Query 010188
Match_columns 516
No_of_seqs 161 out of 1193
Neff 3.8
Searched_HMMs 46136
Date Thu Mar 28 22:04:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010188.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010188hhsearch_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 1.3E-45 2.8E-50 367.8 11.6 276 7-335 4-287 (287)
2 PLN03119 putative ADP-ribosyla 100.0 7.4E-41 1.6E-45 355.0 12.6 161 8-172 3-172 (648)
3 PLN03131 hypothetical protein; 100.0 1.7E-38 3.6E-43 339.3 11.5 157 8-168 3-168 (705)
4 PF01412 ArfGap: Putative GTPa 100.0 1.2E-37 2.6E-42 273.5 5.9 109 17-125 2-116 (116)
5 smart00105 ArfGap Putative GTP 100.0 3.9E-36 8.4E-41 262.7 8.5 103 26-128 1-110 (112)
6 COG5347 GTPase-activating prot 100.0 1.1E-33 2.5E-38 286.7 7.2 115 14-128 6-128 (319)
7 PLN03114 ADP-ribosylation fact 100.0 9.9E-29 2.1E-33 252.5 14.5 112 16-127 10-130 (395)
8 KOG0704 ADP-ribosylation facto 99.9 1.2E-28 2.6E-33 250.6 3.7 110 13-122 4-124 (386)
9 KOG0706 Predicted GTPase-activ 99.9 1.2E-27 2.6E-32 249.1 4.8 85 15-99 10-94 (454)
10 KOG0705 GTPase-activating prot 99.9 2.1E-26 4.6E-31 245.2 5.2 114 15-128 500-619 (749)
11 KOG0521 Putative GTPase activa 99.9 1.5E-23 3.3E-28 233.2 4.0 111 18-128 416-534 (785)
12 KOG0818 GTPase-activating prot 99.8 1.3E-20 2.8E-25 198.9 3.1 102 24-125 4-119 (669)
13 KOG0702 Predicted GTPase-activ 99.8 1.4E-18 3.1E-23 183.4 14.1 125 8-133 5-137 (524)
14 KOG1117 Rho- and Arf-GTPase ac 99.7 3.4E-18 7.3E-23 188.6 2.6 109 19-127 289-405 (1186)
15 KOG0521 Putative GTPase activa 95.0 0.0068 1.5E-07 69.6 0.0 74 23-98 625-699 (785)
16 PRK00085 recO DNA repair prote 78.0 1.2 2.5E-05 43.5 1.5 32 25-56 146-178 (247)
17 TIGR00613 reco DNA repair prot 72.5 3.4 7.3E-05 40.1 3.1 33 25-57 144-177 (241)
18 PRK12495 hypothetical protein; 71.8 1.6 3.5E-05 44.0 0.8 39 15-57 27-67 (226)
19 PF00643 zf-B_box: B-box zinc 62.5 2 4.3E-05 31.3 -0.5 34 27-60 2-36 (42)
20 COG1734 DksA DnaK suppressor p 59.5 6.2 0.00013 36.3 2.0 31 29-59 81-112 (120)
21 PRK11019 hypothetical protein; 57.7 4.6 0.0001 35.4 0.8 37 27-64 35-73 (88)
22 COG1381 RecO Recombinational D 51.9 6.3 0.00014 39.6 0.8 31 25-55 151-182 (251)
23 PRK13715 conjugal transfer pro 47.5 8.5 0.00019 32.4 0.8 33 28-60 34-67 (73)
24 PRK11788 tetratricopeptide rep 47.2 14 0.0003 37.1 2.4 37 15-58 341-378 (389)
25 TIGR02419 C4_traR_proteo phage 45.4 10 0.00023 30.9 1.0 34 24-58 27-62 (63)
26 KOG3362 Predicted BBOX Zn-fing 39.7 7.7 0.00017 37.2 -0.7 34 26-60 116-150 (156)
27 PF11781 RRN7: RNA polymerase 38.9 9.6 0.00021 28.2 -0.1 27 26-55 6-32 (36)
28 TIGR02890 spore_yteA sporulati 38.5 22 0.00047 34.0 2.1 34 26-60 84-119 (159)
29 PRK10778 dksA RNA polymerase-b 38.0 20 0.00042 34.1 1.7 37 25-61 108-145 (151)
30 PF01286 XPA_N: XPA protein N- 37.9 6.9 0.00015 28.9 -1.0 27 29-55 4-31 (34)
31 PF08271 TF_Zn_Ribbon: TFIIB z 30.6 6.1 0.00013 29.5 -2.3 27 30-57 2-28 (43)
32 COG2174 RPL34A Ribosomal prote 30.3 25 0.00054 31.4 1.0 34 23-56 29-79 (93)
33 smart00401 ZnF_GATA zinc finge 30.3 22 0.00047 28.0 0.6 37 27-63 2-40 (52)
34 PHA00080 DksA-like zinc finger 27.7 34 0.00074 28.7 1.4 35 25-60 28-64 (72)
35 cd03031 GRX_GRX_like Glutaredo 25.1 29 0.00064 32.6 0.6 37 16-61 87-123 (147)
36 PF14471 DUF4428: Domain of un 24.6 37 0.0008 26.8 0.9 30 30-60 1-32 (51)
37 KOG0457 Histone acetyltransfer 24.2 2E+02 0.0043 32.1 6.6 94 25-124 10-125 (438)
38 KOG4080 Mitochondrial ribosoma 23.3 50 0.0011 32.5 1.8 32 22-60 86-119 (176)
39 PF04770 ZF-HD_dimer: ZF-HD pr 22.4 26 0.00057 29.1 -0.3 32 30-62 20-53 (60)
40 cd00202 ZnF_GATA Zinc finger D 22.3 82 0.0018 25.1 2.5 33 30-62 1-35 (54)
41 PTZ00218 40S ribosomal protein 21.8 42 0.0009 27.4 0.8 40 25-69 13-52 (54)
42 cd07173 NR_DBD_AR DNA-binding 21.6 60 0.0013 27.8 1.7 31 27-60 2-32 (82)
43 PF00320 GATA: GATA zinc finge 21.5 23 0.00051 25.8 -0.6 32 31-62 1-34 (36)
44 PF01258 zf-dskA_traR: Prokary 21.4 10 0.00023 27.3 -2.5 29 30-58 5-34 (36)
45 PRK00423 tfb transcription ini 21.2 27 0.00058 36.2 -0.5 33 26-59 9-41 (310)
46 cd07171 NR_DBD_ER DNA-binding 21.0 42 0.00091 28.7 0.7 31 27-60 2-32 (82)
No 1
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=1.3e-45 Score=367.81 Aligned_cols=276 Identities=36% Similarity=0.526 Sum_probs=190.7
Q ss_pred ccHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCceecchhHHHHHHhhhhhhcCCCccccccccccCCCCHHHHHHHHh
Q 010188 7 VSKELNARHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQS 86 (516)
Q Consensus 7 ~Sk~~~ar~~kiL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSgIHRsLG~hISkVKSLtLDsWt~eeV~~Lq~ 86 (516)
+.+...++++++|++||+.|+|++|||||+++|+|||+|+|||||++|+||||+||+||||||||+||.|++|+|+.|+.
T Consensus 4 ~~~~~~~~~~~~l~~Ll~~~~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~ 83 (287)
T KOG0703|consen 4 VEKGSNERNKRRLRELLREPDNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMIS 83 (287)
T ss_pred ccccccchHHHHHHHHHcCcccCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHH
Confidence 34456778999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hChHHHHHHHhhcCCCCCChh----HHHHHHHHHHhhcccccCCCCCCCCCCccccccccccCCCCCCCCCCCCCCCcch
Q 010188 87 MGNEKANSYWEAELPPNYDRV----GIENFIRAKYEEKRWVSRDGQANSPPRGLEEKASIHWQRPGEKSGHGYTDNSENL 162 (516)
Q Consensus 87 ~GN~~aN~iwEa~lPps~d~~----~re~FIraKY~eKrFv~k~g~~~~ps~~~~ek~~~~~qr~~~rsgh~~~~s~~~~ 162 (516)
+||.++|.|||+.+|..+++. .+|+|||+|||.|+|+.++..-....+.+++... |...+.++.....+...
