Query 041621
Match_columns 452
No_of_seqs 87 out of 112
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 09:03:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041621.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041621hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03759 PRONE: PRONE (Plant-s 100.0 6E-186 1E-190 1352.9 23.3 338 107-450 2-365 (365)
2 smart00546 CUE Domain that may 81.7 1.7 3.6E-05 31.3 2.9 34 385-418 3-36 (43)
3 PF02845 CUE: CUE domain; Int 77.2 2.9 6.3E-05 30.1 3.0 34 385-418 2-35 (42)
4 PF09539 DUF2385: Protein of u 65.0 1 2.3E-05 39.1 -1.8 31 148-178 10-41 (96)
5 TIGR02301 conserved hypothetic 51.7 2.5 5.5E-05 38.3 -1.8 30 148-177 35-65 (121)
6 KOG2379 Endonuclease MUS81 [Re 51.0 33 0.0007 37.6 5.9 170 150-341 247-450 (501)
7 PF05823 Gp-FAR-1: Nematode fa 45.5 1.2E+02 0.0027 27.8 8.0 96 286-425 1-96 (154)
8 PF03281 Mab-21: Mab-21 protei 36.0 3.6E+02 0.0077 25.9 9.8 134 181-343 115-289 (292)
9 PF08700 Vps51: Vps51/Vps67; 34.0 91 0.002 24.7 4.7 84 313-400 2-86 (87)
10 PF11583 AurF: P-aminobenzoate 30.6 1.2E+02 0.0025 29.5 5.7 65 236-311 44-118 (304)
11 PF10236 DAP3: Mitochondrial r 29.4 66 0.0014 32.0 3.9 80 262-342 81-166 (309)
12 PF02169 LPP20: LPP20 lipoprot 29.1 25 0.00053 27.9 0.7 31 126-156 14-44 (92)
13 PF01343 Peptidase_S49: Peptid 25.5 1.8E+02 0.0038 25.9 5.5 80 174-280 23-108 (154)
14 PF14261 DUF4351: Domain of un 22.8 86 0.0019 24.8 2.7 27 381-409 6-32 (59)
15 PF15002 ERK-JNK_inhib: ERK an 21.4 73 0.0016 31.1 2.5 26 416-441 86-113 (207)
16 PF07528 DZF: DZF domain; Int 21.2 65 0.0014 31.8 2.1 48 387-434 136-190 (248)
17 TIGR03578 EF_0831 conserved hy 20.5 87 0.0019 27.8 2.5 33 129-161 11-47 (96)
No 1
>PF03759 PRONE: PRONE (Plant-specific Rop nucleotide exchanger); InterPro: IPR005512 In plants, the small GTP-binding proteins called Rops work as signalling switches that control growth, development and plant responses to various environmental stimuli. Rop proteins (Rho of plants, Rac-like and atRac in Arabidopsis thaliana (Mouse-ear cress)) belong to the Rho family of Ras-related GTP-binding proteins that turn on signalling pathways by switching from a GDP-bound inactive to a GTP-bound active conformation. Activation depends on guanine nucleotide exchange factors (GEFs) that catalyse the otherwise slow GDP dissociation for subsequent GTP binding. The plant-specific RopGEFs represent a unique family of exchange factor that display no homology to any known RhoGEFs from animals and fungi. They comprise a highly conserved catalytic domain termed PRONE (plant-specific Rop nucleotide exchanger) with exclusive substrate specificity for members of the Rop family. The PRONE domain has been shown to be necessary and sufficient to promote nucleotide release from Rop [, , ]. The PRONE domain can be divided into three highly conserved subdomains separated by two short stretches of variable amino acid residues [, ]. It is approximately 370 residues in length and displays an almost all alpha-helical structure except for a beta-turn that protrudes from the main body of the molecule. The overall structure of the PRONE domain can be divided into two subdomains, the first one including helices alpha1-5 and alpha13, the second alpha6-12 [].; GO: 0005089 Rho guanyl-nucleotide exchange factor activity; PDB: 2NTX_B 2NTY_B 2WBL_A.
