Query 048429
Match_columns 192
No_of_seqs 127 out of 711
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 09:27:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048429.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048429hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00684 Terpene_cyclase_plant_ 100.0 9E-68 2E-72 495.8 18.4 187 5-192 28-244 (542)
2 PLN02279 ent-kaur-16-ene synth 100.0 8.7E-56 1.9E-60 429.1 15.9 165 25-192 267-478 (784)
3 PLN02592 ent-copalyl diphospha 100.0 5.3E-54 1.2E-58 416.4 15.1 166 25-192 307-526 (800)
4 PF01397 Terpene_synth: Terpen 100.0 1.5E-49 3.3E-54 328.9 15.1 135 4-138 22-183 (183)
5 PF14164 YqzH: YqzH-like prote 52.9 7.6 0.00017 27.4 1.1 19 55-73 11-29 (64)
6 PF11848 DUF3368: Domain of un 50.1 8.1 0.00017 25.1 0.9 25 50-74 20-44 (48)
7 KOG3951 Uncharacterized conser 45.9 31 0.00068 30.9 4.1 57 74-138 263-319 (321)
8 PF08373 RAP: RAP domain; Int 33.1 33 0.00072 22.3 1.8 27 48-74 17-43 (58)
9 COG5123 TOA2 Transcription ini 29.5 30 0.00064 26.7 1.2 41 88-137 1-41 (113)
10 PF07862 Nif11: Nitrogen fixat 25.1 36 0.00078 21.7 0.9 13 57-69 35-47 (49)
11 PRK10941 hypothetical protein; 23.3 3E+02 0.0064 24.2 6.5 66 2-68 30-119 (269)
12 PF10229 DUF2246: Uncharacteri 23.3 1.3E+02 0.0028 26.8 4.3 51 7-66 173-240 (278)
13 COG1725 Predicted transcriptio 21.9 4E+02 0.0087 20.9 7.4 68 45-112 46-117 (125)
14 cd06404 PB1_aPKC PB1 domain is 21.5 39 0.00085 25.0 0.5 13 10-22 22-34 (83)
15 PF13369 Transglut_core2: Tran 20.7 3.8E+02 0.0082 20.9 6.1 64 4-68 1-88 (152)
16 PF04983 RNA_pol_Rpb1_3: RNA p 20.3 81 0.0018 24.6 2.2 30 27-68 127-156 (158)
17 cd03569 VHS_Hrs_Vps27p VHS dom 20.3 3.4E+02 0.0074 21.3 5.8 55 12-67 84-141 (142)
18 PF07582 AP_endonuc_2_N: AP en 20.2 55 0.0012 22.2 1.0 12 54-65 5-16 (55)
No 1
>cd00684 Terpene_cyclase_plant_C1 Plant Terpene Cyclases, Class 1. This CD includes a diverse group of monomeric plant terpene cyclases (Tspa-Tspf) that convert the acyclic isoprenoid diphosphates, geranyl diphosphate (GPP), farnesyl diphosphate (FPP), or geranylgeranyl diphosphate (GGPP) into cyclic monoterpenes, diterpenes, or sesquiterpenes, respectively; a few form acyclic species. Terpnoid cyclases are soluble enzymes localized to the cytosol (sesquiterpene synthases) or plastids (mono- and diterpene synthases). All monoterpene and diterpene synthases have restrict substrate specificity, however, some sesquiterpene synthases can accept both FPP and GPP. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl diphosphates, via bridging Mg2+ ions (K+ preferred by gymnosperm cyclases), inducing conformational changes such that an N-terminal regi
Probab=100.00 E-value=9e-68 Score=495.76 Aligned_cols=187 Identities=51% Similarity=0.846 Sum_probs=178.9
Q ss_pred hhHHHHHHHHHHHHHHhhCC--CcChhhhHHHHHHHHHhC----C--------------C-------CCChhhHHHHHHH
Q 048429 5 IDQDEFEALKQKIKNMLISP--TDKSFQKLSLIDAVQRLG----Y--------------D-------GNDVHTVALRFRL 57 (192)
Q Consensus 5 ~~~~~~e~Lk~evr~~l~~~--~~d~~~~L~lID~lqRLG----f--------------~-------~~dL~~~AL~FRL 57 (192)
