Query 009702
Match_columns 528
No_of_seqs 168 out of 1194
Neff 3.7
Searched_HMMs 46136
Date Thu Mar 28 16:19:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009702.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009702hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0703 Predicted GTPase-activ 100.0 5.5E-45 1.2E-49 364.0 11.4 278 6-347 3-287 (287)
2 PLN03119 putative ADP-ribosyla 100.0 1E-39 2.2E-44 347.0 12.4 161 8-184 3-172 (648)
3 PLN03131 hypothetical protein; 100.0 4.3E-37 9.4E-42 329.1 11.5 157 8-180 3-168 (705)
4 PF01412 ArfGap: Putative GTPa 100.0 9.5E-37 2.1E-41 268.2 5.9 109 17-137 2-116 (116)
5 smart00105 ArfGap Putative GTP 100.0 4.8E-35 1E-39 256.3 8.4 103 26-140 1-110 (112)
6 COG5347 GTPase-activating prot 100.0 2.5E-32 5.4E-37 277.5 8.2 113 14-138 6-126 (319)
7 PLN03114 ADP-ribosylation fact 100.0 5.8E-29 1.3E-33 254.7 14.9 112 16-139 10-130 (395)
8 KOG0706 Predicted GTPase-activ 99.9 1.9E-27 4.2E-32 248.0 4.4 85 15-111 10-94 (454)
9 KOG0704 ADP-ribosylation facto 99.9 1.2E-26 2.6E-31 236.6 7.9 109 14-134 5-124 (386)
10 KOG0705 GTPase-activating prot 99.9 5.1E-25 1.1E-29 235.2 5.2 114 16-141 501-620 (749)
11 KOG0521 Putative GTPase activa 99.8 2.7E-22 5.9E-27 223.7 3.8 111 18-140 416-534 (785)
12 KOG0702 Predicted GTPase-activ 99.8 9.9E-20 2.1E-24 192.4 14.1 128 6-146 3-138 (524)
13 KOG0818 GTPase-activating prot 99.7 5.5E-19 1.2E-23 187.2 2.7 102 24-137 4-119 (669)
14 KOG1117 Rho- and Arf-GTPase ac 99.6 4E-17 8.8E-22 180.6 3.4 110 19-140 289-406 (1186)
15 KOG0521 Putative GTPase activa 93.0 0.025 5.5E-07 65.2 -0.3 56 23-78 625-681 (785)
16 PRK00085 recO DNA repair prote 83.7 0.59 1.3E-05 45.6 1.7 32 24-55 145-177 (247)
17 PRK12495 hypothetical protein; 72.9 1.4 3E-05 44.6 0.6 38 16-57 28-67 (226)
18 TIGR00613 reco DNA repair prot 67.5 2.4 5.2E-05 41.2 0.9 34 24-57 143-177 (241)
19 PF00643 zf-B_box: B-box zinc 65.4 1.6 3.5E-05 31.8 -0.5 34 27-60 2-36 (42)
20 COG1734 DksA DnaK suppressor p 60.2 5.8 0.00013 36.6 1.9 40 20-59 70-112 (120)
21 COG1381 RecO Recombinational D 60.1 3.9 8.4E-05 41.2 0.9 32 24-55 150-182 (251)
22 PRK11019 hypothetical protein; 58.7 4.2 9.1E-05 35.7 0.7 36 27-63 35-72 (88)
23 PRK13715 conjugal transfer pro 54.1 5.5 0.00012 33.7 0.7 33 28-60 34-67 (73)
24 PRK11788 tetratricopeptide rep 53.1 9 0.0002 38.5 2.2 40 14-59 340-379 (389)
25 TIGR02419 C4_traR_proteo phage 45.7 10 0.00022 31.1 1.0 34 24-58 27-62 (63)
26 PF11781 RRN7: RNA polymerase 42.0 8.7 0.00019 28.5 0.1 27 26-55 6-32 (36)
27 TIGR02890 spore_yteA sporulati 40.9 19 0.00041 34.6 2.1 44 16-60 72-119 (159)
28 PF01286 XPA_N: XPA protein N- 39.7 6 0.00013 29.4 -1.1 27 29-55 4-31 (34)
29 KOG3362 Predicted BBOX Zn-fing 37.8 8.4 0.00018 37.1 -0.7 34 26-60 116-150 (156)
30 PRK10778 dksA RNA polymerase-b 34.5 20 0.00043 34.2 1.2 46 16-61 97-145 (151)
31 PHA00080 DksA-like zinc finger 29.7 30 0.00065 29.2 1.4 35 25-60 28-64 (72)
32 smart00401 ZnF_GATA zinc finge 27.8 23 0.0005 27.9 0.4 37 27-63 2-40 (52)
33 KOG0457 Histone acetyltransfer 26.7 1.4E+02 0.0031 33.2 6.1 103 24-137 9-126 (438)
34 PF08271 TF_Zn_Ribbon: TFIIB z 26.3 7.7 0.00017 29.0 -2.5 27 30-57 2-28 (43)
35 cd07173 NR_DBD_AR DNA-binding 25.3 47 0.001 28.5 1.8 32 26-60 1-32 (82)
36 COG2174 RPL34A Ribosomal prote 24.6 38 0.00082 30.4 1.1 34 23-56 29-79 (93)
37 PF14471 DUF4428: Domain of un 22.1 44 0.00095 26.5 1.0 31 30-61 1-33 (51)
38 cd07171 NR_DBD_ER DNA-binding 21.8 39 0.00085 28.9 0.7 31 27-60 2-32 (82)
39 TIGR02420 dksA RNA polymerase- 21.8 45 0.00097 29.7 1.1 39 17-55 67-108 (110)
40 PF01258 zf-dskA_traR: Prokary 21.0 11 0.00023 27.4 -2.5 29 30-58 5-34 (36)
41 cd06968 NR_DBD_ROR DNA-binding 20.7 46 0.001 29.3 0.9 31 27-60 4-34 (95)
42 PF00320 GATA: GATA zinc finge 20.4 27 0.00058 25.6 -0.5 32 31-62 1-34 (36)
43 cd00202 ZnF_GATA Zinc finger D 20.3 99 0.0021 24.7 2.6 33 30-62 1-35 (54)
44 PF04770 ZF-HD_dimer: ZF-HD pr 20.1 29 0.00064 28.9 -0.4 31 31-62 21-53 (60)
No 1
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=5.5e-45 Score=363.96 Aligned_cols=278 Identities=36% Similarity=0.521 Sum_probs=189.2
Q ss_pred cccHHHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCcccccccccCCCCCHHHHHHHh
Q 009702 6 NVSKELNARHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQ 85 (528)
Q Consensus 6 ~~SK~l~ar~ekiLr~Ll~~PgNK~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISrVKSLsLD~WT~eEV~~Mq 85 (528)
.+.+...++++++|++|++.|+|++|||||+++|+|||+|+|||||++|+||||+||+||||||||+||.|++|||++|+
T Consensus 3 ~~~~~~~~~~~~~l~~Ll~~~~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~ 82 (287)
T KOG0703|consen 3 RVEKGSNERNKRRLRELLREPDNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMI 82 (287)
T ss_pred cccccccchHHHHHHHHHcCcccCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHH
Confidence 34456678999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcccccccccccccchHHHHHHHhhcCCCCCChH----HHHHHHHHHhhhCccccCCCCCCCCCcccccccccccCCCCC
Q 009702 86 STACDCGFFLYTAMGNEKANSYWEAELPPNYDRV----GIENFIRAKYEEKRWVSRDGQANSPPRGLEEKASIHWQRPGE 161 (528)
Q Consensus 86 ~~~~~~g~~Ll~~gGN~kAN~iwEa~LPpssD~~----~re~FIRaKY~eKrF~~~~~~~~~ps~~~~ek~~~~~~~~~~ 161 (528)
. +||.++|.|||+++|..+++. .+|+|||+|||.|+|+.++..-...++.+++... +...
