~HR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~~~~~~~~~~~~~~~~i~~ 80 (380)
+|||||+++|+|+|++||||||++|+|+||.||+|||||||++||.|+++||++|+.|||.++++||++||+.....|++
T Consensus 24 ~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~Ws~eqL~~Mk~GGN~rA~~fF~qhG~~~~~~~~~ 103 (395)
T PLN03114 24 ICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSSEQLKMMIYGGNNRAQVFFKQYGWSDGGKTEA 103 (395)
T ss_pred cCccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCCCCHHHHHHHHHhcCHHHHHHHHHcCCCCCCCccc
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999987678999
Q ss_pred hhccHHHHHHHHHHHHHHHHHhhhcc-CCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CcCCCCCCCCCC-CCCCcccccc
Q 016929 81 KYTSRAAELYKQILAKEVAKNMAEEA-GLPSSPVASQPAQAANALPDVKIQDAPKE-NYQGRQETQDAP-GSPKVSRTVL 157 (380)
Q Consensus 81 KY~~~~a~~Yr~~l~~~v~~~~~~~~-~~~~~~~~~~~~~~~Dff~~~~~~~~p~~-~~~~~~~~~~~~-~~p~~~~~~~ 157 (380)
||.++++.+||++|+++|++.+.++. .+|+.++++ ...+|+|++.+..+.|.. ++++..+.+... .+|++
T Consensus 104 KY~S~aA~~Yre~L~keVa~~~a~~~~~~p~~~~~~--~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~s~~~----- 176 (395)
T PLN03114 104 KYTSRAADLYKQILAKEVAKSKAEEELDLPPSPPDS--TQVPNGLSSIKTSEALKESNTLKQQEKPDVVPVSPRI----- 176 (395)
T ss_pred ccCCHHHHHHHHHHHHHHHHhhhccccCCCCCCCCc--cccccCcccccccccccccCCcccccCCcccCCCCCC-----
Confidence 99999999999999999999998765 345555543 237899999888776643 234443333222 24543
Q ss_pred cccccCCCccccCCCCCCccccccCCCCCccccCCCCCCCCCCCCCCCCCC-CCCCCCcccchhchhhhcccccCCCCCC
Q 016929 158 TSTVKKPLGAKKSGKTGGLGARKLTSKPSESLYEQKPEEPSVPISSSTSNT-SSVSLPFASRFEYVDNVQSSELSSGGPQ 236 (380)
Q Consensus 158 s~~~kk~~~akk~~K~~~LgakKv~~~~~e~~~d~~~ee~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 236 (380)
+++.|||+|+||.||+|||||+|++++..|.||||++|| .++.+++++.. +...++.++||.|.|+++. +...++..
T Consensus 177 ~~~~kk~~gak~~gktgglg~~klttk~~~~ly~qkp~e-~~~~~~~~~~~~~~~~~~~~srf~y~d~~~~-~~~~~~~~ 254 (395)
T PLN03114 177 SRSVKKPLGAKKTGKTGGLGARKLTTKSSGTLYDQKPEE-SVIIQATSPVSAKSARSSFSSRFDYADNVQN-REDYMSPQ 254 (395)
T ss_pred ccccccccccccccccCCccccccccCCchhhhhcCccc-cCCCCCCCccccccCCCCcchhhhhcccccc-ccccCCcc
Confidence 357899999999999999999999999999999999999 55555555443 3455677899999999998 66677789
Q ss_pred cccccCCCCCCccc-ccCCCCcC-CCCCCC--CcccchhhhHHHHHHhccCCcCccccccCCCCCccchhHHHHhhhccC
Q 016929 237 VLSHVAPPKSSSFF-ADYGMDNG-FQKKSG--SSKVQIQETDEARKKFSNAKSISSSQFFGDQNNSIDMDTQVSLQKFSG 312 (380)
Q Consensus 237 ~~~~~~~~~~~~~~-~~~g~~~~-~~~~~~--~~~~~~~~t~~a~~KFgnaKaISSd~yFGr~~~~a~~ea~~rL~~F~g 312 (380)
..+||+||++..|| .+|||+.+ +++++. +.+.+++++++||+||||||+||||||||+++..+++|++.||++|+|
T Consensus 255 ~~~hvapp~ss~ff~~e~g~~~~~~~k~~~~~~~k~q~~e~~~a~kKF~naKsisS~qfFg~~~~~~d~~~~~~l~kf~g 334 (395)
T PLN03114 255 VVSHVAPPKSSGFFEEELEMNGGRFQKKPITSSSKLQIQETDEARKKFTNAKSISSAQYFGNDNNSADLEAKSSLKKFSG 334 (395)
T ss_pred cccccCCCccchhhHHhhcCCcccccCCCCCccccccccchHHHHHHhcccccccHHhhccccccccchhhHHHHHhhcc
Confidence 99999999999999 68999998 888776 677899999999999999999999999999998889999999999999
Q ss_pred CcccccccccCCCCCCcccchhhHHHHHHhhhchHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 016929 313 SASISSADLFGHDSDNASLDLAASDLINRLSFQAQQDISSLKNIAGETGKKLSSLASSLI 372 (380)
Q Consensus 313 atsISS~~yFg~~~~~~~~~~sA~dl~~~~~~~a~~Dl~~lk~~v~~~A~KLs~~a~~~~ 372 (380)
+++|||+|||||++++.+++++|.||++||++||.+||+.||+++++++.||++||++++
T Consensus 335 s~~ISsad~fg~~~~d~~id~ta~dli~r~s~qa~qd~sslkn~aget~~kl~s~as~~~ 394 (395)
T PLN03114 335 SSAISSADLFGDSDGDFTLDLTAGDLLNRLSLQAQQDISSLKNMAEETKKKLGSVASSLW 394 (395)
T ss_pred ccccchHHhcCCCCccccccccHHHHHHHhhhhhHhHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 999999999999988889999999999999999999999999999999999999999875
No 2
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=1.5e-82 Score=633.51 Aligned_cols=370 Identities=47% Similarity=0.673 Sum_probs=275.4
Q ss_pred CCCCCCCCCCCeeEeccceeecccchhhhhcCCCccccccccCCCCCCHHHHHHHhcCChHHHHHHHhhcCCCCCCchhh
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTDGGKIEA 80 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg~HR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~~~~~~~~~~~~~~~~i~~ 80 (380)
+|||||++||+|+||+|||||||+|+++||+||||||||||++||.|++.|||+|++|||.+|+.||.+|||.. .++++
T Consensus 25 vCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~~FFkqhg~~t-~d~~a 103 (454)
T KOG0706|consen 25 VCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANARVFFKQHGCVT-LDANA 103 (454)
T ss_pred eecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHHHHHHHcCCcc-hhhhh
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999987 69999
Q ss_pred hhccHHHHHHHHHHHHHHHHHhhhcc---CCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCccccc
Q 016929 81 KYTSRAAELYKQILAKEVAKNMAEEA---GLPS-SPVASQPAQAANALPDVKIQDAPKENYQGRQETQDAPGSPKVSRTV 156 (380)
Q Consensus 81 KY~~~~a~~Yr~~l~~~v~~~~~~~~---~~~~-~~~~~~~~~~~Dff~~~~~~~~p~~~~~~~~~~~~~~~~p~~~~~~ 156 (380)
||.+|++++|+++|+++|.+.+.+++ .++. .++..++..+.|||+.+....+-........ ....+|+++.+.