.+.+++++||++||+|+... +.|++++|++||+||||| | | ..||++|||+|||
T Consensus 28 ~~~~~~~~lk~~v~~~~~~~~~~~~~~~~l~liD~lqrLGi~~hF~~EI~~~L~~i~~~~~~~~~~~~~dl~~~al~FRl 107 (542)
T cd00684 28 ELEEEIEELKEEVRKMLEDSEYPVDLFERLWLIDRLQRLGISYHFEDEIKEILDYIYRYWTERGESNEDDLYTTALGFRL 107 (542)
T ss_pred HHHHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHcCchhhhHHHHHHHHHHHHHhhcccccccCCCHHHHHHHHHH
Confidence 47889999999999999865 679999999999999999 3 3 2599999999999
Q ss_pred HhhcCcccccccccccccccCcccccchhhHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHHhhhc---cCCchHHHH
Q 048429 58 LRQQGYRISCDIFGGFKDDRGKFKVSLINDLTGMLSLYEAAHLRIRGEDILDEAVAFTTSHLESMVTQ---VSPQLSDEI 134 (192)
Q Consensus 58 LRqhGy~VS~DvF~~F~d~~G~F~~~l~~dv~glL~LYeAS~l~~~gE~iLdeA~~Ft~~~L~~~~~~---~~~~l~~~V 134 (192)
||||||+||||||++|+|++|+|++++.+||+||||||||||+++|||+|||+|+.||++||++.++. ++++|+++|
T Consensus 108 LR~~Gy~vs~dvf~~F~~~~g~f~~~~~~d~~g~l~Ly~As~l~~~gE~iLdeA~~ft~~~L~~~~~~~~~~~~~l~~~V 187 (542)
T cd00684 108 LRQHGYNVSSDVFKKFKDEDGKFKESLTQDVKGMLSLYEASHLSFPGEDILDEALSFTTKHLEEKLESNWIIDPDLSGEI 187 (542)
T ss_pred HHHcCCCcCHHHHhhhcCCCCCcCchhhhhhHHHHHHHHHhhcCCCCcHHHHHHHHHHHHHHHHHhhccCCCCchHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999986 789999999
Q ss_pred HHhcCCCccCCchhHHHhhhhhhcccCCCCChHHHHHHHHhhhHHHHHHhHHHhhhcC
Q 048429 135 LHALNRPIRRGLPRLEAIYYIDLYSQDDSKDKAILLKFAKLDFSMLQVIHRKELSIIT 192 (192)
Q Consensus 135 ~~aL~~P~~~~l~Rlear~yI~~y~~~~~~n~~~lLeLAklDFn~~Qs~hq~EL~~ls 192 (192)
++||++|||+++||+|||+||++|++++++|++ ||||||+|||+||++||+||++++
T Consensus 188 ~~aL~~P~~~~~~rlear~yi~~Y~~~~~~n~~-lLelAkldfn~~Q~~hq~El~~~~ 244 (542)
T cd00684 188 EYALEIPLHASLPRLEARWYIEFYEQEDDHNET-LLELAKLDFNILQALHQEELKILS 244 (542)
T ss_pred HHHccCchhcCCchHHHHHHHHHhCCCccccHH-HHHHHHHHHHHHhHhHHHHHHHHh
Confidence 999999999999999999999999999999999 999999999999999999999875
No 2
>PLN02279 ent-kaur-16-ene synthase
Probab=100.00 E-value=8.7e-56 Score=429.07 Aligned_cols=165 Identities=33% Similarity=0.536 Sum_probs=154.5
Q ss_pred CcChhhhHHHHHHHHHhC----C--------------C-------CCChhhHHHHHHHHhhcCcccccccccccccccCc
Q 048429 25 TDKSFQKLSLIDAVQRLG----Y--------------D-------GNDVHTVALRFRLLRQQGYRISCDIFGGFKDDRGK 79 (192)
Q Consensus 25 ~~d~~~~L~lID~lqRLG----f--------------~-------~~dL~~~AL~FRLLRqhGy~VS~DvF~~F~d~~G~ 79 (192)
|.++++++|+||+||||| | | ..|+++|||+|||||||||+||||||++|+|+ +
T Consensus 267 p~~~fe~l~lvd~L~rlGi~~hF~~EI~~~L~~~~~~~~~~~~~~~~Dl~~tAl~FRLLR~hGy~VS~dvf~~F~~~-~- 344 (784)
T PLN02279 267 PLDQYARLSMVDTLERLGIDRHFRKEIKSVLDETYRYWLQGEEEIFLDLATCALAFRILRLNGYDVSSDPLKQFAED-H- 344 (784)
T ss_pred cccHHHHhHHHHHHHHhCCccccHHHHHHHHHHHHHhhcccccCCCCCHHHHHHHHHHHHHcCCCCChhHHhhcCCC-c-
Confidence 678999999999999999 3 2 15999999999999999999999999999965 4
Q ss_pred ccccc---hhhHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHHhhhc-------cCCchHHHHHHhcCCCccCCchhH
Q 048429 80 FKVSL---INDLTGMLSLYEAAHLRIRGEDILDEAVAFTTSHLESMVTQ-------VSPQLSDEILHALNRPIRRGLPRL 149 (192)
Q Consensus 80 F~~~l---~~dv~glL~LYeAS~l~~~gE~iLdeA~~Ft~~~L~~~~~~-------~~~~l~~~V~~aL~~P~~~~l~Rl 149 (192)
|++++ .+||+|||+||||||+++|||+|||+|+.||++||++.+++ ++++|+++|++||++|||+++||+
