Query 025108
Match_columns 257
No_of_seqs 181 out of 334
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 02:45:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025108.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025108hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14299 PP2: Phloem protein 2 100.0 5.9E-65 1.3E-69 428.4 20.3 151 100-252 1-154 (154)
2 PF12937 F-box-like: F-box-lik 96.5 0.00091 2E-08 44.9 0.9 38 16-54 1-38 (47)
3 smart00256 FBOX A Receptor for 95.3 0.0057 1.2E-07 38.9 0.4 35 19-54 1-35 (41)
4 PF00646 F-box: F-box domain; 95.2 0.0031 6.8E-08 42.0 -1.2 34 16-50 3-36 (48)
5 PF02018 CBM_4_9: Carbohydrate 89.9 3.8 8.1E-05 31.6 9.2 67 157-231 58-125 (131)
6 PLN03215 ascorbic acid mannose 38.5 13 0.00027 36.1 0.6 36 16-51 4-39 (373)
7 PF13765 PRY: SPRY-associated 27.0 66 0.0014 21.5 2.5 41 95-140 3-43 (49)
8 KOG3233 RNA polymerase III, su 25.4 11 0.00024 35.1 -2.0 48 97-152 137-186 (297)
9 PF06881 Elongin_A: RNA polyme 21.6 37 0.00081 26.7 0.5 65 15-81 3-73 (109)
10 PF13464 DUF4115: Domain of un 18.7 1.3E+02 0.0028 21.8 2.8 25 141-165 6-34 (77)
No 1
>PF14299 PP2: Phloem protein 2
Probab=100.00 E-value=5.9e-65 Score=428.41 Aligned_cols=151 Identities=50% Similarity=0.980 Sum_probs=145.2
Q ss_pred CCeEEEEecccceeeecCCCCceeEeecCCCccccccceEEeeeeEEEEEEEEecCcCCCCceEEEEEEEEEeCCCCCce
Q 025108 100 GCNSFMLFSRALLITWAEDNRFWIWTPVKESSDDIVDVAELVQVCWLEIHARLDTTKLSPGISYEVLFVIMLKDPAYGWE 179 (257)
Q Consensus 100 G~kCymLsAR~L~ItWgdd~rYW~Wi~~~~S~~rF~EVAeL~~VcWLEI~G~i~t~~LSP~t~Y~ay~v~kl~~~~~Gwd 179 (257)
|++|||||||+|+|+||||||||+|+++++| ||.|||||++||||||+|+|++++|||+|+|+||||||+++++|||+
T Consensus 1 G~~cymlsaR~L~I~Wg~~~~yW~w~~~~~s--rf~evAeL~~V~WLeI~G~i~~~~Lsp~t~Y~vy~v~kl~~~~~Gw~ 78 (154)
T PF14299_consen 1 GKKCYMLSARALSITWGDDPRYWKWIPLPDS--RFSEVAELLQVCWLEIRGKINTRMLSPGTTYAVYFVFKLKDDAYGWD 78 (154)
T ss_pred CCEEEEEEhhhCEEecCCCCcceeeccCCcc--cceeeeEEEEEEEEEEEEEEEceEcCCCCEEEEEEEEEecCCCCCCC
Confidence 8999999999999999999999999999988 69999999999999999999999999999999999999999999999
Q ss_pred e-ceEEEEEecCCee--eeeEEeeecCCCCCeEEEeeeeEEeCCCCCeEEEEEEEEEeCCeeeeeEEEEEEEEEec
Q 025108 180 V-PVSLRLLLPNGTK--QEHKENLIVKPRNQWIEIPVGEFKSTPENAGEMEISMYEYEGGKWKKGLVVKGVIIRPK 252 (257)
Q Consensus 180 ~-Pv~~~v~~~~g~~--~~~~~~l~~~~~dgW~EielGeF~~~~~~~~eV~fsl~E~~~~~wK~GLiv~GieIRPk 252 (257)
. ||+++|+++++.. +.++++++..+.||||||++|||+++++++++|+|+|+|+++++||+||||+|||||||
T Consensus 79 ~~pv~~~v~~~~~~~~~~~~~~~~~~~r~dgW~Eie~GeF~~~~~~~~ev~f~~~E~~~~~wK~GLiv~GieIRPK 154 (154)
T PF14299_consen 79 SPPVEFSVKVPDGEKYEQERKVCLPKERGDGWMEIELGEFFNEGGDDGEVEFSMYEVDSGHWKGGLIVEGIEIRPK 154 (154)
T ss_pred cCCEEEEEEeCCCccccceeeEEcCCCCCCCEEEEEcceEEecCCCCcEEEEEEEEecCCcccCeEEEEEEEEecC
Confidence 6 9999999998876 56778888889999999999999999889999999999999999999999999999998
No 2
>PF12937 F-box-like: F-box-like; PDB: 1P22_A 2OVP_B 2OVR_B 2OVQ_B 1FS1_A 1FS2_C 1FQV_I 1LDK_E 2AST_B 2ASS_B.
