Query 011159
Match_columns 492
No_of_seqs 190 out of 1195
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 08:46:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011159.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011159hhsearch_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 3.3E-46 7.2E-51 369.8 12.3 275 8-359 5-287 (287)
2 PLN03119 putative ADP-ribosyla 100.0 9E-41 2E-45 352.5 14.3 160 8-170 3-172 (648)
3 PLN03131 hypothetical protein; 100.0 1.6E-38 3.4E-43 337.7 13.9 161 8-171 3-173 (705)
4 PF01412 ArfGap: Putative GTPa 100.0 6.3E-38 1.4E-42 273.3 7.1 108 17-124 2-115 (116)
5 smart00105 ArfGap Putative GTP 100.0 1.6E-36 3.5E-41 263.3 9.3 103 26-128 1-110 (112)
6 COG5347 GTPase-activating prot 100.0 6E-34 1.3E-38 287.0 10.4 114 14-127 6-127 (319)
7 PLN03114 ADP-ribosylation fact 100.0 8.6E-28 1.9E-32 244.4 19.2 114 14-127 8-130 (395)
8 KOG0704 ADP-ribosylation facto 100.0 2.3E-29 5.1E-34 254.4 5.6 116 12-127 3-121 (386)
9 KOG0706 Predicted GTPase-activ 99.9 6.6E-28 1.4E-32 249.6 6.6 85 15-99 10-94 (454)
10 KOG0705 GTPase-activating prot 99.9 4.4E-26 9.5E-31 241.7 6.0 146 16-161 501-655 (749)
11 KOG0521 Putative GTPase activa 99.9 4.6E-23 9.9E-28 227.9 3.6 112 18-129 416-535 (785)
12 KOG0702 Predicted GTPase-activ 99.8 2.4E-18 5.2E-23 180.7 14.9 125 8-133 5-137 (524)
13 KOG0818 GTPase-activating prot 99.8 2.4E-19 5.2E-24 188.6 3.3 101 25-125 5-119 (669)
14 KOG1117 Rho- and Arf-GTPase ac 99.7 2.9E-18 6.3E-23 188.2 3.2 105 20-124 290-402 (1186)
15 KOG0521 Putative GTPase activa 94.5 0.0092 2E-07 68.1 -0.3 72 24-97 626-698 (785)
16 PRK00085 recO DNA repair prote 83.6 0.69 1.5E-05 44.7 2.1 34 23-56 144-178 (247)
17 TIGR00613 reco DNA repair prot 78.2 2.8 6.2E-05 40.3 4.2 34 24-57 143-177 (241)
18 PF00643 zf-B_box: B-box zinc 73.4 2.2 4.8E-05 30.8 1.6 34 27-60 2-36 (42)
19 PRK12495 hypothetical protein; 68.9 3 6.5E-05 41.9 1.9 38 16-57 28-67 (226)
20 COG1381 RecO Recombinational D 61.9 4.1 8.9E-05 40.6 1.4 37 19-55 145-182 (251)
21 PRK11019 hypothetical protein; 60.7 4 8.8E-05 35.5 1.0 37 27-64 35-73 (88)
22 COG1734 DksA DnaK suppressor p 59.4 5.1 0.00011 36.6 1.4 31 29-59 81-112 (120)
23 TIGR02419 C4_traR_proteo phage 54.1 7.5 0.00016 31.6 1.4 34 24-58 27-62 (63)
24 PRK11788 tetratricopeptide rep 53.2 12 0.00026 37.3 3.0 39 15-59 341-379 (389)
25 PF11781 RRN7: RNA polymerase 50.6 7.6 0.00016 28.5 0.9 27 26-55 6-32 (36)
26 PRK10778 dksA RNA polymerase-b 50.6 9.7 0.00021 35.9 1.8 38 24-61 107-145 (151)
27 PRK13715 conjugal transfer pro 48.3 12 0.00026 31.3 1.8 33 28-60 34-67 (73)
28 KOG3362 Predicted BBOX Zn-fing 43.6 7.7 0.00017 37.0 -0.0 34 26-60 116-150 (156)
29 TIGR02890 spore_yteA sporulati 40.2 16 0.00035 34.7 1.6 36 25-60 83-119 (159)
30 PF01286 XPA_N: XPA protein N- 40.0 7.9 0.00017 28.5 -0.4 27 29-55 4-31 (34)
31 PF08271 TF_Zn_Ribbon: TFIIB z 39.4 8.8 0.00019 28.5 -0.3 27 30-57 2-28 (43)
32 PHA00080 DksA-like zinc finger 34.2 26 0.00057 29.3 1.7 35 25-60 28-64 (72)
33 PF12536 DUF3734: Patatin phos 33.0 18 0.00039 32.1 0.6 11 475-485 68-78 (108)
34 COG2174 RPL34A Ribosomal prote 32.6 27 0.00058 31.1 1.6 33 24-56 30-79 (93)
35 smart00401 ZnF_GATA zinc finge 32.5 27 0.00058 27.3 1.4 37 27-63 2-40 (52)
36 PRK02770 S-adenosylmethionine 29.3 23 0.0005 33.1 0.7 42 360-403 40-90 (139)
37 KOG0457 Histone acetyltransfer 27.2 55 0.0012 36.1 3.1 93 25-123 10-124 (438)
38 TIGR02420 dksA RNA polymerase- 27.1 31 0.00068 30.4 1.1 31 25-55 77-108 (110)
39 PF01258 zf-dskA_traR: Prokary 27.0 9.4 0.0002 27.4 -1.8 30 29-58 4-34 (36)
40 PF00320 GATA: GATA zinc finge 25.9 33 0.00071 24.9 0.8 32 31-62 1-34 (36)
41 cd07173 NR_DBD_AR DNA-binding 25.7 48 0.001 28.2 1.9 31 27-60 2-32 (82)
42 cd07171 NR_DBD_ER DNA-binding 25.0 42 0.00092 28.5 1.5 31 27-60 2-32 (82)
43 PF14471 DUF4428: Domain of un 23.7 37 0.0008 26.7 0.8 30 30-60 1-32 (51)
44 smart00782 PhnA_Zn_Ribbon PhnA 22.3 50 0.0011 25.8 1.3 34 22-56 2-44 (47)
45 KOG3507 DNA-directed RNA polym 22.2 33 0.00071 28.5 0.2 23 29-54 21-43 (62)
46 COG1997 RPL43A Ribosomal prote 21.9 53 0.0011 29.1 1.5 31 25-57 32-62 (89)
47 PTZ00074 60S ribosomal protein 21.2 54 0.0012 30.9 1.5 31 26-56 39-86 (135)
48 PRK04059 rpl34e 50S ribosomal 20.9 51 0.0011 29.0 1.2 31 26-56 32-79 (88)
49 cd07170 NR_DBD_ERR DNA-binding 20.8 53 0.0011 28.9 1.3 30 28-60 4-33 (97)
50 cd06968 NR_DBD_ROR DNA-binding 20.7 57 0.0012 28.5 1.5 31 27-60 4-34 (95)
51 COG2158 Uncharacterized protei 20.4 38 0.00083 30.9 0.4 24 40-63 52-77 (112)
52 PRK00423 tfb transcription ini 20.4 45 0.00097 34.3 0.9 32 26-58 9-40 (310)
53 TIGR01385 TFSII transcription 20.4 76 0.0016 33.1 2.5 30 26-55 256-293 (299)
No 1
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=3.3e-46 Score=369.81 Aligned_cols=275 Identities=32% Similarity=0.438 Sum_probs=191.1
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEcccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhh
Q 011159 8 SKELNAKHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSM 87 (492)
Q Consensus 8 SKrl~ar~ekiL~~Llk~PgNk~CADCGA~nP~WaSvnfGVFLC~~CSGIHRsLGvHISkVKSLsMDtWT~eEV~~Lk~g 87 (492)
.+...++++++|++||+.|+|+.|||||++.|+|||+|+|||||++|+||||+||+||||||||+||.|++|||++|+..