T Consensus 345 F~~~l~~~~~dv~gmL~LY~AS~l~~~gE~iLdeA~~Fs~~~L~~~~~~~~~~~~~~~~~L~~eV~~AL~~P~~~~l~Rl 424 (784)
T PLN02279 345 FSDSLGGYLKDTGAVLELFRASQISYPDESLLEKQNSWTSHFLEQGLSNWSKTADRLRKYIKKEVEDALNFPYYANLERL 424 (784)
T ss_pred ccchhcccchhhHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHHhcccccccccCccHHHHHHHHhcCchhcCccHH
Confidence 99888 59999999999999999999999999999999999998874 578899999999999999999999
Q ss_pred HHhhhhhhcccCCC------------CChHHHHHHHHhhhHHHHHHhHHHhhhcC
Q 048429 150 EAIYYIDLYSQDDS------------KDKAILLKFAKLDFSMLQVIHRKELSIIT 192 (192)
Q Consensus 150 ear~yI~~y~~~~~------------~n~~~lLeLAklDFn~~Qs~hq~EL~~ls 192 (192)
|||+||++|+.++. +|+. ||||||+|||+||++||+||++|+
T Consensus 425 EaR~yI~~Y~~~~~~i~Kt~yr~~~~~n~~-lLeLAklDFN~~Qs~hq~EL~~l~ 478 (784)
T PLN02279 425 ANRRSIENYAVDDTRILKTSYRCSNICNQD-FLKLAVEDFNFCQSIHREELKQLE 478 (784)
T ss_pred HHHHHHHHhccccchhccccccccccccHH-HHHHHHHHHHHHHHHHHHHHHHhC
Confidence 99999999998885 7999 999999999999999999999985
No 3
>PLN02592 ent-copalyl diphosphate synthase
Probab=100.00 E-value=5.3e-54 Score=416.38 Aligned_cols=166 Identities=33% Similarity=0.588 Sum_probs=153.5
Q ss_pred CcChhhhHHHHHHHHHhC----C--------------C---C---------CChhhHHHHHHHHhhcCcccccccccccc
Q 048429 25 TDKSFQKLSLIDAVQRLG----Y--------------D---G---------NDVHTVALRFRLLRQQGYRISCDIFGGFK 74 (192)
Q Consensus 25 ~~d~~~~L~lID~lqRLG----f--------------~---~---------~dL~~~AL~FRLLRqhGy~VS~DvF~~F~ 74 (192)
|.+++++|++||+||||| | | + .|+++|||+|||||||||+||||||++|+
T Consensus 307 P~d~fE~LwlVDtLqRLGIs~hF~~EI~~iLd~iy~~w~~~g~~~a~~~~~~Dld~TALaFRLLRqhGy~VS~DvF~~F~ 386 (800)
T PLN02592 307 PVDLFEHIWAVDRLQRLGISRYFEPEIKECIDYVHRYWTENGICWARNSHVHDIDDTAMGFRLLRLHGHQVSADVFKHFE 386 (800)
T ss_pred CCcHHHHHHHHHHHHHcCCccccHHHHHHHHHHHHHHHhhcCcccccCCCcCCHHHHHHHHHHHHHcCCCCChHHHHhhc
Confidence 579999999999999999 2 2 1 58999999999999999999999999999
Q ss_pred cccCcccccc---hhhHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHHhhh--c------cCCchHHHHHHhcCCCcc
Q 048429 75 DDRGKFKVSL---INDLTGMLSLYEAAHLRIRGEDILDEAVAFTTSHLESMVT--Q------VSPQLSDEILHALNRPIR 143 (192)
Q Consensus 75 d~~G~F~~~l---~~dv~glL~LYeAS~l~~~gE~iLdeA~~Ft~~~L~~~~~--~------~~~~l~~~V~~aL~~P~~ 143 (192)
+ +|.|++.+ .+|++|||+||||||+++|||.|||+|+.||+++|++.++ + ++++|+++|+|||++|||
T Consensus 387 ~-~g~F~~~~ge~~~Dv~glL~LYeAS~l~~~gE~iLdeA~~Fs~~~L~~~~~~~~l~d~~~~~~~L~~eV~~AL~~P~~ 465 (800)
T PLN02592 387 K-GGEFFCFAGQSTQAVTGMFNLYRASQVLFPGEKILENAKEFSSKFLREKQEANELLDKWIIMKDLPGEVGFALEIPWY 465 (800)
T ss_pred C-CCCccccccccccchHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHHHHhhccccccccccCccHHHHHHHhccChhh
Confidence 7 79998655 8999999999999999999999999999999999999753 1 467899999999999999
Q ss_pred CCchhHHHhhhhhhcccCCCC-------------ChHHHHHHHHhhhHHHHHHhHHHhhhcC
Q 048429 144 RGLPRLEAIYYIDLYSQDDSK-------------DKAILLKFAKLDFSMLQVIHRKELSIIT 192 (192)
Q Consensus 144 ~~l~Rlear~yI~~y~~~~~~-------------n~~~lLeLAklDFn~~Qs~hq~EL~~ls 192 (192)
++|||+||||||+.|++++++ |+. ||||||+|||+||++||+||++++
T Consensus 466 ~~l~RlEaR~yI~~Y~~~~~~~i~Kt~yr~~~~~n~~-lLeLAklDFn~~Qs~hq~EL~~ls 526 (800)
