Query psy11137
Match_columns 831
No_of_seqs 244 out of 320
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 18:56:22 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11137.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11137hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3786|consensus 100.0 5.8E-43 1.3E-47 374.3 2.3 219 159-444 1-222 (395)
2 PF05179 CDC73: RNA pol II acc 100.0 1.2E-36 2.5E-41 319.9 8.3 143 14-171 111-267 (273)
3 KOG3786|consensus 100.0 1.7E-37 3.6E-42 332.5 0.1 213 516-796 1-217 (395)
4 COG5157 CDC73 RNA polymerase I 99.9 1.7E-27 3.8E-32 247.5 11.3 141 15-169 200-351 (362)
5 COG5157 CDC73 RNA polymerase I 99.6 1.4E-16 3E-21 166.9 4.4 140 462-619 2-167 (362)
6 PF05179 CDC73: RNA pol II acc 99.0 3.7E-11 8E-16 127.7 0.0 91 703-795 1-95 (273)
7 smart00013 LRRNT Leucine rich 96.6 0.00093 2E-08 50.3 1.5 31 799-829 1-32 (33)
8 PF01462 LRRNT: Leucine rich r 95.4 0.0065 1.4E-07 44.5 0.9 27 799-825 1-28 (28)
9 KOG4237|consensus 86.6 0.24 5.3E-06 56.6 0.5 37 793-829 410-447 (498)
10 KOG4237|consensus 70.9 1.9 4.2E-05 49.7 1.2 33 797-829 34-70 (498)
11 PF14504 CAP_assoc_N: CAP-asso 31.4 54 0.0012 32.6 3.7 49 82-131 45-93 (141)
No 1
>KOG3786|consensus
Probab=100.00 E-value=5.8e-43 Score=374.28 Aligned_cols=219 Identities=52% Similarity=0.732 Sum_probs=186.7
Q ss_pred ehhhHHHHHhccCCchhHHHHHHHhcCCCcccCCchhhHHHHhcCCCCCCCccCcCCCCCcccccccccccccCCcCCCC
Q psy11137 159 TLECLLFFLKNIGLNHTAYVRKAAASNIPVVPRPYRKDILAYLNGEVATSASIDKTAPLEIPTQVKRVGTEELETPAKKP 238 (831)
Q Consensus 159 tLesllf~lkn~~l~H~~Yvr~A~a~~ip~V~rpDRkdllayL~Ge~~~~~~id~~aple~~~~~~r~~~~e~~~~~kk~ 238 (831)
||||||||+||++|+|++||+.+++++||+|+|||||+||.|||| +.+|+|
T Consensus 1 tl~sll~l~kn~~~~h~v~l~~~~~~s~~~v~~~drk~lL~~~ng-----------------------------~~~~~~ 51 (395)
T KOG3786|consen 1 TLDSLLLLLKNVALKHDVYLRASAEESIPVVTRPDRKELLFYLNG-----------------------------PIAKKP 51 (395)
T ss_pred ChhHHHHHHHHHhhcCCeeeecccccCCCccccccHHHHHhhcCC-----------------------------hhhccC
Confidence 799999999999999999999999999999999999999999999 136889
Q ss_pred CcchhhhHHHHHHHHHhhhcCCCcccccccccccCCCCccccccHHHHHHHHHHHHhhhcccccccccCCCCCCCCCccc
Q psy11137 239 RLEDSVHLQHVKQQLAARLDAPKEASVTLDNIKFGPGSLTEAMSVEKIAAIKAKRLAKKRTTIKRVATDTDGTDIGDKDA 318 (831)
Q Consensus 239 r~e~~~~~~~~k~~l~~~l~~~~~~~v~~~~ir~~~~sLse~msvEkIAaiKaKrla~Kr~tIk~~d~~~~~~~~~~~~~ 318 (831)