T Consensus 5 ~~~~~~~~~~~l~~Ll~~~~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~~ 84 (287)
T KOG0703|consen 5 EKGSNERNKRRLRELLREPDNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMISM 84 (287)
T ss_pred cccccchHHHHHHHHHcCcccCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHHH
Confidence 34567889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcHHHHHHHhhcCCCCCChh----hHHHHHHHHhhhCccccCCCCCCCCCCccccccCCCCCCCCCCCCCCCCCCCCCcc
Q 011159 88 GNEKSNSYWEAELPPNYDRV----GIENFIRAKYEEKRWIPRGGNTKSPSRVSEEKASFHRPLPSSSGHRYTNNINRVPD 163 (492)
Q Consensus 88 GN~~aN~iwEA~lPp~~Dr~----~~e~FIRaKYeeKrF~~~~~~~~~ps~~~~e~~~~~~~~~~r~Gh~~~sS~~~~~~ 163 (492)
||.++|+|||+.+|..+++. .+|+|||+|||.|+|+.++.......+.+++.... ...+.+.+|.+.+..+....
T Consensus 85 GN~~an~~~ea~~p~~~~~p~~d~~~e~FIR~KYE~kkf~~~~~~~~s~~~~~~~~~k~-~~~~~~~~~~s~s~~~~~~~ 163 (287)
T KOG0703|consen 85 GNAKANSYYEAKLPDPFRRPGPDDLVEQFIRDKYERKKFLDPEEDITSKPGSRDEESKR-SDKRSRKLSSSLSRSFVKSA 163 (287)
T ss_pred cchhhhhhccccCCccccCCChHHHHHHHHHHHHhhhhhccchhhcccCCCcccccccc-cccCccccccchhhhhhhhc
Confidence 99999999999999877654 39999999999999998762211112222111111 22344555555543222210
Q ss_pred cccCCCCCCCCCCCCCCCCcCCCcccccccccCCCCCCCCCCCCCCCCCCCCcchhhhhhhhhhhhcccCCCCCCCCCCC
Q 011159 164 VRNIAHPPNASNDIAAPKHSSPATVKVVQQVTPSLKIQEPVQNSEPTVPKSEPAKQEAITTAVIQHKKQNSEPAVPKYEP 243 (492)
Q Consensus 164 ~k~~~~~~~~~~~~~atr~~~~~~~~~~~~v~p~~k~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (492)
|-. . .+...+ ++..++ . +.... +.
T Consensus 164 r~~----------~--~~~~~~--------~~s~~~---------------~------~~~~~-----~~---------- 187 (287)
T KOG0703|consen 164 RED----------Q--LKYFLP--------KTSQPV---------------D------DLATF-----QG---------- 187 (287)
T ss_pred ccc----------c--cccccc--------cCCCCc---------------h------hhhhc-----cC----------
Confidence 000 0 000000 000000 0 00000 00
Q ss_pred CCcccCCCCCCcchhhcccccccccCCCCCCCCCCC----CCcccccccccccccccCCCCCCCcccccccchhhhhhhh
Q 011159 244 PKQEASTTPQRKVDYATDLFNLLCTDDSRENDSKTS----NDEKSCANLQSTNASTAEPINSSKATESKVQTRYRIEDLF 319 (492)
Q Consensus 244 ~~~~~~~~~~~k~d~~t~lf~ll~~d~~~en~s~~s----~d~~~~a~fqsa~~~~~~~~~~~~~~es~~~s~~~iedlf 319 (492)
. ........+++ +|+..|.+++ ++.++. +....|+.|+.+...+.+...+..+..+....-...+ ++
T Consensus 188 ---~-~~~i~~~~~~~-~~~s~~n~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~f~~~~-~~ 258 (287)
T KOG0703|consen 188 ---P-IASPHNLQTTY-SLNSTLNIFG---SGKEAADSFTLRAARFAPLAVAFSTVTEDLVPFLQRNSLSEGFMEKT-LS 258 (287)
T ss_pred ---c-cccccchheee-cccccccccc---CccccCCCcccccccccccccccccCccccccccccccccccccCcc-cc
Confidence 0 11456667777 8888888877 333332 7778888998888444477777766666665555555 88
Q ss_pred cCCCCCCCCcccccchhhhhhhhhhhcccCccCCchhhHH
Q 011159 320 MGSPSVIPSVSEKSQKDVKNDVMNLFGKSEMVSPFSIDQQ 359 (492)
Q Consensus 320 kdsp~~~~~~~~~~q~~~kndim~lfeks~~vspf~~hqq 359 (492)
++.+..+. . . .|++|| +-..+.||..++|
T Consensus 259 ~~~~~~~~---~------~-~~~~~~-~~~~~~~~~~~~~ 287 (287)
T KOG0703|consen 259 KPKRWFGT---Q------Q-SKSSLF-FLDGNVPFGSKES 287 (287)
T ss_pred cccccccc---C------c-cccccc-cccccccccccCC
Confidence 88444444 2 5 999999 9999999988765
No 2
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=100.00 E-value=9e-41 Score=352.49 Aligned_cols=160 Identities=27% Similarity=0.518 Sum_probs=148.3
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEcccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhh
Q 011159 8 SKELNAKHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSM 87 (492)
Q Consensus 8 SKrl~ar~ekiL~~Llk~PgNk~CADCGA~nP~WaSvnfGVFLC~~CSGIHRsLGvHISkVKSLsMDtWT~eEV~~Lk~g 87 (492)
|||+++|++++|++|+++|+|++|+|||+++|+|||++||||||++|+||||.|| +|||||+||+|+++||++|+.+
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 7899999999999999999999999999999999999999999999999999998 5999999999999999999999
Q ss_pred CcHHHHHHHhhcCCC-------CCChhhHHHHHHHHhhhCccccCCCCCCCCCCccccccCCCCCCCCCCCCCCCCCCCC
Q 011159 88 GNEKSNSYWEAELPP-------NYDRVGIENFIRAKYEEKRWIPRGGNTKSPSRVSEEKASFHRPLPSSSGHRYTNNINR 160 (492)
Q Consensus 88 GN~~aN~iwEA~lPp-------~~Dr~~~e~FIRaKYeeKrF~~~~~~~~~ps~~~~e~~~~~~~~~~r~Gh~~~sS~~~ 160 (492)
||+++|+|||++|++ ..+...+++|||.||++|||+.+...++++.+.++++..+..+++.++||++++|+.|
T Consensus 80 GN~~AN~iyeanw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~~~~~~d~p~~~~~~~~~~~~~~~~~~s~h~~s~sp~y 159 (648)
T PLN03119 80 GNQRAREIYLKNWDHQRQRLPENSNAERVREFIKNVYVQKKYAGANDADKPSKDSQDHVSSEDMTRRANSYHSYSQSPPY 159 (648)
T ss_pred chHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhccCcCCCCCCcccccccccccccccccccCCCCCCCCCc
Confidence 999999999998753 3355678999999999999999999999998899999988888899999999999997
Q ss_pred C---cccccCCCC
Q 011159 161 V---PDVRNIAHP 170 (492)
Q Consensus 161 ~---~~~k~~~~~ 170 (492)
. |||||+-+.
T Consensus 160 ~~~ye~rr~~~~~ 172 (648)
T PLN03119 160 DYQYEERRYGKIP 172 (648)
T ss_pred ccchhhhhccccc
Confidence 6 899995443
No 3
>PLN03131 hypothetical protein; Provisional
Probab=100.00 E-value=1.6e-38 Score=337.71 Aligned_cols=161 Identities=27% Similarity=0.520 Sum_probs=144.4
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEcccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhh
Q 011159 8 SKELNAKHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSM 87 (492)
Q Consensus 8 SKrl~ar~ekiL~~Llk~PgNk~CADCGA~nP~WaSvnfGVFLC~~CSGIHRsLGvHISkVKSLsMDtWT~eEV~~Lk~g 87 (492)
||+++++++++|++|+++|+|++|+||++++|+|||++||||||++|+||||.|| +|||||+||+|+++||++|+.+
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 6789999999999999999999999999999999999999999999999999998 4999999999999999999999
Q ss_pred CcHHHHHHHhhcCC-------CCCChhhHHHHHHHHhhhCccccCCCCCCCCCCccccccCCCCCCCCCCCCCCCCCCCC
Q 011159 88 GNEKSNSYWEAELP-------PNYDRVGIENFIRAKYEEKRWIPRGGNTKSPSRVSEEKASFHRPLPSSSGHRYTNNINR 160 (492)
Q Consensus 88 GN~~aN~iwEA~lP-------p~~Dr~~~e~FIRaKYeeKrF~~~~~~~~~ps~~~~e~~~~~~~~~~r~Gh~~~sS~~~ 160 (492)
||.++|+|||++|+ ...+...+++|||.||++|||+.....++++......+..+...++..++|++.+|..|
T Consensus 80 GN~~AN~iyeanwd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa~~~s~d~pprd~q~~r~~e~e~rr~~syh~~SqSPpY 159 (705)
T PLN03131 80 GNQRAREIYLKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKYAGGKTHDKPPRDLQRIRSHEDETRRACSYHSYSQSPPY 159 (705)
T ss_pred ccHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhhhcCCCCCCCchhhhhhhcccccccccccccCCCcCCCc
Confidence 99999999998774 33445678999999999999999998888887766666666677778899999999999
Q ss_pred C---cccccCCCCC
Q 011159 161 V---PDVRNIAHPP 171 (492)
Q Consensus 161 ~---~~~k~~~~~~ 171 (492)
. |||||+-+..