T Consensus 84 ~GN~~an~~~ea~~p~~~~~p~~d~~~e~FIR~KYE~kkf~~~~~~~~s~~~~~~~~~k----~~~~~~~~~~~s~s~~~ 159 (287)
T KOG0703|consen 84 MGNAKANSYYEAKLPDPFRRPGPDDLVEQFIRDKYERKKFLDPEEDITSKPGSRDEESK----RSDKRSRKLSSSLSRSF 159 (287)
T ss_pred HcchhhhhhccccCCccccCCChHHHHHHHHHHHHhhhhhccchhhcccCCCccccccc----ccccCccccccchhhhh
Confidence 999999999999999877654 4999999999999999976221111222222221 12222222222222222
Q ss_pred hHhhhcCCCCCCCCCCCccccccCCCCCCCCccccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCcccccccccCCCC
Q 010188 163 SEERKHVQAPSTKDSVPAARISLPLPPRGPDQVVAITKPQQTESTVAPAGATNQSSDANLAVPPPKVDFASDLFDMLSGD 242 (516)
Q Consensus 163 f~e~~~~~~~~~k~a~patr~~~p~~~~~p~~v~p~p~pqekqp~~~~~~~~k~~~~~~~~~~~pkv~~AtDLFdmLsmD 242 (516)
+. .. +...-+.+. +... +.......++..+.......++. +|.+.|.++
T Consensus 160 ~~-~~-------r~~~~~~~~--~~~s--------------------~~~~~~~~~~~~~~~i~~~~~~~-~~~s~~n~~ 208 (287)
T KOG0703|consen 160 VK-SA-------REDQLKYFL--PKTS--------------------QPVDDLATFQGPIASPHNLQTTY-SLNSTLNIF 208 (287)
T ss_pred hh-hc-------ccccccccc--ccCC--------------------CCchhhhhccCccccccchheee-ccccccccc
Confidence 22 11 111111111 1110 11111222222344566777788 888888777
Q ss_pred CCCCCCccc----ccCCCccccccccccccCcccccCCCCcccCCCCCcccccccccCCCCCCCCCCCCCCcchhhhhHH
Q 010188 243 SPNENSSEA----ASADDNLWAGFQSAVETSTAEKKDSTKAVESSPQSATGIEDLFKDSPSLATPSSSEKPQKDLKNDIM 318 (516)
Q Consensus 243 ~~ten~sea----ss~dDn~waGFqSA~~~sta~k~~~~~a~eS~~qStsgiEDlFkds~~~~~~~~~~~~qk~~KndIm 318 (516)
+ +..++ + +.+..|+.|+.+...-+ +...+..+..+....-...+ ++++-+...+ . . .|+
T Consensus 209 ~---~~~~~~~~~~-~~~~~~~~~~~~~~~~~-~~~~~~~~~~s~~~~f~~~~-~~~~~~~~~~----~------~-~~~ 271 (287)
T KOG0703|consen 209 G---SGKEAADSFT-LRAARFAPLAVAFSTVT-EDLVPFLQRNSLSEGFMEKT-LSKPKRWFGT----Q------Q-SKS 271 (287)
T ss_pred c---CccccCCCcc-cccccccccccccccCc-cccccccccccccccccCcc-cccccccccc----C------c-ccc
Confidence 7 22222 3 78888888887766555 66666666666665555555 7777333322 2 5 899
Q ss_pred HhhccCcccCcchhhHH
Q 010188 319 SLFEKSNMVSPFAMHQQ 335 (516)
Q Consensus 319 sLfeksn~~spf~~~qq 335 (516)
+|| +-..+.||..++|
T Consensus 272 ~~~-~~~~~~~~~~~~~ 287 (287)
T KOG0703|consen 272 SLF-FLDGNVPFGSKES 287 (287)
T ss_pred ccc-cccccccccccCC
Confidence 999 9999999987764
No 2
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=100.00 E-value=7.4e-41 Score=354.99 Aligned_cols=161 Identities=29% Similarity=0.569 Sum_probs=148.3
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCceecchhHHHHHHhhhhhhcCCCccccccccccCCCCHHHHHHHHhh
Q 010188 8 SKELNARHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSM 87 (516)
Q Consensus 8 Sk~~~ar~~kiL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSgIHRsLG~hISkVKSLtLDsWt~eeV~~Lq~~ 87 (516)
|||.++|+++||++|+++|+|++|+|||..+|.|||++||||||++|+||||+|| +|||||+||+|+++||++|+.+
T Consensus 3 SKR~qERnekILreLlklPgNk~CADCgs~~P~WASiNlGIFICi~CSGIHRsLG---hRVKSLSLDkWT~EEVe~Mk~g 79 (648)
T PLN03119 3 SKREEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREFT---HRVKSVSMSKFTSKEVEVLQNG 79 (648)
T ss_pred chHHHHHHHHHHHHHhhCcCCCccccCCCCCCCceeeccceEEeccchhhhccCC---ceeeccccCCCCHHHHHHHHHh
Confidence 7999999999999999999999999999999999999999999999999999998 4999999999999999999999
Q ss_pred ChHHHHHHHhhcCCC-------CCChhHHHHHHHHHHhhcccccCCCCCCCCCCccccccccccCCCCCCCCCCCCCCCc
Q 010188 88 GNEKANSYWEAELPP-------NYDRVGIENFIRAKYEEKRWVSRDGQANSPPRGLEEKASIHWQRPGEKSGHGYTDNSE 160 (516)
Q Consensus 88 GN~~aN~iwEa~lPp-------s~d~~~re~FIraKY~eKrFv~k~g~~~~ps~~~~ek~~~~~qr~~~rsgh~~~~s~~ 160 (516)
||.++|+|||++|+. ..+...+|+|||.||++|+|+.+...+++++..+++++.+...| .+++||+|++|++
T Consensus 80 GN~~AN~iyeanw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~~~~~~d~p~~~~~~~~~~~~~~~-~~~s~h~~s~sp~ 158 (648)
T PLN03119 80 GNQRAREIYLKNWDHQRQRLPENSNAERVREFIKNVYVQKKYAGANDADKPSKDSQDHVSSEDMTR-RANSYHSYSQSPP 158 (648)
T ss_pred chHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhccCcCCCCCCccccccccccccccc-ccccCCCCCCCCC
Confidence 999999999998753 34556789999999999999999999998888899998877555 5999999999999
Q ss_pred --chhHhhhcCCCC
Q 010188 161 --NLSEERKHVQAP 172 (516)
Q Consensus 161 --~~f~e~~~~~~~ 172 (516)
++|||||..+-.
