Query 012078
Match_columns 471
No_of_seqs 171 out of 1188
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 08:23:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012078.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012078hhsearch_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 2.6E-46 5.6E-51 370.1 12.4 276 7-335 4-287 (287)
2 PLN03119 putative ADP-ribosyla 100.0 9.5E-41 2.1E-45 351.5 13.9 159 8-170 3-170 (648)
3 PLN03131 hypothetical protein; 100.0 1.6E-38 3.5E-43 336.9 11.6 157 8-168 3-168 (705)
4 PF01412 ArfGap: Putative GTPa 100.0 9.6E-38 2.1E-42 272.6 6.2 109 17-125 2-116 (116)
5 smart00105 ArfGap Putative GTP 100.0 3.9E-36 8.5E-41 261.3 8.8 103 26-128 1-110 (112)
6 COG5347 GTPase-activating prot 100.0 2.5E-33 5.5E-38 282.5 9.8 114 14-127 6-127 (319)
7 PLN03114 ADP-ribosylation fact 100.0 2.6E-28 5.7E-33 247.4 15.6 113 15-127 9-130 (395)
8 KOG0704 ADP-ribosylation facto 99.9 3.8E-28 8.3E-33 244.9 9.2 110 13-122 4-124 (386)
9 KOG0706 Predicted GTPase-activ 99.9 2.9E-27 6.3E-32 244.4 5.7 86 14-99 9-94 (454)
10 KOG0705 GTPase-activating prot 99.9 2.8E-26 6.1E-31 242.4 5.0 114 15-128 500-619 (749)
11 KOG0521 Putative GTPase activa 99.9 5.6E-23 1.2E-27 227.5 3.8 110 18-127 416-533 (785)
12 KOG0702 Predicted GTPase-activ 99.8 1.2E-19 2.7E-24 189.8 14.5 124 9-133 6-137 (524)
13 KOG0818 GTPase-activating prot 99.8 1.7E-20 3.6E-25 196.5 2.8 102 24-125 4-119 (669)
14 KOG1117 Rho- and Arf-GTPase ac 99.7 5.8E-18 1.2E-22 185.4 2.6 107 20-126 290-404 (1186)
15 KOG0521 Putative GTPase activa 94.1 0.013 2.8E-07 66.9 -0.3 73 24-98 626-699 (785)
16 PRK12495 hypothetical protein; 77.4 1.2 2.5E-05 44.4 1.4 40 14-57 26-67 (226)
17 PRK00085 recO DNA repair prote 74.7 1.7 3.7E-05 42.0 1.7 32 25-56 146-178 (247)
18 TIGR00613 reco DNA repair prot 69.0 5.3 0.00012 38.5 3.6 33 25-57 144-177 (241)
19 PF00643 zf-B_box: B-box zinc 69.0 2 4.4E-05 30.8 0.6 34 27-60 2-36 (42)
20 PRK11019 hypothetical protein; 65.8 2.6 5.7E-05 36.4 0.8 37 27-64 35-73 (88)
21 COG1734 DksA DnaK suppressor p 60.5 5.5 0.00012 36.2 1.8 30 30-59 82-112 (120)
22 PRK11788 tetratricopeptide rep 54.9 6.9 0.00015 39.1 1.7 39 15-59 341-379 (389)
23 TIGR02419 C4_traR_proteo phage 53.2 6.9 0.00015 31.6 1.1 34 24-58 27-62 (63)
24 KOG3362 Predicted BBOX Zn-fing 52.7 4 8.6E-05 38.5 -0.4 34 26-60 116-150 (156)
25 COG1381 RecO Recombinational D 52.4 6.5 0.00014 39.1 1.0 31 25-55 151-182 (251)
26 PF11781 RRN7: RNA polymerase 51.4 5.4 0.00012 29.0 0.2 27 26-55 6-32 (36)
27 PRK13715 conjugal transfer pro 51.1 7.4 0.00016 32.4 1.0 33 28-60 34-67 (73)
28 PF03589 Antiterm: Antitermina 47.3 19 0.0004 31.4 2.9 78 29-119 6-90 (95)
29 PRK10778 dksA RNA polymerase-b 45.6 12 0.00027 35.0 1.6 38 24-61 107-145 (151)
30 PF01286 XPA_N: XPA protein N- 45.0 5.3 0.00012 29.0 -0.7 27 29-55 4-31 (34)
31 TIGR02890 spore_yteA sporulati 43.1 15 0.00033 34.7 1.8 34 26-60 84-119 (159)
32 smart00401 ZnF_GATA zinc finge 38.8 14 0.0003 28.6 0.7 37 27-63 2-40 (52)
33 PF08271 TF_Zn_Ribbon: TFIIB z 38.7 5.7 0.00012 29.2 -1.3 27 30-57 2-28 (43)
34 PHA00080 DksA-like zinc finger 34.2 24 0.00053 29.2 1.5 35 25-60 28-64 (72)
35 PF00320 GATA: GATA zinc finge 28.8 16 0.00034 26.3 -0.4 32 31-62 1-34 (36)
36 PTZ00218 40S ribosomal protein 28.1 31 0.00066 27.6 1.1 40 25-69 13-52 (54)
37 TIGR02420 dksA RNA polymerase- 26.0 44 0.00096 29.3 1.8 31 25-55 77-108 (110)
38 cd00202 ZnF_GATA Zinc finger D 25.9 59 0.0013 25.5 2.3 33 30-62 1-35 (54)
39 PF01258 zf-dskA_traR: Prokary 25.5 8.6 0.00019 27.4 -2.2 29 30-58 5-34 (36)
40 COG1592 Rubrerythrin [Energy p 24.8 29 0.00063 33.3 0.5 23 8-30 111-133 (166)
41 cd07173 NR_DBD_AR DNA-binding 22.8 51 0.0011 27.8 1.6 31 27-60 2-32 (82)
42 KOG0457 Histone acetyltransfer 22.6 92 0.002 34.2 3.7 28 415-442 374-401 (438)
43 cd06968 NR_DBD_ROR DNA-binding 22.1 41 0.00089 29.2 0.9 31 27-60 4-34 (95)
44 cd07171 NR_DBD_ER DNA-binding 22.1 39 0.00084 28.5 0.7 31 27-60 2-32 (82)
45 PRK00423 tfb transcription ini 21.8 30 0.00066 35.5 -0.0 34 25-59 8-41 (310)
46 COG2174 RPL34A Ribosomal prote 21.7 47 0.001 29.2 1.1 33 24-56 30-79 (93)
47 smart00782 PhnA_Zn_Ribbon PhnA 20.6 50 0.0011 25.5 1.0 30 27-56 6-44 (47)
48 PF06752 E_Pc_C: Enhancer of P 20.6 61 0.0013 32.7 1.8 15 330-344 7-21 (230)
No 1
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=2.6e-46 Score=370.08 Aligned_cols=276 Identities=36% Similarity=0.525 Sum_probs=191.4
Q ss_pred ccHHHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCceecchhHHHhHhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHh
Q 012078 7 VSKELNARHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQS 86 (471)
Q Consensus 7 ~sk~~~ar~ekiL~~Llk~P~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgIHR~LG~hISkVKSLsLD~Wt~eeV~~Lq~ 86 (471)
+++...++++++|++||+.|+|++|||||+++|+|||+|+|||||++|+||||+||+||||||||+||.|++|+|+.|+.
