Query psy7092
Match_columns 540
No_of_seqs 334 out of 1145
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 17:58:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7092.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7092hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0706|consensus 100.0 1.2E-52 2.7E-57 437.6 17.0 267 26-528 10-277 (454)
2 PLN03114 ADP-ribosylation fact 100.0 1.7E-33 3.7E-38 288.9 13.7 119 25-190 8-127 (395)
3 KOG0704|consensus 100.0 4.1E-34 8.9E-39 291.9 8.0 116 24-186 4-121 (386)
4 KOG0703|consensus 100.0 1.8E-33 4E-38 283.1 7.1 115 22-172 8-122 (287)
5 COG5347 GTPase-activating prot 100.0 4.5E-32 9.7E-37 277.9 10.4 115 25-186 6-122 (319)
6 PF01412 ArfGap: Putative GTPa 100.0 7.4E-32 1.6E-36 239.7 3.3 111 28-172 2-112 (116)
7 smart00105 ArfGap Putative GTP 100.0 2.2E-30 4.8E-35 229.1 5.0 103 37-172 1-103 (112)
8 PLN03119 putative ADP-ribosyla 99.9 1.7E-27 3.7E-32 255.4 6.9 120 18-163 2-121 (648)
9 PLN03131 hypothetical protein; 99.9 3.3E-27 7.1E-32 254.9 6.9 113 18-156 2-114 (705)
10 KOG0703|consensus 99.9 1.5E-24 3.2E-29 219.0 1.2 89 318-441 36-127 (287)
11 KOG0705|consensus 99.8 6.2E-20 1.3E-24 197.4 7.2 115 25-173 499-613 (749)
12 KOG0704|consensus 99.7 6.7E-19 1.5E-23 180.9 4.5 65 320-403 32-112 (386)
13 smart00105 ArfGap Putative GTP 99.7 2E-19 4.3E-24 159.4 -1.1 86 320-440 16-107 (112)
14 PLN03114 ADP-ribosylation fact 99.7 1.2E-18 2.6E-23 180.0 3.8 66 319-403 34-114 (395)
15 KOG0706|consensus 99.7 1E-18 2.2E-23 184.1 0.2 65 320-403 36-114 (454)
16 COG5347 GTPase-activating prot 99.7 2.1E-18 4.6E-23 177.5 2.2 93 319-440 32-125 (319)
17 KOG0521|consensus 99.7 6.2E-18 1.3E-22 190.9 4.1 111 30-162 417-527 (785)
18 PF01412 ArfGap: Putative GTPa 99.7 9E-19 2E-23 156.0 -3.8 90 319-439 25-115 (116)
19 KOG0818|consensus 99.6 3E-17 6.6E-22 174.7 0.9 75 36-118 5-79 (669)
20 PLN03119 putative ADP-ribosyla 99.5 8.2E-15 1.8E-19 158.6 1.1 93 318-443 34-127 (648)
21 PLN03131 hypothetical protein; 99.4 1.4E-14 3E-19 157.9 1.0 95 318-445 34-129 (705)
22 KOG1117|consensus 99.4 5.3E-14 1.1E-18 157.0 4.3 75 36-117 295-370 (1186)
23 KOG0702|consensus 99.2 7.2E-12 1.6E-16 134.1 3.5 114 21-158 6-121 (524)
24 KOG0705|consensus 99.1 7.2E-12 1.6E-16 136.0 -2.0 93 318-431 524-617 (749)
25 KOG0521|consensus 98.7 2.9E-09 6.3E-14 121.4 1.7 81 348-430 450-531 (785)
26 KOG1117|consensus 97.0 0.00032 7E-09 80.4 2.3 55 320-392 311-367 (1186)
27 KOG0818|consensus 97.0 0.00014 3.1E-09 79.4 -0.8 54 320-392 21-75 (669)
28 KOG0702|consensus 83.1 0.53 1.1E-05 52.3 1.1 75 351-438 53-127 (524)
29 PRK00085 recO DNA repair prote 61.9 5.2 0.00011 39.5 2.1 31 37-67 147-178 (247)
30 PRK12495 hypothetical protein; 60.3 7.5 0.00016 39.6 2.9 28 36-67 39-66 (226)
31 PF00643 zf-B_box: B-box zinc 56.8 7.6 0.00017 28.4 1.7 33 39-71 3-36 (42)
32 TIGR00613 reco DNA repair prot 54.4 10 0.00022 37.4 2.7 33 36-68 144-177 (241)
33 PF12662 cEGF: Complement Clr- 50.4 7.6 0.00016 26.6 0.8 13 327-339 1-13 (24)
34 PF07645 EGF_CA: Calcium-bindi 40.9 9.6 0.00021 28.3 0.1 13 325-337 22-34 (42)
35 TIGR02419 C4_traR_proteo phage 37.1 22 0.00047 29.3 1.6 33 36-69 28-62 (63)
36 cd07171 NR_DBD_ER DNA-binding 36.4 19 0.00042 30.9 1.3 31 38-71 2-32 (82)
37 PF01286 XPA_N: XPA protein N- 36.3 13 0.00027 27.6 0.2 27 40-66 4-31 (34)
38 smart00401 ZnF_GATA zinc finge 35.9 32 0.00069 27.2 2.4 37 38-74 2-40 (52)
39 PF08271 TF_Zn_Ribbon: TFIIB z 33.4 23 0.00049 26.6 1.1 27 41-68 2-28 (43)
40 cd06968 NR_DBD_ROR DNA-binding 33.1 24 0.00053 31.1 1.4 31 38-71 4-34 (95)
41 PF00320 GATA: GATA zinc finge 32.8 22 0.00047 26.0 0.9 32 42-73 1-34 (36)
42 PF10764 Gin: Inhibitor of sig 32.7 23 0.00051 27.6 1.1 26 41-67 1-26 (46)
43 COG1381 RecO Recombinational D 32.3 26 0.00056 35.7 1.7 30 37-66 152-182 (251)
44 PRK11788 tetratricopeptide rep 31.7 42 0.0009 34.3 3.1 38 27-70 342-379 (389)
45 PF11781 RRN7: RNA polymerase 31.1 36 0.00077 25.2 1.8 27 37-66 6-32 (36)
46 cd07170 NR_DBD_ERR DNA-binding 29.6 28 0.00061 30.9 1.2 30 39-71 4-33 (97)
47 COG1997 RPL43A Ribosomal prote 29.3 50 0.0011 29.4 2.7 31 37-69 33-63 (89)
48 PF14471 DUF4428: Domain of un 29.3 18 0.0004 28.6 0.0 30 41-71 1-32 (51)
49 cd07173 NR_DBD_AR DNA-binding 28.2 30 0.00066 29.7 1.2 31 38-71 2-32 (82)
50 cd07160 NR_DBD_LXR DNA-binding 27.7 37 0.00081 30.4 1.7 31 38-71 17-47 (101)
51 cd06966 NR_DBD_CAR DNA-binding 27.2 32 0.00069 30.3 1.2 29 40-71 1-29 (94)
52 PRK04023 DNA polymerase II lar 26.8 42 0.00092 41.0 2.4 61 3-65 588-657 (1121)
53 PRK11019 hypothetical protein; 25.8 39 0.00086 29.8 1.5 37 38-75 35-73 (88)
54 KOG0457|consensus 25.7 53 0.0012 36.5 2.7 39 59-97 38-85 (438)
55 PHA00080 DksA-like zinc finger 25.3 55 0.0012 27.7 2.2 32 37-69 29-62 (72)
56 PRK14714 DNA polymerase II lar 25.2 41 0.00089 41.9 1.9 63 3-67 622-700 (1337)
57 cd07169 NR_DBD_GCNF_like DNA-b 24.5 38 0.00083 29.6 1.2 32 37-71 4-35 (90)
58 smart00179 EGF_CA Calcium-bind 24.0 39 0.00084 23.3 0.9 13 325-337 21-33 (39)
59 PF14670 FXa_inhibition: Coagu 23.8 32 0.00069 25.4 0.4 14 325-338 16-29 (36)
60 cd07163 NR_DBD_TLX DNA-binding 22.3 46 0.001 29.1 1.2 31 38-71 5-35 (92)
61 PF07282 OrfB_Zn_ribbon: Putat 21.0 58 0.0013 26.2 1.5 27 38-66 27-53 (69)
62 cd06955 NR_DBD_VDR DNA-binding 20.5 58 0.0012 29.5 1.5 31 38-71 5-35 (107)
63 cd07162 NR_DBD_PXR DNA-binding 20.5 55 0.0012 28.3 1.3 28 41-71 1-28 (87)
64 smart00181 EGF Epidermal growt 20.2 53 0.0011 22.5 0.9 15 325-339 17-31 (35)
No 1
>KOG0706|consensus
Probab=100.00 E-value=1.2e-52 Score=437.63 Aligned_cols=267 Identities=46% Similarity=0.705 Sum_probs=214.1
Q ss_pred hHHHHHHHhcccCCCcccCCCCCCCCceEecccceEcccchhhhccCCCcccceeeccCCCCCCHHHHHHHHhcCcCCcC
Q psy7092 26 NSKLLMLQIITFFPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAP 105 (540)
Q Consensus 26 n~k~l~~l~~~p~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~LGvhiS~VKSl~lDs~Wt~~qL~~m~~gGN~~an 105 (540)
..++++.|...+.||+|||||++||+|+||+||||||++||++||+|||||+||||++||+ |+|.||++|+.|||.+|+
T Consensus 10 ~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDs-Ws~~qLR~M~~GGN~nA~ 88 (454)
T KOG0706|consen 10 IQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDS-WSWEQLRRMQVGGNANAR 88 (454)
T ss_pred HHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeeccccc-CCHHHHhHhhhcCchhHH
Confidence 4566677777899999999999999999999999999999999999999999999999999 999999999999999999
Q ss_pred CCccccchhccccCCCchhHHHHHHHhhhhhcccccCCcchHHHHHHHHhhcCCCCcchhcccCcHHHHHHHHHHHHHHH
Q psy7092 106 NGQNTRLSLWRSWGSFPLAFFKQLVNLWLNIEMYHFSISTTAQALVSFFNQHNCTSKDAQQKYNSRAAQLYREKLQHAAV 185 (540)
Q Consensus 106 ~~~e~~l~~W~~~~~~p~~f~k~~~~~~~~~~~~~~~~~~~~~~l~~F~~~~~~~~~~i~~KY~sraA~~YrekL~~~a~ 185 (540)
.||++|||...+++.||++|+|++||++|..++.
T Consensus 89 ----------------------------------------------~FFkqhg~~t~d~~aKY~SraA~~Yr~kl~~lv~ 122 (454)
T KOG0706|consen 89 ----------------------------------------------VFFKQHGCVTLDANAKYNSRAAKLYREKLKKLVQ 122 (454)
T ss_pred ----------------------------------------------HHHHHcCCcchhhhhhhccHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999
Q ss_pred HHHHHcCCeeeEcCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCccCCCCCCCCCCCCCc
Q psy7092 186 QAMKIHGTKLFLDAMHDATHKKGEEEPVDFFAEHTNGDNFGFDAPAHPIITPTPTPTITASGSTSLAHPQNNNENTGAPS 265 (540)
Q Consensus 186 ~a~~~~~~~~~~d~~~~~~~~~~~~~~~Dff~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 265 (540)
++|.+||+.++++... ++..++.++.|||++|++...