T Consensus 104 KY~SraA~~Yr~kl~~lv~kam~~~~~~l~l~~~~~~~~~~~~~~dffs~~~k~~~~~~~s~~~l---~~~~s~~~S~~v 180 (454)
T KOG0706|consen 104 KYNSRAAKLYREKLKKLVQKAMAEHGTSLLLDSAVSSGSPESEDSDFFSESDKESSKHEPSTDAL---KSLSSPSASNTV 180 (454)
T ss_pred hhccHHHHHHHHHHHHHHHHHHHhcCccccccCCCCCCCCccccccchhhccccccccCCccccc---ccccCCcccccc
Confidence 99999999999999999999998876 2333 2333345667899988755431100000000 111244445455
Q ss_pred ccccccCCCccccCCCCCC--ccccccCCCCCccccCCCCCCCCCCCCCCCCCCCC-CCCCcccchhchh---hhc----
Q 016929 157 LTSTVKKPLGAKKSGKTGG--LGARKLTSKPSESLYEQKPEEPSVPISSSTSNTSS-VSLPFASRFEYVD---NVQ---- 226 (380)
Q Consensus 157 ~s~~~kk~~~akk~~K~~~--LgakKv~~~~~e~~~d~~~ee~~~~~~~~~~~~~~-~~~~~~~~~~~~~---~~~---- 226 (380)
.+...++|.++|++|++++ |||+||.++.+..++.+..+++.....+.++.... .....+.++.|++ +.+
T Consensus 181 ~sg~~k~p~~~k~~g~~k~~~lgarkv~t~s~~~~~~~~~~~~~~~i~a~s~~~~s~~~~~~s~~~~~~e~~dd~~~~E~ 260 (454)
T KOG0706|consen 181 VSGKKKPPVTKKGLGAKKGVTLGARKVNTKSFKSIESQAQEAEKNKIKAASPKPSSEESSARSSRLARQELQDDRKKEEA 260 (454)
T ss_pred ccccccCCccccccccccccccCceecccccccchhhccchhhhccccccCCCcchhhhcccchhhhhhHHHHHHHhhhh
Confidence 5566677777777884444 99999999877777877766544333322222111 0111223333332 211
Q ss_pred ------------ccccCCCCCCccccc-----------CCCCCCcccccCCCCcC-------------CCCCCC------
Q 016929 227 ------------SSELSSGGPQVLSHV-----------APPKSSSFFADYGMDNG-------------FQKKSG------ 264 (380)
Q Consensus 227 ------------~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~g~~~~-------------~~~~~~------ 264 (380)
..+|| +.|+...|+ ++|+..++|..++|... +.+...
T Consensus 261 k~~d~~k~~~~~rlgmg-~~~s~~~hs~~~~~~~i~~~t~~~~k~~~~~~~~~~~~~~~~~s~~~~~~~~~~~ss~ss~~ 339 (454)
T KOG0706|consen 261 KAKDGKKASSSERLGMG-GYRSVMSHSVLGGMQVIEQVTPPKAKPSFLELDMFSDTTKQSSSNYKDAPFGKGSSSSSSKD 339 (454)
T ss_pred hhcCcccccchhhhccc-cccchhhhcccCCceeeecccCccccccccccccccchhccccCCcccCccccCcccccchh
Confidence 12555 335555554 45554444444333221 111111
Q ss_pred ----CcccchhhhHHHHHHhccCCcCccccccCCCCCccchhHHHHhhhccCCcccccccccCCCCCCcccchhhHHHHH
Q 016929 265 ----SSKVQIQETDEARKKFSNAKSISSSQFFGDQNNSIDMDTQVSLQKFSGSASISSADLFGHDSDNASLDLAASDLIN 340 (380)
Q Consensus 265 ----~~~~~~~~t~~a~~KFgnaKaISSd~yFGr~~~~a~~ea~~rL~~F~gatsISS~~yFg~~~~~~~~~~sA~dl~~ 340 (380)
..+.++++|++||+||||||+|||||||||+. ++++|+|+||++|+|+++|||+||||++++ ..++.+++.
T Consensus 340 a~~~~~~~~v~~td~~rkkF~naKaISSdqyFG~~~-~ad~Ea~~~L~~f~gstaISSsd~fG~~~~----~~~~g~~~~ 414 (454)
T KOG0706|consen 340 AKRAKESRPVEETDEARKKFGNAKAISSDQYFGRGS-EADLEARARLQKFSGSTAISSSDLFGEGDD----DHTAGSLAL 414 (454)
T ss_pred hhccccccccccccHHHHhhccccccchhhhcCCcc-hhhhHHHHHHHhccCccccchHhhcCCCCC----CCCccchhh
Confidence 22246788999999999999999999999998 679999999999999999999999999876 356677788
Q ss_pred HhhhchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 016929 341 RLSFQAQQDISSLKNIAGETGKKLSSLASSLITDIQDRIL 380 (380)
Q Consensus 341 ~~~~~a~~Dl~~lk~~v~~~A~KLs~~a~~~~~~iQdry~ 380 (380)
++.+++.+||.+++++|+++|+||+++|++|+++|||||+
T Consensus 415 ~~~~~a~~di~~~k~~~~~~a~kls~~a~~v~~~~qd~~~ 454 (454)
T KOG0706|consen 415 RDSFRAAQDIASFKNSARSVAGKLSVLASKVGSSLQDRYG 454 (454)
T ss_pred cccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 8889999999999999999999999999999999999995
No 3
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=100.00 E-value=6.1e-36 Score=291.54 Aligned_cols=100 Identities=49% Similarity=0.930 Sum_probs=94.8
Q ss_pred CCCCCCCCCCCeeEeccceeecccchhhhhcCCCccccccccCCCCCCHHHHHHHhcCChHHHHHHHhhcCCCCCC-chh
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTDGG-KIE 79 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg~HR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~~~~~~~~~~~~~~~-~i~ 79 (380)
+||||+++||+|+||+||||||++|+|+||.|||||||||||+||+|.+.||+.|+.|||.++++||+.++..... .|+
T Consensus 21 ~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~~~eFL~s~~~~~e~~~i~ 100 (386)
T KOG0704|consen 21 KCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNERFREFLSSQGIYKETWPIR 100 (386)
T ss_pred ceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchhHHHHHhhCccccccccHH
Confidence 5999999999999999999999999999999999999999999999999999999999999999999999865544 899
Q ss_pred hhhccHHHHHHHHHHHHHHHH
Q 016929 80 AKYTSRAAELYKQILAKEVAK 100 (380)
Q Consensus 80 ~KY~~~~a~~Yr~~l~~~v~~ 100 (380)
+||.+++|.+||.+|...++-
T Consensus 101 eKYns~aAa~yRdki~~laeg 121 (386)
T KOG0704|consen 101 EKYNSRAAALYRDKIAALAEG 121 (386)
T ss_pred HhhccHHHHHHHHHHHHHhcC
Confidence 999999999999999987653
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=1.2e-33 Score=277.91 Aligned_cols=102 Identities=47% Similarity=0.759 Sum_probs=95.3
Q ss_pred CCCCCCCCCCCeeEeccceeecccchhhhhcCCCccccccccCCCCCCHHHHHHHhcCChHHHHHHHhhcCCCC-CCchh
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTD-GGKIE 79 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg~HR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~~~~~~~~~~~~~-~~~i~ 79 (380)
+|||||+++|+|+||+||||||++||||||+|||||||||||+||+|+++||++|+.|||.+++.||++|++.. ...|+
T Consensus 22 ~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~wt~~~l~~m~~gGN~~a~~~~e~~~~~~~~~~~k 101 (319)
T COG5347 22 KCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWTEEELRRMEVGGNSNANRFYEKNLLDQLLLPIK 101 (319)
T ss_pred ccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeecccCCHHHHHHHHHhcchhhhhHhccCCCcccccccc
Confidence 59999999999999999999999999999999999999999999999999999999999999999999998863 36899
Q ss_pred hhhccHHHHHHHHHHHHHHHHHh
Q 016929 80 AKYTSRAAELYKQILAKEVAKNM 102 (380)
Q Consensus 80 ~KY~~~~a~~Yr~~l~~~v~~~~ 102 (380)
.||.+.+++.|...+..++...+
T Consensus 102 ~~yd~~v~~~y~~~ky~~~~~~~ 124 (319)
T COG5347 102 AKYDSSVAKKYIRKKYELKKFID 124 (319)
T ss_pred cccCHHHHHHHHHHHHHhhhccc
Confidence 99999999999998887665554
No 5
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.96 E-value=4e-31 Score=254.72 Aligned_cols=88 Identities=41% Similarity=0.802 Sum_probs=79.9
Q ss_pred CCCCCCCCCCCeeEeccceeecccchhhhhcCCCccccccccCCCCCCHHHHHHHhcCChHHHHHHHhhcCCCC------
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTD------ 74 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg~HR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~~~~~~~~~~~~~------ 74 (380)
+|+|||++.|.|||+++|||||+.|+||||+||||||+||||+||.|+++||..|...||.++|.|||+.....