T Consensus 4 ~~~~~~~~~~~~l~~Ll~~~~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~ 83 (287)
T KOG0703|consen 4 VEKGSNERNKRRLRELLREPDNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMIS 83 (287)
T ss_pred ccccccchHHHHHHHHHcCcccCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHH
Confidence 44456789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hCchHHHHHHhhcCCCCCChh----HHHHHHHHHhhhcccccCCCCCCCCCCccccccccccCCCCCCCCCCCCCCCcch
Q 012078 87 MGNEKANSYWEAELPPNYDRV----GIENFIRAKYEEKRWVSRDGQANSPPRGLEEKASIHWQRPGEKSGHGYTDNSENL 162 (471)
Q Consensus 87 ~GN~~aN~iwEa~lPp~~d~~----~~e~FIraKY~eKrFv~~~~~~~~ps~~~dek~~~~~~r~~~~~g~~~~~s~~~~ 162 (471)
+||.++|.|||+++|..++++ .+|+|||+|||.|+|+.++..-....+.+++.. .|...+..+.+...++..
T Consensus 84 ~GN~~an~~~ea~~p~~~~~p~~d~~~e~FIR~KYE~kkf~~~~~~~~s~~~~~~~~~----k~~~~~~~~~~~s~s~~~ 159 (287)
T KOG0703|consen 84 MGNAKANSYYEAKLPDPFRRPGPDDLVEQFIRDKYERKKFLDPEEDITSKPGSRDEES----KRSDKRSRKLSSSLSRSF 159 (287)
T ss_pred HcchhhhhhccccCCccccCCChHHHHHHHHHHHHhhhhhccchhhcccCCCcccccc----cccccCccccccchhhhh
Confidence 999999999999999887664 499999999999999997621111122222221 112233344444444433
Q ss_pred hHhhhcCCCCCCCCCCccccccCCCCCCCCCcccccCCCCCCCCccCCCCcCCcCcCCCCCCCCCcccccccccccCCCC
Q 012078 163 SEERKHVQAPSTKDSVPAARISLPLPPRGPDQVVAITKPQQTESTVAPAGATNQSSDANLAVPPPKVDFASDLFDMLSGD 242 (471)
Q Consensus 163 f~e~~~~~~~~~~~a~pasr~~~pa~~~~~~~v~p~Pkpq~~eP~~~~~~~~~~~~d~~~~~~~pkvd~atdlfnmLsmD 242 (471)
+. ... ...-..+. +... +.......++..........++. ++.+.++++
T Consensus 160 ~~-~~r-------~~~~~~~~--~~~s--------------------~~~~~~~~~~~~~~~i~~~~~~~-~~~s~~n~~ 208 (287)
T KOG0703|consen 160 VK-SAR-------EDQLKYFL--PKTS--------------------QPVDDLATFQGPIASPHNLQTTY-SLNSTLNIF 208 (287)
T ss_pred hh-hcc-------cccccccc--ccCC--------------------CCchhhhhccCccccccchheee-ccccccccc
Confidence 33 110 11111111 1111 00001111122233455677777 888888888
Q ss_pred CCCCCCCcc----ccCCCCccccccccccccccccCCCCCcCCCCCCCcccccccccCCCCCCCCCCCCCCcchhhhhHH
Q 012078 243 SPNENSSEA----ASADDNLWAGFQSAVETSTAEKKDSTKAVESSPQSATGIEDLFKDSPSLATPSSSEKPQKDLKNDIM 318 (471)
Q Consensus 243 ~~tengS~A----ss~dd~~wagFqsA~~~sta~k~~~a~a~eS~~~S~sg~eDlFkds~~~~~~~~~~~~qk~~KndIm 318 (471)
+ +++++ + +.+..|+.|+.+...-+ +...+..+..+....-.+.+ ++++-+..+. . . .|+
T Consensus 209 ~---~~~~~~~~~~-~~~~~~~~~~~~~~~~~-~~~~~~~~~~s~~~~f~~~~-~~~~~~~~~~----~------~-~~~ 271 (287)
T KOG0703|consen 209 G---SGKEAADSFT-LRAARFAPLAVAFSTVT-EDLVPFLQRNSLSEGFMEKT-LSKPKRWFGT----Q------Q-SKS 271 (287)
T ss_pred c---CccccCCCcc-cccccccccccccccCc-cccccccccccccccccCcc-cccccccccc----C------c-ccc
Confidence 8 33333 4 78888999998765555 66666666666555555555 7777333322 2 5 899
Q ss_pred HhhccCCcCCCchhhHH
Q 012078 319 SLFEKSNMVSPFAMHQQ 335 (471)
Q Consensus 319 sLfeksn~~spf~~~qq 335 (471)
+|| +-..+.||..++|
T Consensus 272 ~~~-~~~~~~~~~~~~~ 287 (287)
T KOG0703|consen 272 SLF-FLDGNVPFGSKES 287 (287)
T ss_pred ccc-cccccccccccCC
Confidence 999 9999999987764
No 2
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=100.00 E-value=9.5e-41 Score=351.54 Aligned_cols=159 Identities=28% Similarity=0.562 Sum_probs=147.4
Q ss_pred cHHHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCceecchhHHHhHhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhh
Q 012078 8 SKELNARHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSM 87 (471)
Q Consensus 8 sk~~~ar~ekiL~~Llk~P~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgIHR~LG~hISkVKSLsLD~Wt~eeV~~Lq~~ 87 (471)
|||+++|+++||++|++.|+|++|+|||..+|+|||++||||||++|+||||+|| +|||||+||+|+++||++|+.+
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 4999999999999999999999
Q ss_pred CchHHHHHHhhcCCC-------CCChhHHHHHHHHHhhhcccccCCCCCCCCCCccccccccccCCCCCCCCCCCCCCCc
Q 012078 88 GNEKANSYWEAELPP-------NYDRVGIENFIRAKYEEKRWVSRDGQANSPPRGLEEKASIHWQRPGEKSGHGYTDNSE 160 (471)
Q Consensus 88 GN~~aN~iwEa~lPp-------~~d~~~~e~FIraKY~eKrFv~~~~~~~~ps~~~dek~~~~~~r~~~~~g~~~~~s~~ 160 (471)
||.++|+|||++|++ ..+...+++|||.||++|+|+.+...++++++.+++++.+...| .+++||+|++|++
T Consensus 80 GN~~AN~iyeanw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~~~~~~d~p~~~~~~~~~~~~~~~-~~~s~h~~s~sp~ 158 (648)
T PLN03119 80 GNQRAREIYLKNWDHQRQRLPENSNAERVREFIKNVYVQKKYAGANDADKPSKDSQDHVSSEDMTR-RANSYHSYSQSPP 158 (648)
T ss_pred chHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhccCcCCCCCCccccccccccccccc-ccccCCCCCCCCC
Confidence 999999999998853 34456789999999999999999999999998999998887555 5899999999998
Q ss_pred --chhHhhhcCC
Q 012078 161 --NLSEERKHVQ 170 (471)
Q Consensus 161 --~~f~e~~~~~ 170 (471)
+.|||||..+
T Consensus 159 y~~~ye~rr~~~ 170 (648)
T PLN03119 159 YDYQYEERRYGK 170 (648)
T ss_pred cccchhhhhccc
Confidence 8899999775
No 3
>PLN03131 hypothetical protein; Provisional
Probab=100.00 E-value=1.6e-38 Score=336.93 Aligned_cols=157 Identities=29% Similarity=0.549 Sum_probs=141.7
Q ss_pred cHHHHHHHHHHHHHhhcCCCCCCCcCCCCCCCCceecchhHHHhHhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhh
Q 012078 8 SKELNARHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSM 87 (471)
Q Consensus 8 sk~~~ar~ekiL~~Llk~P~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgIHR~LG~hISkVKSLsLD~Wt~eeV~~Lq~~ 87 (471)
||++++|++++|++|++.|+|++|+|||+++|+|||++||||||++|+||||+|| +|||||+||+|+++||++|+.+
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 012078 88 GNEKANSYWEAELP-------PNYDRVGIENFIRAKYEEKRWVSRDGQANSPPRGLEEKASIHWQRPGEKSGHGYTDNSE 160 (471)
Q Consensus 88 GN~~aN~iwEa~lP-------p~~d~~~~e~FIraKY~eKrFv~~~~~~~~ps~~~dek~~~~~~r~~~~~g~~~~~s~~ 160 (471)
||.++|+|||++|+ ...+...+++|||.||++|+|+.+...++++...+..+..+.+.|+ ..++|+|++|+.