T Consensus 123 kam~~~~~~l~l~~~~--~~~~~~~~~~dffs~~~k~~~----------------------------------------- 159 (454)
T KOG0706|consen 123 KAMAEHGTSLLLDSAV--SSGSPESEDSDFFSESDKESS----------------------------------------- 159 (454)
T ss_pred HHHHhcCccccccCCC--CCCCCccccccchhhcccccc-----------------------------------------
Confidence 9999999999999933 556778889999999987431
Q ss_pred chhhcccCCCCCcccccccCCCCCCCCCCCCCCCCCcccccccCCCCCcccccccccCCCCcccccCCcccccccccCCC
Q psy7092 266 VEKAFSEAKPSNLGVKKIQSKKPSGPQNNNENTGAPSVEKAFSDAKPSNLGVKKIQSKKPSGFVCRCPPFYQANVLTTTP 345 (540)
Q Consensus 266 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~crc~~~~~~~~~~~~~ 345 (540)
.++|+++.+.... .+++. .+...|.+|+..+
T Consensus 160 ----------------------~~~~s~~~l~~~~--s~~~S---~~v~sg~~k~p~~---------------------- 190 (454)
T KOG0706|consen 160 ----------------------KHEPSTDALKSLS--SPSAS---NTVVSGKKKPPVT---------------------- 190 (454)
T ss_pred ----------------------ccCCccccccccc--CCccc---cccccccccCCcc----------------------
Confidence 1344444444311 11111 1112255544333
Q ss_pred CCCccccccccCceeeeeeeecccCCCCCHHHHHHHHhcccccchhcccCCCCCCCCCCCCCCCCCCCCCCCCCCCcccc
Q psy7092 346 PRQSLVAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAMKAEFGPFNAGQFDSPPPDCTHTLPLAFTPSGMGFA 425 (540)
Q Consensus 346 ~~~~~sgIHR~LGVHISkVkS~~LDs~Wt~EQv~~Mq~gGN~~a~~~kY~~~~A~~yK~~~P~s~~~lp~~~~~s~~~~~ 425 (540)
T Consensus 191 -------------------------------------------------------------------------------- 190 (454)
T KOG0706|consen 191 -------------------------------------------------------------------------------- 190 (454)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred cccccCCCCCcccCCCCCCCccccc-chHHHHHHHHHHhHhhhhhccCCCCccccccccccccccchhhHHHHHHHHHHH
Q psy7092 426 SMSRSGGLGGKKLGKGGLGAQKVKA-NFAELEKEAELADSLKMQSATSKPQSVADVERENEDSIENISLRLAYQDISKQQ 504 (540)
Q Consensus 426 ~fir~~~~~~k~~~~g~~~a~kvst-sFs~iE~qAq~adk~ke~kk~~~~~~~~~~k~e~e~~~~~sSlRlAykdle~q~ 504 (540)
.+.++.++. +.+|++++.+ +|..|+.+++.++++..+... .+... ++ ....+++++|+|+..++
T Consensus 191 ----~k~~g~~k~--~~lgarkv~t~s~~~~~~~~~~~~~~~i~a~s-------~~~~s-~~-~~~~s~~~~~~e~~dd~ 255 (454)
T KOG0706|consen 191 ----KKGLGAKKG--VTLGARKVNTKSFKSIESQAQEAEKNKIKAAS-------PKPSS-EE-SSARSSRLARQELQDDR 255 (454)
T ss_pred ----ccccccccc--cccCceecccccccchhhccchhhhccccccC-------CCcch-hh-hcccchhhhhhHHHHHH
Confidence 222333332 2489999965 799999999999998877652 11111 22 34467899999999999
Q ss_pred HHHHHHHHhcCCCchhHHHhhccc
Q psy7092 505 KQEEEKLKAYNPKKAEQIERLGMY 528 (540)
Q Consensus 505 K~~e~klk~~dPkKa~QaERLGM~ 528 (540)
+++|++ ++ ||+|+.++|||||.
T Consensus 256 ~~~E~k-~~-d~~k~~~~~rlgmg 277 (454)
T KOG0706|consen 256 KKEEAK-AK-DGKKASSSERLGMG 277 (454)
T ss_pred Hhhhhh-hc-Ccccccchhhhccc
Confidence 999998 56 99999999999994
No 2
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=100.00 E-value=1.7e-33 Score=288.95 Aligned_cols=119 Identities=49% Similarity=0.840 Sum_probs=111.4
Q ss_pred chHHHHHHHhcccCCCcccCCCCCCCCceEecccceEcccchhhhccCCCcccceeeccCCCCCCHHHHHHHHhcCcCCc
Q psy7092 25 KNSKLLMLQIITFFPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANA 104 (540)
Q Consensus 25 ~n~k~l~~l~~~p~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~LGvhiS~VKSl~lDs~Wt~~qL~~m~~gGN~~a 104 (540)
...+.++.|+..|+|+.|||||+++|+|+|++||||||++|+|+||+||+||++|||++||. |++++|++|+.|||.+|
T Consensus 8 d~~~vfrkL~~kPgNk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~-Ws~eqL~~Mk~GGN~rA 86 (395)
T PLN03114 8 DKISVFKKLKAKSDNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDS-WSSEQLKMMIYGGNNRA 86 (395)
T ss_pred cHHHHHHHHHhCcCCCcCccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCC-CCHHHHHHHHHhcCHHH
Confidence 34567888999999999999999999999999999999999999999999999999999999 99999999999999999
Q ss_pred CCCccccchhccccCCCchhHHHHHHHhhhhhcccccCCcchHHHHHHHHhhcCCCC-cchhcccCcHHHHHHHHHHHHH
Q psy7092 105 PNGQNTRLSLWRSWGSFPLAFFKQLVNLWLNIEMYHFSISTTAQALVSFFNQHNCTS-KDAQQKYNSRAAQLYREKLQHA 183 (540)
Q Consensus 105 n~~~e~~l~~W~~~~~~p~~f~k~~~~~~~~~~~~~~~~~~~~~~l~~F~~~~~~~~-~~i~~KY~sraA~~YrekL~~~ 183 (540)
+ +||.+||+.. ..++.||++++|++||++|.+.
T Consensus 87 ~----------------------------------------------~fF~qhG~~~~~~~~~KY~S~aA~~Yre~L~ke 120 (395)
T PLN03114 87 Q----------------------------------------------VFFKQYGWSDGGKTEAKYTSRAADLYKQILAKE 120 (395)
T ss_pred H----------------------------------------------HHHHHcCCCCCCCcccccCCHHHHHHHHHHHHH
Confidence 9 9999999864 5799999999999999999999
Q ss_pred HHHHHHH
Q psy7092 184 AVQAMKI 190 (540)
Q Consensus 184 a~~a~~~ 190 (540)
++.+...
T Consensus 121 Va~~~a~ 127 (395)
T PLN03114 121 VAKSKAE 127 (395)
T ss_pred HHHhhhc
Confidence 9887543
No 3
>KOG0704|consensus
Probab=100.00 E-value=4.1e-34 Score=291.93 Aligned_cols=116 Identities=42% Similarity=0.827 Sum_probs=105.9
Q ss_pred hchHHHHHHHhcccCCCcccCCCCCCCCceEecccceEcccchhhhccCCCcccceeeccCCCCCCHHHHHHHHhcCcCC
Q psy7092 24 VKNSKLLMLQIITFFPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNAN 103 (540)
Q Consensus 24 ~~n~k~l~~l~~~p~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~LGvhiS~VKSl~lDs~Wt~~qL~~m~~gGN~~ 103 (540)
.+.++.|+.|....+|+.||||+++||+|||++||||||++|||+||+|||||||||||+||. |.+.||+.|+.|||.+
T Consensus 4 prtrr~L~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~-wkeiel~kMeaGGN~~ 82 (386)
T KOG0704|consen 4 PRTRRVLLELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDK-WKEIELKKMEAGGNER 82 (386)
T ss_pred hHHHHHHHhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeeccc-ccHHHHHHHHhccchh
Confidence 456677777766669999999999999999999999999999999999999999999999999 9999999999999999
Q ss_pred cCCCccccchhccccCCCchhHHHHHHHhhhhhcccccCCcchHHHHHHHHhhcCCC--CcchhcccCcHHHHHHHHHHH
Q psy7092 104 APNGQNTRLSLWRSWGSFPLAFFKQLVNLWLNIEMYHFSISTTAQALVSFFNQHNCT--SKDAQQKYNSRAAQLYREKLQ 181 (540)
Q Consensus 104 an~~~e~~l~~W~~~~~~p~~f~k~~~~~~~~~~~~~~~~~~~~~~l~~F~~~~~~~--~~~i~~KY~sraA~~YrekL~ 181 (540)
++ +||.++++- .-+|++||++++|.+||++|.
T Consensus 83 ~~----------------------------------------------eFL~s~~~~~e~~~i~eKYns~aAa~yRdki~ 116 (386)
T KOG0704|consen 83 FR----------------------------------------------EFLSSQGIYKETWPIREKYNSRAAALYRDKIA 116 (386)
T ss_pred HH----------------------------------------------HHHhhCccccccccHHHhhccHHHHHHHHHHH
Confidence 99 999999864 348999999999999999999
Q ss_pred HHHHH
Q psy7092 182 HAAVQ 186 (540)
Q Consensus 182 ~~a~~ 186 (540)
.++.-
T Consensus 117 ~laeg 121 (386)
T KOG0704|consen 117 ALAEG 121 (386)
T ss_pred HHhcC
Confidence 87543
No 4
>KOG0703|consensus
Probab=99.98 E-value=1.8e-33 Score=283.14 Aligned_cols=115 Identities=36% Similarity=0.604 Sum_probs=102.3
Q ss_pred hhhchHHHHHHHhcccCCCcccCCCCCCCCceEecccceEcccchhhhccCCCcccceeeccCCCCCCHHHHHHHHhcCc
Q psy7092 22 EKVKNSKLLMLQIITFFPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGN 101 (540)
Q Consensus 22 e~~~n~k~l~~l~~~p~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~LGvhiS~VKSl~lDs~Wt~~qL~~m~~gGN 101 (540)
..+++.+.|++||+.|+|++|+|||++.|.|||+|+|||||+.|+||||+||+|||+||||+||. |+++||+.|...||
T Consensus 8 ~~~~~~~~l~~Ll~~~~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~-W~~eqv~~m~~~GN 86 (287)
T KOG0703|consen 8 SNERNKRRLRELLREPDNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDE-WTDEQVDFMISMGN 86 (287)
T ss_pred ccchHHHHHHHHHcCcccCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccc-cCHHHHHHHHHHcc
Confidence 45788999999999999999999999999999999999999999999999999999999999999 99999999999999
Q ss_pred CCcCCCccccchhccccCCCchhHHHHHHHhhhhhcccccCCcchHHHHHHHHhhcCCCCcchhcccCcHH
Q psy7092 102 ANAPNGQNTRLSLWRSWGSFPLAFFKQLVNLWLNIEMYHFSISTTAQALVSFFNQHNCTSKDAQQKYNSRA 172 (540)
Q Consensus 102 ~~an~~~e~~l~~W~~~~~~p~~f~k~~~~~~~~~~~~~~~~~~~~~~l~~F~~~~~~~~~~i~~KY~sra 172 (540)
.+|| +|||+. +|. .+..+.++..++.| |+.||+.+-
T Consensus 87 ~~an-------~~~ea~--~p~----------------~~~~p~~d~~~e~F----------IR~KYE~kk 122 (287)
T KOG0703|consen 87 AKAN-------SYYEAK--LPD----------------PFRRPGPDDLVEQF----------IRDKYERKK 122 (287)
T ss_pred hhhh-------hhcccc--CCc----------------cccCCChHHHHHHH----------HHHHHhhhh
Confidence 9999 778772 333 35567777789999 567776544
No 5
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=99.97 E-value=4.5e-32 Score=277.94 Aligned_cols=115 Identities=43% Similarity=0.740 Sum_probs=103.1
Q ss_pred chHHHHHHHhcccCCCcccCCCCCCCCceEecccceEcccchhhhccCCCcccceeeccCCCCCCHHHHHHHHhcCcCCc
Q psy7092 25 KNSKLLMLQIITFFPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANA 104 (540)
Q Consensus 25 ~n~k~l~~l~~~p~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~LGvhiS~VKSl~lDs~Wt~~qL~~m~~gGN~~a 104 (540)
..++++..|...++|+.|||||+++|+|+|+|||||||++||||||+||+|||+||||+||. |+.+||+.|..|||.+|
T Consensus 6 ~~~~~l~~l~~~~~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~-wt~~~l~~m~~gGN~~a 84 (319)
T COG5347 6 EDRKLLKLLKSDSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDN-WTEEELRRMEVGGNSNA 84 (319)
T ss_pred HHHHHHHHHhhccccCccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeeccc-CCHHHHHHHHHhcchhh
Confidence 35667777777899999999999999999999999999999999999999999999999999 99999999999999999
Q ss_pred CCCccccchhccccCCCchhHHHHHHHhhhhhcccccCCcchHHHHHHHHhhcCCCC--cchhcccCcHHHHHHHHHHHH
Q psy7092 105 PNGQNTRLSLWRSWGSFPLAFFKQLVNLWLNIEMYHFSISTTAQALVSFFNQHNCTS--KDAQQKYNSRAAQLYREKLQH 182 (540)
Q Consensus 105 n~~~e~~l~~W~~~~~~p~~f~k~~~~~~~~~~~~~~~~~~~~~~l~~F~~~~~~~~--~~i~~KY~sraA~~YrekL~~ 182 (540)
| .||..|++.. .+++.||.+..++.|.+++..