T PLN02592 466 ASLPRVETRFYIEQYGGEDDVWIGKTLYRMPYVNNNE-YLELAKLDYNNCQALHQLEWDNFQ 526 (800)
T ss_pred cCcchHHHHHHHHHhcCCcccchhhhhccccccCCHH-HHHHHHHHHHHHHHHhHHHHHHHh
Confidence 999999999999999987764 999 999999999999999999999885
No 4
>PF01397 Terpene_synth: Terpene synthase, N-terminal domain; InterPro: IPR001906 Sequences containing this domain belong to the terpene synthase family. It has been suggested that this gene family be designated tps (for terpene synthase). Sequence comparisons reveal similarities between the monoterpene (C10) synthases, sesquiterpene (C15) synthases and the diterpene (C20) synthases. It has been split into six subgroups on the basis of phylogeny, called Tpsa-Tpsf []. Tpsa includes vetispiridiene synthase Q39979 from SWISSPROT, 5-epi- aristolochene synthase, Q40577 from SWISSPROT and (+)-delta-cadinene synthase P93665 from SWISSPROT . Tpsb includes (-)-limonene synthase, Q40322 from SWISSPROT. Tpsc includes copalyl diphosphate synthase (kaurene synthase A), O04408 from SWISSPROT. Tpsd includes taxadiene synthase, Q41594 from SWISSPROT, pinene synthase, O24475 from SWISSPROT and myrcene synthase, O24474 from SWISSPROT. Tpse includes ent-kaurene synthase B Q39548 from SWISSPROT. Tpsf includes linalool synthase Q9ZPN5 from SWISSPROT. In the fungus Phaeosphaeria sp. (strain L487) the synthesis of ent-kaurene from geranylgeranyl dophosphate is promoted by a single bifunctional protein [].; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 2ONH_A 2ONG_B 3P5R_A 3P5P_A 3N0F_A 3N0G_B 3PYB_A 3PYA_A 3G4F_A 3G4D_B ....
Probab=100.00 E-value=1.5e-49 Score=328.94 Aligned_cols=135 Identities=53% Similarity=0.836 Sum_probs=118.0
Q ss_pred hhhHHHHHHHHHHHHHHhhCCCcChhhhHHHHHHHHHhC----C--------------C------CCChhhHHHHHHHHh
Q 048429 4 TIDQDEFEALKQKIKNMLISPTDKSFQKLSLIDAVQRLG----Y--------------D------GNDVHTVALRFRLLR 59 (192)
Q Consensus 4 ~~~~~~~e~Lk~evr~~l~~~~~d~~~~L~lID~lqRLG----f--------------~------~~dL~~~AL~FRLLR 59 (192)
+.+.+++++||++||.||.....|++++|+|||+||||| | | ..||++|||+|||||
T Consensus 22 ~~~~~~~~~Lk~~v~~~l~~~~~d~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~~~~~~~~~~~dL~~~AL~FRLLR 101 (183)
T PF01397_consen 22 EKCKERAEELKEEVRNMLPASYPDPLEKLELIDTLQRLGISYHFEDEIKEILDSIYRSWDEDNEEIDDLYTTALRFRLLR 101 (183)
T ss_dssp HHHHHHHHHHHHHHHHHHHSSSSHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHHTTTTTSHTSSCHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHhhhccccccccCchhHHHHHHHHHH
Confidence 567889999999999999875458999999999999999 3 2 149999999999999
Q ss_pred hcCcccccccccccccccCcccccchhhHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHHhhhccCC---chHHHHHH
Q 048429 60 QQGYRISCDIFGGFKDDRGKFKVSLINDLTGMLSLYEAAHLRIRGEDILDEAVAFTTSHLESMVTQVSP---QLSDEILH 136 (192)
Q Consensus 60 qhGy~VS~DvF~~F~d~~G~F~~~l~~dv~glL~LYeAS~l~~~gE~iLdeA~~Ft~~~L~~~~~~~~~---~l~~~V~~ 136 (192)
||||+||||||++|+|++|+|+.++++||+|||+||||||++++||+|||+|+.||++||++.+++..+ +|+++|+|
T Consensus 102 qhGy~VS~DvF~~F~d~~g~F~~~l~~Dv~glLsLYeAS~l~~~gE~iLdeA~~Ft~~~L~~~~~~~~~~~~~L~~~V~~ 181 (183)