T Consensus 80 GN~~AN~iyeanwd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa~~~s~d~pprd~q~~r~~e~e~rr-~~syh~~SqSPp 158 (705)
T PLN03131 80 GNQRAREIYLKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKYAGGKTHDKPPRDLQRIRSHEDETRR-ACSYHSYSQSPP 158 (705)
T ss_pred ccHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhhhcCCCCCCCchhhhhhhcccccccc-cccccCCCcCCC
Confidence 99999999999875 2344567899999999999999998888888777777777766776 679999999988
Q ss_pred --chhHhhhc
Q 012078 161 --NLSEERKH 168 (471)
Q Consensus 161 --~~f~e~~~ 168 (471)
++|||||.
T Consensus 159 Y~~~yedrRy 168 (705)
T PLN03131 159 YDFQYEDRRY 168 (705)
T ss_pred cccccccccc
Confidence 56899876
No 4
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=100.00 E-value=9.6e-38 Score=272.62 Aligned_cols=109 Identities=58% Similarity=1.053 Sum_probs=91.1
Q ss_pred HHHHHhhcCCCCCCCcCCCCCCCCceecchhHHHhHhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhCchHHHHHH
Q 012078 17 KILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYW 96 (471)
Q Consensus 17 kiL~~Llk~P~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgIHR~LG~hISkVKSLsLD~Wt~eeV~~Lq~~GN~~aN~iw 96 (471)
++|+.|++.|+|+.|+|||+++|+|||++||||||+.|+|+||+||+|||+||||+||+|+++||+.|+.+||.++|++|
T Consensus 2 ~~l~~l~~~~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~VkSi~~d~w~~~ev~~~~~~GN~~~n~~~ 81 (116)
T PF01412_consen 2 KILRELLKKPGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRVKSITMDNWSPEEVQRMREGGNKRANSIW 81 (116)
T ss_dssp HHHHHHHCSTTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--EEETTTS---HHHHHHHHHSHHHHHHHHH
T ss_pred HHHHHHHcCcCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhccccccCCCCHHHHHHHHHHChHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCC------CCCChhHHHHHHHHHhhhcccccC
Q 012078 97 EAELP------PNYDRVGIENFIRAKYEEKRWVSR 125 (471)
Q Consensus 97 Ea~lP------p~~d~~~~e~FIraKY~eKrFv~~ 125 (471)
|++.+ +..+...+++||++||++++|+.+
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 233456799999999999999863
No 5
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=100.00 E-value=3.9e-36 Score=261.27 Aligned_cols=103 Identities=58% Similarity=1.018 Sum_probs=96.0
Q ss_pred CCCCCCcCCCCCCCCceecchhHHHhHhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhCchHHHHHHhhcCCCCC-
Q 012078 26 PENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYWEAELPPNY- 104 (471)
Q Consensus 26 P~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgIHR~LG~hISkVKSLsLD~Wt~eeV~~Lq~~GN~~aN~iwEa~lPp~~- 104 (471)
|+|+.|+|||+++|+|||++||||||+.|+|+||.||+|||+||||+||+|++++|++|+.+||.++|+|||+++++..
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 012078 105 ------DRVGIENFIRAKYEEKRWVSRDGQ 128 (471)
Q Consensus 105 ------d~~~~e~FIraKY~eKrFv~~~~~ 128 (471)
+...+++||+.||++++|+.+.+.
T Consensus 81 ~~~~~~~~~~~~~fI~~KY~~k~f~~~~~~ 110 (112)
T smart00105 81 KPPDSDDQQKYESFIAAKYEEKLFVPPESA 110 (112)
T ss_pred CCCCCchHHHHHHHHHHHHHhhhccccccC
Confidence 356799999999999999987653
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=2.5e-33 Score=282.54 Aligned_cols=114 Identities=47% Similarity=0.911 Sum_probs=105.3
Q ss_pred HHHHHHHHhhcCCCCCCCcCCCCCCCCceecchhHHHhHhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhCchHHH
Q 012078 14 RHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKAN 93 (471)
Q Consensus 14 r~ekiL~~Llk~P~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgIHR~LG~hISkVKSLsLD~Wt~eeV~~Lq~~GN~~aN 93 (471)
+.+++|..|.+.++|+.|||||+++|+||||+||||||++|+||||+||+|||+||||+||+|+++||++|..+||.++|
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 56788899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcC------C--CCCChhHHHHHHHHHhhhcccccCCC
Q 012078 94 SYWEAEL------P--PNYDRVGIENFIRAKYEEKRWVSRDG 127 (471)
Q Consensus 94 ~iwEa~l------P--p~~d~~~~e~FIraKY~eKrFv~~~~ 127 (471)
.||+.++ | ..||...+++||+.||++++|+....
T Consensus 86 ~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~~~ 127 (319)
T COG5347 86 RFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDDSS 127 (319)
T ss_pred hHhccCCCcccccccccccCHHHHHHHHHHHHHhhhcccccc
Confidence 9999864 2 34566789999999999999998633
No 7
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.96 E-value=2.6e-28 Score=247.36 Aligned_cols=113 Identities=38% Similarity=0.666 Sum_probs=97.8
Q ss_pred HHHHHHHhhcCCCCCCCcCCCCCCCCceecchhHHHhHhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhCchHHHH
Q 012078 15 HRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANS 94 (471)
Q Consensus 15 ~ekiL~~Llk~P~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgIHR~LG~hISkVKSLsLD~Wt~eeV~~Lq~~GN~~aN~ 94 (471)
..++|+.|+..|+|+.|+|||+++|+|+|++||||||+.|+|+||.||+||++|||++||.|++++|++|+.+||.++|.
T Consensus 9 ~~~vfrkL~~kPgNk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~Ws~eqL~~Mk~GGN~rA~~ 88 (395)
T PLN03114 9 KISVFKKLKAKSDNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSSEQLKMMIYGGNNRAQV 88 (395)
T ss_pred HHHHHHHHHhCcCCCcCccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCCCCHHHHHHHHHhcCHHHHH
Confidence 46779999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcC-CC------CCCh--hHHHHHHHHHhhhcccccCCC
Q 012078 95 YWEAEL-PP------NYDR--VGIENFIRAKYEEKRWVSRDG 127 (471)
Q Consensus 95 iwEa~l-Pp------~~d~--~~~e~FIraKY~eKrFv~~~~ 127 (471)
||+.+. .. .|.- ..+.+.+.+|++++.+..+..