Probab=96.54 E-value=0.00091 Score=44.86 Aligned_cols=38 Identities=16% Similarity=0.135 Sum_probs=31.6
Q ss_pred CCCCCcchhhhhcccccCcccchhhhhcchhhhhhCcCC
Q 025108 16 PNEKPSQNESQNFAIAAKPADNTKETKVCEAKEAEVKLP 54 (257)
Q Consensus 16 ~~~lp~~~~~~~~~~~~~p~d~cr~a~v~~af~~~~fLP 54 (257)
+++||++.+.+|+++ .+|.|.++++.||+.++....-+
T Consensus 1 i~~LP~Eil~~If~~-L~~~dl~~~~~vcr~w~~~~~~~ 38 (47)
T PF12937_consen 1 ISSLPDEILLEIFSY-LDPRDLLRLSLVCRRWRRIANDN 38 (47)
T ss_dssp CCCS-HHHHHHHHTT-S-HHHHHHHTTSSHHHHHHHTCC
T ss_pred ChHhHHHHHHHHHhc-CCHHHHHHHHHHHHHHHHHHCCh
Confidence 468999999999999 79999999999999999765444
No 3
>smart00256 FBOX A Receptor for Ubiquitination Targets.
Probab=95.31 E-value=0.0057 Score=38.86 Aligned_cols=35 Identities=14% Similarity=0.096 Sum_probs=31.3
Q ss_pred CCcchhhhhcccccCcccchhhhhcchhhhhhCcCC
Q 025108 19 KPSQNESQNFAIAAKPADNTKETKVCEAKEAEVKLP 54 (257)
Q Consensus 19 lp~~~~~~~~~~~~~p~d~cr~a~v~~af~~~~fLP 54 (257)
||++++.+|+++ -+|.|.++++.||+.|+.....+
T Consensus 1 lP~~ll~~I~~~-l~~~d~~~~~~vc~~~~~~~~~~ 35 (41)
T smart00256 1 LPDEILEEILSK-LPPKDLLRLRKVSRRWRSLIDSH 35 (41)
T ss_pred CCHHHHHHHHHc-CCHHHHHHHHHHHHHHHHHhcCh
Confidence 799999999999 89999999999999999765444
No 4
>PF00646 F-box: F-box domain; InterPro: IPR001810 The F-box domain was first described as a sequence motif found in cyclin-F that interacts with the protein SKP1 [, ]. This relatively conserved structural motif is present in numerous proteins and serves as a link between a target protein and a ubiquitin-conjugating enzyme. The SCF complex (e.g., Skp1-Cullin-F-box) plays a similar role as an E3 ligase in the ubiquitin protein degradation pathway [, ]. Different F-box proteins as a part of SCF complex recruit particular substrates for ubiquitination through specific protein-protein interaction domains. Many mammalian F-box domains contain leucine-rich or WD-40 repeats (IPR001680 from INTERPRO). However, several F-box proteins either have other previously described domains such as Sec7 domain found in FBS protein or do not contain defined protein-protein interaction domains or motifs.; GO: 0005515 protein binding; PDB: 2E32_A 2E31_A 3V7D_B 1NEX_B 3MKS_D 3L2O_B.
Probab=95.15 E-value=0.0031 Score=41.97 Aligned_cols=34 Identities=12% Similarity=0.104 Sum_probs=28.6
Q ss_pred CCCCCcchhhhhcccccCcccchhhhhcchhhhhh
Q 025108 16 PNEKPSQNESQNFAIAAKPADNTKETKVCEAKEAE 50 (257)
Q Consensus 16 ~~~lp~~~~~~~~~~~~~p~d~cr~a~v~~af~~~ 50 (257)
+.+||++++.+|+.. .+|.|.++++.||+.++..
