Query psy16569
Match_columns 385
No_of_seqs 200 out of 224
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 16:22:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16569.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16569hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3635|consensus 100.0 4.9E-96 1E-100 768.8 23.9 267 57-365 858-1142(1150)
2 PF00723 Glyco_hydro_15: Glyco 97.3 3.5E-06 7.6E-11 85.9 -8.9 99 26-125 349-448 (448)
3 TIGR00589 ogt O-6-methylguanin 80.2 3.2 7E-05 33.9 4.5 53 188-254 1-59 (80)
4 PRK03887 methylated-DNA--prote 79.1 15 0.00033 34.6 9.1 106 119-255 37-149 (175)
5 PF01035 DNA_binding_1: 6-O-me 75.5 3.8 8.2E-05 33.5 3.6 52 189-254 2-59 (85)
6 KOG4062|consensus 70.7 5.9 0.00013 37.2 4.1 59 188-255 88-147 (178)
7 PRK10286 O-6-alkylguanine-DNA: 63.4 10 0.00022 35.4 4.1 78 150-254 60-145 (171)
8 cd06445 ATase The DNA repair p 54.8 25 0.00054 28.2 4.5 51 190-254 1-57 (79)
9 PRK00901 methylated-DNA--prote 50.7 25 0.00054 32.1 4.4 53 188-254 72-130 (155)
10 PRK15435 bifunctional DNA-bind 48.1 25 0.00055 35.8 4.5 54 188-255 269-328 (353)
11 PRK10572 DNA-binding transcrip 28.8 1.9E+02 0.0041 27.5 6.8 70 107-184 169-242 (290)
12 COG4422 Bacteriophage protein 26.2 35 0.00075 33.1 1.3 20 184-203 94-113 (250)
13 PRK10100 DNA-binding transcrip 21.6 2.9E+02 0.0063 26.0 6.5 92 66-161 105-196 (216)
14 COG1711 DNA replication initia 21.6 30 0.00065 33.9 -0.1 92 182-277 18-110 (223)
15 PF11543 UN_NPL4: Nuclear pore 21.5 68 0.0015 26.1 2.0 67 7-73 7-80 (80)
16 COG3437 Response regulator con 20.9 1.9E+02 0.0041 30.3 5.4 83 66-149 113-219 (360)
17 KOG3635|consensus 20.5 49 0.0011 38.2 1.3 73 1-75 465-537 (1150)
18 PF01900 RNase_P_Rpp14: Rpp14/ 20.1 29 0.00062 28.7 -0.5 57 145-201 16-78 (107)
No 1
>KOG3635|consensus
Probab=100.00 E-value=4.9e-96 Score=768.79 Aligned_cols=267 Identities=41% Similarity=0.720 Sum_probs=252.1
Q ss_pred eeeeecCCceeEecCCCCHHHHHHHHHhhcCCCchHHHHHHHHHHHHHhHHHhcCCccccchhhHhHHHHHHHHHHHHHH
Q psy16569 57 LAVGVIGQKETVFDKPLSPSEIRSVIYSTIQPYDVIQAVLQQEIVLYCGRLIATSPDMFNGILKIRVGWVIEAIKVYLEI 136 (385)
Q Consensus 57 l~VGr~g~eE~vIs~PL~p~ei~~~i~~~~~~~d~~~~vL~QEii~ylg~lIrt~P~LF~gml~iRvG~ii~~m~~eL~~ 136 (385)
+|||.++.+|.+|+.|+||.||+++||++++ +|.+.+|||||+++||||+|||+|+||.||||||||||||+|+.||.+
T Consensus 858 lTvG~pp~~E~~isapl~p~el~~lIy~a~~-~D~~~avl~qE~vvy~am~irt~P~lf~emlrlRiGlii~~m~~el~~ 936 (1150)
T KOG3635|consen 858 LTVGLPPQREKVISAPLPPEELQNLIYEASG-YDESIAVLTQELVVYLAMYIRTNPSLFREMLRLRIGLIIQVMAIELQI 936 (1150)
T ss_pred eeecCCCccceeccCCCCHHHHHHHHHHHhc-ccHHHHHHHHHHHHHhHhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999986 999999999999999999999999999999999999999999999999
Q ss_pred hccc-c-hhhccCChHHHHHHHHHHhcccccc-ccccchhhHHhhhccccccCCccchHHHHHHHhhCCCceEecceecC
Q psy16569 137 IGKD-V-NAMYNYSPFEIRQLLWKVLNVREWA-DEEHLTVLQLRRLEGCWCRVPSHFYNQVWDIMIRTPEGISVQGHILP 213 (385)
Q Consensus 137 ~~~e-a-e~L~~lSP~eik~lL~~vLs~~~w~-~~~~l~wl~~R~l~GaLnRvP~~FY~~VW~iL~~~p~Gl~I~g~~~~ 213 (385)
++.| | ++||||||||||++|+|||++++|+ +....+||||||+||||||||.+||++||++|+||||||+|+|++
T Consensus 937 sl~e~as~~l~nLsP~e~k~ll~~ils~~efg~vs~~r~wLrrRrlDGaLnRVP~gFY~rvW~iLqk~p~Gl~i~g~v-- 1014 (1150)