Probab=100.00 E-value=6.4e-186 Score=1352.86 Aligned_cols=338 Identities=68% Similarity=1.095 Sum_probs=265.9
Q ss_pred hHHHHHHHHHHHHhhhccCCCCCCCchhhHHHHHHHHHHHHHhhhhccccccCCChhHHHhhhhhccccccccCeeEEee
Q 041621 107 DLELELMKERFAKLLLGEDMSGSGKGVCTAVTISNAITNLYATVFGQNLRLAPLKPEKKALWKREMDCLLSVCDYIVEFV 186 (452)
Q Consensus 107 ~se~E~MKErFaKLLLGEDMSGggKGV~tALAiSNAITNL~AtVFGelwrLEPl~~ekK~~WrREmdwLLSV~D~IVElv 186 (452)
.+|+||||||||||||||||||||||||||||||||||||||||||||||||||++|||+||||||||||||||||||||
T Consensus 2 ~se~e~mKErFaKLLLGEDmSG~gkGV~tAlAiSNAITNL~AtvFGe~~rLEPl~~ekk~~WrrEm~wLLsv~d~iVE~v 81 (365)
T PF03759_consen 2 PSEVEMMKERFAKLLLGEDMSGGGKGVCTALAISNAITNLAATVFGELWRLEPLSPEKKAMWRREMDWLLSVTDYIVELV 81 (365)
T ss_dssp HHHHHHHHHHHHHHHTTTBTTSSS-S--HHHHHHHHHHHHHHHHHTT--SSS---HHHHHHHHHHHHHHHGGGGG-EEEE
T ss_pred chHHHHHHHHHHHHhccCCCCCCCCcccHHHHHHHHHHHHHHHHhhhhhccCCCChHHHHHHHHhcceeecchhhhhhcc
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecccccCCCcchh-------------------------HhhhccCCCeeEeeeCCCCCCCCCCCCCcccccccccCcccc
Q 041621 187 SESQNLRDGREVE-------------------------DILESFQDTEFWYAEQGSMSSNSTRSGSFRRVIVQRKEEKWW 241 (452)
Q Consensus 187 Ps~Q~~~dG~~~E-------------------------e~LDsf~~tEFWYv~~g~~~~~~~~s~s~r~~~~~R~eeKWW 241 (452)
|++|++|||+++| |+||||+|||||||++|+++ .++.+++||+ ..+||++|||
T Consensus 82 Ps~Q~~~dG~~~EvM~~r~RsDl~~NlPALrKLD~MLie~LDsf~dtEFwYv~~g~~~-~~~~~~~~~~-~~~r~~~KWW 159 (365)
T PF03759_consen 82 PSKQTFPDGTTMEVMTTRPRSDLYMNLPALRKLDAMLIEILDSFKDTEFWYVDQGIVA-DSDSSSSFRR-SSQRQEEKWW 159 (365)
T ss_dssp EEEEE-TTS-EEEEEEEEE-HHHHTHHHHHHHHHHHHHHHHHTTCS-SSEE--TT-------SHHHHT-------CCCTT
T ss_pred cceeecCCCceEEEEecCccchhhcCcHHHHHHHHHHHHHHHhCCCCeeEEecCCccc-ccccCccccC-cccccCCccc
Confidence 9999999999999 99999999999999999988 5666788887 9999999999
Q ss_pred ccCCcCCCCCCCHHHHHhhhhhhhhHHHHHHHHHHhhhhhhhcCCCchHHHhhccccCccchhHHHHHhhccCCCCChhh
Q 041621 242 LPVPCVPPGGLSEKSRKHLRHKRDCANQIHKAAMAINSTILAEMEIPDSYMANLPKSGKACLGDFIYRYMYTTEKFSPDH 321 (452)
Q Consensus 242 LP~p~VP~~GLSe~~RK~L~~qrd~~nQIlKAAmAIN~~vL~EMeIPe~y~esLPKnGrasLGD~iYr~i~t~e~Fspe~ 321 (452)
||+|||||+||||++||+|||||||||||||||||||++||+|||||++|+|+||||||+||||.|||+| |+|+||||+
T Consensus 160 LP~p~VP~~GLse~~rK~L~~~rd~~~QilKAAmaIN~~vL~EMeiP~~y~esLPKnGrasLGd~iYr~i-t~~~Fspe~ 238 (365)
T PF03759_consen 160 LPVPRVPPNGLSEESRKWLQHQRDCVNQILKAAMAINSQVLAEMEIPESYLESLPKNGRASLGDSIYRYI-TSEQFSPEQ 238 (365)
T ss_dssp S--EE--TT---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS---HHHHHCS-SSHHHHHHHHHHHHC-TSSS--HHH
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHhcccccHHHHHHHH-hccCcCHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999 999999999
Q ss_pred HhhhcCchhhhHHHhhhhhhHHHHHHHHHhhhccCCCcch-hhhhhhhcccCcchhHHHHHHHHHHHHHHHHhhCCCCCc
Q 041621 322 LLDCLSIASEHEALELADHVEASMYTWRRKACMSHSKSSW-DMVKDLMSETDRSDKNHLLAARAESLLFYLKQRYPELAQ 400 (452)
Q Consensus 322 lL~~ldLssEH~aLe~anRvEAsi~iWrrK~~~~~~kssW-~~vk~l~~~~~~~dK~e~laeRAEtlL~~LKqRfPgLpQ 400 (452)
||+||||||||+|||+|||||||||+||||++++++|+|| ++|||+|++. |||++|++|||+||+|||||||||||
T Consensus 239 ll~~ldlssEH~~le~~NRvEAai~vWrrK~~~k~~ksSWg~~vkdl~~~~---dK~e~l~eRAEtlL~~LK~RfPgl~Q 315 (365)
T PF03759_consen 239 LLDCLDLSSEHKALELANRVEAAIYVWRRKICEKDSKSSWGSMVKDLMSDG---DKRELLAERAETLLLCLKQRFPGLPQ 315 (365)
T ss_dssp HHHTS--SSHHHHHHHHHHHHHHHHHHCH---------------------H---HHHHHHHHHHHHHHHHHHHHSTT---
T ss_pred HHHhcccccHHHHHHHHHHHHHHHHHHHHHhcCCCCccchhhhcccccccc---hHHHHHHHHHHHHHHHHHHhCCCCCc
Confidence 9999999999999999999999999999999999999999 5999999987 89999999999999999999999999
Q ss_pred chhhhhhhhhchhhHHHHHHHHHHHHHHhHHHHHHhhhhHHhhchhhhcc
Q 041621 401 TSLDTCKIQCNQDVGQAVLESYSRVLEGLAFNTVAWVEDVLFVDRSVRNQ 450 (452)
Q Consensus 401 T~LD~sKIQyNkDVG~aILESYSRVLEsLAfnI~sRIdDVL~~D~~~~~~ 450 (452)
|+||++|||||||||||||||||||||||||||++|||||||+|+++++.