T Consensus 89 fF~qhG~~~~~~~~~KY~S~aA~~Yre~L~keVa~~~a~~~~ 130 (395)
T PLN03114 89 FFKQYGWSDGGKTEAKYTSRAADLYKQILAKEVAKSKAEEEL 130 (395)
T ss_pred HHHHcCCCCCCCcccccCCHHHHHHHHHHHHHHHHhhhcccc
Confidence 998763 11 1221 234455888889888876543
No 8
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=99.95 E-value=3.8e-28 Score=244.89 Aligned_cols=110 Identities=39% Similarity=0.740 Sum_probs=93.7
Q ss_pred HHHHHHHHHhhcCCCCCCCcCCCCCCCCceecchhHHHhHhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhCchHH
Q 012078 13 ARHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKA 92 (471)
Q Consensus 13 ar~ekiL~~Llk~P~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgIHR~LG~hISkVKSLsLD~Wt~eeV~~Lq~~GN~~a 92 (471)
.|.++.|.+|....+|+.|+||++.+|+|||++||||||++|+|+||.||+|||+|||||||+|.+.||+.|+.+||+++
T Consensus 4 prtrr~L~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~~ 83 (386)
T KOG0704|consen 4 PRTRRVLLELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNERF 83 (386)
T ss_pred hHHHHHHHhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchhH
Confidence 46788888888888999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhcC--CCC------CCh---hHHHHHHHHHhhhccc
Q 012078 93 NSYWEAEL--PPN------YDR---VGIENFIRAKYEEKRW 122 (471)
Q Consensus 93 N~iwEa~l--Pp~------~d~---~~~e~FIraKY~eKrF 122 (471)
+.|++.+- .+. |+- ..+++-|.+--+.+.|
T Consensus 84 ~eFL~s~~~~~e~~~i~eKYns~aAa~yRdki~~laegr~w 124 (386)
T KOG0704|consen 84 REFLSSQGIYKETWPIREKYNSRAAALYRDKIAALAEGREW 124 (386)
T ss_pred HHHHhhCccccccccHHHhhccHHHHHHHHHHHHHhcCCcc
Confidence 99998652 222 221 1245556666666666
No 9
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.93 E-value=2.9e-27 Score=244.36 Aligned_cols=86 Identities=45% Similarity=0.842 Sum_probs=83.0
Q ss_pred HHHHHHHHhhcCCCCCCCcCCCCCCCCceecchhHHHhHhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhCchHHH
Q 012078 14 RHRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKAN 93 (471)
Q Consensus 14 r~ekiL~~Llk~P~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgIHR~LG~hISkVKSLsLD~Wt~eeV~~Lq~~GN~~aN 93 (471)
....+++.|...++||.|+|||+++|.|+||+||||||+.|+++||+||+||++|||..||+|+.+||++|+.+||.+|+
T Consensus 9 d~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~ 88 (454)
T KOG0706|consen 9 DIQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANAR 88 (454)
T ss_pred hHHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHH
Confidence 35788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhc
Q 012078 94 SYWEAE 99 (471)
Q Consensus 94 ~iwEa~ 99 (471)
.|+..+
T Consensus 89 ~FFkqh 94 (454)
T KOG0706|consen 89 VFFKQH 94 (454)
T ss_pred HHHHHc
Confidence 999875
No 10
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.92 E-value=2.8e-26 Score=242.38 Aligned_cols=114 Identities=42% Similarity=0.841 Sum_probs=104.6
Q ss_pred HHHHHHHhhcCCCCCCCcCCCCCCCCceecchhHHHhHhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhCchHHHH
Q 012078 15 HRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANS 94 (471)
Q Consensus 15 ~ekiL~~Llk~P~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgIHR~LG~hISkVKSLsLD~Wt~eeV~~Lq~~GN~~aN~ 94 (471)
....|+.|...+||.+|+||+.++|.|+|+|+|+.+|++|+||||.||.|+|+|+||.||.|..|.+..|..+||+.||.
T Consensus 500 ea~a~qairn~rgn~~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl~~Vm~aiGN~~AN~ 579 (749)
T KOG0705|consen 500 EAMALQAIRNMRGNSHCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVELLKVMSAIGNDLANS 579 (749)
T ss_pred hHHHHHHHhcCcCCceeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHHHHHHHHhhhhHHHH
Confidence 45678888899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcC-----C-CCCChhHHHHHHHHHhhhcccccCCCC
Q 012078 95 YWEAEL-----P-PNYDRVGIENFIRAKYEEKRWVSRDGQ 128 (471)
Q Consensus 95 iwEa~l-----P-p~~d~~~~e~FIraKY~eKrFv~~~~~ 128 (471)
+||..+ | +...|.++|+|||+||++|.|..+...
T Consensus 580 vWE~~~~G~~KPs~~s~REEkErwIr~KYeqklFLaPl~~ 619 (749)
T KOG0705|consen 580 VWEGSSQGQTKPSPDSSREEKERWIRAKYEQKLFLAPLPC 619 (749)
T ss_pred HhhhhccCCcCCCccccHHHHHHHHHHHHHHHhhcCCCCC
Confidence 999754 2 345678999999999999999986554
No 11
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.86 E-value=5.6e-23 Score=227.54 Aligned_cols=110 Identities=47% Similarity=0.926 Sum_probs=101.5
Q ss_pred HHHHhhcCCCCCCCcCCCCCCCCceecchhHHHhHhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhCchHHHHHHh
Q 012078 18 ILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYWE 97 (471)
Q Consensus 18 iL~~Llk~P~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgIHR~LG~hISkVKSLsLD~Wt~eeV~~Lq~~GN~~aN~iwE 97 (471)
.+..+.+.|+|..|+|||++.|+|+|+|+||.+|++|+|+||+||+|||||+||+||.|.++.+..++.+||..+|.+||
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 37788899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCC--------CChhHHHHHHHHHhhhcccccCCC
Q 012078 98 AELPPN--------YDRVGIENFIRAKYEEKRWVSRDG 127 (471)
Q Consensus 98 a~lPp~--------~d~~~~e~FIraKY~eKrFv~~~~ 127 (471)
+.++.. .++..++.||++||++++|.-+..