T PF01397_consen 102 QHGYYVSSDVFNKFKDEKGNFKESLSNDVKGLLSLYEASHLRFHGEDILDEARAFTTKHLKSLLSNLSIPDPHLAKEVKH 181 (183)
T ss_dssp HTT----GGGGGGGBETTSSBSGGGGGHHHHHHHHHHHHTT--TT-HHHHHHHHHHHHHHHHHHTTTCTTSCHHHHHHHH
T ss_pred HcCCcccHHHHhCcccCCCccchhhhHhHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999985543 49999999
Q ss_pred hc
Q 048429 137 AL 138 (192)
Q Consensus 137 aL 138 (192)
||
T Consensus 182 AL 183 (183)
T PF01397_consen 182 AL 183 (183)
T ss_dssp HH
T ss_pred hC
Confidence 97
No 5
>PF14164 YqzH: YqzH-like protein
Probab=52.88 E-value=7.6 Score=27.37 Aligned_cols=19 Identities=32% Similarity=0.551 Sum_probs=16.1
Q ss_pred HHHHhhcCccccccccccc
Q 048429 55 FRLLRQQGYRISCDIFGGF 73 (192)
Q Consensus 55 FRLLRqhGy~VS~DvF~~F 73 (192)
=+-|||.||+++++++...
T Consensus 11 ~~~l~QYg~d~~~~pls~~ 29 (64)
T PF14164_consen 11 INCLRQYGYDVECMPLSDE 29 (64)
T ss_pred HHHHHHhCCcccCCCCCHH
Confidence 3579999999999998864
No 6
>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Probab=50.11 E-value=8.1 Score=25.11 Aligned_cols=25 Identities=28% Similarity=0.361 Sum_probs=18.6
Q ss_pred hHHHHHHHHhhcCcccccccccccc
Q 048429 50 TVALRFRLLRQQGYRISCDIFGGFK 74 (192)
Q Consensus 50 ~~AL~FRLLRqhGy~VS~DvF~~F~ 74 (192)
.+.=.+.-|+++||++|+++++.+.
T Consensus 20 ~~~~~l~~l~~~g~~is~~l~~~~L 44 (48)
T PF11848_consen 20 EVKPLLDRLQQAGFRISPKLIEEIL 44 (48)
T ss_pred hHHHHHHHHHHcCcccCHHHHHHHH
Confidence 3444455669999999999888765
No 7
>KOG3951 consensus Uncharacterized conserved protein [Function unknown]
Probab=45.93 E-value=31 Score=30.87 Aligned_cols=57 Identities=26% Similarity=0.344 Sum_probs=41.2
Q ss_pred ccccCcccccchhhHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHHhhhccCCchHHHHHHhc
Q 048429 74 KDDRGKFKVSLINDLTGMLSLYEAAHLRIRGEDILDEAVAFTTSHLESMVTQVSPQLSDEILHAL 138 (192)
Q Consensus 74 ~d~~G~F~~~l~~dv~glL~LYeAS~l~~~gE~iLdeA~~Ft~~~L~~~~~~~~~~l~~~V~~aL 138 (192)
.+.+|-|.....-|+||-..|-.+-- .... +.|=.|..||++||.. .+-++++++-|
T Consensus 263 Vhp~GAFv~~s~iDmkgcvrllk~q~-p~~~-e~LLnaLRfTTKHlNd------esTpK~ir~ll 319 (321)
T KOG3951|consen 263 VHPNGAFVSNSSIDMKGCVRLLKLQP-PEQS-ECLLNALRFTTKHLND------ESTPKSIRHLL 319 (321)
T ss_pred ccccccccccCcCcHHHHHHHHHcCC-chhh-HHHHHHHHHHHhhcCC------CCChHHHHHHh
Confidence 45789998888999999999888753 2233 4466799999999973 33455565554
No 8
>PF08373 RAP: RAP domain; InterPro: IPR013584 The ~60-residue RAP (an acronym for RNA-binding domain abundant in Apicomplexans) domain is found in various proteins in eukaryotes. It is particularly abundant in apicomplexans and might mediate a range of cellular functions through its potential interactions with RNA []. The RAP domain consists of multiple blocks of charged and aromatics residues and is predicted to be composed of alpha helical and beta strand structures. Two predicted loop regions that are dominated by glycine and tryptophan residues are found before and after the central beta sheet []. Some proteins known to contain a RAP domain are listed below: Human hypothetical protein MGC5297, Mammalian FAST kinase domain-containing proteins (FASTKDs), Chlamydomonas reinhardtii chloroplastic trans-splicing factor Raa3.