T KOG3635|consen 937 SLREKASEDLMNLSPFEMKNLLHHILSGKEFGAVSTERQWLRRRRLDGALNRVPVGFYQRVWKILQKCPHGLSIEGTV-- 1014 (1150)
T ss_pred hhcchhchhhcCCChHHHHHHHHHhhchhhhcccchhHHHHHHHhhccchhcCchHHHHHHHHHHHhCCCceeECcEe--
Confidence 9874 4 9999999999999999999999996 666679999999999999999999999999999999999999999
Q ss_pred CCccccccchhhHHHHHHHHHHHhhcCCCCccccccccCCCccccccCcchhhHHHHHHHHHcCCCCCcchhHHHHHHHH
Q psy16569 214 QQPTLSNMTQSELTFALVAVWDIMIRTPEGISVQGHILPQQPTLSNMTQSELTFALLIEEILNHITYPEYRQIIVELLSI 293 (385)
Q Consensus 214 ~~~~~~n~~~~~~~~~~~~~~~~~~~~p~~i~~~~~~L~~~~tlseMT~gE~~FAl~VE~lLn~I~~PEYRQl~VE~L~v 293 (385)
||++ |++||||||+|||++||+.||+|++||||||+||+||+
T Consensus 1015 -------------------------------------Lp~s-tt~eMT~~EikFal~vE~~Ln~I~qPEyRQlvVE~lmv 1056 (1150)
T KOG3635|consen 1015 -------------------------------------LPQS-TTQEMTPGEIKFALLVEETLNRIPQPEYRQLVVEALMV 1056 (1150)
T ss_pred -------------------------------------cchh-hhhhcCccceeeeeEhHHHhccCCcHHHHHHHHHHHHH
Confidence 8999 77999999999999999999999999999999999999
Q ss_pred HHHHHhhCCCCccCCcccHHHHHHHHHHHhhhhhch------------hHHhHHHHhccCcchhhh---HHHHHHHHHHh
Q psy16569 294 VSTILLRNPELSFRKQLDLDELVNNAYHMFCKDNNI------------ERKDMKSFYAAKQSITTG---YLARAVVNNVL 358 (385)
Q Consensus 294 l~~i~e~np~l~f~~~i~ld~lv~~A~~~f~~d~~~------------~~~~~~~Fy~~~P~~~~~---yl~~Av~~~ll 358 (385)
+++++++||+++|++.||+|.||+.|+.+|++|+.. .+.+|++|||+||+|.+| ||+|||+| +.
T Consensus 1057 ltlvl~~np~l~~~~~idvd~ivh~AnqlF~~dq~~lq~~~~~~~~~~a~~ic~~fYdsaPsG~ygT~tYl~rAv~n-l~ 1135 (1150)
T KOG3635|consen 1057 LTLVLERNPELSFGGIIDVDHIVHEANQLFLKDQKHLQADDTELREDGARGICKHFYDSAPSGEYGTMTYLTRAVAN-LY 1135 (1150)
T ss_pred HHHHHhcCCCcccCCeeeHHHHHHHHHHHHHhhhhhhcccchhhhhcchhhHHHHHhcCCCCCccchhHHHHHHHHH-HH
Confidence 999999999999999999999999999999999621 178999999999987555 99999999 66
Q ss_pred cCCcccc
Q psy16569 359 KGGELAT 365 (385)
Q Consensus 359 ~~~~~~t 365 (385)
.|+.+++
T Consensus 1136 ~~ev~p~ 1142 (1150)
T KOG3635|consen 1136 LGEVLPN 1142 (1150)
T ss_pred hcccCCC
Confidence 6666543
No 2
>PF00723 Glyco_hydro_15: Glycosyl hydrolases family 15; InterPro: IPR011613 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 15 GH15 from CAZY comprises enzymes with several known activities; glucoamylase (3.2.1.3 from EC); alpha-glucosidase (3.2.1.20 from EC); glucodextranase (3.2.1.70 from EC). Glucoamylase (GA) catalyses the release of D-glucose from the non-reducing ends of starch and other oligo- or poly-saccharides. Studies of fungal GA have indicated 3 closely-clustered acidic residues that play a role in the catalytic mechanism []. This region is also conserved in a recently sequenced bacterial GA []. The 3D structure of the pseudo-tetrasaccharide acarbose complexed with glucoamylase II(471) from Aspergillus awamori var. X100 has been determined to 2.4A resolution []. The protein belongs to the mainly-alpha class, and contains 19 helices and 9 strands. This protein is found in higher organisms, and is represented by phosphorylase kinase subunits.; GO: 0004339 glucan 1,4-alpha-glucosidase activity, 0005976 polysaccharide metabolic process; PDB: 1GAI_A 1GAH_A 1LF6_B 1LF9_A 3EQA_A 1AYX_A 2F6D_A 2FBA_A 1DOG_A 1GLM_A ....
