Query 010564
Match_columns 507
No_of_seqs 163 out of 1170
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 02:00:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010564.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010564hhsearch_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 4.7E-45 1E-49 363.1 13.3 272 2-326 8-287 (287)
2 PLN03119 putative ADP-ribosyla 100.0 6.7E-40 1.4E-44 347.2 12.4 157 3-163 7-172 (648)
3 PLN03131 hypothetical protein; 100.0 5.8E-38 1.3E-42 334.6 11.0 153 3-159 7-168 (705)
4 PF01412 ArfGap: Putative GTPa 100.0 2.1E-37 4.5E-42 271.4 6.7 109 8-116 2-116 (116)
5 smart00105 ArfGap Putative GTP 100.0 6E-36 1.3E-40 261.1 8.8 103 17-119 1-110 (112)
6 COG5347 GTPase-activating prot 100.0 4.8E-33 1E-37 281.7 9.8 115 5-119 6-128 (319)
7 PLN03114 ADP-ribosylation fact 100.0 2.5E-29 5.4E-34 256.4 14.8 115 4-118 7-130 (395)
8 KOG0704 ADP-ribosylation facto 99.9 1.7E-28 3.7E-33 249.1 5.0 90 1-90 1-90 (386)
9 KOG0706 Predicted GTPase-activ 99.9 5.7E-27 1.2E-31 243.6 5.9 87 4-90 8-94 (454)
10 KOG0705 GTPase-activating prot 99.9 4.2E-26 9E-31 242.6 5.3 119 3-121 497-621 (749)
11 KOG0521 Putative GTPase activa 99.9 4.1E-23 8.9E-28 229.4 4.1 111 9-119 416-534 (785)
12 KOG0702 Predicted GTPase-activ 99.8 1.7E-18 3.8E-23 182.4 14.8 122 3-125 9-138 (524)
13 KOG0818 GTPase-activating prot 99.8 1.3E-19 2.9E-24 191.1 3.1 102 15-116 4-119 (669)
14 KOG1117 Rho- and Arf-GTPase ac 99.7 2.2E-18 4.7E-23 189.8 2.8 108 11-118 290-405 (1186)
15 KOG0521 Putative GTPase activa 94.1 0.013 2.8E-07 67.2 -0.4 72 15-88 626-698 (785)
16 PRK00085 recO DNA repair prote 79.2 1.1 2.3E-05 43.6 1.7 33 15-47 145-178 (247)
17 TIGR00613 reco DNA repair prot 77.9 2.4 5.2E-05 41.0 3.6 66 15-92 143-209 (241)
18 PF00643 zf-B_box: B-box zinc 68.8 2 4.3E-05 31.2 0.5 34 18-51 2-36 (42)
19 PRK12495 hypothetical protein; 59.9 3.9 8.5E-05 41.3 0.8 38 7-48 28-67 (226)
20 COG1381 RecO Recombinational D 55.2 5.6 0.00012 39.9 1.0 31 16-46 151-182 (251)
21 COG1734 DksA DnaK suppressor p 49.3 8.5 0.00018 35.3 1.1 31 20-50 81-112 (120)
22 PF11781 RRN7: RNA polymerase 47.6 6.5 0.00014 29.0 0.1 28 17-47 6-33 (36)
23 KOG3362 Predicted BBOX Zn-fing 44.8 6.2 0.00013 37.7 -0.4 34 17-51 116-150 (156)
24 PRK11019 hypothetical protein; 41.2 8.4 0.00018 33.7 -0.1 36 18-54 35-72 (88)
25 PF01286 XPA_N: XPA protein N- 38.9 6.7 0.00014 29.0 -0.9 27 20-46 4-31 (34)
26 smart00401 ZnF_GATA zinc finge 36.1 15 0.00033 28.7 0.6 37 18-54 2-40 (52)
27 TIGR02419 C4_traR_proteo phage 35.9 13 0.00027 30.4 0.1 34 15-49 27-62 (63)
28 PF08271 TF_Zn_Ribbon: TFIIB z 34.6 6.2 0.00013 29.4 -1.7 27 21-48 2-28 (43)
29 PF00320 GATA: GATA zinc finge 27.7 18 0.00039 26.3 -0.3 32 22-53 1-34 (36)
30 cd00202 ZnF_GATA Zinc finger D 26.8 58 0.0012 25.9 2.4 33 21-53 1-35 (54)
31 TIGR02890 spore_yteA sporulati 26.5 31 0.00067 33.0 1.0 34 17-51 84-119 (159)
32 COG2174 RPL34A Ribosomal prote 26.0 36 0.00078 30.4 1.2 33 15-47 30-79 (93)
33 cd07171 NR_DBD_ER DNA-binding 24.6 33 0.00071 29.3 0.7 31 18-51 2-32 (82)
34 PF01258 zf-dskA_traR: Prokary 24.4 9.7 0.00021 27.4 -2.1 30 20-49 4-34 (36)
35 cd07173 NR_DBD_AR DNA-binding 24.2 49 0.0011 28.3 1.7 31 18-51 2-32 (82)
36 PHA00080 DksA-like zinc finger 23.5 42 0.00091 28.2 1.2 34 17-51 29-64 (72)
37 PRK13715 conjugal transfer pro 23.1 30 0.00065 29.1 0.2 33 19-51 34-67 (73)
38 COG1997 RPL43A Ribosomal prote 22.3 34 0.00075 30.3 0.4 33 15-49 31-63 (89)
39 PRK10778 dksA RNA polymerase-b 22.2 55 0.0012 31.0 1.8 37 15-51 107-144 (151)
40 PRK00423 tfb transcription ini 22.1 27 0.00059 36.0 -0.3 34 16-50 8-41 (310)
41 cd06968 NR_DBD_ROR DNA-binding 21.4 44 0.00095 29.3 0.9 31 18-51 4-34 (95)
42 cd07170 NR_DBD_ERR DNA-binding 21.0 40 0.00087 29.7 0.6 30 19-51 4-33 (97)
43 KOG0457 Histone acetyltransfer 20.3 90 0.002 34.6 3.1 28 406-433 374-401 (438)
No 1
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=4.7e-45 Score=363.12 Aligned_cols=272 Identities=35% Similarity=0.495 Sum_probs=189.1
Q ss_pred ChHHHHHHHHHHhcCCCCCCcccCCCCCCCceecchhHHHhHHhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhchh
Q 010564 2 NFYVFMQILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNE 81 (507)
Q Consensus 2 ~~~k~ekiL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISkVKSLsLD~Wt~eEV~~Mq~gGN~ 81 (507)
..+.++++|++||+.|+|+.|||||+++|+|||+|+|||||++|+||||+||+|||+||||+||.|++|+|+.|+..||.