|.|+. +++.+ .|....|+ +|+++|++|+||+||||++++|+++|+..+- ++ .+
T Consensus 52 ~~e~~-~~~~d--------------~~~~~~i~----~l~~amsd~~ia~ykak~~~~~~~~~k~~~~----~d----~i 104 (395)
T KOG3786|consen 52 RTEET-ELEND--------------SVFDLRIK----SLSEAMSDESIAEYKAKCLAKKRTNIKFLVR----TD----LI 104 (395)
T ss_pred Cccce-eeeec--------------ccccHHHH----HHHHHhccHHHHHHhHHHHHhcccchhcccc----hH----HH
Confidence 99888 54422 25577888 9999999999999999999999999987652 11 12
Q ss_pred ccccchhhhchhhhhhhhhHhhhccccccccccccCCcchhHhHHHHHHHHHHhhhcCCCCCCC---CCCCCCCCCCCCC
Q psy11137 319 EKDNLKDMLAFDVDVTKNIISRERQWRTRTSIFHTSGKIFSKNIFAILQSIKAREEGRHRPAPP---TPLVPSTPVNKSV 395 (831)
Q Consensus 319 ~~~~~r~~ld~d~d~tr~i~sRER~wRtR~svLqs~~k~F~~nil~iL~svk~ree~~~~~~~~---~~p~~~~~~~~~~ 395 (831)
. .+....++|++++++|++|||+||||+++||+.+++|+||++++|+.++.+++++.....+ -+|.++ .....+
T Consensus 105 ~--~~~g~~~~d~d~~~~i~k~Er~~rt~~~il~~~~~~~~k~~~s~l~~~~~~~e~~~~v~~~~~~~~~v~~-~~~~~~ 181 (395)
T KOG3786|consen 105 V--WLKGNTESDVDLIRDILKRERPWRTRTTILQSTGREFVKNIFSKLQEVKAREEDRKTVEEHNPNFMPVDP-AIRIDG 181 (395)
T ss_pred H--HhhCCccccHHHHhhhhccCCccchHHHHHhhcchhhhhhHHHHhhccceeeecCcccccccccccCCCH-HHhcCC
Confidence 2 2233679999999999999999999999999999999999999999999999999865432 345544 445677
Q ss_pred CCCcccccchhhhhcccccccCCeeecccccccccccceecccCCCCCC
Q psy11137 396 PQPIVYNRYDQERFIKSREETEGFKIDTMGTYHGMTLKSVTEGNTPRKP 444 (831)
Q Consensus 396 ~~p~~YnRYdQERF~~k~eet~gF~Idt~Gt~hg~~lksv~~G~~~~~~ 444 (831)
|.|+.||||+||||. .|+||++|| |||+|+++++|+..+..
T Consensus 182 p~~~~y~ryi~~rf~-------~~~~~~~Gs-~g~~l~~~~e~~~~~~~ 222 (395)
T KOG3786|consen 182 PKPIDYNRYIQERFL-------SFGIDTYGS-HGMKLKPVHEGARKRRK 222 (395)
T ss_pred ccchhhhhhhhhhhh-------ccccccccc-ccccCCccchhhhhccc
Confidence 779999999999993 299999999 99999999999965544
No 2
>PF05179 CDC73: RNA pol II accessory factor, Cdc73 family; InterPro: IPR007852 Paf1 is an RNA polymerase II-associated protein in yeast, which defines a complex that is distinct from the Srb/Mediator holoenzyme. The Paf1 complex, which also contains Cdc73, Ctr9, Hpr1, Ccr4, Rtf1 and Leo1, is required for full expression of a subset of yeast genes, particularly those responsive to signals from the Pkc1/MAP kinase cascade. The complex appears to play an essential role in RNA elongation []. ; PDB: 3V46_A.