T Consensus 160 ~~~yedrRygk~~~ 173 (705)
T PLN03131 160 DFQYEDRRYGKQAG 173 (705)
T ss_pred cccccccccccccc
Confidence 7 8888855443
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=6.3e-38 Score=273.30 Aligned_cols=108 Identities=57% Similarity=1.049 Sum_probs=90.6
Q ss_pred HHHHHHhcCCCCCCCcCCCCCCCCeeEcccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhCcHHHHHHH
Q 011159 17 KILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYW 96 (492)
Q Consensus 17 kiL~~Llk~PgNk~CADCGA~nP~WaSvnfGVFLC~~CSGIHRsLGvHISkVKSLsMDtWT~eEV~~Lk~gGN~~aN~iw 96 (492)
++|+.|++.|+|++|||||+++|+|||++||||||+.|+|+||.||+|||+||||+||+|+++||+.|+.+||.++|++|
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------CCCChhhHHHHHHHHhhhCcccc
Q 011159 97 EAELP------PNYDRVGIENFIRAKYEEKRWIP 124 (492)
Q Consensus 97 EA~lP------p~~Dr~~~e~FIRaKYeeKrF~~ 124 (492)
|++.+ +..+...+++||++||++++|+.
T Consensus 82 e~~~~~~~~~~~~~~~~~~~~fI~~KY~~k~f~~ 115 (116)
T PF01412_consen 82 EANSPPPKKPPPSSDQEKREQFIRAKYVEKAFIS 115 (116)
T ss_dssp TTTSTTTTTHCTTSHHHHHHHHHHHHHTTHTTS-
T ss_pred HcCCCCCCCCCCCCcHHHHHHHHHHHHHhhhhcc
Confidence 99842 23345678999999999999985
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=1.6e-36 Score=263.29 Aligned_cols=103 Identities=57% Similarity=1.023 Sum_probs=96.1
Q ss_pred CCCCCCcCCCCCCCCeeEcccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhCcHHHHHHHhhcCCCCC-
Q 011159 26 PENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYWEAELPPNY- 104 (492)
Q Consensus 26 PgNk~CADCGA~nP~WaSvnfGVFLC~~CSGIHRsLGvHISkVKSLsMDtWT~eEV~~Lk~gGN~~aN~iwEA~lPp~~- 104 (492)
|+|++|||||+++|+|||++||||||+.|+|+||.||+|||+||||+||+|++++|++|+.+||.++|+|||+++++..
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 011159 105 ------DRVGIENFIRAKYEEKRWIPRGGN 128 (492)
Q Consensus 105 ------Dr~~~e~FIRaKYeeKrF~~~~~~ 128 (492)
+...+++||+.||++++|+.+++.
T Consensus 81 ~~~~~~~~~~~~~fI~~KY~~k~f~~~~~~ 110 (112)
T smart00105 81 KPPDSDDQQKYESFIAAKYEEKLFVPPESA 110 (112)
T ss_pred CCCCCchHHHHHHHHHHHHHhhhccccccC
Confidence 356789999999999999987664
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=6e-34 Score=286.96 Aligned_cols=114 Identities=46% Similarity=0.881 Sum_probs=104.5
Q ss_pred HHHHHHHHHhcCCCCCCCcCCCCCCCCeeEcccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhCcHHHH
Q 011159 14 KHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSN 93 (492)
Q Consensus 14 r~ekiL~~Llk~PgNk~CADCGA~nP~WaSvnfGVFLC~~CSGIHRsLGvHISkVKSLsMDtWT~eEV~~Lk~gGN~~aN 93 (492)
..+++|..|...++|+.|||||+++|+|||++||||||++|+||||+||+||++||||+||+|+.+||++|+.+||.++|
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 45778888899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcCC--------CCCChhhHHHHHHHHhhhCccccCCC
Q 011159 94 SYWEAELP--------PNYDRVGIENFIRAKYEEKRWIPRGG 127 (492)
Q Consensus 94 ~iwEA~lP--------p~~Dr~~~e~FIRaKYeeKrF~~~~~ 127 (492)
+||+.++- ..+|...+++||+.||++++|...+.
T Consensus 86 ~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~~~ 127 (319)
T COG5347 86 RFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDDSS 127 (319)
T ss_pred hHhccCCCcccccccccccCHHHHHHHHHHHHHhhhcccccc
Confidence 99998642 34566678999999999999987633
No 7
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.96 E-value=8.6e-28 Score=244.35 Aligned_cols=114 Identities=38% Similarity=0.640 Sum_probs=97.1
Q ss_pred HHHHHHHHHhcCCCCCCCcCCCCCCCCeeEcccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhCcHHHH
Q 011159 14 KHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSN 93 (492)
Q Consensus 14 r~ekiL~~Llk~PgNk~CADCGA~nP~WaSvnfGVFLC~~CSGIHRsLGvHISkVKSLsMDtWT~eEV~~Lk~gGN~~aN 93 (492)
...++|++|+..|+|++|+|||+++|+|++++||||||+.|+|+||.||+||++||||+||.|++++|++|+.+||.++|
T Consensus 8 d~~~vfrkL~~kPgNk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~Ws~eqL~~Mk~GGN~rA~ 87 (395)
T PLN03114 8 DKISVFKKLKAKSDNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSSEQLKMMIYGGNNRAQ 87 (395)
T ss_pred cHHHHHHHHHhCcCCCcCccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCCCCHHHHHHHHHhcCHHHH
Confidence 34677999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcCC-C------CCC-h-hhHHHHHHHHhhhCccccCCC
Q 011159 94 SYWEAELP-P------NYD-R-VGIENFIRAKYEEKRWIPRGG 127 (492)
Q Consensus 94 ~iwEA~lP-p------~~D-r-~~~e~FIRaKYeeKrF~~~~~ 127 (492)
.||+.+.- . .|. + ..+.+.+.+|++++.+..+..
T Consensus 88 ~fF~qhG~~~~~~~~~KY~S~aA~~Yre~L~keVa~~~a~~~~ 130 (395)
T PLN03114 88 VFFKQYGWSDGGKTEAKYTSRAADLYKQILAKEVAKSKAEEEL 130 (395)
T ss_pred HHHHHcCCCCCCCcccccCCHHHHHHHHHHHHHHHHhhhcccc
Confidence 99987631 1 111 1 123455778888887765443
No 8
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=99.95 E-value=2.3e-29 Score=254.44 Aligned_cols=116 Identities=36% Similarity=0.659 Sum_probs=94.9
Q ss_pred HHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEcccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhCcHH
Q 011159 12 NAKHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEK 91 (492)
Q Consensus 12 ~ar~ekiL~~Llk~PgNk~CADCGA~nP~WaSvnfGVFLC~~CSGIHRsLGvHISkVKSLsMDtWT~eEV~~Lk~gGN~~ 91 (492)
..|+++.|.+|....+|+.|+||+++||+|||++||||||++|+|+||+||||||+|||||||+|.+.||+.|+.+||++
T Consensus 3 sprtrr~L~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~ 82 (386)
T KOG0704|consen 3 SPRTRRVLLELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNER 82 (386)
T ss_pred ChHHHHHHHhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchh
Confidence 34778888888888899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcC--CCCCC-hhhHHHHHHHHhhhCccccCCC
Q 011159 92 SNSYWEAEL--PPNYD-RVGIENFIRAKYEEKRWIPRGG 127 (492)
Q Consensus 92 aN~iwEA~l--Pp~~D-r~~~e~FIRaKYeeKrF~~~~~ 127 (492)
++.|++..- .+..+ ++++..-+.+-|++|.=+..++
T Consensus 83 ~~eFL~s~~~~~e~~~i~eKYns~aAa~yRdki~~laeg 121 (386)
T KOG0704|consen 83 FREFLSSQGIYKETWPIREKYNSRAAALYRDKIAALAEG 121 (386)
T ss_pred HHHHHhhCccccccccHHHhhccHHHHHHHHHHHHHhcC
Confidence 999998652 12211 2333344555555554333333
No 9
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.94 E-value=6.6e-28 Score=249.64 Aligned_cols=85 Identities=45% Similarity=0.850 Sum_probs=82.8
Q ss_pred HHHHHHHHhcCCCCCCCcCCCCCCCCeeEcccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhCcHHHHH
Q 011159 15 HRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNS 94 (492)
Q Consensus 15 ~ekiL~~Llk~PgNk~CADCGA~nP~WaSvnfGVFLC~~CSGIHRsLGvHISkVKSLsMDtWT~eEV~~Lk~gGN~~aN~ 94 (492)
-+.+++.|..+++||+|||||+++|+|++|+||||||+.|+++||.|||||++|||..||+|+.+||+.|+.|||.+|+.