T Consensus 27 ~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~~GN~~an~~~ea~~p~~~~~p~~ 106 (287)
T KOG0703|consen 27 VCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMISMGNAKANSYYEAKLPDPFRRPGP 106 (287)
T ss_pred cccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHHHcchhhhhhccccCCccccCCCh
Confidence 69999999999999999999999999999999999999999999999999999999999999999999872211
Q ss_pred ----CCchhhhhccHHHH
Q 016929 75 ----GGKIEAKYTSRAAE 88 (380)
Q Consensus 75 ----~~~i~~KY~~~~a~ 88 (380)
+.|||.||+.+...
T Consensus 107 d~~~e~FIR~KYE~kkf~ 124 (287)
T KOG0703|consen 107 DDLVEQFIRDKYERKKFL 124 (287)
T ss_pred HHHHHHHHHHHHhhhhhc
Confidence 25899999877543
No 6
>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=99.96 E-value=4e-30 Score=218.57 Aligned_cols=93 Identities=48% Similarity=0.874 Sum_probs=79.5
Q ss_pred CCCCCCCCCCCeeEeccceeecccchhhhhcCCCccccccccCCCCCCHHHHHHHhcCChHHHHHHHhhcCCCCC-----
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTDG----- 75 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg~HR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~~~~~~~~~~~~~~----- 75 (380)
+|+|||+++|+|+|++||||||++|+|+||.||+|||+||||+||+|++++|++|+.+||..+|+||++++....
T Consensus 5 ~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~VkSl~md~w~~~~i~~~~~~GN~~~n~~~e~~~~~~~~~~~~ 84 (112)
T smart00105 5 KCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTLDTWTEEELRLLQKGGNENANSIWESNLDDFSLKPPD 84 (112)
T ss_pred cccCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCeeeecccCCCCHHHHHHHHHhhhHHHHHHHHhhCCccccCCCC
Confidence 599999999999999999999999999999999999999999999999999999999999999999999865321
Q ss_pred CchhhhhccHHHHHHHHH
Q 016929 76 GKIEAKYTSRAAELYKQI 93 (380)
Q Consensus 76 ~~i~~KY~~~~a~~Yr~~ 93 (380)
.....+|+..+...|+.+
T Consensus 85 ~~~~~~~~~fI~~KY~~k 102 (112)
T smart00105 85 SDDQQKYESFIAAKYEEK 102 (112)
T ss_pred CchHHHHHHHHHHHHHhh
Confidence 123445555555555443
No 7
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=99.96 E-value=4.5e-30 Score=219.43 Aligned_cols=70 Identities=54% Similarity=1.113 Sum_probs=59.2
Q ss_pred CCCCCCCCCCCeeEeccceeecccchhhhhcCCCccccccccCCCCCCHHHHHHHhcCChHHHHHHHhhc
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQH 70 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg~HR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~~~~~~~~~ 70 (380)
+|+|||+++|+|+|++||||||+.|+|+||.||+|||+||||+||.|++++|++|+.+||..+|+||+++
T Consensus 15 ~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~VkSi~~d~w~~~ev~~~~~~GN~~~n~~~e~~ 84 (116)
T PF01412_consen 15 VCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRVKSITMDNWSPEEVQRMREGGNKRANSIWEAN 84 (116)
T ss_dssp B-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--EEETTTS---HHHHHHHHHSHHHHHHHHHTTT
T ss_pred cCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhccccccCCCCHHHHHHHHHHChHHHHHHHHcC
Confidence 5999999999999999999999999999999999999999999999999999999999999999999998
No 8
>PLN03131 hypothetical protein; Provisional
Probab=99.89 E-value=8.3e-24 Score=218.95 Aligned_cols=82 Identities=26% Similarity=0.704 Sum_probs=74.4
Q ss_pred CCCCCCCCCCCeeEeccceeecccchhhhhcCCCccccccccCCCCCCHHHHHHHhcCChHHHHHHHhhcCCCC------
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTD------ 74 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg~HR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~~~~~~~~~~~~~------ 74 (380)
+|+||++++|+|+|++||||||+.|+||||.|| | +||||+||.|+++||+.|+.+||.++|+||+++ |..
T Consensus 25 ~CADCga~~P~WASiNlGIFICi~CSGIHRsLg-h--RVKSVTLD~WtdeEV~~Mk~gGN~~AN~iyean-wd~~r~~lP 100 (705)
T PLN03131 25 RCINCNSLGPQFVCTNFWTFICMTCSGIHREFT-H--RVKSVSMSKFTSQDVEALQNGGNQRAREIYLKD-WDQQRQRLP 100 (705)
T ss_pred ccccCCCCCCCeeEeccceEEchhchhhhcccC-c--ccccccCCCCCHHHHHHHHHhccHHHHHHHHhh-cccccCCCC
Confidence 599999999999999999999999999999997 3 899999999999999999999999999999975 211
Q ss_pred --------CCchhhhhccHH
Q 016929 75 --------GGKIEAKYTSRA 86 (380)
Q Consensus 75 --------~~~i~~KY~~~~ 86 (380)
..||+.||+++.
T Consensus 101 ~~sd~ekrr~FIR~KYVeKR 120 (705)
T PLN03131 101 DNSKVDKIREFIKDIYVDKK 120 (705)
T ss_pred CCccHHHHHHHHHHHHhhhh
Confidence 258899998875
No 9
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=99.89 E-value=7.7e-24 Score=217.71 Aligned_cols=83 Identities=24% Similarity=0.602 Sum_probs=74.2
Q ss_pred CCCCCCCCCCCeeEeccceeecccchhhhhcCCCccccccccCCCCCCHHHHHHHhcCChHHHHHHHhhcCCC------C
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWT------D 74 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg~HR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~~~~~~~~~~~~------~ 74 (380)
+|+|||+++|+|+|++||||||+.|+||||.|| ++||||+||+|+++||++|+.+||.++|+||+++.-. .
T Consensus 25 ~CADCgs~~P~WASiNlGIFICi~CSGIHRsLG---hRVKSLSLDkWT~EEVe~Mk~gGN~~AN~iyeanw~~~~~~~P~ 101 (648)
T PLN03119 25 RCINCNSLGPQYVCTTFWTFVCMACSGIHREFT---HRVKSVSMSKFTSKEVEVLQNGGNQRAREIYLKNWDHQRQRLPE 101 (648)
T ss_pred ccccCCCCCCCceeeccceEEeccchhhhccCC---ceeeccccCCCCHHHHHHHHHhchHHHHHHHHhhcccccCCCCC
Confidence 599999999999999999999999999999998 4899999999999999999999999999999986211 0
Q ss_pred -------CCchhhhhccHH
Q 016929 75 -------GGKIEAKYTSRA 86 (380)
Q Consensus 75 -------~~~i~~KY~~~~ 86 (380)
..||+.||+++.
T Consensus 102 ~sD~e~lr~FIR~KYVeKR 120 (648)
T PLN03119 102 NSNAERVREFIKNVYVQKK 120 (648)
T ss_pred CccHHHHHHHHHHHHhhhh
Confidence 147888888874
No 10
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.82 E-value=1.2e-20 Score=194.02 Aligned_cols=86 Identities=44% Similarity=0.844 Sum_probs=78.7
Q ss_pred CCCCCCCCCCCeeEeccceeecccchhhhhcCCCccccccccCCCCCCHHHHHHHhcCChHHHHHHHhhc--CCC-----
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQH--GWT----- 73 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg~HR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~~~~~~~~~--~~~----- 73 (380)
.|+||+++||.|||+|+||++|++|+||||+||+|+|+|||+.||.|..+.+..|...||+.||.+|+.- |-.
T Consensus 515 ~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl~~Vm~aiGN~~AN~vWE~~~~G~~KPs~~ 594 (749)
T KOG0705|consen 515 HCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVELLKVMSAIGNDLANSVWEGSSQGQTKPSPD 594 (749)
T ss_pred eeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHHHHHHHHhhhhHHHHHhhhhccCCcCCCcc
Confidence 5999999999999999999999999999999999999999999999999999999999999999999963 211
Q ss_pred -----CCCchhhhhccHH
Q 016929 74 -----DGGKIEAKYTSRA 86 (380)
Q Consensus 74 -----~~~~i~~KY~~~~ 86 (380)
.+.||+.||+.+.
