Query psy13914
Match_columns 87
No_of_seqs 57 out of 59
Neff 3.0
Searched_HMMs 46136
Date Fri Aug 16 23:42:11 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13914.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13914hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2717|consensus 100.0 5.6E-50 1.2E-54 314.9 8.1 87 1-87 200-294 (313)
2 PF03643 Vps26: Vacuolar prote 100.0 1.1E-32 2.3E-37 211.9 9.1 81 2-82 188-270 (275)
3 KOG3063|consensus 96.6 0.0087 1.9E-07 48.3 7.0 72 8-79 201-274 (301)
4 PF09064 Tme5_EGF_like: Thromb 54.9 6.7 0.00015 22.9 0.9 13 22-34 19-31 (34)
5 PF01826 TIL: Trypsin Inhibito 44.5 18 0.00038 20.9 1.6 18 17-34 29-46 (55)
6 COG4888 Uncharacterized Zn rib 35.4 15 0.00032 26.1 0.4 16 57-72 18-33 (104)
7 PF08004 DUF1699: Protein of u 33.3 17 0.00037 26.7 0.4 29 19-47 42-77 (131)
8 PF02752 Arrestin_C: Arrestin 30.3 1.4E+02 0.003 18.5 7.4 24 5-28 31-54 (136)
9 PF12662 cEGF: Complement Clr- 23.8 43 0.00094 17.7 0.9 11 22-32 3-13 (24)
10 PF08290 Hep_core_N: Hepatitis 22.8 30 0.00065 19.3 0.1 10 62-71 12-21 (27)
11 PF00399 PIR: Yeast PIR protei 22.0 33 0.00072 17.6 0.2 7 40-46 6-12 (18)
12 KOG0443|consensus 21.7 54 0.0012 30.3 1.5 26 51-78 612-637 (827)
13 COG1644 RPB10 DNA-directed RNA 20.7 26 0.00056 22.9 -0.5 16 56-71 1-17 (63)
14 PF01194 RNA_pol_N: RNA polyme 20.5 36 0.00078 21.8 0.1 17 56-72 1-18 (60)
No 1
>KOG2717|consensus
Probab=100.00 E-value=5.6e-50 Score=314.87 Aligned_cols=87 Identities=56% Similarity=0.993 Sum_probs=85.4
Q ss_pred CeeeecCCCceeEEEEEEEEeeeeeCCceeecccceeeEEEeeCcccCCCccCeEEEeeeeeccCccCccceEEEEEe--
Q psy13914 1 IVIEQTELPIKSVELQLVRVETCGCAEGYSRDATEIQNIQIGEGNVFTGIPIPIYMVFPRLFTCPTLITSNFKIGERL-- 78 (87)
Q Consensus 1 l~ve~s~~pIkSIelQLvRVEt~~~~eg~~reaTEIQniQIadGdVcr~l~IPiymvfPRlftCPt~~t~~FkveFev-- 78 (87)
|+||+|+++|+|||+||+|||||||+|||++||||||+|||||||||||+++||||+|||||||||+.|+||||||||
T Consensus 200 ltVe~seaaI~Sie~qLvRVEtcgc~Egy~~dateIQsiQIADGdVcr~l~lPIymvlPRLftCPtl~t~nFkvEFevni 279 (313)
T KOG2717|consen 200 LTVEASEAAITSIEIQLVRVETCGCGEGYVTDATEIQSIQIADGDVCRNLTLPIYMVLPRLFTCPTLFTGNFKVEFEVNI 279 (313)
T ss_pred EEEEeeccceeEEEEEEEEEEEeecccceecccceeeeEEeccCccccCCceeEEEEechhhcCCceeccccEEEEEEEE
Confidence 589999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ------ceeeeccCC
Q psy13914 79 ------DHYTTKNLK 87 (87)
Q Consensus 79 ------~~liteNfp 87 (87)
||.++||||
T Consensus 280 ~v~fk~d~~~~enf~ 294 (313)
T KOG2717|consen 280 TVSFKSDLAKAENFA 294 (313)
T ss_pred EEEEccchhhccCCc
Confidence 799999996
No 2
>PF03643 Vps26: Vacuolar protein sorting-associated protein 26 ; InterPro: IPR005377 The movement of lipid and protein components between intracellular organelles requires the regulated interactions of many molecules. Vacuolar protein sorting-associated protein (Vps)5 is a yeast protein that is a subunit of a large multimeric complex, termed the retromer complex, involved in retrograde transport of proteins from endosomes to the trans-Golgi network. Sorting nexin (SNX) 1 and SNX2 are its mammalian orthologs []. To carry out its biological functions, Vps5 forms the retromer complex with at least four other proteins: Vps17, Vps26, Vps29, and Vps35 []. This family of Vps26-proteins also contains Down syndrome critical region 3/A.; GO: 0007034 vacuolar transport, 0030904 retromer complex; PDB: 3LHA_A 3LH9_A 2R51_A 3LH8_B 2FAU_A.