T Consensus 10 ~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~~ 89 (454)
T KOG0706|consen 10 IQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANARV 89 (454)
T ss_pred HHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHHH
Confidence 47789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhc
Q 011159 95 YWEAE 99 (492)
Q Consensus 95 iwEA~ 99 (492)
|+..+
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=4.4e-26 Score=241.65 Aligned_cols=146 Identities=36% Similarity=0.670 Sum_probs=120.7
Q ss_pred HHHHHHHhcCCCCCCCcCCCCCCCCeeEcccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhCcHHHHHH
Q 011159 16 RKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSY 95 (492)
Q Consensus 16 ekiL~~Llk~PgNk~CADCGA~nP~WaSvnfGVFLC~~CSGIHRsLGvHISkVKSLsMDtWT~eEV~~Lk~gGN~~aN~i 95 (492)
...|+.|...+||..|+||+.++|.|+++|+|+.||++|+||||.||.|+|+||+|.||.|..|.+..|..+||+.||++
T Consensus 501 a~a~qairn~rgn~~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl~~Vm~aiGN~~AN~v 580 (749)
T KOG0705|consen 501 AMALQAIRNMRGNSHCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVELLKVMSAIGNDLANSV 580 (749)
T ss_pred HHHHHHHhcCcCCceeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHHHHHHHHhhhhHHHHH
Confidence 45678888899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcC-----C-CCCChhhHHHHHHHHhhhCccccCCCCCCCCCCccccc---cCCCCCCCCCCCCCCCCCCCCC
Q 011159 96 WEAEL-----P-PNYDRVGIENFIRAKYEEKRWIPRGGNTKSPSRVSEEK---ASFHRPLPSSSGHRYTNNINRV 161 (492)
Q Consensus 96 wEA~l-----P-p~~Dr~~~e~FIRaKYeeKrF~~~~~~~~~ps~~~~e~---~~~~~~~~~r~Gh~~~sS~~~~ 161 (492)
||..+ | +...++++|+|||+||++|.|..+......+-++.--+ ....++......|+++..++..
T Consensus 581 WE~~~~G~~KPs~~s~REEkErwIr~KYeqklFLaPl~~te~~lgqqLl~A~~~~Dl~t~~lLLAhg~~~e~~~t 655 (749)
T KOG0705|consen 581 WEGSSQGQTKPSPDSSREEKERWIRAKYEQKLFLAPLPCTEEPLGQQLLRAVAAEDLQTAILLLAHGSREEVNET 655 (749)
T ss_pred hhhhccCCcCCCccccHHHHHHHHHHHHHHHhhcCCCCCCCCchHHHHHHHHHHHHHHHHHHHHhccCchhhhcc
Confidence 99753 2 34457889999999999999998877655554432211 1122444455677777666665
No 11
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.86 E-value=4.6e-23 Score=227.92 Aligned_cols=112 Identities=46% Similarity=0.889 Sum_probs=102.8
Q ss_pred HHHHHhcCCCCCCCcCCCCCCCCeeEcccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhCcHHHHHHHh
Q 011159 18 ILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYWE 97 (492)
Q Consensus 18 iL~~Llk~PgNk~CADCGA~nP~WaSvnfGVFLC~~CSGIHRsLGvHISkVKSLsMDtWT~eEV~~Lk~gGN~~aN~iwE 97 (492)
.+..+...|||..|+|||++.|+|+++|+||.+|+.|+|+||.||+|||||+||+||.|.++.+.+++.+||..+|.+||
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 37888899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCC--------CChhhHHHHHHHHhhhCccccCCCCC
Q 011159 98 AELPPN--------YDRVGIENFIRAKYEEKRWIPRGGNT 129 (492)
Q Consensus 98 A~lPp~--------~Dr~~~e~FIRaKYeeKrF~~~~~~~ 129 (492)
+.++.. .++..++.||++||++++|.......
T Consensus 496 ~~l~~~~~~~~~~~~~~~~r~~~i~~kyve~~F~~k~~~~ 535 (785)
T KOG0521|consen 496 ALLPSYDSSKPTASSSRQAREAWIKAKYVERRFSVKEPQI 535 (785)
T ss_pred cccccccccCCCCccchhhhhHhhhcccceeeEeecccch
Confidence 998643 23557899999999999998765543
No 12
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.78 E-value=2.4e-18 Score=180.71 Aligned_cols=125 Identities=30% Similarity=0.559 Sum_probs=111.8
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCC-CeeEcccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHh
Q 011159 8 SKELNAKHRKILDGLLKLPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQS 86 (492)
Q Consensus 8 SKrl~ar~ekiL~~Llk~PgNk~CADCGA~nP-~WaSvnfGVFLC~~CSGIHRsLGvHISkVKSLsMDtWT~eEV~~Lk~ 86 (492)
.|+.++.++++||+|+++|+|++|++|..+.+ +|+++.-|-|+|+.|+|+.|.|.. -+|||+|+|.+|+..||.+|+.
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 45666677999999999999999999999988 999999999999999999999974 4799999999999999999999
Q ss_pred hCcHHHHHHHhhc-------CCCCCChhhHHHHHHHHhhhCccccCCCCCCCCC
Q 011159 87 MGNEKSNSYWEAE-------LPPNYDRVGIENFIRAKYEEKRWIPRGGNTKSPS 133 (492)
Q Consensus 87 gGN~~aN~iwEA~-------lPp~~Dr~~~e~FIRaKYeeKrF~~~~~~~~~ps 133 (492)
+||+.+.++|..- +|+..+....++||+.||+.|||+......+.++
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 9999999999753 5777778889999999999999997766555443
No 13
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.75 E-value=2.4e-19 Score=188.56 Aligned_cols=101 Identities=42% Similarity=0.812 Sum_probs=90.3
Q ss_pred CCCCCCCcCCCCCCCCeeEcccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhCcHHHHHHHhhcCCC--
Q 011159 25 LPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYWEAELPP-- 102 (492)
Q Consensus 25 ~PgNk~CADCGA~nP~WaSvnfGVFLC~~CSGIHRsLGvHISkVKSLsMDtWT~eEV~~Lk~gGN~~aN~iwEA~lPp-- 102 (492)
...-+.|+|||+++|.|+|++-|+|||.+|+.+||.||.|||.||+|.-..|.++.|.+...+.|..+|.|||..|-+
T Consensus 5 ~l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaNsIWEh~Lld~s 84 (669)
T KOG0818|consen 5 LLSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGANSIWEHSLLDPA 84 (669)
T ss_pred chhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcchhhhhhccCch
Confidence 455679999999999999999999999999999999999999999999999999999999999999999999987522
Q ss_pred ----------CCChh--hHHHHHHHHhhhCccccC
Q 011159 103 ----------NYDRV--GIENFIRAKYEEKRWIPR 125 (492)
Q Consensus 103 ----------~~Dr~--~~e~FIRaKYeeKrF~~~ 125 (492)
..|+. .+++|||+||+...|+.+
T Consensus 85 t~~sg~rk~~pqD~~Hp~K~eFIkaKy~~LtFv~~ 119 (669)
T KOG0818|consen 85 TIMSGRRKANPQDKVHPNKAEFIRAKYQMLAFVHR 119 (669)
T ss_pred hhhcccCCCCCcCCCCccHHHHHHHHHHheeeecc
Confidence 12332 478999999999999974
No 14
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.71 E-value=2.9e-18 Score=188.20 Aligned_cols=105 Identities=42% Similarity=0.816 Sum_probs=96.2
Q ss_pred HHHhcCCCCCCCcCCCCCCCCeeEcccchHhhHhhhhhhhcCCCccceeeecccCC--CCHHHHHHHHhhCcHHHHHHHh
Q 011159 20 DGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDT--WLPEQVAVIQSMGNEKSNSYWE 97 (492)
Q Consensus 20 ~~Llk~PgNk~CADCGA~nP~WaSvnfGVFLC~~CSGIHRsLGvHISkVKSLsMDt--WT~eEV~~Lk~gGN~~aN~iwE 97 (492)
+++.....|+.|+|||++.|.|+++|+++.||-.|+|-||+||.-+|+|+|++||. |+.+-|+++...||.++|+||.