T Consensus 83 ~------------~GN~~an~~~ea~~p~~~~~p~~d~~~e~FIR~KYE~kkf~~~~~~~~s~~~~~~~~~k----~~~~ 146 (287)
T KOG0703|consen 83 S------------MGNAKANSYYEAKLPDPFRRPGPDDLVEQFIRDKYERKKFLDPEEDITSKPGSRDEESK----RSDK 146 (287)
T ss_pred H------------HcchhhhhhccccCCccccCCChHHHHHHHHHHHHhhhhhccchhhcccCCCccccccc----cccc
Confidence 9 999999999999999887654 3999999999999999876222222222222211 1111
Q ss_pred CCCCCCCCCCcchhhhhhcCCCCCCCCCCCccccccCCCCCCCCccccCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCc
Q 009702 162 KSGHGYTDNSENLSEERKHVQAPSTKDSVPAARISLPLPPRGPDQVVAITKPQQTESTVAPAGATNQSSDANLAVPPPKV 241 (528)
Q Consensus 162 ~sg~~~~~s~~~~f~e~~~~~~~~~k~~~~atr~~~pa~~~~p~~v~~~pkpq~~eP~~~~~~~~~~~~~~~~~~~pPKv 241 (528)
+........+..++. .. +...-..+. +... +.......++..........
T Consensus 147 ~~~~~~~s~s~~~~~-~~-------r~~~~~~~~--~~~s--------------------~~~~~~~~~~~~~~~i~~~~ 196 (287)
T KOG0703|consen 147 RSRKLSSSLSRSFVK-SA-------REDQLKYFL--PKTS--------------------QPVDDLATFQGPIASPHNLQ 196 (287)
T ss_pred Cccccccchhhhhhh-hc-------ccccccccc--ccCC--------------------CCchhhhhccCccccccchh
Confidence 122222222222221 11 111111111 1000 11111222222234456666
Q ss_pred ccccccccccCCCCCCCCCccc---cCCCCCccccccccccccccccCCCCCcccCCccccccccccccCCCCCCCCCCC
Q 009702 242 DFASDLFDMLSGDSPNENSSEA---ASADDNLWAGFQSAVETSTAEKKDSTKAVESSPQSATGIEDLFKDSPSLATPSSS 318 (528)
Q Consensus 242 d~AtdLFdlLsmD~~~en~s~a---~~~dDn~waGFqSA~~~sta~k~~~~~~~eS~~~StsgiEDlFkdsp~~~~~~~~ 318 (528)
+++ +|.+.|.+++ +..++ -.+.+..|+.|+.+...-+ +...+..+..+....-...+ ++++-+...+
T Consensus 197 ~~~-~~~s~~n~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~s~~~~f~~~~-~~~~~~~~~~---- 266 (287)
T KOG0703|consen 197 TTY-SLNSTLNIFG---SGKEAADSFTLRAARFAPLAVAFSTVT-EDLVPFLQRNSLSEGFMEKT-LSKPKRWFGT---- 266 (287)
T ss_pred eee-cccccccccc---CccccCCCcccccccccccccccccCc-cccccccccccccccccCcc-cccccccccc----
Confidence 778 8888888888 22222 1277888888887765555 66666666666555555555 7777333322
Q ss_pred CCCcchhhhhHHHhhccCcccCcchhhHH
Q 009702 319 EKPQKDLKNDIMSLFEKSNMVSPFAMHQQ 347 (528)
Q Consensus 319 ~~~qk~~KndImsLfeksn~~spf~~~qq 347 (528)
. . .|++|| +-..+.||..++|
T Consensus 267 ~------~-~~~~~~-~~~~~~~~~~~~~ 287 (287)
T KOG0703|consen 267 Q------Q-SKSSLF-FLDGNVPFGSKES 287 (287)
T ss_pred C------c-cccccc-cccccccccccCC
Confidence 2 5 899999 9999999987764
No 2
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=100.00 E-value=1e-39 Score=346.96 Aligned_cols=161 Identities=29% Similarity=0.569 Sum_probs=147.5
Q ss_pred cHHHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCcccccccccCCCCCHHHHHHHhhc
Q 009702 8 SKELNARHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQST 87 (528)
Q Consensus 8 SK~l~ar~ekiLr~Ll~~PgNK~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISrVKSLsLD~WT~eEV~~Mq~~ 87 (528)
|||+++|+++||++|+++|+|++|+|||+++|.|||++||||||+.|+||||.|| +|||||+||+|+++||++|+.
T Consensus 3 SKR~qERnekILreLlklPgNk~CADCgs~~P~WASiNlGIFICi~CSGIHRsLG---hRVKSLSLDkWT~EEVe~Mk~- 78 (648)
T PLN03119 3 SKREEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREFT---HRVKSVSMSKFTSKEVEVLQN- 78 (648)
T ss_pred chHHHHHHHHHHHHHhhCcCCCccccCCCCCCCceeeccceEEeccchhhhccCC---ceeeccccCCCCHHHHHHHHH-
Confidence 7999999999999999999999999999999999999999999999999999998 599999999999999999998
Q ss_pred ccccccccccccchHHHHHHHhhcCCC-------CCChHHHHHHHHHHhhhCccccCCCCCCCCCcccccccccccCCCC
Q 009702 88 ACDCGFFLYTAMGNEKANSYWEAELPP-------NYDRVGIENFIRAKYEEKRWVSRDGQANSPPRGLEEKASIHWQRPG 160 (528)
Q Consensus 88 ~~~~g~~Ll~~gGN~kAN~iwEa~LPp-------ssD~~~re~FIRaKY~eKrF~~~~~~~~~ps~~~~ek~~~~~~~~~ 160 (528)
+||.++|+|||++|++ ..+...+++|||.||++|+|+.+....+++++.++++..+...+ .
T Consensus 79 -----------gGN~~AN~iyeanw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~~~~~~d~p~~~~~~~~~~~~~~~-~ 146 (648)
T PLN03119 79 -----------GGNQRAREIYLKNWDHQRQRLPENSNAERVREFIKNVYVQKKYAGANDADKPSKDSQDHVSSEDMTR-R 146 (648)
T ss_pred -----------hchHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhccCcCCCCCCccccccccccccccc-c
Confidence 9999999999998853 34567789999999999999999999998888888988776445 4
Q ss_pred CCCCCCCCCCCc--chhhhhhcCCCC
Q 009702 161 EKSGHGYTDNSE--NLSEERKHVQAP 184 (528)
Q Consensus 161 ~~sg~~~~~s~~--~~f~e~~~~~~~ 184 (528)
+++||+|..|++ ++|||||..+-.
T Consensus 147 ~~s~h~~s~sp~y~~~ye~rr~~~~~ 172 (648)
T PLN03119 147 ANSYHSYSQSPPYDYQYEERRYGKIP 172 (648)
T ss_pred cccCCCCCCCCCcccchhhhhccccc
Confidence 899999999988 799999976544
No 3
>PLN03131 hypothetical protein; Provisional
Probab=100.00 E-value=4.3e-37 Score=329.12 Aligned_cols=157 Identities=29% Similarity=0.552 Sum_probs=137.4
Q ss_pred cHHHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCcccccccccCCCCCHHHHHHHhhc
Q 009702 8 SKELNARHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQST 87 (528)
Q Consensus 8 SK~l~ar~ekiLr~Ll~~PgNK~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISrVKSLsLD~WT~eEV~~Mq~~ 87 (528)
||+++++++++|++|+++|+|++|+|||+++|.|||++||||||+.|+||||.|| +|||||+||+|+++||++|+.