T Consensus 85 ~----------------------------------------------~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~ 118 (319)
T COG5347 85 N----------------------------------------------RFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYE 118 (319)
T ss_pred h----------------------------------------------hHhccCCCcccccccccccCHHHHHHHHHHHHH
Confidence 9 6666666652 679999999999999999877
Q ss_pred HHHH
Q psy7092 183 AAVQ 186 (540)
Q Consensus 183 ~a~~ 186 (540)
++.-
T Consensus 119 ~~~~ 122 (319)
T COG5347 119 LKKF 122 (319)
T ss_pred hhhc
Confidence 6544
No 6
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=99.97 E-value=7.4e-32 Score=239.65 Aligned_cols=111 Identities=35% Similarity=0.688 Sum_probs=89.3
Q ss_pred HHHHHHhcccCCCcccCCCCCCCCceEecccceEcccchhhhccCCCcccceeeccCCCCCCHHHHHHHHhcCcCCcCCC
Q psy7092 28 KLLMLQIITFFPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAPNG 107 (540)
Q Consensus 28 k~l~~l~~~p~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~LGvhiS~VKSl~lDs~Wt~~qL~~m~~gGN~~an~~ 107 (540)
++|+.|+..|+|++|+|||+++|+|+|++||||||+.|+|+||.||+|+|+||||+||+ |+.++|+.|+.+||..+|
T Consensus 2 ~~l~~l~~~~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~VkSi~~d~-w~~~ev~~~~~~GN~~~n-- 78 (116)
T PF01412_consen 2 KILRELLKKPGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRVKSITMDN-WSPEEVQRMREGGNKRAN-- 78 (116)
T ss_dssp HHHHHHHCSTTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--EEETTTS----HHHHHHHHHSHHHHHH--
T ss_pred HHHHHHHcCcCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhccccccCC-CCHHHHHHHHHHChHHHH--
Confidence 67889999999999999999999999999999999999999999999999999999999 999999999999999999
Q ss_pred ccccchhccccCCCchhHHHHHHHhhhhhcccccCCcchHHHHHHHHhhcCCCCcchhcccCcHH
Q psy7092 108 QNTRLSLWRSWGSFPLAFFKQLVNLWLNIEMYHFSISTTAQALVSFFNQHNCTSKDAQQKYNSRA 172 (540)
Q Consensus 108 ~e~~l~~W~~~~~~p~~f~k~~~~~~~~~~~~~~~~~~~~~~l~~F~~~~~~~~~~i~~KY~sra 172 (540)
++|+++ ......++.+++...+++| |+.||..+.
T Consensus 79 -----~~~e~~----------------~~~~~~~~~~~~~~~~~~f----------I~~KY~~k~ 112 (116)
T PF01412_consen 79 -----SIWEAN----------------SPPPKKPPPSSDQEKREQF----------IRAKYVEKA 112 (116)
T ss_dssp -----HHHTTT----------------STTTTTHCTTSHHHHHHHH----------HHHHHTTHT
T ss_pred -----HHHHcC----------------CCCCCCCCCCCcHHHHHHH----------HHHHHHhhh
Confidence 888882 2233456778889999999 557777654
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=99.96 E-value=2.2e-30 Score=229.14 Aligned_cols=103 Identities=50% Similarity=0.812 Sum_probs=87.8
Q ss_pred cCCCcccCCCCCCCCceEecccceEcccchhhhccCCCcccceeeccCCCCCCHHHHHHHHhcCcCCcCCCccccchhcc
Q psy7092 37 FFPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAPNGQNTRLSLWR 116 (540)
Q Consensus 37 p~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~LGvhiS~VKSl~lDs~Wt~~qL~~m~~gGN~~an~~~e~~l~~W~ 116 (540)
|+|+.||||++++|+|+|++||||||++|+|+||+||+|||+||||+||+ |++++|+.|+.+||.++| ++|+
T Consensus 1 ~~N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~VkSl~md~-w~~~~i~~~~~~GN~~~n-------~~~e 72 (112)
T smart00105 1 PGNKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTLDT-WTEEELRLLQKGGNENAN-------SIWE 72 (112)
T ss_pred CCCCcccCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCeeeecccCC-CCHHHHHHHHHhhhHHHH-------HHHH
Confidence 58999999999999999999999999999999999999999999999999 999999999999999999 6776
Q ss_pred ccCCCchhHHHHHHHhhhhhcccccCCcchHHHHHHHHhhcCCCCcchhcccCcHH
Q psy7092 117 SWGSFPLAFFKQLVNLWLNIEMYHFSISTTAQALVSFFNQHNCTSKDAQQKYNSRA 172 (540)
Q Consensus 117 ~~~~~p~~f~k~~~~~~~~~~~~~~~~~~~~~~l~~F~~~~~~~~~~i~~KY~sra 172 (540)
+. ++.....++...+...+++| |+.||..+.
T Consensus 73 ~~---------------~~~~~~~~~~~~~~~~~~~f----------I~~KY~~k~ 103 (112)
T smart00105 73 SN---------------LDDFSLKPPDSDDQQKYESF----------IAAKYEEKL 103 (112)
T ss_pred hh---------------CCccccCCCCCchHHHHHHH----------HHHHHHhhh
Confidence 62 12222334455567788888 567776655
No 8
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=99.94 E-value=1.7e-27 Score=255.39 Aligned_cols=120 Identities=22% Similarity=0.403 Sum_probs=102.0
Q ss_pred hhhhhhhchHHHHHHHhcccCCCcccCCCCCCCCceEecccceEcccchhhhccCCCcccceeeccCCCCCCHHHHHHHH
Q psy7092 18 LFHLEKVKNSKLLMLQIITFFPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQ 97 (540)
Q Consensus 18 ~~~~e~~~n~k~l~~l~~~p~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~LGvhiS~VKSl~lDs~Wt~~qL~~m~ 97 (540)
..++++++++++|++|++.|+|+.|+||++++|.|+|++||||||+.|+||||+|| ++||||+||+ |+++||+.|+
T Consensus 2 ~SKR~qERnekILreLlklPgNk~CADCgs~~P~WASiNlGIFICi~CSGIHRsLG---hRVKSLSLDk-WT~EEVe~Mk 77 (648)
T PLN03119 2 GSKREEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREFT---HRVKSVSMSK-FTSKEVEVLQ 77 (648)
T ss_pred cchHHHHHHHHHHHHHhhCcCCCccccCCCCCCCceeeccceEEeccchhhhccCC---ceeeccccCC-CCHHHHHHHH
Confidence 45788999999999999999999999999999999999999999999999999998 4999999999 9999999999
Q ss_pred hcCcCCcCCCccccchhccccCCCchhHHHHHHHhhhhhcccccCCcchHHHHHHHHhhcCCCCcc
Q psy7092 98 LGGNANAPNGQNTRLSLWRSWGSFPLAFFKQLVNLWLNIEMYHFSISTTAQALVSFFNQHNCTSKD 163 (540)
Q Consensus 98 ~gGN~~an~~~e~~l~~W~~~~~~p~~f~k~~~~~~~~~~~~~~~~~~~~~~l~~F~~~~~~~~~~ 163 (540)
.+||.+|| .||++ .|- .....++...++..+++||+..|+..++
T Consensus 78 ~gGN~~AN-------~iyea--------------nw~-~~~~~~P~~sD~e~lr~FIR~KYVeKRF 121 (648)
T PLN03119 78 NGGNQRAR-------EIYLK--------------NWD-HQRQRLPENSNAERVREFIKNVYVQKKY 121 (648)
T ss_pred HhchHHHH-------HHHHh--------------hcc-cccCCCCCCccHHHHHHHHHHHHhhhhc
Confidence 99999999 45544 222 2223456677888899998865554433
No 9
>PLN03131 hypothetical protein; Provisional
Probab=99.94 E-value=3.3e-27 Score=254.87 Aligned_cols=113 Identities=21% Similarity=0.442 Sum_probs=97.0
Q ss_pred hhhhhhhchHHHHHHHhcccCCCcccCCCCCCCCceEecccceEcccchhhhccCCCcccceeeccCCCCCCHHHHHHHH
Q psy7092 18 LFHLEKVKNSKLLMLQIITFFPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQ 97 (540)
Q Consensus 18 ~~~~e~~~n~k~l~~l~~~p~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~LGvhiS~VKSl~lDs~Wt~~qL~~m~ 97 (540)
..++++++++++|+.|++.|+|+.|+||++++|.|+|++||||||+.|+||||+|| ++||||+||+ |++++|+.|+
T Consensus 2 ~SkkqqErnekiLreLlk~PgNk~CADCga~~P~WASiNlGIFICi~CSGIHRsLg---hRVKSVTLD~-WtdeEV~~Mk 77 (705)
T PLN03131 2 GSRKEEERNEKIIRGLMKLPPNRRCINCNSLGPQFVCTNFWTFICMTCSGIHREFT---HRVKSVSMSK-FTSQDVEALQ 77 (705)
T ss_pred cchHHHHHHHHHHHHHhhCcCCCccccCCCCCCCeeEeccceEEchhchhhhcccC---cccccccCCC-CCHHHHHHHH
Confidence 35778999999999999999999999999999999999999999999999999997 4999999999 9999999999
Q ss_pred hcCcCCcCCCccccchhccccCCCchhHHHHHHHhhhhhcccccCCcchHHHHHHHHhh
Q psy7092 98 LGGNANAPNGQNTRLSLWRSWGSFPLAFFKQLVNLWLNIEMYHFSISTTAQALVSFFNQ 156 (540)
Q Consensus 98 ~gGN~~an~~~e~~l~~W~~~~~~p~~f~k~~~~~~~~~~~~~~~~~~~~~~l~~F~~~ 156 (540)
.+||.+|| .+|++ .| +.....++...+...+++||+.
T Consensus 78 ~gGN~~AN-------~iyea--------------nw-d~~r~~lP~~sd~ekrr~FIR~ 114 (705)
T PLN03131 78 NGGNQRAR-------EIYLK--------------DW-DQQRQRLPDNSKVDKIREFIKD 114 (705)
T ss_pred HhccHHHH-------HHHHh--------------hc-ccccCCCCCCccHHHHHHHHHH
Confidence 99999999 44443 22 2222345666777889999663
No 10
>KOG0703|consensus
Probab=99.89 E-value=1.5e-24 Score=218.95 Aligned_cols=89 Identities=34% Similarity=0.409 Sum_probs=78.1
Q ss_pred cccccCCCCcccc-cCCcccccccccCCCCCCccccccccCceeeeeeeecccCCCCCHHHHHHHHhcccccchhcccCC
Q psy7092 318 KKIQSKKPSGFVC-RCPPFYQANVLTTTPPRQSLVAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAMKAEFGP 396 (540)
Q Consensus 318 ~~~~~~~~~~f~c-rc~~~~~~~~~~~~~~~~~~sgIHR~LGVHISkVkS~~LDs~Wt~EQv~~Mq~gGN~~a~~~kY~~ 396 (540)
-+|++-|-|+||| || +||||+||||||+||||+||+ |++|||++|+.+||.+||.+
T Consensus 36 P~WaSwnlGvFiC~~C------------------~giHR~lg~hiSkVkSv~LD~-W~~eqv~~m~~~GN~~an~~---- 92 (287)
T KOG0703|consen 36 PRWASWNLGVFICLRC------------------AGIHRSLGVHISKVKSVTLDE-WTDEQVDFMISMGNAKANSY---- 92 (287)
T ss_pred CCeEEeecCeEEEeec------------------ccccccccchhheeeeeeccc-cCHHHHHHHHHHcchhhhhh----
Confidence 4688889999999 99 999999999999999999999 99999999999999999999
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCC--CCcccccccccCCCCCcccCCC
Q psy7092 397 FNAGQFDSPPPDCTHTLPLAFTP--SGMGFASMSRSGGLGGKKLGKG 441 (540)
Q Consensus 397 ~~A~~yK~~~P~s~~~lp~~~~~--s~~~~~~fir~~~~~~k~~~~g 441 (540)
|++.||..|.+ .+..++.|||.||+.+||++.+
T Consensus 93 ------------~ea~~p~~~~~p~~d~~~e~FIR~KYE~kkf~~~~ 127 (287)
T KOG0703|consen 93 ------------YEAKLPDPFRRPGPDDLVEQFIRDKYERKKFLDPE 127 (287)
T ss_pred ------------ccccCCccccCCChHHHHHHHHHHHHhhhhhccch
Confidence 55566666655 2346899999999999998754
No 11
>KOG0705|consensus
Probab=99.79 E-value=6.2e-20 Score=197.42 Aligned_cols=115 Identities=32% Similarity=0.543 Sum_probs=94.5
Q ss_pred chHHHHHHHhcccCCCcccCCCCCCCCceEecccceEcccchhhhccCCCcccceeeccCCCCCCHHHHHHHHhcCcCCc
Q psy7092 25 KNSKLLMLQIITFFPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANA 104 (540)
Q Consensus 25 ~n~k~l~~l~~~p~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~LGvhiS~VKSl~lDs~Wt~~qL~~m~~gGN~~a 104 (540)
.+.-+|..+..-+||..|+||+.++|.|||+|+|+.+|+.|+||||.||.|+|+|||+.||. |..+.+..|...||+.|
T Consensus 499 sea~a~qairn~rgn~~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDd-WPvEl~~Vm~aiGN~~A 577 (749)
T KOG0705|consen 499 SEAMALQAIRNMRGNSHCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDD-WPVELLKVMSAIGNDLA 577 (749)
T ss_pred hhHHHHHHHhcCcCCceeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhcccccc-CcHHHHHHHHHhhhhHH
Confidence 34445555556789999999999999999999999999999999999999999999999999 99999999999999999
Q ss_pred CCCccccchhccccCCCchhHHHHHHHhhhhhcccccCCcchHHHHHHHHhhcCCCCcchhcccCcHHH
Q psy7092 105 PNGQNTRLSLWRSWGSFPLAFFKQLVNLWLNIEMYHFSISTTAQALVSFFNQHNCTSKDAQQKYNSRAA 173 (540)
Q Consensus 105 n~~~e~~l~~W~~~~~~p~~f~k~~~~~~~~~~~~~~~~~~~~~~l~~F~~~~~~~~~~i~~KY~sraA 173 (540)
| ++||.. +.-. ....+++....-+.| |+.||+.+.+
T Consensus 578 N-------~vWE~~---------------~~G~-~KPs~~s~REEkErw----------Ir~KYeqklF 613 (749)
T KOG0705|consen 578 N-------SVWEGS---------------SQGQ-TKPSPDSSREEKERW----------IRAKYEQKLF 613 (749)
T ss_pred H-------HHhhhh---------------ccCC-cCCCccccHHHHHHH----------HHHHHHHHhh
Confidence 9 889872 1111 123445556667778 5678877765
No 12
>KOG0704|consensus
Probab=99.74 E-value=6.7e-19 Score=180.94 Aligned_cols=65 Identities=37% Similarity=0.721 Sum_probs=59.7
Q ss_pred cccCCCCcccc-cCCcccccccccCCCCCCccccccccCceeeeeeeecccCCCCCHHHHHHHHhcccccchh-------
Q psy7092 320 IQSKKPSGFVC-RCPPFYQANVLTTTPPRQSLVAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAMK------- 391 (540)
Q Consensus 320 ~~~~~~~~f~c-rc~~~~~~~~~~~~~~~~~~sgIHR~LGVHISkVkS~~LDs~Wt~EQv~~Mq~gGN~~a~~------- 391 (540)
+.+-.+|-||| -| ||+||+|||||||||||+||. |.+.||..|..|||.+.+.