T Consensus 316 T~LD~~KIQyNkDVG~aILESYSRVLEsLAfnI~sRIdDVL~~D~~~~~~ 365 (365)
T PF03759_consen 316 TSLDISKIQYNKDVGQAILESYSRVLESLAFNILSRIDDVLYADDLTKNS 365 (365)
T ss_dssp -HHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred hHHHHHHHHccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCC
Confidence 99999999999999999999999999999999999999999999999863
No 2
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=81.66 E-value=1.7 Score=31.32 Aligned_cols=34 Identities=21% Similarity=0.347 Sum_probs=29.2
Q ss_pred HHHHHHHHhhCCCCCcchhhhhhhhhchhhHHHH
Q 041621 385 ESLLFYLKQRYPELAQTSLDTCKIQCNQDVGQAV 418 (452)
Q Consensus 385 EtlL~~LKqRfPgLpQT~LD~sKIQyNkDVG~aI 418 (452)
+..+..|++-||.++...+-.+=.++|.||..+|
T Consensus 3 ~~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i 36 (43)
T smart00546 3 DEALHDLKDMFPNLDEEVIKAVLEANNGNVEATI 36 (43)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHH
Confidence 3467789999999999999888888999998876
No 3
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=77.24 E-value=2.9 Score=30.08 Aligned_cols=34 Identities=24% Similarity=0.438 Sum_probs=29.3
Q ss_pred HHHHHHHHhhCCCCCcchhhhhhhhhchhhHHHH
Q 041621 385 ESLLFYLKQRYPELAQTSLDTCKIQCNQDVGQAV 418 (452)
Q Consensus 385 EtlL~~LKqRfPgLpQT~LD~sKIQyNkDVG~aI 418 (452)
+..+..|+.-||.++...+-..=.++|.||-.+|
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai 35 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAI 35 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHH
Confidence 3567899999999999999999999999998876
No 4
>PF09539 DUF2385: Protein of unknown function (DUF2385); InterPro: IPR012645 Members of this uncharacterised protein family are found in a number of alphaproteobacteria, including root nodule bacteria, Brucella suis, Caulobacter crescentus (Caulobacter vibrioides), and Rhodopseudomonas palustris. Conserved residues include two well-separated cysteines, suggesting a disulphide bond. The function is unknown.
Probab=65.01 E-value=1 Score=39.15 Aligned_cols=31 Identities=26% Similarity=0.462 Sum_probs=27.2
Q ss_pred HhhhhccccccCCCh-hHHHhhhhhccccccc
Q 041621 148 ATVFGQNLRLAPLKP-EKKALWKREMDCLLSV 178 (452)
Q Consensus 148 AtVFGelwrLEPl~~-ekK~~WrREmdwLLSV 178 (452)
|-|+|+++-|.+|+. +....||.+|.=||-+
T Consensus 10 AeiLGalHyLR~LCg~~~~~~WR~~M~~Ll~~ 41 (96)
T PF09539_consen 10 AEILGALHYLRNLCGGNEDQYWRDRMQALLDA 41 (96)
T ss_pred HHHHHHHHHHHHHhCCCCcchHHHHHHHHHHh
Confidence 679999999999999 8899999999776643
No 5
>TIGR02301 conserved hypothetical protein TIGR02301. Members of this uncharacterized protein family are found in a number of alphaProteobacteria, including root nodule bacteria, Brucella suis, Caulobacter crescentus, and Rhodopseudomonas palustris. Conserved residues include two well-separated cysteines, suggesting a disulfide bond. The function is unknown.
Probab=51.70 E-value=2.5 Score=38.25 Aligned_cols=30 Identities=27% Similarity=0.464 Sum_probs=25.9
Q ss_pred HhhhhccccccCCChhHH-Hhhhhhcccccc
Q 041621 148 ATVFGQNLRLAPLKPEKK-ALWKREMDCLLS 177 (452)
Q Consensus 148 AtVFGelwrLEPl~~ekK-~~WrREmdwLLS 177 (452)
|.|+|+++-|.+|+.... ..||.+|.=||-
T Consensus 35 AeiLG~lHyLR~LC~~~~~~~WR~~M~~Ll~ 65 (121)
T TIGR02301 35 AEILGSLHYLRNLCGSKGDDYWRSRMQALID 65 (121)
T ss_pred HHHHHHHHHHHHHhCCCcchHHHHHHHHHHH
Confidence 678999999999998665 899999977764
No 6
>KOG2379 consensus Endonuclease MUS81 [Replication, recombination and repair]
Probab=51.03 E-value=33 Score=37.58 Aligned_cols=170 Identities=24% Similarity=0.325 Sum_probs=100.2
Q ss_pred hhhccccccCCChhHHHhhhhhccccc--------cccCeeEE------eeecccccCCCcchhH--hhh-ccCCCeeEe
Q 041621 150 VFGQNLRLAPLKPEKKALWKREMDCLL--------SVCDYIVE------FVSESQNLRDGREVED--ILE-SFQDTEFWY 212 (452)
Q Consensus 150 VFGelwrLEPl~~ekK~~WrREmdwLL--------SV~D~IVE------lvPs~Q~~~dG~~~Ee--~LD-sf~~tEFWY 212 (452)
+||+..-++-+..|-|..=-.+.=|.- .|+|+||| |+-|- -||+-.|. =|. |=-..=|+.