T Consensus 159 y~~~ye~rr~~~~~ 172 (648)
T PLN03119 159 YDYQYEERRYGKIP 172 (648)
T ss_pred cccchhhhhccccc
Confidence 799999976654
No 3
>PLN03131 hypothetical protein; Provisional
Probab=100.00 E-value=1.7e-38 Score=339.30 Aligned_cols=157 Identities=29% Similarity=0.552 Sum_probs=140.0
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCceecchhHHHHHHhhhhhhcCCCccccccccccCCCCHHHHHHHHhh
Q 010188 8 SKELNARHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSM 87 (516)
Q Consensus 8 Sk~~~ar~~kiL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSgIHRsLG~hISkVKSLtLDsWt~eeV~~Lq~~ 87 (516)
||+.+++++++|++|++.|+|++|+|||+++|.|||++||||||++|+||||+|| +|||||+||+|++++|++|+.+
T Consensus 3 SkkqqErnekiLreLlk~PgNk~CADCga~~P~WASiNlGIFICi~CSGIHRsLg---hRVKSVTLD~WtdeEV~~Mk~g 79 (705)
T PLN03131 3 SRKEEERNEKIIRGLMKLPPNRRCINCNSLGPQFVCTNFWTFICMTCSGIHREFT---HRVKSVSMSKFTSQDVEALQNG 79 (705)
T ss_pred chHHHHHHHHHHHHHhhCcCCCccccCCCCCCCeeEeccceEEchhchhhhcccC---cccccccCCCCCHHHHHHHHHh
Confidence 7889999999999999999999999999999999999999999999999999998 4999999999999999999999
Q ss_pred ChHHHHHHHhhcCC-------CCCChhHHHHHHHHHHhhcccccCCCCCCCCCCccccccccccCCCCCCCCCCCCCCCc
Q 010188 88 GNEKANSYWEAELP-------PNYDRVGIENFIRAKYEEKRWVSRDGQANSPPRGLEEKASIHWQRPGEKSGHGYTDNSE 160 (516)
Q Consensus 88 GN~~aN~iwEa~lP-------ps~d~~~re~FIraKY~eKrFv~k~g~~~~ps~~~~ek~~~~~qr~~~rsgh~~~~s~~ 160 (516)
||.++|+|||++|+ ...+...+|+|||.||++|+|+.....++++......+..+...|. ..++|+|++|++
T Consensus 80 GN~~AN~iyeanwd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa~~~s~d~pprd~q~~r~~e~e~rr-~~syh~~SqSPp 158 (705)
T PLN03131 80 GNQRAREIYLKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKYAGGKTHDKPPRDLQRIRSHEDETRR-ACSYHSYSQSPP 158 (705)
T ss_pred ccHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhhhcCCCCCCCchhhhhhhcccccccc-cccccCCCcCCC
Confidence 99999999999874 2344567899999999999999998777766655555555554555 789999999999
Q ss_pred c--hhHhhhc
Q 010188 161 N--LSEERKH 168 (516)
Q Consensus 161 ~--~f~e~~~ 168 (516)
+ +|||||.
T Consensus 159 Y~~~yedrRy 168 (705)
T PLN03131 159 YDFQYEDRRY 168 (705)
T ss_pred cccccccccc
Confidence 6 8999876
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=1.2e-37 Score=273.48 Aligned_cols=109 Identities=58% Similarity=1.053 Sum_probs=91.2
Q ss_pred HHHHHHhcCCCCCCCcCCCCCCCCceecchhHHHHHHhhhhhhcCCCccccccccccCCCCHHHHHHHHhhChHHHHHHH
Q 010188 17 KILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYW 96 (516)
Q Consensus 17 kiL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSgIHRsLG~hISkVKSLtLDsWt~eeV~~Lq~~GN~~aN~iw 96 (516)
++|+.|++.|+|+.|+|||+++|+|||++||||||+.|+|+||+||+|||+||||+||+|++++|+.|+.+||.++|++|
T Consensus 2 ~~l~~l~~~~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~VkSi~~d~w~~~ev~~~~~~GN~~~n~~~ 81 (116)
T PF01412_consen 2 KILRELLKKPGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRVKSITMDNWSPEEVQRMREGGNKRANSIW 81 (116)
T ss_dssp HHHHHHHCSTTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--EEETTTS---HHHHHHHHHSHHHHHHHHH
T ss_pred HHHHHHHcCcCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhccccccCCCCHHHHHHHHHHChHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCC------CCCChhHHHHHHHHHHhhcccccC
Q 010188 97 EAELP------PNYDRVGIENFIRAKYEEKRWVSR 125 (516)
Q Consensus 97 Ea~lP------ps~d~~~re~FIraKY~eKrFv~k 125 (516)
|++.+ +..+...+++||++||++++|+.+
T Consensus 82 e~~~~~~~~~~~~~~~~~~~~fI~~KY~~k~f~~~ 116 (116)
T PF01412_consen 82 EANSPPPKKPPPSSDQEKREQFIRAKYVEKAFISK 116 (116)
T ss_dssp TTTSTTTTTHCTTSHHHHHHHHHHHHHTTHTTS-C
T ss_pred HcCCCCCCCCCCCCcHHHHHHHHHHHHHhhhhccC
Confidence 99842 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=3.9e-36 Score=262.74 Aligned_cols=103 Identities=58% Similarity=1.018 Sum_probs=96.3
Q ss_pred CCCCCCcCCCCCCCCceecchhHHHHHHhhhhhhcCCCccccccccccCCCCHHHHHHHHhhChHHHHHHHhhcCCCCC-
Q 010188 26 PENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYWEAELPPNY- 104 (516)
Q Consensus 26 PgNk~CADCGA~~P~WASvn~GVFLC~~CSgIHRsLG~hISkVKSLtLDsWt~eeV~~Lq~~GN~~aN~iwEa~lPps~- 104 (516)
|+|+.|||||+++|+|||++||||||+.|+|+||.||+|||+||||+||+|++++|++|+.+||.++|+|||+++++..
T Consensus 1 ~~N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~VkSl~md~w~~~~i~~~~~~GN~~~n~~~e~~~~~~~~ 80 (112)
T smart00105 1 PGNKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTLDTWTEEELRLLQKGGNENANSIWESNLDDFSL 80 (112)
T ss_pred CCCCcccCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCeeeecccCCCCHHHHHHHHHhhhHHHHHHHHhhCCcccc
Confidence 5899999999999999999999999999999999999999999999999999999999999999999999999986432
Q ss_pred ------ChhHHHHHHHHHHhhcccccCCCC
Q 010188 105 ------DRVGIENFIRAKYEEKRWVSRDGQ 128 (516)
Q Consensus 105 ------d~~~re~FIraKY~eKrFv~k~g~ 128 (516)
+...+++||+.||++|+|+.+.+.
T Consensus 81 ~~~~~~~~~~~~~fI~~KY~~k~f~~~~~~ 110 (112)
T smart00105 81 KPPDSDDQQKYESFIAAKYEEKLFVPPESA 110 (112)
T ss_pred CCCCCchHHHHHHHHHHHHHhhhccccccC
Confidence 356899999999999999988664
No 6
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=100.00 E-value=1.1e-33 Score=286.73 Aligned_cols=115 Identities=46% Similarity=0.876 Sum_probs=105.7
Q ss_pred HHHHHHHHHhcCCCCCCCcCCCCCCCCceecchhHHHHHHhhhhhhcCCCccccccccccCCCCHHHHHHHHhhChHHHH
Q 010188 14 RHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKAN 93 (516)
Q Consensus 14 r~~kiL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSgIHRsLG~hISkVKSLtLDsWt~eeV~~Lq~~GN~~aN 93 (516)
..+++|..|.+.++|+.|||||+++|+||||+||||||++|+||||+||+|||+||||+||+|+.+||++|+.+||.++|
T Consensus 6 ~~~~~l~~l~~~~~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~wt~~~l~~m~~gGN~~a~ 85 (319)
T COG5347 6 EDRKLLKLLKSDSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWTEEELRRMEVGGNSNAN 85 (319)
T ss_pred HHHHHHHHHhhccccCccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeecccCCHHHHHHHHHhcchhhh
Confidence 46788888999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcCC--------CCCChhHHHHHHHHHHhhcccccCCCC
Q 010188 94 SYWEAELP--------PNYDRVGIENFIRAKYEEKRWVSRDGQ 128 (516)
Q Consensus 94 ~iwEa~lP--------ps~d~~~re~FIraKY~eKrFv~k~g~ 128 (516)
.||+.++- ..+|...+++||+.||++++|+.....