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 45566789999999999999999999999999999999999999999999999997 9999999999999999999999
Q ss_pred hcCCCCC------ChhhHHHHHHHHhhhCcccc
Q 011159 98 AELPPNY------DRVGIENFIRAKYEEKRWIP 124 (492)
Q Consensus 98 A~lPp~~------Dr~~~e~FIRaKYeeKrF~~ 124 (492)
.++|++. ....+++||.+||++..|-.
T Consensus 370 ~nl~~~e~lh~dssp~~r~~fi~~Kykeg~fRk 402 (1186)
T KOG1117|consen 370 GNLPPNEHLHPDSSPSTRRQFIKEKYKEGKFRK 402 (1186)
T ss_pred cCCCCccccCCCCCcchhhhHHHHHhhcccccc
Confidence 9998754 24568999999999987754
No 15
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=94.53 E-value=0.0092 Score=68.11 Aligned_cols=72 Identities=21% Similarity=0.237 Sum_probs=61.1
Q ss_pred cCCCCCCCcCCCCC-CCCeeEcccchHhhHhhhhhhhcCCCccceeeecccCCCCHHHHHHHHhhCcHHHHHHHh
Q 011159 24 KLPENRECADCKAK-GPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYWE 97 (492)
Q Consensus 24 k~PgNk~CADCGA~-nP~WaSvnfGVFLC~~CSGIHRsLGvHISkVKSLsMDtWT~eEV~~Lk~gGN~~aN~iwE 97 (492)
....+..|++|++. ...|+++++.+-+|+.|+++|+.++.|++..+++.|++..+ |..+...|+...+..|.
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 44567899999985 78999999999999999999999999999999999998777 77777777776666554
No 16
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=83.63 E-value=0.69 Score=44.66 Aligned_cols=34 Identities=29% Similarity=0.465 Sum_probs=28.3
Q ss_pred hcCCCCCCCcCCCCCCC-CeeEcccchHhhHhhhh
Q 011159 23 LKLPENRECADCKAKGP-RWASVNLGIFICMQCSG 56 (492)
Q Consensus 23 lk~PgNk~CADCGA~nP-~WaSvnfGVFLC~~CSG 56 (492)
--.|.-..|+-||.... .|.+..-|.|+|..|..
T Consensus 144 G~~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~ 178 (247)
T PRK00085 144 GYGLDLDHCAVCGAPGDHRYFSPKEGGAVCSECGD 178 (247)
T ss_pred CCccchhhHhcCCCCCCceEEecccCCcccccccC
Confidence 34577789999998754 78899999999999973
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=78.18 E-value=2.8 Score=40.31 Aligned_cols=34 Identities=26% Similarity=0.462 Sum_probs=28.0
Q ss_pred cCCCCCCCcCCCCCCC-CeeEcccchHhhHhhhhh
Q 011159 24 KLPENRECADCKAKGP-RWASVNLGIFICMQCSGI 57 (492)
Q Consensus 24 k~PgNk~CADCGA~nP-~WaSvnfGVFLC~~CSGI 57 (492)
=.|.-..|+.||..++ .|.++..|.|+|..|...
T Consensus 143 ~~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 143 YALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred CCcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 3577789999998544 688999999999999764
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=73.41 E-value=2.2 Score=30.77 Aligned_cols=34 Identities=12% Similarity=0.335 Sum_probs=29.4
Q ss_pred CCCCCcCCCCCCCCeeEcccchHhhHhhhhh-hhc
Q 011159 27 ENRECADCKAKGPRWASVNLGIFICMQCSGI-HRS 60 (492)
Q Consensus 27 gNk~CADCGA~nP~WaSvnfGVFLC~~CSGI-HRs 60 (492)
.+..|..|......|.+.+-+++||..|... |+.
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 3568999999888999999999999999998 886
No 19
>PRK12495 hypothetical protein; Provisional
Probab=68.95 E-value=3 Score=41.90 Aligned_cols=38 Identities=24% Similarity=0.397 Sum_probs=28.0
Q ss_pred HHHHHHHhc--CCCCCCCcCCCCCCCCeeEcccchHhhHhhhhh
Q 011159 16 RKILDGLLK--LPENRECADCKAKGPRWASVNLGIFICMQCSGI 57 (492)
Q Consensus 16 ekiL~~Llk--~PgNk~CADCGA~nP~WaSvnfGVFLC~~CSGI 57 (492)
+++-+.|++ ...++.|-+||.+=|.+ -|+.+|..|..+
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 344444444 47899999999998832 699999999654
No 20
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=61.87 E-value=4.1 Score=40.59 Aligned_cols=37 Identities=32% Similarity=0.588 Sum_probs=29.5
Q ss_pred HHHHhcCCCCCCCcCCCCCC-CCeeEcccchHhhHhhh
Q 011159 19 LDGLLKLPENRECADCKAKG-PRWASVNLGIFICMQCS 55 (492)
Q Consensus 19 L~~Llk~PgNk~CADCGA~n-P~WaSvnfGVFLC~~CS 55 (492)
|..+-=.+.=..|+.||.+. +..++.-.|-++|.+|.