T Consensus 32 WvSvsyGIfICLEC------------------SG~HRgLGVhiSFVRSVTMD~-wkeiel~kMeaGGN~~~~eFL~s~~~ 92 (386)
T KOG0704|consen 32 WVSVSYGIFICLEC------------------SGKHRGLGVHISFVRSVTMDK-WKEIELKKMEAGGNERFREFLSSQGI 92 (386)
T ss_pred eEeecccEEEEEec------------------CCcccccceeeEEEEeeeccc-ccHHHHHHHHhccchhHHHHHhhCcc
Confidence 44667899999 78 999999999999999999999 9999999999999999655
Q ss_pred --------cccCCCCCCCCC
Q psy7092 392 --------AEFGPFNAGQFD 403 (540)
Q Consensus 392 --------~kY~~~~A~~yK 403 (540)
.||++.+|+.||
T Consensus 93 ~~e~~~i~eKYns~aAa~yR 112 (386)
T KOG0704|consen 93 YKETWPIREKYNSRAAALYR 112 (386)
T ss_pred ccccccHHHhhccHHHHHHH
Confidence 779999999988
No 13
>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=99.73 E-value=2e-19 Score=159.41 Aligned_cols=86 Identities=34% Similarity=0.411 Sum_probs=71.7
Q ss_pred cccCCCCcccc-cCCcccccccccCCCCCCccccccccCceeeeeeeecccCCCCCHHHHHHHHhcccccchhcccCCCC
Q psy7092 320 IQSKKPSGFVC-RCPPFYQANVLTTTPPRQSLVAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAMKAEFGPFN 398 (540)
Q Consensus 320 ~~~~~~~~f~c-rc~~~~~~~~~~~~~~~~~~sgIHR~LGVHISkVkS~~LDs~Wt~EQv~~Mq~gGN~~a~~~kY~~~~ 398 (540)
+.+-++|.||| .| |||||+||+|||+||||+||+ |++++|+.|+.+||.++++.
T Consensus 16 w~s~~~GifvC~~C------------------sgiHR~lg~his~VkSl~md~-w~~~~i~~~~~~GN~~~n~~------ 70 (112)
T smart00105 16 WASVNLGVFLCIEC------------------SGIHRSLGVHISKVRSLTLDT-WTEEELRLLQKGGNENANSI------ 70 (112)
T ss_pred cEEeccceeEhHHh------------------HHHHHhcCCCcCeeeecccCC-CCHHHHHHHHHhhhHHHHHH------
Confidence 55778999999 89 999999999999999999999 99999999999999999998
Q ss_pred CCCCCCCCCCCCCCCCCCCCC-----CCcccccccccCCCCCcccCC
Q psy7092 399 AGQFDSPPPDCTHTLPLAFTP-----SGMGFASMSRSGGLGGKKLGK 440 (540)
Q Consensus 399 A~~yK~~~P~s~~~lp~~~~~-----s~~~~~~fir~~~~~~k~~~~ 440 (540)
++..+|+...+ .....+.|||.||+.++++..
T Consensus 71 ----------~e~~~~~~~~~~~~~~~~~~~~~fI~~KY~~k~f~~~ 107 (112)
T smart00105 71 ----------WESNLDDFSLKPPDSDDQQKYESFIAAKYEEKLFVPP 107 (112)
T ss_pred ----------HHhhCCccccCCCCCchHHHHHHHHHHHHHhhhcccc
Confidence 33444333222 235678899999999998754
No 14
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.73 E-value=1.2e-18 Score=180.02 Aligned_cols=66 Identities=45% Similarity=0.725 Sum_probs=61.3
Q ss_pred ccccCCCCcccc-cCCcccccccccCCCCCCccccccccCceeeeeeeecccCCCCCHHHHHHHHhcccccchh------
Q psy7092 319 KIQSKKPSGFVC-RCPPFYQANVLTTTPPRQSLVAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAMK------ 391 (540)
Q Consensus 319 ~~~~~~~~~f~c-rc~~~~~~~~~~~~~~~~~~sgIHR~LGVHISkVkS~~LDs~Wt~EQv~~Mq~gGN~~a~~------ 391 (540)
.|.+.++|.||| .| |||||+||||||||||++||+ |+++||+.|+.|||.+++.
T Consensus 34 tWASvn~GIFLCl~C------------------SGVHRsLGvHISfVRSltLD~-Ws~eqL~~Mk~GGN~rA~~fF~qhG 94 (395)
T PLN03114 34 TWASVTYGIFLCIDC------------------SAVHRSLGVHISFVRSTNLDS-WSSEQLKMMIYGGNNRAQVFFKQYG 94 (395)
T ss_pred Cceeeccceeehhhh------------------hHhhccCCCCCceeecccCCC-CCHHHHHHHHHhcCHHHHHHHHHcC
Confidence 466788999999 89 999999999999999999999 9999999999999999765
Q ss_pred --------cccCCCCCCCCC
Q psy7092 392 --------AEFGPFNAGQFD 403 (540)
Q Consensus 392 --------~kY~~~~A~~yK 403 (540)
.||++.+|..||
T Consensus 95 ~~~~~~~~~KY~S~aA~~Yr 114 (395)
T PLN03114 95 WSDGGKTEAKYTSRAADLYK 114 (395)
T ss_pred CCCCCCcccccCCHHHHHHH
Confidence 679999999988
No 15
>KOG0706|consensus
Probab=99.71 E-value=1e-18 Score=184.06 Aligned_cols=65 Identities=54% Similarity=0.907 Sum_probs=61.4
Q ss_pred cccCCCCcccc-cCCcccccccccCCCCCCccccccccCceeeeeeeecccCCCCCHHHHHHHHhcccccchh-------
Q psy7092 320 IQSKKPSGFVC-RCPPFYQANVLTTTPPRQSLVAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAMK------- 391 (540)
Q Consensus 320 ~~~~~~~~f~c-rc~~~~~~~~~~~~~~~~~~sgIHR~LGVHISkVkS~~LDs~Wt~EQv~~Mq~gGN~~a~~------- 391 (540)
|.+.-+|.||| -| |++||+||||||||||++||+ |+|+||++|+.|||.+|+.
T Consensus 36 WaSVTYGIFLCiDC------------------SAvHRnLGVHiSFVRSTnLDs-Ws~~qLR~M~~GGN~nA~~FFkqhg~ 96 (454)
T KOG0706|consen 36 WASVTYGIFLCIDC------------------SAVHRNLGVHISFVRSTNLDS-WSWEQLRRMQVGGNANARVFFKQHGC 96 (454)
T ss_pred ceeecceEEEEEec------------------chhhhccccceEEEeeccccc-CCHHHHhHhhhcCchhHHHHHHHcCC
Confidence 56777899999 89 999999999999999999999 9999999999999999887
Q ss_pred ------cccCCCCCCCCC
Q psy7092 392 ------AEFGPFNAGQFD 403 (540)
Q Consensus 392 ------~kY~~~~A~~yK 403 (540)
+||++++|.+|+
T Consensus 97 ~t~d~~aKY~SraA~~Yr 114 (454)
T KOG0706|consen 97 VTLDANAKYNSRAAKLYR 114 (454)
T ss_pred cchhhhhhhccHHHHHHH
Confidence 779999999998
No 16
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=99.71 E-value=2.1e-18 Score=177.55 Aligned_cols=93 Identities=33% Similarity=0.440 Sum_probs=70.4
Q ss_pred ccccCCCCcccc-cCCcccccccccCCCCCCccccccccCceeeeeeeecccCCCCCHHHHHHHHhcccccchhcccCCC
Q psy7092 319 KIQSKKPSGFVC-RCPPFYQANVLTTTPPRQSLVAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAMKAEFGPF 397 (540)
Q Consensus 319 ~~~~~~~~~f~c-rc~~~~~~~~~~~~~~~~~~sgIHR~LGVHISkVkS~~LDs~Wt~EQv~~Mq~gGN~~a~~~kY~~~ 397 (540)
.|.+-++|.||| +| |||||+|||||||||||+||+ |+++||++|..|||.+++.. |+..
T Consensus 32 ~W~S~nlGvfiCi~C------------------agvHRsLGvhiS~VKSitLD~-wt~~~l~~m~~gGN~~a~~~-~e~~ 91 (319)
T COG5347 32 TWASVNLGVFLCIDC------------------AGVHRSLGVHISKVKSLTLDN-WTEEELRRMEVGGNSNANRF-YEKN 91 (319)
T ss_pred ceEecccCeEEEeec------------------chhhhccccceeeeeeeeccc-CCHHHHHHHHHhcchhhhhH-hccC
Confidence 577889999999 99 999999999999999999999 99999999999999999997 4322
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCcccccccccCCCCCcccCC
Q psy7092 398 NAGQFDSPPPDCTHTLPLAFTPSGMGFASMSRSGGLGGKKLGK 440 (540)
Q Consensus 398 ~A~~yK~~~P~s~~~lp~~~~~s~~~~~~fir~~~~~~k~~~~ 440 (540)
..-. ..+|..-......++.||+++|.-+++...
T Consensus 92 ~~~~---------~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~ 125 (319)
T COG5347 92 LLDQ---------LLLPIKAKYDSSVAKKYIRKKYELKKFIDD 125 (319)
T ss_pred CCcc---------cccccccccCHHHHHHHHHHHHHhhhcccc
Confidence 1110 001211122334566788888877777643
No 17
>KOG0521|consensus
Probab=99.70 E-value=6.2e-18 Score=190.86 Aligned_cols=111 Identities=32% Similarity=0.454 Sum_probs=89.5
Q ss_pred HHHHhcccCCCcccCCCCCCCCceEecccceEcccchhhhccCCCcccceeeccCCCCCCHHHHHHHHhcCcCCcCCCcc
Q psy7092 30 LMLQIITFFPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAPNGQN 109 (540)
Q Consensus 30 l~~l~~~p~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~LGvhiS~VKSl~lDs~Wt~~qL~~m~~gGN~~an~~~e 109 (540)
+..+...|+|..|+|||++.|+|+|+|+||.+||.|+|+||+||+|+|+|+|++||. |..+.+..|+.+||..+|.+||
T Consensus 417 ~~~vq~~pgN~~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~-~~~~l~~l~~~lgn~~~N~i~e 495 (785)
T KOG0521|consen 417 IEEVQSVPGNAQCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDV-WEPELLLLFKNLGNKYVNEIYE 495 (785)
T ss_pred hhhhhcCCchhhhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhc-cCcHHHHHHHHhCcchhhhhhh
Confidence 444445799999999999999999999999999999999999999999999999999 9999999999999999995555
Q ss_pred ccchhccccCCCchhHHHHHHHhhhhhcccccCCcchHHHHHHHHhhcCCCCc
Q psy7092 110 TRLSLWRSWGSFPLAFFKQLVNLWLNIEMYHFSISTTAQALVSFFNQHNCTSK 162 (540)
Q Consensus 110 ~~l~~W~~~~~~p~~f~k~~~~~~~~~~~~~~~~~~~~~~l~~F~~~~~~~~~ 162 (540)
..| |.. . ........++.+.+.|+++.|+...