T Consensus 3 SkkqqErnekiLreLlk~PgNk~CADCga~~P~WASiNlGIFICi~CSGIHRsLg---hRVKSVTLD~WtdeEV~~Mk~- 78 (705)
T PLN03131 3 SRKEEERNEKIIRGLMKLPPNRRCINCNSLGPQFVCTNFWTFICMTCSGIHREFT---HRVKSVSMSKFTSQDVEALQN- 78 (705)
T ss_pred chHHHHHHHHHHHHHhhCcCCCccccCCCCCCCeeEeccceEEchhchhhhcccC---cccccccCCCCCHHHHHHHHH-
Confidence 6889999999999999999999999999999999999999999999999999998 599999999999999999998
Q ss_pred ccccccccccccchHHHHHHHhhcCC-------CCCChHHHHHHHHHHhhhCccccCCCCCCCCCcccccccccccCCCC
Q 009702 88 ACDCGFFLYTAMGNEKANSYWEAELP-------PNYDRVGIENFIRAKYEEKRWVSRDGQANSPPRGLEEKASIHWQRPG 160 (528)
Q Consensus 88 ~~~~g~~Ll~~gGN~kAN~iwEa~LP-------pssD~~~re~FIRaKY~eKrF~~~~~~~~~ps~~~~ek~~~~~~~~~ 160 (528)
+||.++|+|||++|+ ++.+...+++|||.||++|||+.......++...+.-+..+...|.
T Consensus 79 -----------gGN~~AN~iyeanwd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa~~~s~d~pprd~q~~r~~e~e~rr- 146 (705)
T PLN03131 79 -----------GGNQRAREIYLKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKYAGGKTHDKPPRDLQRIRSHEDETRR- 146 (705)
T ss_pred -----------hccHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhhhcCCCCCCCchhhhhhhcccccccc-
Confidence 999999999999874 3345567899999999999999988777766554444444444455
Q ss_pred CCCCCCCCCCCcc--hhhhhhc
Q 009702 161 EKSGHGYTDNSEN--LSEERKH 180 (528)
Q Consensus 161 ~~sg~~~~~s~~~--~f~e~~~ 180 (528)
..++|+|..|+.| +|||||.
T Consensus 147 ~~syh~~SqSPpY~~~yedrRy 168 (705)
T PLN03131 147 ACSYHSYSQSPPYDFQYEDRRY 168 (705)
T ss_pred cccccCCCcCCCcccccccccc
Confidence 4689999999985 8899876
No 4
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=100.00 E-value=9.5e-37 Score=268.20 Aligned_cols=109 Identities=58% Similarity=1.053 Sum_probs=90.9
Q ss_pred HHHHHhhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCcccccccccCCCCCHHHHHHHhhcccccccccc
Q 009702 17 KILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSTACDCGFFLY 96 (528)
Q Consensus 17 kiLr~Ll~~PgNK~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISrVKSLsLD~WT~eEV~~Mq~~~~~~g~~Ll 96 (528)
++|+.|++.|+|++|||||+++|+|||++||||||+.|+|+||+||+|||+||||+||+|+++||+.|+.
T Consensus 2 ~~l~~l~~~~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~VkSi~~d~w~~~ev~~~~~---------- 71 (116)
T PF01412_consen 2 KILRELLKKPGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRVKSITMDNWSPEEVQRMRE---------- 71 (116)
T ss_dssp HHHHHHHCSTTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--EEETTTS---HHHHHHHHH----------
T ss_pred HHHHHHHcCcCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhccccccCCCCHHHHHHHHH----------
Confidence 6899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccchHHHHHHHhhcCC------CCCChHHHHHHHHHHhhhCccccC
Q 009702 97 TAMGNEKANSYWEAELP------PNYDRVGIENFIRAKYEEKRWVSR 137 (528)
Q Consensus 97 ~~gGN~kAN~iwEa~LP------pssD~~~re~FIRaKY~eKrF~~~ 137 (528)
+||.++|++||++.+ +..+...+++||++||++++|+.+
T Consensus 72 --~GN~~~n~~~e~~~~~~~~~~~~~~~~~~~~fI~~KY~~k~f~~~ 116 (116)
T PF01412_consen 72 --GGNKRANSIWEANSPPPKKPPPSSDQEKREQFIRAKYVEKAFISK 116 (116)
T ss_dssp --SHHHHHHHHHTTTSTTTTTHCTTSHHHHHHHHHHHHHTTHTTS-C
T ss_pred --HChHHHHHHHHcCCCCCCCCCCCCcHHHHHHHHHHHHHhhhhccC
Confidence 999999999999842 233456899999999999999863
No 5
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=100.00 E-value=4.8e-35 Score=256.31 Aligned_cols=103 Identities=58% Similarity=1.015 Sum_probs=95.8
Q ss_pred CCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCcccccccccCCCCCHHHHHHHhhcccccccccccccchHHHH
Q 009702 26 PENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSTACDCGFFLYTAMGNEKAN 105 (528)
Q Consensus 26 PgNK~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISrVKSLsLD~WT~eEV~~Mq~~~~~~g~~Ll~~gGN~kAN 105 (528)
|+|++|||||+++|+||+++||||||+.|+|+||.||+|||+||||+||+|++++|++|+. +||.++|
T Consensus 1 ~~N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~VkSl~md~w~~~~i~~~~~------------~GN~~~n 68 (112)
T smart00105 1 PGNKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTLDTWTEEELRLLQK------------GGNENAN 68 (112)
T ss_pred CCCCcccCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCeeeecccCCCCHHHHHHHHH------------hhhHHHH
Confidence 5899999999999999999999999999999999999999999999999999999999998 9999999
Q ss_pred HHHhhcCCCC-------CChHHHHHHHHHHhhhCccccCCCC
Q 009702 106 SYWEAELPPN-------YDRVGIENFIRAKYEEKRWVSRDGQ 140 (528)
Q Consensus 106 ~iwEa~LPps-------sD~~~re~FIRaKY~eKrF~~~~~~ 140 (528)
++||+++++. .+...+++||+.||++++|+.+.+.
T Consensus 69 ~~~e~~~~~~~~~~~~~~~~~~~~~fI~~KY~~k~f~~~~~~ 110 (112)
T smart00105 69 SIWESNLDDFSLKPPDSDDQQKYESFIAAKYEEKLFVPPESA 110 (112)
T ss_pred HHHHhhCCccccCCCCCchHHHHHHHHHHHHHhhhccccccC
Confidence 9999998643 2357899999999999999987654
No 6
>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=2.5e-32 Score=277.49 Aligned_cols=113 Identities=47% Similarity=0.889 Sum_probs=104.1
Q ss_pred HHHHHHHHhhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCcccccccccCCCCCHHHHHHHhhccccccc
Q 009702 14 RHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSTACDCGF 93 (528)
Q Consensus 14 r~ekiLr~Ll~~PgNK~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISrVKSLsLD~WT~eEV~~Mq~~~~~~g~ 93 (528)
..+++|..|++.++|+.|||||+++|+|||++||||||++|+||||+||+||++||||+||+|+++||++|..
T Consensus 6 ~~~~~l~~l~~~~~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~wt~~~l~~m~~------- 78 (319)
T COG5347 6 EDRKLLKLLKSDSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWTEEELRRMEV------- 78 (319)
T ss_pred HHHHHHHHHhhccccCccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeecccCCHHHHHHHHH-------
Confidence 4577888899999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccccchHHHHHHHhhcCC--------CCCChHHHHHHHHHHhhhCccccCC
Q 009702 94 FLYTAMGNEKANSYWEAELP--------PNYDRVGIENFIRAKYEEKRWVSRD 138 (528)
Q Consensus 94 ~Ll~~gGN~kAN~iwEa~LP--------pssD~~~re~FIRaKY~eKrF~~~~ 138 (528)
+||.++|.|||.++- ..+|...+++||+.||++++|+...
T Consensus 79 -----gGN~~a~~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~~ 126 (319)
T COG5347 79 -----GGNSNANRFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDDS 126 (319)
T ss_pred -----hcchhhhhHhccCCCcccccccccccCHHHHHHHHHHHHHhhhccccc
Confidence 999999999998742 2356677999999999999999863
No 7
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.96 E-value=5.8e-29 Score=254.69 Aligned_cols=112 Identities=38% Similarity=0.668 Sum_probs=97.1
Q ss_pred HHHHHHhhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCcccccccccCCCCCHHHHHHHhhccccccccc
Q 009702 16 RKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSTACDCGFFL 95 (528)
Q Consensus 16 ekiLr~Ll~~PgNK~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISrVKSLsLD~WT~eEV~~Mq~~~~~~g~~L 95 (528)
.++|+.|+.+|+|++|+|||+++|+|++++||||||+.|+||||.||+||++|||++||.|++++|++|+.