Probab=100.00 E-value=1.2e-36 Score=319.87 Aligned_cols=143 Identities=42% Similarity=0.704 Sum_probs=96.2
Q ss_pred cCCCCCCCEEEecCCccceeecccchHHHHH-----------cCCCCCCeEEEEeecCCC--ceeeEEEEeCCCCCCCCC
Q psy11137 14 QKRISRTPIIIIPAANTSLITMFVTTEAKRA-----------AGSKRENEILIQRSKGDG--TTVPYRVIDNPLKLARTD 80 (831)
Q Consensus 14 qkr~~k~PIIIVPss~TSLITL~Ni~d~l~~-----------~g~~~~~~V~I~R~~~~g--~~v~yrVVDn~~~f~ped 80 (831)
.++.+++||||||||+||||||+|+++||.. .++.++++|+|+|...++ .+++|+|||||.+|+|+|
T Consensus 111 ~k~~~~~PIIiVp~s~sSlitm~NiK~FLed~~fv~~~~~~~~~~~~~~~v~i~r~~~~~~~~~v~f~VvD~~~~~~ped 190 (273)
T PF05179_consen 111 SKRRSKDPIIIVPPSASSLITMYNIKQFLEDGKFVPPDEKRKSGSSKPNEVTIQRKFDRIKPGPVRFRVVDNPEKFTPED 190 (273)
T ss_dssp -----S--EEE----TT-SS-TTTHHHHHHH--------GGGS---TTSEEEEEE--TTSSS--EEEEEESSSTT--GGG
T ss_pred cccCCCCCEEEECCcccchhHHHHHHHHHHcCeeecCccccccCCCCCCEEEEEeccCCCCCCceeEEEecChhhCCccc
Confidence 3567889999999999999999999999863 245678999999987544 389999999999999999
Q ss_pred CCeEEEEEeeCCcccccCCCCCCChHHHhhhcceeEEeeeccCCcceeEeccccccccccc-ceeEeeccCCCCccceee
Q psy11137 81 WDRVVAVFVMGPAWQFKGWPWDANPVEIFSKNLAVSRNFIQTTSCNQIIFGEFSWPKDVNT-NYLHYQSSREGAVKKYYT 159 (831)
Q Consensus 81 WdRVVAVFvtGq~WQFK~wpw~~dP~eLF~~V~Gfyv~f~~de~ds~VIFGd~a~pk~VkT-ny~~~~~~~~g~~~eyYt 159 (831)
|+|||||||+|++||||+|||+ +|++||++||||||+|+++. .|.+|+- |..+....|+ +-+=.
T Consensus 191 W~RVVAVF~~G~~WQFk~w~~~-~P~~LF~~v~gf~~~~~~~~-----------~p~~v~~WnV~~l~l~r~---kRh~D 255 (273)
T PF05179_consen 191 WDRVVAVFVTGQAWQFKGWPWS-DPVELFQKVKGFYVHYDGDK-----------VPPNVKQWNVKVLRLSRN---KRHLD 255 (273)
T ss_dssp GGGEEEEE--S-GGGGTTSSS--SHHHHHHHSEEEEEEETTS--------------HHHHHSSEEEEEE-SS-----TTH
T ss_pred CCeEEEEEeECchhhhCCCCCC-CHHHHhhcCcEEEEEecCCC-----------CChhHhcCCCeEEEeCCC---cccch
Confidence 9999999999999999999999 99999999999999999888 4555555 5556555553 45667
Q ss_pred hhhHHHHHhccC
Q psy11137 160 LECLLFFLKNIG 171 (831)
Q Consensus 160 Lesllf~lkn~~ 171 (831)
-+++..||..++
T Consensus 256 ~~~~~~FW~~Le 267 (273)
T PF05179_consen 256 REVVEEFWEKLE 267 (273)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 788888887664
No 3
>KOG3786|consensus
Probab=100.00 E-value=1.7e-37 Score=332.50 Aligned_cols=213 Identities=50% Similarity=0.724 Sum_probs=181.9
Q ss_pred eHHHHHHHHHcCCCChHHHHHHHHHCCCCCCCCCcccchhhhhcCCccccccccccCCCCCCccccccCcccCCCcCCCC