T Consensus 496 ~~l--~~~------------------~-~~~~~~~~~~~~r~~~i~~kyve~~ 527 (785)
T KOG0521|consen 496 ALL--PSY------------------D-SSKPTASSSRQAREAWIKAKYVERR 527 (785)
T ss_pred ccc--ccc------------------c-ccCCCCccchhhhhHhhhcccceee
Confidence 543 111 0 1122233447888889877776544
No 18
>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=99.68 E-value=9e-19 Score=155.95 Aligned_cols=90 Identities=27% Similarity=0.461 Sum_probs=63.3
Q ss_pred ccccCCCCcccc-cCCcccccccccCCCCCCccccccccCceeeeeeeecccCCCCCHHHHHHHHhcccccchhcccCCC
Q psy7092 319 KIQSKKPSGFVC-RCPPFYQANVLTTTPPRQSLVAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAMKAEFGPF 397 (540)
Q Consensus 319 ~~~~~~~~~f~c-rc~~~~~~~~~~~~~~~~~~sgIHR~LGVHISkVkS~~LDs~Wt~EQv~~Mq~gGN~~a~~~kY~~~ 397 (540)
.+.+-++|.|+| .| |||||.||||||+||||+||+ |++++|+.|+.+||..++.. |+..
T Consensus 25 ~w~s~~~GiflC~~C------------------ag~HR~lg~~is~VkSi~~d~-w~~~ev~~~~~~GN~~~n~~-~e~~ 84 (116)
T PF01412_consen 25 TWASLNYGIFLCLEC------------------AGIHRSLGVHISRVKSITMDN-WSPEEVQRMREGGNKRANSI-WEAN 84 (116)
T ss_dssp -EEETTTTEEE-HHH------------------HHHHHHHTTTT--EEETTTS----HHHHHHHHHSHHHHHHHH-HTTT
T ss_pred CEEEeecChhhhHHH------------------HHHHHHhcccchhccccccCC-CCHHHHHHHHHHChHHHHHH-HHcC
Confidence 566778999999 89 999999999999999999999 99999999999999999998 4433
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCcccccccccCCCCCcccC
Q psy7092 398 NAGQFDSPPPDCTHTLPLAFTPSGMGFASMSRSGGLGGKKLG 439 (540)
Q Consensus 398 ~A~~yK~~~P~s~~~lp~~~~~s~~~~~~fir~~~~~~k~~~ 439 (540)
....+++.++ .+....+.||+.+|+.++++.
T Consensus 85 -~~~~~~~~~~----------~~~~~~~~fI~~KY~~k~f~~ 115 (116)
T PF01412_consen 85 -SPPPKKPPPS----------SDQEKREQFIRAKYVEKAFIS 115 (116)
T ss_dssp -STTTTTHCTT----------SHHHHHHHHHHHHHTTHTTS-
T ss_pred -CCCCCCCCCC----------CcHHHHHHHHHHHHHhhhhcc
Confidence 1111111111 123456779999999887763
No 19
>KOG0818|consensus
Probab=99.64 E-value=3e-17 Score=174.65 Aligned_cols=75 Identities=35% Similarity=0.730 Sum_probs=71.4
Q ss_pred ccCCCcccCCCCCCCCceEecccceEcccchhhhccCCCcccceeeccCCCCCCHHHHHHHHhcCcCCcCCCccccchhc
Q psy7092 36 TFFPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAPNGQNTRLSLW 115 (540)
Q Consensus 36 ~p~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~LGvhiS~VKSl~lDs~Wt~~qL~~m~~gGN~~an~~~e~~l~~W 115 (540)
...-++|+|||+++|.||||+-|+|||.+|+.+||+||.|||.||++.... |.+..|++...+.|..|| ++|
T Consensus 5 ~l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~-W~pt~l~~V~tLn~~gaN-------sIW 76 (669)
T KOG0818|consen 5 LLSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTP-WPPTLLQMVETLNNNGAN-------SIW 76 (669)
T ss_pred chhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCC-CCHHHHHHHHHHHhcCcc-------hhh
Confidence 456789999999999999999999999999999999999999999999998 999999999999999999 899
Q ss_pred ccc
Q psy7092 116 RSW 118 (540)
Q Consensus 116 ~~~ 118 (540)
|.+
T Consensus 77 Eh~ 79 (669)
T KOG0818|consen 77 EHS 79 (669)
T ss_pred hhh
Confidence 886
No 20
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=99.47 E-value=8.2e-15 Score=158.59 Aligned_cols=93 Identities=20% Similarity=0.266 Sum_probs=72.2
Q ss_pred cccccCCCCcccc-cCCcccccccccCCCCCCccccccccCceeeeeeeecccCCCCCHHHHHHHHhcccccchhcccCC
Q psy7092 318 KKIQSKKPSGFVC-RCPPFYQANVLTTTPPRQSLVAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAMKAEFGP 396 (540)
Q Consensus 318 ~~~~~~~~~~f~c-rc~~~~~~~~~~~~~~~~~~sgIHR~LGVHISkVkS~~LDs~Wt~EQv~~Mq~gGN~~a~~~kY~~ 396 (540)
-++.+-++|.||| +| |||||+|| | +||||+||+ |++|||+.|+.+||.+++++ |+.
T Consensus 34 P~WASiNlGIFICi~C------------------SGIHRsLG-h--RVKSLSLDk-WT~EEVe~Mk~gGN~~AN~i-yea 90 (648)
T PLN03119 34 PQYVCTTFWTFVCMAC------------------SGIHREFT-H--RVKSVSMSK-FTSKEVEVLQNGGNQRAREI-YLK 90 (648)
T ss_pred CCceeeccceEEeccc------------------hhhhccCC-c--eeeccccCC-CCHHHHHHHHHhchHHHHHH-HHh
Confidence 3566789999999 99 99999998 4 999999999 99999999999999999998 654
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCcccccccccCCCCCcccCCCCC
Q psy7092 397 FNAGQFDSPPPDCTHTLPLAFTPSGMGFASMSRSGGLGGKKLGKGGL 443 (540)
Q Consensus 397 ~~A~~yK~~~P~s~~~lp~~~~~s~~~~~~fir~~~~~~k~~~~g~~ 443 (540)
......++ .|.. .....++.|||.||+.+||++....
T Consensus 91 nw~~~~~~-~P~~---------sD~e~lr~FIR~KYVeKRF~~~~~~ 127 (648)
T PLN03119 91 NWDHQRQR-LPEN---------SNAERVREFIKNVYVQKKYAGANDA 127 (648)
T ss_pred hcccccCC-CCCC---------ccHHHHHHHHHHHHhhhhccCcCCC
Confidence 43322221 1111 1224567899999999999976543
No 21
>PLN03131 hypothetical protein; Provisional
Probab=99.45 E-value=1.4e-14 Score=157.89 Aligned_cols=95 Identities=20% Similarity=0.242 Sum_probs=72.0
Q ss_pred cccccCCCCcccc-cCCcccccccccCCCCCCccccccccCceeeeeeeecccCCCCCHHHHHHHHhcccccchhcccCC
Q psy7092 318 KKIQSKKPSGFVC-RCPPFYQANVLTTTPPRQSLVAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAMKAEFGP 396 (540)
Q Consensus 318 ~~~~~~~~~~f~c-rc~~~~~~~~~~~~~~~~~~sgIHR~LGVHISkVkS~~LDs~Wt~EQv~~Mq~gGN~~a~~~kY~~ 396 (540)
-++.+.++|.||| +| |||||+|| | |||||+||+ |+++||+.|+.+||.+++.+ |+.
T Consensus 34 P~WASiNlGIFICi~C------------------SGIHRsLg-h--RVKSVTLD~-WtdeEV~~Mk~gGN~~AN~i-yea 90 (705)
T PLN03131 34 PQFVCTNFWTFICMTC------------------SGIHREFT-H--RVKSVSMSK-FTSQDVEALQNGGNQRAREI-YLK 90 (705)
T ss_pred CCeeEeccceEEchhc------------------hhhhcccC-c--ccccccCCC-CCHHHHHHHHHhccHHHHHH-HHh
Confidence 3567889999999 99 99999998 4 999999999 99999999999999999988 653
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCcccccccccCCCCCcccCCCCCCC
Q psy7092 397 FNAGQFDSPPPDCTHTLPLAFTPSGMGFASMSRSGGLGGKKLGKGGLGA 445 (540)
Q Consensus 397 ~~A~~yK~~~P~s~~~lp~~~~~s~~~~~~fir~~~~~~k~~~~g~~~a 445 (540)
......+ +.|... ....++.|||.||+.+||.+.....+
T Consensus 91 nwd~~r~-~lP~~s---------d~ekrr~FIR~KYVeKRFa~~~s~d~ 129 (705)
T PLN03131 91 DWDQQRQ-RLPDNS---------KVDKIREFIKDIYVDKKYAGGKTHDK 129 (705)
T ss_pred hcccccC-CCCCCc---------cHHHHHHHHHHHHhhhhhhcCCCCCC
Confidence 3321111 111111 12356789999999999997544433
No 22
>KOG1117|consensus
Probab=99.44 E-value=5.3e-14 Score=156.95 Aligned_cols=75 Identities=33% Similarity=0.656 Sum_probs=72.0
Q ss_pred ccCCCcccCCCCCCCCceEecccceEcccchhhhccCCCcccceeeccCCCC-CCHHHHHHHHhcCcCCcCCCccccchh
Q psy7092 36 TFFPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTN-WTWVQLRQMQLGGNANAPNGQNTRLSL 114 (540)
Q Consensus 36 ~p~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~LGvhiS~VKSl~lDs~-Wt~~qL~~m~~gGN~~an~~~e~~l~~ 114 (540)
...|+.|+||+++.|.|||+|++|.||-.|+|-||+||..+|+|+|++||.. |+.+-|+.+-..||..+| +|
T Consensus 295 ne~nr~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an-------~F 367 (1186)
T KOG1117|consen 295 NEENRECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRAN-------RF 367 (1186)
T ss_pred ccccccccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCcccc-------cc
Confidence 4689999999999999999999999999999999999999999999999977 999999999999999999 88
Q ss_pred ccc
Q psy7092 115 WRS 117 (540)
Q Consensus 115 W~~ 117 (540)
|..
T Consensus 368 wa~ 370 (1186)
T KOG1117|consen 368 WAG 370 (1186)
T ss_pred ccc
Confidence 876
No 23
>KOG0702|consensus
Probab=99.20 E-value=7.2e-12 Score=134.07 Aligned_cols=114 Identities=23% Similarity=0.327 Sum_probs=95.1
Q ss_pred hhhhch-HHHHHHHhcccCCCcccCCCCCCC-CceEecccceEcccchhhhccCCCcccceeeccCCCCCCHHHHHHHHh
Q psy7092 21 LEKVKN-SKLLMLQIITFFPQECFDCNAKNP-TWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQL 98 (540)
Q Consensus 21 ~e~~~n-~k~l~~l~~~p~Nk~CaDCga~nP-~WaSv~~GVflC~~CSgvHR~LGvhiS~VKSl~lDs~Wt~~qL~~m~~ 98 (540)
++.|+. +++||.|+++|+|++|++|....+ +|++++-|-|+|..|+|..|.| ..-++|||+.|.+ ++..++..++.