T Consensus 86 ~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~~~~ 128 (319)
T COG5347 86 RFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDDSSS 128 (319)
T ss_pred hHhccCCCcccccccccccCHHHHHHHHHHHHHhhhccccccC
Confidence 99998742 245667899999999999999986433
No 7
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.96 E-value=9.9e-29 Score=252.48 Aligned_cols=112 Identities=38% Similarity=0.670 Sum_probs=97.4
Q ss_pred HHHHHHHhcCCCCCCCcCCCCCCCCceecchhHHHHHHhhhhhhcCCCccccccccccCCCCHHHHHHHHhhChHHHHHH
Q 010188 16 RKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSY 95 (516)
Q Consensus 16 ~kiL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSgIHRsLG~hISkVKSLtLDsWt~eeV~~Lq~~GN~~aN~i 95 (516)
.++|+.|+..|+|+.|+|||+++|.|+|++||||||+.|+||||.||+||++||||+||.|++++|++|+.+||.++|.|
T Consensus 10 ~~vfrkL~~kPgNk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~Ws~eqL~~Mk~GGN~rA~~f 89 (395)
T PLN03114 10 ISVFKKLKAKSDNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSSEQLKMMIYGGNNRAQVF 89 (395)
T ss_pred HHHHHHHHhCcCCCcCccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCCCCHHHHHHHHHhcCHHHHHH
Confidence 56799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcC-CC------CCCh--hHHHHHHHHHHhhcccccCCC
Q 010188 96 WEAEL-PP------NYDR--VGIENFIRAKYEEKRWVSRDG 127 (516)
Q Consensus 96 wEa~l-Pp------s~d~--~~re~FIraKY~eKrFv~k~g 127 (516)
|+.+. .. .|+- ..+-+.+.+|++++.+.....
T Consensus 90 F~qhG~~~~~~~~~KY~S~aA~~Yre~L~keVa~~~a~~~~ 130 (395)
T PLN03114 90 FKQYGWSDGGKTEAKYTSRAADLYKQILAKEVAKSKAEEEL 130 (395)
T ss_pred HHHcCCCCCCCcccccCCHHHHHHHHHHHHHHHHhhhcccc
Confidence 98763 11 1221 234455888899988876544
No 8
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=99.95 E-value=1.2e-28 Score=250.61 Aligned_cols=110 Identities=39% Similarity=0.740 Sum_probs=93.5
Q ss_pred HHHHHHHHHHhcCCCCCCCcCCCCCCCCceecchhHHHHHHhhhhhhcCCCccccccccccCCCCHHHHHHHHhhChHHH
Q 010188 13 ARHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKA 92 (516)
Q Consensus 13 ar~~kiL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSgIHRsLG~hISkVKSLtLDsWt~eeV~~Lq~~GN~~a 92 (516)
.|+++.|.+|....+|+.|+||++++|+|||++||||||++|+|+||.||+|||+|||||||+|.+.||+.|+.+||+++
T Consensus 4 prtrr~L~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~~ 83 (386)
T KOG0704|consen 4 PRTRRVLLELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNERF 83 (386)
T ss_pred hHHHHHHHhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchhH
Confidence 46788898888888999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhcC--CCC------CCh---hHHHHHHHHHHhhccc
Q 010188 93 NSYWEAEL--PPN------YDR---VGIENFIRAKYEEKRW 122 (516)
Q Consensus 93 N~iwEa~l--Pps------~d~---~~re~FIraKY~eKrF 122 (516)
++|++.+- .+. |+. ...++-|.+--+.+.|
T Consensus 84 ~eFL~s~~~~~e~~~i~eKYns~aAa~yRdki~~laegr~w 124 (386)
T KOG0704|consen 84 REFLSSQGIYKETWPIREKYNSRAAALYRDKIAALAEGREW 124 (386)
T ss_pred HHHHhhCccccccccHHHhhccHHHHHHHHHHHHHhcCCcc
Confidence 99998652 111 211 1245556666666666
No 9
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.94 E-value=1.2e-27 Score=249.11 Aligned_cols=85 Identities=46% Similarity=0.853 Sum_probs=82.5
Q ss_pred HHHHHHHHhcCCCCCCCcCCCCCCCCceecchhHHHHHHhhhhhhcCCCccccccccccCCCCHHHHHHHHhhChHHHHH
Q 010188 15 HRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANS 94 (516)
Q Consensus 15 ~~kiL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSgIHRsLG~hISkVKSLtLDsWt~eeV~~Lq~~GN~~aN~ 94 (516)
...+++.|+..++|+.|+|||+++|.|+||+||||||+.|+++||+|||||++|||..||+|+.+||++|+.+||.+|+.
T Consensus 10 ~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~~ 89 (454)
T KOG0706|consen 10 IQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANARV 89 (454)
T ss_pred HHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHHH
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhc
Q 010188 95 YWEAE 99 (516)
Q Consensus 95 iwEa~ 99 (516)
|+..+
T Consensus 90 FFkqh 94 (454)
T KOG0706|consen 90 FFKQH 94 (454)
T ss_pred HHHHc
Confidence 99876
No 10
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.92 E-value=2.1e-26 Score=245.22 Aligned_cols=114 Identities=42% Similarity=0.841 Sum_probs=105.1
Q ss_pred HHHHHHHHhcCCCCCCCcCCCCCCCCceecchhHHHHHHhhhhhhcCCCccccccccccCCCCHHHHHHHHhhChHHHHH
Q 010188 15 HRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANS 94 (516)
Q Consensus 15 ~~kiL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSgIHRsLG~hISkVKSLtLDsWt~eeV~~Lq~~GN~~aN~ 94 (516)
..-.|+.|...+||.+|+||+.++|.|||+|+|+++|++|+||||.||.|+|+||+|.||.|..|.+..|..+||+.+|.
T Consensus 500 ea~a~qairn~rgn~~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl~~Vm~aiGN~~AN~ 579 (749)
T KOG0705|consen 500 EAMALQAIRNMRGNSHCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVELLKVMSAIGNDLANS 579 (749)
T ss_pred hHHHHHHHhcCcCCceeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHHHHHHHHhhhhHHHH
Confidence 45678888999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcC-----C-CCCChhHHHHHHHHHHhhcccccCCCC
Q 010188 95 YWEAEL-----P-PNYDRVGIENFIRAKYEEKRWVSRDGQ 128 (516)
Q Consensus 95 iwEa~l-----P-ps~d~~~re~FIraKY~eKrFv~k~g~ 128 (516)
+||..+ | +...++++|+|||+||++|.|..+...
T Consensus 580 vWE~~~~G~~KPs~~s~REEkErwIr~KYeqklFLaPl~~ 619 (749)
T KOG0705|consen 580 VWEGSSQGQTKPSPDSSREEKERWIRAKYEQKLFLAPLPC 619 (749)
T ss_pred HhhhhccCCcCCCccccHHHHHHHHHHHHHHHhhcCCCCC
Confidence 999754 2 345678999999999999999987655
No 11
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.88 E-value=1.5e-23 Score=233.23 Aligned_cols=111 Identities=48% Similarity=0.926 Sum_probs=102.6
Q ss_pred HHHHHhcCCCCCCCcCCCCCCCCceecchhHHHHHHhhhhhhcCCCccccccccccCCCCHHHHHHHHhhChHHHHHHHh
Q 010188 18 ILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYWE 97 (516)
Q Consensus 18 iL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSgIHRsLG~hISkVKSLtLDsWt~eeV~~Lq~~GN~~aN~iwE 97 (516)
.+..+.+.|+|..|+|||++.|+|+|+|+||.+|++|+|+||+||+|||+|+||+||.|.++.+..++.+||..+|.+||
T Consensus 416 ~~~~vq~~pgN~~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~~~~l~~l~~~lgn~~~N~i~e 495 (785)
T KOG0521|consen 416 VIEEVQSVPGNAQCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVWEPELLLLFKNLGNKYVNEIYE 495 (785)
T ss_pred hhhhhhcCCchhhhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhccCcHHHHHHHHhCcchhhhhhh
Confidence 37888999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCC--------CChhHHHHHHHHHHhhcccccCCCC
Q 010188 98 AELPPN--------YDRVGIENFIRAKYEEKRWVSRDGQ 128 (516)
Q Consensus 98 a~lPps--------~d~~~re~FIraKY~eKrFv~k~g~ 128 (516)
+.++.. .++..++.||++||++++|..+...