T Consensus 10 ~~vfrkL~~kPgNk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~Ws~eqL~~Mk~--------- 80 (395)
T PLN03114 10 ISVFKKLKAKSDNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSSEQLKMMIY--------- 80 (395)
T ss_pred HHHHHHHHhCcCCCcCccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCCCCHHHHHHHHH---------
Confidence 56899999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccchHHHHHHHhhcC-CCC------CC--hHHHHHHHHHHhhhCccccCCC
Q 009702 96 YTAMGNEKANSYWEAEL-PPN------YD--RVGIENFIRAKYEEKRWVSRDG 139 (528)
Q Consensus 96 l~~gGN~kAN~iwEa~L-Pps------sD--~~~re~FIRaKY~eKrF~~~~~ 139 (528)
+||.++|.||+.+. ... |+ -..+.+.+.+|++++.+..+..
T Consensus 81 ---GGN~rA~~fF~qhG~~~~~~~~~KY~S~aA~~Yre~L~keVa~~~a~~~~ 130 (395)
T PLN03114 81 ---GGNNRAQVFFKQYGWSDGGKTEAKYTSRAADLYKQILAKEVAKSKAEEEL 130 (395)
T ss_pred ---hcCHHHHHHHHHcCCCCCCCcccccCCHHHHHHHHHHHHHHHHhhhcccc
Confidence 99999999998753 111 11 1234566888899988875543
No 8
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.93 E-value=1.9e-27 Score=248.01 Aligned_cols=85 Identities=46% Similarity=0.853 Sum_probs=82.0
Q ss_pred HHHHHHHhhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCcccccccccCCCCCHHHHHHHhhcccccccc
Q 009702 15 HRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSTACDCGFF 94 (528)
Q Consensus 15 ~ekiLr~Ll~~PgNK~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISrVKSLsLD~WT~eEV~~Mq~~~~~~g~~ 94 (528)
...+++.|+..++||.|||||+++|+|++|+||||||++|+++||+|||||++|||..||+|+++||++|+.
T Consensus 10 ~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~-------- 81 (454)
T KOG0706|consen 10 IQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQV-------- 81 (454)
T ss_pred HHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhh--------
Confidence 467899999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cccccchHHHHHHHhhc
Q 009702 95 LYTAMGNEKANSYWEAE 111 (528)
Q Consensus 95 Ll~~gGN~kAN~iwEa~ 111 (528)
+||.+|+.|+..+
T Consensus 82 ----GGN~nA~~FFkqh 94 (454)
T KOG0706|consen 82 ----GGNANARVFFKQH 94 (454)
T ss_pred ----cCchhHHHHHHHc
Confidence 9999999999875
No 9
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=99.93 E-value=1.2e-26 Score=236.58 Aligned_cols=109 Identities=39% Similarity=0.740 Sum_probs=91.7
Q ss_pred HHHHHHHHhhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCcccccccccCCCCCHHHHHHHhhccccccc
Q 009702 14 RHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSTACDCGF 93 (528)
Q Consensus 14 r~ekiLr~Ll~~PgNK~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISrVKSLsLD~WT~eEV~~Mq~~~~~~g~ 93 (528)
|.++.|..|+...+|+.|+||++.+|+|||++||||||++|+|+||.||+||++|||||||+|.+.||+.|+.
T Consensus 5 rtrr~L~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMea------- 77 (386)
T KOG0704|consen 5 RTRRVLLELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEA------- 77 (386)
T ss_pred HHHHHHHhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHh-------
Confidence 5677787777777999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccccchHHHHHHHhhcC--CCCCC-h--------HHHHHHHHHHhhhCcc
Q 009702 94 FLYTAMGNEKANSYWEAEL--PPNYD-R--------VGIENFIRAKYEEKRW 134 (528)
Q Consensus 94 ~Ll~~gGN~kAN~iwEa~L--PpssD-~--------~~re~FIRaKY~eKrF 134 (528)
+||.++++|++..- .+..+ + ...++-|.+--+.+.|
T Consensus 78 -----GGN~~~~eFL~s~~~~~e~~~i~eKYns~aAa~yRdki~~laegr~w 124 (386)
T KOG0704|consen 78 -----GGNERFREFLSSQGIYKETWPIREKYNSRAAALYRDKIAALAEGREW 124 (386)
T ss_pred -----ccchhHHHHHhhCccccccccHHHhhccHHHHHHHHHHHHHhcCCcc
Confidence 99999999997642 22211 1 1245566666666666
No 10
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.90 E-value=5.1e-25 Score=235.24 Aligned_cols=114 Identities=41% Similarity=0.819 Sum_probs=104.1
Q ss_pred HHHHHHhhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCcccccccccCCCCCHHHHHHHhhccccccccc
Q 009702 16 RKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSTACDCGFFL 95 (528)
Q Consensus 16 ekiLr~Ll~~PgNK~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISrVKSLsLD~WT~eEV~~Mq~~~~~~g~~L 95 (528)
...|+.|+..+||.+|+||+.++|.|+++|+|+.+|++|+||||.||.|+||||+|.||.|..|-+..|..
T Consensus 501 a~a~qairn~rgn~~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl~~Vm~a--------- 571 (749)
T KOG0705|consen 501 AMALQAIRNMRGNSHCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVELLKVMSA--------- 571 (749)
T ss_pred HHHHHHHhcCcCCceeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHHHHHHHH---------
Confidence 45678888999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccchHHHHHHHhhcCC------CCCChHHHHHHHHHHhhhCccccCCCCC
Q 009702 96 YTAMGNEKANSYWEAELP------PNYDRVGIENFIRAKYEEKRWVSRDGQA 141 (528)
Q Consensus 96 l~~gGN~kAN~iwEa~LP------pssD~~~re~FIRaKY~eKrF~~~~~~~ 141 (528)
+||+.||++||..+- +.+.|+.+|+|||+||++|.|..+.+..
T Consensus 572 ---iGN~~AN~vWE~~~~G~~KPs~~s~REEkErwIr~KYeqklFLaPl~~t 620 (749)
T KOG0705|consen 572 ---IGNDLANSVWEGSSQGQTKPSPDSSREEKERWIRAKYEQKLFLAPLPCT 620 (749)
T ss_pred ---hhhhHHHHHhhhhccCCcCCCccccHHHHHHHHHHHHHHHhhcCCCCCC
Confidence 999999999997541 3345889999999999999999876653
No 11
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.85 E-value=2.7e-22 Score=223.67 Aligned_cols=111 Identities=48% Similarity=0.926 Sum_probs=101.7
Q ss_pred HHHHhhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCcccccccccCCCCCHHHHHHHhhccccccccccc
Q 009702 18 ILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSTACDCGFFLYT 97 (528)
Q Consensus 18 iLr~Ll~~PgNK~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISrVKSLsLD~WT~eEV~~Mq~~~~~~g~~Ll~ 97 (528)
.+..+++.|+|..|+|||++.|+|+++|+||.+|++|+|+||+||+|||||+||+||.|.++.+..++.
T Consensus 416 ~~~~vq~~pgN~~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~~~~l~~l~~~----------- 484 (785)
T KOG0521|consen 416 VIEEVQSVPGNAQCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVWEPELLLLFKN----------- 484 (785)
T ss_pred hhhhhhcCCchhhhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhccCcHHHHHHHH-----------
Confidence 378889999999999999999999999999999999999999999999999999999999999988888
Q ss_pred ccchHHHHHHHhhcCCCC--------CChHHHHHHHHHHhhhCccccCCCC
Q 009702 98 AMGNEKANSYWEAELPPN--------YDRVGIENFIRAKYEEKRWVSRDGQ 140 (528)
Q Consensus 98 ~gGN~kAN~iwEa~LPps--------sD~~~re~FIRaKY~eKrF~~~~~~ 140 (528)
+||..+|.+||+.++.- .++..++.||++||++++|..+...