Probab=97.28 E-value=3.5e-06 Score=85.86 Aligned_cols=99 Identities=14% Similarity=0.273 Sum_probs=77.1
Q ss_pred HHHHHHhcCCCCcceecCCCCCCcccc-ccceeeeeecCCceeEecCCCCHHHHHHHHHhhcCCCchHHHHHHHHHHHHH
Q psy16569 26 LVKVYQHLGVNKKLKLSGRPPRPIGAL-GTSKLAVGVIGQKETVFDKPLSPSEIRSVIYSTIQPYDVIQAVLQQEIVLYC 104 (385)
Q Consensus 26 L~~iY~~lG~n~kLgLSGRP~r~vg~L-~TSkl~VGr~g~eE~vIs~PL~p~ei~~~i~~~~~~~d~~~~vL~QEii~yl 104 (385)
+..+|.+.|+.+-|.+.-....-...+ +.+++++|.+++++..++.|.++.++.+.+.++|.. +....+|+||+..|.
T Consensus 349 ~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~k~~~~g~~~~~~~~~~~~~~~~~~~d~~l~~~~~-~~~~g~lsEq~~~~~ 427 (448)
T PF00723_consen 349 YAEAYRRAGRGRDWPIVREARGFFEKFVSSKQITVGIPYNSEDFISLPKALFEYADSFLRVVRE-ANRNGLLSEQFNRYT 427 (448)
T ss_dssp HHHHHHHHHHTEBEEECTTTHHHHHHHTTTGSSESEEEETSHHHHHHHHHHHHHHHHHHHHHHH-S-TTS---SEE-TTT
T ss_pred HHHHHHHHhcCCcccchHHHHHHHHHHhcccccccccccCchhhhhcccchHHHHHHHHHHHhc-CCcCcEeeeeeeccc
Confidence 788899999988888864333222222 227899999999999999999999999999999986 889999999999999
Q ss_pred hHHHhcCCccccchhhHhHHH
Q psy16569 105 GRLIATSPDMFNGILKIRVGW 125 (385)
Q Consensus 105 g~lIrt~P~LF~gml~iRvG~ 125 (385)
|+++.++|..|+++..||+||
T Consensus 428 G~~~ga~pltwS~~~~l~~~~ 448 (448)
T PF00723_consen 428 GFMQGARPLTWSYASFLRAGW 448 (448)
T ss_dssp --EESSSS-HHHHHHHHHHH-
T ss_pred CCcCCCCchhhhhhhhHhhcC
Confidence 999999999999999999998
No 3
>TIGR00589 ogt O-6-methylguanine DNA methyltransferase. All proteins in this family for which functions are known are involved alkyl-DNA transferases which remove alkyl groups from DNA as part of alkylation DNA repair. Some of the proteins in this family are also transcription regulators and have a distinct transcription regulatory domain. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=80.18 E-value=3.2 Score=33.90 Aligned_cols=53 Identities=26% Similarity=0.333 Sum_probs=41.4
Q ss_pred ccchHHHHHHHhhCCCceEecceecCCCccccccchhhHHH------HHHHHHHHhhcCCCCccccccccCCC
Q psy16569 188 SHFYNQVWDIMIRTPEGISVQGHILPQQPTLSNMTQSELTF------ALVAVWDIMIRTPEGISVQGHILPQQ 254 (385)
Q Consensus 188 ~~FY~~VW~iL~~~p~Gl~I~g~~~~~~~~~~n~~~~~~~~------~~~~~~~~~~~~p~~i~~~~~~L~~~ 254 (385)
.+|+.+||+.+.+-|.| ++ .|-+++-= |-++|=..|-+.|-.+.|++||.-..
T Consensus 1 t~f~~~V~~~l~~IP~G-----~v---------~TYg~iA~~~g~p~~~RaVg~al~~np~~~~iPcHRVv~s 59 (80)
T TIGR00589 1 TPFQQRVWQALRTIPYG-----ET---------KSYGQLAARIGNPKAVRAVGGANGRNPLAILVPCHRVIGK 59 (80)
T ss_pred ChHHHHHHHHHhCCCCC-----Cc---------CCHHHHHHHhCCCChHHHHHHHHHhCCCCCCCCCceeECC
Confidence 36999999999999984 44 34455433 45788889999999999999998664
No 4
>PRK03887 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=79.09 E-value=15 Score=34.59 Aligned_cols=106 Identities=26% Similarity=0.296 Sum_probs=67.2
Q ss_pred hhHhHHHHHHHHHHHHHHhcccchhhccCChHHHHHHHHHHhccc--cccccccchhhHHhhhccccccCCccchHHHHH
Q psy16569 119 LKIRVGWVIEAIKVYLEIIGKDVNAMYNYSPFEIRQLLWKVLNVR--EWADEEHLTVLQLRRLEGCWCRVPSHFYNQVWD 196 (385)
Q Consensus 119 l~iRvG~ii~~m~~eL~~~~~eae~L~~lSP~eik~lL~~vLs~~--~w~~~~~l~wl~~R~l~GaLnRvP~~FY~~VW~ 196 (385)
|+=|+.-++..+..+. -.|+-.- .|.+..+++.++|.+. ++..... +. +.| -..|+.+||+
T Consensus 37 ~~~~~~~~~~~l~~~f----~~a~l~~--~~~~~~~~l~~~l~g~~~~~~~~~~---l~---~~g-----~T~Fq~rV~~ 99 (175)
T PRK03887 37 LRERISNLAEFLKKRG----VKVSLKE--RPSDYPELVFKVLIGKISNEEGLEE---LS---FEG-----LTPFERKVYE 99 (175)
T ss_pred HHHHHHHHHHHHHHhC----cCceecC--CChhHHHHHHHHHcCCccccccCcc---cC---cCC-----CCHHHHHHHH
Confidence 4445555555555542 1222222 4555789999999986 3321111 21 112 2789999999
Q ss_pred HH-hhCCCceEecceecCCCccccccchhhHH----HHHHHHHHHhhcCCCCccccccccCCCc
Q psy16569 197 IM-IRTPEGISVQGHILPQQPTLSNMTQSELT----FALVAVWDIMIRTPEGISVQGHILPQQP 255 (385)
Q Consensus 197 iL-~~~p~Gl~I~g~~~~~~~~~~n~~~~~~~----~~~~~~~~~~~~~p~~i~~~~~~L~~~~ 255 (385)
.| ...|. |++ +|-+|+- .|-++|=..|-+.|-.+.|++||.-...