T Consensus 8 ~~~~~~~~l~~Ll~~~~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~~GN~ 87 (287)
T KOG0703|consen 8 SNERNKRRLRELLREPDNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMISMGNA 87 (287)
T ss_pred ccchHHHHHHHHHcCcccCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHHHcch
Confidence 35688999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCCChh----hHHHHHHHHhhhcccccCCCCCCCCCCccccccccccCCCCCCCCCCCCCCCcchhHhh
Q 010564 82 KANSYWEAELPPNYDRV----GIENFIRAKYEEKRWVSRDGQANSPPRGLEEKASIHWQRPGEKSGHGYTDNSENLSEER 157 (507)
Q Consensus 82 raN~iwEa~lPps~d~~----~re~FIraKY~eKrF~~~~g~~~~Ps~~~~ek~~~~~qr~~~~sg~~~~~s~~~~f~er 157 (507)
++|.|||++||..++++ .+|+|||+|||.|+|+.++..-....+..++... |...+..+.....+...+ ..
T Consensus 88 ~an~~~ea~~p~~~~~p~~d~~~e~FIR~KYE~kkf~~~~~~~~s~~~~~~~~~k----~~~~~~~~~~~s~s~~~~-~~ 162 (287)
T KOG0703|consen 88 KANSYYEAKLPDPFRRPGPDDLVEQFIRDKYERKKFLDPEEDITSKPGSRDEESK----RSDKRSRKLSSSLSRSFV-KS 162 (287)
T ss_pred hhhhhccccCCccccCCChHHHHHHHHHHHHhhhhhccchhhcccCCCccccccc----ccccCccccccchhhhhh-hh
Confidence 99999999999887654 4999999999999999986221222222222211 121222222222222222 21
Q ss_pred hcCCCCCCCCCCCccccccCCCCCCCCCcccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCcccccccccCCCCCCCC
Q 010564 158 KHVQAPSTKDSVPAARISLPLPPRGPDQVVAITKPQQTESTVAPAGATNQSSDANLAVPPPKVDFASDLFDMLSGDSPNE 237 (507)
Q Consensus 158 ~~~~~~~~k~~~patr~~~p~~~~~p~~v~p~pkpq~~eP~~~~~~~~~~~~~~~~~a~pPKvd~AtDLFdmLsmD~~te 237 (507)
.+ ...-+.+. +... +.......++..+.......++. +|.+.|.+++
T Consensus 163 ~r-------~~~~~~~~--~~~s--------------------~~~~~~~~~~~~~~~i~~~~~~~-~~~s~~n~~~--- 209 (287)
T KOG0703|consen 163 AR-------EDQLKYFL--PKTS--------------------QPVDDLATFQGPIASPHNLQTTY-SLNSTLNIFG--- 209 (287)
T ss_pred cc-------cccccccc--ccCC--------------------CCchhhhhccCccccccchheee-cccccccccc---
Confidence 11 11111111 1110 11111222222234456666777 8888888777
Q ss_pred CCccc----ccCCCccccccccccccCcccccCCCCcccCCCCCcccccccccCCCCCCCCCCCCCCchhhhhhHHhhhc
Q 010564 238 NSSEA----ASADDNLWAGFQSAVETSTAEKKDSTKAVESSPQSATGIEDLFKDSPSLATPSSSEKPQKDLKNDIMSLFE 313 (507)
Q Consensus 238 n~sea----ss~dDn~waGFqsA~~~sta~k~~~~~a~eS~~qStsgiEDlFkdsp~~~~~~~~~~~qk~~KndImsLfe 313 (507)
+..++ + +.+..|+.|+.+...-+ +...+..+..+....-...+ ++++.+.... . . .|++||
T Consensus 210 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~-~~~~~~~~~~s~~~~f~~~~-~~~~~~~~~~----~------~-~~~~~~- 274 (287)
T KOG0703|consen 210 SGKEAADSFT-LRAARFAPLAVAFSTVT-EDLVPFLQRNSLSEGFMEKT-LSKPKRWFGT----Q------Q-SKSSLF- 274 (287)
T ss_pred CccccCCCcc-cccccccccccccccCc-cccccccccccccccccCcc-cccccccccc----C------c-cccccc-
Confidence 22222 3 78888888887766655 76777777777666666666 7777333322 1 5 899999
Q ss_pred cCcccCcchhhHH
Q 010564 314 KSNMVSPFAMHQQ 326 (507)
Q Consensus 314 ksn~~spf~~~qq 326 (507)
+-..+.||..++|
T Consensus 275 ~~~~~~~~~~~~~ 287 (287)
T KOG0703|consen 275 FLDGNVPFGSKES 287 (287)
T ss_pred cccccccccccCC
Confidence 9999999988764
No 2
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=100.00 E-value=6.7e-40 Score=347.16 Aligned_cols=157 Identities=27% Similarity=0.531 Sum_probs=144.2
Q ss_pred hHHHHHHHHHHhcCCCCCCcccCCCCCCCceecchhHHHhHHhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhchhH
Q 010564 3 FYVFMQILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEK 82 (507)
Q Consensus 3 ~~k~ekiL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISkVKSLsLD~Wt~eEV~~Mq~gGN~r 82 (507)
.+++++||++|++.|+|++|+|||+.+|.|||+|||||||++|+||||+|| +|||||+||+|+++||++|+.+||.+
T Consensus 7 qERnekILreLlklPgNk~CADCgs~~P~WASiNlGIFICi~CSGIHRsLG---hRVKSLSLDkWT~EEVe~Mk~gGN~~ 83 (648)
T PLN03119 7 EERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREFT---HRVKSVSMSKFTSKEVEVLQNGGNQR 83 (648)
T ss_pred HHHHHHHHHHHhhCcCCCccccCCCCCCCceeeccceEEeccchhhhccCC---ceeeccccCCCCHHHHHHHHHhchHH
Confidence 378999999999999999999999999999999999999999999999998 59999999999999999999999999
Q ss_pred HHHHHhhcCC-------CCCChhhHHHHHHHHhhhcccccCCCCCCCCCCccccccccccCCCCCCCCCCCCCCCc--ch
Q 010564 83 ANSYWEAELP-------PNYDRVGIENFIRAKYEEKRWVSRDGQANSPPRGLEEKASIHWQRPGEKSGHGYTDNSE--NL 153 (507)
Q Consensus 83 aN~iwEa~lP-------ps~d~~~re~FIraKY~eKrF~~~~g~~~~Ps~~~~ek~~~~~qr~~~~sg~~~~~s~~--~~ 153 (507)
+|+|||++|+ ...+...+|+|||.||++|+|+.+...++++++.+++++.+...| .+++||+|.++++ ++
T Consensus 84 AN~iyeanw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~~~~~~d~p~~~~~~~~~~~~~~~-~~~s~h~~s~sp~y~~~ 162 (648)
T PLN03119 84 AREIYLKNWDHQRQRLPENSNAERVREFIKNVYVQKKYAGANDADKPSKDSQDHVSSEDMTR-RANSYHSYSQSPPYDYQ 162 (648)
T ss_pred HHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhccCcCCCCCCccccccccccccccc-ccccCCCCCCCCCcccc
Confidence 9999999875 334566789999999999999999999999988899998877555 4999999999999 79
Q ss_pred hHhhhcCCCC
Q 010564 154 SEERKHVQAP 163 (507)
Q Consensus 154 f~er~~~~~~ 163 (507)
|||||..+-.