T Consensus 247 ~~~~~~~~~~v~~evR~L~vGD~lWVa~~k~~g~E~VLd~IVERKr~DDl~SSI---rDgRf~EQK~RLq~sGik~~iYl 323 (501)
T KOG2379|consen 247 FFGEYFELEGVKHEVRSLEVGDFLWVARHKYDGTELVLDFIVERKRLDDLVSSI---RDGRFKEQKNRLQRSGIKRIIYL 323 (501)
T ss_pred hhhhhhhhccceeeEEEecccceEEEecccCCCceEeeeeheeecchHHHHHHH---hccchHHHHHHHHhcCcceEEEE
Confidence 577777777777766655444455554 49999999 34333 36666661 111 111234566
Q ss_pred eeCCCCCCCCCC-CCCcccc--cccccCccccccCCcCCCCCCCHHHHHhhhhhhhhHHHHHHHHHHhh-------hhhh
Q 041621 213 AEQGSMSSNSTR-SGSFRRV--IVQRKEEKWWLPVPCVPPGGLSEKSRKHLRHKRDCANQIHKAAMAIN-------STIL 282 (452)
Q Consensus 213 v~~g~~~~~~~~-s~s~r~~--~~~R~eeKWWLP~p~VP~~GLSe~~RK~L~~qrd~~nQIlKAAmAIN-------~~vL 282 (452)
++..- .++-.. ..+.+.- .++ -.+.. --+-..||-+..+|-=.-+|. .-||.+-.+-=+ .|..
T Consensus 324 vE~~~-~~n~~~~~eslktA~~~t~-v~~GF----~V~RT~~l~et~s~l~y~tr~-~~~~~~~~~~~~~d~~~~~~q~~ 396 (501)
T KOG2379|consen 324 VEEDG-NPNQSKPAESLKTAVTNTL-VLEGF----DVIRTRDLGETVSKLAYLTRG-LLQIYASLLLDKEDYRERDDQLK 396 (501)
T ss_pred EeccC-CcccccHHHHHHHHHHHHh-hhcce----EEEEecChhHHHHHHHHHhHH-HHHHHHHhhccccccccchhhhh
Confidence 66531 111000 0000000 000 00000 012245677777766444444 467777777555 7899
Q ss_pred hcCCCch-------HHHhhccccCccchhHHHHHhhccCCCCChhhHhhhcCchhhhHHHhhhhhh
Q 041621 283 AEMEIPD-------SYMANLPKSGKACLGDFIYRYMYTTEKFSPDHLLDCLSIASEHEALELADHV 341 (452)
Q Consensus 283 ~EMeIPe-------~y~esLPKnGrasLGD~iYr~i~t~e~Fspe~lL~~ldLssEH~aLe~anRv 341 (452)
-+|.+|. .+.+-++|++.-++||..++.| +.+.+||-| .|.+|++|-
T Consensus 397 ~~~~~p~~~~~~f~~F~~~~~K~~~~TV~evf~~qL-----------Mqvkg~S~e-rAiAI~d~Y 450 (501)
T KOG2379|consen 397 GAMTVPSETELSFSAFQERLSKGKALTVGEVFARQL-----------MQVKGMSLE-RAIAIADRY 450 (501)
T ss_pred cccCCCCcccccHHHHHHHhhhcccccHHHHHHHHH-----------HhccCccHH-HHHHHHHhc
Confidence 9999995 8899999999999999999988 447777777 777777764
No 7
>PF05823 Gp-FAR-1: Nematode fatty acid retinoid binding protein (Gp-FAR-1); InterPro: IPR008632 Parasitic nematodes produce at least two structurally novel classes of small helix-rich retinol- and fatty-acid-binding proteins that have no counterparts in their plant or animal hosts and thus represent potential targets for new nematicides. Gp-FAR-1 is a member of the nematode-specific fatty-acid- and retinol-binding (FAR) family of proteins but localises to the surface of the organism, placing it in a strategic position for interaction with the host. Gp-FAR-1 functions as a broad-spectrum retinol- and fatty-acid-binding protein, and it is thought that it is involved in the evasion of primary host plant defence systems [].; GO: 0008289 lipid binding; PDB: 2W9Y_A.
