Query 012502
Match_columns 462
No_of_seqs 183 out of 1193
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 03:19:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012502.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012502hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0703 Predicted GTPase-activ 100.0 4.4E-45 9.6E-50 359.7 12.7 275 8-359 5-287 (287)
2 PLN03119 putative ADP-ribosyla 100.0 3.5E-40 7.6E-45 346.1 14.7 156 8-166 3-168 (648)
3 PLN03131 hypothetical protein; 100.0 6.6E-38 1.4E-42 331.1 13.2 156 8-166 3-168 (705)
4 PF01412 ArfGap: Putative GTPa 100.0 1.3E-37 2.7E-42 269.9 7.3 109 17-125 2-116 (116)
5 smart00105 ArfGap Putative GTP 100.0 4.8E-36 1E-40 258.9 9.3 103 26-128 1-110 (112)
6 COG5347 GTPase-activating prot 100.0 5.3E-33 1.1E-37 278.6 11.1 114 14-127 6-127 (319)
7 PLN03114 ADP-ribosylation fact 100.0 3.8E-27 8.1E-32 238.3 18.8 113 15-127 9-130 (395)
8 KOG0704 ADP-ribosylation facto 99.9 2.3E-28 5E-33 245.8 6.4 88 12-99 3-90 (386)
9 KOG0706 Predicted GTPase-activ 99.9 5.7E-27 1.2E-31 241.3 7.1 85 15-99 10-94 (454)
10 KOG0705 GTPase-activating prot 99.9 7.4E-26 1.6E-30 238.6 6.7 147 15-161 500-655 (749)
11 KOG0521 Putative GTPase activa 99.9 1.6E-22 3.5E-27 222.4 3.6 112 18-129 416-535 (785)
12 KOG0702 Predicted GTPase-activ 99.8 3.7E-18 7.9E-23 178.3 15.2 124 8-132 5-136 (524)
13 KOG0818 GTPase-activating prot 99.7 6.3E-19 1.4E-23 184.4 3.9 101 25-125 5-119 (669)
14 KOG1117 Rho- and Arf-GTPase ac 99.7 3.5E-18 7.6E-23 186.5 4.1 107 20-126 290-404 (1186)
15 KOG0521 Putative GTPase activa 93.8 0.016 3.5E-07 65.8 -0.2 72 24-97 626-698 (785)
16 PRK00085 recO DNA repair prote 82.3 0.93 2E-05 43.5 2.4 35 21-55 142-177 (247)
17 PF00643 zf-B_box: B-box zinc 76.9 2 4.3E-05 30.8 2.1 34 27-60 2-36 (42)
18 TIGR00613 reco DNA repair prot 71.3 3 6.4E-05 39.9 2.4 34 24-57 143-177 (241)
19 PRK12495 hypothetical protein; 63.9 5.4 0.00012 39.9 2.6 38 16-57 28-67 (226)
20 COG1381 RecO Recombinational D 62.4 4.3 9.3E-05 40.2 1.6 37 19-55 145-182 (251)
21 PF11781 RRN7: RNA polymerase 55.7 7.4 0.00016 28.3 1.5 27 26-55 6-32 (36)
22 COG1734 DksA DnaK suppressor p 54.7 5.9 0.00013 35.9 1.0 31 29-59 81-112 (120)
23 PRK11788 tetratricopeptide rep 53.0 9.4 0.0002 37.8 2.3 38 15-58 341-378 (389)
24 PF08271 TF_Zn_Ribbon: TFIIB z 52.1 6 0.00013 29.1 0.5 28 30-58 2-29 (43)
25 KOG3362 Predicted BBOX Zn-fing 49.7 6.3 0.00014 37.3 0.4 34 26-60 116-150 (156)
26 PRK13715 conjugal transfer pro 49.5 12 0.00026 31.1 2.0 33 28-60 34-67 (73)
27 PRK11019 hypothetical protein; 48.4 9.3 0.0002 33.1 1.2 36 27-63 35-72 (88)
28 PRK10778 dksA RNA polymerase-b 48.0 12 0.00025 35.1 1.8 38 23-60 106-144 (151)
29 TIGR02419 C4_traR_proteo phage 46.3 13 0.00027 30.0 1.6 34 24-58 27-62 (63)
30 PF01286 XPA_N: XPA protein N- 45.1 7.3 0.00016 28.4 0.1 27 29-55 4-31 (34)
31 TIGR02890 spore_yteA sporulati 37.1 21 0.00045 33.7 1.7 36 25-60 83-119 (159)
32 smart00401 ZnF_GATA zinc finge 37.0 27 0.00058 27.0 2.1 37 27-63 2-40 (52)
33 PHA00080 DksA-like zinc finger 33.9 28 0.00061 28.8 1.8 35 25-60 28-64 (72)
34 PF00320 GATA: GATA zinc finge 30.7 30 0.00064 24.8 1.3 32 31-62 1-34 (36)
35 TIGR02420 dksA RNA polymerase- 28.9 37 0.0008 29.7 1.8 31 25-55 77-108 (110)
36 PRK02770 S-adenosylmethionine 28.1 26 0.00056 32.5 0.8 41 360-402 40-89 (139)
37 COG2174 RPL34A Ribosomal prote 27.8 38 0.00081 29.9 1.7 33 24-56 30-79 (93)
38 cd07173 NR_DBD_AR DNA-binding 26.4 45 0.00097 28.1 1.8 31 27-60 2-32 (82)
39 PF01258 zf-dskA_traR: Prokary 26.2 11 0.00024 26.8 -1.6 29 30-58 5-34 (36)
40 cd07171 NR_DBD_ER DNA-binding 25.8 43 0.00094 28.2 1.7 31 27-60 2-32 (82)
41 PRK00423 tfb transcription ini 25.0 37 0.00081 34.6 1.4 33 26-59 9-41 (310)
42 COG2158 Uncharacterized protei 24.9 34 0.00074 31.0 0.9 24 40-63 52-77 (112)
43 KOG0457 Histone acetyltransfer 24.4 64 0.0014 35.3 3.0 93 25-123 10-124 (438)
44 smart00782 PhnA_Zn_Ribbon PhnA 24.0 48 0.001 25.6 1.4 34 22-56 2-44 (47)
45 COG1997 RPL43A Ribosomal prote 23.9 58 0.0013 28.6 2.1 30 26-57 33-62 (89)
46 cd06968 NR_DBD_ROR DNA-binding 23.8 50 0.0011 28.6 1.7 31 27-60 4-34 (95)
47 PF07282 OrfB_Zn_ribbon: Putat 22.8 38 0.00083 26.6 0.8 28 27-56 27-54 (69)
48 smart00290 ZnF_UBP Ubiquitin C 22.5 53 0.0011 24.2 1.4 24 30-53 1-24 (50)
49 cd07160 NR_DBD_LXR DNA-binding 22.4 52 0.0011 28.9 1.6 31 27-60 17-47 (101)
50 cd07170 NR_DBD_ERR DNA-binding 22.2 51 0.0011 28.7 1.5 30 28-60 4-33 (97)
51 KOG0119 Splicing factor 1/bran 21.9 80 0.0017 35.3 3.2 77 7-88 240-327 (554)
52 COG1592 Rubrerythrin [Energy p 21.8 54 0.0012 31.5 1.7 23 8-30 111-133 (166)
53 COG0675 Transposase and inacti 21.6 33 0.00071 33.1 0.2 23 28-57 309-331 (364)
54 TIGR00373 conserved hypothetic 21.3 45 0.00098 31.1 1.0 29 30-59 111-139 (158)
55 PF12763 EF-hand_4: Cytoskelet 20.7 51 0.0011 28.9 1.2 11 448-458 64-74 (104)
No 1
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=4.4e-45 Score=359.72 Aligned_cols=275 Identities=32% Similarity=0.443 Sum_probs=184.8
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEcccchhcchhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhh
Q 012502 8 SKELNAKHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSM 87 (462)
Q Consensus 8 SKrl~ar~ekiL~~Llk~PgNk~CADCGA~~P~WaSlnfGVFLC~~CSGIHRsLG~hISkVKSLsMDtWT~eEV~~Lq~g 87 (462)
.+...++++++|++||+.|+|+.|||||+++|+|||+|+|||||++|+||||+||+||||||||+||.|++|+|+.|+..