T Consensus 595 s~REEkErwIr~KYeqkl 612 (749)
T KOG0705|consen 595 SSREEKERWIRAKYEQKL 612 (749)
T ss_pred ccHHHHHHHHHHHHHHHh
Confidence 1268999999884
No 11
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.72 E-value=7.5e-19 Score=190.79 Aligned_cols=85 Identities=47% Similarity=0.800 Sum_probs=78.3
Q ss_pred CCCCCCCCCCCeeEeccceeecccchhhhhcCCCccccccccCCCCCCHHHHHHHhcCChHHHHHHHhhcCCCC------
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTD------ 74 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg~HR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~~~~~~~~~~~~~------ 74 (380)
+|+|||++.|+|+|+|+||.+||+|+|+||+||||||+|||++||.|..+.+.+|+.+||..+|.+|+.+.+..
T Consensus 428 ~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~~~~l~~l~~~lgn~~~N~i~e~~l~~~~~~~~~ 507 (785)
T KOG0521|consen 428 QCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVWEPELLLLFKNLGNKYVNEIYEALLPSYDSSKPT 507 (785)
T ss_pred hhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhccCcHHHHHHHHhCcchhhhhhhcccccccccCCC
Confidence 59999999999999999999999999999999999999999999999999999999999999999999875422
Q ss_pred --------CCchhhhhccH
Q 016929 75 --------GGKIEAKYTSR 85 (380)
Q Consensus 75 --------~~~i~~KY~~~ 85 (380)
..+|++||..+
T Consensus 508 ~~~~~~~r~~~i~~kyve~ 526 (785)
T KOG0521|consen 508 ASSSRQAREAWIKAKYVER 526 (785)
T ss_pred CccchhhhhHhhhccccee
Confidence 14688888876
No 12
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.66 E-value=2.2e-17 Score=167.80 Aligned_cols=86 Identities=41% Similarity=0.696 Sum_probs=78.6
Q ss_pred CCCCCCCCCCCeeEeccceeecccchhhhhcCCCccccccccCCCCCCHHHHHHHhcCChHHHHHHHhhcCCCC------
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQHGWTD------ 74 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg~HR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~~~~~~~~~~~~~------ 74 (380)
+|.|||++.|.||||+-|+|||.+|..+||+||.|||.||++....|.+..|++.....|..+|.+|+.+.++.
T Consensus 10 vC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaNsIWEh~Lld~st~~sg 89 (669)
T KOG0818|consen 10 VCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGANSIWEHSLLDPATIMSG 89 (669)
T ss_pred hhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcchhhhhhccCchhhhcc
Confidence 69999999999999999999999999999999999999999999999999999999999999999999873221
Q ss_pred --------------CCchhhhhccHH
Q 016929 75 --------------GGKIEAKYTSRA 86 (380)
Q Consensus 75 --------------~~~i~~KY~~~~ 86 (380)
..||++||...+
T Consensus 90 ~rk~~pqD~~Hp~K~eFIkaKy~~Lt 115 (669)
T KOG0818|consen 90 RRKANPQDKVHPNKAEFIRAKYQMLA 115 (669)
T ss_pred cCCCCCcCCCCccHHHHHHHHHHhee
Confidence 257999998764
No 13
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.47 E-value=9.9e-15 Score=155.71 Aligned_cols=86 Identities=35% Similarity=0.644 Sum_probs=78.3
Q ss_pred CCCCCCCCCCCeeEeccceeecccchhhhhcCCCccccccccCCCC--CCHHHHHHHhcCChHHHHHHHhhcCCCC----
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDS--WSAEQLKMMVYGGNNRAQVFFKQHGWTD---- 74 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg~HR~LG~hiS~VkS~~lD~--W~~~~l~~m~~gGN~~~~~~~~~~~~~~---- 74 (380)
.|+|||++.|.|||+|++|.||-.|+|-||+||..+|+|+|+.||. |+.+-++++-+.||..+|.||..+....
T Consensus 300 ~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~Fwa~nl~~~e~lh 379 (1186)
T KOG1117|consen 300 ECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANRFWAGNLPPNEHLH 379 (1186)
T ss_pred cccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCcccccccccCCCCccccC
Confidence 4999999999999999999999999999999999999999999996 9999999999999999999998763221
Q ss_pred --------CCchhhhhccHH
Q 016929 75 --------GGKIEAKYTSRA 86 (380)
Q Consensus 75 --------~~~i~~KY~~~~ 86 (380)
..+|++||++-.
T Consensus 380 ~dssp~~r~~fi~~Kykeg~ 399 (1186)
T KOG1117|consen 380 PDSSPSTRRQFIKEKYKEGK 399 (1186)
T ss_pred CCCCcchhhhHHHHHhhccc
Confidence 268999998864
No 14
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=98.44 E-value=9.9e-08 Score=98.19 Aligned_cols=68 Identities=22% Similarity=0.483 Sum_probs=63.8
Q ss_pred CCCCCCCCCC-CeeEeccceeecccchhhhhcCCCccccccccCCCCCCHHHHHHHhcCChHHHHHHHhh
Q 016929 1 MCFDCNAKNP-TWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFFKQ 69 (380)
Q Consensus 1 ~C~DCga~~P-~WaSv~~GiflC~~Csg~HR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~~~~~~~~ 69 (380)
+|++|....+ +|.+++-|-|+|+.|+|..|.| .--++||||.|-.++..++..++.+||+.++++|.+
T Consensus 27 rC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l-~~ahRvksiSmttft~qevs~lQshgNq~~k~i~fk 95 (524)
T KOG0702|consen 27 RCINCNSLVAATYVVYTVGSFVCTMCSGLLSGL-NPAHRVKSISMTTFTDQEVSFLQSHGNQVCKEIWFK 95 (524)
T ss_pred ceeeccccccceEEEeeccceeeeccchhhccC-CCccccceeeeeeccccchHHHhhcchhhhhhhhhc
Confidence 5999999888 9999999999999999999998 456799999999999999999999999999999975
No 15
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=92.92 E-value=0.023 Score=63.28 Aligned_cols=65 Identities=18% Similarity=0.208 Sum_probs=52.0
Q ss_pred CCCCCCC-CCCCeeEeccceeecccchhhhhcCCCccccccccCCCCCCHHHHHHHhcCChHHHHHHH
Q 016929 1 MCFDCNA-KNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSAEQLKMMVYGGNNRAQVFF 67 (380)
Q Consensus 1 ~C~DCga-~~P~WaSv~~GiflC~~Csg~HR~LG~hiS~VkS~~lD~W~~~~l~~m~~gGN~~~~~~~ 67 (380)
.|.+|++ ..-.|+++++.+-+|++|+++|+.++.|++.++++.|++-.+ +.....-||...+.-+
T Consensus 632 ~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~~~ 697 (785)
T KOG0521|consen 632 ECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHHAT 697 (785)
T ss_pred cchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchhhh
Confidence 3788886 679999999999999999999999999999999999888766 5444444444444433
No 16
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=87.78 E-value=0.89 Score=46.42 Aligned_cols=20 Identities=50% Similarity=0.846 Sum_probs=17.7
Q ss_pred hhccCCcccccccccCCCCC
Q 016929 308 QKFSGSASISSADLFGHDSD 327 (380)
Q Consensus 308 ~~F~gatsISS~~yFg~~~~ 327 (380)
++|.|+.+|||++|||+...