Q psy11137 516 TLECLLFFLKNIGLNHTAYVRKAAASNIPVVPRPYRKDILAYLNGEVATSASIDKTAPLEIPTQVKRVGTEELETPAKKP 595 (831)
Q Consensus 516 TLealvf~w~n~dlsh~dYv~~a~a~~Ip~VS~~DRKdLl~yL~Ge~dts~~ID~sAp~~~p~~~~r~~~~~~~~~~KK~ 595 (831)
||+||+++.+|..++|..||++|.+..+|+|+++|||+||.||+| | .+||+
T Consensus 1 tl~sll~l~kn~~~~h~v~l~~~~~~s~~~v~~~drk~lL~~~ng------------~-----------------~~~~~ 51 (395)
T KOG3786|consen 1 TLDSLLLLLKNVALKHDVYLRASAEESIPVVTRPDRKELLFYLNG------------P-----------------IAKKP 51 (395)
T ss_pred ChhHHHHHHHHHhhcCCeeeecccccCCCccccccHHHHHhhcCC------------h-----------------hhccC
Confidence 699999999999999999999999999999999999999999999 3 27778
Q ss_pred CCCChHHHHHHHHHHHhHhcCCCCccccccccccCCCCcccccCHHHHHHHHHHHHhhccceeeccc-cCCCCCCCCCCc
Q psy11137 596 RLEDSVHLQHVKQQLAARLDAPKEASVTLDNIKFGPGSLTEAMSVEKIAAIKAKRLAKKRTTIKRVA-TDTDGTDIGDKD 674 (831)
Q Consensus 596 r~eD~e~~~r~kerl~a~L~~~k~~~v~~~~i~~~~~~lse~~s~ekiaaikaK~~a~kr~tIk~~~-~~~~~~~~~~~~ 674 (831)
+.|+.| ++. + ++....|+ +|+++||+++||++|||++++||++||... +| .
T Consensus 52 ~~e~~~-~~~-------------d-~~~~~~i~----~l~~amsd~~ia~ykak~~~~~~~~~k~~~~~d---------~ 103 (395)
T KOG3786|consen 52 RTEETE-LEN-------------D-SVFDLRIK----SLSEAMSDESIAEYKAKCLAKKRTNIKFLVRTD---------L 103 (395)
T ss_pred Ccccee-eee-------------c-ccccHHHH----HHHHHhccHHHHHHhHHHHHhcccchhcccchH---------H
Confidence 888883 431 1 14556688 999999999999999999999999999554 22 1
Q ss_pred cccccchhhhcchhhhhhhhhhhhhccccccceecccCcchhhhHHHHHHHhHhhhccCCCCCCCCC---CCCCCCCCCC
Q psy11137 675 AEKDNLKDMLAFDVDVTKNIISRERQWRTRTSIFHTSGKIFSKNIFAILQSIKAREEGRHRPAPPTP---LVPSTPVNKS 751 (831)
Q Consensus 675 ~~~~~~r~~~~~d~d~~~~i~srEr~wrtRtsvlqs~~k~F~kni~~iL~~vk~reeg~~~~~~~~~---~~~~~~~~~~ 751 (831)
+. .+..+.++|+|.+++|++|||.||||+++||+.|+.|+||||++|+.+|+|||++...+.+.+ +++| .....
T Consensus 104 i~--~~~g~~~~d~d~~~~i~k~Er~~rt~~~il~~~~~~~~k~~~s~l~~~~~~~e~~~~v~~~~~~~~~v~~-~~~~~ 180 (395)
T KOG3786|consen 104 IV--WLKGNTESDVDLIRDILKRERPWRTRTTILQSTGREFVKNIFSKLQEVKAREEDRKTVEEHNPNFMPVDP-AIRID 180 (395)
T ss_pred HH--HhhCCccccHHHHhhhhccCCccchHHHHHhhcchhhhhhHHHHhhccceeeecCcccccccccccCCCH-HHhcC
Confidence 22 334478999999999999999999999999999999999999999999999999995433333 5555 33356
Q ss_pred CCCCccccchhhhhhcccccccCCeeeeeccccceeEEEeecccc
Q psy11137 752 VPQPIVYNRYDQERFIKSREETEGFKIDTMGKGHMFVISTQSVST 796 (831)
Q Consensus 752 ~~~~~~y~rydqerf~~~keet~gfkidt~gtyh~~~~~~~~~~~ 796 (831)
+|.|+.||||+||||.+ |+|||+|+ |||.|++++.+.