T Consensus 496 ~~l~~~~~~~~~~~~~~~~r~~~i~~kyve~~F~~k~~~ 534 (785)
T KOG0521|consen 496 ALLPSYDSSKPTASSSRQAREAWIKAKYVERRFSVKEPQ 534 (785)
T ss_pred cccccccccCCCCccchhhhhHhhhcccceeeEeecccc
Confidence 998632 2356799999999999999977554
No 12
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.80 E-value=1.3e-20 Score=198.95 Aligned_cols=102 Identities=42% Similarity=0.804 Sum_probs=91.6
Q ss_pred cCCCCCCCcCCCCCCCCceecchhHHHHHHhhhhhhcCCCccccccccccCCCCHHHHHHHHhhChHHHHHHHhhcCCC-
Q 010188 24 KLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYWEAELPP- 102 (516)
Q Consensus 24 k~PgNk~CADCGA~~P~WASvn~GVFLC~~CSgIHRsLG~hISkVKSLtLDsWt~eeV~~Lq~~GN~~aN~iwEa~lPp- 102 (516)
+...-+.|+|||+++|.||||+-|+|||.+|+.+||.||.|||.||+|.-..|.++.|+++..+.|..+|.|||..|-+
T Consensus 4 ~~l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaNsIWEh~Lld~ 83 (669)
T KOG0818|consen 4 RLLSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGANSIWEHSLLDP 83 (669)
T ss_pred cchhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcchhhhhhccCc
Confidence 3456688999999999999999999999999999999999999999999999999999999999999999999987622
Q ss_pred -----------CCCh--hHHHHHHHHHHhhcccccC
Q 010188 103 -----------NYDR--VGIENFIRAKYEEKRWVSR 125 (516)
Q Consensus 103 -----------s~d~--~~re~FIraKY~eKrFv~k 125 (516)
..|+ ..+++|||+||+...|+.+
T Consensus 84 st~~sg~rk~~pqD~~Hp~K~eFIkaKy~~LtFv~~ 119 (669)
T KOG0818|consen 84 ATIMSGRRKANPQDKVHPNKAEFIRAKYQMLAFVHR 119 (669)
T ss_pred hhhhcccCCCCCcCCCCccHHHHHHHHHHheeeecc
Confidence 1233 2589999999999999984
No 13
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.78 E-value=1.4e-18 Score=183.36 Aligned_cols=125 Identities=30% Similarity=0.578 Sum_probs=110.9
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCC-CceecchhHHHHHHhhhhhhcCCCccccccccccCCCCHHHHHHHHh
Q 010188 8 SKELNARHRKILEGLLKLPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQS 86 (516)
Q Consensus 8 Sk~~~ar~~kiL~~Llk~PgNk~CADCGA~~P-~WASvn~GVFLC~~CSgIHRsLG~hISkVKSLtLDsWt~eeV~~Lq~ 86 (516)
.|+.++.++++||.|+++|+|++|++|....+ +|+++.-|-|+|+.|+|.-|.|.. -+|||+|+|.+++..||..|+.
T Consensus 5 ~ke~E~~~ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~~-ahRvksiSmttft~qevs~lQs 83 (524)
T KOG0702|consen 5 KKEDEYDYEKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLNP-AHRVKSISMTTFTDQEVSFLQS 83 (524)
T ss_pred cccchhHHHHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccCCC-ccccceeeeeeccccchHHHhh
Confidence 45555667999999999999999999999988 999999999999999999999864 4799999999999999999999
Q ss_pred hChHHHHHHHhhc-------CCCCCChhHHHHHHHHHHhhcccccCCCCCCCCC
Q 010188 87 MGNEKANSYWEAE-------LPPNYDRVGIENFIRAKYEEKRWVSRDGQANSPP 133 (516)
Q Consensus 87 ~GN~~aN~iwEa~-------lPps~d~~~re~FIraKY~eKrFv~k~g~~~~ps 133 (516)
.||+.+.+||..- +|+..+....++|||.||+.|+|+......+.++
T Consensus 84 hgNq~~k~i~fkl~D~q~S~vPD~rn~~~~kef~q~~y~~kr~~v~~n~~k~~s 137 (524)
T KOG0702|consen 84 HGNQVCKEIWFKLFDFQRSNVPDSRNPQKVKEFQQEKYVKKRYYVPKNQMKIPS 137 (524)
T ss_pred cchhhhhhhhhcchhhhhccCCCcccchhhHHHHhhhhccceeecCcccccccc
Confidence 9999999999763 4667777889999999999999998766655444
No 14
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.70 E-value=3.4e-18 Score=188.62 Aligned_cols=109 Identities=42% Similarity=0.791 Sum_probs=99.0
Q ss_pred HHHHhcCCCCCCCcCCCCCCCCceecchhHHHHHHhhhhhhcCCCccccccccccCC--CCHHHHHHHHhhChHHHHHHH
Q 010188 19 LEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDT--WLPEQVAFIQSMGNEKANSYW 96 (516)
Q Consensus 19 L~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSgIHRsLG~hISkVKSLtLDs--Wt~eeV~~Lq~~GN~~aN~iw 96 (516)
-+++.....|+.|+|||++.|.||++|++|.||-.|+|-||.||..+|+|+|++||. |+.+.|+++..+||.++|.||
T Consensus 289 aeriW~ne~nr~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~Fw 368 (1186)
T KOG1117|consen 289 AERIWLNEENRECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANRFW 368 (1186)
T ss_pred HHHHHhccccccccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCccccccc
Confidence 345667789999999999999999999999999999999999999999999999995 999999999999999999999
Q ss_pred hhcCCCCC------ChhHHHHHHHHHHhhcccccCCC
Q 010188 97 EAELPPNY------DRVGIENFIRAKYEEKRWVSRDG 127 (516)
Q Consensus 97 Ea~lPps~------d~~~re~FIraKY~eKrFv~k~g 127 (516)
-.++|++. ....|++||..||.+.+|.....
T Consensus 369 a~nl~~~e~lh~dssp~~r~~fi~~Kykeg~fRk~~~ 405 (1186)
T KOG1117|consen 369 AGNLPPNEHLHPDSSPSTRRQFIKEKYKEGKFRKEHP 405 (1186)
T ss_pred ccCCCCccccCCCCCcchhhhHHHHHhhccccccccc
Confidence 99998754 34579999999999998876544
No 15
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=94.97 E-value=0.0068 Score=69.60 Aligned_cols=74 Identities=20% Similarity=0.235 Sum_probs=63.0
Q ss_pred hcCCCCCCCcCCCC-CCCCceecchhHHHHHHhhhhhhcCCCccccccccccCCCCHHHHHHHHhhChHHHHHHHhh
Q 010188 23 LKLPENRECADCKA-KGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYWEA 98 (516)
Q Consensus 23 lk~PgNk~CADCGA-~~P~WASvn~GVFLC~~CSgIHRsLG~hISkVKSLtLDsWt~eeV~~Lq~~GN~~aN~iwEa 98 (516)
.....+-.|++|++ ....|+++++.+-+|+.|+++|+.++.|++..+++.|++..+ |..+..-|+...+..|..
T Consensus 625 ~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~~~~~ 699 (785)
T KOG0521|consen 625 VKASSDGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHHATAS 699 (785)
T ss_pred HHhccCccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchhhhhh
Confidence 34456788999987 489999999999999999999999999999999999998766 777777788777776643
No 16
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=78.03 E-value=1.2 Score=43.45 Aligned_cols=32 Identities=31% Similarity=0.561 Sum_probs=27.2
Q ss_pred CCCCCCCcCCCCCCC-CceecchhHHHHHHhhh
Q 010188 25 LPENRECADCKAKGP-RWASVNLGIFICMQCSG 56 (516)
Q Consensus 25 ~PgNk~CADCGA~~P-~WASvn~GVFLC~~CSg 56 (516)
.|.-..|+-||.... .|.+...|.++|..|..