T Consensus 100 ~Lv~~IP~-----G~v---------~TYgqIA~~~G~aaRAVG~Al~~NP~~i~IPCHRVV~s~ 149 (175)
T PRK03887 100 WLTKNVKR-----GEV---------ITYGELAKALNTSPRAVGGAMKRNPYPIIVPCHRVVGRK 149 (175)
T ss_pred HHHHhCCC-----CCC---------CcHHHHHHHHCchHHHHHHHHHhCCCCCccCCeeEECCC
Confidence 65 57887 444 3444442 3779999999999999999999987653
No 5
>PF01035 DNA_binding_1: 6-O-methylguanine DNA methyltransferase, DNA binding domain; InterPro: IPR014048 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase This entry represents the DNA binding region of 6-O-methylguanine-DNA methyltransferases. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme []. This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources [].; GO: 0003824 catalytic activity, 0006281 DNA repair; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A 2KIM_A 2KIF_A ....
Probab=75.47 E-value=3.8 Score=33.54 Aligned_cols=52 Identities=27% Similarity=0.422 Sum_probs=39.2
Q ss_pred cchHHHHHHHhhCCCceEecceecCCCccccccchhhHHHHH------HHHHHHhhcCCCCccccccccCCC
Q psy16569 189 HFYNQVWDIMIRTPEGISVQGHILPQQPTLSNMTQSELTFAL------VAVWDIMIRTPEGISVQGHILPQQ 254 (385)
Q Consensus 189 ~FY~~VW~iL~~~p~Gl~I~g~~~~~~~~~~n~~~~~~~~~~------~~~~~~~~~~p~~i~~~~~~L~~~ 254 (385)
+|+.+||+.+..-|.| ++ +|-+|+--++ ++|=..|-+.|..+.|++||.-..
T Consensus 2 ~f~~~V~~~v~~IP~G-----~v---------~TYg~iA~~~g~p~~ar~Vg~al~~np~~~~iP~HRVv~~ 59 (85)
T PF01035_consen 2 PFQRRVWEAVRQIPYG-----KV---------TTYGEIARLLGRPKAARAVGSALARNPIPIIIPCHRVVNS 59 (85)
T ss_dssp HHHHHHHHHHTTS-TT------B---------EEHHHHHHHTT-TTCHHHHHHHHHTSSCTTTSGGGGEEBT
T ss_pred hHHHHHHHHHHcCCCC-----ce---------EeHHHHHHHHhhcccHHHHHHHhccccccCCCCeEEEECC
Confidence 6999999999999984 44 3455554433 477788999999999999998665
No 6
>KOG4062|consensus
Probab=70.74 E-value=5.9 Score=37.18 Aligned_cols=59 Identities=25% Similarity=0.290 Sum_probs=44.1
Q ss_pred ccchHHHHHHHhhCCCceEec-ceecCCCccccccchhhHHHHHHHHHHHhhcCCCCccccccccCCCc
Q psy16569 188 SHFYNQVWDIMIRTPEGISVQ-GHILPQQPTLSNMTQSELTFALVAVWDIMIRTPEGISVQGHILPQQP 255 (385)
Q Consensus 188 ~~FY~~VW~iL~~~p~Gl~I~-g~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~p~~i~~~~~~L~~~~ 255 (385)
.+||.+||+.|.+-|+|=++. |++ ++ |-.| .=|.++|=.-|-+.+--|.|++||.-++.