T Consensus 163 ye~rr~~~~~ 172 (648)
T PLN03119 163 YEERRYGKIP 172 (648)
T ss_pred hhhhhccccc
Confidence 9999977654
No 3
>PLN03131 hypothetical protein; Provisional
Probab=100.00 E-value=5.8e-38 Score=334.60 Aligned_cols=153 Identities=28% Similarity=0.510 Sum_probs=138.0
Q ss_pred hHHHHHHHHHHhcCCCCCCcccCCCCCCCceecchhHHHhHHhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhchhH
Q 010564 3 FYVFMQILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEK 82 (507)
Q Consensus 3 ~~k~ekiL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISkVKSLsLD~Wt~eEV~~Mq~gGN~r 82 (507)
-++++++|++|++.|+|++|+||++++|.|||++||||||++|+||||.|| +|||||+||+|++++|++|+.+||.+
T Consensus 7 qErnekiLreLlk~PgNk~CADCga~~P~WASiNlGIFICi~CSGIHRsLg---hRVKSVTLD~WtdeEV~~Mk~gGN~~ 83 (705)
T PLN03131 7 EERNEKIIRGLMKLPPNRRCINCNSLGPQFVCTNFWTFICMTCSGIHREFT---HRVKSVSMSKFTSQDVEALQNGGNQR 83 (705)
T ss_pred HHHHHHHHHHHhhCcCCCccccCCCCCCCeeEeccceEEchhchhhhcccC---cccccccCCCCCHHHHHHHHHhccHH
Confidence 478999999999999999999999999999999999999999999999998 49999999999999999999999999
Q ss_pred HHHHHhhcCC-------CCCChhhHHHHHHHHhhhcccccCCCCCCCCCCccccccccccCCCCCCCCCCCCCCCcc--h
Q 010564 83 ANSYWEAELP-------PNYDRVGIENFIRAKYEEKRWVSRDGQANSPPRGLEEKASIHWQRPGEKSGHGYTDNSEN--L 153 (507)
Q Consensus 83 aN~iwEa~lP-------ps~d~~~re~FIraKY~eKrF~~~~g~~~~Ps~~~~ek~~~~~qr~~~~sg~~~~~s~~~--~ 153 (507)
+|+|||++|+ ...+...+|+|||.|||+|||+.+...++++...+.-+..+...|+ ..++|+|++|++| +
T Consensus 84 AN~iyeanwd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa~~~s~d~pprd~q~~r~~e~e~rr-~~syh~~SqSPpY~~~ 162 (705)
T PLN03131 84 AREIYLKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKYAGGKTHDKPPRDLQRIRSHEDETRR-ACSYHSYSQSPPYDFQ 162 (705)
T ss_pred HHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhhhcCCCCCCCchhhhhhhcccccccc-cccccCCCcCCCcccc
Confidence 9999998874 3445567899999999999999998887877776666666666677 7899999999995 9
Q ss_pred hHhhhc
Q 010564 154 SEERKH 159 (507)
Q Consensus 154 f~er~~ 159 (507)
|||||.
T Consensus 163 yedrRy 168 (705)
T PLN03131 163 YEDRRY 168 (705)
T ss_pred cccccc
Confidence 999987
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=2.1e-37 Score=271.41 Aligned_cols=109 Identities=57% Similarity=1.048 Sum_probs=91.3
Q ss_pred HHHHHHhcCCCCCCcccCCCCCCCceecchhHHHhHHhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhchhHHHHHH
Q 010564 8 QILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYW 87 (507)
Q Consensus 8 kiL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISkVKSLsLD~Wt~eEV~~Mq~gGN~raN~iw 87 (507)
++|+.|++.|+|++|||||+++|+|||++||||||+.|+|+||.||+|||+||||+||+|++++|+.|+.+||.++|++|
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 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCC------CCCChhhHHHHHHHHhhhcccccC
Q 010564 88 EAELP------PNYDRVGIENFIRAKYEEKRWVSR 116 (507)
Q Consensus 88 Ea~lP------ps~d~~~re~FIraKY~eKrF~~~ 116 (507)
|++.+ +..+...+++||++||++++|+.+
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=6e-36 Score=261.06 Aligned_cols=103 Identities=58% Similarity=1.015 Sum_probs=96.3
Q ss_pred CCCCCcccCCCCCCCceecchhHHHhHHhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhchhHHHHHHhhcCCCC--
Q 010564 17 PENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYWEAELPPN-- 94 (507)
Q Consensus 17 PgNk~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISkVKSLsLD~Wt~eEV~~Mq~gGN~raN~iwEa~lPps-- 94 (507)
|+|++||||++++|+|||++||||||+.|+|+||.||+|||+||||+||+|++++|++|+.+||.++|+|||+++++.
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 589999999999999999999999999999999999999999999999999999999999999999999999998642
Q ss_pred -----CChhhHHHHHHHHhhhcccccCCCC
Q 010564 95 -----YDRVGIENFIRAKYEEKRWVSRDGQ 119 (507)
Q Consensus 95 -----~d~~~re~FIraKY~eKrF~~~~g~ 119 (507)
.+...+++||+.||++++|+.+.+.
T Consensus 81 ~~~~~~~~~~~~~fI~~KY~~k~f~~~~~~ 110 (112)
T smart00105 81 KPPDSDDQQKYESFIAAKYEEKLFVPPESA 110 (112)
T ss_pred CCCCCchHHHHHHHHHHHHHhhhccccccC
Confidence 2356899999999999999988664
No 6
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=99.98 E-value=4.8e-33 Score=281.72 Aligned_cols=115 Identities=45% Similarity=0.860 Sum_probs=105.7
Q ss_pred HHHHHHHHHhcCCCCCCcccCCCCCCCceecchhHHHhHHhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhchhHHH
Q 010564 5 VFMQILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKAN 84 (507)
Q Consensus 5 k~ekiL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISkVKSLsLD~Wt~eEV~~Mq~gGN~raN 84 (507)
..+++|..|.+.++|+.|||||+.+|+|||+|||||||++|+||||+||+||++||||+||+|+.+||++|+.+||.++|
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 45788889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcC------C--CCCChhhHHHHHHHHhhhcccccCCCC
Q 010564 85 SYWEAEL------P--PNYDRVGIENFIRAKYEEKRWVSRDGQ 119 (507)
Q Consensus 85 ~iwEa~l------P--ps~d~~~re~FIraKY~eKrF~~~~g~ 119 (507)
.||+.++ | ..||...+++||+.||++++|+.....