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----HHHHHHHHHhhcCccccCCCCCCCCCcccccccCCCCCCCCCCCCCCCCCCCCCcc
Q 012502 88 GNEKSNSYWEAELPPNYDRV----GIENFIRAKYEEKRWIPRGGNTKSPSRVSEEKASFHRPLPSSSGHRYTNNINRVPD 163 (462)
Q Consensus 88 GN~~aN~iwEa~lPp~~D~~----~~e~FIraKY~eKrF~~~~~~~~~ps~~~~e~~~~~~~~~~r~Gh~~~sS~~~~ed 163 (462)
||.+||+|||+.+|+.+++. .+|+|||+|||.|+|+.++.......+..++.... ...+.+.+|++.+..+....
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 49999999999999998762211112222111111 22234444444433222211
Q ss_pred cccCCCCCCCCCCCCCCCccCCCCccccccccCCCCccCCCCCCCCCCCCCccchhhhhhhhhhhhcccCCCCCCCCCCC
Q 012502 164 VRNIAHPPNASNDIAAPKHSSPATVKVVQQVTPSLKIQEPVQNSEPTVPKSEPAKQEAITTAVIQHKKQNSEPAVPKYEP 243 (462)
Q Consensus 164 RK~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~k~q~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (462)
|-. ..+...+- + . ++ .-+...+ -++
T Consensus 164 r~~------------~~~~~~~~--------~----------s-~~----------~~~~~~~------------~~~-- 188 (287)
T KOG0703|consen 164 RED------------QLKYFLPK--------T----------S-QP----------VDDLATF------------QGP-- 188 (287)
T ss_pred ccc------------cccccccc--------C----------C-CC----------chhhhhc------------cCc--
Confidence 111 00000000 0 0 00 0000000 000
Q ss_pred CCCCCCCCCCCccccccccccccccCCCCCCCCCCC----CCcccccccccccccCCCCCCCCCcccccccchhhhhhhh
Q 012502 244 PKQEASTTPQRKVDYATDLFNLLCTDDSRENDSKTS----NDEKSCANLQSTNASTAEPINSSKATESKVQTRYRIEDLF 319 (462)
Q Consensus 244 ~~~~~~~~~~pKvd~atdlf~ll~~d~~~en~s~~s----~dd~~~~gfqsa~~~~~~~~~~~~~~es~~~s~~~~edlf 319 (462)
........+++ +|...|.+++ ++.+++ +.+..|+.++.+...+.+...+..+..+....-...+ ++
T Consensus 189 -----~~~i~~~~~~~-~~~s~~n~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~f~~~~-~~ 258 (287)
T KOG0703|consen 189 -----IASPHNLQTTY-SLNSTLNIFG---SGKEAADSFTLRAARFAPLAVAFSTVTEDLVPFLQRNSLSEGFMEKT-LS 258 (287)
T ss_pred -----cccccchheee-cccccccccc---CccccCCCcccccccccccccccccCccccccccccccccccccCcc-cc
Confidence 01244555777 9888888888 333332 6777788888877443365555555555554444444 77
Q ss_pred cCCCCCCCCccccchhhhhhhhHhhhccccccCCcchhHH
Q 012502 320 MGSPSVIPSVSEKSQKDVKNDVMNLFGKSEMVSPFSIDQQ 359 (462)
Q Consensus 320 ~~~~~~~~~~~~~~qk~~kndim~lf~ks~~vspf~~hqq 359 (462)
++-+.... . . .|++|| +-..+.||..++|
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 77222232 1 5 899999 9999999988764
No 2
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=100.00 E-value=3.5e-40 Score=346.07 Aligned_cols=156 Identities=27% Similarity=0.530 Sum_probs=146.1
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEcccchhcchhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhh
Q 012502 8 SKELNAKHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSM 87 (462)
Q Consensus 8 SKrl~ar~ekiL~~Llk~PgNk~CADCGA~~P~WaSlnfGVFLC~~CSGIHRsLG~hISkVKSLsMDtWT~eEV~~Lq~g 87 (462)
|||+++|++++|++|++.|+|++|+|||+++|.|||++||||||++|+||||+|| +|||||+||+|+++||++|+.+
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-------CCChhHHHHHHHHHhhcCccccCCCCCCCCCcccccccCCCCCCCCCCCCCCCCCCCC
Q 012502 88 GNEKSNSYWEAELPP-------NYDRVGIENFIRAKYEEKRWIPRGGNTKSPSRVSEEKASFHRPLPSSSGHRYTNNINR 160 (462)
Q Consensus 88 GN~~aN~iwEa~lPp-------~~D~~~~e~FIraKY~eKrF~~~~~~~~~ps~~~~e~~~~~~~~~~r~Gh~~~sS~~~ 160 (462)
||.++|+|||++|++ ..+...+++|||.||++|+|+.+...++++++.++++..+....+.++||++.+|..+
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 3455678999999999999999999999999899999998877889999999999996
Q ss_pred C---ccccc
Q 012502 161 V---PDVRN 166 (462)
Q Consensus 161 ~---edRK~ 166 (462)
. |||||
T Consensus 160 ~~~ye~rr~ 168 (648)
T PLN03119 160 DYQYEERRY 168 (648)
T ss_pred ccchhhhhc
Confidence 6 89999
No 3
>PLN03131 hypothetical protein; Provisional
Probab=100.00 E-value=6.6e-38 Score=331.11 Aligned_cols=156 Identities=28% Similarity=0.547 Sum_probs=141.6
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEcccchhcchhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhh
Q 012502 8 SKELNAKHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSM 87 (462)
Q Consensus 8 SKrl~ar~ekiL~~Llk~PgNk~CADCGA~~P~WaSlnfGVFLC~~CSGIHRsLG~hISkVKSLsMDtWT~eEV~~Lq~g 87 (462)
|||++++++++|++|++.|+|++|+|||+++|+|||++||||||+.|+||||.|| +|||||+||+|+++||++|+.+
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 6899999999999999999999999999999999999999999999999999998 4999999999999999999999
Q ss_pred cchhHHHHHhhcCC-------CCCChhHHHHHHHHHhhcCccccCCCCCCCCCcccccccCCCCCCCCCCCCCCCCCCCC
Q 012502 88 GNEKSNSYWEAELP-------PNYDRVGIENFIRAKYEEKRWIPRGGNTKSPSRVSEEKASFHRPLPSSSGHRYTNNINR 160 (462)
Q Consensus 88 GN~~aN~iwEa~lP-------p~~D~~~~e~FIraKY~eKrF~~~~~~~~~ps~~~~e~~~~~~~~~~r~Gh~~~sS~~~ 160 (462)
||.++|+|||++|+ +..+...+++|||.||++|+|+.+...++++......+..+....+..++|++..|..+
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 99999999999874 33445678999999999999999998888887777777777666677899999999998
Q ss_pred C---ccccc
Q 012502 161 V---PDVRN 166 (462)
Q Consensus 161 ~---edRK~ 166 (462)
. ||||+
T Consensus 160 ~~~yedrRy 168 (705)
T PLN03131 160 DFQYEDRRY 168 (705)
T ss_pred ccccccccc
Confidence 7 78877
No 4
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=100.00 E-value=1.3e-37 Score=269.90 Aligned_cols=109 Identities=57% Similarity=1.048 Sum_probs=91.0
Q ss_pred HHHHHHhcCCCCCCCcCCCCCCCCeeEcccchhcchhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhcchhHHHHH
Q 012502 17 KILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYW 96 (462)
Q Consensus 17 kiL~~Llk~PgNk~CADCGA~~P~WaSlnfGVFLC~~CSGIHRsLG~hISkVKSLsMDtWT~eEV~~Lq~gGN~~aN~iw 96 (462)
++|+.|++.|+|+.|||||+++|+|||++||||||+.|+|+||+||+|||+||||+||+|+++||+.|+.+||.++|++|
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------CCCChhHHHHHHHHHhhcCccccC
Q 012502 97 EAELP------PNYDRVGIENFIRAKYEEKRWIPR 125 (462)
Q Consensus 97 Ea~lP------p~~D~~~~e~FIraKY~eKrF~~~ 125 (462)
|++.+ +..+...+++||++||++++|+.+
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 233456789999999999999863
No 5
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=100.00 E-value=4.8e-36 Score=258.90 Aligned_cols=103 Identities=57% Similarity=1.023 Sum_probs=96.1
Q ss_pred CCCCCCcCCCCCCCCeeEcccchhcchhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhcchhHHHHHhhcCCCCC-
Q 012502 26 PENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYWEAELPPNY- 104 (462)
Q Consensus 26 PgNk~CADCGA~~P~WaSlnfGVFLC~~CSGIHRsLG~hISkVKSLsMDtWT~eEV~~Lq~gGN~~aN~iwEa~lPp~~- 104 (462)
|+|+.|||||+++|+|||++||||||+.|+|+||.||+|||+||||+||+|++++|++|+.+||.++|++||+++++..