T Consensus 88 t~F~~kVw~al~~i~~Gev~tY~~i-A~---~iG~-----PsaaRaVg~A~~~n~la~lvPcHRVv~s~ 147 (178)
T KOG4062|consen 88 TDFQRKVWDALCEIPYGEVSTYGQI-AR---RIGN-----PSAARAVGSAMAHNNLAILVPCHRVVGSN 147 (178)
T ss_pred chHHHHHHHHHhccCCCceeeHHHH-HH---HhCC-----cHHHHHHHHHHccCCCcEEecceeeecCC
Confidence 489999999999999976552 111 00 0000 24889999999999999999999998763
No 7
>PRK10286 O-6-alkylguanine-DNA:cysteine-protein methyltransferase; Provisional
Probab=63.43 E-value=10 Score=35.40 Aligned_cols=78 Identities=19% Similarity=0.126 Sum_probs=54.2
Q ss_pred HHHHHHHHHHhcccc--ccccccchhhHHhhhccccccCCccchHHHHHHHhhCCCceEecceecCCCccccccchhhHH
Q psy16569 150 FEIRQLLWKVLNVRE--WADEEHLTVLQLRRLEGCWCRVPSHFYNQVWDIMIRTPEGISVQGHILPQQPTLSNMTQSELT 227 (385)
Q Consensus 150 ~eik~lL~~vLs~~~--w~~~~~l~wl~~R~l~GaLnRvP~~FY~~VW~iL~~~p~Gl~I~g~~~~~~~~~~n~~~~~~~ 227 (385)
.++++.|...++|+. |. ++- +..--..|..+||+.|.+-|.|=+. |-+||-
T Consensus 60 ~~~~~~l~~Yf~g~~~~f~------~~p-------l~~~gt~fq~~V~~~l~~IP~G~~~--------------tYg~iA 112 (171)
T PRK10286 60 GGLSDKLRDYFAGNLSIID------TLP-------TATGGTPFQREVWQTLRTIPCGQVM--------------HYGQLA 112 (171)
T ss_pred HHHHHHHHHHHCCCCCCCC------ccc-------ccCCCCHHHHHHHHHHHcCCCCCcE--------------eHHHHH
Confidence 456777777777763 42 010 1112257999999999999985443 344432
Q ss_pred H------HHHHHHHHhhcCCCCccccccccCCC
Q psy16569 228 F------ALVAVWDIMIRTPEGISVQGHILPQQ 254 (385)
Q Consensus 228 ~------~~~~~~~~~~~~p~~i~~~~~~L~~~ 254 (385)
= |.++|=..|-+.|-.|.|++||.-..
T Consensus 113 ~~~g~p~aaRaVG~A~~~Np~~i~iPCHRVv~~ 145 (171)
T PRK10286 113 EQLGRPGAARAVGAANGSNPISIVVPCHRVIGR 145 (171)
T ss_pred HHhCCCChHHHHHHHHHhCCCCCccCCceEECC
Confidence 2 67889999999999999999998654
No 8
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=54.78 E-value=25 Score=28.19 Aligned_cols=51 Identities=25% Similarity=0.423 Sum_probs=39.1
Q ss_pred chHHHHHHHhhCCCceEecceecCCCccccccchhhHHH------HHHHHHHHhhcCCCCccccccccCCC
Q psy16569 190 FYNQVWDIMIRTPEGISVQGHILPQQPTLSNMTQSELTF------ALVAVWDIMIRTPEGISVQGHILPQQ 254 (385)
Q Consensus 190 FY~~VW~iL~~~p~Gl~I~g~~~~~~~~~~n~~~~~~~~------~~~~~~~~~~~~p~~i~~~~~~L~~~ 254 (385)
|+.+||+.+..-|. |++ +|-+++-= +-++|=..|-+.|..+.|++||.-..
T Consensus 1 ~~~~V~~~v~~IP~-----G~v---------~TYg~iA~~~g~p~~~R~Vg~al~~np~~~~vP~HRVv~~ 57 (79)
T cd06445 1 FQRRVWEALRQIPY-----GEV---------TTYGQIAKLAGTPKAARAVGSALARNPIPILIPCHRVVRS 57 (79)
T ss_pred CHHHHHHHHhcCCC-----CCc---------CcHHHHHHHHCCCCcHHHHHHHHHhCCCCCCCCceeEECC
Confidence 88999999999998 444 34444422 45677778999999999999998664
No 9
>PRK00901 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=50.75 E-value=25 Score=32.14 Aligned_cols=53 Identities=23% Similarity=0.278 Sum_probs=42.0
Q ss_pred ccchHHHHHHHhhCCCceEecceecCCCccccccchhhHHH------HHHHHHHHhhcCCCCccccccccCCC
Q psy16569 188 SHFYNQVWDIMIRTPEGISVQGHILPQQPTLSNMTQSELTF------ALVAVWDIMIRTPEGISVQGHILPQQ 254 (385)
Q Consensus 188 ~~FY~~VW~iL~~~p~Gl~I~g~~~~~~~~~~n~~~~~~~~------~~~~~~~~~~~~p~~i~~~~~~L~~~ 254 (385)
.+|-.+||+.|..-|.|=++ |-+||-= |.++|=..|-+.|--|.|++||.-..
T Consensus 72 t~fq~~Vw~~l~~Ip~G~t~--------------tY~~lA~~~g~p~a~RAVg~A~~~NP~~iiIPCHRVv~~ 130 (155)
T PRK00901 72 TEFQKKVWKALQEIPYGETR--------------SYKEIAVNIGNPKACRAVGLANNKNPIPIFIPCHRVIGA 130 (155)
T ss_pred ChHHHHHHHHHccCCCCCcC--------------CHHHHHHHHCCCchHHHHHHHHHhCCCCCccCCceEECC
Confidence 58999999999999985333 3333322 67899999999999999999998765
No 10
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=48.06 E-value=25 Score=35.85 Aligned_cols=54 Identities=22% Similarity=0.305 Sum_probs=42.9
Q ss_pred ccchHHHHHHHhhCCCceEecceecCCCccccccchhhHHH------HHHHHHHHhhcCCCCccccccccCCCc
Q psy16569 188 SHFYNQVWDIMIRTPEGISVQGHILPQQPTLSNMTQSELTF------ALVAVWDIMIRTPEGISVQGHILPQQP 255 (385)
Q Consensus 188 ~~FY~~VW~iL~~~p~Gl~I~g~~~~~~~~~~n~~~~~~~~------~~~~~~~~~~~~p~~i~~~~~~L~~~~ 255 (385)
..|..+||+.|..-|.| ++ +|-+||-= |.++|=..|-+.|-.|.|++||.-...