Probab=33.13 E-value=33 Score=22.28 Aligned_cols=27 Identities=19% Similarity=0.381 Sum_probs=22.5
Q ss_pred hhhHHHHHHHHhhcCcccccccccccc
Q 048429 48 VHTVALRFRLLRQQGYRISCDIFGGFK 74 (192)
Q Consensus 48 L~~~AL~FRLLRqhGy~VS~DvF~~F~ 74 (192)
...++|.=|+|+..||.|-+=.|-.+.
T Consensus 17 ~g~t~lk~r~L~~~G~~Vi~Ip~~eW~ 43 (58)
T PF08373_consen 17 TGSTKLKHRHLKALGYKVISIPYYEWN 43 (58)
T ss_pred chHHHHHHHHHHHCCCEEEEecHHHHH
Confidence 357899999999999999887776664
No 9
>COG5123 TOA2 Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=29.49 E-value=30 Score=26.71 Aligned_cols=41 Identities=29% Similarity=0.470 Sum_probs=25.7
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHHhhhccCCchHHHHHHh
Q 048429 88 LTGMLSLYEAAHLRIRGEDILDEAVAFTTSHLESMVTQVSPQLSDEILHA 137 (192)
Q Consensus 88 v~glL~LYeAS~l~~~gE~iLdeA~~Ft~~~L~~~~~~~~~~l~~~V~~a 137 (192)
+.|+.+||+-|-++--=|++||+-++ ...++|+++..|-..
T Consensus 1 v~~yYElYRrs~ig~~L~dalD~lis---------~g~isp~lam~vLet 41 (113)
T COG5123 1 VPGYYELYRRSMIGKVLEDALDELIS---------AGVISPNLAMHVLET 41 (113)
T ss_pred CccHHHHHHHHHHHHHHHHHHHHHHh---------cCCcCHHHHHHHHHH
Confidence 35899999999876444666665321 113567676666443
No 10
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=25.07 E-value=36 Score=21.74 Aligned_cols=13 Identities=31% Similarity=0.580 Sum_probs=10.2
Q ss_pred HHhhcCccccccc
Q 048429 57 LLRQQGYRISCDI 69 (192)
Q Consensus 57 LLRqhGy~VS~Dv 69 (192)
+-|.+||.+|++-
T Consensus 35 lA~~~Gy~ft~~e 47 (49)
T PF07862_consen 35 LAREAGYDFTEEE 47 (49)
T ss_pred HHHHcCCCCCHHH
Confidence 4599999998753
No 11
>PRK10941 hypothetical protein; Provisional
Probab=23.30 E-value=3e+02 Score=24.21 Aligned_cols=66 Identities=15% Similarity=0.114 Sum_probs=45.3
Q ss_pred CchhhHHHHHHHHHHHHHHhhCCCcChhhhHHHHHHH--HHhCCC----------------------CCChhhHHHHHHH
Q 048429 2 DATIDQDEFEALKQKIKNMLISPTDKSFQKLSLIDAV--QRLGYD----------------------GNDVHTVALRFRL 57 (192)
Q Consensus 2 ~~~~~~~~~e~Lk~evr~~l~~~~~d~~~~L~lID~l--qRLGf~----------------------~~dL~~~AL~FRL 57 (192)
|.+.+..+++.|..+|+..+.. ..++.+++..+-.+ +.+||. +.-+.-.++.--+
T Consensus 30 ~~~~~~~~L~~l~~~~~~~l~~-~~~~~~~l~~L~~~fy~~lgF~Gn~~~Y~~p~ns~L~~VL~~R~G~PisL~il~l~i 108 (269)
T PRK10941 30 PSQDVYDELERLVSLAREEISQ-LLPQDEQLEKLIALFYGEWGFGGASGVYRLSDALWLDKVLKTRQGSAVSLGAILLWI 108 (269)
T ss_pred CHHHHHHHHHHHHHHHHHhccc-cCCHHHHHHHHHHHHHHHhCCCCCccccCCchhhHHHHHHHccCCCcHHHHHHHHHH
Confidence 5566778999999999999865 45667777766666 778851 1233334455567
Q ss_pred HhhcCcccccc
Q 048429 58 LRQQGYRISCD 68 (192)
Q Consensus 58 LRqhGy~VS~D 68 (192)
-|+-|.+|.+=
T Consensus 109 A~~lglp~~gV 119 (269)
T PRK10941 109 ANRLDLPLMPV 119 (269)
T ss_pred HHHcCCCeeee
Confidence 78888877653
No 12
>PF10229 DUF2246: Uncharacterized conserved protein (DUF2246); InterPro: IPR019362 This entry represents conserved proteins found in the metazoa but absent from fungi. They are all approximately 300 residues in length and have no known function.