T Consensus 145 L~~~G~~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 145 LGELGIGPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred HHHcCCccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 33333356667999999985 57999999999999998
No 21
>PRK11019 hypothetical protein; Provisional
Probab=60.69 E-value=4 Score=35.54 Aligned_cols=37 Identities=22% Similarity=0.518 Sum_probs=25.5
Q ss_pred CCCCCcCCCCCCC--CeeEcccchHhhHhhhhhhhcCCCc
Q 011159 27 ENRECADCKAKGP--RWASVNLGIFICMQCSGIHRSLGVH 64 (492)
Q Consensus 27 gNk~CADCGA~nP--~WaSvnfGVFLC~~CSGIHRsLGvH 64 (492)
.-.+|.|||.+=| .|--+ -++-.|+.|...+...+.|
T Consensus 35 syg~C~~CG~~Ip~~Rl~A~-P~a~~Cv~Cq~~~E~~~k~ 73 (88)
T PRK11019 35 SLTECEECGEPIPEARRKAI-PGVRLCVACQQEKDLQQAA 73 (88)
T ss_pred cCCeeCcCCCcCcHHHHhhc-CCccccHHHHHHHHHHHhH
Confidence 3579999999844 33322 2688999999987654433
No 22
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=59.40 E-value=5.1 Score=36.60 Aligned_cols=31 Identities=16% Similarity=0.429 Sum_probs=20.9
Q ss_pred CCCcCCCCCCC-CeeEcccchHhhHhhhhhhh
Q 011159 29 RECADCKAKGP-RWASVNLGIFICMQCSGIHR 59 (492)
Q Consensus 29 k~CADCGA~nP-~WaSvnfGVFLC~~CSGIHR 59 (492)
.+|.+||.+=| .=.-.--+..+|+.|...|-
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 48999999822 11112236789999998774
No 23
>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=54.08 E-value=7.5 Score=31.58 Aligned_cols=34 Identities=35% Similarity=0.638 Sum_probs=23.6
Q ss_pred cCCCCCCCcCCCCCCC--CeeEcccchHhhHhhhhhh
Q 011159 24 KLPENRECADCKAKGP--RWASVNLGIFICMQCSGIH 58 (492)
Q Consensus 24 k~PgNk~CADCGA~nP--~WaSvnfGVFLC~~CSGIH 58 (492)
..++...|.|||.+=| ++. .--|+..|..|...+
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 4567789999999743 222 233788999997754
No 24
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=53.16 E-value=12 Score=37.31 Aligned_cols=39 Identities=18% Similarity=0.406 Sum_probs=29.3
Q ss_pred HHHHHHHHhcCCCCCCCcCCCCCCCCeeEcccchHhhHhhhhhhh
Q 011159 15 HRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHR 59 (492)
Q Consensus 15 ~ekiL~~Llk~PgNk~CADCGA~nP~WaSvnfGVFLC~~CSGIHR 59 (492)
-++.++..++......|-.||.....|. ++|-.|.+.|-
T Consensus 341 ~~~~~~~~~~~~p~~~c~~cg~~~~~~~------~~c~~c~~~~~ 379 (389)
T PRK11788 341 LRDLVGEQLKRKPRYRCRNCGFTARTLY------WHCPSCKAWET 379 (389)
T ss_pred HHHHHHHHHhCCCCEECCCCCCCCccce------eECcCCCCccC
Confidence 4666665555444455999999999995 79999998873
No 25
>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=50.65 E-value=7.6 Score=28.53 Aligned_cols=27 Identities=26% Similarity=0.812 Sum_probs=22.9
Q ss_pred CCCCCCcCCCCCCCCeeEcccchHhhHhhh
Q 011159 26 PENRECADCKAKGPRWASVNLGIFICMQCS 55 (492)
Q Consensus 26 PgNk~CADCGA~nP~WaSvnfGVFLC~~CS 55 (492)
..|..|..|++. |....=|.|+|.+|-
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCc
Confidence 345679999998 888899999999994
No 26
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=50.55 E-value=9.7 Score=35.85 Aligned_cols=38 Identities=13% Similarity=0.270 Sum_probs=24.1
Q ss_pred cCCCCCCCcCCCCCCC-CeeEcccchHhhHhhhhhhhcC
Q 011159 24 KLPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRSL 61 (492)
Q Consensus 24 k~PgNk~CADCGA~nP-~WaSvnfGVFLC~~CSGIHRsL 61 (492)
..+.-.+|-+||.+=| .=.-+--++.+|+.|...|-..
T Consensus 107 ~~gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~E~~ 145 (151)
T PRK10778 107 EDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIR 145 (151)
T ss_pred hCCCCceeccCCCcccHHHHhcCCCccccHHHHHHHHHH
Confidence 4567779999998711 1111112357899999877643
No 27
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=48.32 E-value=12 Score=31.34 Aligned_cols=33 Identities=18% Similarity=0.496 Sum_probs=22.2
Q ss_pred CCCCcCCCCCCCCe-eEcccchHhhHhhhhhhhc
Q 011159 28 NRECADCKAKGPRW-ASVNLGIFICMQCSGIHRS 60 (492)
Q Consensus 28 Nk~CADCGA~nP~W-aSvnfGVFLC~~CSGIHRs 60 (492)
...|.|||.+=|.= .-.--|+..|..|...+-.
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 45899999984421 1122378899999886644
No 28
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=43.59 E-value=7.7 Score=36.99 Aligned_cols=34 Identities=29% Similarity=0.640 Sum_probs=28.2
Q ss_pred CCCCCCcCCCCCCCCeeEcccchHhhH-hhhhhhhc
Q 011159 26 PENRECADCKAKGPRWASVNLGIFICM-QCSGIHRS 60 (492)
Q Consensus 26 PgNk~CADCGA~nP~WaSvnfGVFLC~-~CSGIHRs 60 (492)
|--+.|+-|| -...|.+++.|.-+|. .|-.+|..
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 6667999999998885 89999864
No 29
>TIGR02890 spore_yteA sporulation protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to PFAM family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. The function of proteins in this family is unknown. YteA was detected in mature spores of Bacillus subtilis by Kuwana, et al., and appears to be expressed under control of sigma-K.
Probab=40.22 E-value=16 Score=34.67 Aligned_cols=36 Identities=14% Similarity=0.223 Sum_probs=22.2
Q ss_pred CCCCCCCcCCCCCCC-CeeEcccchHhhHhhhhhhhc
Q 011159 25 LPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRS 60 (492)
Q Consensus 25 ~PgNk~CADCGA~nP-~WaSvnfGVFLC~~CSGIHRs 60 (492)
...=.+|.+||.+=| .=.-+--++-.|+.|...+-.
T Consensus 83 ~G~YG~Ce~CGe~I~~~RL~a~P~a~~Ci~Cq~~~E~ 119 (159)
T TIGR02890 83 NGTYGICEVCGKPIPYERLEAIPTATTCVECQNRKEV 119 (159)
T ss_pred CCCCCeecccCCcccHHHHhhCCCcchhHHHHHHhhh
Confidence 345558999998711 111112246789999987643
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=39.99 E-value=7.9 Score=28.47 Aligned_cols=27 Identities=19% Similarity=0.582 Sum_probs=16.6
Q ss_pred CCCcCCCCC-CCCeeEcccchHhhHhhh
Q 011159 29 RECADCKAK-GPRWASVNLGIFICMQCS 55 (492)
Q Consensus 29 k~CADCGA~-nP~WaSvnfGVFLC~~CS 55 (492)
..|.+|+.. .-.|..-+|+.-||..|.
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 677999999999999994
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=39.37 E-value=8.8 Score=28.46 Aligned_cols=27 Identities=22% Similarity=0.600 Sum_probs=21.1
Q ss_pred CCcCCCCCCCCeeEcccchHhhHhhhhh
Q 011159 30 ECADCKAKGPRWASVNLGIFICMQCSGI 57 (492)
Q Consensus 30 ~CADCGA~nP~WaSvnfGVFLC~~CSGI 57 (492)
+|-.||+.. ......-|-++|..|-.+
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 599999977 455677899999999443
No 32
>PHA00080 DksA-like zinc finger domain containing protein
Probab=34.24 E-value=26 Score=29.26 Aligned_cols=35 Identities=29% Similarity=0.619 Sum_probs=23.5
Q ss_pred CCCCCCCcCCCCCCC--CeeEcccchHhhHhhhhhhhc
Q 011159 25 LPENRECADCKAKGP--RWASVNLGIFICMQCSGIHRS 60 (492)
Q Consensus 25 ~PgNk~CADCGA~nP--~WaSvnfGVFLC~~CSGIHRs 60 (492)
..+..+|.|||.+=| .|.-+ -|+..|+.|...+-.
T Consensus 28 ~~~~~~C~~Cg~~Ip~~Rl~a~-P~~~~Cv~Cq~~~E~ 64 (72)
T PHA00080 28 APSATHCEECGDPIPEARREAV-PGCRTCVSCQEILEL 64 (72)
T ss_pred CCCCCEecCCCCcCcHHHHHhC-CCccCcHHHHHHHHH
Confidence 355669999999733 33222 367779999887643
No 33
>PF12536 DUF3734: Patatin phospholipase ; InterPro: IPR021095 This entry represents bacterial proteins of approximately 110 amino acids in length. These proteins are found in association with PF01734 from PFAM. There are two completely conserved residues (F and G) that may be functionally important. The proteins in this family are frequently annotated as patatin family phospholipases however there is little accompanying literature to confirm this.
Probab=33.01 E-value=18 Score=32.06 Aligned_cols=11 Identities=36% Similarity=0.558 Sum_probs=7.4
Q ss_pred CCCccccchhc
Q 011159 475 NGKDHDFSSLT 485 (492)
Q Consensus 475 ~gkdydfsslt 485 (492)
..||||||-.+
T Consensus 68 ~sKDyeFSr~s 78 (108)
T PF12536_consen 68 HSKDYEFSRSS 78 (108)
T ss_pred cccCccCCHHH
Confidence 45888887653
No 34
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=32.65 E-value=27 Score=31.06 Aligned_cols=33 Identities=24% Similarity=0.507 Sum_probs=23.3
Q ss_pred cCCCCCCCcCCCCCC-----------------CCeeEcccchHhhHhhhh
Q 011159 24 KLPENRECADCKAKG-----------------PRWASVNLGIFICMQCSG 56 (492)
Q Consensus 24 k~PgNk~CADCGA~n-----------------P~WaSvnfGVFLC~~CSG 56 (492)
+.++--.|+|||.+- -.=+.=.||-.+|..|..