Probab=45.52 E-value=1.2e+02 Score=27.78 Aligned_cols=96 Identities=19% Similarity=0.233 Sum_probs=52.4
Q ss_pred CCchHHHhhccccCccchhHHHHHhhccCCCCChhhHhhhcCchhhhHHHhhhhhhHHHHHHHHHhhhccCCCcchhhhh
Q 041621 286 EIPDSYMANLPKSGKACLGDFIYRYMYTTEKFSPDHLLDCLSIASEHEALELADHVEASMYTWRRKACMSHSKSSWDMVK 365 (452)
Q Consensus 286 eIPe~y~esLPKnGrasLGD~iYr~i~t~e~Fspe~lL~~ldLssEH~aLe~anRvEAsi~iWrrK~~~~~~kssW~~vk 365 (452)
+||+.|.+-||..-. ++++.|.-.....+.|+++.- . .-.++.-+
T Consensus 1 ~i~~~~k~~iP~ev~--------------------~~~~~Lt~eeK~~lkev~~~~-------~-------~~~~~de~- 45 (154)
T PF05823_consen 1 DIPEEYKELIPSEVV--------------------EFYKNLTPEEKAELKEVAKNY-------A-------KFKNEDEM- 45 (154)
T ss_dssp -S-HHHHTT--HHHH--------------------HHHHH--TTTHHHHHHHHTT---------------------TTH-
T ss_pred CchHHHHHhCcHHHH--------------------HHHHcCCHHHHHHHHHHHHHc-------c-------ccCCHHHH-
Confidence 488888888886421 122444555556677777662 1 11345433
Q ss_pred hhhcccCcchhHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhchhhHHHHHHHHHHH
Q 041621 366 DLMSETDRSDKNHLLAARAESLLFYLKQRYPELAQTSLDTCKIQCNQDVGQAVLESYSRV 425 (452)
Q Consensus 366 ~l~~~~~~~dK~e~laeRAEtlL~~LKqRfPgLpQT~LD~sKIQyNkDVG~aILESYSRV 425 (452)
+... ..|..-|.++++.+...+|.+|=+|...+- +|=+.|....+.-|...
T Consensus 46 --i~~L--K~ksP~L~~k~~~l~~~~k~ki~~L~peak-----~Fv~~li~~~~~l~~~~ 96 (154)
T PF05823_consen 46 --IAAL--KEKSPSLYEKAEKLRDKLKKKIDKLSPEAK-----AFVKELIAKARSLYAQY 96 (154)
T ss_dssp --HHHH--HHH-HHHHHHHHHHHHHHHHTTTT--HHHH-----HHHHHHHHHHHHHHHHH
T ss_pred --HHHH--HHhCHHHHHHHHHHHHHHHHHHHcCCHHHH-----HHHHHHHHHHHHHHHHh
Confidence 3332 268899999999999999999999966553 44455555555555553
No 8
>PF03281 Mab-21: Mab-21 protein
Probab=35.96 E-value=3.6e+02 Score=25.92 Aligned_cols=134 Identities=22% Similarity=0.338 Sum_probs=80.4
Q ss_pred eeEEeeeccccc------CCCcch-------hHhhhccCCCeeEeeeCCCCCCCCCCCCCcccccccccCccccccCCcC
Q 041621 181 YIVEFVSESQNL------RDGREV-------EDILESFQDTEFWYAEQGSMSSNSTRSGSFRRVIVQRKEEKWWLPVPCV 247 (452)
Q Consensus 181 ~IVElvPs~Q~~------~dG~~~-------Ee~LDsf~~tEFWYv~~g~~~~~~~~s~s~r~~~~~R~eeKWWLP~p~V 247 (452)
+-|+|||.-+-. .++-.. ..+.+..++..|..|.+ ... .....+.-|-+=
T Consensus 115 i~vdlVPa~~~~~~WP~~a~~~~~~~~~Wp~~~~~~~~~~~~~~lvpk-~~~------------~~~~~~~~Wrls---- 177 (292)
T PF03281_consen 115 ISVDLVPAFEFPGGWPRSAQEWLRRFNGWPSPKLIQEIKSFGFHLVPK-PCS------------PNSDSENSWRLS---- 177 (292)
T ss_pred EEEEEEEEEEEcCCCCcccccccccccCCCchhhhhhcccCceEEeee-ccC------------CCCCCCceEEEe----
Confidence 789999998861 111111 14455566667777766 111 111233344433
Q ss_pred CCCCCCHHHHHhhhhhhhhHHHHHHHHHHhhhhhhhcCCCchHH---------Hhhcccc---CccchhHHHHHhhccCC
Q 041621 248 PPGGLSEKSRKHLRHKRDCANQIHKAAMAINSTILAEMEIPDSY---------MANLPKS---GKACLGDFIYRYMYTTE 315 (452)
Q Consensus 248 P~~GLSe~~RK~L~~qrd~~nQIlKAAmAIN~~vL~EMeIPe~y---------~esLPKn---GrasLGD~iYr~i~t~e 315 (452)
.+..+++.|++...|-.++|+..++|.......+..=.+| .+..|.+ -...||+.+++.|
T Consensus 178 ----f~~~E~~ll~~~~~~~~~~l~llk~l~~~~~~~~~~l~syhLkt~ll~~~~~~p~~~~W~~~~l~~~l~~~l---- 249 (292)
T PF03281_consen 178 ----FSVAERQLLKNLNGCRKKCLRLLKALRDRHLTNLSGLSSYHLKTVLLWLCEKHPSSSDWSEENLGERLLDLL---- 249 (292)
T ss_pred ----hHHHHHHHHHhccccHHHHHHHHHHHHHhccccCCCccHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHHH----
Confidence 3467788887756677777777777777766666666665 3455655 2578999999888
Q ss_pred CCChhhHhhhc-------------Cc---hhhhHHHhhhhhhHH
Q 041621 316 KFSPDHLLDCL-------------SI---ASEHEALELADHVEA 343 (452)
Q Consensus 316 ~Fspe~lL~~l-------------dL---ssEH~aLe~anRvEA 343 (452)
++|..|| || -+++.+.+++++|+.