T Consensus 300 kKF~naKsisS~qfFg~~~~ 319 (395)
T PLN03114 300 KKFTNAKSISSAQYFGNDNN 319 (395)
T ss_pred HHhcccccccHHhhcccccc
Confidence 56999999999999998753
No 17
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=86.86 E-value=1.6 Score=45.59 Aligned_cols=75 Identities=24% Similarity=0.295 Sum_probs=50.7
Q ss_pred hhhhHHHHHHhccCCcCccccccCCCCCccchhHHHHhhhccCCcccccccccCCCCCCcccchhhHHHHHHhhhchHHH
Q 016929 270 IQETDEARKKFSNAKSISSSQFFGDQNNSIDMDTQVSLQKFSGSASISSADLFGHDSDNASLDLAASDLINRLSFQAQQD 349 (380)
Q Consensus 270 ~~~t~~a~~KFgnaKaISSd~yFGr~~~~a~~ea~~rL~~F~gatsISS~~yFg~~~~~~~~~~sA~dl~~~~~~~a~~D 349 (380)
.-++....+||.++-+|||-.|||.+++ .+...++.++.. +.... ||+. |. .=
T Consensus 378 d~Ea~~~L~~f~gstaISSsd~fG~~~~-----------------~~~~g~~~~~~~----~~a~~-di~~-~k----~~ 430 (454)
T KOG0706|consen 378 DLEARARLQKFSGSTAISSSDLFGEGDD-----------------DHTAGSLALRDS----FRAAQ-DIAS-FK----NS 430 (454)
T ss_pred hhHHHHHHHhccCccccchHhhcCCCCC-----------------CCCccchhhccc----ccccc-cHHH-HH----HH
Confidence 3466777899999999999999999984 334444444431 22222 5554 32 23
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 016929 350 ISSLKNIAGETGKKLSSLASSL 371 (380)
Q Consensus 350 l~~lk~~v~~~A~KLs~~a~~~ 371 (380)
+.+++.-+..+|.||.+..+..
T Consensus 431 ~~~~a~kls~~a~~v~~~~qd~ 452 (454)
T KOG0706|consen 431 ARSVAGKLSVLASKVGSSLQDR 452 (454)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh
Confidence 3458999999999988876654
No 18
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=78.99 E-value=1.3 Score=41.90 Aligned_cols=28 Identities=25% Similarity=0.496 Sum_probs=23.7
Q ss_pred CCCCCCCCCC-CeeEeccceeecccchhh
Q 016929 1 MCFDCNAKNP-TWASVTYGIFLCIDCSAV 28 (380)
Q Consensus 1 ~C~DCga~~P-~WaSv~~GiflC~~Csg~ 28 (380)
.|.-||.+.. .|.++..|.++|..|...
T Consensus 151 ~C~~Cg~~~~~~~f~~~~gg~~c~~c~~~ 179 (247)
T PRK00085 151 HCAVCGAPGDHRYFSPKEGGAVCSECGDP 179 (247)
T ss_pred hHhcCCCCCCceEEecccCCcccccccCc
Confidence 4999998755 788999999999999733
No 19
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=66.09 E-value=3.6 Score=38.77 Aligned_cols=28 Identities=36% Similarity=0.721 Sum_probs=23.3
Q ss_pred CCCCCCCCCC-CeeEeccceeecccchhh
Q 016929 1 MCFDCNAKNP-TWASVTYGIFLCIDCSAV 28 (380)
Q Consensus 1 ~C~DCga~~P-~WaSv~~GiflC~~Csg~ 28 (380)
.|..||..++ .|.++..|.++|.+|...
T Consensus 149 ~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 149 KCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred ccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 4999998654 688999999999999654
No 20
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=62.36 E-value=5.7 Score=27.13 Aligned_cols=32 Identities=28% Similarity=0.731 Sum_probs=23.6
Q ss_pred CCCCCCC-CCCeeEecccee-ecccchhhhhcCC
Q 016929 2 CFDCNAK-NPTWASVTYGIF-LCIDCSAVHRSLG 33 (380)
Q Consensus 2 C~DCga~-~P~WaSv~~Gif-lC~~Csg~HR~LG 33 (380)
|..|+.. -|.|-..+.|-. ||-.|--.+|..|
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 8899974 699999999988 9999977666544
No 21
>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=56.41 E-value=6.2 Score=28.71 Aligned_cols=26 Identities=31% Similarity=0.821 Sum_probs=20.6
Q ss_pred CCCCCCCCCCCeeEeccceeecccchh
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSA 27 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg 27 (380)
+|+=|+...+. .=+=+|.|||.+|-.
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHH
Confidence 58889988877 445589999999954
No 22
>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=55.96 E-value=6.6 Score=26.97 Aligned_cols=31 Identities=16% Similarity=0.351 Sum_probs=26.1
Q ss_pred CCCCCCCCCCCeeEeccceeecccchhh-hhc
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSAV-HRS 31 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg~-HR~ 31 (380)
.|..|+.....|-+.+=.++||..|... |+.
T Consensus 5 ~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~ 36 (42)
T PF00643_consen 5 KCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG 36 (42)
T ss_dssp B-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT
T ss_pred cCccCCccceEEEecCCCCccCccCCCCCCCC
Confidence 4777888778899999999999999987 886
No 23
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=51.05 E-value=9.3 Score=26.84 Aligned_cols=25 Identities=24% Similarity=0.635 Sum_probs=20.0
Q ss_pred CCCCCCCCCCCeeEeccceeecccch
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCS 26 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Cs 26 (380)
+|-.||+.. .-..-..|-++|..|-
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG 26 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCG 26 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCC
Confidence 588999977 5556778999999993
No 24
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=48.15 E-value=15 Score=27.13 Aligned_cols=35 Identities=26% Similarity=0.591 Sum_probs=28.4
Q ss_pred CCCCCCC-CCCCeeEeccce-eecccchhhhhcCCCc
Q 016929 1 MCFDCNA-KNPTWASVTYGI-FLCIDCSAVHRSLGVH 35 (380)
Q Consensus 1 ~C~DCga-~~P~WaSv~~Gi-flC~~Csg~HR~LG~h 35 (380)
.|..|+. .-|.|=..+.|- +||-.|--..+..|..
T Consensus 5 ~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 5 SCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC
Confidence 5999997 458999999996 9999997777765543
No 25
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=44.19 E-value=11 Score=36.45 Aligned_cols=26 Identities=35% Similarity=0.783 Sum_probs=23.3
Q ss_pred CCCCCCCCC-CCeeEeccceeecccch
Q 016929 1 MCFDCNAKN-PTWASVTYGIFLCIDCS 26 (380)
Q Consensus 1 ~C~DCga~~-P~WaSv~~GiflC~~Cs 26 (380)
.|+.||.+- |...|+-.|-++|..|.
T Consensus 156 ~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 156 SCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred HHhCcCCcCCCcceeeccCcccchhcc
Confidence 499999975 57999999999999998
No 26
>PRK12495 hypothetical protein; Provisional
Probab=41.82 E-value=13 Score=35.67 Aligned_cols=23 Identities=22% Similarity=0.475 Sum_probs=19.0
Q ss_pred CCCCCCCCCCCeeEeccceeecccchh
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSA 27 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg 27 (380)
.|-+||.+-|. --|+.+|..|..
T Consensus 44 hC~~CG~PIpa----~pG~~~Cp~CQ~ 66 (226)
T PRK12495 44 HCDECGDPIFR----HDGQEFCPTCQQ 66 (226)
T ss_pred hcccccCcccC----CCCeeECCCCCC
Confidence 59999999993 269999999963
No 27
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=39.71 E-value=22 Score=29.49 Aligned_cols=25 Identities=32% Similarity=0.711 Sum_probs=20.5
Q ss_pred CCCCCCCCCCCeeEeccceeecccchh
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSA 27 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg 27 (380)
.|-.|+.+ +--=+..||+.|..|-.
T Consensus 37 ~Cp~C~~~--~VkR~a~GIW~C~kCg~ 61 (89)
T COG1997 37 VCPFCGRT--TVKRIATGIWKCRKCGA 61 (89)
T ss_pred cCCCCCCc--ceeeeccCeEEcCCCCC
Confidence 48899987 56677899999999943
No 28
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=38.57 E-value=18 Score=26.98 Aligned_cols=34 Identities=29% Similarity=0.691 Sum_probs=27.4
Q ss_pred CCCCCCCC-CCCeeEec-cceeecccchhhhhcCCC
Q 016929 1 MCFDCNAK-NPTWASVT-YGIFLCIDCSAVHRSLGV 34 (380)
Q Consensus 1 ~C~DCga~-~P~WaSv~-~GiflC~~Csg~HR~LG~ 34 (380)
+|..|+.. -|.|-..+ -+..||-.|--..+..|.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~ 36 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGV 36 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCC
Confidence 69999974 58899876 788999999776666663
No 29
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=37.62 E-value=13 Score=26.64 Aligned_cols=27 Identities=26% Similarity=0.598 Sum_probs=19.1
Q ss_pred CCCCCCCCCCCeeEeccceeecccchhhhhcC
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRSL 32 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg~HR~L 32 (380)
+|.+||...... .....-|..| -||.|
T Consensus 4 ~C~~Cg~~~~~~---~~~~irC~~C--G~rIl 30 (44)
T smart00659 4 ICGECGRENEIK---SKDVVRCREC--GYRIL 30 (44)
T ss_pred ECCCCCCEeecC---CCCceECCCC--CceEE
Confidence 599999865543 5677899998 34543
No 30
>PRK11019 hypothetical protein; Provisional
Probab=36.11 E-value=6 Score=32.70 Aligned_cols=35 Identities=20% Similarity=0.542 Sum_probs=24.7
Q ss_pred CCCCCCCCCC--CeeEeccceeecccchhhhhcCCCcc
Q 016929 1 MCFDCNAKNP--TWASVTYGIFLCIDCSAVHRSLGVHI 36 (380)
Q Consensus 1 ~C~DCga~~P--~WaSv~~GiflC~~Csg~HR~LG~hi 36 (380)
+|.|||.+=| .|.-++ ++-+|++|...+-..+.|.