T Consensus 146 ~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~ 178 (247)
T PRK00085 146 GLDLDHCAVCGAPGDHRYFSPKEGGAVCSECGD 178 (247)
T ss_pred ccchhhHhcCCCCCCceEEecccCCcccccccC
Confidence 466789999998744 78999999999999973
No 17
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=72.54 E-value=3.4 Score=40.12 Aligned_cols=33 Identities=27% Similarity=0.497 Sum_probs=27.3
Q ss_pred CCCCCCCcCCCCCCC-CceecchhHHHHHHhhhh
Q 010188 25 LPENRECADCKAKGP-RWASVNLGIFICMQCSGI 57 (516)
Q Consensus 25 ~PgNk~CADCGA~~P-~WASvn~GVFLC~~CSgI 57 (516)
.|.-..|+.||..++ .|.++..|.|+|..|...
T Consensus 144 ~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 144 ALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred CcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 467789999998544 688999999999999763
No 18
>PRK12495 hypothetical protein; Provisional
Probab=71.79 E-value=1.6 Score=43.96 Aligned_cols=39 Identities=26% Similarity=0.392 Sum_probs=28.5
Q ss_pred HHHHHHHHhc--CCCCCCCcCCCCCCCCceecchhHHHHHHhhhh
Q 010188 15 HRKILEGLLK--LPENRECADCKAKGPRWASVNLGIFICMQCSGI 57 (516)
Q Consensus 15 ~~kiL~~Llk--~PgNk~CADCGA~~P~WASvn~GVFLC~~CSgI 57 (516)
.+++-+.|++ ...+.+|-+||.+=|.+ -|+.+|..|..+
T Consensus 27 ~~~ma~lL~~gatmsa~hC~~CG~PIpa~----pG~~~Cp~CQ~~ 67 (226)
T PRK12495 27 TERMSELLLQGATMTNAHCDECGDPIFRH----DGQEFCPTCQQP 67 (226)
T ss_pred HHHHHHHHHhhcccchhhcccccCcccCC----CCeeECCCCCCc
Confidence 3444444554 47899999999988732 699999999754
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=62.51 E-value=2 Score=31.28 Aligned_cols=34 Identities=12% Similarity=0.335 Sum_probs=29.4
Q ss_pred CCCCCcCCCCCCCCceecchhHHHHHHhhhh-hhc
Q 010188 27 ENRECADCKAKGPRWASVNLGIFICMQCSGI-HRS 60 (516)
Q Consensus 27 gNk~CADCGA~~P~WASvn~GVFLC~~CSgI-HRs 60 (516)
.+..|..|+.....|.+.+-+++||..|... |+.
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 3578999998889999999999999999998 886
No 20
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=59.45 E-value=6.2 Score=36.31 Aligned_cols=31 Identities=16% Similarity=0.429 Sum_probs=21.0
Q ss_pred CCCcCCCCCCC-CceecchhHHHHHHhhhhhh
Q 010188 29 RECADCKAKGP-RWASVNLGIFICMQCSGIHR 59 (516)
Q Consensus 29 k~CADCGA~~P-~WASvn~GVFLC~~CSgIHR 59 (516)
-+|.+||.+=| .=.-.-=+..+|+.|...|-
T Consensus 81 G~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~~E 112 (120)
T COG1734 81 GICEECGEPIPEARLEARPTARLCIECQERAE 112 (120)
T ss_pred cchhccCCcCCHHHHhhCcchHHHHHHHHHHH
Confidence 38999998722 11222336789999998774
No 21
>PRK11019 hypothetical protein; Provisional
Probab=57.73 E-value=4.6 Score=35.41 Aligned_cols=37 Identities=22% Similarity=0.530 Sum_probs=25.7
Q ss_pred CCCCCcCCCCCCC--CceecchhHHHHHHhhhhhhcCCCc
Q 010188 27 ENRECADCKAKGP--RWASVNLGIFICMQCSGIHRSLGVH 64 (516)
Q Consensus 27 gNk~CADCGA~~P--~WASvn~GVFLC~~CSgIHRsLG~h 64 (516)
.-.+|.|||.+=| +|--+. ++-.|+.|...+...+.|
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 4579999998733 343333 778899999987654433
No 22
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=51.88 E-value=6.3 Score=39.60 Aligned_cols=31 Identities=32% Similarity=0.693 Sum_probs=27.1
Q ss_pred CCCCCCCcCCCCCC-CCceecchhHHHHHHhh
Q 010188 25 LPENRECADCKAKG-PRWASVNLGIFICMQCS 55 (516)
Q Consensus 25 ~PgNk~CADCGA~~-P~WASvn~GVFLC~~CS 55 (516)
.+.=..|+.||.+. +..+++-.|-++|..|.
T Consensus 151 ~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 151 GPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred ccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 35668999999984 57999999999999998
No 23
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=47.53 E-value=8.5 Score=32.44 Aligned_cols=33 Identities=18% Similarity=0.496 Sum_probs=21.8
Q ss_pred CCCCcCCCCCCCCc-eecchhHHHHHHhhhhhhc
Q 010188 28 NRECADCKAKGPRW-ASVNLGIFICMQCSGIHRS 60 (516)
Q Consensus 28 Nk~CADCGA~~P~W-ASvn~GVFLC~~CSgIHRs 60 (516)
...|.|||.+=|.= .-.-=|+..|+.|...+-.
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 46899999873321 1122377889999886643
No 24
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=47.19 E-value=14 Score=37.14 Aligned_cols=37 Identities=22% Similarity=0.505 Sum_probs=28.2
Q ss_pred HHHHHHHHhc-CCCCCCCcCCCCCCCCceecchhHHHHHHhhhhh
Q 010188 15 HRKILEGLLK-LPENRECADCKAKGPRWASVNLGIFICMQCSGIH 58 (516)
Q Consensus 15 ~~kiL~~Llk-~PgNk~CADCGA~~P~WASvn~GVFLC~~CSgIH 58 (516)
-++.++..++ .|.| .|-.||.....|. ++|..|.+.|
T Consensus 341 ~~~~~~~~~~~~p~~-~c~~cg~~~~~~~------~~c~~c~~~~ 378 (389)
T PRK11788 341 LRDLVGEQLKRKPRY-RCRNCGFTARTLY------WHCPSCKAWE 378 (389)
T ss_pred HHHHHHHHHhCCCCE-ECCCCCCCCccce------eECcCCCCcc
Confidence 3556665544 5565 5999999999997 7899999887
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=45.35 E-value=10 Score=30.94 Aligned_cols=34 Identities=35% Similarity=0.638 Sum_probs=23.2
Q ss_pred cCCCCCCCcCCCCCCC--CceecchhHHHHHHhhhhh
Q 010188 24 KLPENRECADCKAKGP--RWASVNLGIFICMQCSGIH 58 (516)
Q Consensus 24 k~PgNk~CADCGA~~P--~WASvn~GVFLC~~CSgIH 58 (516)
..++..+|.|||.+=| +|. ..-|+..|+.|...+
T Consensus 27 ~~~s~g~C~~Cg~~Ip~~Rl~-a~p~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 27 IGPSLRECEDCGEPIPEARRE-ALPGVTRCVSCQEIL 62 (63)
T ss_pred cCCCCCeeccCCCcChHHHHh-hcCCcCCcHHHHhhc
Confidence 3466789999998733 232 233778899997654
No 26
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=39.67 E-value=7.7 Score=37.19 Aligned_cols=34 Identities=29% Similarity=0.640 Sum_probs=27.9
Q ss_pred CCCCCCcCCCCCCCCceecchhHHHHH-Hhhhhhhc
Q 010188 26 PENRECADCKAKGPRWASVNLGIFICM-QCSGIHRS 60 (516)
Q Consensus 26 PgNk~CADCGA~~P~WASvn~GVFLC~-~CSgIHRs 60 (516)
|--+.|+-|| -..-|.+++.|.-.|. .|-.+|..