Probab=23.29 E-value=1.3e+02 Score=26.81 Aligned_cols=51 Identities=27% Similarity=0.470 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHHhhCCCcChhhhHHHHHHHHHhCCC-----------------CCChhhHHHHHHHHhhcCcccc
Q 048429 7 QDEFEALKQKIKNMLISPTDKSFQKLSLIDAVQRLGYD-----------------GNDVHTVALRFRLLRQQGYRIS 66 (192)
Q Consensus 7 ~~~~e~Lk~evr~~l~~~~~d~~~~L~lID~lqRLGf~-----------------~~dL~~~AL~FRLLRqhGy~VS 66 (192)
..++|.=|+..++-|... --.+-+.|+..||| ...++.+.-+||+| ||.|.
T Consensus 173 s~~vE~Ere~l~e~Fv~~------A~~ic~~L~~~GYWADFIDP~SG~p~~~~~~~~~l~etd~~~~~L---gf~i~ 240 (278)
T PF10229_consen 173 SEEVEQEREQLLEKFVLF------AKEICDALRSQGYWADFIDPFSGRPYFGPYTNNTLFETDERFRLL---GFPIE 240 (278)
T ss_pred cHHHHHHHHHHHHHHHHH------HHHHHHHHHhCCEeeeeecCCCCccccCCCcCCccccHHHHHHhc---Cceee
Confidence 345555566655555421 13477899999975 13688999999875 99995
No 13
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=21.86 E-value=4e+02 Score=20.95 Aligned_cols=68 Identities=24% Similarity=0.204 Sum_probs=39.7
Q ss_pred CCChhhHHHHHHHHhhcCcccccccccccccccCc-ccccc-hhhHHHHHH--HHHHhhcCCCCchHHHHHH
Q 048429 45 GNDVHTVALRFRLLRQQGYRISCDIFGGFKDDRGK-FKVSL-INDLTGMLS--LYEAAHLRIRGEDILDEAV 112 (192)
Q Consensus 45 ~~dL~~~AL~FRLLRqhGy~VS~DvF~~F~d~~G~-F~~~l-~~dv~glL~--LYeAS~l~~~gE~iLdeA~ 112 (192)
.-+.+|++=+|+.|.+.||=-+---...|.-++|. -.... ..=+...|+ +.+|..+++.-|+|++=..
T Consensus 46 ~VNpnTv~raY~eLE~eG~i~t~rg~G~fV~~~~~~~~~~~~~~~~~~~l~~~I~~~~~~G~s~eei~~~~~ 117 (125)
T COG1725 46 GVNPNTVQRAYQELEREGIVETKRGKGTFVTEDAKEILDQLKRELAEEELEEFIEEAKALGLSLEEILELLK 117 (125)
T ss_pred CCCHHHHHHHHHHHHHCCCEEEecCeeEEEcCCchhhHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 35899999999999999986665544444433332 00000 111222222 5677777777666665433
No 14
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=21.47 E-value=39 Score=24.97 Aligned_cols=13 Identities=23% Similarity=0.439 Sum_probs=9.1
Q ss_pred HHHHHHHHHHHhh
Q 048429 10 FEALKQKIKNMLI 22 (192)
Q Consensus 10 ~e~Lk~evr~~l~ 22 (192)
.+.|.++||.+..