T Consensus 496 ~~l~~~~~~~~~~~~~~~~r~~~i~~kyve~~F~~k~~ 533 (785)
T KOG0521|consen 496 ALLPSYDSSKPTASSSRQAREAWIKAKYVERRFSVKEP 533 (785)
T ss_pred cccccccccCCCCccchhhhhHhhhcccceeeEeeccc
Confidence 998632 235679999999999999987643
No 12
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.82 E-value=1.2e-19 Score=189.84 Aligned_cols=124 Identities=31% Similarity=0.582 Sum_probs=109.9
Q ss_pred HHHHHHHHHHHHHhhcCCCCCCCcCCCCCCC-CceecchhHHHhHhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhh
Q 012078 9 KELNARHRKILEGLLKLPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSM 87 (471)
Q Consensus 9 k~~~ar~ekiL~~Llk~P~Nk~CADCGa~~P-~WaSvn~GVFLC~~CSgIHR~LG~hISkVKSLsLD~Wt~eeV~~Lq~~ 87 (471)
|+.++.++|+||.|+++|+||+|++|+...+ +|+++..|-|+|..|+|.-|.|.. -+|||||+|.+|+..||..|+.+
T Consensus 6 ke~E~~~ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~~-ahRvksiSmttft~qevs~lQsh 84 (524)
T KOG0702|consen 6 KEDEYDYEKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLNP-AHRVKSISMTTFTDQEVSFLQSH 84 (524)
T ss_pred ccchhHHHHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccCCC-ccccceeeeeeccccchHHHhhc
Confidence 4555567999999999999999999999988 999999999999999999999864 47999999999999999999999
Q ss_pred CchHHHHHHhhc-------CCCCCChhHHHHHHHHHhhhcccccCCCCCCCCC
Q 012078 88 GNEKANSYWEAE-------LPPNYDRVGIENFIRAKYEEKRWVSRDGQANSPP 133 (471)
Q Consensus 88 GN~~aN~iwEa~-------lPp~~d~~~~e~FIraKY~eKrFv~~~~~~~~ps 133 (471)
||+.+.+||..- +|+..+....++|||.||+.|+|+......+.++
T Consensus 85 gNq~~k~i~fkl~D~q~S~vPD~rn~~~~kef~q~~y~~kr~~v~~n~~k~~s 137 (524)
T KOG0702|consen 85 GNQVCKEIWFKLFDFQRSNVPDSRNPQKVKEFQQEKYVKKRYYVPKNQMKIPS 137 (524)
T ss_pred chhhhhhhhhcchhhhhccCCCcccchhhHHHHhhhhccceeecCcccccccc
Confidence 999999999864 4667777789999999999999998766555443
No 13
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.79 E-value=1.7e-20 Score=196.51 Aligned_cols=102 Identities=42% Similarity=0.804 Sum_probs=91.5
Q ss_pred cCCCCCCCcCCCCCCCCceecchhHHHhHhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhCchHHHHHHhhcCCC-
Q 012078 24 KLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYWEAELPP- 102 (471)
Q Consensus 24 k~P~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgIHR~LG~hISkVKSLsLD~Wt~eeV~~Lq~~GN~~aN~iwEa~lPp- 102 (471)
+...-+.|+|||+++|.|+||+-|+|||.+|+.+||.||.|||.||+|....|.++.|++...+.|..+|.|||..|-+
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 3456688999999999999999999999999999999999999999999999999999999999999999999987621
Q ss_pred -----------CCCh--hHHHHHHHHHhhhcccccC
Q 012078 103 -----------NYDR--VGIENFIRAKYEEKRWVSR 125 (471)
Q Consensus 103 -----------~~d~--~~~e~FIraKY~eKrFv~~ 125 (471)
..|. +.+++|||+||+...|+.+
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 1222 3589999999999999984
No 14
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.69 E-value=5.8e-18 Score=185.39 Aligned_cols=107 Identities=43% Similarity=0.814 Sum_probs=97.7
Q ss_pred HHhhcCCCCCCCcCCCCCCCCceecchhHHHhHhhhhhhhcCCCccceeeeccCCC--CCHHHHHHHHhhCchHHHHHHh
Q 012078 20 EGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDT--WLPEQVAFIQSMGNEKANSYWE 97 (471)
Q Consensus 20 ~~Llk~P~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgIHR~LG~hISkVKSLsLD~--Wt~eeV~~Lq~~GN~~aN~iwE 97 (471)
+++.....|+.|+|||++.|.|+++|++|.||-.|+|-||+||..+|+|+|++||. |+.+-|+++..+||.++|+||-
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 45666889999999999999999999999999999999999999999999999995 9999999999999999999999
Q ss_pred hcCCCCC------ChhHHHHHHHHHhhhcccccCC
Q 012078 98 AELPPNY------DRVGIENFIRAKYEEKRWVSRD 126 (471)
Q Consensus 98 a~lPp~~------d~~~~e~FIraKY~eKrFv~~~ 126 (471)
.++|++. ....+++||..||.+.+|....
T Consensus 370 ~nl~~~e~lh~dssp~~r~~fi~~Kykeg~fRk~~ 404 (1186)
T KOG1117|consen 370 GNLPPNEHLHPDSSPSTRRQFIKEKYKEGKFRKEH 404 (1186)
T ss_pred cCCCCccccCCCCCcchhhhHHHHHhhcccccccc
Confidence 9998754 2356899999999999887643
No 15
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=94.09 E-value=0.013 Score=66.94 Aligned_cols=73 Identities=21% Similarity=0.232 Sum_probs=61.5
Q ss_pred cCCCCCCCcCCCCC-CCCceecchhHHHhHhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhCchHHHHHHhh
Q 012078 24 KLPENRECADCKAK-GPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYWEA 98 (471)
Q Consensus 24 k~P~Nk~CADCGa~-~P~WaSvn~GVFLC~~CSgIHR~LG~hISkVKSLsLD~Wt~eeV~~Lq~~GN~~aN~iwEa 98 (471)
....+-.|++|++. ...|+++++.+-+|..|+++|+.++.|++..+++.|++..+ |..+..-|+...+..|..
T Consensus 626 ~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~~~~~ 699 (785)
T KOG0521|consen 626 KASSDGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHHATAS 699 (785)
T ss_pred HhccCccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchhhhhh
Confidence 44567889999975 88899999999999999999999999999999999988766 777777777777666643
No 16
>PRK12495 hypothetical protein; Provisional
Probab=77.44 E-value=1.2 Score=44.45 Aligned_cols=40 Identities=25% Similarity=0.377 Sum_probs=29.8
Q ss_pred HHHHHHHHhhc--CCCCCCCcCCCCCCCCceecchhHHHhHhhhhh
Q 012078 14 RHRKILEGLLK--LPENRECADCKAKGPRWASVNLGIFICMQCSGI 57 (471)
Q Consensus 14 r~ekiL~~Llk--~P~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgI 57 (471)
..+++-+.|++ ...+++|-+||.+=|.+ -|+.+|..|..+
T Consensus 26 ~~~~ma~lL~~gatmsa~hC~~CG~PIpa~----pG~~~Cp~CQ~~ 67 (226)
T PRK12495 26 ATERMSELLLQGATMTNAHCDECGDPIFRH----DGQEFCPTCQQP 67 (226)
T ss_pred HHHHHHHHHHhhcccchhhcccccCcccCC----CCeeECCCCCCc
Confidence 34455555555 47899999999998832 699999999754
No 17
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=74.66 E-value=1.7 Score=42.03 Aligned_cols=32 Identities=31% Similarity=0.561 Sum_probs=27.2
Q ss_pred CCCCCCCcCCCCCCC-CceecchhHHHhHhhhh
Q 012078 25 LPENRECADCKAKGP-RWASVNLGIFICMQCSG 56 (471)
Q Consensus 25 ~P~Nk~CADCGa~~P-~WaSvn~GVFLC~~CSg 56 (471)
.|.-..|+-||.... .|.+...|.++|..|..
T Consensus 146 ~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~ 178 (247)
T PRK00085 146 GLDLDHCAVCGAPGDHRYFSPKEGGAVCSECGD 178 (247)
T ss_pred ccchhhHhcCCCCCCceEEecccCCcccccccC
Confidence 466779999998744 78999999999999973
No 18
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=69.01 E-value=5.3 Score=38.50 Aligned_cols=33 Identities=27% Similarity=0.497 Sum_probs=27.3
Q ss_pred CCCCCCCcCCCCCCC-CceecchhHHHhHhhhhh
Q 012078 25 LPENRECADCKAKGP-RWASVNLGIFICMQCSGI 57 (471)
Q Consensus 25 ~P~Nk~CADCGa~~P-~WaSvn~GVFLC~~CSgI 57 (471)
.|.-..|+.||..++ .|.++..|.|+|..|...
T Consensus 144 ~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 144 ALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred CcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 467789999998544 688999999999999763
No 19
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=68.97 E-value=2 Score=30.83 Aligned_cols=34 Identities=12% Similarity=0.335 Sum_probs=29.4
Q ss_pred CCCCCcCCCCCCCCceecchhHHHhHhhhhh-hhc
Q 012078 27 ENRECADCKAKGPRWASVNLGIFICMQCSGI-HRS 60 (471)
Q Consensus 27 ~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgI-HR~ 60 (471)
.+..|..|+.....|.+.+=+++||..|... |+.