T Consensus 181 ~p~~~~y~ryi~~rf~~-------~~~~~~Gs-~g~~l~~~~e~~ 217 (395)
T KOG3786|consen 181 GPKPIDYNRYIQERFLS-------FGIDTYGS-HGMKLKPVHEGA 217 (395)
T ss_pred Cccchhhhhhhhhhhhc-------cccccccc-ccccCCccchhh
Confidence 77799999999999933 99999999 999999998875
No 4
>COG5157 CDC73 RNA polymerase II assessory factor [Transcription]
Probab=99.94 E-value=1.7e-27 Score=247.53 Aligned_cols=141 Identities=20% Similarity=0.311 Sum_probs=105.9
Q ss_pred CCCCCCCEEEecCCccceeecccchHHHHHcC-------CCCCCe--EEEEeecCC--CceeeEEEEeCCCCCCCCCCCe
Q psy11137 15 KRISRTPIIIIPAANTSLITMFVTTEAKRAAG-------SKRENE--ILIQRSKGD--GTTVPYRVIDNPLKLARTDWDR 83 (831)
Q Consensus 15 kr~~k~PIIIVPss~TSLITL~Ni~d~l~~~g-------~~~~~~--V~I~R~~~~--g~~v~yrVVDn~~~f~pedWdR 83 (831)
|.++++||||||+|+||++||.||++|+..+. ..-++. +.-..+.+. ..+++|-+||++..|+||||+|
T Consensus 200 k~~~kDPIIlvp~saSS~lt~~NIK~FleEgkyV~P~n~~~~~~G~~i~~~eK~~~~~~g~~rfIiVd~t~~FkpeyWdR 279 (362)
T COG5157 200 KYYAKDPIILVPQSASSPLTLSNIKEFLEEGKYVNPRNLPSCSDGIRISEVEKVELDLDGPFRFIIVDDTGGFKPEYWDR 279 (362)
T ss_pred ccccCCceEEeccccccceeHHHHHHHHHhcCccCccccccCCCCceEEeeeehhhcccCceEEEEEcCCCCcChhhhce
Confidence 44678999999999999999999999997532 112333 332333332 2467888999999999999999
Q ss_pred EEEEEeeCCcccccCCCCCCChHHHhhhcceeEEeeeccCCcceeEecccccccccccceeEeeccCCCCccceeehhhH
Q psy11137 84 VVAVFVMGPAWQFKGWPWDANPVEIFSKNLAVSRNFIQTTSCNQIIFGEFSWPKDVNTNYLHYQSSREGAVKKYYTLECL 163 (831)
Q Consensus 84 VVAVFvtGq~WQFK~wpw~~dP~eLF~~V~Gfyv~f~~de~ds~VIFGd~a~pk~VkTny~~~~~~~~g~~~eyYtLesl 163 (831)
|||||+||++|||.+|+|+ +|.+||++++|||+.|.++...-++. ||-+-|.|=+-. +-|-.-|.+
T Consensus 280 VVciFttG~~WQf~~y~w~-~p~elF~~~kgfyf~~~Gd~~~~~~~------------~wNve~i~v~~~-kR~~drevv 345 (362)
T COG5157 280 VVCIFTTGSKWQFGRYNWR-DPGELFNTIKGFYFARRGDQSNLYMR------------NWNVEEIGVHDG-KRFVDREVV 345 (362)
T ss_pred EEEEEecCCeeeecCcccC-CHHHHHhhCCceEEEEcCCCCChhhh------------ccCceeEEeecC-cccccHHHH
Confidence 9999999999999999999 99999999999999999998532221 233333332222 556677777
Q ss_pred HHHHhc
Q psy11137 164 LFFLKN 169 (831)
Q Consensus 164 lf~lkn 169 (831)
-+||..