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 ------ChhHHHHHHHHHhhcCccccCCCC
Q 012502 105 ------DRVGIENFIRAKYEEKRWIPRGGN 128 (462)
Q Consensus 105 ------D~~~~e~FIraKY~eKrF~~~~~~ 128 (462)
+...+++||++||++++|+.+++.
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=99.98 E-value=5.3e-33 Score=278.57 Aligned_cols=114 Identities=46% Similarity=0.881 Sum_probs=104.4
Q ss_pred HHHHHHHHHhcCCCCCCCcCCCCCCCCeeEcccchhcchhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhcchhHH
Q 012502 14 KHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSN 93 (462)
Q Consensus 14 r~ekiL~~Llk~PgNk~CADCGA~~P~WaSlnfGVFLC~~CSGIHRsLG~hISkVKSLsMDtWT~eEV~~Lq~gGN~~aN 93 (462)
..+++|..|...++|+.|||||+++|+|||++||||||++||||||+||+||++||||+||+|+.+||++|+.+||.++|
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 45778888999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcCC--------CCCChhHHHHHHHHHhhcCccccCCC
Q 012502 94 SYWEAELP--------PNYDRVGIENFIRAKYEEKRWIPRGG 127 (462)
Q Consensus 94 ~iwEa~lP--------p~~D~~~~e~FIraKY~eKrF~~~~~ 127 (462)
+||+.+.- ..+|...+++||++||+.++|.....
T Consensus 86 ~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~~~ 127 (319)
T COG5347 86 RFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDDSS 127 (319)
T ss_pred hHhccCCCcccccccccccCHHHHHHHHHHHHHhhhcccccc
Confidence 99998742 24456678999999999999987633
No 7
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.95 E-value=3.8e-27 Score=238.29 Aligned_cols=113 Identities=38% Similarity=0.660 Sum_probs=97.7
Q ss_pred HHHHHHHHhcCCCCCCCcCCCCCCCCeeEcccchhcchhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhcchhHHH
Q 012502 15 HRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNS 94 (462)
Q Consensus 15 ~ekiL~~Llk~PgNk~CADCGA~~P~WaSlnfGVFLC~~CSGIHRsLG~hISkVKSLsMDtWT~eEV~~Lq~gGN~~aN~ 94 (462)
..++|+.|+..|+|+.|+|||+++|+|++++||||||+.|+|+||.||+||++|||++||.|++++|++|+.+||.++|.
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 45779999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcC-CC------CCC-h-hHHHHHHHHHhhcCccccCCC
Q 012502 95 YWEAEL-PP------NYD-R-VGIENFIRAKYEEKRWIPRGG 127 (462)
Q Consensus 95 iwEa~l-Pp------~~D-~-~~~e~FIraKY~eKrF~~~~~ 127 (462)
||+.+. .. .|. + ..+.+.+.+|++++.+..+..
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 11 111 1 234456888899988875443
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-28 Score=245.78 Aligned_cols=88 Identities=42% Similarity=0.841 Sum_probs=84.0
Q ss_pred HHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEcccchhcchhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhcchh
Q 012502 12 NAKHRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEK 91 (462)
Q Consensus 12 ~ar~ekiL~~Llk~PgNk~CADCGA~~P~WaSlnfGVFLC~~CSGIHRsLG~hISkVKSLsMDtWT~eEV~~Lq~gGN~~ 91 (462)
+.|+++.|.+|....+|+.|+||++++|+|||++||||||++|+|+||+||+|||+||||+||+|.+.||+.|+.+||++
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 35778889998888899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhc
Q 012502 92 SNSYWEAE 99 (462)
Q Consensus 92 aN~iwEa~ 99 (462)
++.|++..
T Consensus 83 ~~eFL~s~ 90 (386)
T KOG0704|consen 83 FREFLSSQ 90 (386)
T ss_pred HHHHHhhC
Confidence 99999765
No 9
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.93 E-value=5.7e-27 Score=241.29 Aligned_cols=85 Identities=45% Similarity=0.850 Sum_probs=82.6
Q ss_pred HHHHHHHHhcCCCCCCCcCCCCCCCCeeEcccchhcchhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhcchhHHH
Q 012502 15 HRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNS 94 (462)
Q Consensus 15 ~ekiL~~Llk~PgNk~CADCGA~~P~WaSlnfGVFLC~~CSGIHRsLG~hISkVKSLsMDtWT~eEV~~Lq~gGN~~aN~ 94 (462)
-.++++.|..+++||.|||||+++|.|++++||||||+.|+++||+||+||++|||..||+|+.+||++|+.|||.+|+.
T Consensus 10 ~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~~ 89 (454)
T KOG0706|consen 10 IQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANARV 89 (454)
T ss_pred HHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHHH
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhc
Q 012502 95 YWEAE 99 (462)
Q Consensus 95 iwEa~ 99 (462)
|+..+
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=7.4e-26 Score=238.58 Aligned_cols=147 Identities=36% Similarity=0.667 Sum_probs=119.9
Q ss_pred HHHHHHHHhcCCCCCCCcCCCCCCCCeeEcccchhcchhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhcchhHHH
Q 012502 15 HRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNS 94 (462)
Q Consensus 15 ~ekiL~~Llk~PgNk~CADCGA~~P~WaSlnfGVFLC~~CSGIHRsLG~hISkVKSLsMDtWT~eEV~~Lq~gGN~~aN~ 94 (462)
+...|+.|...+||..|+||+.++|.|+++|+|+.+|++|+||||.||+|+|+||||.||.|..|.+..|..+||+.||.