T Consensus 250 ----~~L~~~L~~~~Lphff~~~~NLf~~~~~~~~~~~~~~~~~ 289 (292)
T PF03281_consen 250 ----DFLIKCLQEGRLPHFFIPNLNLFQHLSPEELDELARKLER 289 (292)
T ss_pred ----HHHHHHHhcCCCCccCCCCcccCCCCCHHHHHHHHHHHHH
Confidence 3444443 21 256777888887764
No 9
>PF08700 Vps51: Vps51/Vps67; InterPro: IPR014812 The VFT tethering complex (also known as GARP complex, Golgi associated retrograde protein complex, Vps53 tethering complex) is a conserved eukaryotic docking complex which is involved in recycling of proteins from endosomes to the late Golgi. Vps51 (also known as Vps67) is a subunit of VFT and interacts with the SNARE Tlg1 [].
Probab=33.96 E-value=91 Score=24.69 Aligned_cols=84 Identities=17% Similarity=0.196 Sum_probs=47.8
Q ss_pred cCCCCChhhHhh-hcCchhhhHHHhhhhhhHHHHHHHHHhhhccCCCcchhhhhhhhcccCcchhHHHHHHHHHHHHHHH
Q 041621 313 TTEKFSPDHLLD-CLSIASEHEALELADHVEASMYTWRRKACMSHSKSSWDMVKDLMSETDRSDKNHLLAARAESLLFYL 391 (452)
Q Consensus 313 t~e~Fspe~lL~-~ldLssEH~aLe~anRvEAsi~iWrrK~~~~~~kssW~~vk~l~~~~~~~dK~e~laeRAEtlL~~L 391 (452)
.++.|+|+.++. .|-=.+.+++..+.+++..-+-.=...+..- --+.-.+|+.-.+...+.+--...-.++|..|
T Consensus 2 ~~~~fd~~~~~~~~l~~~s~~~i~~~~~~L~~~i~~~~~eLr~~----V~~nY~~fI~as~~I~~m~~~~~~l~~~l~~l 77 (87)
T PF08700_consen 2 DSENFDVDEYFKDLLKNSSIKEIRQLENKLRQEIEEKDEELRKL----VYENYRDFIEASDEISSMENDLSELRNLLSEL 77 (87)
T ss_pred CCCcCCHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHH----HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578999999987 3444556788888888886665544444321 12233444444333334444444555566666
Q ss_pred HhhCCCCCc
Q 041621 392 KQRYPELAQ 400 (452)
Q Consensus 392 KqRfPgLpQ 400 (452)
++....|.+
T Consensus 78 ~~~~~~l~~ 86 (87)
T PF08700_consen 78 QQSIQSLQE 86 (87)
T ss_pred HHHHHHhhc
Confidence 665555444
No 10
>PF11583 AurF: P-aminobenzoate N-oxygenase AurF; PDB: 3CHI_B 3CHT_A 3CHH_A 2JCD_B 3CHU_A.
Probab=30.58 E-value=1.2e+02 Score=29.50 Aligned_cols=65 Identities=28% Similarity=0.312 Sum_probs=35.3
Q ss_pred cCccccccCCcCCCCC------CCHHHHHhhhhhhhhHHHHHHHHHHhhhhhhhcCCCc----hHHHhhccccCccchhH
Q 041621 236 KEEKWWLPVPCVPPGG------LSEKSRKHLRHKRDCANQIHKAAMAINSTILAEMEIP----DSYMANLPKSGKACLGD 305 (452)
Q Consensus 236 ~eeKWWLP~p~VP~~G------LSe~~RK~L~~qrd~~nQIlKAAmAIN~~vL~EMeIP----e~y~esLPKnGrasLGD 305 (452)
.++|||+|.-.||-.| |+++.|.+|..+ ++++. ++-.+..|..|- ...+...... ..++
T Consensus 44 ~~~~~~~p~~~~pl~gtp~~~~l~~~~r~~l~~~-~~~~~-------~~~~i~~E~~l~~~~~~~l~~~~~~~---~~~~ 112 (304)
T PF11583_consen 44 DPDRPWLPPELLPLYGTPLWERLSEEQRIELLRH-EWANY-------LSQGIWFEQGLVNPAFRMLARDRFPS---DPDD 112 (304)
T ss_dssp -TTS-SS-GGGSTTTT-HHHHTS-HHHHHHHHHH-HHHHH-------HHHHHHHHHHTHHHHHHHHHTT-STT---TT-H
T ss_pred CCcccCCCcccCccCCCHHHHhCCHHHHHHHHHH-HHHHH-------HHHHHHHHHHHHHHHHHHHHHHHhcc---CCCc
Confidence 6899999999999987 778887777654 33333 333455566665 3333332221 2455
Q ss_pred HHHHhh
Q 041621 306 FIYRYM 311 (452)
Q Consensus 306 ~iYr~i 311 (452)
..++|+
T Consensus 113 ~~~~~~ 118 (304)
T PF11583_consen 113 DAKRYA 118 (304)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 556555
No 11
>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).