T Consensus 3 ~~~LP~~il~~Il~~-l~~~~~~~l~~vsk~~~~~ 36 (48)
T PF00646_consen 3 LSDLPDEILQEILSY-LDPKDLLRLSLVSKRWRSL 36 (48)
T ss_dssp HHHS-HHHHHHHHHT-S-HHHHHHHCTT-HHHHHH
T ss_pred HHHCCHHHHHHHHHH-CcHHHHHHHHHHhhHHHHH
Confidence 467999999999999 9999999999999999964
No 5
>PF02018 CBM_4_9: Carbohydrate binding domain; InterPro: IPR003305 The 1,4-beta-glucanase CenC from Cellulomonas fimi contains two cellulose-binding domains, CBD(N1) and CBD(N2), arranged in tandem at its N terminus. These homologous CBDs are distinct in their selectivity for binding amorphous and not crystalline cellulose []. Multidimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy was used to determine the tertiary structure of the 152 amino acid N-terminal cellulose-binding domain from C. fimi 1,4-beta-glucanase CenC (CBDN1) []. The tertiary structure of CBDN1 is strikingly similar to that of the bacterial 1,3-1,4-beta-glucanases, as well as other sugar-binding proteins with jelly-roll folds.; GO: 0016798 hydrolase activity, acting on glycosyl bonds; PDB: 3OEA_B 2ZEX_B 3OEB_A 2ZEY_A 2ZEW_A 1GUI_A 2W5F_A 2WZE_A 2WYS_A 2ZEZ_B ....
Probab=89.88 E-value=3.8 Score=31.59 Aligned_cols=67 Identities=21% Similarity=0.350 Sum_probs=44.4
Q ss_pred CCCCceEEEEEEEEEeCCCCCceeceEEEEEecCCe-eeeeEEeeecCCCCCeEEEeeeeEEeCCCCCeEEEEEEE
Q 025108 157 LSPGISYEVLFVIMLKDPAYGWEVPVSLRLLLPNGT-KQEHKENLIVKPRNQWIEIPVGEFKSTPENAGEMEISMY 231 (257)
Q Consensus 157 LSP~t~Y~ay~v~kl~~~~~Gwd~Pv~~~v~~~~g~-~~~~~~~l~~~~~dgW~EielGeF~~~~~~~~eV~fsl~ 231 (257)
|-||.+|.+.|-++.... .++.+.+...++. ...-... .....+.|.+++ ++|... .+...+.|.+.
T Consensus 58 l~~G~~Y~~s~~vk~~~~-----~~~~~~~~~~~~~~~~~~~~~-~~~~~~~W~~~s-~~ft~~-~~~~~~~l~~~ 125 (131)
T PF02018_consen 58 LKPGKTYTVSFWVKADSG-----GTVSVSLRDEDGSPYNWYTGQ-TVTITGEWTKYS-GTFTAP-SDDDTVRLYFE 125 (131)
T ss_dssp E-TTSEEEEEEEEEESSS-----EEEEEEEEESSTTTEEEEEEE-EEEETSSEEEEE-EEEEEE-SSCEEEEEEEE
T ss_pred ecCCCEEEEEEEEEeCCC-----CEEEEEEEEcCCCCcEEEEEE-EEECCCCcEEEE-EEEEEC-CCCceEEEEEE
Confidence 569999999999999764 6777777776662 1111110 122458999999 589887 45566666554
No 6
>PLN03215 ascorbic acid mannose pathway regulator 1; Provisional
Probab=38.46 E-value=13 Score=36.09 Aligned_cols=36 Identities=8% Similarity=0.014 Sum_probs=32.6
Q ss_pred CCCCCcchhhhhcccccCcccchhhhhcchhhhhhC
Q 025108 16 PNEKPSQNESQNFAIAAKPADNTKETKVCEAKEAEV 51 (257)
Q Consensus 16 ~~~lp~~~~~~~~~~~~~p~d~cr~a~v~~af~~~~ 51 (257)
-.+||++.+.-|.....+..|.-|..+||.+-|++.
T Consensus 4 Ws~Lp~dll~~i~~~l~~~~d~~~~~~vC~sWr~a~ 39 (373)
T PLN03215 4 WSTLPEELLHMIAGRLFSNVELKRFRSICRSWRSSV 39 (373)
T ss_pred hhhCCHHHHHHHHhhCCcHHHHHHHHhhhhhHHHhc
Confidence 458999999999997689999999999999999973
No 7
>PF13765 PRY: SPRY-associated domain; PDB: 3KB5_A 2VOK_A 2VOL_B 2FBE_B 2WL1_A 2IWG_E.
Probab=26.98 E-value=66 Score=21.55 Aligned_cols=41 Identities=7% Similarity=0.200 Sum_probs=25.2
Q ss_pred EEecCCCeEEEEecccceeeecCCCCceeEeecCCCccccccceEE
Q 025108 95 VEKKSGCNSFMLFSRALLITWAEDNRFWIWTPVKESSDDIVDVAEL 140 (257)
Q Consensus 95 ldk~sG~kCymLsAR~L~ItWgdd~rYW~Wi~~~~S~~rF~EVAeL 140 (257)
||..|...+..||.-.-++.+++.++ ..+++..||...+..