T Consensus 86 ~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~~~~ 128 (319)
T COG5347 86 RFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDDSSS 128 (319)
T ss_pred hHhccCCCcccccccccccCHHHHHHHHHHHHHhhhccccccC
Confidence 9999864 2 345677899999999999999987443
No 7
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.96 E-value=2.5e-29 Score=256.39 Aligned_cols=115 Identities=37% Similarity=0.645 Sum_probs=99.7
Q ss_pred HHHHHHHHHHhcCCCCCCcccCCCCCCCceecchhHHHhHHhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhchhHH
Q 010564 4 YVFMQILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKA 83 (507)
Q Consensus 4 ~k~ekiL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISkVKSLsLD~Wt~eEV~~Mq~gGN~ra 83 (507)
+...++|+.|+..|+|++|+|||+++|.|+|++||||||+.|+||||.||+||++||||+||+|++++|++|+.+||.++
T Consensus 7 ~d~~~vfrkL~~kPgNk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~Ws~eqL~~Mk~GGN~rA 86 (395)
T PLN03114 7 NDKISVFKKLKAKSDNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSSEQLKMMIYGGNNRA 86 (395)
T ss_pred ccHHHHHHHHHhCcCCCcCccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCCCCHHHHHHHHHhcCHHH
Confidence 44567899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhcC-CC------CCCh--hhHHHHHHHHhhhcccccCCC
Q 010564 84 NSYWEAEL-PP------NYDR--VGIENFIRAKYEEKRWVSRDG 118 (507)
Q Consensus 84 N~iwEa~l-Pp------s~d~--~~re~FIraKY~eKrF~~~~g 118 (507)
|.||+.+. .. .|+- ..+.+-+.+|++++.+.....
T Consensus 87 ~~fF~qhG~~~~~~~~~KY~S~aA~~Yre~L~keVa~~~a~~~~ 130 (395)
T PLN03114 87 QVFFKQYGWSDGGKTEAKYTSRAADLYKQILAKEVAKSKAEEEL 130 (395)
T ss_pred HHHHHHcCCCCCCCcccccCCHHHHHHHHHHHHHHHHhhhcccc
Confidence 99998763 11 1221 234555889999988875544
No 8
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=99.95 E-value=1.7e-28 Score=249.09 Aligned_cols=90 Identities=41% Similarity=0.759 Sum_probs=85.4
Q ss_pred CChHHHHHHHHHHhcCCCCCCcccCCCCCCCceecchhHHHhHHhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhch
Q 010564 1 MNFYVFMQILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGN 80 (507)
Q Consensus 1 m~~~k~ekiL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISkVKSLsLD~Wt~eEV~~Mq~gGN 80 (507)
|-+-+.++.|..|....+|+.|+||++.+|+|||++||||||++|+|+||.||+|||+|||||||+|.+.||+.|+.+||
T Consensus 1 masprtrr~L~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN 80 (386)
T KOG0704|consen 1 MASPRTRRVLLELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGN 80 (386)
T ss_pred CCChHHHHHHHhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccc
Confidence 55678889998888778999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHhhc
Q 010564 81 EKANSYWEAE 90 (507)
Q Consensus 81 ~raN~iwEa~ 90 (507)
+++++|++.+
T Consensus 81 ~~~~eFL~s~ 90 (386)
T KOG0704|consen 81 ERFREFLSSQ 90 (386)
T ss_pred hhHHHHHhhC
Confidence 9999999865
No 9
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.93 E-value=5.7e-27 Score=243.61 Aligned_cols=87 Identities=45% Similarity=0.818 Sum_probs=83.5
Q ss_pred HHHHHHHHHHhcCCCCCCcccCCCCCCCceecchhHHHhHHhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhchhHH
Q 010564 4 YVFMQILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKA 83 (507)
Q Consensus 4 ~k~ekiL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISkVKSLsLD~Wt~eEV~~Mq~gGN~ra 83 (507)
+....+++.|...++||.|||||+++|.|+||+||||||+.|+++||+||+||++|||..||+|+.+||+.|+.+||.+|
T Consensus 8 ~d~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA 87 (454)
T KOG0706|consen 8 QDIQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANA 87 (454)
T ss_pred hhHHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhH
Confidence 44567899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhc
Q 010564 84 NSYWEAE 90 (507)
Q Consensus 84 N~iwEa~ 90 (507)
+.|+..+
T Consensus 88 ~~FFkqh 94 (454)
T KOG0706|consen 88 RVFFKQH 94 (454)
T ss_pred HHHHHHc
Confidence 9999876
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=4.2e-26 Score=242.62 Aligned_cols=119 Identities=40% Similarity=0.784 Sum_probs=107.7
Q ss_pred hHHHHHHHHHHhcCCCCCCcccCCCCCCCceecchhHHHhHHhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhchhH
Q 010564 3 FYVFMQILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEK 82 (507)
Q Consensus 3 ~~k~ekiL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISkVKSLsLD~Wt~eEV~~Mq~gGN~r 82 (507)
++-....|+.|...+||..|+||+.++|.|||+|+|+++|++|+||||.||.|+|+||+|.||.|..|.+..|..+||+.
T Consensus 497 sqsea~a~qairn~rgn~~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl~~Vm~aiGN~~ 576 (749)
T KOG0705|consen 497 SQSEAMALQAIRNMRGNSHCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVELLKVMSAIGNDL 576 (749)
T ss_pred hhhhHHHHHHHhcCcCCceeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHHHHHHHHhhhhH
Confidence 34456678889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcC-----C-CCCChhhHHHHHHHHhhhcccccCCCCCC
Q 010564 83 ANSYWEAEL-----P-PNYDRVGIENFIRAKYEEKRWVSRDGQAN 121 (507)
Q Consensus 83 aN~iwEa~l-----P-ps~d~~~re~FIraKY~eKrF~~~~g~~~ 121 (507)
+|.+||..+ | +.+.++.+|+|||+||++|.|..+.....