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 34567888889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcC-----C-CCCChhHHHHHHHHHhhcCccccCCCCCCCCCcccccc---cCCCCCCCCCCCCCCCCCCCCC
Q 012502 95 YWEAEL-----P-PNYDRVGIENFIRAKYEEKRWIPRGGNTKSPSRVSEEK---ASFHRPLPSSSGHRYTNNINRV 161 (462)
Q Consensus 95 iwEa~l-----P-p~~D~~~~e~FIraKY~eKrF~~~~~~~~~ps~~~~e~---~~~~~~~~~r~Gh~~~sS~~~~ 161 (462)
+||... | +.+.++++|+|||+||++|.|..+.....-+-++.-.. ....+.....+.|+++..++..
T Consensus 580 vWE~~~~G~~KPs~~s~REEkErwIr~KYeqklFLaPl~~te~~lgqqLl~A~~~~Dl~t~~lLLAhg~~~e~~~t 655 (749)
T KOG0705|consen 580 VWEGSSQGQTKPSPDSSREEKERWIRAKYEQKLFLAPLPCTEEPLGQQLLRAVAAEDLQTAILLLAHGSREEVNET 655 (749)
T ss_pred HhhhhccCCcCCCccccHHHHHHHHHHHHHHHhhcCCCCCCCCchHHHHHHHHHHHHHHHHHHHHhccCchhhhcc
Confidence 999854 2 34457899999999999999998877655554433222 1111333445666666555554
No 11
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.85 E-value=1.6e-22 Score=222.42 Aligned_cols=112 Identities=46% Similarity=0.889 Sum_probs=102.6
Q ss_pred HHHHHhcCCCCCCCcCCCCCCCCeeEcccchhcchhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhcchhHHHHHh
Q 012502 18 ILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYWE 97 (462)
Q Consensus 18 iL~~Llk~PgNk~CADCGA~~P~WaSlnfGVFLC~~CSGIHRsLG~hISkVKSLsMDtWT~eEV~~Lq~gGN~~aN~iwE 97 (462)
.+..+...|||..|+|||++.|+|+++|+||.+|++|+|+||+||+|||||+|++||.|.++.+.+++.+||..+|.+||
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--------CChhHHHHHHHHHhhcCccccCCCCC
Q 012502 98 AELPPN--------YDRVGIENFIRAKYEEKRWIPRGGNT 129 (462)
Q Consensus 98 a~lPp~--------~D~~~~e~FIraKY~eKrF~~~~~~~ 129 (462)
+.++.. .++..++.||++||++++|..+....
T Consensus 496 ~~l~~~~~~~~~~~~~~~~r~~~i~~kyve~~F~~k~~~~ 535 (785)
T KOG0521|consen 496 ALLPSYDSSKPTASSSRQAREAWIKAKYVERRFSVKEPQI 535 (785)
T ss_pred cccccccccCCCCccchhhhhHhhhcccceeeEeecccch
Confidence 998632 23567899999999999998765543
No 12
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.77 E-value=3.7e-18 Score=178.31 Aligned_cols=124 Identities=30% Similarity=0.558 Sum_probs=111.2
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCCCcCCCCCCC-CeeEcccchhcchhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHh
Q 012502 8 SKELNAKHRKILDGLLKLPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQS 86 (462)
Q Consensus 8 SKrl~ar~ekiL~~Llk~PgNk~CADCGA~~P-~WaSlnfGVFLC~~CSGIHRsLG~hISkVKSLsMDtWT~eEV~~Lq~ 86 (462)
.|+.++.++++||.|+++|+|++|++|..+.+ .|+++.-|-|+|+.|+|..|.|.. -+|||||+|.+|+..||..|+.
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 45556667999999999999999999999988 999999999999999999999875 5899999999999999999999
Q ss_pred hcchhHHHHHhhc-------CCCCCChhHHHHHHHHHhhcCccccCCCCCCCC
Q 012502 87 MGNEKSNSYWEAE-------LPPNYDRVGIENFIRAKYEEKRWIPRGGNTKSP 132 (462)
Q Consensus 87 gGN~~aN~iwEa~-------lPp~~D~~~~e~FIraKY~eKrF~~~~~~~~~p 132 (462)
+||+.+.++|... +|+..+....++||+.||+.|||+-......-+
T Consensus 84 hgNq~~k~i~fkl~D~q~S~vPD~rn~~~~kef~q~~y~~kr~~v~~n~~k~~ 136 (524)
T KOG0702|consen 84 HGNQVCKEIWFKLFDFQRSNVPDSRNPQKVKEFQQEKYVKKRYYVPKNQMKIP 136 (524)
T ss_pred cchhhhhhhhhcchhhhhccCCCcccchhhHHHHhhhhccceeecCccccccc
Confidence 9999999999864 578888888999999999999999766554444
No 13
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.74 E-value=6.3e-19 Score=184.36 Aligned_cols=101 Identities=41% Similarity=0.795 Sum_probs=90.5
Q ss_pred CCCCCCCcCCCCCCCCeeEcccchhcchhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhcchhHHHHHhhcCCC--
Q 012502 25 LPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYWEAELPP-- 102 (462)
Q Consensus 25 ~PgNk~CADCGA~~P~WaSlnfGVFLC~~CSGIHRsLG~hISkVKSLsMDtWT~eEV~~Lq~gGN~~aN~iwEa~lPp-- 102 (462)
...-+.|+|||+++|.|+|++-|+|||.+|..+||+||.|||.||+|.-..|.++.|.+...+.|..+|.|||..+-+
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 455678999999999999999999999999999999999999999999999999999999999999999999987532
Q ss_pred ----------CCCh--hHHHHHHHHHhhcCccccC
Q 012502 103 ----------NYDR--VGIENFIRAKYEEKRWIPR 125 (462)
Q Consensus 103 ----------~~D~--~~~e~FIraKY~eKrF~~~ 125 (462)
..|. ..+++|||+||+.-.|+.+
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 1222 2478999999999999974
No 14
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.71 E-value=3.5e-18 Score=186.52 Aligned_cols=107 Identities=41% Similarity=0.798 Sum_probs=97.3
Q ss_pred HHHhcCCCCCCCcCCCCCCCCeeEcccchhcchhhhhhhhcCCCccceeeeccCCC--CCHHHHHHHHhhcchhHHHHHh
Q 012502 20 DGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDT--WLPEQVAVIQSMGNEKSNSYWE 97 (462)
Q Consensus 20 ~~Llk~PgNk~CADCGA~~P~WaSlnfGVFLC~~CSGIHRsLG~hISkVKSLsMDt--WT~eEV~~Lq~gGN~~aN~iwE 97 (462)
+++.....|+.|+|||++.|.|+++|+++.||-.|+|-||+||..+|+|+|++||. |+.+-|+++...||.++|+||.
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 45566789999999999999999999999999999999999999999999999996 9999999999999999999999
Q ss_pred hcCCCCC------ChhHHHHHHHHHhhcCccccCC
Q 012502 98 AELPPNY------DRVGIENFIRAKYEEKRWIPRG 126 (462)
Q Consensus 98 a~lPp~~------D~~~~e~FIraKY~eKrF~~~~ 126 (462)
+++|+++ ....+++||.+||.+..|-...