T Consensus 346 s~~w~~ 351 (362)
T COG5157 346 SSIWER 351 (362)
T ss_pred HHHHHH
Confidence 777754
No 5
>COG5157 CDC73 RNA polymerase II assessory factor [Transcription]
Probab=99.63 E-value=1.4e-16 Score=166.88 Aligned_cols=140 Identities=15% Similarity=0.181 Sum_probs=106.0
Q ss_pred cchhcccCccccCCCceEE-------------ecceEEeCC-----ccccCCCcccccccccccCCCccceeeHHHHHHH
Q psy11137 462 ANAAASPAPYNINKKEIIE-------------RENQIIFGE-----FSWPKDVNTNYLHYQSSREGAVKKYYTLECLLFF 523 (831)
Q Consensus 462 ~~~L~~LR~~~i~kk~I~~-------------~~~~i~Fgd-----~sfpk~~~Tny~~~g~sk~g~~~e~YTLealvf~ 523 (831)
|+.|.+||.++.+++.-.+ .+..+.|.+ ++|+.+..|...+ +. .+.|+.||||
T Consensus 2 ~n~ldllk~~l~~~d~~~l~~~E~~s~~~kv~~~q~~~f~~~~S~~~~fe~ne~~eiE~------DS---~~qLR~v~f~ 72 (362)
T COG5157 2 ANSLDLLKKALRDPDACQLSPEEIVSGGKKVPPKQMVKFKGTESKEYTFEQNEETEIEI------DS---LVQLRIVLFY 72 (362)
T ss_pred ccHHHHHHHHhcCccceecchhhccccCcccCceeEEEecCCCCceeecCcccceeecc------cc---hhhhhhhhhh
Confidence 5677777777777654433 557788853 6899999999876 34 8999999999
Q ss_pred HHcCCCChHHHHHHHHHCCCCCCCCCcccchhhhhcCCccccccccccCCCCCCccccccCcccCCCcCCCC--CCCChH
Q psy11137 524 LKNIGLNHTAYVRKAAASNIPVVPRPYRKDILAYLNGEVATSASIDKTAPLEIPTQVKRVGTEELETPAKKP--RLEDSV 601 (831)
Q Consensus 524 w~n~dlsh~dYv~~a~a~~Ip~VS~~DRKdLl~yL~Ge~dts~~ID~sAp~~~p~~~~r~~~~~~~~~~KK~--r~eD~e 601 (831)
|+|+|.|.++||++|++.||++|+|+||+||++||+|+++++++|....|- ++....+. . +..- -..||+
T Consensus 73 wlnrD~s~a~Y~~~C~e~gi~ni~fl~rtdlI~wlegnteSsq~l~~~~~k--~EtSs~ts----~--s~~~D~~~sd~~ 144 (362)
T COG5157 73 WLNRDKSYAVYMTLCRESGIGNIYFLDRTDLIEWLEGNTESSQYLKAPGQK--KETSSTTS----I--SARIDSEVSDPV 144 (362)
T ss_pred hhhccchHHHHHHHHHHcCcccEEEeeHHHHHHHHhCCcchhhhhcCCCCC--CCCccccc----c--eeecccccccHH
Confidence 999999999999999999999999999999999999999999999865543 33222100 0 1111 123774
Q ss_pred HHHHH--HHH----HHhHhcCCCC
Q psy11137 602 HLQHV--KQQ----LAARLDAPKE 619 (831)
Q Consensus 602 ~~~r~--ker----l~a~L~~~k~ 619 (831)
+... +|| ||++|.|-|.
T Consensus 145 -V~~~~k~eR~l~~hns~l~G~kp 167 (362)
T COG5157 145 -VVETMKHERILVGHNSRLIGLKP 167 (362)
T ss_pred -HhhhhhcceeecCCCceeecccc
Confidence 4444 777 8999998773
No 6
>PF05179 CDC73: RNA pol II accessory factor, Cdc73 family; InterPro: IPR007852 Paf1 is an RNA polymerase II-associated protein in yeast, which defines a complex that is distinct from the Srb/Mediator holoenzyme. The Paf1 complex, which also contains Cdc73, Ctr9, Hpr1, Ccr4, Rtf1 and Leo1, is required for full expression of a subset of yeast genes, particularly those responsive to signals from the Pkc1/MAP kinase cascade. The complex appears to play an essential role in RNA elongation []. ; PDB: 3V46_A.