T Consensus 22 ~e~L~~~v~~~c~ 34 (83)
T cd06404 22 LEELCNEVRDMCR 34 (83)
T ss_pred HHHHHHHHHHHhC
Confidence 5677777777764
No 15
>PF13369 Transglut_core2: Transglutaminase-like superfamily
Probab=20.71 E-value=3.8e+02 Score=20.94 Aligned_cols=64 Identities=19% Similarity=0.307 Sum_probs=41.6
Q ss_pred hhhHHHHHHHHHHHHHHhhCCCcChhhhHHHHHH-H-HHhCCC----------------------CCChhhHHHHHHHHh
Q 048429 4 TIDQDEFEALKQKIKNMLISPTDKSFQKLSLIDA-V-QRLGYD----------------------GNDVHTVALRFRLLR 59 (192)
Q Consensus 4 ~~~~~~~e~Lk~evr~~l~~~~~d~~~~L~lID~-l-qRLGf~----------------------~~dL~~~AL~FRLLR 59 (192)
+.+..+++.+-.+|+..+.+ ..++.+++..|.. + +++||. +.-+.-+++.=-+.|
T Consensus 1 ~~~~~~Ld~la~~v~~~~~~-~~~~~~~l~al~~~l~~~~gF~~~~~~y~~~~n~~l~~vL~~r~G~Pi~L~ily~~va~ 79 (152)
T PF13369_consen 1 EAVLQRLDALAAQVRQRLPA-RASPREKLEALNDVLYQELGFSGNSENYYDPENSFLHKVLERRRGIPISLAILYLEVAR 79 (152)
T ss_pred ChHHHHHHHHHHHHHHHccc-cCCHHHHHHHHHHHHHHHcCCCCCccccCChHhhhHHHHHhcCCCCcHHHHHHHHHHHH
Confidence 34678999999999999865 3466667766654 3 788851 123334444445667
Q ss_pred hcCcccccc
Q 048429 60 QQGYRISCD 68 (192)
Q Consensus 60 qhGy~VS~D 68 (192)
.-|.++.+=
T Consensus 80 rlGl~~~~v 88 (152)
T PF13369_consen 80 RLGLPAEPV 88 (152)
T ss_pred HcCCeEEEE
Confidence 777776653
No 16
>PF04983 RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; InterPro: IPR007066 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=20.29 E-value=81 Score=24.59 Aligned_cols=30 Identities=33% Similarity=0.721 Sum_probs=21.4
Q ss_pred ChhhhHHHHHHHHHhCCCCCChhhHHHHHHHHhhcCcccccc
Q 048429 27 KSFQKLSLIDAVQRLGYDGNDVHTVALRFRLLRQQGYRISCD 68 (192)
Q Consensus 27 d~~~~L~lID~lqRLGf~~~dL~~~AL~FRLLRqhGy~VS~D 68 (192)
.+-.-..++|.+|+|| |+-+..+|+-|+-+
T Consensus 127 G~~~~~~~ld~i~~lg------------~~~~t~~GfSvgi~ 156 (158)
T PF04983_consen 127 GPEATVQFLDAIKRLG------------FRYLTRSGFSVGID 156 (158)
T ss_dssp HHHHHHHHHHHHHHHH------------HHHHHHHTBB-SGG
T ss_pred CHHHHHHHHHHHHHHH------------HHHHHHcCeeEecc
Confidence 3456688999999887 77777778777643
No 17
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=20.29 E-value=3.4e+02 Score=21.29 Aligned_cols=55 Identities=11% Similarity=0.331 Sum_probs=31.4
Q ss_pred HHHHHHHHHhhCCCcChhhhHHHHHHHHHhC--CC-CCChhhHHHHHHHHhhcCccccc
Q 048429 12 ALKQKIKNMLISPTDKSFQKLSLIDAVQRLG--YD-GNDVHTVALRFRLLRQQGYRISC 67 (192)
Q Consensus 12 ~Lk~evr~~l~~~~~d~~~~L~lID~lqRLG--f~-~~dL~~~AL~FRLLRqhGy~VS~ 67 (192)
++-++..+++.. ..++.-+=.++..|+..+ |. ..++..+.=.+..||..||..++
T Consensus 84 ~fl~~l~~l~~~-~~~~~Vk~kil~li~~W~~~f~~~~~l~~i~~~y~~L~~~G~~FP~ 141 (142)
T cd03569 84 EFMDELKDLIKT-TKNEEVRQKILELIQAWALAFRNKPQLKYVVDTYQILKAEGHKFPE 141 (142)
T ss_pred HHHHHHHHHHcc-cCCHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHcCCCCCC
Confidence 334445555543 222222233334444444 43 34777788889999999998764
No 18
>PF07582 AP_endonuc_2_N: AP endonuclease family 2 C terminus; InterPro: IPR011418 DNA damaging agents such as the anti-tumour drugs bleomycin and neocarzinostatin or those that generate oxygen radicals produce a variety of lesions in DNA. Amongst these is base-loss which forms apurinic/apyrimidinic (AP) sites or strand breaks with atypical 3' termini. DNA repair at the AP sites is initiated by specific endonuclease cleavage of the phosphodiester backbone. Such endonucleases are also generally capable of removing blocking groups from the 3' terminus of DNA strand breaks. AP endonucleases can be classified into two families based on sequence similarity []. This entry represents a highly-conserved sequence found at the C terminus of several apurinic/apyrimidinic (AP) endonucleases in a range of Gram-positive and Gram-negative bacteria. ; PDB: 3LMZ_A 2ZDS_D.
Probab=20.21 E-value=55 Score=22.19 Aligned_cols=12 Identities=42% Similarity=0.592 Sum_probs=8.4
Q ss_pred HHHHHhhcCccc
Q 048429 54 RFRLLRQQGYRI 65 (192)
Q Consensus 54 ~FRLLRqhGy~V 65 (192)
.|+-||+.||+=
T Consensus 5 i~~~L~~~GYdG 16 (55)
T PF07582_consen 5 IFSALREIGYDG 16 (55)
T ss_dssp HHHHHHHTT--S
T ss_pred HHHHHHHcCCCc
Confidence 488999999973
Done!