T Consensus 577 AN~vWE~~~~G~~KPs~~s~REEkErwIr~KYeqklFLaPl~~te 621 (749)
T KOG0705|consen 577 ANSVWEGSSQGQTKPSPDSSREEKERWIRAKYEQKLFLAPLPCTE 621 (749)
T ss_pred HHHHhhhhccCCcCCCccccHHHHHHHHHHHHHHHhhcCCCCCCC
Confidence 999999754 2 34568899999999999999998766533
No 11
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.87 E-value=4.1e-23 Score=229.35 Aligned_cols=111 Identities=48% Similarity=0.926 Sum_probs=102.6
Q ss_pred HHHHHhcCCCCCCcccCCCCCCCceecchhHHHhHHhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhchhHHHHHHh
Q 010564 9 ILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYWE 88 (507)
Q Consensus 9 iL~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISkVKSLsLD~Wt~eEV~~Mq~gGN~raN~iwE 88 (507)
.++.+.+.|+|..|+|||++.|+|+++|+||.+|++|+|+||+||+|||+|+||+||.|.++.+.+++.+||..+|.+||
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 36788899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCC--------CChhhHHHHHHHHhhhcccccCCCC
Q 010564 89 AELPPN--------YDRVGIENFIRAKYEEKRWVSRDGQ 119 (507)
Q Consensus 89 a~lPps--------~d~~~re~FIraKY~eKrF~~~~g~ 119 (507)
+.++.. .++..++.||++||++++|..+...
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
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.78 E-value=1.7e-18 Score=182.43 Aligned_cols=122 Identities=30% Similarity=0.605 Sum_probs=109.8
Q ss_pred hHHHHHHHHHHhcCCCCCCcccCCCCCC-CceecchhHHHhHHhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhchh
Q 010564 3 FYVFMQILEGLLKLPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNE 81 (507)
Q Consensus 3 ~~k~ekiL~~Llk~PgNk~CADCGA~~P-~WASvn~GVFLC~~CSGIHRsLG~hISkVKSLsLD~Wt~eEV~~Mq~gGN~ 81 (507)
-+.|+|+||.|+++|+|++|++|+...+ .|+++.-|-|+|+.|+|..|.|.. -+|||+|+|.+++..||..|+.+||+
T Consensus 9 E~~~ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~~-ahRvksiSmttft~qevs~lQshgNq 87 (524)
T KOG0702|consen 9 EYDYEKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLNP-AHRVKSISMTTFTDQEVSFLQSHGNQ 87 (524)
T ss_pred hhHHHHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccCCC-ccccceeeeeeccccchHHHhhcchh
Confidence 4567999999999999999999999988 999999999999999999999875 48999999999999999999999999
Q ss_pred HHHHHHhh-------cCCCCCChhhHHHHHHHHhhhcccccCCCCCCCCCC
Q 010564 82 KANSYWEA-------ELPPNYDRVGIENFIRAKYEEKRWVSRDGQANSPPR 125 (507)
Q Consensus 82 raN~iwEa-------~lPps~d~~~re~FIraKY~eKrF~~~~g~~~~Ps~ 125 (507)
.+.+||.. .+|+..+....++|||.||+.|||+....+.+-++.
T Consensus 88 ~~k~i~fkl~D~q~S~vPD~rn~~~~kef~q~~y~~kr~~v~~n~~k~~s~ 138 (524)
T KOG0702|consen 88 VCKEIWFKLFDFQRSNVPDSRNPQKVKEFQQEKYVKKRYYVPKNQMKIPSY 138 (524)
T ss_pred hhhhhhhcchhhhhccCCCcccchhhHHHHhhhhccceeecCccccccccc
Confidence 99999975 357777778899999999999999988776654443
No 13
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.76 E-value=1.3e-19 Score=191.07 Aligned_cols=102 Identities=42% Similarity=0.804 Sum_probs=91.7
Q ss_pred cCCCCCCcccCCCCCCCceecchhHHHhHHhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhchhHHHHHHhhcCCC-
Q 010564 15 KLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYWEAELPP- 93 (507)
Q Consensus 15 k~PgNk~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISkVKSLsLD~Wt~eEV~~Mq~gGN~raN~iwEa~lPp- 93 (507)
+...-+.|+|||+++|.|||++-|+|||.+|+.+||.||.|||.||+|.-..|.++.|++...+.|..+|.|||..|-+
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 4556789999999999999999999999999999999999999999999999999999999999999999999987621
Q ss_pred -----------CCCh--hhHHHHHHHHhhhcccccC
Q 010564 94 -----------NYDR--VGIENFIRAKYEEKRWVSR 116 (507)
Q Consensus 94 -----------s~d~--~~re~FIraKY~eKrF~~~ 116 (507)
..|. +.+++|||+||+...|+.+
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 1122 3589999999999999984
No 14
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.71 E-value=2.2e-18 Score=189.80 Aligned_cols=108 Identities=43% Similarity=0.802 Sum_probs=97.8
Q ss_pred HHHhcCCCCCCcccCCCCCCCceecchhHHHhHHhhhhhhcCCCccceeeeccCCC--CCHHHHHHHHhhchhHHHHHHh
Q 010564 11 EGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDT--WLPEQVAFIQSMGNEKANSYWE 88 (507)
Q Consensus 11 ~~Llk~PgNk~CADCGA~~P~WASvn~GVFLC~~CSGIHRsLG~hISkVKSLsLD~--Wt~eEV~~Mq~gGN~raN~iwE 88 (507)
+.+.....|+.|+|||+..|.||++|+++.||-.|+|-||.||..+|+|+|++||. |+.+-|+++..+||.++|.||.
T Consensus 290 eriW~ne~nr~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~Fwa 369 (1186)
T KOG1117|consen 290 ERIWLNEENRECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANRFWA 369 (1186)
T ss_pred HHHHhccccccccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCcccccccc
Confidence 34445789999999999999999999999999999999999999999999999995 9999999999999999999999
Q ss_pred hcCCCCC------ChhhHHHHHHHHhhhcccccCCC
Q 010564 89 AELPPNY------DRVGIENFIRAKYEEKRWVSRDG 118 (507)
Q Consensus 89 a~lPps~------d~~~re~FIraKY~eKrF~~~~g 118 (507)
.++|++. ....|++||.+||.+.+|.....
T Consensus 370 ~nl~~~e~lh~dssp~~r~~fi~~Kykeg~fRk~~~ 405 (1186)
T KOG1117|consen 370 GNLPPNEHLHPDSSPSTRRQFIKEKYKEGKFRKEHP 405 (1186)
T ss_pred cCCCCccccCCCCCcchhhhHHHHHhhccccccccc
Confidence 9998754 24579999999999998876544
No 15
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=94.05 E-value=0.013 Score=67.24 Aligned_cols=72 Identities=21% Similarity=0.230 Sum_probs=61.5
Q ss_pred cCCCCCCcccCCCC-CCCceecchhHHHhHHhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhchhHHHHHHh
Q 010564 15 KLPENRECADCKAK-GPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYWE 88 (507)
Q Consensus 15 k~PgNk~CADCGA~-~P~WASvn~GVFLC~~CSGIHRsLG~hISkVKSLsLD~Wt~eEV~~Mq~gGN~raN~iwE 88 (507)
....+-.|++|++. ...|+++++.+-+|..|+++|+.++.+++..+++.|++..+ |..+...||...+..|.