T Consensus 2 ~~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~ 36 (42)
T PF00643_consen 2 QEPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG 36 (42)
T ss_dssp SSSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT
T ss_pred cCccCccCCccceEEEecCCCCccCccCCCCCCCC
Confidence 3578999999889999999999999999998 886
No 20
>PRK11019 hypothetical protein; Provisional
Probab=65.82 E-value=2.6 Score=36.40 Aligned_cols=37 Identities=22% Similarity=0.530 Sum_probs=26.0
Q ss_pred CCCCCcCCCCCCC--CceecchhHHHhHhhhhhhhcCCCc
Q 012078 27 ENRECADCKAKGP--RWASVNLGIFICMQCSGIHRSLGVH 64 (471)
Q Consensus 27 ~Nk~CADCGa~~P--~WaSvn~GVFLC~~CSgIHR~LG~h 64 (471)
.-.+|.|||.+=| +|--+. ++-.|+.|...+...+.|
T Consensus 35 syg~C~~CG~~Ip~~Rl~A~P-~a~~Cv~Cq~~~E~~~k~ 73 (88)
T PRK11019 35 SLTECEECGEPIPEARRKAIP-GVRLCVACQQEKDLQQAA 73 (88)
T ss_pred cCCeeCcCCCcCcHHHHhhcC-CccccHHHHHHHHHHHhH
Confidence 4579999999743 344333 678999999987654433
No 21
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=60.51 E-value=5.5 Score=36.18 Aligned_cols=30 Identities=17% Similarity=0.454 Sum_probs=20.6
Q ss_pred CCcCCCCCCC-CceecchhHHHhHhhhhhhh
Q 012078 30 ECADCKAKGP-RWASVNLGIFICMQCSGIHR 59 (471)
Q Consensus 30 ~CADCGa~~P-~WaSvn~GVFLC~~CSgIHR 59 (471)
+|.+||.+=| .=.-.--+..+|..|...|-
T Consensus 82 ~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~~E 112 (120)
T COG1734 82 ICEECGEPIPEARLEARPTARLCIECQERAE 112 (120)
T ss_pred chhccCCcCCHHHHhhCcchHHHHHHHHHHH
Confidence 8999999722 11122335789999998774
No 22
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=54.95 E-value=6.9 Score=39.12 Aligned_cols=39 Identities=18% Similarity=0.399 Sum_probs=29.4
Q ss_pred HHHHHHHhhcCCCCCCCcCCCCCCCCceecchhHHHhHhhhhhhh
Q 012078 15 HRKILEGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHR 59 (471)
Q Consensus 15 ~ekiL~~Llk~P~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgIHR 59 (471)
-+++++..++......|..||.....|. ++|..|.+.|-
T Consensus 341 ~~~~~~~~~~~~p~~~c~~cg~~~~~~~------~~c~~c~~~~~ 379 (389)
T PRK11788 341 LRDLVGEQLKRKPRYRCRNCGFTARTLY------WHCPSCKAWET 379 (389)
T ss_pred HHHHHHHHHhCCCCEECCCCCCCCccce------eECcCCCCccC
Confidence 4666666655444455999999999996 78999998873
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=53.20 E-value=6.9 Score=31.58 Aligned_cols=34 Identities=35% Similarity=0.647 Sum_probs=23.5
Q ss_pred cCCCCCCCcCCCCCCC--CceecchhHHHhHhhhhhh
Q 012078 24 KLPENRECADCKAKGP--RWASVNLGIFICMQCSGIH 58 (471)
Q Consensus 24 k~P~Nk~CADCGa~~P--~WaSvn~GVFLC~~CSgIH 58 (471)
..++...|.|||.+=| +|.- .-|+..|..|...+
T Consensus 27 ~~~s~g~C~~Cg~~Ip~~Rl~a-~p~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 27 IGPSLRECEDCGEPIPEARREA-LPGVTRCVSCQEIL 62 (63)
T ss_pred cCCCCCeeccCCCcChHHHHhh-cCCcCCcHHHHhhc
Confidence 4567789999999733 2322 23688899998654
No 24
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=52.69 E-value=4 Score=38.54 Aligned_cols=34 Identities=29% Similarity=0.640 Sum_probs=28.4
Q ss_pred CCCCCCcCCCCCCCCceecchhHHHhH-hhhhhhhc
Q 012078 26 PENRECADCKAKGPRWASVNLGIFICM-QCSGIHRS 60 (471)
Q Consensus 26 P~Nk~CADCGa~~P~WaSvn~GVFLC~-~CSgIHR~ 60 (471)
|--+.|+-|| ....|.|++-|.-+|. .|-.+|..
T Consensus 116 P~r~fCaVCG-~~S~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 116 PLRKFCAVCG-YDSKYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred CcchhhhhcC-CCchhHHHhcCCceeechhhhhccc
Confidence 4557899999 6677999999999985 89999965
No 25
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=52.39 E-value=6.5 Score=39.15 Aligned_cols=31 Identities=32% Similarity=0.729 Sum_probs=27.1
Q ss_pred CCCCCCCcCCCCC-CCCceecchhHHHhHhhh
Q 012078 25 LPENRECADCKAK-GPRWASVNLGIFICMQCS 55 (471)
Q Consensus 25 ~P~Nk~CADCGa~-~P~WaSvn~GVFLC~~CS 55 (471)
.+.=..|+.||.+ ++...+.-.|-++|.+|.
T Consensus 151 ~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 151 GPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred ccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 4566789999998 557999999999999998
No 26
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=51.36 E-value=5.4 Score=29.00 Aligned_cols=27 Identities=26% Similarity=0.812 Sum_probs=23.3
Q ss_pred CCCCCCcCCCCCCCCceecchhHHHhHhhh
Q 012078 26 PENRECADCKAKGPRWASVNLGIFICMQCS 55 (471)
Q Consensus 26 P~Nk~CADCGa~~P~WaSvn~GVFLC~~CS 55 (471)
..|..|..|++. |....=|.++|.+|-
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCc
Confidence 456679999998 888999999999995
No 27
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=51.09 E-value=7.4 Score=32.39 Aligned_cols=33 Identities=18% Similarity=0.496 Sum_probs=22.2
Q ss_pred CCCCcCCCCCCCCce-ecchhHHHhHhhhhhhhc
Q 012078 28 NRECADCKAKGPRWA-SVNLGIFICMQCSGIHRS 60 (471)
Q Consensus 28 Nk~CADCGa~~P~Wa-Svn~GVFLC~~CSgIHR~ 60 (471)
...|.|||.+=|.== -.--|+..|..|...+-.
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 468999999744211 122378899999886643
No 28
>PF03589 Antiterm: Antitermination protein; InterPro: IPR003222 This entry consists of antitermination proteins found in bacteriophages, such as protein Q from phage lambda, and some bacterial homologues. Protein Q positively regulates expression of the phage late gene operon by binding to the bacterial host RNA polymerase (RNAP) and modifying it. The modified RNAP transcribes through termination sites that otherwise prevent expression of the regulated genes [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=47.28 E-value=19 Score=31.40 Aligned_cols=78 Identities=18% Similarity=0.452 Sum_probs=48.5
Q ss_pred CCCcCCCCCCC------CceecchhHH-HhHhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhCchHHHHHHhhcCC
Q 012078 29 RECADCKAKGP------RWASVNLGIF-ICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAFIQSMGNEKANSYWEAELP 101 (471)
Q Consensus 29 k~CADCGa~~P------~WaSvn~GVF-LC~~CSgIHR~LG~hISkVKSLsLD~Wt~eeV~~Lq~~GN~~aN~iwEa~lP 101 (471)
..|.+|+..+- +-+-+-+-+| .|.+|++ ..||++.+ ..-++.|...-.......|..+|.