T Consensus 485 -lgn~~~N~i~e~~l~~~~~~~~~~~~~~~~r~~~i~~kyve~~F~~k~~~ 534 (785)
T KOG0521|consen 485 -LGNKYVNEIYEALLPSYDSSKPTASSSRQAREAWIKAKYVERRFSVKEPQ 534 (785)
T ss_pred -hCcchhhhhhhcccccccccCCCCccchhhhhHhhhcccceeeEeecccc
Confidence 99999999999998632 2456799999999999999977554
No 12
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.82 E-value=9.9e-20 Score=192.42 Aligned_cols=128 Identities=30% Similarity=0.558 Sum_probs=114.1
Q ss_pred cccHHHHHHHHHHHHHhhcCCCCCCCcCCCCCCC-CeeecchhHHHHHHhhhhhhcCCCcccccccccCCCCCHHHHHHH
Q 009702 6 NVSKELNARHRKILEGLLKLPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFI 84 (528)
Q Consensus 6 ~~SK~l~ar~ekiLr~Ll~~PgNK~CADCGA~~P-~WASvn~GVFLC~~CSGIHRsLG~hISrVKSLsLD~WT~eEV~~M 84 (528)
...|+.++.++++||.|+++|+|++|++|....+ +|+++..|.|+|+.|+|..|.|.. -||||+|+|.+|+..||.+|
T Consensus 3 ~~~ke~E~~~ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~~-ahRvksiSmttft~qevs~l 81 (524)
T KOG0702|consen 3 GYKKEDEYDYEKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLNP-AHRVKSISMTTFTDQEVSFL 81 (524)
T ss_pred cccccchhHHHHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccCCC-ccccceeeeeeccccchHHH
Confidence 4456767778999999999999999999999987 999999999999999999999875 58999999999999999999
Q ss_pred hhcccccccccccccchHHHHHHHhhc-------CCCCCChHHHHHHHHHHhhhCccccCCCCCCCCCc
Q 009702 85 QSTACDCGFFLYTAMGNEKANSYWEAE-------LPPNYDRVGIENFIRAKYEEKRWVSRDGQANSPPR 146 (528)
Q Consensus 85 q~~~~~~g~~Ll~~gGN~kAN~iwEa~-------LPpssD~~~re~FIRaKY~eKrF~~~~~~~~~ps~ 146 (528)
|+ +||+.+.+||.+- +|+..+....++|||.||+.|||+-.....+.++.
T Consensus 82 Qs------------hgNq~~k~i~fkl~D~q~S~vPD~rn~~~~kef~q~~y~~kr~~v~~n~~k~~s~ 138 (524)
T KOG0702|consen 82 QS------------HGNQVCKEIWFKLFDFQRSNVPDSRNPQKVKEFQQEKYVKKRYYVPKNQMKIPSY 138 (524)
T ss_pred hh------------cchhhhhhhhhcchhhhhccCCCcccchhhHHHHhhhhccceeecCccccccccc
Confidence 99 9999999999763 46777778899999999999999987776665543
No 13
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.74 E-value=5.5e-19 Score=187.16 Aligned_cols=102 Identities=43% Similarity=0.821 Sum_probs=90.3
Q ss_pred cCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCcccccccccCCCCCHHHHHHHhhcccccccccccccchHH
Q 009702 24 KLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSTACDCGFFLYTAMGNEK 103 (528)
Q Consensus 24 ~~PgNK~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISrVKSLsLD~WT~eEV~~Mq~~~~~~g~~Ll~~gGN~k 103 (528)
+...-+.|+|||+++|.|+||+-|+|||.+|..+||.||.|||.||+|....|.++-|+++.. +.|..
T Consensus 4 ~~l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~t------------Ln~~g 71 (669)
T KOG0818|consen 4 RLLSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVET------------LNNNG 71 (669)
T ss_pred cchhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHH------------HHhcC
Confidence 445668899999999999999999999999999999999999999999999999999999988 88899
Q ss_pred HHHHHhhcCCCC------------CChH--HHHHHHHHHhhhCccccC
Q 009702 104 ANSYWEAELPPN------------YDRV--GIENFIRAKYEEKRWVSR 137 (528)
Q Consensus 104 AN~iwEa~LPps------------sD~~--~re~FIRaKY~eKrF~~~ 137 (528)
+|.|||..|-+. .|.. .+++|||+||+...|+.+
T Consensus 72 aNsIWEh~Lld~st~~sg~rk~~pqD~~Hp~K~eFIkaKy~~LtFv~~ 119 (669)
T KOG0818|consen 72 ANSIWEHSLLDPATIMSGRRKANPQDKVHPNKAEFIRAKYQMLAFVHR 119 (669)
T ss_pred cchhhhhhccCchhhhcccCCCCCcCCCCccHHHHHHHHHHheeeecc
Confidence 999999876221 1222 479999999999999985
No 14
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.65 E-value=4e-17 Score=180.59 Aligned_cols=110 Identities=42% Similarity=0.779 Sum_probs=99.2
Q ss_pred HHHhhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhcCCCcccccccccCCC--CCHHHHHHHhhcccccccccc
Q 009702 19 LEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDT--WLPEQVAFIQSTACDCGFFLY 96 (528)
Q Consensus 19 Lr~Ll~~PgNK~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISrVKSLsLD~--WT~eEV~~Mq~~~~~~g~~Ll 96 (528)
-+++.....|+.|+|||+..|.|+++|+++.||-.|+|-||+||..+|+|+|++||. |+.+-|+++..
T Consensus 289 aeriW~ne~nr~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfiv---------- 358 (1186)
T KOG1117|consen 289 AERIWLNEENRECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIV---------- 358 (1186)
T ss_pred HHHHHhccccccccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhhee----------
Confidence 345667789999999999999999999999999999999999999999999999998 99999998877
Q ss_pred cccchHHHHHHHhhcCCCCC------ChHHHHHHHHHHhhhCccccCCCC
Q 009702 97 TAMGNEKANSYWEAELPPNY------DRVGIENFIRAKYEEKRWVSRDGQ 140 (528)
Q Consensus 97 ~~gGN~kAN~iwEa~LPpss------D~~~re~FIRaKY~eKrF~~~~~~ 140 (528)
+||.++|.||-.+++++. ....|++||..||.+.+|......
T Consensus 359 --lgn~~an~Fwa~nl~~~e~lh~dssp~~r~~fi~~Kykeg~fRk~~~~ 406 (1186)
T KOG1117|consen 359 --LGNPRANRFWAGNLPPNEHLHPDSSPSTRRQFIKEKYKEGKFRKEHPV 406 (1186)
T ss_pred --ecCcccccccccCCCCccccCCCCCcchhhhHHHHHhhcccccccccc
Confidence 999999999999998753 345799999999999999876554
No 15
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=93.00 E-value=0.025 Score=65.18 Aligned_cols=56 Identities=21% Similarity=0.272 Sum_probs=49.5
Q ss_pred hcCCCCCCCcCCCCC-CCCeeecchhHHHHHHhhhhhhcCCCcccccccccCCCCCH
Q 009702 23 LKLPENRECADCKAK-GPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLP 78 (528)
Q Consensus 23 l~~PgNK~CADCGA~-~P~WASvn~GVFLC~~CSGIHRsLG~hISrVKSLsLD~WT~ 78 (528)
.....+-.|++|++. ...|+++++.+-+|+.|+++|+.++.|++..+++.|++..+
T Consensus 625 ~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~ 681 (785)
T KOG0521|consen 625 VKASSDGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD 681 (785)
T ss_pred HHhccCccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc
Confidence 344567889999984 78999999999999999999999999999999999888766
No 16
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=83.74 E-value=0.59 Score=45.57 Aligned_cols=32 Identities=31% Similarity=0.538 Sum_probs=27.6
Q ss_pred cCCCCCCCcCCCCCCC-CeeecchhHHHHHHhh
Q 009702 24 KLPENRECADCKAKGP-RWASVNLGIFICMQCS 55 (528)
Q Consensus 24 ~~PgNK~CADCGA~~P-~WASvn~GVFLC~~CS 55 (528)
-.|.-..|+-||.... .|.++..|.++|..|.