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 456677899999871 111234789999999964
No 35
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=32.52 E-value=27 Score=27.29 Aligned_cols=37 Identities=24% Similarity=0.587 Sum_probs=30.0
Q ss_pred CCCCCcCCCCC-CCCeeEcccch-HhhHhhhhhhhcCCC
Q 011159 27 ENRECADCKAK-GPRWASVNLGI-FICMQCSGIHRSLGV 63 (492)
Q Consensus 27 gNk~CADCGA~-nP~WaSvnfGV-FLC~~CSGIHRsLGv 63 (492)
..+.|..|+.. .|.|=....|- +||-.|.-..+..+.
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~ 40 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCC
Confidence 45789999986 68898888886 999999887776654
No 36
>PRK02770 S-adenosylmethionine decarboxylase proenzyme; Provisional
Probab=29.27 E-value=23 Score=33.09 Aligned_cols=42 Identities=21% Similarity=0.444 Sum_probs=24.9
Q ss_pred HHHHHHhccccCCCCcccCCCcCCCCCCC---------CCccccccCCCCcCC
Q 011159 360 QSFLAAASVNSNGGSQSFPINVHQPGSNG---------IHVPIQSWGVVGHQV 403 (492)
Q Consensus 360 Q~llmaaa~~~~~~~~~~p~~~~q~~~ng---------~~~p~qnw~~~Gyq~ 403 (492)
+.+|..|+ +..|.. .+....++=.+.| +||.+|.||..||-.
T Consensus 40 ~~~l~~Aa-~~~gat-iv~~~~h~F~P~GvTgv~lLaESHisIHTwPE~gyaa 90 (139)
T PRK02770 40 RTTLTEAA-KRAGAT-LLNLITHRFEPQGVTALALLAESHISIHTWPESGYAA 90 (139)
T ss_pred HHHHHHHH-HHcCCE-EEEEEeEEcCCCeEEEEEEecccEEEEEeCcCCCcEE
Confidence 44555555 555544 2333333333333 469999999999953
No 37
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=27.16 E-value=55 Score=36.06 Aligned_cols=93 Identities=14% Similarity=0.303 Sum_probs=47.0
Q ss_pred CCCCCCCcC-CCCC--CCCeeEccc--chHhhHhhhhhhhcCCCcc-----ceeee----cccCCCCH-HHHHHHHh---
Q 011159 25 LPENRECAD-CKAK--GPRWASVNL--GIFICMQCSGIHRSLGVHI-----SKVRS----ATLDTWLP-EQVAVIQS--- 86 (492)
Q Consensus 25 ~PgNk~CAD-CGA~--nP~WaSvnf--GVFLC~~CSGIHRsLGvHI-----SkVKS----LsMDtWT~-eEV~~Lk~--- 86 (492)
.+|++.|+| |-.. +...+...- -.+||+.|-..=-.+|.|- -.|.. |---.|+. ||+.+|+.
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 455564433 6543 333222221 1579999987655555541 11222 12234995 67877754
Q ss_pred --hCc--HHHHHHHhhcCCCCCChhhHHHHHHHHhhhCccc
Q 011159 87 --MGN--EKSNSYWEAELPPNYDRVGIENFIRAKYEEKRWI 123 (492)
Q Consensus 87 --gGN--~~aN~iwEA~lPp~~Dr~~~e~FIRaKYeeKrF~ 123 (492)
.|| +.|+.| ...+....+++-...|++..+.
T Consensus 90 ~G~GNW~dIA~hI------GtKtkeeck~hy~k~fv~s~~~ 124 (438)
T KOG0457|consen 90 YGFGNWQDIADHI------GTKTKEECKEHYLKHFVNSPIF 124 (438)
T ss_pred hCCCcHHHHHHHH------cccchHHHHHHHHHHHhcCccc
Confidence 466 222221 1223445666667777776443
No 38
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=27.11 E-value=31 Score=30.35 Aligned_cols=31 Identities=16% Similarity=0.336 Sum_probs=18.1
Q ss_pred CCCCCCCcCCCCCCCC-eeEcccchHhhHhhh
Q 011159 25 LPENRECADCKAKGPR-WASVNLGIFICMQCS 55 (492)
Q Consensus 25 ~PgNk~CADCGA~nP~-WaSvnfGVFLC~~CS 55 (492)
.+.-.+|.|||.+=|. =.-.--++..|..|.
T Consensus 77 ~g~yG~C~~Cge~I~~~RL~a~P~a~~Cv~Cq 108 (110)
T TIGR02420 77 DGEYGYCEECGEEIGLRRLEARPTATLCIDCK 108 (110)
T ss_pred CCCCCchhccCCcccHHHHhhCCCccccHHhH
Confidence 3566799999987211 001111356788885
No 39
>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=27.02 E-value=9.4 Score=27.38 Aligned_cols=30 Identities=23% Similarity=0.533 Sum_probs=16.4
Q ss_pred CCCcCCCCCCC-CeeEcccchHhhHhhhhhh
Q 011159 29 RECADCKAKGP-RWASVNLGIFICMQCSGIH 58 (492)
Q Consensus 29 k~CADCGA~nP-~WaSvnfGVFLC~~CSGIH 58 (492)
.+|.+||..=+ .=.-+--+..+|..|...|
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 35999997622 1111223678899998765
No 40
>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=25.86 E-value=33 Score=24.85 Aligned_cols=32 Identities=25% Similarity=0.694 Sum_probs=23.0
Q ss_pred CcCCCCC-CCCeeEcccchH-hhHhhhhhhhcCC
Q 011159 31 CADCKAK-GPRWASVNLGIF-ICMQCSGIHRSLG 62 (492)
Q Consensus 31 CADCGA~-nP~WaSvnfGVF-LC~~CSGIHRsLG 62 (492)
|..|+.. .|.|=....|-. ||-.|--.+|..|
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 699998888877 9999987777644
No 41
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=25.74 E-value=48 Score=28.16 Aligned_cols=31 Identities=16% Similarity=0.540 Sum_probs=25.6
Q ss_pred CCCCCcCCCCCCCCeeEcccchHhhHhhhhhhhc
Q 011159 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (492)
Q Consensus 27 gNk~CADCGA~nP~WaSvnfGVFLC~~CSGIHRs 60 (492)
..+.|.=||.+.- ...||++.|..|.+..|-
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 4567999998765 458999999999998874
No 42
>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=25.03 E-value=42 Score=28.47 Aligned_cols=31 Identities=19% Similarity=0.613 Sum_probs=25.7
Q ss_pred CCCCCcCCCCCCCCeeEcccchHhhHhhhhhhhc
Q 011159 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (492)
Q Consensus 27 gNk~CADCGA~nP~WaSvnfGVFLC~~CSGIHRs 60 (492)
+|..|.=||.+.. ...||++.|..|.+..|-
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 4678999998665 468999999999998874
No 43
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=23.70 E-value=37 Score=26.65 Aligned_cols=30 Identities=27% Similarity=0.563 Sum_probs=19.9
Q ss_pred CCcCCCCCCCCee--EcccchHhhHhhhhhhhc
Q 011159 30 ECADCKAKGPRWA--SVNLGIFICMQCSGIHRS 60 (492)
Q Consensus 30 ~CADCGA~nP~Wa--SvnfGVFLC~~CSGIHRs 60 (492)
.|+=||..-.-.- -+.=| +||..|..--..
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 4888888744333 34557 899999864433
No 44
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=22.32 E-value=50 Score=25.77 Aligned_cols=34 Identities=26% Similarity=0.676 Sum_probs=22.2
Q ss_pred HhcCCCCCCCcCCCCCCC--Cee-------EcccchHhhHhhhh
Q 011159 22 LLKLPENRECADCKAKGP--RWA-------SVNLGIFICMQCSG 56 (492)
Q Consensus 22 Llk~PgNk~CADCGA~nP--~Wa-------SvnfGVFLC~~CSG 56 (492)
|+++.+| .|-=|++..+ .|. +..-.|+||..|..