T Consensus 6 ke~E~~~ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l-~~ahRvksiSmtt-ft~qevs~lQs 83 (524)
T KOG0702|consen 6 KEDEYDYEKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGL-NPAHRVKSISMTT-FTDQEVSFLQS 83 (524)
T ss_pred ccchhHHHHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccC-CCccccceeeeee-ccccchHHHhh
Confidence 455656 999999999999999999999988 9999999999999999999998 4578999999999 99999999999
Q ss_pred cCcCCcCCCccccchhccccCCCchhHHHHHHHhhhhhcccccCCcchHHHHHHHHhhcC
Q psy7092 99 GGNANAPNGQNTRLSLWRSWGSFPLAFFKQLVNLWLNIEMYHFSISTTAQALVSFFNQHN 158 (540)
Q Consensus 99 gGN~~an~~~e~~l~~W~~~~~~p~~f~k~~~~~~~~~~~~~~~~~~~~~~l~~F~~~~~ 158 (540)
+||..+. ++|..- .||- --..++..+.+.+++|+++.|
T Consensus 84 hgNq~~k-------~i~fkl----~D~q-----------~S~vPD~rn~~~~kef~q~~y 121 (524)
T KOG0702|consen 84 HGNQVCK-------EIWFKL----FDFQ-----------RSNVPDSRNPQKVKEFQQEKY 121 (524)
T ss_pred cchhhhh-------hhhhcc----hhhh-----------hccCCCcccchhhHHHHhhhh
Confidence 9999999 667551 1111 122577788888999965433
No 24
>KOG0705|consensus
Probab=99.10 E-value=7.2e-12 Score=136.01 Aligned_cols=93 Identities=27% Similarity=0.363 Sum_probs=78.4
Q ss_pred cccccCCCCcccc-cCCcccccccccCCCCCCccccccccCceeeeeeeecccCCCCCHHHHHHHHhcccccchhcccCC
Q psy7092 318 KKIQSKKPSGFVC-RCPPFYQANVLTTTPPRQSLVAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAMKAEFGP 396 (540)
Q Consensus 318 ~~~~~~~~~~f~c-rc~~~~~~~~~~~~~~~~~~sgIHR~LGVHISkVkS~~LDs~Wt~EQv~~Mq~gGN~~a~~~kY~~ 396 (540)
-++++-|-|..+| -| +||||.||+|+|+|||+.||. |..|-+..|..+||+.||.. +|.
T Consensus 524 ~~wAslnlg~l~cieC------------------sgihr~lgt~lSrvr~LeLDd-WPvEl~~Vm~aiGN~~AN~v-WE~ 583 (749)
T KOG0705|consen 524 PKWASLNLGVLMCIEC------------------SGIHRNLGTHLSRVRSLELDD-WPVELLKVMSAIGNDLANSV-WEG 583 (749)
T ss_pred cccccccCCeEEEEEc------------------hhhhhhhhhhhhhhhcccccc-CcHHHHHHHHHhhhhHHHHH-hhh
Confidence 3566777778888 77 999999999999999999999 99999999999999999997 554
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCcccccccccC
Q psy7092 397 FNAGQFDSPPPDCTHTLPLAFTPSGMGFASMSRSG 431 (540)
Q Consensus 397 ~~A~~yK~~~P~s~~~lp~~~~~s~~~~~~fir~~ 431 (540)
..+.+.+|.|++..++.+-||+++|...-|..+-
T Consensus 584 -~~~G~~KPs~~s~REEkErwIr~KYeqklFLaPl 617 (749)
T KOG0705|consen 584 -SSQGQTKPSPDSSREEKERWIRAKYEQKLFLAPL 617 (749)
T ss_pred -hccCCcCCCccccHHHHHHHHHHHHHHHhhcCCC
Confidence 5567789999999888777777777666666653
No 25
>KOG0521|consensus
Probab=98.74 E-value=2.9e-09 Score=121.37 Aligned_cols=81 Identities=25% Similarity=0.262 Sum_probs=60.2
Q ss_pred CccccccccCceeeeeeeecccCCCCCHHHHHHHHhcccccchhcccCCCCCCC-CCCCCCCCCCCCCCCCCCCCccccc
Q psy7092 348 QSLVAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAMKAEFGPFNAGQ-FDSPPPDCTHTLPLAFTPSGMGFAS 426 (540)
Q Consensus 348 ~~~sgIHR~LGVHISkVkS~~LDs~Wt~EQv~~Mq~gGN~~a~~~kY~~~~A~~-yK~~~P~s~~~lp~~~~~s~~~~~~ 426 (540)
..||||||+||||||+|||++||. |.++.++.|+.+||...|.. |+..+... .+.+.+.+.......|+..++-...
T Consensus 450 IecSGvhRslGvh~SkvrsLtLD~-~~~~l~~l~~~lgn~~~N~i-~e~~l~~~~~~~~~~~~~~~~r~~~i~~kyve~~ 527 (785)
T KOG0521|consen 450 IECSGVHRSLGVHISKVRSLTLDV-WEPELLLLFKNLGNKYVNEI-YEALLPSYDSSKPTASSSRQAREAWIKAKYVERR 527 (785)
T ss_pred hhccccccccCchhhhhhhhhhhc-cCcHHHHHHHHhCcchhhhh-hhcccccccccCCCCccchhhhhHhhhcccceee
Confidence 467999999999999999999999 99999999999999999988 77666544 4455555444444444444444444
Q ss_pred cccc
Q psy7092 427 MSRS 430 (540)
Q Consensus 427 fir~ 430 (540)
|.+.
T Consensus 528 F~~k 531 (785)
T KOG0521|consen 528 FSVK 531 (785)
T ss_pred Eeec
Confidence 4433
No 26
>KOG1117|consensus
Probab=97.01 E-value=0.00032 Score=80.43 Aligned_cols=55 Identities=29% Similarity=0.406 Sum_probs=49.3
Q ss_pred cccCCCCcccc-cCCcccccccccCCCCCCccccccccCceeeeeeeecccCC-CCCHHHHHHHHhcccccchhc
Q psy7092 320 IQSKKPSGFVC-RCPPFYQANVLTTTPPRQSLVAVHRGLGVHLSFVRSTQLDT-NWTWVQLRQMQLGGNANAMKA 392 (540)
Q Consensus 320 ~~~~~~~~f~c-rc~~~~~~~~~~~~~~~~~~sgIHR~LGVHISkVkS~~LDs-~Wt~EQv~~Mq~gGN~~a~~~ 392 (540)
|++-|-.+-|| +| +|-||+||.-+|+|+|+.||. -|+.|-++.+...||..+|.-
T Consensus 311 wasiNL~vvIck~c------------------aGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~F 367 (1186)
T KOG1117|consen 311 WASINLCVVICKPC------------------AGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANRF 367 (1186)
T ss_pred ccccccceEEcccC------------------CCccccCCCccccccccccCcccccchhhhhheeecCcccccc
Confidence 45567777888 78 999999999999999999995 499999999999999999886
No 27
>KOG0818|consensus
Probab=96.97 E-value=0.00014 Score=79.38 Aligned_cols=54 Identities=31% Similarity=0.510 Sum_probs=46.7
Q ss_pred cccCCCCcccc-cCCcccccccccCCCCCCccccccccCceeeeeeeecccCCCCCHHHHHHHHhcccccchhc
Q psy7092 320 IQSKKPSGFVC-RCPPFYQANVLTTTPPRQSLVAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAMKA 392 (540)
Q Consensus 320 ~~~~~~~~f~c-rc~~~~~~~~~~~~~~~~~~sgIHR~LGVHISkVkS~~LDs~Wt~EQv~~Mq~gGN~~a~~~ 392 (540)
|++.|-|.|+| -| -.+||+||-|||.||++-=-- |.++-|+..-..-|..+|.+
T Consensus 21 WASvnrGt~lC~eC------------------csvHrsLGrhIS~vrhLR~s~-W~pt~l~~V~tLn~~gaNsI 75 (669)
T KOG0818|consen 21 WASVNRGTFLCDEC------------------CSVHRSLGRHISQVRHLRHTP-WPPTLLQMVETLNNNGANSI 75 (669)
T ss_pred ceeecCceEehHhh------------------hHHHhhhcchHHHHHHhccCC-CCHHHHHHHHHHHhcCcchh
Confidence 56777899999 67 689999999999999999776 99998888777888888876
No 28
>KOG0702|consensus
Probab=83.07 E-value=0.53 Score=52.25 Aligned_cols=75 Identities=19% Similarity=0.157 Sum_probs=51.4
Q ss_pred ccccccCceeeeeeeecccCCCCCHHHHHHHHhcccccchhcccCCCCCCCCCCCCCCCCCCCCCCCCCCCccccccccc
Q psy7092 351 VAVHRGLGVHLSFVRSTQLDTNWTWVQLRQMQLGGNANAMKAEFGPFNAGQFDSPPPDCTHTLPLAFTPSGMGFASMSRS 430 (540)
Q Consensus 351 sgIHR~LGVHISkVkS~~LDs~Wt~EQv~~Mq~gGN~~a~~~kY~~~~A~~yK~~~P~s~~~lp~~~~~s~~~~~~fir~ 430 (540)
+|+-|+|-. --+|||++|-+ .|.-++-.+|.+||.....+-|.-+ ...+...||+. .-+.+..|+|.
T Consensus 53 sg~ls~l~~-ahRvksiSmtt-ft~qevs~lQshgNq~~k~i~fkl~--D~q~S~vPD~r---------n~~~~kef~q~ 119 (524)
T KOG0702|consen 53 SGLLSGLNP-AHRVKSISMTT-FTDQEVSFLQSHGNQVCKEIWFKLF--DFQRSNVPDSR---------NPQKVKEFQQE 119 (524)
T ss_pred chhhccCCC-ccccceeeeee-ccccchHHHhhcchhhhhhhhhcch--hhhhccCCCcc---------cchhhHHHHhh
Confidence 777777653 34799999999 9999999999999988777633210 01111122211 22466779999
Q ss_pred CCCCCccc
Q psy7092 431 GGLGGKKL 438 (540)
Q Consensus 431 ~~~~~k~~ 438 (540)
+|+++||+
T Consensus 120 ~y~~kr~~ 127 (524)
T KOG0702|consen 120 KYVKKRYY 127 (524)
T ss_pred hhccceee
Confidence 99999987
No 29
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=61.86 E-value=5.2 Score=39.48 Aligned_cols=31 Identities=23% Similarity=0.465 Sum_probs=26.3
Q ss_pred cCCCcccCCCCCCC-CceEecccceEcccchh
Q psy7092 37 FFPQECFDCNAKNP-TWSSVTYGVFICIDCSA 67 (540)
Q Consensus 37 p~Nk~CaDCga~nP-~WaSv~~GVflC~~CSg 67 (540)
|.-..|+-||.... .|.++..|.++|..|..
T Consensus 147 p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~ 178 (247)
T PRK00085 147 LDLDHCAVCGAPGDHRYFSPKEGGAVCSECGD 178 (247)
T ss_pred cchhhHhcCCCCCCceEEecccCCcccccccC
Confidence 56678999998755 78899999999999973
No 30
>PRK12495 hypothetical protein; Provisional
Probab=60.28 E-value=7.5 Score=39.56 Aligned_cols=28 Identities=21% Similarity=0.407 Sum_probs=23.5
Q ss_pred ccCCCcccCCCCCCCCceEecccceEcccchh
Q psy7092 36 TFFPQECFDCNAKNPTWSSVTYGVFICIDCSA 67 (540)
Q Consensus 36 ~p~Nk~CaDCga~nP~WaSv~~GVflC~~CSg 67 (540)
...+..|-+||.+-|.. -|+.+|..|..
T Consensus 39 tmsa~hC~~CG~PIpa~----pG~~~Cp~CQ~ 66 (226)
T PRK12495 39 TMTNAHCDECGDPIFRH----DGQEFCPTCQQ 66 (226)
T ss_pred ccchhhcccccCcccCC----CCeeECCCCCC
Confidence 46899999999999832 59999999964
No 31
>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=56.78 E-value=7.6 Score=28.36 Aligned_cols=33 Identities=15% Similarity=0.402 Sum_probs=28.1
Q ss_pred CCcccCCCCCCCCceEecccceEcccchhh-hcc
Q psy7092 39 PQECFDCNAKNPTWSSVTYGVFICIDCSAV-HRG 71 (540)
Q Consensus 39 Nk~CaDCga~nP~WaSv~~GVflC~~CSgv-HR~ 71 (540)
+..|..|......+-+.+-+++||..|... |+.
T Consensus 3 ~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~ 36 (42)
T PF00643_consen 3 EPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG 36 (42)
T ss_dssp SSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT
T ss_pred CccCccCCccceEEEecCCCCccCccCCCCCCCC
Confidence 567889998778899999999999999987 886
No 32
>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=54.40 E-value=10 Score=37.35 Aligned_cols=33 Identities=27% Similarity=0.600 Sum_probs=26.9
Q ss_pred ccCCCcccCCCCCCC-CceEecccceEcccchhh
Q psy7092 36 TFFPQECFDCNAKNP-TWSSVTYGVFICIDCSAV 68 (540)
Q Consensus 36 ~p~Nk~CaDCga~nP-~WaSv~~GVflC~~CSgv 68 (540)
.|.-..|..||..++ .|.|+..|.++|.+|...