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 3457899999999998886443
No 15
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=93.84 E-value=0.016 Score=65.81 Aligned_cols=72 Identities=21% Similarity=0.237 Sum_probs=61.2
Q ss_pred cCCCCCCCcCCCCC-CCCeeEcccchhcchhhhhhhhcCCCccceeeeccCCCCCHHHHHHHHhhcchhHHHHHh
Q 012502 24 KLPENRECADCKAK-GPRWASVNLGIFICMQCSGIHRSLGVHISKVRSATLDTWLPEQVAVIQSMGNEKSNSYWE 97 (462)
Q Consensus 24 k~PgNk~CADCGA~-~P~WaSlnfGVFLC~~CSGIHRsLG~hISkVKSLsMDtWT~eEV~~Lq~gGN~~aN~iwE 97 (462)
....+..|++|++. ...|+++++.+-+|+.|+++|+.++.+++..+++.+++..+ |..+...|+...+..|.
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 34557899999975 78899999999999999999999999999999999988776 77777777777666654
No 16
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=82.35 E-value=0.93 Score=43.47 Aligned_cols=35 Identities=31% Similarity=0.481 Sum_probs=28.6
Q ss_pred HHhcCCCCCCCcCCCCCCC-CeeEcccchhcchhhh
Q 012502 21 GLLKLPENRECADCKAKGP-RWASVNLGIFICMQCS 55 (462)
Q Consensus 21 ~Llk~PgNk~CADCGA~~P-~WaSlnfGVFLC~~CS 55 (462)
.+--.|.-..|+-||.... .|.+..-|.++|..|.
T Consensus 142 ~~G~~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 142 ELGYGLDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred HcCCccchhhHhcCCCCCCceEEecccCCccccccc
Confidence 3333577789999998754 7889999999999997
No 17
>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=76.88 E-value=2 Score=30.81 Aligned_cols=34 Identities=12% Similarity=0.335 Sum_probs=29.4
Q ss_pred CCCCCcCCCCCCCCeeEcccchhcchhhhhh-hhc
Q 012502 27 ENRECADCKAKGPRWASVNLGIFICMQCSGI-HRS 60 (462)
Q Consensus 27 gNk~CADCGA~~P~WaSlnfGVFLC~~CSGI-HRs 60 (462)
.+..|..|......+.+.+-+++||..|... |+.
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 3568999999889999999999999999998 886
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=71.32 E-value=3 Score=39.92 Aligned_cols=34 Identities=26% Similarity=0.462 Sum_probs=27.9
Q ss_pred cCCCCCCCcCCCCCCC-CeeEcccchhcchhhhhh
Q 012502 24 KLPENRECADCKAKGP-RWASVNLGIFICMQCSGI 57 (462)
Q Consensus 24 k~PgNk~CADCGA~~P-~WaSlnfGVFLC~~CSGI 57 (462)
-.|.=..|+.||..++ .|.+...|.|+|..|...
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 19
>PRK12495 hypothetical protein; Provisional
Probab=63.91 E-value=5.4 Score=39.86 Aligned_cols=38 Identities=24% Similarity=0.397 Sum_probs=27.8
Q ss_pred HHHHHHHhc--CCCCCCCcCCCCCCCCeeEcccchhcchhhhhh
Q 012502 16 RKILDGLLK--LPENRECADCKAKGPRWASVNLGIFICMQCSGI 57 (462)
Q Consensus 16 ekiL~~Llk--~PgNk~CADCGA~~P~WaSlnfGVFLC~~CSGI 57 (462)
+++-+.|++ ...++.|-+||.+=|.+ -|+.+|..|..+
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 334444444 46899999999998833 699999999654
No 20
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=62.38 E-value=4.3 Score=40.18 Aligned_cols=37 Identities=32% Similarity=0.588 Sum_probs=29.6
Q ss_pred HHHHhcCCCCCCCcCCCCCC-CCeeEcccchhcchhhh
Q 012502 19 LDGLLKLPENRECADCKAKG-PRWASVNLGIFICMQCS 55 (462)
Q Consensus 19 L~~Llk~PgNk~CADCGA~~-P~WaSlnfGVFLC~~CS 55 (462)
|..+-=.+.=..|+.||.+. +..++.-.|-++|.+|.
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
>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=55.74 E-value=7.4 Score=28.32 Aligned_cols=27 Identities=26% Similarity=0.812 Sum_probs=23.0
Q ss_pred CCCCCCcCCCCCCCCeeEcccchhcchhhh
Q 012502 26 PENRECADCKAKGPRWASVNLGIFICMQCS 55 (462)
Q Consensus 26 PgNk~CADCGA~~P~WaSlnfGVFLC~~CS 55 (462)
..|..|..|++. |....=|.++|.+|-
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 22
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=54.68 E-value=5.9 Score=35.89 Aligned_cols=31 Identities=16% Similarity=0.429 Sum_probs=20.8
Q ss_pred CCCcCCCCCCC-CeeEcccchhcchhhhhhhh
Q 012502 29 RECADCKAKGP-RWASVNLGIFICMQCSGIHR 59 (462)
Q Consensus 29 k~CADCGA~~P-~WaSlnfGVFLC~~CSGIHR 59 (462)
.+|.+||.+=| .=.-.--+..+|+.|...|-
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 38999999822 11122236789999988774
No 23
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=53.05 E-value=9.4 Score=37.75 Aligned_cols=38 Identities=18% Similarity=0.419 Sum_probs=28.5
Q ss_pred HHHHHHHHhcCCCCCCCcCCCCCCCCeeEcccchhcchhhhhhh
Q 012502 15 HRKILDGLLKLPENRECADCKAKGPRWASVNLGIFICMQCSGIH 58 (462)
Q Consensus 15 ~ekiL~~Llk~PgNk~CADCGA~~P~WaSlnfGVFLC~~CSGIH 58 (462)
-++.++..++......|-.||.....|. ++|..|.+.|
T Consensus 341 ~~~~~~~~~~~~p~~~c~~cg~~~~~~~------~~c~~c~~~~ 378 (389)
T PRK11788 341 LRDLVGEQLKRKPRYRCRNCGFTARTLY------WHCPSCKAWE 378 (389)
T ss_pred HHHHHHHHHhCCCCEECCCCCCCCccce------eECcCCCCcc
Confidence 4566665555433345999999999994 7999998887
No 24
>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=52.08 E-value=6 Score=29.10 Aligned_cols=28 Identities=21% Similarity=0.557 Sum_probs=21.7
Q ss_pred CCcCCCCCCCCeeEcccchhcchhhhhhh
Q 012502 30 ECADCKAKGPRWASVNLGIFICMQCSGIH 58 (462)
Q Consensus 30 ~CADCGA~~P~WaSlnfGVFLC~~CSGIH 58 (462)
+|-.||+.. ....-.-|-++|..|..|-
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-BBE
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCCCEe
Confidence 599999987 4556778999999995543
No 25
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=49.69 E-value=6.3 Score=37.28 Aligned_cols=34 Identities=29% Similarity=0.640 Sum_probs=28.5
Q ss_pred CCCCCCcCCCCCCCCeeEcccchhcch-hhhhhhhc
Q 012502 26 PENRECADCKAKGPRWASVNLGIFICM-QCSGIHRS 60 (462)
Q Consensus 26 PgNk~CADCGA~~P~WaSlnfGVFLC~-~CSGIHRs 60 (462)
|--+.|+-|| -...|.+++.|.-+|. .|-.+|..
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 26
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=49.50 E-value=12 Score=31.10 Aligned_cols=33 Identities=18% Similarity=0.516 Sum_probs=22.2
Q ss_pred CCCCcCCCCCCCC-eeEcccchhcchhhhhhhhc
Q 012502 28 NRECADCKAKGPR-WASVNLGIFICMQCSGIHRS 60 (462)
Q Consensus 28 Nk~CADCGA~~P~-WaSlnfGVFLC~~CSGIHRs 60 (462)
...|.|||.+=|. =.-.--|+..|..|...+-.