T Consensus 269 t~f~~~v~~~l~~ip~G-----~~---------~tY~~~a~~~g~p~a~ravg~a~~~np~~~~iPchRvv~~~ 328 (353)
T PRK15435 269 TAFQQQVWQALRTIPCG-----ET---------VSYQQLANAIGKPKAVRAVASACAANKLAIVIPCHRVVRGD 328 (353)
T ss_pred CHHHHHHHHHHhcCCCC-----Cc---------CcHHHHHHHhCCCChHHHHHHHHHhCCCCcccCCceeECCC
Confidence 45999999999999984 44 34555533 558899999999999999999987653
No 11
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=28.75 E-value=1.9e+02 Score=27.54 Aligned_cols=70 Identities=19% Similarity=0.194 Sum_probs=42.1
Q ss_pred HHhcCCccccchhhHhHHHHHHHHHHHHH--HhcccchhhccCChHHHHHHHHHHhc--cccccccccchhhHHhhhccc
Q psy16569 107 LIATSPDMFNGILKIRVGWVIEAIKVYLE--IIGKDVNAMYNYSPFEIRQLLWKVLN--VREWADEEHLTVLQLRRLEGC 182 (385)
Q Consensus 107 lIrt~P~LF~gml~iRvG~ii~~m~~eL~--~~~~eae~L~~lSP~eik~lL~~vLs--~~~w~~~~~l~wl~~R~l~Ga 182 (385)
.++.+|..-.....-|+.-+++.|...+. ++-++-....++||+-+.++.++..- .++| ++.+|++-|
T Consensus 169 ~~~~~~~~~~~~~~~~i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~~~G~tp~~~--------l~~~Rl~~A 240 (290)
T PRK10572 169 CMEAIPESLHPPMDPRVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRW--------REDQRISRA 240 (290)
T ss_pred HHHhCcccccccccHHHHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHH--------HHHHHHHHH
Confidence 34444443322222355566666655542 22223366789999999999998743 3344 889888776
Q ss_pred cc
Q psy16569 183 WC 184 (385)
Q Consensus 183 Ln 184 (385)
..
T Consensus 241 ~~ 242 (290)
T PRK10572 241 KL 242 (290)
T ss_pred HH
Confidence 43
No 12
>COG4422 Bacteriophage protein gp37 [Function unknown]
Probab=26.18 E-value=35 Score=33.13 Aligned_cols=20 Identities=40% Similarity=0.883 Sum_probs=18.5
Q ss_pred ccCCccchHHHHHHHhhCCC
Q psy16569 184 CRVPSHFYNQVWDIMIRTPE 203 (385)
Q Consensus 184 nRvP~~FY~~VW~iL~~~p~ 203 (385)
-+||.+|..+||.+|..+|+
T Consensus 94 ~~V~~~FI~~Vw~VM~~TP~ 113 (250)
T COG4422 94 ADVPLDFIREVWEVMRATPR 113 (250)
T ss_pred ccchHHHHHHHHHHHHhCcc
Confidence 47999999999999999986
No 13
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=21.57 E-value=2.9e+02 Score=25.96 Aligned_cols=92 Identities=10% Similarity=0.135 Sum_probs=57.9
Q ss_pred eeEecCCCCHHHHHHHHHhhcCCCchHHHHHHHHHHHHHhHHHhcCCccccchhhHhHHHHHHHHHHHHHHhcccchhhc
Q psy16569 66 ETVFDKPLSPSEIRSVIYSTIQPYDVIQAVLQQEIVLYCGRLIATSPDMFNGILKIRVGWVIEAIKVYLEIIGKDVNAMY 145 (385)
Q Consensus 66 E~vIs~PL~p~ei~~~i~~~~~~~d~~~~vL~QEii~ylg~lIrt~P~LF~gml~iRvG~ii~~m~~eL~~~~~eae~L~ 145 (385)
.-.|.++.++++|.+.|+....+.-....-+.+.++-+.+.....+.. +. -|+=|=--++.+++. +.+..|-..-+
T Consensus 105 ~G~l~K~~~~~~L~~aI~~v~~G~~~~~~~~~~~l~~~~~~~~~~~~~-~~-~Lt~rE~~Vl~l~~~--G~s~~eIA~~L 180 (216)
T PRK10100 105 NGVFYAMEDQERVVNGLQGVLRGECYFTQKLASYLITHSGNYRYNSTE-SA-LLTHREKEILNKLRI--GASNNEIARSL 180 (216)
T ss_pred eEEEECCCCHHHHHHHHHHHHcCCcccCHHHHHHHHHhhcccccCCCc-cC-CCCHHHHHHHHHHHc--CCCHHHHHHHh
Confidence 456888999999999999987665333333333333222111111111 22 266676666766665 44555655668
Q ss_pred cCChHHHHHHHHHHhc
Q psy16569 146 NYSPFEIRQLLWKVLN 161 (385)
Q Consensus 146 ~lSP~eik~lL~~vLs 161 (385)
++|+.-+|..+.+++.