T Consensus 144 ~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 144 ALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred CcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 356678999998654 677899999999999764
No 33
>PF12662 cEGF: Complement Clr-like EGF-like
Probab=50.35 E-value=7.6 Score=26.57 Aligned_cols=13 Identities=46% Similarity=1.242 Sum_probs=11.2
Q ss_pred cccccCCcccccc
Q psy7092 327 GFVCRCPPFYQAN 339 (540)
Q Consensus 327 ~f~crc~~~~~~~ 339 (540)
+|.|.|++.|+.+
T Consensus 1 sy~C~C~~Gy~l~ 13 (24)
T PF12662_consen 1 SYTCSCPPGYQLS 13 (24)
T ss_pred CEEeeCCCCCcCC
Confidence 5899999999865
No 34
>PF07645 EGF_CA: Calcium-binding EGF domain; InterPro: IPR001881 A sequence of about forty amino-acid residues found in epidermal growth factor (EGF) has been shown [, , , , , ] to be present in a large number of membrane-bound and extracellular, mostly animal, proteins. Many of these proteins require calcium for their biological function and a calcium-binding site has been found at the N terminus of some EGF-like domains []. Calcium-binding may be crucial for numerous protein-protein interactions. For human coagulation factor IX it has been shown [] that the calcium-ligands form a pentagonal bipyramid. The first, third and fourth conserved negatively charged or polar residues are side chain ligands. The latter is possibly hydroxylated (see aspartic acid and asparagine hydroxylation site) []. A conserved aromatic residue, as well as the second conserved negative residue, are thought to be involved in stabilising the calcium-binding site. As in non-calcium binding EGF-like domains, there are six conserved cysteines and the structure of both types is very similar as calcium-binding induces only strictly local structural changes []. +------------------+ +---------+ | | | | nxnnC-x(3,14)-C-x(3,7)-CxxbxxxxaxC-x(1,6)-C-x(8,13)-Cx | | +------------------+ 'n': negatively charged or polar residue [DEQN] 'b': possibly beta-hydroxylated residue [DN] 'a': aromatic amino acid 'C': cysteine, involved in disulphide bond 'x': any amino acid. ; GO: 0005509 calcium ion binding; PDB: 2VJ3_A 1TOZ_A 1LMJ_A 1UZQ_A 1UZK_A 1UZJ_B 1UZP_A 1EMO_A 1EMN_A 2RR0_A ....
Probab=40.92 E-value=9.6 Score=28.27 Aligned_cols=13 Identities=38% Similarity=1.196 Sum_probs=12.1
Q ss_pred CCcccccCCcccc
Q psy7092 325 PSGFVCRCPPFYQ 337 (540)
Q Consensus 325 ~~~f~crc~~~~~ 337 (540)
+|+|.|.|++.|+
T Consensus 22 ~Gsy~C~C~~Gy~ 34 (42)
T PF07645_consen 22 EGSYSCSCPPGYE 34 (42)
T ss_dssp TTEEEEEESTTEE
T ss_pred CCCEEeeCCCCcE
Confidence 6899999999998
No 35
>TIGR02419 C4_traR_proteo phage/conjugal plasmid C-4 type zinc finger protein, TraR family. Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA.
Probab=37.06 E-value=22 Score=29.26 Aligned_cols=33 Identities=27% Similarity=0.526 Sum_probs=23.3
Q ss_pred ccCCCcccCCCCCCC--CceEecccceEcccchhhh
Q psy7092 36 TFFPQECFDCNAKNP--TWSSVTYGVFICIDCSAVH 69 (540)
Q Consensus 36 ~p~Nk~CaDCga~nP--~WaSv~~GVflC~~CSgvH 69 (540)
.++...|.|||.+=| .+.- --|+..|++|...+
T Consensus 28 ~~s~g~C~~Cg~~Ip~~Rl~a-~p~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 28 GPSLRECEDCGEPIPEARREA-LPGVTRCVSCQEIL 62 (63)
T ss_pred CCCCCeeccCCCcChHHHHhh-cCCcCCcHHHHhhc
Confidence 456789999999755 3322 23788999997653
No 36
>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=36.44 E-value=19 Score=30.88 Aligned_cols=31 Identities=26% Similarity=0.565 Sum_probs=25.5
Q ss_pred CCCcccCCCCCCCCceEecccceEcccchhhhcc
Q psy7092 38 FPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 71 (540)
Q Consensus 38 ~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~ 71 (540)
.|..|.-||.+.- ...||++.|..|.++.|-
T Consensus 2 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 2 DTHFCAVCSDYAS---GYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 4678999997553 579999999999998864
No 37
>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=36.29 E-value=13 Score=27.58 Aligned_cols=27 Identities=15% Similarity=0.546 Sum_probs=16.6
Q ss_pred CcccCCCCC-CCCceEecccceEcccch
Q psy7092 40 QECFDCNAK-NPTWSSVTYGVFICIDCS 66 (540)
Q Consensus 40 k~CaDCga~-nP~WaSv~~GVflC~~CS 66 (540)
..|.+|+.. .-+|..-+|+.-||..|.
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 469999996 558999999999999994
No 38
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=35.87 E-value=32 Score=27.16 Aligned_cols=37 Identities=22% Similarity=0.542 Sum_probs=29.7
Q ss_pred CCCcccCCCCC-CCCceEecccc-eEcccchhhhccCCC
Q psy7092 38 FPQECFDCNAK-NPTWSSVTYGV-FICIDCSAVHRGLGV 74 (540)
Q Consensus 38 ~Nk~CaDCga~-nP~WaSv~~GV-flC~~CSgvHR~LGv 74 (540)
....|..|+.. .|.|=.-..|- +||-.|.-..+..|.
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~ 40 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCC
Confidence 35789999985 67898888886 999999776666554
No 39
>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=33.42 E-value=23 Score=26.57 Aligned_cols=27 Identities=26% Similarity=0.667 Sum_probs=20.1
Q ss_pred cccCCCCCCCCceEecccceEcccchhh
Q psy7092 41 ECFDCNAKNPTWSSVTYGVFICIDCSAV 68 (540)
Q Consensus 41 ~CaDCga~nP~WaSv~~GVflC~~CSgv 68 (540)
.|-.||+.. .-..-..|-++|..|-.|
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 589999976 444567799999999433
No 40
>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=33.14 E-value=24 Score=31.13 Aligned_cols=31 Identities=29% Similarity=0.629 Sum_probs=25.6
Q ss_pred CCCcccCCCCCCCCceEecccceEcccchhhhcc
Q psy7092 38 FPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 71 (540)
Q Consensus 38 ~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~ 71 (540)
.+..|.-||.+.- ...||++.|..|.++.|-
T Consensus 4 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 4 EVIPCKICGDKSS---GIHYGVITCEGCKGFFRR 34 (95)
T ss_pred cccCCcccCCcCc---ceEECceeehhhHHhhHH
Confidence 5678999998654 468999999999998874
No 41
>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=32.76 E-value=22 Score=26.02 Aligned_cols=32 Identities=25% Similarity=0.717 Sum_probs=22.9
Q ss_pred ccCCCCC-CCCceEecccce-EcccchhhhccCC
Q psy7092 42 CFDCNAK-NPTWSSVTYGVF-ICIDCSAVHRGLG 73 (540)
Q Consensus 42 CaDCga~-nP~WaSv~~GVf-lC~~CSgvHR~LG 73 (540)
|..|+.. .|.|-....|-. ||-.|--.+|..|
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~ 34 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYG 34 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhC
Confidence 8899985 789999999988 9999977666543
No 42
>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=32.69 E-value=23 Score=27.61 Aligned_cols=26 Identities=35% Similarity=0.874 Sum_probs=20.1
Q ss_pred cccCCCCCCCCceEecccceEcccchh
Q psy7092 41 ECFDCNAKNPTWSSVTYGVFICIDCSA 67 (540)
Q Consensus 41 ~CaDCga~nP~WaSv~~GVflC~~CSg 67 (540)
.|+=|+...+. .=.=+|.|||.+|-.
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHH
Confidence 48889998776 344579999999954
No 43
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=32.29 E-value=26 Score=35.67 Aligned_cols=30 Identities=23% Similarity=0.497 Sum_probs=26.0
Q ss_pred cCCCcccCCCCCCC-CceEecccceEcccch
Q psy7092 37 FFPQECFDCNAKNP-TWSSVTYGVFICIDCS 66 (540)
Q Consensus 37 p~Nk~CaDCga~nP-~WaSv~~GVflC~~CS 66 (540)
+.=..|+.||.+.+ ...|+-.|-++|..|+
T Consensus 152 ~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 152 PNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred cchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 45567999999854 7999999999999998
No 44
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=31.69 E-value=42 Score=34.30 Aligned_cols=38 Identities=21% Similarity=0.308 Sum_probs=27.7
Q ss_pred HHHHHHHhcccCCCcccCCCCCCCCceEecccceEcccchhhhc
Q psy7092 27 SKLLMLQIITFFPQECFDCNAKNPTWSSVTYGVFICIDCSAVHR 70 (540)
Q Consensus 27 ~k~l~~l~~~p~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR 70 (540)
++.++..+.....-.|-.||.....|. ++|..|.+.|-
T Consensus 342 ~~~~~~~~~~~p~~~c~~cg~~~~~~~------~~c~~c~~~~~ 379 (389)
T PRK11788 342 RDLVGEQLKRKPRYRCRNCGFTARTLY------WHCPSCKAWET 379 (389)
T ss_pred HHHHHHHHhCCCCEECCCCCCCCccce------eECcCCCCccC
Confidence 445554445333345999999999995 89999988874
No 45
>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=31.08 E-value=36 Score=25.23 Aligned_cols=27 Identities=22% Similarity=0.592 Sum_probs=22.6
Q ss_pred cCCCcccCCCCCCCCceEecccceEcccch
Q psy7092 37 FFPQECFDCNAKNPTWSSVTYGVFICIDCS 66 (540)
Q Consensus 37 p~Nk~CaDCga~nP~WaSv~~GVflC~~CS 66 (540)
..|..|..|++. |....=|-+.|..|-
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCc
Confidence 356679999998 888888999999983
No 46
>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=29.58 E-value=28 Score=30.94 Aligned_cols=30 Identities=27% Similarity=0.614 Sum_probs=24.5
Q ss_pred CCcccCCCCCCCCceEecccceEcccchhhhcc
Q psy7092 39 PQECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 71 (540)
Q Consensus 39 Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~ 71 (540)
+..|.-||.+.- ...||++.|..|.++.|-
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 456999997654 468999999999998874
No 47
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=29.34 E-value=50 Score=29.42 Aligned_cols=31 Identities=23% Similarity=0.460 Sum_probs=24.3
Q ss_pred cCCCcccCCCCCCCCceEecccceEcccchhhh
Q psy7092 37 FFPQECFDCNAKNPTWSSVTYGVFICIDCSAVH 69 (540)
Q Consensus 37 p~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvH 69 (540)
..--.|-.|+.+ .---+..||+.|..|-..-
T Consensus 33 ~~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 33 RAKHVCPFCGRT--TVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred hcCCcCCCCCCc--ceeeeccCeEEcCCCCCee
Confidence 356789999998 5556789999999995543
No 48
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=29.27 E-value=18 Score=28.62 Aligned_cols=30 Identities=30% Similarity=0.679 Sum_probs=20.4
Q ss_pred cccCCCCCCCCceE--ecccceEcccchhhhcc
Q psy7092 41 ECFDCNAKNPTWSS--VTYGVFICIDCSAVHRG 71 (540)
Q Consensus 41 ~CaDCga~nP~WaS--v~~GVflC~~CSgvHR~ 71 (540)
.|+=||.+-.-... +.=| +||.+|..--..