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 4589999998442 11122378899999886643
No 27
>PRK11019 hypothetical protein; Provisional
Probab=48.36 E-value=9.3 Score=33.05 Aligned_cols=36 Identities=22% Similarity=0.485 Sum_probs=25.0
Q ss_pred CCCCCcCCCCCCC--CeeEcccchhcchhhhhhhhcCCC
Q 012502 27 ENRECADCKAKGP--RWASVNLGIFICMQCSGIHRSLGV 63 (462)
Q Consensus 27 gNk~CADCGA~~P--~WaSlnfGVFLC~~CSGIHRsLG~ 63 (462)
.-..|.|||.+=| .+-. --++-.|+.|...+...+.
T Consensus 35 syg~C~~CG~~Ip~~Rl~A-~P~a~~Cv~Cq~~~E~~~k 72 (88)
T PRK11019 35 SLTECEECGEPIPEARRKA-IPGVRLCVACQQEKDLQQA 72 (88)
T ss_pred cCCeeCcCCCcCcHHHHhh-cCCccccHHHHHHHHHHHh
Confidence 3579999999844 2322 2378899999998765443
No 28
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=48.01 E-value=12 Score=35.10 Aligned_cols=38 Identities=13% Similarity=0.305 Sum_probs=24.3
Q ss_pred hcCCCCCCCcCCCCCCC-CeeEcccchhcchhhhhhhhc
Q 012502 23 LKLPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRS 60 (462)
Q Consensus 23 lk~PgNk~CADCGA~~P-~WaSlnfGVFLC~~CSGIHRs 60 (462)
+..+.-..|-+||.+=| .=.-.--++..|+.|...|-.
T Consensus 106 i~~gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~E~ 144 (151)
T PRK10778 106 VEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEI 144 (151)
T ss_pred HhCCCCceeccCCCcccHHHHhcCCCccccHHHHHHHHH
Confidence 34567779999998811 111112246789999987754
No 29
>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=46.26 E-value=13 Score=30.04 Aligned_cols=34 Identities=35% Similarity=0.638 Sum_probs=23.6
Q ss_pred cCCCCCCCcCCCCCCC--CeeEcccchhcchhhhhhh
Q 012502 24 KLPENRECADCKAKGP--RWASVNLGIFICMQCSGIH 58 (462)
Q Consensus 24 k~PgNk~CADCGA~~P--~WaSlnfGVFLC~~CSGIH 58 (462)
..++...|.|||.+=| ++. .--|+..|..|...+
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 4567789999999843 222 234788999997654
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=45.08 E-value=7.3 Score=28.39 Aligned_cols=27 Identities=19% Similarity=0.582 Sum_probs=16.7
Q ss_pred CCCcCCCCC-CCCeeEcccchhcchhhh
Q 012502 29 RECADCKAK-GPRWASVNLGIFICMQCS 55 (462)
Q Consensus 29 k~CADCGA~-~P~WaSlnfGVFLC~~CS 55 (462)
..|.+|+.. .-+|..-+|+.-||..|.
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=37.12 E-value=21 Score=33.72 Aligned_cols=36 Identities=14% Similarity=0.223 Sum_probs=22.3
Q ss_pred CCCCCCCcCCCCCCC-CeeEcccchhcchhhhhhhhc
Q 012502 25 LPENRECADCKAKGP-RWASVNLGIFICMQCSGIHRS 60 (462)
Q Consensus 25 ~PgNk~CADCGA~~P-~WaSlnfGVFLC~~CSGIHRs 60 (462)
...=..|.+||.+=| .=.-+--++-.|+.|...+-.
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 345557999998711 111122256789999887643
No 32
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=36.99 E-value=27 Score=27.04 Aligned_cols=37 Identities=24% Similarity=0.587 Sum_probs=30.2
Q ss_pred CCCCCcCCCCC-CCCeeEcccch-hcchhhhhhhhcCCC
Q 012502 27 ENRECADCKAK-GPRWASVNLGI-FICMQCSGIHRSLGV 63 (462)
Q Consensus 27 gNk~CADCGA~-~P~WaSlnfGV-FLC~~CSGIHRsLG~ 63 (462)
....|..|+.. .|.|=.-..|- +||-.|.-..+..+.
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 58898888886 999999888777654
No 33
>PHA00080 DksA-like zinc finger domain containing protein
Probab=33.87 E-value=28 Score=28.82 Aligned_cols=35 Identities=26% Similarity=0.565 Sum_probs=23.5
Q ss_pred CCCCCCCcCCCCCCC--CeeEcccchhcchhhhhhhhc
Q 012502 25 LPENRECADCKAKGP--RWASVNLGIFICMQCSGIHRS 60 (462)
Q Consensus 25 ~PgNk~CADCGA~~P--~WaSlnfGVFLC~~CSGIHRs 60 (462)
..+...|.|||.+=| .+.. .-|+..|+.|...+-.
T Consensus 28 ~~~~~~C~~Cg~~Ip~~Rl~a-~P~~~~Cv~Cq~~~E~ 64 (72)
T PHA00080 28 APSATHCEECGDPIPEARREA-VPGCRTCVSCQEILEL 64 (72)
T ss_pred CCCCCEecCCCCcCcHHHHHh-CCCccCcHHHHHHHHH
Confidence 355668999998733 2322 2367789999887643
No 34
>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=30.67 E-value=30 Score=24.85 Aligned_cols=32 Identities=25% Similarity=0.694 Sum_probs=23.2
Q ss_pred CcCCCCC-CCCeeEcccchh-cchhhhhhhhcCC
Q 012502 31 CADCKAK-GPRWASVNLGIF-ICMQCSGIHRSLG 62 (462)
Q Consensus 31 CADCGA~-~P~WaSlnfGVF-LC~~CSGIHRsLG 62 (462)
|.+|++. .|.|=....|-. ||-.|.-.+|..|
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 699998888887 9999987777644
No 35
>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=28.90 E-value=37 Score=29.67 Aligned_cols=31 Identities=19% Similarity=0.410 Sum_probs=18.3
Q ss_pred CCCCCCCcCCCCCCC-CeeEcccchhcchhhh
Q 012502 25 LPENRECADCKAKGP-RWASVNLGIFICMQCS 55 (462)
Q Consensus 25 ~PgNk~CADCGA~~P-~WaSlnfGVFLC~~CS 55 (462)
.+.-..|.|||.+=| .=.-.--++..|..|.
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 356679999998822 1111111356788885
No 36
>PRK02770 S-adenosylmethionine decarboxylase proenzyme; Provisional
Probab=28.13 E-value=26 Score=32.48 Aligned_cols=41 Identities=22% Similarity=0.454 Sum_probs=24.4
Q ss_pred HHHHHHhhhccCCCCcccCCCcCCCCCCC---------CCccccccCCCCcC
Q 012502 360 QSFLAAASVNSNGGSQSFPINVHQPGSNG---------IHVPIQSWGVVGHQ 402 (462)
Q Consensus 360 q~~lmaaa~~~~~~~~~~p~~~~q~~~ng---------~~~p~qnw~~~Gyq 402 (462)
+.+|..|+ +..|.. .+....++=.+.| +||.+|.||-.||=
T Consensus 40 ~~~l~~Aa-~~~gat-iv~~~~h~F~P~GvTgv~lLaESHisIHTwPE~gya 89 (139)
T PRK02770 40 RTTLTEAA-KRAGAT-LLNLITHRFEPQGVTALALLAESHISIHTWPESGYA 89 (139)
T ss_pred HHHHHHHH-HHcCCE-EEEEEeEEcCCCeEEEEEEecccEEEEEeCcCCCcE
Confidence 44555555 565544 2333333333333 46999999999994
No 37
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=27.83 E-value=38 Score=29.90 Aligned_cols=33 Identities=24% Similarity=0.504 Sum_probs=23.1
Q ss_pred cCCCCCCCcCCCCCC--------C---------CeeEcccchhcchhhhh
Q 012502 24 KLPENRECADCKAKG--------P---------RWASVNLGIFICMQCSG 56 (462)
Q Consensus 24 k~PgNk~CADCGA~~--------P---------~WaSlnfGVFLC~~CSG 56 (462)
+.++--.|+|||.+- . .=++=.||-.+|..|..