T Consensus 2 L~~Rs~~-kCELC~a~~~L~vy~Vpp~~~~~~d~~iliC~tC~~ 44 (47)
T smart00782 2 LLARCES-KCELCGSDSPLVVYAVPPSSDVTADNSVMLCDTCHS 44 (47)
T ss_pred hhHHcCC-cccCcCCCCCceEEecCCCCCCCccceeeechHHHH
Confidence 3444444 4999998753 121 34668999999965
No 45
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=22.17 E-value=33 Score=28.46 Aligned_cols=23 Identities=22% Similarity=0.593 Sum_probs=16.1
Q ss_pred CCCcCCCCCCCCeeEcccchHhhHhh
Q 011159 29 RECADCKAKGPRWASVNLGIFICMQC 54 (492)
Q Consensus 29 k~CADCGA~nP~WaSvnfGVFLC~~C 54 (492)
-+|+|||+.+.- -.--++-|-+|
T Consensus 21 YiCgdC~~en~l---k~~D~irCReC 43 (62)
T KOG3507|consen 21 YICGDCGQENTL---KRGDVIRCREC 43 (62)
T ss_pred EEeccccccccc---cCCCcEehhhc
Confidence 379999998752 12346778888
No 46
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=21.88 E-value=53 Score=29.08 Aligned_cols=31 Identities=19% Similarity=0.495 Sum_probs=23.7
Q ss_pred CCCCCCCcCCCCCCCCeeEcccchHhhHhhhhh
Q 011159 25 LPENRECADCKAKGPRWASVNLGIFICMQCSGI 57 (492)
Q Consensus 25 ~PgNk~CADCGA~nP~WaSvnfGVFLC~~CSGI 57 (492)
.-.-..|-.|+.+ .---+..||+.|..|-..
T Consensus 32 ~~~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~~ 62 (89)
T COG1997 32 QRAKHVCPFCGRT--TVKRIATGIWKCRKCGAK 62 (89)
T ss_pred HhcCCcCCCCCCc--ceeeeccCeEEcCCCCCe
Confidence 3455689999998 444678999999999543
No 47
>PTZ00074 60S ribosomal protein L34; Provisional
Probab=21.17 E-value=54 Score=30.88 Aligned_cols=31 Identities=26% Similarity=0.562 Sum_probs=21.8
Q ss_pred CCCCCCcCCCCC-----------------CCCeeEcccchHhhHhhhh
Q 011159 26 PENRECADCKAK-----------------GPRWASVNLGIFICMQCSG 56 (492)
Q Consensus 26 PgNk~CADCGA~-----------------nP~WaSvnfGVFLC~~CSG 56 (492)
+.--.|.|||.+ .-.-++=.||-.+|..|.-
T Consensus 39 ~~~pkC~~cg~~L~GI~~~Rp~e~~rlsK~~KtvsRaYGG~lC~~CVr 86 (135)
T PTZ00074 39 SSGPKCGDCGKVLAGIKALRPTEYKQLSRRERTVSRAYGGVLCHKCVR 86 (135)
T ss_pred CCCCCCCCCCCccCCccCCchHHHHHccccCCCccCCCccchhHHHHH
Confidence 344469999987 1223455799999999954
No 48
>PRK04059 rpl34e 50S ribosomal protein L34e; Validated
Probab=20.92 E-value=51 Score=28.95 Aligned_cols=31 Identities=23% Similarity=0.553 Sum_probs=21.4
Q ss_pred CCCCCCcCCCCCC-----------------CCeeEcccchHhhHhhhh
Q 011159 26 PENRECADCKAKG-----------------PRWASVNLGIFICMQCSG 56 (492)
Q Consensus 26 PgNk~CADCGA~n-----------------P~WaSvnfGVFLC~~CSG 56 (492)
+.--.|.|||.+- -.-++=.||-.+|..|.-
T Consensus 32 ~~~pkC~~c~~~L~Gi~~~Rp~~~~rlsK~~K~vsRaYGG~lc~~cvr 79 (88)
T PRK04059 32 PSKAKCAICGKPLNGVPRGRPVEIRKLGKTEKRPERPYGGYLCPKCLK 79 (88)
T ss_pred CCCCcCCCCCCccCCccCcchHHHHhcccccCCcccCcCceecHHHHH
Confidence 3334699999861 123455789999999964
No 49
>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=20.79 E-value=53 Score=28.87 Aligned_cols=30 Identities=20% Similarity=0.540 Sum_probs=24.7
Q ss_pred CCCCcCCCCCCCCeeEcccchHhhHhhhhhhhc
Q 011159 28 NRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (492)
Q Consensus 28 Nk~CADCGA~nP~WaSvnfGVFLC~~CSGIHRs 60 (492)
+..|.=||.+.-. ..||++.|..|.+..|-
T Consensus 4 ~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 33 (97)
T cd07170 4 KRLCLVCGDIASG---YHYGVASCEACKAFFKR 33 (97)
T ss_pred CCCCeecCCcCcc---eEECceeehhhhHHHHH
Confidence 3569999987654 48999999999998874
No 50
>cd06968 NR_DBD_ROR DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RORS are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum particularly in the regulation of the maturation and survival of Purkinje cells. RORbe
Probab=20.71 E-value=57 Score=28.45 Aligned_cols=31 Identities=29% Similarity=0.703 Sum_probs=25.7
Q ss_pred CCCCCcCCCCCCCCeeEcccchHhhHhhhhhhhc
Q 011159 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (492)
Q Consensus 27 gNk~CADCGA~nP~WaSvnfGVFLC~~CSGIHRs 60 (492)
.+..|.=||.+... ..||++.|..|.+..|-
T Consensus 4 ~~~~C~VCg~~~~g---~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 4 EVIPCKICGDKSSG---IHYGVITCEGCKGFFRR 34 (95)
T ss_pred cccCCcccCCcCcc---eEECceeehhhHHhhHH
Confidence 46679999987654 48999999999998874
No 51
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=20.45 E-value=38 Score=30.93 Aligned_cols=24 Identities=38% Similarity=0.826 Sum_probs=21.2
Q ss_pred CeeEcccc--hHhhHhhhhhhhcCCC
Q 011159 40 RWASVNLG--IFICMQCSGIHRSLGV 63 (492)
Q Consensus 40 ~WaSvnfG--VFLC~~CSGIHRsLGv 63 (492)
.|++-.-| |.-|.+|-.|||.-++
T Consensus 52 ewi~~~~G~~VwSC~dC~~iH~ke~~ 77 (112)
T COG2158 52 EWISDSNGRKVWSCSDCHWIHRKEGA 77 (112)
T ss_pred ceeEcCCCCEEeeccccceecccchH
Confidence 89998889 9999999999997553
No 52
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=20.42 E-value=45 Score=34.32 Aligned_cols=32 Identities=19% Similarity=0.471 Sum_probs=22.8
Q ss_pred CCCCCCcCCCCCCCCeeEcccchHhhHhhhhhh
Q 011159 26 PENRECADCKAKGPRWASVNLGIFICMQCSGIH 58 (492)
Q Consensus 26 PgNk~CADCGA~nP~WaSvnfGVFLC~~CSGIH 58 (492)
.....|-+||.... =....-|-.||..|--|.
T Consensus 9 ~~~~~Cp~Cg~~~i-v~d~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 9 EEKLVCPECGSDKL-IYDYERGEIVCADCGLVI 40 (310)
T ss_pred ccCCcCcCCCCCCe-eEECCCCeEeecccCCcc
Confidence 34568999997432 234567999999996654
No 53
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=20.37 E-value=76 Score=33.12 Aligned_cols=30 Identities=20% Similarity=0.517 Sum_probs=22.1
Q ss_pred CCCCCCcCCCCCCCCeeEc-------c-cchHhhHhhh
Q 011159 26 PENRECADCKAKGPRWASV-------N-LGIFICMQCS 55 (492)
Q Consensus 26 PgNk~CADCGA~nP~WaSv-------n-fGVFLC~~CS 55 (492)
.+...|..||.....|.-+ . --.|+|..|.
T Consensus 256 t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg 293 (299)
T TIGR01385 256 TDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECG 293 (299)
T ss_pred cccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCC
Confidence 4467999999999888744 1 2356899985
Done!