T Consensus 626 ~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~~~~ 698 (785)
T KOG0521|consen 626 KASSDGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHHATA 698 (785)
T ss_pred HhccCccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchhhhh
Confidence 44568899999985 88899999999999999999999999999999999888766 77777778877776664
No 16
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=79.22 E-value=1.1 Score=43.58 Aligned_cols=33 Identities=30% Similarity=0.523 Sum_probs=27.6
Q ss_pred cCCCCCCcccCCCCCC-CceecchhHHHhHHhhh
Q 010564 15 KLPENRECADCKAKGP-RWASVNLGIFICMQCSG 47 (507)
Q Consensus 15 k~PgNk~CADCGA~~P-~WASvn~GVFLC~~CSG 47 (507)
-.|.-..|+-||.... .|.+...|.++|..|..
T Consensus 145 ~~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~ 178 (247)
T PRK00085 145 YGLDLDHCAVCGAPGDHRYFSPKEGGAVCSECGD 178 (247)
T ss_pred CccchhhHhcCCCCCCceEEecccCCcccccccC
Confidence 4466689999998744 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=77.87 E-value=2.4 Score=41.04 Aligned_cols=66 Identities=18% Similarity=0.285 Sum_probs=41.8
Q ss_pred cCCCCCCcccCCCCCC-CceecchhHHHhHHhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhchhHHHHHHhhcCC
Q 010564 15 KLPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYWEAELP 92 (507)
Q Consensus 15 k~PgNk~CADCGA~~P-~WASvn~GVFLC~~CSGIHRsLG~hISkVKSLsLD~Wt~eEV~~Mq~gGN~raN~iwEa~lP 92 (507)
-.|.-..|+.||..++ .|.++..|.|+|..|..... +. ..++.+.+..++.+=+.....+.+.+++
T Consensus 143 ~~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~~~----~~--------~~~~~~~l~~~~~l~~~~~~~~~~~~~~ 209 (241)
T TIGR00613 143 YALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEKDP----HA--------IPIDPKLLRLLRYLLKLDLEKLLSIEIK 209 (241)
T ss_pred CCcccCccCCCCCcCCCceEchhcCeEEChhhCccCC----Cc--------eecCHHHHHHHHHHHcCCHHHhceeecC
Confidence 3467789999998544 68899999999999976421 10 1245566666665544444444444443
No 18
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=68.85 E-value=2 Score=31.16 Aligned_cols=34 Identities=12% Similarity=0.335 Sum_probs=29.4
Q ss_pred CCCCcccCCCCCCCceecchhHHHhHHhhhh-hhc
Q 010564 18 ENRECADCKAKGPRWASVNLGIFICMQCSGI-HRS 51 (507)
Q Consensus 18 gNk~CADCGA~~P~WASvn~GVFLC~~CSGI-HRs 51 (507)
.+..|..|......|.+.+-+++||..|... |+.
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 3678999999889999999999999999998 886
No 19
>PRK12495 hypothetical protein; Provisional
Probab=59.90 E-value=3.9 Score=41.26 Aligned_cols=38 Identities=26% Similarity=0.373 Sum_probs=27.6
Q ss_pred HHHHHHHhc--CCCCCCcccCCCCCCCceecchhHHHhHHhhhh
Q 010564 7 MQILEGLLK--LPENRECADCKAKGPRWASVNLGIFICMQCSGI 48 (507)
Q Consensus 7 ekiL~~Llk--~PgNk~CADCGA~~P~WASvn~GVFLC~~CSGI 48 (507)
+++-+.|++ ...++.|-+||.+=|.+ -|+.+|..|..+
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 344444443 36899999999998832 699999999754
No 20
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=55.20 E-value=5.6 Score=39.89 Aligned_cols=31 Identities=32% Similarity=0.729 Sum_probs=26.9
Q ss_pred CCCCCCcccCCCC-CCCceecchhHHHhHHhh
Q 010564 16 LPENRECADCKAK-GPRWASVNLGIFICMQCS 46 (507)
Q Consensus 16 ~PgNk~CADCGA~-~P~WASvn~GVFLC~~CS 46 (507)
.+.=..|+.||.. ++..++.-.|-++|.+|.
T Consensus 151 ~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 151 GPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred ccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 3555899999998 557999999999999998
No 21
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=49.31 E-value=8.5 Score=35.35 Aligned_cols=31 Identities=16% Similarity=0.429 Sum_probs=21.4
Q ss_pred CCcccCCCCCC-CceecchhHHHhHHhhhhhh
Q 010564 20 RECADCKAKGP-RWASVNLGIFICMQCSGIHR 50 (507)
Q Consensus 20 k~CADCGA~~P-~WASvn~GVFLC~~CSGIHR 50 (507)
-+|.+||.+=| .=.-.--+..+|+.|...|-
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 38999999722 22223346789999998774
No 22
>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=47.58 E-value=6.5 Score=28.97 Aligned_cols=28 Identities=25% Similarity=0.767 Sum_probs=23.7
Q ss_pred CCCCCcccCCCCCCCceecchhHHHhHHhhh
Q 010564 17 PENRECADCKAKGPRWASVNLGIFICMQCSG 47 (507)
Q Consensus 17 PgNk~CADCGA~~P~WASvn~GVFLC~~CSG 47 (507)
..|..|..|++. |....=|.++|.+|-.
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCce
Confidence 456679999998 8889999999999953
No 23
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=44.81 E-value=6.2 Score=37.73 Aligned_cols=34 Identities=29% Similarity=0.640 Sum_probs=28.2
Q ss_pred CCCCCcccCCCCCCCceecchhHHHhH-Hhhhhhhc
Q 010564 17 PENRECADCKAKGPRWASVNLGIFICM-QCSGIHRS 51 (507)
Q Consensus 17 PgNk~CADCGA~~P~WASvn~GVFLC~-~CSGIHRs 51 (507)
|--+.|+-|| -..-|.+++.|.-+|. .|-.+|.+
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 4567999999 6666999999998875 89999965
No 24
>PRK11019 hypothetical protein; Provisional
Probab=41.20 E-value=8.4 Score=33.72 Aligned_cols=36 Identities=22% Similarity=0.553 Sum_probs=25.3
Q ss_pred CCCCcccCCCCCC--CceecchhHHHhHHhhhhhhcCCC
Q 010564 18 ENRECADCKAKGP--RWASVNLGIFICMQCSGIHRSLGV 54 (507)
Q Consensus 18 gNk~CADCGA~~P--~WASvn~GVFLC~~CSGIHRsLG~ 54 (507)
.-.+|.|||..=| +|--+. ++-.|+.|...+...+.
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 4579999999743 343333 67889999998754433
No 25
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=38.86 E-value=6.7 Score=28.95 Aligned_cols=27 Identities=19% Similarity=0.582 Sum_probs=16.8
Q ss_pred CCcccCCCC-CCCceecchhHHHhHHhh
Q 010564 20 RECADCKAK-GPRWASVNLGIFICMQCS 46 (507)
Q Consensus 20 k~CADCGA~-~P~WASvn~GVFLC~~CS 46 (507)
..|.+|+.. .-+|..-+|+.-||..|.