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 456667899999871 1 11234689999999964
No 38
>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=26.40 E-value=45 Score=28.13 Aligned_cols=31 Identities=16% Similarity=0.525 Sum_probs=25.5
Q ss_pred CCCCCcCCCCCCCCeeEcccchhcchhhhhhhhc
Q 012502 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (462)
Q Consensus 27 gNk~CADCGA~~P~WaSlnfGVFLC~~CSGIHRs 60 (462)
..+.|.=||..... ..||++.|..|.+..|-
T Consensus 2 ~~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 32 (82)
T cd07173 2 PQKTCLICGDEASG---CHYGALTCGSCKVFFKR 32 (82)
T ss_pred CCCCCeecCCcCcc---eEECcchhhhHHHHHHH
Confidence 45679999987654 58999999999998874
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=26.17 E-value=11 Score=26.79 Aligned_cols=29 Identities=24% Similarity=0.563 Sum_probs=16.3
Q ss_pred CCcCCCCCCC-CeeEcccchhcchhhhhhh
Q 012502 30 ECADCKAKGP-RWASVNLGIFICMQCSGIH 58 (462)
Q Consensus 30 ~CADCGA~~P-~WaSlnfGVFLC~~CSGIH 58 (462)
.|.+||..=+ .=.-+--+..+|..|+..|
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 5999997621 1112223678899998765
No 40
>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=25.78 E-value=43 Score=28.16 Aligned_cols=31 Identities=19% Similarity=0.613 Sum_probs=25.6
Q ss_pred CCCCCcCCCCCCCCeeEcccchhcchhhhhhhhc
Q 012502 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (462)
Q Consensus 27 gNk~CADCGA~~P~WaSlnfGVFLC~~CSGIHRs 60 (462)
.|..|.=||.... ...||++.|..|.+..|-
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 458999999999998863
No 41
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=24.95 E-value=37 Score=34.63 Aligned_cols=33 Identities=18% Similarity=0.461 Sum_probs=23.7
Q ss_pred CCCCCCcCCCCCCCCeeEcccchhcchhhhhhhh
Q 012502 26 PENRECADCKAKGPRWASVNLGIFICMQCSGIHR 59 (462)
Q Consensus 26 PgNk~CADCGA~~P~WaSlnfGVFLC~~CSGIHR 59 (462)
.....|-+||+... =....-|-.+|..|.-|..
T Consensus 9 ~~~~~Cp~Cg~~~i-v~d~~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 9 EEKLVCPECGSDKL-IYDYERGEIVCADCGLVIE 41 (310)
T ss_pred ccCCcCcCCCCCCe-eEECCCCeEeecccCCccc
Confidence 34568999997432 2345779999999977653
No 42
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=24.89 E-value=34 Score=30.99 Aligned_cols=24 Identities=38% Similarity=0.826 Sum_probs=21.1
Q ss_pred CeeEcccc--hhcchhhhhhhhcCCC
Q 012502 40 RWASVNLG--IFICMQCSGIHRSLGV 63 (462)
Q Consensus 40 ~WaSlnfG--VFLC~~CSGIHRsLG~ 63 (462)
.|++-.-| |.-|..|-.|||.=+.
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 43
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=24.43 E-value=64 Score=35.26 Aligned_cols=93 Identities=14% Similarity=0.314 Sum_probs=46.3
Q ss_pred CCCCCCCcC-CCCC--CCCeeEccc--chhcchhhhhhhhcCCCcc----ce-eee----ccCCCCCH-HHHHHHHh---
Q 012502 25 LPENRECAD-CKAK--GPRWASVNL--GIFICMQCSGIHRSLGVHI----SK-VRS----ATLDTWLP-EQVAVIQS--- 86 (462)
Q Consensus 25 ~PgNk~CAD-CGA~--~P~WaSlnf--GVFLC~~CSGIHRsLG~hI----Sk-VKS----LsMDtWT~-eEV~~Lq~--- 86 (462)
.+|++.|+| |-.. +...+...- -.+||+.|-.+=-.+|.|- =+ |.. |---.||. ||+.+|+.
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 1578999977555555541 11 222 11225995 67777764
Q ss_pred --hcc--hhHHHHHhhcCCCCCChhHHHHHHHHHhhcCccc
Q 012502 87 --MGN--EKSNSYWEAELPPNYDRVGIENFIRAKYEEKRWI 123 (462)
Q Consensus 87 --gGN--~~aN~iwEa~lPp~~D~~~~e~FIraKY~eKrF~ 123 (462)
.|| +.|+.| ...+..+.+++-.+.|++-.++
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 366 222222 1233455666666777766443
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=23.98 E-value=48 Score=25.65 Aligned_cols=34 Identities=26% Similarity=0.676 Sum_probs=22.2
Q ss_pred HhcCCCCCCCcCCCCCCC--Cee-------Ecccchhcchhhhh
Q 012502 22 LLKLPENRECADCKAKGP--RWA-------SVNLGIFICMQCSG 56 (462)
Q Consensus 22 Llk~PgNk~CADCGA~~P--~Wa-------SlnfGVFLC~~CSG 56 (462)
|+++.+| .|-=|++..+ .|. +..-.|+||..|..
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 3344444 4999998753 222 34668999999965
No 45
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=23.94 E-value=58 Score=28.55 Aligned_cols=30 Identities=20% Similarity=0.530 Sum_probs=23.4
Q ss_pred CCCCCCcCCCCCCCCeeEcccchhcchhhhhh
Q 012502 26 PENRECADCKAKGPRWASVNLGIFICMQCSGI 57 (462)
Q Consensus 26 PgNk~CADCGA~~P~WaSlnfGVFLC~~CSGI 57 (462)
..-..|-.|+.+ .---+..||+.|..|-..
T Consensus 33 ~~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~~ 62 (89)
T COG1997 33 RAKHVCPFCGRT--TVKRIATGIWKCRKCGAK 62 (89)
T ss_pred hcCCcCCCCCCc--ceeeeccCeEEcCCCCCe
Confidence 445689999998 444678999999999553
No 46
>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=23.76 E-value=50 Score=28.58 Aligned_cols=31 Identities=29% Similarity=0.703 Sum_probs=25.6
Q ss_pred CCCCCcCCCCCCCCeeEcccchhcchhhhhhhhc
Q 012502 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (462)
Q Consensus 27 gNk~CADCGA~~P~WaSlnfGVFLC~~CSGIHRs 60 (462)
++..|.=||..... ..||++.|..|.+..|-
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 47999999999998873
No 47
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=22.84 E-value=38 Score=26.63 Aligned_cols=28 Identities=18% Similarity=0.570 Sum_probs=22.9
Q ss_pred CCCCCcCCCCCCCCeeEcccchhcchhhhh
Q 012502 27 ENRECADCKAKGPRWASVNLGIFICMQCSG 56 (462)
Q Consensus 27 gNk~CADCGA~~P~WaSlnfGVFLC~~CSG 56 (462)
--+.|..||..... ..+-.+|.|..|.-
T Consensus 27 TSq~C~~CG~~~~~--~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK--RRSGRVFTCPNCGF 54 (69)
T ss_pred CccCccCccccccc--ccccceEEcCCCCC
Confidence 45689999999877 67888999999943
No 48
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=22.45 E-value=53 Score=24.17 Aligned_cols=24 Identities=21% Similarity=0.540 Sum_probs=18.1
Q ss_pred CCcCCCCCCCCeeEcccchhcchh
Q 012502 30 ECADCKAKGPRWASVNLGIFICMQ 53 (462)
Q Consensus 30 ~CADCGA~~P~WaSlnfGVFLC~~ 53 (462)
+|.+|+..+.-|+++.-+-..|..