T Consensus 38 ~C~~CG~~Ip~~Rl~A~P-~a~~Cv~Cq~~~E~~~k~~ 74 (88)
T PRK11019 38 ECEECGEPIPEARRKAIP-GVRLCVACQQEKDLQQAAF 74 (88)
T ss_pred eeCcCCCcCcHHHHhhcC-CccccHHHHHHHHHHHhHh
Confidence 5999998655 355454 6779999998776555443
No 31
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=32.66 E-value=14 Score=25.38 Aligned_cols=26 Identities=15% Similarity=0.544 Sum_probs=15.6
Q ss_pred CCCCCCCC-CCCeeEeccceeecccch
Q 016929 1 MCFDCNAK-NPTWASVTYGIFLCIDCS 26 (380)
Q Consensus 1 ~C~DCga~-~P~WaSv~~GiflC~~Cs 26 (380)
.|.+|+.+ .-+|..-+|+.-+|..|.
T Consensus 5 ~C~eC~~~f~dSyL~~~F~~~VCD~CR 31 (34)
T PF01286_consen 5 KCDECGKPFMDSYLLNNFDLPVCDKCR 31 (34)
T ss_dssp E-TTT--EES-SSCCCCTS-S--TTT-
T ss_pred hHhHhCCHHHHHHHHHhCCcccccccc
Confidence 49999974 578999999999999994
No 32
>PHA00080 DksA-like zinc finger domain containing protein
Probab=32.64 E-value=9.6 Score=30.19 Aligned_cols=29 Identities=21% Similarity=0.572 Sum_probs=19.5
Q ss_pred CCCCCCCCC--CCeeEeccceeecccchhhhh
Q 016929 1 MCFDCNAKN--PTWASVTYGIFLCIDCSAVHR 30 (380)
Q Consensus 1 ~C~DCga~~--P~WaSv~~GiflC~~Csg~HR 30 (380)
+|.+||.+= ..|.-++ ++..|++|...+-
T Consensus 33 ~C~~Cg~~Ip~~Rl~a~P-~~~~Cv~Cq~~~E 63 (72)
T PHA00080 33 HCEECGDPIPEARREAVP-GCRTCVSCQEILE 63 (72)
T ss_pred EecCCCCcCcHHHHHhCC-CccCcHHHHHHHH
Confidence 499999854 3444455 4556999987653
No 33
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=31.75 E-value=33 Score=23.59 Aligned_cols=21 Identities=29% Similarity=0.925 Sum_probs=19.0
Q ss_pred CCCCCCCCCCeeEeccceeecccc
Q 016929 2 CFDCNAKNPTWASVTYGIFLCIDC 25 (380)
Q Consensus 2 C~DCga~~P~WaSv~~GiflC~~C 25 (380)
|..|++. |....=|-+.|..|
T Consensus 11 C~~C~~~---~~~~~dG~~yC~~c 31 (36)
T PF11781_consen 11 CPVCGSR---WFYSDDGFYYCDRC 31 (36)
T ss_pred CCCCCCe---EeEccCCEEEhhhC
Confidence 8888887 99999999999998
No 34
>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=30.09 E-value=26 Score=29.31 Aligned_cols=27 Identities=26% Similarity=0.716 Sum_probs=22.0
Q ss_pred CCCCCCCCCCeeEeccceeecccchhhhhc
Q 016929 2 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 31 (380)
Q Consensus 2 C~DCga~~P~WaSv~~GiflC~~Csg~HR~ 31 (380)
|.-||.+. ....||++.|..|.++.|-
T Consensus 7 C~VCg~~a---~g~hyGv~sC~aCk~FFRR 33 (97)
T cd07170 7 CLVCGDIA---SGYHYGVASCEACKAFFKR 33 (97)
T ss_pred CeecCCcC---cceEECceeehhhhHHHHH
Confidence 77788654 4568999999999998874
No 35
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=30.07 E-value=13 Score=25.01 Aligned_cols=22 Identities=23% Similarity=0.587 Sum_probs=13.8
Q ss_pred CCCCCCCCCCCeeEeccceeecccc
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDC 25 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~C 25 (380)
+|.+||+.+. .. .....-|..|
T Consensus 2 ~C~~Cg~~~~--~~-~~~~irC~~C 23 (32)
T PF03604_consen 2 ICGECGAEVE--LK-PGDPIRCPEC 23 (32)
T ss_dssp BESSSSSSE---BS-TSSTSSBSSS
T ss_pred CCCcCCCeeE--cC-CCCcEECCcC
Confidence 5899998765 11 2334578888
No 36
>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=28.56 E-value=36 Score=27.70 Aligned_cols=28 Identities=18% Similarity=0.613 Sum_probs=22.5
Q ss_pred CCCCCCCCCCCeeEeccceeecccchhhhhc
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 31 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg~HR~ 31 (380)
+|.-||.+.- ...||++.|..|.++.|-
T Consensus 1 ~C~VCg~~~~---g~hygv~sC~aC~~FFRR 28 (87)
T cd07162 1 ICRVCGDRAT---GYHFNAMTCEGCKGFFRR 28 (87)
T ss_pred CCcccCCcCc---ceEECcceehhhHHHHHh
Confidence 4888887544 358999999999998874
No 37
>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=28.10 E-value=32 Score=28.62 Aligned_cols=27 Identities=30% Similarity=0.828 Sum_probs=22.1
Q ss_pred CCCCCCCCCCeeEeccceeecccchhhhhc
Q 016929 2 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 31 (380)
Q Consensus 2 C~DCga~~P~WaSv~~GiflC~~Csg~HR~ 31 (380)
|.-||.+. ....||++.|..|.++.|-
T Consensus 8 C~VCg~~~---~g~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 8 CKICGDKS---SGIHYGVITCEGCKGFFRR 34 (95)
T ss_pred CcccCCcC---cceEECceeehhhHHhhHH
Confidence 77888754 4568999999999998874
No 38
>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=27.81 E-value=35 Score=25.87 Aligned_cols=24 Identities=25% Similarity=0.695 Sum_probs=20.1
Q ss_pred CCCCCCCCCCCeeEeccceeecccch
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCS 26 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Cs 26 (380)
.|..||..... ..+.-+|.|..|-
T Consensus 30 ~C~~CG~~~~~--~~~~r~~~C~~Cg 53 (69)
T PF07282_consen 30 TCPRCGHRNKK--RRSGRVFTCPNCG 53 (69)
T ss_pred CccCccccccc--ccccceEEcCCCC
Confidence 48899988877 7788899999983
No 39
>PF14376 Haem_bd: Haem-binding domain
Probab=27.14 E-value=28 Score=30.63 Aligned_cols=13 Identities=31% Similarity=1.091 Sum_probs=10.5
Q ss_pred CCCCCCCCCCCee
Q 016929 1 MCFDCNAKNPTWA 13 (380)
Q Consensus 1 ~C~DCga~~P~Wa 13 (380)
-|.||++.+..|-
T Consensus 43 ~CydCHSn~T~~P 55 (137)
T PF14376_consen 43 SCYDCHSNNTRYP 55 (137)
T ss_pred cccccCCCCCCCc
Confidence 3999999887665
No 40
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=26.38 E-value=31 Score=28.77 Aligned_cols=14 Identities=36% Similarity=0.954 Sum_probs=11.4
Q ss_pred Eeccceeecccchh
Q 016929 14 SVTYGIFLCIDCSA 27 (380)
Q Consensus 14 Sv~~GiflC~~Csg 27 (380)
+=+||-.+|..|..