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 4567899999 6678999999998875 78888864
No 27
>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=38.90 E-value=9.6 Score=28.16 Aligned_cols=27 Identities=26% Similarity=0.812 Sum_probs=23.0
Q ss_pred CCCCCCcCCCCCCCCceecchhHHHHHHhh
Q 010188 26 PENRECADCKAKGPRWASVNLGIFICMQCS 55 (516)
Q Consensus 26 PgNk~CADCGA~~P~WASvn~GVFLC~~CS 55 (516)
..|..|..|++. |....=|-+.|.+|-
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCc
Confidence 345679999987 999999999999995
No 28
>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=38.49 E-value=22 Score=34.04 Aligned_cols=34 Identities=15% Similarity=0.333 Sum_probs=21.1
Q ss_pred CCCCCCcCCCCC--CCCceecchhHHHHHHhhhhhhc
Q 010188 26 PENRECADCKAK--GPRWASVNLGIFICMQCSGIHRS 60 (516)
Q Consensus 26 PgNk~CADCGA~--~P~WASvn~GVFLC~~CSgIHRs 60 (516)
..=-+|.+||.+ ..++-.+. ++-.|+.|...+-.
T Consensus 84 G~YG~Ce~CGe~I~~~RL~a~P-~a~~Ci~Cq~~~E~ 119 (159)
T TIGR02890 84 GTYGICEVCGKPIPYERLEAIP-TATTCVECQNRKEV 119 (159)
T ss_pred CCCCeecccCCcccHHHHhhCC-CcchhHHHHHHhhh
Confidence 334569999987 11222222 45689999987643
No 29
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=38.02 E-value=20 Score=34.09 Aligned_cols=37 Identities=14% Similarity=0.267 Sum_probs=23.2
Q ss_pred CCCCCCCcCCCCCCC-CceecchhHHHHHHhhhhhhcC
Q 010188 25 LPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRSL 61 (516)
Q Consensus 25 ~PgNk~CADCGA~~P-~WASvn~GVFLC~~CSgIHRsL 61 (516)
.+.--+|-+||.+=| .=.-+-=++..|+.|...|-..
T Consensus 108 ~gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~E~~ 145 (151)
T PRK10778 108 DEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIR 145 (151)
T ss_pred CCCCceeccCCCcccHHHHhcCCCccccHHHHHHHHHH
Confidence 466689999998711 1111112446899999877543
No 30
>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=37.89 E-value=6.9 Score=28.94 Aligned_cols=27 Identities=19% Similarity=0.582 Sum_probs=16.8
Q ss_pred CCCcCCCCC-CCCceecchhHHHHHHhh
Q 010188 29 RECADCKAK-GPRWASVNLGIFICMQCS 55 (516)
Q Consensus 29 k~CADCGA~-~P~WASvn~GVFLC~~CS 55 (516)
..|.+||.. .-+|..-+|+.-||..|.
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 778999999999999994
No 31
>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=30.59 E-value=6.1 Score=29.47 Aligned_cols=27 Identities=22% Similarity=0.600 Sum_probs=20.5
Q ss_pred CCcCCCCCCCCceecchhHHHHHHhhhh
Q 010188 30 ECADCKAKGPRWASVNLGIFICMQCSGI 57 (516)
Q Consensus 30 ~CADCGA~~P~WASvn~GVFLC~~CSgI 57 (516)
+|-.||+.. ....-..|-++|..|..|
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 589999876 455667899999999544
No 32
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=30.26 E-value=25 Score=31.43 Aligned_cols=34 Identities=24% Similarity=0.524 Sum_probs=24.1
Q ss_pred hcCCCCCCCcCCCCC--------CCCc---------eecchhHHHHHHhhh
Q 010188 23 LKLPENRECADCKAK--------GPRW---------ASVNLGIFICMQCSG 56 (516)
Q Consensus 23 lk~PgNk~CADCGA~--------~P~W---------ASvn~GVFLC~~CSg 56 (516)
.+.++-..|+|||.+ ..++ .+=.||-.+|..|..
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 456777899999987 1112 234689999999964
No 33
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=30.25 E-value=22 Score=27.98 Aligned_cols=37 Identities=24% Similarity=0.587 Sum_probs=30.2
Q ss_pred CCCCCcCCCCC-CCCceecchhH-HHHHHhhhhhhcCCC
Q 010188 27 ENRECADCKAK-GPRWASVNLGI-FICMQCSGIHRSLGV 63 (516)
Q Consensus 27 gNk~CADCGA~-~P~WASvn~GV-FLC~~CSgIHRsLG~ 63 (516)
..+.|..|+.. .|.|=....|- +||-.|.-..+..+.
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~ 40 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCC
Confidence 45789999975 78898888886 999999887777654
No 34
>PHA00080 DksA-like zinc finger domain containing protein
Probab=27.73 E-value=34 Score=28.75 Aligned_cols=35 Identities=26% Similarity=0.598 Sum_probs=23.4
Q ss_pred CCCCCCCcCCCCC--CCCceecchhHHHHHHhhhhhhc
Q 010188 25 LPENRECADCKAK--GPRWASVNLGIFICMQCSGIHRS 60 (516)
Q Consensus 25 ~PgNk~CADCGA~--~P~WASvn~GVFLC~~CSgIHRs 60 (516)
..+..+|.|||.. ..+|.-+. |+..|+.|...+-.
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 3456789999987 33343333 56679999887643
No 35
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=25.10 E-value=29 Score=32.64 Aligned_cols=37 Identities=27% Similarity=0.698 Sum_probs=26.3
Q ss_pred HHHHHHHhcCCCCCCCcCCCCCCCCceecchhHHHHHHhhhhhhcC
Q 010188 16 RKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSL 61 (516)
Q Consensus 16 ~kiL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSgIHRsL 61 (516)
+++|+.+........|.-||. .+|+ +|..|.|-|+.+
T Consensus 87 ~~lL~~~~~~~~~~~C~~Cgg--~rfv-------~C~~C~Gs~k~~ 123 (147)
T cd03031 87 RKLLKGIRARAGGGVCEGCGG--ARFV-------PCSECNGSCKVF 123 (147)
T ss_pred HHHHhhcccccCCCCCCCCCC--cCeE-------ECCCCCCcceEE
Confidence 445555544456667999994 4666 899999999865
No 36
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=24.57 E-value=37 Score=26.82 Aligned_cols=30 Identities=27% Similarity=0.563 Sum_probs=19.9
Q ss_pred CCcCCCCCCCCce--ecchhHHHHHHhhhhhhc
Q 010188 30 ECADCKAKGPRWA--SVNLGIFICMQCSGIHRS 60 (516)
Q Consensus 30 ~CADCGA~~P~WA--Svn~GVFLC~~CSgIHRs 60 (516)
.|+=||..-.-+- -+.=| +||..|..--..
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 4888988744333 35557 899999864333
No 37
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=24.22 E-value=2e+02 Score=32.10 Aligned_cols=94 Identities=15% Similarity=0.262 Sum_probs=47.5
Q ss_pred CCCCCCCcC-CCCC--CCCceecchh--HHHHHHhhhhhhcCCCcc-----ccccc----cccCCCCH-HHHHHHHh---
Q 010188 25 LPENRECAD-CKAK--GPRWASVNLG--IFICMQCSGIHRSLGVHI-----SKVRS----ATLDTWLP-EQVAFIQS--- 86 (516)
Q Consensus 25 ~PgNk~CAD-CGA~--~P~WASvn~G--VFLC~~CSgIHRsLG~hI-----SkVKS----LtLDsWt~-eeV~~Lq~--- 86 (516)
.++++.|+| |-.- +...+.+.-+ ..||+.|-.+=-++|+|- -.|.. +---.|+. |||++|..