Probab=29.36 E-value=66 Score=32.00 Aligned_cols=80 Identities=18% Similarity=0.196 Sum_probs=60.5
Q ss_pred hhhhhHHHHHHHHHHhhhhhhhcCCCchHHHhh--ccccCccchhHHHHHhhccCCCCChhh---HhhhcCchhh-hHHH
Q 041621 262 HKRDCANQIHKAAMAINSTILAEMEIPDSYMAN--LPKSGKACLGDFIYRYMYTTEKFSPDH---LLDCLSIASE-HEAL 335 (452)
Q Consensus 262 ~qrd~~nQIlKAAmAIN~~vL~EMeIPe~y~es--LPKnGrasLGD~iYr~i~t~e~Fspe~---lL~~ldLssE-H~aL 335 (452)
.|-..+.++||.-.+.|..+|..|.+...|.-+ -+..+..+|-|.+=..+ ....+++++ |++.|...++ ..+|
T Consensus 81 ~qP~~a~~~L~~~~~~N~~~L~~i~~s~~~~~~~~~~~~~g~tL~dLv~~g~-~~~~~a~~~~~~l~~EL~~~~~~~PVL 159 (309)
T PF10236_consen 81 DQPMYAAKWLKKFLKANEELLKKIKLSKDYKWSKRESTPKGSTLLDLVEQGI-NDPKYAWDVFQALIRELKAQSKRPPVL 159 (309)
T ss_pred ecHHHHHHHHHHHHHHhHHHHHhccccccccccccccCCCCCCHHHHHHhhc-ccchhHHHHHHHHHHHHHhcccCCceE
Confidence 345788999999999999999999999999776 44555578888888788 777788754 5666777777 6666
Q ss_pred hhhhhhH
Q 041621 336 ELADHVE 342 (452)
Q Consensus 336 e~anRvE 342 (452)
=..|-+-
T Consensus 160 ~avD~~n 166 (309)
T PF10236_consen 160 VAVDGFN 166 (309)
T ss_pred EEehhhH
Confidence 5444443
No 12
>PF02169 LPP20: LPP20 lipoprotein; InterPro: IPR002217 A major antigen has been recognised in Helicobacter pylori, a protein with an apparent molecular weight of 20,000 and mass 18,283 kDa []. DNA sequence analysis revealed a 525 bp gene, encoding a 175-amino acid residue product with a typical 21-residue lipoprotein signal peptide and consensus prolipoprotein processing site []. Results of experimental work with Lpp20 are consistent with it being a nonessential lipoprotein []. Prokaryotic membrane lipoproteins are synthesised with precursor signal peptides that are cleaved by specific peptidases (signal peptidase II). The enzyme recognises a conserved sequence, cutting upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached [].; GO: 0009279 cell outer membrane
Probab=29.06 E-value=25 Score=27.86 Aligned_cols=31 Identities=16% Similarity=0.209 Sum_probs=25.9
Q ss_pred CCCCCCchhhHHHHHHHHHHHHHhhhhcccc
Q 041621 126 MSGSGKGVCTAVTISNAITNLYATVFGQNLR 156 (452)
Q Consensus 126 MSGggKGV~tALAiSNAITNL~AtVFGelwr 156 (452)
+.|-|.|-..-.|.-||..||+..|+|..-.
T Consensus 14 l~a~G~~~~~~~A~~~A~~~la~~i~~~v~~ 44 (92)
T PF02169_consen 14 LYAVGSGSSREQAKQDALANLAEQISVVVIS 44 (92)
T ss_pred EEEEEcccChHHHHHHHHHHHHHheeEEEEe
Confidence 5667777777999999999999999998643
No 13
>PF01343 Peptidase_S49: Peptidase family S49 peptidase classification.; InterPro: IPR002142 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. The domain defines sequences in viruses, archaea, bacteria and plants. These sequences are variously annotated in the different taxonomic groups, examples are: Viruses: capsid protein Archaea: proteinase IV homolog Bacteria: proteinase IV, sohB, SppA, pfaP, putative protease Plants: SppA, protease IV This group also contains proteins classified as non-peptidase homologues that either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases. Related proteins, non-peptidase homologs and unclassified S49 members are also to be found in IPR002810 from INTERPRO.; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3RST_B 3BEZ_D 3BF0_A.
Probab=25.51 E-value=1.8e+02 Score=25.87 Aligned_cols=80 Identities=23% Similarity=0.174 Sum_probs=51.5
Q ss_pred ccccccCeeEEeeecccccCCCcchh-----HhhhccCC-CeeEeeeCCCCCCCCCCCCCcccccccccCccccccCCcC
Q 041621 174 CLLSVCDYIVEFVSESQNLRDGREVE-----DILESFQD-TEFWYAEQGSMSSNSTRSGSFRRVIVQRKEEKWWLPVPCV 247 (452)
Q Consensus 174 wLLSV~D~IVElvPs~Q~~~dG~~~E-----e~LDsf~~-tEFWYv~~g~~~~~~~~s~s~r~~~~~R~eeKWWLP~p~V 247 (452)
||.|.||+|+ .-|+.-...-|..++ +.||.+.= .++-+ .|... + . --
T Consensus 23 ~lAs~ad~I~-~~p~s~vgsiGv~~~~~~~~~~l~k~GV~~~~~~--~g~~K---~--~-------------------~~ 75 (154)
T PF01343_consen 23 YLASAADEIY-ANPSSSVGSIGVSAERLFFKGLLEKLGVKVEVVR--SGEYK---S--A-------------------GF 75 (154)
T ss_dssp HHHTTSSEEE-E-TT-EEE---EEEEEEE-HHHHHHTT-EEEEEE--SSTTC---C--C-------------------CC
T ss_pred HHHHcCCEEE-ecCCCEEEEeChhhccccHHHHHHHCCCeEEEEe--cCccc---c--c-------------------cC
Confidence 7899999997 667777777776665 88887753 33222 22111 0 0 04
Q ss_pred CCCCCCHHHHHhhhhhhhhHHHHHHHHHHhhhh
Q 041621 248 PPGGLSEKSRKHLRHKRDCANQIHKAAMAINST 280 (452)
Q Consensus 248 P~~GLSe~~RK~L~~qrd~~nQIlKAAmAIN~~ 280 (452)
|...+|++.|..++..=+-+.+.+....|-|..