Probab=99.03 E-value=3.7e-11 Score=127.70 Aligned_cols=91 Identities=32% Similarity=0.444 Sum_probs=0.0
Q ss_pred cccceecccCcch-hhhHHHHHHHhHhhhccCCCCCCCCCCCCC---CCCCCCCCCCccccchhhhhhcccccccCCeee
Q psy11137 703 TRTSIFHTSGKIF-SKNIFAILQSIKAREEGRHRPAPPTPLVPS---TPVNKSVPQPIVYNRYDQERFIKSREETEGFKI 778 (831)
Q Consensus 703 tRtsvlqs~~k~F-~kni~~iL~~vk~reeg~~~~~~~~~~~~~---~~~~~~~~~~~~y~rydqerf~~~keet~gfki 778 (831)
||++||++++|.| .+||+++|++.++++|++...+.......+ ......+..+..|+||+||||.+ +++.||+|
T Consensus 1 t~~~v~~~~~~~~~~~~l~~~l~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~--~~~~~~~~ 78 (273)
T PF05179_consen 1 TRTTVLISNGKFFERLDLITWLQGASDEEEIKEKEPVLAETAAPERKKGDKNSQQRPSKYNRYDQERFDG--EVLRGFKI 78 (273)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CceehhhhcCcchhhhhHHHHhhcchHhhhcccccccccccccccccccccccccchhhhhhHHHHHhhh--hhcccccc
Confidence 7999999999988 899999999999999988643332222222 11222334478999999999955 79999999
Q ss_pred eeccccceeEEEeeccc
Q psy11137 779 DTMGKGHMFVISTQSVS 795 (831)
Q Consensus 779 dt~gtyh~~~~~~~~~~ 795 (831)
+++|+||||.++++...
T Consensus 79 ~~~~s~~~~~~~~~~~~ 95 (273)
T PF05179_consen 79 DDFGSLRGSALKSVSQG 95 (273)
T ss_dssp -----------------
T ss_pred ccchhcccccccccccc
Confidence 99999999999987665
No 7
>smart00013 LRRNT Leucine rich repeat N-terminal domain.
Probab=96.63 E-value=0.00093 Score=50.29 Aligned_cols=31 Identities=42% Similarity=0.712 Sum_probs=28.7
Q ss_pred CCCCcceEeccccchhhhhccccC-CCCCCCC
Q psy11137 799 QCPFRCICFRTTVRCMFQHLEYVP-RVSNDTT 829 (831)
Q Consensus 799 ~CP~~C~C~~ttVrC~~~~l~~ip-~vp~~t~ 829 (831)
.||..|.|...+|.|....|..|| .||.+|+
T Consensus 1 ~CP~~C~C~~~~V~C~~~~L~~vP~~iP~~t~ 32 (33)
T smart00013 1 ACPAPCNCSGTAVDCSGRGLTEVPLDLPPDTT 32 (33)
T ss_pred CcCCCCEECCCEeEeCCCCcCccCCCCCcccc
Confidence 499999999999999999999999 4998886
No 8
>PF01462 LRRNT: Leucine rich repeat N-terminal domain; InterPro: IPR000372 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. LRRs are often flanked by cysteine-rich domains: an N-terminal LRR domain and a C-terminal LRR domain (IPR000483 from INTERPRO). This entry represents the N-terminal LRR domain. ; PDB: 3E6J_A 1W8A_A 2V9S_C 2V9T_B 3TWI_D 3ZYN_A 3ZYO_A 1OOK_G 1QYY_G 1SQ0_B ....