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 479999986 777999999999999994
No 26
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=36.12 E-value=15 Score=28.74 Aligned_cols=37 Identities=24% Similarity=0.587 Sum_probs=30.5
Q ss_pred CCCCcccCCCC-CCCceecchhH-HHhHHhhhhhhcCCC
Q 010564 18 ENRECADCKAK-GPRWASVNLGI-FICMQCSGIHRSLGV 54 (507)
Q Consensus 18 gNk~CADCGA~-~P~WASvn~GV-FLC~~CSGIHRsLG~ 54 (507)
..+.|..|+.. -|.|=....|- +||-.|.-..+..+.
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~ 40 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCC
Confidence 45789999985 78898888886 999999988877654
No 27
>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=35.93 E-value=13 Score=30.40 Aligned_cols=34 Identities=35% Similarity=0.638 Sum_probs=23.3
Q ss_pred cCCCCCCcccCCCCCC--CceecchhHHHhHHhhhhh
Q 010564 15 KLPENRECADCKAKGP--RWASVNLGIFICMQCSGIH 49 (507)
Q Consensus 15 k~PgNk~CADCGA~~P--~WASvn~GVFLC~~CSGIH 49 (507)
..++...|.|||..=| +|. ..-|+..|..|...+
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 3466789999999733 222 233778899998754
No 28
>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=34.64 E-value=6.2 Score=29.38 Aligned_cols=27 Identities=22% Similarity=0.600 Sum_probs=21.0
Q ss_pred CcccCCCCCCCceecchhHHHhHHhhhh
Q 010564 21 ECADCKAKGPRWASVNLGIFICMQCSGI 48 (507)
Q Consensus 21 ~CADCGA~~P~WASvn~GVFLC~~CSGI 48 (507)
+|-.||+.. ......-|-++|..|..|
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-BB
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCCCE
Confidence 699999977 455677899999999654
No 29
>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=27.71 E-value=18 Score=26.31 Aligned_cols=32 Identities=25% Similarity=0.694 Sum_probs=23.1
Q ss_pred cccCCCC-CCCceecchhHH-HhHHhhhhhhcCC
Q 010564 22 CADCKAK-GPRWASVNLGIF-ICMQCSGIHRSLG 53 (507)
Q Consensus 22 CADCGA~-~P~WASvn~GVF-LC~~CSGIHRsLG 53 (507)
|..|+.. .|.|=....|-. ||-.|.-.+|..+
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 889988887776 9999988877654
No 30
>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=26.84 E-value=58 Score=25.87 Aligned_cols=33 Identities=24% Similarity=0.637 Sum_probs=27.2
Q ss_pred CcccCCCC-CCCceecc-hhHHHhHHhhhhhhcCC
Q 010564 21 ECADCKAK-GPRWASVN-LGIFICMQCSGIHRSLG 53 (507)
Q Consensus 21 ~CADCGA~-~P~WASvn-~GVFLC~~CSGIHRsLG 53 (507)
.|..|+.. -|.|=... -+..||-.|.-..|..+
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~ 35 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHG 35 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcC
Confidence 59999986 67788765 78899999998887766
No 31
>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=26.51 E-value=31 Score=32.96 Aligned_cols=34 Identities=15% Similarity=0.319 Sum_probs=21.5
Q ss_pred CCCCCcccCCCC--CCCceecchhHHHhHHhhhhhhc
Q 010564 17 PENRECADCKAK--GPRWASVNLGIFICMQCSGIHRS 51 (507)
Q Consensus 17 PgNk~CADCGA~--~P~WASvn~GVFLC~~CSGIHRs 51 (507)
..=-.|.+||.. ..++-.+ -++-.|+.|...+-.
T Consensus 84 G~YG~Ce~CGe~I~~~RL~a~-P~a~~Ci~Cq~~~E~ 119 (159)
T TIGR02890 84 GTYGICEVCGKPIPYERLEAI-PTATTCVECQNRKEV 119 (159)
T ss_pred CCCCeecccCCcccHHHHhhC-CCcchhHHHHHHhhh
Confidence 344679999987 1122222 246789999987643
No 32
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=26.00 E-value=36 Score=30.37 Aligned_cols=33 Identities=27% Similarity=0.624 Sum_probs=23.5
Q ss_pred cCCCCCCcccCCCC-------CC----------CceecchhHHHhHHhhh
Q 010564 15 KLPENRECADCKAK-------GP----------RWASVNLGIFICMQCSG 47 (507)
Q Consensus 15 k~PgNk~CADCGA~-------~P----------~WASvn~GVFLC~~CSG 47 (507)
+.++--.|+|||.+ -| .=+.=.||-.+|..|..
T Consensus 30 K~~~~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~ 79 (93)
T COG2174 30 KKPTIPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVR 79 (93)
T ss_pred ccCCCCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHHH
Confidence 55677899999987 11 11234789999999974
No 33
>cd07171 NR_DBD_ER DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ER interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Estrogen receptor is a transcription regulator that mediates the biological effects of hormone estrogen. The binding of estrogen to the receptor triggers the dimerization and the binding of the receptor dimer to estrogen response element, which is a palindromic inverted repeat: 5'GGTCAnnnTGACC-3', of target genes. Through ER, estrogen regulates development, reproduction and homeostasis. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well-conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserv
Probab=24.63 E-value=33 Score=29.26 Aligned_cols=31 Identities=19% Similarity=0.613 Sum_probs=25.5
Q ss_pred CCCCcccCCCCCCCceecchhHHHhHHhhhhhhc
Q 010564 18 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 51 (507)
Q Consensus 18 gNk~CADCGA~~P~WASvn~GVFLC~~CSGIHRs 51 (507)
.|..|.=||.... ...||++.|..|.+..|-
T Consensus 2 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 2 DTHFCAVCSDYAS---GYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 4678999997553 578999999999998874
No 34
>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=24.38 E-value=9.7 Score=27.41 Aligned_cols=30 Identities=23% Similarity=0.533 Sum_probs=16.3
Q ss_pred CCcccCCCCCC-CceecchhHHHhHHhhhhh
Q 010564 20 RECADCKAKGP-RWASVNLGIFICMQCSGIH 49 (507)
Q Consensus 20 k~CADCGA~~P-~WASvn~GVFLC~~CSGIH 49 (507)
..|.+||..=+ .=.-+--+..+|..|...|
T Consensus 4 g~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~~ 34 (36)
T PF01258_consen 4 GICEDCGEPIPEERLVAVPGATLCVECQERR 34 (36)
T ss_dssp SB-TTTSSBEEHHHHHHCTTECS-HHHHHHH
T ss_pred CCccccCChHHHHHHHhCCCcEECHHHhCcc
Confidence 35999998511 1112223677899998765
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=24.16 E-value=49 Score=28.26 Aligned_cols=31 Identities=16% Similarity=0.540 Sum_probs=25.4
Q ss_pred CCCCcccCCCCCCCceecchhHHHhHHhhhhhhc
Q 010564 18 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 51 (507)
Q Consensus 18 gNk~CADCGA~~P~WASvn~GVFLC~~CSGIHRs 51 (507)
..+.|.=||.... ...||++.|..|.+..|-
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 4677999997654 568999999999998874
No 36
>PHA00080 DksA-like zinc finger domain containing protein
Probab=23.50 E-value=42 Score=28.17 Aligned_cols=34 Identities=26% Similarity=0.591 Sum_probs=23.1
Q ss_pred CCCCCcccCCCCC--CCceecchhHHHhHHhhhhhhc
Q 010564 17 PENRECADCKAKG--PRWASVNLGIFICMQCSGIHRS 51 (507)
Q Consensus 17 PgNk~CADCGA~~--P~WASvn~GVFLC~~CSGIHRs 51 (507)
.+...|.|||..= .+|.-+. |+..|+.|...+-.