T Consensus 6 ~~c~~c~g~g~al~~~~s~~~~G~pvfk~c~rcgg------~G~sr~~~-------~~a~~al~~~a~~~~~~~w~rk~k 72 (95)
T PF03589_consen 6 DSCRRCAGDGAALDMKQSKAQFGVPVFKDCERCGG------RGYSRLPS-------SRAIEALTQYAPKLAPRTWLRKWK 72 (95)
T ss_pred CCcCccCCcceeccHHHhHhccCCchhhhhhhhcC------CCCCCCCh-------HHHHHHHHHHHHHHCHHHHHHHhh
Confidence 46778887651 1111233455 7888876 33556554 345677777888888889999999
Q ss_pred CCCChhHHHHHHHHHhhh
Q 012078 102 PNYDRVGIENFIRAKYEE 119 (471)
Q Consensus 102 p~~d~~~~e~FIraKY~e 119 (471)
+.++..-.+-++..-|.+
T Consensus 73 ~~~~~lv~~~~aeea~ad 90 (95)
T PF03589_consen 73 PFYEALVMKCLAEEAFAD 90 (95)
T ss_pred hHHHHHHHHHHHHHHHHH
Confidence 887654444444444443
No 29
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=45.63 E-value=12 Score=35.04 Aligned_cols=38 Identities=13% Similarity=0.270 Sum_probs=24.0
Q ss_pred cCCCCCCCcCCCCCCC-CceecchhHHHhHhhhhhhhcC
Q 012078 24 KLPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRSL 61 (471)
Q Consensus 24 k~P~Nk~CADCGa~~P-~WaSvn~GVFLC~~CSgIHR~L 61 (471)
..+.-..|-+||.+=| .=.-+--++.+|+.|...|-..
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 4567779999998621 1111122357899999877543
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=45.03 E-value=5.3 Score=29.02 Aligned_cols=27 Identities=19% Similarity=0.582 Sum_probs=16.8
Q ss_pred CCCcCCCCC-CCCceecchhHHHhHhhh
Q 012078 29 RECADCKAK-GPRWASVNLGIFICMQCS 55 (471)
Q Consensus 29 k~CADCGa~-~P~WaSvn~GVFLC~~CS 55 (471)
..|.+|+.. .-+|..-+|+.-||..|.
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 469999987 677999999999999994
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=43.10 E-value=15 Score=34.72 Aligned_cols=34 Identities=15% Similarity=0.333 Sum_probs=22.0
Q ss_pred CCCCCCcCCCCC--CCCceecchhHHHhHhhhhhhhc
Q 012078 26 PENRECADCKAK--GPRWASVNLGIFICMQCSGIHRS 60 (471)
Q Consensus 26 P~Nk~CADCGa~--~P~WaSvn~GVFLC~~CSgIHR~ 60 (471)
..=-.|.+||.+ ..++-.+. ++-.|+.|...+-.
T Consensus 84 G~YG~Ce~CGe~I~~~RL~a~P-~a~~Ci~Cq~~~E~ 119 (159)
T TIGR02890 84 GTYGICEVCGKPIPYERLEAIP-TATTCVECQNRKEV 119 (159)
T ss_pred CCCCeecccCCcccHHHHhhCC-CcchhHHHHHHhhh
Confidence 444579999986 22222333 46789999987643
No 32
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=38.75 E-value=14 Score=28.64 Aligned_cols=37 Identities=24% Similarity=0.587 Sum_probs=30.3
Q ss_pred CCCCCcCCCCC-CCCceecchhH-HHhHhhhhhhhcCCC
Q 012078 27 ENRECADCKAK-GPRWASVNLGI-FICMQCSGIHRSLGV 63 (471)
Q Consensus 27 ~Nk~CADCGa~-~P~WaSvn~GV-FLC~~CSgIHR~LG~ 63 (471)
..+.|.+|+.. .|.|=....|- +||-.|.-..+..+.
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~ 40 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCC
Confidence 46789999986 78898888886 999999887777654
No 33
>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=38.66 E-value=5.7 Score=29.24 Aligned_cols=27 Identities=22% Similarity=0.600 Sum_probs=20.8
Q ss_pred CCcCCCCCCCCceecchhHHHhHhhhhh
Q 012078 30 ECADCKAKGPRWASVNLGIFICMQCSGI 57 (471)
Q Consensus 30 ~CADCGa~~P~WaSvn~GVFLC~~CSgI 57 (471)
+|-.||+.. ....-..|-++|..|..+
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 455667899999999544
No 34
>PHA00080 DksA-like zinc finger domain containing protein
Probab=34.18 E-value=24 Score=29.23 Aligned_cols=35 Identities=26% Similarity=0.563 Sum_probs=23.8
Q ss_pred CCCCCCCcCCCCCC--CCceecchhHHHhHhhhhhhhc
Q 012078 25 LPENRECADCKAKG--PRWASVNLGIFICMQCSGIHRS 60 (471)
Q Consensus 25 ~P~Nk~CADCGa~~--P~WaSvn~GVFLC~~CSgIHR~ 60 (471)
..+...|.|||..= .+|.-+. |+..|..|...+-.
T Consensus 28 ~~~~~~C~~Cg~~Ip~~Rl~a~P-~~~~Cv~Cq~~~E~ 64 (72)
T PHA00080 28 APSATHCEECGDPIPEARREAVP-GCRTCVSCQEILEL 64 (72)
T ss_pred CCCCCEecCCCCcCcHHHHHhCC-CccCcHHHHHHHHH
Confidence 35566899999973 3343333 56779999987643
No 35
>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=28.84 E-value=16 Score=26.29 Aligned_cols=32 Identities=25% Similarity=0.694 Sum_probs=22.8
Q ss_pred CcCCCCC-CCCceecchhHH-HhHhhhhhhhcCC
Q 012078 31 CADCKAK-GPRWASVNLGIF-ICMQCSGIHRSLG 62 (471)
Q Consensus 31 CADCGa~-~P~WaSvn~GVF-LC~~CSgIHR~LG 62 (471)
|.+|+.. .|.|=....|-. ||-.|.-.+|..|
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 889998887776 9999987777644
No 36
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=28.11 E-value=31 Score=27.64 Aligned_cols=40 Identities=23% Similarity=0.375 Sum_probs=28.4
Q ss_pred CCCCCCCcCCCCCCCCceecchhHHHhHhhhhhhhcCCCccceee
Q 012078 25 LPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVR 69 (471)
Q Consensus 25 ~P~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgIHR~LG~hISkVK 69 (471)
.++-+.|.-||... =+--.||..+|..|- |++...|.++|
T Consensus 13 GkGsr~C~vCg~~~--gliRkygL~~CRqCF---Re~A~~iGF~K 52 (54)
T PTZ00218 13 GKGSRQCRVCSNRH--GLIRKYGLNVCRQCF---RENAELIGFHK 52 (54)
T ss_pred CCCCCeeecCCCcc--hhhhhcCcchhhHHH---HHhhHhcCeee
Confidence 35778999999864 334489999999996 55544555554
No 37
>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=25.95 E-value=44 Score=29.28 Aligned_cols=31 Identities=16% Similarity=0.336 Sum_probs=17.9
Q ss_pred CCCCCCCcCCCCCCCC-ceecchhHHHhHhhh
Q 012078 25 LPENRECADCKAKGPR-WASVNLGIFICMQCS 55 (471)
Q Consensus 25 ~P~Nk~CADCGa~~P~-WaSvn~GVFLC~~CS 55 (471)
.+.-..|.|||.+=|. =.-.-=++..|..|.