T Consensus 10 ~~g~ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLea~~t 89 (438)
T KOG0457|consen 10 DPGGKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSVGAETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLEAAET 89 (438)
T ss_pred cCCCCCCCccHhHHhccceEEEeecCCCcchhHHHHhcccccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHHHHHH
Confidence 455555554 5432 3333333222 478999987555555441 22332 22235996 46777764
Q ss_pred --hChH--HHHHHHhhcCCCCCChhHHHHHHHHHHhhccccc
Q 010188 87 --MGNE--KANSYWEAELPPNYDRVGIENFIRAKYEEKRWVS 124 (516)
Q Consensus 87 --~GN~--~aN~iwEa~lPps~d~~~re~FIraKY~eKrFv~ 124 (516)
+||= .++.|= ..+..+.+++-.+.|++-.+..
T Consensus 90 ~G~GNW~dIA~hIG------tKtkeeck~hy~k~fv~s~~~~ 125 (438)
T KOG0457|consen 90 YGFGNWQDIADHIG------TKTKEECKEHYLKHFVNSPIFP 125 (438)
T ss_pred hCCCcHHHHHHHHc------ccchHHHHHHHHHHHhcCcccc
Confidence 3662 121111 2334556666677777654443
No 38
>KOG4080 consensus Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=23.33 E-value=50 Score=32.46 Aligned_cols=32 Identities=31% Similarity=0.744 Sum_probs=23.6
Q ss_pred HhcCCCC-CCCcCCCCCCCCceecchhHHHHHHhhh-hhhc
Q 010188 22 LLKLPEN-RECADCKAKGPRWASVNLGIFICMQCSG-IHRS 60 (516)
Q Consensus 22 Llk~PgN-k~CADCGA~~P~WASvn~GVFLC~~CSg-IHRs 60 (516)
+++.-.| +.|-.||.-.+.-+ ||.-|-+ ||+.
T Consensus 86 ~Lk~k~nl~~CP~CGh~k~a~~-------LC~~Cy~kV~ke 119 (176)
T KOG4080|consen 86 LLKPKDNLNTCPACGHIKPAHT-------LCDYCYAKVHKE 119 (176)
T ss_pred cccchhccccCcccCccccccc-------cHHHHHHHHHHH
Confidence 5665554 89999998877655 8999975 5654
No 39
>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors. HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.
Probab=22.41 E-value=26 Score=29.08 Aligned_cols=32 Identities=25% Similarity=0.479 Sum_probs=25.4
Q ss_pred CCcC-CCCCCCC-ceecchhHHHHHHhhhhhhcCC
Q 010188 30 ECAD-CKAKGPR-WASVNLGIFICMQCSGIHRSLG 62 (516)
Q Consensus 30 ~CAD-CGA~~P~-WASvn~GVFLC~~CSgIHRsLG 62 (516)
.+.| |+.--|. +..-+...+.|..| |.||+|-
T Consensus 20 ~a~DGCgEFm~~~g~eg~~~al~CaAC-gCHRnFH 53 (60)
T PF04770_consen 20 HAVDGCGEFMPSPGEEGTPEALKCAAC-GCHRNFH 53 (60)
T ss_pred cccccccccccCCCCCCCcccceeccc-Ccchhcc
Confidence 3667 8887777 77677888999999 7899873
No 40
>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=22.25 E-value=82 Score=25.08 Aligned_cols=33 Identities=24% Similarity=0.637 Sum_probs=26.8
Q ss_pred CCcCCCCC-CCCceecc-hhHHHHHHhhhhhhcCC
Q 010188 30 ECADCKAK-GPRWASVN-LGIFICMQCSGIHRSLG 62 (516)
Q Consensus 30 ~CADCGA~-~P~WASvn-~GVFLC~~CSgIHRsLG 62 (516)
.|..|+.. -|.|=... -+..||-.|.-..|..|
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~ 35 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG 35 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC
Confidence 59999975 67888765 78899999987777766
No 41
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=21.75 E-value=42 Score=27.36 Aligned_cols=40 Identities=23% Similarity=0.392 Sum_probs=27.8
Q ss_pred CCCCCCCcCCCCCCCCceecchhHHHHHHhhhhhhcCCCcccccc
Q 010188 25 LPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVR 69 (516)
Q Consensus 25 ~PgNk~CADCGA~~P~WASvn~GVFLC~~CSgIHRsLG~hISkVK 69 (516)
.+|-+.|.-||.. .-+--.||..+|..|- |++-..|.++|
T Consensus 13 GkGsr~C~vCg~~--~gliRkygL~~CRqCF---Re~A~~iGF~K 52 (54)
T PTZ00218 13 GKGSRQCRVCSNR--HGLIRKYGLNVCRQCF---RENAELIGFHK 52 (54)
T ss_pred CCCCCeeecCCCc--chhhhhcCcchhhHHH---HHhhHhcCeee
Confidence 3577999999975 3445589999999996 44444444443
No 42
>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=21.57 E-value=60 Score=27.78 Aligned_cols=31 Identities=16% Similarity=0.540 Sum_probs=25.1
Q ss_pred CCCCCcCCCCCCCCceecchhHHHHHHhhhhhhc
Q 010188 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (516)
Q Consensus 27 gNk~CADCGA~~P~WASvn~GVFLC~~CSgIHRs 60 (516)
..+.|.=||.... ...||++.|..|.+..|-
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 468999999999998874
No 43
>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=21.50 E-value=23 Score=25.77 Aligned_cols=32 Identities=25% Similarity=0.694 Sum_probs=22.9
Q ss_pred CcCCCCC-CCCceecchhHH-HHHHhhhhhhcCC
Q 010188 31 CADCKAK-GPRWASVNLGIF-ICMQCSGIHRSLG 62 (516)
Q Consensus 31 CADCGA~-~P~WASvn~GVF-LC~~CSgIHRsLG 62 (516)
|..|+.. .|.|=....|-. ||-.|.-.+|..|
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 8899975 889998888776 9999988777644
No 44
>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=21.37 E-value=10 Score=27.33 Aligned_cols=29 Identities=24% Similarity=0.563 Sum_probs=15.0
Q ss_pred CCcCCCCCCC-CceecchhHHHHHHhhhhh
Q 010188 30 ECADCKAKGP-RWASVNLGIFICMQCSGIH 58 (516)
Q Consensus 30 ~CADCGA~~P-~WASvn~GVFLC~~CSgIH 58 (516)
.|.+||..=+ .=.-+-=+..+|..|...|
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 4889986511 1111122667788888765
No 45
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=21.17 E-value=27 Score=36.18 Aligned_cols=33 Identities=18% Similarity=0.462 Sum_probs=23.4
Q ss_pred CCCCCCcCCCCCCCCceecchhHHHHHHhhhhhh
Q 010188 26 PENRECADCKAKGPRWASVNLGIFICMQCSGIHR 59 (516)
Q Consensus 26 PgNk~CADCGA~~P~WASvn~GVFLC~~CSgIHR 59 (516)
.....|-+||... -=....-|-.||..|.-|..
T Consensus 9 ~~~~~Cp~Cg~~~-iv~d~~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 9 EEKLVCPECGSDK-LIYDYERGEIVCADCGLVIE 41 (310)
T ss_pred ccCCcCcCCCCCC-eeEECCCCeEeecccCCccc
Confidence 4456899999742 22245679999999987653
No 46
>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=21.02 E-value=42 Score=28.69 Aligned_cols=31 Identities=19% Similarity=0.613 Sum_probs=25.2
Q ss_pred CCCCCcCCCCCCCCceecchhHHHHHHhhhhhhc
Q 010188 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (516)
Q Consensus 27 gNk~CADCGA~~P~WASvn~GVFLC~~CSgIHRs 60 (516)
.|..|.=||.... ...||++.|..|.+..|-
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 4678999997543 468999999999998874
Done!