T Consensus 3 lDp~TAh~~L~lS~d~k~v~~~~~~~-----~~p~~peRF~~~~~V 43 (49)
T PF13765_consen 3 LDPNTAHPSLVLSEDGKSVRYSEQPQ-----NYPDNPERFDHWPQV 43 (49)
T ss_dssp B-TTTS-TTEEEETTSSEEEE-SST------S--S-TTS-SSSSEE
T ss_pred ECcccCCCCeEECCCCeEEEEccCCc-----cCCCCCCccCCcCeE
Confidence 68888999999999999999988764 334445589755433
No 8
>KOG3233 consensus RNA polymerase III, subunit C34 [Transcription]
Probab=25.44 E-value=11 Score=35.13 Aligned_cols=48 Identities=19% Similarity=0.322 Sum_probs=32.5
Q ss_pred ecCCCeEEEEec--ccceeeecCCCCceeEeecCCCccccccceEEeeeeEEEEEEEE
Q 025108 97 KKSGCNSFMLFS--RALLITWAEDNRFWIWTPVKESSDDIVDVAELVQVCWLEIHARL 152 (257)
Q Consensus 97 k~sG~kCymLsA--R~L~ItWgdd~rYW~Wi~~~~S~~rF~EVAeL~~VcWLEI~G~i 152 (257)
+.+++|||||.- -..+||.| .|.+..+-...| |+-|+++||.=+.-+-
T Consensus 137 ~n~~~KvYmLy~leP~~elTGG------~WytDqdlDvEf--Ie~L~~~c~~fl~~~~ 186 (297)
T KOG3233|consen 137 KNSRKKVYMLYDLEPDSELTGG------TWYTDQDLDVEF--IEVLKQICVRFLESKR 186 (297)
T ss_pred cCCCceEEEEecccccccccCC------cccccccccHHH--HHHHHHHHHHHHHhcc
Confidence 568899999974 56788888 477655432235 5568999985444333
No 9
>PF06881 Elongin_A: RNA polymerase II transcription factor SIII (Elongin) subunit A; InterPro: IPR010684 This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0016021 integral to membrane
Probab=21.63 E-value=37 Score=26.66 Aligned_cols=65 Identities=12% Similarity=0.126 Sum_probs=45.1
Q ss_pred CCCCCCcchhhhhcccccCcccchhhhhcchhhhhh------CcCCCCchhhhcccCCCCCCCcHHHHHHHhh
Q 025108 15 QPNEKPSQNESQNFAIAAKPADNTKETKVCEAKEAE------VKLPHMYEAIVKDADSPIDKSSVDKLYDQLY 81 (257)
Q Consensus 15 ~~~~lp~~~~~~~~~~~~~p~d~cr~a~v~~af~~~------~fLP~dy~~il~~~~~~~~~sskKeLy~~L~ 81 (257)
++.++|.+++..||.. -+|..-.+...-|+-+..+ .|+=.||+.-... ..|....|-+++|.++.
T Consensus 3 dvG~~py~ll~piL~~-~~~~QL~~iE~~np~l~~~tdeLW~~~i~rdFp~~~~~-~~~~~~~~Wr~~Y~~~~ 73 (109)
T PF06881_consen 3 DVGDVPYHLLRPILEK-CSPEQLRRIEDNNPHLIEDTDELWKKLIKRDFPEESKR-QKPKEPESWRELYEKLK 73 (109)
T ss_pred ccCCCCHHHHHHHHcc-CCHHHHHHHHHhCCCcchhhHHHHHHHHHhHCcChhhc-ccccccchHHHHHHHHH
Confidence 5789999999999999 5999999999888777653 3333444331111 12334456788999985
No 10
>PF13464 DUF4115: Domain of unknown function (DUF4115)
Probab=18.68 E-value=1.3e+02 Score=21.83 Aligned_cols=25 Identities=20% Similarity=0.332 Sum_probs=17.1
Q ss_pred eeeeEEEEE---E-EEecCcCCCCceEEE
Q 025108 141 VQVCWLEIH---A-RLDTTKLSPGISYEV 165 (257)
Q Consensus 141 ~~VcWLEI~---G-~i~t~~LSP~t~Y~a 165 (257)
..-||++|+ | .+-..+|.+|.+|+.
T Consensus 6 ~~~sWv~V~d~dG~~~~~~~l~~G~~~~~ 34 (77)
T PF13464_consen 6 TGDSWVEVTDADGKVLFSGTLKAGETKTF 34 (77)
T ss_pred eCCeEEEEEeCCCcEeeeeeeCCCcEEEE
Confidence 356999998 4 344456778876665
Done!