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 3456799999987221 111111346788885
No 38
>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=25.89 E-value=59 Score=25.47 Aligned_cols=33 Identities=24% Similarity=0.637 Sum_probs=26.8
Q ss_pred CCcCCCCC-CCCceecc-hhHHHhHhhhhhhhcCC
Q 012078 30 ECADCKAK-GPRWASVN-LGIFICMQCSGIHRSLG 62 (471)
Q Consensus 30 ~CADCGa~-~P~WaSvn-~GVFLC~~CSgIHR~LG 62 (471)
.|..|+.. -|.|=... -+..||-.|.-..+..|
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 78899999987777765
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=25.45 E-value=8.6 Score=27.36 Aligned_cols=29 Identities=24% Similarity=0.563 Sum_probs=15.7
Q ss_pred CCcCCCCCCC-CceecchhHHHhHhhhhhh
Q 012078 30 ECADCKAKGP-RWASVNLGIFICMQCSGIH 58 (471)
Q Consensus 30 ~CADCGa~~P-~WaSvn~GVFLC~~CSgIH 58 (471)
.|.+||..=+ .=.-+--+..+|..|...|
T Consensus 5 ~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~~ 34 (36)
T PF01258_consen 5 ICEDCGEPIPEERLVAVPGATLCVECQERR 34 (36)
T ss_dssp B-TTTSSBEEHHHHHHCTTECS-HHHHHHH
T ss_pred CccccCChHHHHHHHhCCCcEECHHHhCcc
Confidence 4999997621 1111223677899998765
No 40
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=24.77 E-value=29 Score=33.30 Aligned_cols=23 Identities=26% Similarity=0.485 Sum_probs=18.1
Q ss_pred cHHHHHHHHHHHHHhhcCCCCCC
Q 012078 8 SKELNARHRKILEGLLKLPENRE 30 (471)
Q Consensus 8 sk~~~ar~ekiL~~Llk~P~Nk~ 30 (471)
..+.+.+|.+.++.++..+.+..
T Consensus 111 ~~~~Ek~H~~~~~~~Le~~~~~~ 133 (166)
T COG1592 111 AAKAEKRHAEMFRGLLERLEEGK 133 (166)
T ss_pred HHHHHHHHHHHHHHHHHhhhcCC
Confidence 34667889999999998876654
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=22.82 E-value=51 Score=27.82 Aligned_cols=31 Identities=16% Similarity=0.540 Sum_probs=25.3
Q ss_pred CCCCCcCCCCCCCCceecchhHHHhHhhhhhhhc
Q 012078 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (471)
Q Consensus 27 ~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgIHR~ 60 (471)
..+.|.=||.... ...||++.|..|.+..|-
T Consensus 2 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 32 (82)
T cd07173 2 PQKTCLICGDEAS---GCHYGALTCGSCKVFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECcchhhhHHHHHHH
Confidence 4567999997654 468999999999998874
No 42
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=22.55 E-value=92 Score=34.17 Aligned_cols=28 Identities=14% Similarity=0.264 Sum_probs=20.8
Q ss_pred hhHHHHHHhhhccccccccCCchhHHHH
Q 012078 415 ADLQKLMQAMSMVPTHQVAAGPADIQKL 442 (471)
Q Consensus 415 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 442 (471)
.|.+.|.+....+|.+-++-+-+-++++
T Consensus 374 e~E~~lc~~~~~~p~~yLe~~~vl~~e~ 401 (438)
T KOG0457|consen 374 EDEKRLCQELKILPKLYLELKEVLSREI 401 (438)
T ss_pred hhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence 5778899999999988877655544443
No 43
>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=22.10 E-value=41 Score=29.15 Aligned_cols=31 Identities=29% Similarity=0.718 Sum_probs=25.4
Q ss_pred CCCCCcCCCCCCCCceecchhHHHhHhhhhhhhc
Q 012078 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (471)
Q Consensus 27 ~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgIHR~ 60 (471)
++..|.=||.... ...||++.|..|.+..|-
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 44
>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=22.06 E-value=39 Score=28.53 Aligned_cols=31 Identities=19% Similarity=0.613 Sum_probs=25.4
Q ss_pred CCCCCcCCCCCCCCceecchhHHHhHhhhhhhhc
Q 012078 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (471)
Q Consensus 27 ~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgIHR~ 60 (471)
.|..|.=||.... ...||++.|..|.+..|-
T Consensus 2 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 2 DTHFCAVCSDYAS---GYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 4678999997554 468999999999998874
No 45
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=21.76 E-value=30 Score=35.50 Aligned_cols=34 Identities=18% Similarity=0.420 Sum_probs=23.8
Q ss_pred CCCCCCCcCCCCCCCCceecchhHHHhHhhhhhhh
Q 012078 25 LPENRECADCKAKGPRWASVNLGIFICMQCSGIHR 59 (471)
Q Consensus 25 ~P~Nk~CADCGa~~P~WaSvn~GVFLC~~CSgIHR 59 (471)
......|-+||.... -....-|-.||..|.-|..
T Consensus 8 ~~~~~~Cp~Cg~~~i-v~d~~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 8 EEEKLVCPECGSDKL-IYDYERGEIVCADCGLVIE 41 (310)
T ss_pred cccCCcCcCCCCCCe-eEECCCCeEeecccCCccc
Confidence 344568999997432 2245679999999987653
No 46
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=21.66 E-value=47 Score=29.24 Aligned_cols=33 Identities=24% Similarity=0.561 Sum_probs=23.1
Q ss_pred cCCCCCCCcCCCCC--------CCCc---------eecchhHHHhHhhhh
Q 012078 24 KLPENRECADCKAK--------GPRW---------ASVNLGIFICMQCSG 56 (471)
Q Consensus 24 k~P~Nk~CADCGa~--------~P~W---------aSvn~GVFLC~~CSg 56 (471)
+.++--.|++||.+ ..++ .+=.||-.+|..|..
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 45666789999986 1112 234689999999974
No 47
>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=20.64 E-value=50 Score=25.53 Aligned_cols=30 Identities=17% Similarity=0.639 Sum_probs=20.6
Q ss_pred CCCCCcCCCCCCC--Cc-------eecchhHHHhHhhhh
Q 012078 27 ENRECADCKAKGP--RW-------ASVNLGIFICMQCSG 56 (471)
Q Consensus 27 ~Nk~CADCGa~~P--~W-------aSvn~GVFLC~~CSg 56 (471)
.+..|-=|++..+ .| .+..-.|+||..|..
T Consensus 6 s~~kCELC~a~~~L~vy~Vpp~~~~~~d~~iliC~tC~~ 44 (47)
T smart00782 6 CESKCELCGSDSPLVVYAVPPSSDVTADNSVMLCDTCHS 44 (47)
T ss_pred cCCcccCcCCCCCceEEecCCCCCCCccceeeechHHHH
Confidence 3445999998643 12 244668999999964
No 48
>PF06752 E_Pc_C: Enhancer of Polycomb C-terminus; InterPro: IPR009607 This entry represents the C terminus of eukaryotic enhancer of polycomb proteins, which have roles in heterochromatin formation []. This family contains several conserved motifs.
Probab=20.63 E-value=61 Score=32.73 Aligned_cols=15 Identities=47% Similarity=0.762 Sum_probs=10.9
Q ss_pred chhhHHHHHHHHHHH
Q 012078 330 FAMHQQQLTMLAQQQ 344 (471)
Q Consensus 330 f~~~qqq~~~~~qqq 344 (471)
|--|||||+.|-.||
T Consensus 7 yQqHQqQL~~MQkQQ 21 (230)
T PF06752_consen 7 YQQHQQQLVLMQKQQ 21 (230)
T ss_pred HHHHHHHHHHHHHHH
Confidence 456888888886655
Done!