T Consensus 145 ~~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 145 YGLDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred CccchhhHhcCCCCCCceEEecccCCccccccc
Confidence 3677789999998744 7999999999999997
No 17
>PRK12495 hypothetical protein; Provisional
Probab=72.95 E-value=1.4 Score=44.58 Aligned_cols=38 Identities=26% Similarity=0.405 Sum_probs=28.2
Q ss_pred HHHHHHhhc--CCCCCCCcCCCCCCCCeeecchhHHHHHHhhhh
Q 009702 16 RKILEGLLK--LPENRECADCKAKGPRWASVNLGIFICMQCSGI 57 (528)
Q Consensus 16 ekiLr~Ll~--~PgNK~CADCGA~~P~WASvn~GVFLC~~CSGI 57 (528)
+++-+.|++ ...+++|-+||.+-|.+ -|+.+|..|..+
T Consensus 28 ~~ma~lL~~gatmsa~hC~~CG~PIpa~----pG~~~Cp~CQ~~ 67 (226)
T PRK12495 28 ERMSELLLQGATMTNAHCDECGDPIFRH----DGQEFCPTCQQP 67 (226)
T ss_pred HHHHHHHHhhcccchhhcccccCcccCC----CCeeECCCCCCc
Confidence 444445554 57899999999998832 588999999644
No 18
>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=67.47 E-value=2.4 Score=41.20 Aligned_cols=34 Identities=26% Similarity=0.462 Sum_probs=28.0
Q ss_pred cCCCCCCCcCCCCCCC-CeeecchhHHHHHHhhhh
Q 009702 24 KLPENRECADCKAKGP-RWASVNLGIFICMQCSGI 57 (528)
Q Consensus 24 ~~PgNK~CADCGA~~P-~WASvn~GVFLC~~CSGI 57 (528)
-.|.-..|+.||..++ .|.++..|.|+|..|...
T Consensus 143 ~~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 143 YALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred CCcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 3677789999998543 688999999999999763
No 19
>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=65.37 E-value=1.6 Score=31.79 Aligned_cols=34 Identities=12% Similarity=0.335 Sum_probs=29.5
Q ss_pred CCCCCcCCCCCCCCeeecchhHHHHHHhhhh-hhc
Q 009702 27 ENRECADCKAKGPRWASVNLGIFICMQCSGI-HRS 60 (528)
Q Consensus 27 gNK~CADCGA~~P~WASvn~GVFLC~~CSGI-HRs 60 (528)
.+..|..|+.....|.+.+-+++||..|... |+.
T Consensus 2 ~~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~ 36 (42)
T PF00643_consen 2 QEPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG 36 (42)
T ss_dssp SSSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT
T ss_pred cCccCccCCccceEEEecCCCCccCccCCCCCCCC
Confidence 3578999999889999999999999999998 886
No 20
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=60.15 E-value=5.8 Score=36.57 Aligned_cols=40 Identities=18% Similarity=0.420 Sum_probs=24.6
Q ss_pred HHhhcCCCCC--CCcCCCCCCC-CeeecchhHHHHHHhhhhhh
Q 009702 20 EGLLKLPENR--ECADCKAKGP-RWASVNLGIFICMQCSGIHR 59 (528)
Q Consensus 20 r~Ll~~PgNK--~CADCGA~~P-~WASvn~GVFLC~~CSGIHR 59 (528)
..|.++..+. +|.+||.+=| .=.-.--+..+|+.|...|-
T Consensus 70 ~al~rIe~gtYG~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~~E 112 (120)
T COG1734 70 SALDRIEEGTYGICEECGEPIPEARLEARPTARLCIECQERAE 112 (120)
T ss_pred HHHHHHHcCCccchhccCCcCCHHHHhhCcchHHHHHHHHHHH
Confidence 3444444444 8999999832 11122235789999998774
No 21
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=60.08 E-value=3.9 Score=41.16 Aligned_cols=32 Identities=31% Similarity=0.649 Sum_probs=27.9
Q ss_pred cCCCCCCCcCCCCCC-CCeeecchhHHHHHHhh
Q 009702 24 KLPENRECADCKAKG-PRWASVNLGIFICMQCS 55 (528)
Q Consensus 24 ~~PgNK~CADCGA~~-P~WASvn~GVFLC~~CS 55 (528)
=.+.=..|+.||.+. +..+++-.|-++|..|.
T Consensus 150 ~~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 150 IGPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred CccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 356777999999985 57999999999999998
No 22
>PRK11019 hypothetical protein; Provisional
Probab=58.70 E-value=4.2 Score=35.75 Aligned_cols=36 Identities=22% Similarity=0.553 Sum_probs=25.3
Q ss_pred CCCCCcCCCCCCC--CeeecchhHHHHHHhhhhhhcCCC
Q 009702 27 ENRECADCKAKGP--RWASVNLGIFICMQCSGIHRSLGV 63 (528)
Q Consensus 27 gNK~CADCGA~~P--~WASvn~GVFLC~~CSGIHRsLG~ 63 (528)
.-.+|.|||.+=| +|--+. ++-.|+.|...+...+.
T Consensus 35 syg~C~~CG~~Ip~~Rl~A~P-~a~~Cv~Cq~~~E~~~k 72 (88)
T PRK11019 35 SLTECEECGEPIPEARRKAIP-GVRLCVACQQEKDLQQA 72 (88)
T ss_pred cCCeeCcCCCcCcHHHHhhcC-CccccHHHHHHHHHHHh
Confidence 4569999999743 344333 67789999998755443
No 23
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=54.15 E-value=5.5 Score=33.67 Aligned_cols=33 Identities=18% Similarity=0.516 Sum_probs=21.5
Q ss_pred CCCCcCCCCCCCC-eeecchhHHHHHHhhhhhhc
Q 009702 28 NRECADCKAKGPR-WASVNLGIFICMQCSGIHRS 60 (528)
Q Consensus 28 NK~CADCGA~~P~-WASvn~GVFLC~~CSGIHRs 60 (528)
..+|.|||.+=|. =.-.--|+..|+.|...+-.
T Consensus 34 ~~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~E~ 67 (73)
T PRK13715 34 VYLCEACGNPIPEARRKIFPGVTLCVECQAYQER 67 (73)
T ss_pred cccHhhcCCcCCHHHHhcCCCcCCCHHHHHHHHH
Confidence 4589999997441 11112367889999886543
No 24
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=53.15 E-value=9 Score=38.53 Aligned_cols=40 Identities=18% Similarity=0.370 Sum_probs=29.4
Q ss_pred HHHHHHHHhhcCCCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhh
Q 009702 14 RHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHR 59 (528)
Q Consensus 14 r~ekiLr~Ll~~PgNK~CADCGA~~P~WASvn~GVFLC~~CSGIHR 59 (528)
..++.++..++....-.|-.||.....|. ++|..|.+.|-
T Consensus 340 ~~~~~~~~~~~~~p~~~c~~cg~~~~~~~------~~c~~c~~~~~ 379 (389)
T PRK11788 340 LLRDLVGEQLKRKPRYRCRNCGFTARTLY------WHCPSCKAWET 379 (389)
T ss_pred HHHHHHHHHHhCCCCEECCCCCCCCccce------eECcCCCCccC
Confidence 34666665555433445999999999996 68999988873
No 25
>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=45.68 E-value=10 Score=31.14 Aligned_cols=34 Identities=35% Similarity=0.647 Sum_probs=23.0
Q ss_pred cCCCCCCCcCCCCCCC--CeeecchhHHHHHHhhhhh
Q 009702 24 KLPENRECADCKAKGP--RWASVNLGIFICMQCSGIH 58 (528)
Q Consensus 24 ~~PgNK~CADCGA~~P--~WASvn~GVFLC~~CSGIH 58 (528)
..++..+|.|||..=| +|.- --|+..|+.|...+
T Consensus 27 ~~~s~g~C~~Cg~~Ip~~Rl~a-~p~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 27 IGPSLRECEDCGEPIPEARREA-LPGVTRCVSCQEIL 62 (63)
T ss_pred cCCCCCeeccCCCcChHHHHhh-cCCcCCcHHHHhhc
Confidence 3466789999999733 2322 23677899997654
No 26
>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=42.04 E-value=8.7 Score=28.47 Aligned_cols=27 Identities=26% Similarity=0.812 Sum_probs=22.9
Q ss_pred CCCCCCcCCCCCCCCeeecchhHHHHHHhh
Q 009702 26 PENRECADCKAKGPRWASVNLGIFICMQCS 55 (528)
Q Consensus 26 PgNK~CADCGA~~P~WASvn~GVFLC~~CS 55 (528)
..|..|..|++. |....=|.++|.+|-
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCc
Confidence 346679999998 888999999999994
No 27
>TIGR02890 spore_yteA sporulation protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to PFAM family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. The function of proteins in this family is unknown. YteA was detected in mature spores of Bacillus subtilis by Kuwana, et al., and appears to be expressed under control of sigma-K.