T Consensus 66 ~RpYGG~lc~~c~~ 79 (93)
T COG2174 66 ERPYGGYLCANCVR 79 (93)
T ss_pred CCCcCceecHHHHH
Confidence 45699999999954
No 41
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=26.38 E-value=42 Score=33.40 Aligned_cols=28 Identities=25% Similarity=0.628 Sum_probs=20.1
Q ss_pred CCCCCCCCCCCeeEeccceeecccchhhh
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSAVH 29 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg~H 29 (380)
.|.+||..+.. ....-|-.+|.+|--|.
T Consensus 13 ~Cp~Cg~~~iv-~d~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 13 VCPECGSDKLI-YDYERGEIVCADCGLVI 40 (310)
T ss_pred cCcCCCCCCee-EECCCCeEeecccCCcc
Confidence 59999974332 23567999999996543
No 42
>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=26.28 E-value=27 Score=28.39 Aligned_cols=27 Identities=22% Similarity=0.592 Sum_probs=22.0
Q ss_pred CCCCCCCCCCeeEeccceeecccchhhhhc
Q 016929 2 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 31 (380)
Q Consensus 2 C~DCga~~P~WaSv~~GiflC~~Csg~HR~ 31 (380)
|.-||.+. ....||++.|..|.++.|-
T Consensus 3 C~VCg~~a---~g~hyGv~sC~aCk~FFRR 29 (86)
T cd07157 3 CQVCGEPA---AGFHHGAYVCEACKKFFMR 29 (86)
T ss_pred CcccCCcC---cccEECcceeeEeeeEEec
Confidence 77788654 4569999999999998875
No 43
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=25.24 E-value=14 Score=29.35 Aligned_cols=31 Identities=26% Similarity=0.674 Sum_probs=18.6
Q ss_pred CCCCCCCCCCCee-Eeccceeecccchhhhhc
Q 016929 1 MCFDCNAKNPTWA-SVTYGIFLCIDCSAVHRS 31 (380)
Q Consensus 1 ~C~DCga~~P~Wa-Sv~~GiflC~~Csg~HR~ 31 (380)
.|.|||.+=|.=- -.-=|+..|+.|...+-.
T Consensus 36 ~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~E~ 67 (73)
T PRK13715 36 LCEACGNPIPEARRKIFPGVTLCVECQAYQER 67 (73)
T ss_pred cHhhcCCcCCHHHHhcCCCcCCCHHHHHHHHH
Confidence 4888887644221 111267789998775543
No 44
>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=24.70 E-value=16 Score=28.06 Aligned_cols=28 Identities=25% Similarity=0.725 Sum_probs=16.9
Q ss_pred CCCCCCCCCC--CeeEeccceeecccchhhh
Q 016929 1 MCFDCNAKNP--TWASVTYGIFLCIDCSAVH 29 (380)
Q Consensus 1 ~C~DCga~~P--~WaSv~~GiflC~~Csg~H 29 (380)
.|.|||.+=| .|.-++ |+..|++|...|
T Consensus 33 ~C~~Cg~~Ip~~Rl~a~p-~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 33 ECEDCGEPIPEARREALP-GVTRCVSCQEIL 62 (63)
T ss_pred eeccCCCcChHHHHhhcC-CcCCcHHHHhhc
Confidence 4888887544 222222 667788886543
No 45
>PF13119 DUF3973: Domain of unknown function (DUF3973)
Probab=24.61 E-value=32 Score=24.43 Aligned_cols=13 Identities=38% Similarity=1.134 Sum_probs=10.8
Q ss_pred eecccchhhhhcC
Q 016929 20 FLCIDCSAVHRSL 32 (380)
Q Consensus 20 flC~~Csg~HR~L 32 (380)
|-|+.||.+|-.-
T Consensus 2 yYCi~Cs~~h~e~ 14 (41)
T PF13119_consen 2 YYCINCSEIHHEK 14 (41)
T ss_pred EEEEEhHHhHHhh
Confidence 6799999999753
No 46
>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=24.30 E-value=31 Score=27.93 Aligned_cols=27 Identities=30% Similarity=0.776 Sum_probs=21.8
Q ss_pred CCCCCCCCCCeeEeccceeecccchhhhhc
Q 016929 2 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 31 (380)
Q Consensus 2 C~DCga~~P~WaSv~~GiflC~~Csg~HR~ 31 (380)
|.-||.+. ....||++.|..|.+++|-
T Consensus 2 C~VCg~~~---~g~hyGv~sC~aCk~FFRR 28 (84)
T cd06965 2 CRVCGDKA---SGFHYGVHACEGCKGFFRR 28 (84)
T ss_pred CcccCccC---cceEEChhhhhhhhhheee
Confidence 77788644 3467999999999999875
No 47
>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=24.23 E-value=39 Score=27.08 Aligned_cols=27 Identities=30% Similarity=0.715 Sum_probs=21.6
Q ss_pred CCCCCCCCCCeeEeccceeecccchhhhhc
Q 016929 2 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 31 (380)
Q Consensus 2 C~DCga~~P~WaSv~~GiflC~~Csg~HR~ 31 (380)
|.-||.+.- ...||++.|..|.++.|-
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 666876443 569999999999998885
No 48
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=23.67 E-value=54 Score=23.16 Aligned_cols=22 Identities=27% Similarity=0.637 Sum_probs=15.5
Q ss_pred CCCCCCCCCCCeeEeccceeec
Q 016929 1 MCFDCNAKNPTWASVTYGIFLC 22 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC 22 (380)
.|.+|+..+.-|+++.-+-..|
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c 22 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGC 22 (50)
T ss_pred CcccCCCcCCeEEecCCCCccc
Confidence 5999998777776666555555
No 49
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=23.26 E-value=52 Score=28.30 Aligned_cols=32 Identities=31% Similarity=0.725 Sum_probs=26.0
Q ss_pred CCCCCCCCCCeeEeccc--eeecccchhhhhcCCCc
Q 016929 2 CFDCNAKNPTWASVTYG--IFLCIDCSAVHRSLGVH 35 (380)
Q Consensus 2 C~DCga~~P~WaSv~~G--iflC~~Csg~HR~LG~h 35 (380)
|.+|+-- .|.+-.-| |.-|.+|--+||.-++.