T Consensus 181 ~iS~~TVk~~~~~i~~ 196 (216)
T PRK10100 181 FISENTVKTHLYNLFK 196 (216)
T ss_pred CCCHHHHHHHHHHHHH
Confidence 9999999999999987
No 14
>COG1711 DNA replication initiation complex subunit, GINS family [Replication, recombination, and repair]
Probab=21.57 E-value=30 Score=33.86 Aligned_cols=92 Identities=14% Similarity=0.107 Sum_probs=51.8
Q ss_pred ccccCCccchHHHHHHHhhCCCceEecceecCCCccccccchhhHHHHHHHHHHHhhcCCCCccccccccC-CCcccccc
Q psy16569 182 CWCRVPSHFYNQVWDIMIRTPEGISVQGHILPQQPTLSNMTQSELTFALVAVWDIMIRTPEGISVQGHILP-QQPTLSNM 260 (385)
Q Consensus 182 aLnRvP~~FY~~VW~iL~~~p~Gl~I~g~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~p~~i~~~~~~L~-~~~tlseM 260 (385)
-|.+++.+||.+|=.-.+--. .-++....++.++ +-|+-.++.-|....=.+.+|-=+- +|+.-.++ +..|.+.|
T Consensus 18 ~L~~Id~dFY~~v~~~I~eLe--~~~~~~~~~~D~e-~~~~~~~~et~~~~~r~ifqrR~~K-iv~~A~~~~~~~~~~~L 93 (223)
T COG1711 18 GLTEIDEDFYRDVRSFIKELE--DEAGRAEEARDIE-KYLLTDRIETAKSDARSIFQRRYGK-IVSRAIYDVPGETISNL 93 (223)
T ss_pred hhhhcCHHHHHHHHHHHHHHH--HHhhccccccCHH-HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHhccccchhcC
Confidence 478999999999987765541 3343444343333 3334334444544443443333222 22222222 33457899
Q ss_pred CcchhhHHHHHHHHHcC
Q psy16569 261 TQSELTFALLIEEILNH 277 (385)
Q Consensus 261 T~gE~~FAl~VE~lLn~ 277 (385)
|+.|..|--.|..+++.
T Consensus 94 t~eEk~ly~~l~~~I~~ 110 (223)
T COG1711 94 TPEEKELYEDLVNFIED 110 (223)
T ss_pred CHHHHHHHHHHHHHHhh
Confidence 99999998777766553
No 15
>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.
Probab=21.46 E-value=68 Score=26.14 Aligned_cols=67 Identities=9% Similarity=0.222 Sum_probs=30.4
Q ss_pred CcccCcCCccCeEeechhHHHHHHHhc----CCC-CcceecCCCCCCccccccceeeeeec--CCceeEecCCC
Q psy16569 7 IQTQTPHEVEPVQIWSSNELVKVYQHL----GVN-KKLKLSGRPPRPIGALGTSKLAVGVI--GQKETVFDKPL 73 (385)
Q Consensus 7 i~vqT~~ev~PI~V~pa~~L~~iY~~l----G~n-~kLgLSGRP~r~vg~L~TSkl~VGr~--g~eE~vIs~PL 73 (385)
|.+++++....|.|.|.+.++++|.++ +.+ ..+.|+--+...-...+...-+|... .+.+.+|..|+
T Consensus 7 lRvrS~dG~~Rie~~~~~t~~~L~~kI~~~l~~~~~~~~L~~~~~~~~~l~s~~~~tl~~lglkHGdmlyL~~~ 80 (80)
T PF11543_consen 7 LRVRSKDGMKRIEVSPSSTLSDLKEKISEQLSIPDSSQSLSKDRNNKEELKSSDSKTLSSLGLKHGDMLYLKPM 80 (80)
T ss_dssp EEEE-SSEEEEEEE-TTSBHHHHHHHHHHHS---TTT---BSSGGGGGCSSS-TT-CCCCT---TT-EEE----
T ss_pred EEEECCCCCEEEEcCCcccHHHHHHHHHHHcCCCCcceEEEecCCCCcccccCCcCCHHHcCCCCccEEEEecC
Confidence 578899889999999999988888764 444 34555432222111111112233222 35667777664
No 16
>COG3437 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]
Probab=20.86 E-value=1.9e+02 Score=30.31 Aligned_cols=83 Identities=22% Similarity=0.237 Sum_probs=52.6
Q ss_pred eeEecCCCCHHHHHHHHHhhcCCC------------------chH-HHHHHH-----HHHHHHhHHHhcCCccccchhhH
Q psy16569 66 ETVFDKPLSPSEIRSVIYSTIQPY------------------DVI-QAVLQQ-----EIVLYCGRLIATSPDMFNGILKI 121 (385)
Q Consensus 66 E~vIs~PL~p~ei~~~i~~~~~~~------------------d~~-~~vL~Q-----Eii~ylg~lIrt~P~LF~gml~i 121 (385)
.--+++|++|.|+...+....+-. ..+ +.+-++ |.+--|.+++ -.=+.+.|=...