Probab=95.36 E-value=0.0065 Score=44.49 Aligned_cols=27 Identities=37% Similarity=0.709 Sum_probs=22.2
Q ss_pred CCCCcceEeccccchhhhhccccCC-CC
Q psy11137 799 QCPFRCICFRTTVRCMFQHLEYVPR-VS 825 (831)
Q Consensus 799 ~CP~~C~C~~ttVrC~~~~l~~ip~-vp 825 (831)
.||..|.|...+|.|....|..||. ||
T Consensus 1 ~CP~~C~C~~~~V~C~~~~L~~vP~~lP 28 (28)
T PF01462_consen 1 ACPRPCTCSGLTVDCSGRGLTAVPSDLP 28 (28)
T ss_dssp SSETTSEEETTEEEETTSS-SSS-STS-
T ss_pred CcCCCCEecCCEeECCCCCCCccCCCCc
Confidence 4999999999999999999999995 54
No 9
>KOG4237|consensus
Probab=86.58 E-value=0.24 Score=56.60 Aligned_cols=37 Identities=35% Similarity=0.712 Sum_probs=33.4
Q ss_pred ccccCCCCCCcceEeccccchhhhhccccC-CCCCCCC
Q psy11137 793 SVSTEPQCPFRCICFRTTVRCMFQHLEYVP-RVSNDTT 829 (831)
Q Consensus 793 ~~~~~~~CP~~C~C~~ttVrC~~~~l~~ip-~vp~~t~ 829 (831)
..++...||+.|.|-.|-|||.-..|..+| +||.+++
T Consensus 410 ~~~~s~~cP~~c~c~~tVvRcSnk~lk~lp~~iP~d~t 447 (498)
T KOG4237|consen 410 GCLTSSPCPPPCTCLDTVVRCSNKLLKLLPRGIPVDVT 447 (498)
T ss_pred CCCCCCCCCCCcchhhhhHhhcccchhhcCCCCCchhH
Confidence 356778999999999999999999999997 9999876
No 10
>KOG4237|consensus
Probab=70.90 E-value=1.9 Score=49.65 Aligned_cols=33 Identities=30% Similarity=0.612 Sum_probs=30.1
Q ss_pred CCCCCCcceEec---cccchhhhhccccC-CCCCCCC
Q psy11137 797 EPQCPFRCICFR---TTVRCMFQHLEYVP-RVSNDTT 829 (831)
Q Consensus 797 ~~~CP~~C~C~~---ttVrC~~~~l~~ip-~vp~~t~ 829 (831)
+..||.-|+|-. ..|.|--.-|..|| .+|+.|+
T Consensus 34 ~~~CP~pC~Cs~~~g~~VdCr~~GL~eVP~~LP~~tv 70 (498)
T KOG4237|consen 34 ASACPAPCTCSDVEGGIVDCRGKGLTEVPANLPPETV 70 (498)
T ss_pred cccCCCCcccCCCCCceEEccCCCcccCcccCCCcce
Confidence 568999999999 99999999999999 8888875
No 11
>PF14504 CAP_assoc_N: CAP-associated N-terminal
Probab=31.38 E-value=54 Score=32.58 Aligned_cols=49 Identities=20% Similarity=0.352 Sum_probs=35.8
Q ss_pred CeEEEEEeeCCcccccCCCCCCChHHHhhhcceeEEeeeccCCcceeEec
Q psy11137 82 DRVVAVFVMGPAWQFKGWPWDANPVEIFSKNLAVSRNFIQTTSCNQIIFG 131 (831)
Q Consensus 82 dRVVAVFvtGq~WQFK~wpw~~dP~eLF~~V~Gfyv~f~~de~ds~VIFG 131 (831)
++||++|+.|..|...+++....-.++|+ ..||...+.-..++..+.|-
T Consensus 45 ~kV~~lyt~~~~~~~~p~kiG~s~~~v~~-~~~~~p~~~i~~~~~~Y~~e 93 (141)
T PF14504_consen 45 GKVVALYTNGNDINVSPFKIGMSKSEVFK-KLGIEPEFSIKKGNNSYQFE 93 (141)
T ss_pred CEEEEEEECCcccccCCeecCCCHHHHHH-hcCCCccEEEEECCEEEEEe
Confidence 89999999999999999998756677775 55665555444444444443
Done!