T Consensus 76 ~~~~~s~~~r~~~~~~l~~~~~~f~~~Va~~R~ 108 (154)
T PF01343_consen 76 PRDPMSEEERENLQELLDELYDQFVNDVAEGRG 108 (154)
T ss_dssp TTSS--HHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred cCCCCCHHHHHHHHHHHHHHHHHHHHHHHHccC
Confidence 567899999999999999999999888888875
No 14
>PF14261 DUF4351: Domain of unknown function (DUF4351)
Probab=22.80 E-value=86 Score=24.80 Aligned_cols=27 Identities=33% Similarity=0.381 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHhhCCCCCcchhhhhhhh
Q 041621 381 AARAESLLFYLKQRYPELAQTSLDTCKIQ 409 (452)
Q Consensus 381 aeRAEtlL~~LKqRfPgLpQT~LD~sKIQ 409 (452)
.+.+.-++..|++||..+|...- .||+
T Consensus 6 eg~~~lllRlL~rrFG~lp~~~~--~~I~ 32 (59)
T PF14261_consen 6 EGEARLLLRLLTRRFGELPPEIQ--ERIQ 32 (59)
T ss_pred HHHHHHHHHHHHHHcCCCCHHHH--HHHH
Confidence 35677899999999999998653 5554
No 15
>PF15002 ERK-JNK_inhib: ERK and JNK pathways, inhibitor
Probab=21.41 E-value=73 Score=31.10 Aligned_cols=26 Identities=31% Similarity=0.465 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHhHH--HHHHhhhhHH
Q 041621 416 QAVLESYSRVLEGLAF--NTVAWVEDVL 441 (452)
Q Consensus 416 ~aILESYSRVLEsLAf--nI~sRIdDVL 441 (452)
..|.++||.|||+.|| .|+-|.=|+.
T Consensus 86 ~~~kdAls~vlENtAffgDl~LrfPdi~ 113 (207)
T PF15002_consen 86 DKLKDALSSVLENTAFFGDLVLRFPDIV 113 (207)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHccHHH
Confidence 4899999999999999 5666665554
No 16
>PF07528 DZF: DZF domain; InterPro: IPR006561 This domain is found in proteins containing the double-stranded RNA-binding motif, DSRM (IPR001159 from INTERPRO), or the zinc finger domain C2H2 (IPR007087 from INTERPRO). This domain is found exclusively in the metazoa.
Probab=21.15 E-value=65 Score=31.83 Aligned_cols=48 Identities=29% Similarity=0.323 Sum_probs=30.0
Q ss_pred HHHHHHhhCCCCCcc---hhh--hhhhhhch--hhHHHHHHHHHHHHHHhHHHHH
Q 041621 387 LLFYLKQRYPELAQT---SLD--TCKIQCNQ--DVGQAVLESYSRVLEGLAFNTV 434 (452)
Q Consensus 387 lL~~LKqRfPgLpQT---~LD--~sKIQyNk--DVG~aILESYSRVLEsLAfnI~ 434 (452)
||.-|++|||++..= .+| +.|.=.|- .-...+=+++.||||-||.-|+
T Consensus 136 IlrDl~~R~p~w~~L~~W~leLL~~~~i~~~~~~~~l~~g~a~RRvle~lasGil 190 (248)
T PF07528_consen 136 ILRDLRQRVPTWQPLSSWALELLVEKAISNNSSRQPLSPGDAFRRVLECLASGIL 190 (248)
T ss_pred hHHHHHHhCCCCCCCChhHHHHHHHHHeeeCCCCCCCChHHHHHHHHHHHhCcee
Confidence 678899999997542 111 22222211 1123466999999999998764
No 17
>TIGR03578 EF_0831 conserved hypothetical protein EF_0831/AHA_3912. Members of this family of small (about 100 amino acid), relatively rare proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. The function is unknown.
Probab=20.53 E-value=87 Score=27.76 Aligned_cols=33 Identities=27% Similarity=0.525 Sum_probs=29.1
Q ss_pred CCCchhhHHHHHHHHHHHHHhhh----hccccccCCC
Q 041621 129 SGKGVCTAVTISNAITNLYATVF----GQNLRLAPLK 161 (452)
Q Consensus 129 ggKGV~tALAiSNAITNL~AtVF----GelwrLEPl~ 161 (452)
+|||=+=+-|+..|+.++-.+|- |=+.|+||..
T Consensus 11 sgkG~tK~~Afa~als~iq~~v~~~~~~illRIEP~d 47 (96)
T TIGR03578 11 SGKGNTKQLAFASALSKIQKKVMKENPAVLLRIEPVD 47 (96)
T ss_pred EcCCccHHHHHHHHHHHHHHHHHhcCCceEEEEccce
Confidence 68888999999999999999998 4489999975
Done!