Probab=40.92 E-value=19 Score=34.57 Aligned_cols=44 Identities=20% Similarity=0.390 Sum_probs=25.7
Q ss_pred HHHHHHhhcCC--CCCCCcCCCCC--CCCeeecchhHHHHHHhhhhhhc
Q 009702 16 RKILEGLLKLP--ENRECADCKAK--GPRWASVNLGIFICMQCSGIHRS 60 (528)
Q Consensus 16 ekiLr~Ll~~P--gNK~CADCGA~--~P~WASvn~GVFLC~~CSGIHRs 60 (528)
.+|-+.|.++. .=-+|.+||.+ ..++-.+. ++-.|+.|...+-.
T Consensus 72 ~~Ie~AL~Ri~~G~YG~Ce~CGe~I~~~RL~a~P-~a~~Ci~Cq~~~E~ 119 (159)
T TIGR02890 72 REIEHALQKIENGTYGICEVCGKPIPYERLEAIP-TATTCVECQNRKEV 119 (159)
T ss_pred HHHHHHHHHHhCCCCCeecccCCcccHHHHhhCC-CcchhHHHHHHhhh
Confidence 34444454443 33469999987 22222223 35689999987643
No 28
>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=39.71 E-value=6 Score=29.37 Aligned_cols=27 Identities=19% Similarity=0.582 Sum_probs=16.8
Q ss_pred CCCcCCCCC-CCCeeecchhHHHHHHhh
Q 009702 29 RECADCKAK-GPRWASVNLGIFICMQCS 55 (528)
Q Consensus 29 K~CADCGA~-~P~WASvn~GVFLC~~CS 55 (528)
..|.+|+.. .-+|..-+|+.-||..|.
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 469999986 678999999999999994
No 29
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=37.75 E-value=8.4 Score=37.05 Aligned_cols=34 Identities=29% Similarity=0.640 Sum_probs=27.7
Q ss_pred CCCCCCcCCCCCCCCeeecchhHHHHH-Hhhhhhhc
Q 009702 26 PENRECADCKAKGPRWASVNLGIFICM-QCSGIHRS 60 (528)
Q Consensus 26 PgNK~CADCGA~~P~WASvn~GVFLC~-~CSGIHRs 60 (528)
|--+.|+-|| -...|.+++.|.-.|. .|-.+|.+
T Consensus 116 P~r~fCaVCG-~~S~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 116 PLRKFCAVCG-YDSKYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred CcchhhhhcC-CCchhHHHhcCCceeechhhhhccc
Confidence 4557899999 5666999999998875 79999965
No 30
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=34.49 E-value=20 Score=34.17 Aligned_cols=46 Identities=20% Similarity=0.304 Sum_probs=26.4
Q ss_pred HHHHHHhhc--CCCCCCCcCCCCCCC-CeeecchhHHHHHHhhhhhhcC
Q 009702 16 RKILEGLLK--LPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRSL 61 (528)
Q Consensus 16 ekiLr~Ll~--~PgNK~CADCGA~~P-~WASvn~GVFLC~~CSGIHRsL 61 (528)
.+|-+.|.+ .+.--+|-+||.+=| .=.-+--++..|+.|...|-..
T Consensus 97 ~~I~~AL~Ri~~gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~E~~ 145 (151)
T PRK10778 97 KKIEKTLKKVEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIR 145 (151)
T ss_pred HHHHHHHHHHhCCCCceeccCCCcccHHHHhcCCCccccHHHHHHHHHH
Confidence 334444444 455668999998711 1111111356899999877543
No 31
>PHA00080 DksA-like zinc finger domain containing protein
Probab=29.68 E-value=30 Score=29.20 Aligned_cols=35 Identities=26% Similarity=0.563 Sum_probs=23.4
Q ss_pred CCCCCCCcCCCCCC--CCeeecchhHHHHHHhhhhhhc
Q 009702 25 LPENRECADCKAKG--PRWASVNLGIFICMQCSGIHRS 60 (528)
Q Consensus 25 ~PgNK~CADCGA~~--P~WASvn~GVFLC~~CSGIHRs 60 (528)
..+..+|.|||..= .+|.-+. ++..|+.|...+-.
T Consensus 28 ~~~~~~C~~Cg~~Ip~~Rl~a~P-~~~~Cv~Cq~~~E~ 64 (72)
T PHA00080 28 APSATHCEECGDPIPEARREAVP-GCRTCVSCQEILEL 64 (72)
T ss_pred CCCCCEecCCCCcCcHHHHHhCC-CccCcHHHHHHHHH
Confidence 34566899999973 3443333 46679999887643
No 32
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=27.84 E-value=23 Score=27.90 Aligned_cols=37 Identities=24% Similarity=0.587 Sum_probs=30.2
Q ss_pred CCCCCcCCCCC-CCCeeecchhH-HHHHHhhhhhhcCCC
Q 009702 27 ENRECADCKAK-GPRWASVNLGI-FICMQCSGIHRSLGV 63 (528)
Q Consensus 27 gNK~CADCGA~-~P~WASvn~GV-FLC~~CSGIHRsLG~ 63 (528)
..+.|..|+.. -|.|=....|- +||-.|.-..+..+.
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~ 40 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCC
Confidence 46789999986 68898888886 999999888877664
No 33
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=26.66 E-value=1.4e+02 Score=33.22 Aligned_cols=103 Identities=14% Similarity=0.249 Sum_probs=52.1
Q ss_pred cCCCCCCCcC-CCCC--CCCeeecchh--HHHHHHhhhhhhcCCCcc----cc-ccc----ccCCCCCH-HHHHHHhhcc
Q 009702 24 KLPENRECAD-CKAK--GPRWASVNLG--IFICMQCSGIHRSLGVHI----SK-VRS----ATLDTWLP-EQVAFIQSTA 88 (528)
Q Consensus 24 ~~PgNK~CAD-CGA~--~P~WASvn~G--VFLC~~CSGIHRsLG~hI----Sr-VKS----LsLD~WT~-eEV~~Mq~~~ 88 (528)
..+++++|+| |-.. +...|...-+ ..||+.|-.+=-++|.|- =+ |.. +---.|+. ||+..|...
T Consensus 9 ~~~g~ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLea~- 87 (438)
T KOG0457|consen 9 DDPGGKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSVGAETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLEAA- 87 (438)
T ss_pred hcCCCCCCCccHhHHhccceEEEeecCCCcchhHHHHhcccccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHHHH-
Confidence 3466675544 7653 4443322222 579999987644555441 11 222 12234985 677766651
Q ss_pred cccccccccccchHHHHHHHhhcCCCCCChHHHHHHHHHHhhhCccccC
Q 009702 89 CDCGFFLYTAMGNEKANSYWEAELPPNYDRVGIENFIRAKYEEKRWVSR 137 (528)
Q Consensus 89 ~~~g~~Ll~~gGN~kAN~iwEa~LPpssD~~~re~FIRaKY~eKrF~~~ 137 (528)
..+| +||=. .|-+. =...+.+..+++-.+.|++-.+...