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c~~ 24 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGCGR 24 (50)
T ss_pred CcccCCCcCCeEEecCCCCcccCC
Confidence 599999888788877766666643
No 49
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family 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. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=22.45 E-value=52 Score=28.88 Aligned_cols=31 Identities=26% Similarity=0.662 Sum_probs=25.7
Q ss_pred CCCCCcCCCCCCCCeeEcccchhcchhhhhhhhc
Q 012502 27 ENRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (462)
Q Consensus 27 gNk~CADCGA~~P~WaSlnfGVFLC~~CSGIHRs 60 (462)
++..|.=||..... ..||+..|..|.+..|-
T Consensus 17 ~~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 47 (101)
T cd07160 17 GNEVCSVCGDKASG---FHYNVLSCEGCKGFFRR 47 (101)
T ss_pred CCCCCeecCCcCcc---eEECcceehhhhhhhhh
Confidence 46789999987654 48999999999998873
No 50
>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=22.23 E-value=51 Score=28.72 Aligned_cols=30 Identities=20% Similarity=0.540 Sum_probs=24.6
Q ss_pred CCCCcCCCCCCCCeeEcccchhcchhhhhhhhc
Q 012502 28 NRECADCKAKGPRWASVNLGIFICMQCSGIHRS 60 (462)
Q Consensus 28 Nk~CADCGA~~P~WaSlnfGVFLC~~CSGIHRs 60 (462)
+..|.=||..... ..||++.|..|.+..|-
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 48999999999998873
No 51
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=21.93 E-value=80 Score=35.29 Aligned_cols=77 Identities=25% Similarity=0.503 Sum_probs=47.2
Q ss_pred ccHHHHHHHHHHHHHHhcCCCCCCCcCCCCCC-CCeeEccc---chhcchhhhhhhhcCCCccce---ee--eccCCC--
Q 012502 7 VSKELNAKHRKILDGLLKLPENRECADCKAKG-PRWASVNL---GIFICMQCSGIHRSLGVHISK---VR--SATLDT-- 75 (462)
Q Consensus 7 ~SKrl~ar~ekiL~~Llk~PgNk~CADCGA~~-P~WaSlnf---GVFLC~~CSGIHRsLG~hISk---VK--SLsMDt-- 75 (462)
.=||+|.|....|..-++..+|+.|-.||..+ -+|.|-+- ..-+|..|-.+ | ||++ ++ -+.|+.
T Consensus 240 ~l~~~Qlrela~lNgt~r~~d~~~c~~cg~~~H~q~~cp~r~~~~~n~c~~cg~~----g-H~~~dc~~~~q~~~~~~~~ 314 (554)
T KOG0119|consen 240 DLKRLQLRELARLNGTLRDDDNRACRNCGSTGHKQYDCPGRIPNTTNVCKICGPL----G-HISIDCKVNDQQMPMSSAN 314 (554)
T ss_pred cccHHHHHHHHHhCCCCCccccccccccCCCccccccCCcccccccccccccCCc----c-cccccCCCcccccchhhhc
Confidence 34677777777777778888999999999986 44554322 33378888542 2 3221 22 222333
Q ss_pred CCHHHHHHHHhhc
Q 012502 76 WLPEQVAVIQSMG 88 (462)
Q Consensus 76 WT~eEV~~Lq~gG 88 (462)
|..|-..+|..+|
T Consensus 315 ~d~ey~~lm~e~~ 327 (554)
T KOG0119|consen 315 FDREYASLMLELG 327 (554)
T ss_pred cCHHHHhhhcccc
Confidence 5566566666666
No 52
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=21.83 E-value=54 Score=31.46 Aligned_cols=23 Identities=22% Similarity=0.446 Sum_probs=18.0
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCC
Q 012502 8 SKELNAKHRKILDGLLKLPENRE 30 (462)
Q Consensus 8 SKrl~ar~ekiL~~Llk~PgNk~ 30 (462)
..+...+|.+.++.+|..+.+..
T Consensus 111 ~~~~Ek~H~~~~~~~Le~~~~~~ 133 (166)
T COG1592 111 AAKAEKRHAEMFRGLLERLEEGK 133 (166)
T ss_pred HHHHHHHHHHHHHHHHHhhhcCC
Confidence 34667889999999999876654
No 53
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.63 E-value=33 Score=33.11 Aligned_cols=23 Identities=22% Similarity=0.683 Sum_probs=19.2
Q ss_pred CCCCcCCCCCCCCeeEcccchhcchhhhhh
Q 012502 28 NRECADCKAKGPRWASVNLGIFICMQCSGI 57 (462)
Q Consensus 28 Nk~CADCGA~~P~WaSlnfGVFLC~~CSGI 57 (462)
-+.|.-||. +.-+.|.|..|...
T Consensus 309 S~~C~~cg~-------~~~r~~~C~~cg~~ 331 (364)
T COG0675 309 SKTCPCCGH-------LSGRLFKCPRCGFV 331 (364)
T ss_pred cccccccCC-------ccceeEECCCCCCe
Confidence 379999999 66789999999763
No 54
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=21.28 E-value=45 Score=31.08 Aligned_cols=29 Identities=17% Similarity=0.380 Sum_probs=19.5
Q ss_pred CCcCCCCCCCCeeEcccchhcchhhhhhhh
Q 012502 30 ECADCKAKGPRWASVNLGIFICMQCSGIHR 59 (462)
Q Consensus 30 ~CADCGA~~P~WaSlnfGVFLC~~CSGIHR 59 (462)
.|..|+.+-..==.+++ -|.|..|.+.-.
T Consensus 111 ~Cp~c~~r~tf~eA~~~-~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 111 ICPNMCVRFTFNEAMEL-NFTCPRCGAMLD 139 (158)
T ss_pred ECCCCCcEeeHHHHHHc-CCcCCCCCCEee
Confidence 69999966433223344 599999987643
No 55
>PF12763 EF-hand_4: Cytoskeletal-regulatory complex EF hand; PDB: 2QPT_A 2KSP_A 2KFG_A 2JQ6_A 2KFH_A 2KFF_A 1IQ3_A 3FIA_A 2KHN_A 2KGR_A ....
Probab=20.68 E-value=51 Score=28.94 Aligned_cols=11 Identities=45% Similarity=0.730 Sum_probs=7.8
Q ss_pred HHHHHHHHhhc
Q 012502 448 LFLICMHLVYH 458 (462)
Q Consensus 448 ~~~~~~~~~~~ 458 (462)
-|.|+|||+++
T Consensus 64 EF~iAm~Li~~ 74 (104)
T PF12763_consen 64 EFAIAMHLINR 74 (104)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHHH
Confidence 36778888765
Done!