T Consensus 45 c~~~~~g--ewi~~~~G~~VwSC~dC~~iH~ke~~~ 78 (112)
T COG2158 45 CENEELG--EWISDSNGRKVWSCSDCHWIHRKEGAE 78 (112)
T ss_pred ccccccC--ceeEcCCCCEEeeccccceecccchHH
Confidence 5566554 99999999 99999999999976543
No 50
>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=23.05 E-value=41 Score=28.33 Aligned_cols=27 Identities=26% Similarity=0.720 Sum_probs=21.7
Q ss_pred CCCCCCCCCCeeEeccceeecccchhhhhc
Q 016929 2 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 31 (380)
Q Consensus 2 C~DCga~~P~WaSv~~GiflC~~Csg~HR~ 31 (380)
|.-||.+. ....||+..|..|.++.|-
T Consensus 21 C~VCg~~a---~g~hyGv~sC~aCk~FFRR 47 (101)
T cd07160 21 CSVCGDKA---SGFHYNVLSCEGCKGFFRR 47 (101)
T ss_pred CeecCCcC---cceEECcceehhhhhhhhh
Confidence 77788643 3578999999999998874
No 51
>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=22.99 E-value=42 Score=27.78 Aligned_cols=28 Identities=25% Similarity=0.610 Sum_probs=22.0
Q ss_pred CCCCCCCCCCCeeEeccceeecccchhhhhc
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRS 31 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg~HR~ 31 (380)
.|.-||.+. ....||++.|..|.++.|-
T Consensus 2 ~C~VCg~~a---~g~hyGv~sC~aC~~FFRR 29 (94)
T cd06966 2 ICGVCGDKA---LGYNFNAITCESCKAFFRR 29 (94)
T ss_pred CCeeCCCcC---cceEECcceeeeehheehh
Confidence 377788643 3568999999999998875
No 52
>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=22.68 E-value=43 Score=27.01 Aligned_cols=27 Identities=26% Similarity=0.747 Sum_probs=21.7
Q ss_pred CCCCCCCCCCeeEeccceeecccchhhhhc
Q 016929 2 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 31 (380)
Q Consensus 2 C~DCga~~P~WaSv~~GiflC~~Csg~HR~ 31 (380)
|.-||.+. ....||++.|..|.++.|-
T Consensus 6 C~VCg~~~---~g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 6 CAVCSDYA---SGYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CeecCCcC---cceEECceeehhhHHhHHH
Confidence 67787643 4579999999999998874
No 53
>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=22.65 E-value=44 Score=27.39 Aligned_cols=27 Identities=30% Similarity=0.790 Sum_probs=21.9
Q ss_pred CCCCCCCCCCeeEeccceeecccchhhhhc
Q 016929 2 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 31 (380)
Q Consensus 2 C~DCga~~P~WaSv~~GiflC~~Csg~HR~ 31 (380)
|.-||.+. ....||++.|..|.++.|-
T Consensus 9 C~VCg~~~---~g~hyGv~sC~aCk~FFRR 35 (90)
T cd07168 9 CSICEDKA---TGLHYGIITCEGCKGFFKR 35 (90)
T ss_pred CcccCCcC---cceEECceehhhhhHhhhh
Confidence 77788644 3579999999999998874
No 54
>PTZ00074 60S ribosomal protein L34; Provisional
Probab=22.28 E-value=41 Score=30.02 Aligned_cols=25 Identities=40% Similarity=0.753 Sum_probs=17.2
Q ss_pred CCCCCCCCC-------C----------CeeEeccceeecccc
Q 016929 1 MCFDCNAKN-------P----------TWASVTYGIFLCIDC 25 (380)
Q Consensus 1 ~C~DCga~~-------P----------~WaSv~~GiflC~~C 25 (380)
.|.|||.+- | .-++=.||-.||..|
T Consensus 43 kC~~cg~~L~GI~~~Rp~e~~rlsK~~KtvsRaYGG~lC~~C 84 (135)
T PTZ00074 43 KCGDCGKVLAGIKALRPTEYKQLSRRERTVSRAYGGVLCHKC 84 (135)
T ss_pred CCCCCCCccCCccCCchHHHHHccccCCCccCCCccchhHHH
Confidence 499999652 1 123556888888888
No 55
>cd07156 NR_DBD_VDR_like The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemi
Probab=22.15 E-value=52 Score=25.71 Aligned_cols=27 Identities=19% Similarity=0.581 Sum_probs=20.9
Q ss_pred CCCCCCCCCCeeEeccceeecccchhhhhc
Q 016929 2 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 31 (380)
Q Consensus 2 C~DCga~~P~WaSv~~GiflC~~Csg~HR~ 31 (380)
|.-||.+.- ...||++.|..|.++.|-
T Consensus 1 C~VC~~~~~---g~hygv~sC~aC~~FFRR 27 (72)
T cd07156 1 CGVCGDRAT---GYHFNAMTCEGCKGFFRR 27 (72)
T ss_pred CCccCccCc---ccEECcceehhhhhhhch
Confidence 566776444 358999999999998874
No 56
>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors. HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.
Probab=22.13 E-value=38 Score=26.14 Aligned_cols=29 Identities=28% Similarity=0.540 Sum_probs=23.1
Q ss_pred CC-CCCCCCC-eeEeccceeecccchhhhhcC
Q 016929 3 FD-CNAKNPT-WASVTYGIFLCIDCSAVHRSL 32 (380)
Q Consensus 3 ~D-Cga~~P~-WaSv~~GiflC~~Csg~HR~L 32 (380)
+| |+.--|. |.--+-.-++|.-| |.||++
T Consensus 22 ~DGCgEFm~~~g~eg~~~al~CaAC-gCHRnF 52 (60)
T PF04770_consen 22 VDGCGEFMPSPGEEGTPEALKCAAC-GCHRNF 52 (60)
T ss_pred cccccccccCCCCCCCcccceeccc-Ccchhc
Confidence 44 8877777 76667788999999 899986
No 57
>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=21.66 E-value=51 Score=27.17 Aligned_cols=27 Identities=22% Similarity=0.711 Sum_probs=21.7
Q ss_pred CCCCCCCCCCeeEeccceeecccchhhhhc
Q 016929 2 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 31 (380)
Q Consensus 2 C~DCga~~P~WaSv~~GiflC~~Csg~HR~ 31 (380)
|.-||.+.- ...||++.|..|.++.|-
T Consensus 4 C~VCg~~a~---g~hyGv~sC~aCk~FFRR 30 (91)
T cd07161 4 CLVCGDRAS---GYHYNALTCEGCKGFFRR 30 (91)
T ss_pred CeeCCCcCc---ceEECceeehhhHHHHHH
Confidence 777886443 468999999999998874
No 58
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=21.64 E-value=49 Score=25.81 Aligned_cols=27 Identities=30% Similarity=0.755 Sum_probs=21.0
Q ss_pred CCCCCCCCCCeeEeccceeecccchhhhhc
Q 016929 2 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 31 (380)
Q Consensus 2 C~DCga~~P~WaSv~~GiflC~~Csg~HR~ 31 (380)
|.-||.+.- ...||++.|..|.++.|-
T Consensus 1 C~VCg~~~~---g~hyGv~~C~aC~~FFRR 27 (73)
T cd07158 1 CKVCGDKAS---GFHYGVHSCEGCKGFFRR 27 (73)
T ss_pred CcccCccCc---ceEECcchhhHHHHHHhh
Confidence 566776443 468999999999998874
No 59
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=21.62 E-value=35 Score=26.34 Aligned_cols=27 Identities=30% Similarity=0.593 Sum_probs=18.2
Q ss_pred CCCCCCCCCCCeeEeccceeecccchhhhhcC
Q 016929 1 MCFDCNAKNPTWASVTYGIFLCIDCSAVHRSL 32 (380)
Q Consensus 1 ~C~DCga~~P~WaSv~~GiflC~~Csg~HR~L 32 (380)
+|.|||+.|--= .--++-|.+| -||.|
T Consensus 22 iCgdC~~en~lk---~~D~irCReC--G~RIl 48 (62)
T KOG3507|consen 22 ICGDCGQENTLK---RGDVIRCREC--GYRIL 48 (62)
T ss_pred Eecccccccccc---CCCcEehhhc--chHHH
Confidence 599999987421 2346789999 45553
No 60
>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=20.93 E-value=46 Score=27.33 Aligned_cols=27 Identities=26% Similarity=0.827 Sum_probs=21.7
Q ss_pred CCCCCCCCCCeeEeccceeecccchhhhhc
Q 016929 2 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 31 (380)
Q Consensus 2 C~DCga~~P~WaSv~~GiflC~~Csg~HR~ 31 (380)
|.-||.+. ....||+..|..|.++.|-
T Consensus 9 C~VCg~~a---~g~hyGv~sC~aCk~FFRR 35 (90)
T cd07169 9 CLICGDRA---TGLHYGIISCEGCKGFFKR 35 (90)
T ss_pred CeecCCcC---cceEECcceehhhHHHHHH
Confidence 77788643 4578999999999998874
No 61
>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=20.00 E-value=47 Score=26.82 Aligned_cols=27 Identities=22% Similarity=0.733 Sum_probs=21.8
Q ss_pred CCCCCCCCCCeeEeccceeecccchhhhhc
Q 016929 2 CFDCNAKNPTWASVTYGIFLCIDCSAVHRS 31 (380)
Q Consensus 2 C~DCga~~P~WaSv~~GiflC~~Csg~HR~ 31 (380)
|.-||.+. ....||++.|..|.++.|-
T Consensus 6 C~VCg~~a---~g~hyGv~sC~aCk~FFRR 32 (82)
T cd07173 6 CLICGDEA---SGCHYGALTCGSCKVFFKR 32 (82)
T ss_pred CeecCCcC---cceEECcchhhhHHHHHHH
Confidence 77788644 3578999999999998875
Done!