T Consensus 88 ~t~G------~GNW~--dIA~h--IGtKtkeeck~hy~k~fv~s~~~~~ 126 (438)
T KOG0457|consen 88 ETYG------FGNWQ--DIADH--IGTKTKEECKEHYLKHFVNSPIFPL 126 (438)
T ss_pred HHhC------CCcHH--HHHHH--HcccchHHHHHHHHHHHhcCccccc
Confidence 1122 56522 11111 0123456677777788887655543
No 34
>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=26.26 E-value=7.7 Score=29.05 Aligned_cols=27 Identities=22% Similarity=0.600 Sum_probs=20.9
Q ss_pred CCcCCCCCCCCeeecchhHHHHHHhhhh
Q 009702 30 ECADCKAKGPRWASVNLGIFICMQCSGI 57 (528)
Q Consensus 30 ~CADCGA~~P~WASvn~GVFLC~~CSGI 57 (528)
+|-.||+.. ....-.-|-++|..|..|
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 589999977 456677899999999544
No 35
>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=25.33 E-value=47 Score=28.49 Aligned_cols=32 Identities=19% Similarity=0.603 Sum_probs=25.7
Q ss_pred CCCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhc
Q 009702 26 PENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (528)
Q Consensus 26 PgNK~CADCGA~~P~WASvn~GVFLC~~CSGIHRs 60 (528)
+..+.|.=||.... ...||++.|..|.++.|-
T Consensus 1 ~~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 32 (82)
T cd07173 1 PPQKTCLICGDEAS---GCHYGALTCGSCKVFFKR 32 (82)
T ss_pred CCCCCCeecCCcCc---ceEECcchhhhHHHHHHH
Confidence 34667999997654 458999999999998874
No 36
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=24.56 E-value=38 Score=30.41 Aligned_cols=34 Identities=26% Similarity=0.552 Sum_probs=23.7
Q ss_pred hcCCCCCCCcCCCCCC-------C----------CeeecchhHHHHHHhhh
Q 009702 23 LKLPENRECADCKAKG-------P----------RWASVNLGIFICMQCSG 56 (528)
Q Consensus 23 l~~PgNK~CADCGA~~-------P----------~WASvn~GVFLC~~CSG 56 (528)
.+.++--.|+|||.+- | .=++=.||-.+|..|..
T Consensus 29 kK~~~~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~ 79 (93)
T COG2174 29 KKKPTIPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVR 79 (93)
T ss_pred eccCCCCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHHH
Confidence 3466777899999871 1 11234789999999965
No 37
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=22.10 E-value=44 Score=26.47 Aligned_cols=31 Identities=26% Similarity=0.546 Sum_probs=20.5
Q ss_pred CCcCCCCCCCCe--eecchhHHHHHHhhhhhhcC
Q 009702 30 ECADCKAKGPRW--ASVNLGIFICMQCSGIHRSL 61 (528)
Q Consensus 30 ~CADCGA~~P~W--ASvn~GVFLC~~CSGIHRsL 61 (528)
.|+=||.+-.-+ +-+.=| +||..|..--..+
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl~~~ 33 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKLSGF 33 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHhcCc
Confidence 488898874433 345557 8999998644443
No 38
>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=21.78 E-value=39 Score=28.94 Aligned_cols=31 Identities=19% Similarity=0.613 Sum_probs=25.3
Q ss_pred CCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhc
Q 009702 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (528)
Q Consensus 27 gNK~CADCGA~~P~WASvn~GVFLC~~CSGIHRs 60 (528)
.|..|.=||.... ...||++.|..|.++.|-
T Consensus 2 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 2 DTHFCAVCSDYAS---GYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 4678999997554 468999999999998864
No 39
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=21.77 E-value=45 Score=29.67 Aligned_cols=39 Identities=23% Similarity=0.427 Sum_probs=20.9
Q ss_pred HHHHHhhcC--CCCCCCcCCCCCCCC-eeecchhHHHHHHhh
Q 009702 17 KILEGLLKL--PENRECADCKAKGPR-WASVNLGIFICMQCS 55 (528)
Q Consensus 17 kiLr~Ll~~--PgNK~CADCGA~~P~-WASvn~GVFLC~~CS 55 (528)
.|-+.|.+. +.--+|.|||.+=|. =.-.--++..|+.|.
T Consensus 67 ~i~~AL~ri~~g~yG~C~~Cge~I~~~RL~a~P~a~~Cv~Cq 108 (110)
T TIGR02420 67 KIDEALKRIEDGEYGYCEECGEEIGLRRLEARPTATLCIDCK 108 (110)
T ss_pred HHHHHHHHHhCCCCCchhccCCcccHHHHhhCCCccccHHhH
Confidence 444455443 355699999987220 000111245688885
No 40
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=20.98 E-value=11 Score=27.39 Aligned_cols=29 Identities=24% Similarity=0.563 Sum_probs=15.5
Q ss_pred CCcCCCCCCC-CeeecchhHHHHHHhhhhh
Q 009702 30 ECADCKAKGP-RWASVNLGIFICMQCSGIH 58 (528)
Q Consensus 30 ~CADCGA~~P-~WASvn~GVFLC~~CSGIH 58 (528)
+|.+||..=+ .=.-+--+..+|..|...|
T Consensus 5 ~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~~ 34 (36)
T PF01258_consen 5 ICEDCGEPIPEERLVAVPGATLCVECQERR 34 (36)
T ss_dssp B-TTTSSBEEHHHHHHCTTECS-HHHHHHH
T ss_pred CccccCChHHHHHHHhCCCcEECHHHhCcc
Confidence 4899987622 1111223567888888765
No 41
>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=20.72 E-value=46 Score=29.29 Aligned_cols=31 Identities=29% Similarity=0.718 Sum_probs=25.2
Q ss_pred CCCCCcCCCCCCCCeeecchhHHHHHHhhhhhhc
Q 009702 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (528)
Q Consensus 27 gNK~CADCGA~~P~WASvn~GVFLC~~CSGIHRs 60 (528)
++..|.=||.... ...||++.|..|.++.|-
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 4667999998654 358999999999999874
No 42
>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=20.42 E-value=27 Score=25.56 Aligned_cols=32 Identities=25% Similarity=0.694 Sum_probs=23.1
Q ss_pred CcCCCCC-CCCeeecchhHH-HHHHhhhhhhcCC
Q 009702 31 CADCKAK-GPRWASVNLGIF-ICMQCSGIHRSLG 62 (528)
Q Consensus 31 CADCGA~-~P~WASvn~GVF-LC~~CSGIHRsLG 62 (528)
|.+|+.. .|.|=....|-. ||-.|.-.+|..+
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~ 34 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYG 34 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhC
Confidence 8899986 699998887776 9999988877654
No 43
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=20.27 E-value=99 Score=24.70 Aligned_cols=33 Identities=24% Similarity=0.637 Sum_probs=27.0
Q ss_pred CCcCCCCC-CCCeeecc-hhHHHHHHhhhhhhcCC
Q 009702 30 ECADCKAK-GPRWASVN-LGIFICMQCSGIHRSLG 62 (528)
Q Consensus 30 ~CADCGA~-~P~WASvn-~GVFLC~~CSGIHRsLG 62 (528)
+|..|+.. -|.|=... -+..||-.|.-..|..+
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~ 35 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG 35 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC
Confidence 59999986 57788765 78899999988777766
No 44
>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors. HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.
Probab=20.14 E-value=29 Score=28.89 Aligned_cols=31 Identities=26% Similarity=0.490 Sum_probs=25.1
Q ss_pred CcC-CCCCCCC-eeecchhHHHHHHhhhhhhcCC
Q 009702 31 CAD-CKAKGPR-WASVNLGIFICMQCSGIHRSLG 62 (528)
Q Consensus 31 CAD-CGA~~P~-WASvn~GVFLC~~CSGIHRsLG 62 (528)
+.| |+.-.|. +..-+...+.|..| |.||+|-
T Consensus 21 a~DGCgEFm~~~g~eg~~~al~CaAC-gCHRnFH 53 (60)
T PF04770_consen 21 AVDGCGEFMPSPGEEGTPEALKCAAC-GCHRNFH 53 (60)
T ss_pred ccccccccccCCCCCCCcccceeccc-Ccchhcc
Confidence 666 9988777 77677888999999 7899873
Done!