T Consensus 113 ~dyl~KP~~~~~l~~rv~~~~q~k~~~~~~~~~~~~le~~e~~~~~~e~~~~~~~~~~t~~~L~~~~-E~R~~etg~H~~ 191 (360)
T COG3437 113 DDYLSKPISPKELVARVSSHLQLKRNEDFLLDQNLYLELQELRRRTEELAQIEDNLDETLEELAALL-EVRDYETGDHLE 191 (360)
T ss_pred HHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HhcccchhhHHH
Confidence 456788999999998874332111 000 001111 2233344444 345667788889
Q ss_pred hHHHHHHHHHHHHHHhcccchhhccCCh
Q psy16569 122 RVGWVIEAIKVYLEIIGKDVNAMYNYSP 149 (385)
Q Consensus 122 RvG~ii~~m~~eL~~~~~eae~L~~lSP 149 (385)
|+++..++++..++++..+++.++.-+|
T Consensus 192 Rv~~~~~~lAe~lgLse~~v~~i~~Aap 219 (360)
T COG3437 192 RVAQYSELLAELLGLSEEEVDLIKKAAP 219 (360)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHhccc
Confidence 9999999999998877777777766666
No 17
>KOG3635|consensus
Probab=20.49 E-value=49 Score=38.19 Aligned_cols=73 Identities=52% Similarity=0.700 Sum_probs=69.0
Q ss_pred CcCcCCCcccCcCCccCeEeechhHHHHHHHhcCCCCcceecCCCCCCccccccceeeeeecCCceeEecCCCCH
Q psy16569 1 MMGTYGIQTQTPHEVEPVQIWSSNELVKVYQHLGVNKKLKLSGRPPRPIGALGTSKLAVGVIGQKETVFDKPLSP 75 (385)
Q Consensus 1 ~L~~~Gi~vqT~~ev~PI~V~pa~~L~~iY~~lG~n~kLgLSGRP~r~vg~L~TSkl~VGr~g~eE~vIs~PL~p 75 (385)
+|++|||+|||++||+||||||++.|+++|.++|+|+|+||||||.|++|+|+|||+| ++.+..++|+|.+-.
T Consensus 465 ~L~~~gI~vQti~eV~PIqi~pa~~L~~~y~~LG~N~klgLSGRP~RpiG~LgTSKlY--~I~~~~v~ftPqf~D 537 (1150)
T KOG3635|consen 465 ELATHGIQVQTIAEVEPIQIQPARELSHLYAKLGRNNKLGLSGRPDRPIGVLGTSKLY--RIRGKIVTFTPQFFD 537 (1150)
T ss_pred HHHhcCccccccccccceeeccHHHHHHHHHHhCccccCCCCCCCCCcccccchhhHH--hhcCcEEEEehhhhh
Confidence 4789999999999999999999999999999999999999999999999999999999 588888999887754
No 18
>PF01900 RNase_P_Rpp14: Rpp14/Pop5 family; InterPro: IPR002759 This family contains proteins found in some eukaryotes and archaebacteria that are related to yeast ribonuclease P. This enzyme is essential for tRNA processing generating 5'-termini of mature tRNA molecules []. tRNA processing enzyme ribonuclease P (RNase P) consists of an RNA molecule associated with at least eight protein subunits, hPop1, Rpp14, Rpp20, Rpp25, Rpp29, Rpp30, Rpp38, and Rpp40 [].; GO: 0004540 ribonuclease activity, 0008033 tRNA processing; PDB: 2CZV_D 2AV5_B.
Probab=20.14 E-value=29 Score=28.66 Aligned_cols=57 Identities=14% Similarity=0.342 Sum_probs=33.4
Q ss_pred ccCChHHHHHHHHHHhccc--cccccccchhhHHhhhcc----ccccCCccchHHHHHHHhhC
Q psy16569 145 YNYSPFEIRQLLWKVLNVR--EWADEEHLTVLQLRRLEG----CWCRVPSHFYNQVWDIMIRT 201 (385)
Q Consensus 145 ~~lSP~eik~lL~~vLs~~--~w~~~~~l~wl~~R~l~G----aLnRvP~~FY~~VW~iL~~~ 201 (385)
..++|.++++.+++-+..- +++......|++-.-.+. ++-|++.++|..||..|--.
T Consensus 16 ~~~~~~~l~~~I~~a~~~l~G~~G~~~~~~~l~v~~~~~~t~~~IiR~~r~~~~~v~~aL~~i 78 (107)
T PF01900_consen 16 AELSPSDLKKAIREAVKELFGDFGAAAISPSLQVKYFNPKTGIGIIRCRREYYKKVWSALTLI 78 (107)
T ss_dssp S---HHHHHHHHHHHHHHHCHHHHHHHH--EEE--EEETTTTEEEEEEEGGGHHHHHHHHHT-
T ss_pred CcCCHHHHHHHHHHHHHHHcChhhhhhcccccceeeEcCCCCEEEEEEcchhhhHHHHHHHHH
Confidence 5678889999888877621 121111112344333322 89999999999999999766
Done!