T Consensus 29 ~~~~~C~~Cg~~Ip~~Rl~a~P-~~~~Cv~Cq~~~E~ 64 (72)
T PHA00080 29 PSATHCEECGDPIPEARREAVP-GCRTCVSCQEILEL 64 (72)
T ss_pred CCCCEecCCCCcCcHHHHHhCC-CccCcHHHHHHHHH
Confidence 4556899999873 3333333 56779999987643
No 37
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=23.11 E-value=30 Score=29.15 Aligned_cols=33 Identities=18% Similarity=0.516 Sum_probs=22.1
Q ss_pred CCCcccCCCCCCC-ceecchhHHHhHHhhhhhhc
Q 010564 19 NRECADCKAKGPR-WASVNLGIFICMQCSGIHRS 51 (507)
Q Consensus 19 Nk~CADCGA~~P~-WASvn~GVFLC~~CSGIHRs 51 (507)
...|.|||..=|. =.-.--|+..|+.|...+-.
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 4689999997442 11223378899999886643
No 38
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=22.27 E-value=34 Score=30.28 Aligned_cols=33 Identities=18% Similarity=0.480 Sum_probs=25.3
Q ss_pred cCCCCCCcccCCCCCCCceecchhHHHhHHhhhhh
Q 010564 15 KLPENRECADCKAKGPRWASVNLGIFICMQCSGIH 49 (507)
Q Consensus 15 k~PgNk~CADCGA~~P~WASvn~GVFLC~~CSGIH 49 (507)
+...-..|-.|+.. .---+..||+.|..|-..-
T Consensus 31 ~~~~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 31 QQRAKHVCPFCGRT--TVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred HHhcCCcCCCCCCc--ceeeeccCeEEcCCCCCee
Confidence 34556799999998 4556788999999996543
No 39
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=22.23 E-value=55 Score=31.03 Aligned_cols=37 Identities=14% Similarity=0.297 Sum_probs=23.6
Q ss_pred cCCCCCCcccCCCCCC-CceecchhHHHhHHhhhhhhc
Q 010564 15 KLPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRS 51 (507)
Q Consensus 15 k~PgNk~CADCGA~~P-~WASvn~GVFLC~~CSGIHRs 51 (507)
..+.--+|-+||..=| .=.-+--++..|+.|...|-.
T Consensus 107 ~~gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~E~ 144 (151)
T PRK10778 107 EDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEI 144 (151)
T ss_pred hCCCCceeccCCCcccHHHHhcCCCccccHHHHHHHHH
Confidence 3456689999998711 111112245789999987754
No 40
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=22.13 E-value=27 Score=36.05 Aligned_cols=34 Identities=18% Similarity=0.421 Sum_probs=24.4
Q ss_pred CCCCCCcccCCCCCCCceecchhHHHhHHhhhhhh
Q 010564 16 LPENRECADCKAKGPRWASVNLGIFICMQCSGIHR 50 (507)
Q Consensus 16 ~PgNk~CADCGA~~P~WASvn~GVFLC~~CSGIHR 50 (507)
......|-+||... --....-|-.||..|.-|..
T Consensus 8 ~~~~~~Cp~Cg~~~-iv~d~~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 8 EEEKLVCPECGSDK-LIYDYERGEIVCADCGLVIE 41 (310)
T ss_pred cccCCcCcCCCCCC-eeEECCCCeEeecccCCccc
Confidence 34557899999742 22345779999999988654
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=21.39 E-value=44 Score=29.30 Aligned_cols=31 Identities=29% Similarity=0.718 Sum_probs=25.5
Q ss_pred CCCCcccCCCCCCCceecchhHHHhHHhhhhhhc
Q 010564 18 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 51 (507)
Q Consensus 18 gNk~CADCGA~~P~WASvn~GVFLC~~CSGIHRs 51 (507)
++..|.=||.... ...||++.|..|.+..|-
T Consensus 4 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 4 EVIPCKICGDKSS---GIHYGVITCEGCKGFFRR 34 (95)
T ss_pred cccCCcccCCcCc---ceEECceeehhhHHhhHH
Confidence 5678999998654 458999999999998874
No 42
>cd07170 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription
Probab=21.04 E-value=40 Score=29.72 Aligned_cols=30 Identities=20% Similarity=0.555 Sum_probs=24.4
Q ss_pred CCCcccCCCCCCCceecchhHHHhHHhhhhhhc
Q 010564 19 NRECADCKAKGPRWASVNLGIFICMQCSGIHRS 51 (507)
Q Consensus 19 Nk~CADCGA~~P~WASvn~GVFLC~~CSGIHRs 51 (507)
+..|.=||.... ...||++.|..|.+..|-
T Consensus 4 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 33 (97)
T cd07170 4 KRLCLVCGDIAS---GYHYGVASCEACKAFFKR 33 (97)
T ss_pred CCCCeecCCcCc---ceEECceeehhhhHHHHH
Confidence 457999997654 458999999999998874
No 43
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=20.33 E-value=90 Score=34.59 Aligned_cols=28 Identities=14% Similarity=0.264 Sum_probs=19.5
Q ss_pred hhHHHHHHhhhccccccccCCchhHHHH
Q 010564 406 ADLQKLMQAMSMVPTHQVAAGPADIQKL 433 (507)
Q Consensus 406 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 433 (507)
.|.++|.+....+|.+-++-+-+.+++.
T Consensus 374 e~E~~lc~~~~~~p~~yLe~~~vl~~e~ 401 (438)
T KOG0457|consen 374 EDEKRLCQELKILPKLYLELKEVLSREI 401 (438)
T ss_pred hhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence 5677888888888888776655544443
Done!