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl~~ 32 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKLSG 32 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHhcC
Confidence 48889987665543 3447 899999864433
No 49
>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=28.22 E-value=30 Score=29.73 Aligned_cols=31 Identities=19% Similarity=0.612 Sum_probs=25.3
Q ss_pred CCCcccCCCCCCCCceEecccceEcccchhhhcc
Q psy7092 38 FPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 71 (540)
Q Consensus 38 ~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~ 71 (540)
..+.|.-||.+.- ...|||+.|..|.++.|-
T Consensus 2 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 32 (82)
T cd07173 2 PQKTCLICGDEAS---GCHYGALTCGSCKVFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECcchhhhHHHHHHH
Confidence 4567999997654 568999999999998874
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=27.66 E-value=37 Score=30.41 Aligned_cols=31 Identities=26% Similarity=0.550 Sum_probs=25.4
Q ss_pred CCCcccCCCCCCCCceEecccceEcccchhhhcc
Q psy7092 38 FPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 71 (540)
Q Consensus 38 ~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~ 71 (540)
.+..|.-||...- ...||+..|..|.++.|-
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 4667999998654 569999999999998874
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=27.23 E-value=32 Score=30.29 Aligned_cols=29 Identities=24% Similarity=0.543 Sum_probs=23.2
Q ss_pred CcccCCCCCCCCceEecccceEcccchhhhcc
Q psy7092 40 QECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 71 (540)
Q Consensus 40 k~CaDCga~nP~WaSv~~GVflC~~CSgvHR~ 71 (540)
+.|.-||.+.- ...||++.|..|.++.|-
T Consensus 1 ~~C~VCg~~a~---g~hyGv~sC~aC~~FFRR 29 (94)
T cd06966 1 KICGVCGDKAL---GYNFNAITCESCKAFFRR 29 (94)
T ss_pred CCCeeCCCcCc---ceEECcceeeeehheehh
Confidence 45888987544 458999999999998874
No 52
>PRK04023 DNA polymerase II large subunit; Validated
Probab=26.85 E-value=42 Score=40.96 Aligned_cols=61 Identities=18% Similarity=0.230 Sum_probs=36.9
Q ss_pred CCCCCch-hhhhhhhhhhhhhhhchHHHHH--HHhc-ccCCCcccCCCCCCCCceEeccc-----ceEcccc
Q psy7092 3 KLSTPPL-CQMLAGQYLFHLEKVKNSKLLM--LQII-TFFPQECFDCNAKNPTWSSVTYG-----VFICIDC 65 (540)
Q Consensus 3 ~~~~~p~-~~~~~~~~~~~~e~~~n~k~l~--~l~~-~p~Nk~CaDCga~nP~WaSv~~G-----VflC~~C 65 (540)
|-++||+ .+++++-+.= ......++.. -.+. ..+.+.|..||...+...|-+.| +..|.+|
T Consensus 588 RkMkP~~h~LFPiG~~GG--~~R~i~~A~~~~g~~eVEVg~RfCpsCG~~t~~frCP~CG~~Te~i~fCP~C 657 (1121)
T PRK04023 588 RKMKPPVHVLFPIGNAGG--STRDINKAAKYKGTIEVEIGRRKCPSCGKETFYRRCPFCGTHTEPVYRCPRC 657 (1121)
T ss_pred ccCCCCCcccccccccCc--ccccHHHHHhcCCceeecccCccCCCCCCcCCcccCCCCCCCCCcceeCccc
Confidence 6667766 8888876663 1111222222 1121 34888999999986666665555 5677777
No 53
>PRK11019 hypothetical protein; Provisional
Probab=25.79 E-value=39 Score=29.82 Aligned_cols=37 Identities=22% Similarity=0.484 Sum_probs=26.1
Q ss_pred CCCcccCCCCCCC--CceEecccceEcccchhhhccCCCc
Q psy7092 38 FPQECFDCNAKNP--TWSSVTYGVFICIDCSAVHRGLGVH 75 (540)
Q Consensus 38 ~Nk~CaDCga~nP--~WaSv~~GVflC~~CSgvHR~LGvh 75 (540)
.-..|.|||.+=| .|.-++ ++-.|++|...+-..+.|
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 3579999999755 444333 788999999876544333
No 54
>KOG0457|consensus
Probab=25.71 E-value=53 Score=36.53 Aligned_cols=39 Identities=26% Similarity=0.456 Sum_probs=22.7
Q ss_pred ceEcccchhhhccCCCc----ccceeec----cCCCCCC-HHHHHHHH
Q psy7092 59 VFICIDCSAVHRGLGVH----LSFVRST----QLDTNWT-WVQLRQMQ 97 (540)
Q Consensus 59 VflC~~CSgvHR~LGvh----iS~VKSl----~lDs~Wt-~~qL~~m~ 97 (540)
..||+.|-.+=-.+|.| --+|-+. -++..|+ ++||.++.
T Consensus 38 fdLCl~CFs~GaE~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLe 85 (438)
T KOG0457|consen 38 FDLCLQCFSVGAETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLE 85 (438)
T ss_pred cchhHHHHhcccccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHH
Confidence 57999998654445544 2333332 2334499 56776665
No 55
>PHA00080 DksA-like zinc finger domain containing protein
Probab=25.25 E-value=55 Score=27.67 Aligned_cols=32 Identities=22% Similarity=0.563 Sum_probs=22.9
Q ss_pred cCCCcccCCCCCCC--CceEecccceEcccchhhh
Q psy7092 37 FFPQECFDCNAKNP--TWSSVTYGVFICIDCSAVH 69 (540)
Q Consensus 37 p~Nk~CaDCga~nP--~WaSv~~GVflC~~CSgvH 69 (540)
.+...|.+||..=| .|.-++ |+..|++|...+
T Consensus 29 ~~~~~C~~Cg~~Ip~~Rl~a~P-~~~~Cv~Cq~~~ 62 (72)
T PHA00080 29 PSATHCEECGDPIPEARREAVP-GCRTCVSCQEIL 62 (72)
T ss_pred CCCCEecCCCCcCcHHHHHhCC-CccCcHHHHHHH
Confidence 45668999999754 444334 667799998764
No 56
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=25.16 E-value=41 Score=41.91 Aligned_cols=63 Identities=19% Similarity=0.264 Sum_probs=33.9
Q ss_pred CCCCCch-hhhhhhhhhhhhhhhchHHHHHHH---hccc-------CCCcccCCCCCCCCceEeccc-----ceEcccch
Q psy7092 3 KLSTPPL-CQMLAGQYLFHLEKVKNSKLLMLQ---IITF-------FPQECFDCNAKNPTWSSVTYG-----VFICIDCS 66 (540)
Q Consensus 3 ~~~~~p~-~~~~~~~~~~~~e~~~n~k~l~~l---~~~p-------~Nk~CaDCga~nP~WaSv~~G-----VflC~~CS 66 (540)
|-+.||+ .+++++-+.= .+....++.... .... +...|-.||...+.+.|-..| ++.|.+|-
T Consensus 622 R~mkP~~h~LFPig~aGG--~qR~I~kAa~~a~~~~d~~G~ieVEV~~rkCPkCG~~t~~~fCP~CGs~te~vy~CPsCG 699 (1337)
T PRK14714 622 RKMKPPVHTLFPIGEAGG--AQRDVAKAAKHAPDMSDEGGVIEVEVGRRRCPSCGTETYENRCPDCGTHTEPVYVCPDCG 699 (1337)
T ss_pred cccCCCCcccccccccCc--ccccHHHHHHhhhhccccCCeEEEEEEEEECCCCCCccccccCcccCCcCCCceeCccCC
Confidence 5667766 8888877653 111122222111 0112 337788888876665555555 44566664
Q ss_pred h
Q psy7092 67 A 67 (540)
Q Consensus 67 g 67 (540)
.
T Consensus 700 a 700 (1337)
T PRK14714 700 A 700 (1337)
T ss_pred C
Confidence 3
No 57
>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=24.52 E-value=38 Score=29.57 Aligned_cols=32 Identities=19% Similarity=0.641 Sum_probs=25.9
Q ss_pred cCCCcccCCCCCCCCceEecccceEcccchhhhcc
Q psy7092 37 FFPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 71 (540)
Q Consensus 37 p~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~ 71 (540)
.++..|.-||.+. ....||+..|..|.++.|-
T Consensus 4 ~~~~~C~VCg~~a---~g~hyGv~sC~aCk~FFRR 35 (90)
T cd07169 4 AEQRTCLICGDRA---TGLHYGIISCEGCKGFFKR 35 (90)
T ss_pred ccCCCCeecCCcC---cceEECcceehhhHHHHHH
Confidence 3567799999755 3568999999999998864
No 58
>smart00179 EGF_CA Calcium-binding EGF-like domain.
Probab=23.96 E-value=39 Score=23.29 Aligned_cols=13 Identities=38% Similarity=1.109 Sum_probs=10.8
Q ss_pred CCcccccCCcccc
Q psy7092 325 PSGFVCRCPPFYQ 337 (540)
Q Consensus 325 ~~~f~crc~~~~~ 337 (540)
.++|.|.|++.|.
T Consensus 21 ~g~~~C~C~~g~~ 33 (39)
T smart00179 21 VGSYRCECPPGYT 33 (39)
T ss_pred CCCeEeECCCCCc
Confidence 5789999988775
No 59
>PF14670 FXa_inhibition: Coagulation Factor Xa inhibitory site; PDB: 3Q3K_B 1NFY_B 1LQD_A 1G2L_B 1IQF_L 2UWP_B 2VH6_B 3KQC_L 2P93_L 2BQW_A ....
Probab=23.82 E-value=32 Score=25.45 Aligned_cols=14 Identities=43% Similarity=1.246 Sum_probs=10.8
Q ss_pred CCcccccCCccccc
Q psy7092 325 PSGFVCRCPPFYQA 338 (540)
Q Consensus 325 ~~~f~crc~~~~~~ 338 (540)
+++|.|.||+.|.-
T Consensus 16 ~g~~~C~C~~Gy~L 29 (36)
T PF14670_consen 16 PGSYRCSCPPGYKL 29 (36)
T ss_dssp TTSEEEE-STTEEE
T ss_pred CCceEeECCCCCEE
Confidence 67899999998864
No 60
>cd07163 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=22.29 E-value=46 Score=29.14 Aligned_cols=31 Identities=23% Similarity=0.685 Sum_probs=25.1
Q ss_pred CCCcccCCCCCCCCceEecccceEcccchhhhcc
Q psy7092 38 FPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 71 (540)
Q Consensus 38 ~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~ 71 (540)
-+..|.-||.+.- ...||+..|..|.++.|-
T Consensus 5 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (92)
T cd07163 5 LDIPCKVCGDRSS---GKHYGIYACDGCSGFFKR 35 (92)
T ss_pred cCCCCcccCCcCc---ccEECceeeeeeeeEEee
Confidence 3677999998554 469999999999998764
No 61
>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=21.04 E-value=58 Score=26.19 Aligned_cols=27 Identities=30% Similarity=0.647 Sum_probs=22.6
Q ss_pred CCCcccCCCCCCCCceEecccceEcccch
Q psy7092 38 FPQECFDCNAKNPTWSSVTYGVFICIDCS 66 (540)
Q Consensus 38 ~Nk~CaDCga~nP~WaSv~~GVflC~~CS 66 (540)
.-+.|..||..... ..+..+|.|..|-
T Consensus 27 TSq~C~~CG~~~~~--~~~~r~~~C~~Cg 53 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK--RRSGRVFTCPNCG 53 (69)
T ss_pred CccCccCccccccc--ccccceEEcCCCC
Confidence 45679999998887 7788899999983
No 62
>cd06955 NR_DBD_VDR DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of core
Probab=20.54 E-value=58 Score=29.55 Aligned_cols=31 Identities=19% Similarity=0.597 Sum_probs=24.9
Q ss_pred CCCcccCCCCCCCCceEecccceEcccchhhhcc
Q psy7092 38 FPQECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 71 (540)
Q Consensus 38 ~Nk~CaDCga~nP~WaSv~~GVflC~~CSgvHR~ 71 (540)
..+.|.-||...- ...||+..|..|.++.|-
T Consensus 5 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (107)
T cd06955 5 VPRICGVCGDRAT---GFHFNAMTCEGCKGFFRR 35 (107)
T ss_pred CCCCCeecCCcCc---ccEECcceeeeecceecc
Confidence 3467999998655 459999999999998874
No 63
>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=20.53 E-value=55 Score=28.32 Aligned_cols=28 Identities=18% Similarity=0.543 Sum_probs=22.3
Q ss_pred cccCCCCCCCCceEecccceEcccchhhhcc
Q psy7092 41 ECFDCNAKNPTWSSVTYGVFICIDCSAVHRG 71 (540)
Q Consensus 41 ~CaDCga~nP~WaSv~~GVflC~~CSgvHR~ 71 (540)
.|.-||.+... ..||+..|..|.++.|-
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 37778876553 58999999999998864
No 64
>smart00181 EGF Epidermal growth factor-like domain.
Probab=20.22 E-value=53 Score=22.47 Aligned_cols=15 Identities=40% Similarity=1.260 Sum_probs=12.5
Q ss_pred CCcccccCCcccccc
Q psy7092 325 PSGFVCRCPPFYQAN 339 (540)
Q Consensus 325 ~~~f~crc~~~~~~~ 339 (540)
.++|.|+|++.|..+
T Consensus 17 ~~~~~C~C~~g~~g~ 31 (35)
T smart00181 17 PGSYTCSCPPGYTGD 31 (35)
T ss_pred CCCeEeECCCCCccC
Confidence 578999999888765
Done!