Probab=99.98 E-value=1.1e-32 Score=211.93 Aligned_cols=81 Identities=44% Similarity=0.790 Sum_probs=66.0
Q ss_pred eeeecCCCceeEEEEEEEEeeeeeCCceeecccceeeEEEeeCcccCCCccCeEEEeeeeeccCccCc--cceEEEEEec
Q psy13914 2 VIEQTELPIKSVELQLVRVETCGCAEGYSRDATEIQNIQIGEGNVFTGIPIPIYMVFPRLFTCPTLIT--SNFKIGERLD 79 (87)
Q Consensus 2 ~ve~s~~pIkSIelQLvRVEt~~~~eg~~reaTEIQniQIadGdVcr~l~IPiymvfPRlftCPt~~t--~~FkveFev~ 79 (87)
.+..++.+||||||||+|+|||||++|+++|+|+||++||+|||+|||..|||||+|||||+|||+.+ +.|||+|+++
T Consensus 188 ~f~lv~~kIk~~elqLiR~Et~g~~~~~~~e~t~i~~~eImDG~p~rge~IPirl~l~~l~l~Pt~~~~~~~FsV~y~ln 267 (275)
T PF03643_consen 188 YFLLVRIKIKSMELQLIRVETCGCGENYAKESTEIQKIEIMDGAPCRGESIPIRLFLPRLFLCPTYKNVNNKFSVEYELN 267 (275)
T ss_dssp EEEEESS-EEEEEEEEEEEEEECECCCEEEEEEEEEEEEEESS---TT-EEEEEEECCCT-----EEEECTTEEEEEEEE
T ss_pred EEEEEeecceEEEEEEEEEEEEecCCcccccceEEEEEEeecCCccccceeeEEEEcCCcccCCcchhcCCcEEEEEEEE
Confidence 46778899999999999999999999999999999999999999999999999999999999999994 5699999997
Q ss_pred eee
Q psy13914 80 HYT 82 (87)
Q Consensus 80 ~li 82 (87)
-.+
T Consensus 268 lvl 270 (275)
T PF03643_consen 268 LVL 270 (275)
T ss_dssp EEE
T ss_pred EEE
Confidence 543
No 3
>KOG3063|consensus
Probab=96.61 E-value=0.0087 Score=48.27 Aligned_cols=72 Identities=24% Similarity=0.397 Sum_probs=62.3
Q ss_pred CCceeEEEEEEEEeeeeeCCceeecccceeeEEEeeCcccCCCccCeEEEeeeeeccCccC--ccceEEEEEec
Q psy13914 8 LPIKSVELQLVRVETCGCAEGYSRDATEIQNIQIGEGNVFTGIPIPIYMVFPRLFTCPTLI--TSNFKIGERLD 79 (87)
Q Consensus 8 ~pIkSIelQLvRVEt~~~~eg~~reaTEIQniQIadGdVcr~l~IPiymvfPRlftCPt~~--t~~FkveFev~ 79 (87)
.+||-.||+++|-|+.|.+-....+..-|..-+|-||.-.||=.|||-|.+--.=--||+. .+.|||..=++
T Consensus 201 ikIk~Mel~iikrEstG~gpn~~~e~eTiakyeIMDGapvrGEsIPiRlFLagYdlTPtmrdinkkFsVkyyLn 274 (301)
T KOG3063|consen 201 IKIKHMELSIIKRESTGTGPNTYVETETIAKYEIMDGAPVRGESIPIRLFLAGYDLTPTMRDINKKFSVKYYLN 274 (301)
T ss_pred EEeeeeEEEEEEeecccCCCcceeccceeeeEEeccCCCcCCCeeeeEEEecccCCCcchhhhcceeeeeeEEE
Confidence 4689999999999999998887778888999999999999999999988877776778887 77788876663
No 4
>PF09064 Tme5_EGF_like: Thrombomodulin like fifth domain, EGF-like; InterPro: IPR015149 This domain adopts a fold similar to other EGF domains, with a flat major and a twisted minor beta sheet. Disulphide pairing, however, is not of the usual 1-3, 2-4, 5-6 type; rather 1-2, 3-4, 5-6 pairing is found. Its extended major sheet (strands beta-2 and beta-3 and the connecting loop) projects into thrombin's active site groove. This domain is required for interaction of thrombomodulin with thrombin, and subsequent activation of protein-C []. ; GO: 0004888 transmembrane signaling receptor activity, 0016021 integral to membrane
Probab=54.93 E-value=6.7 Score=22.86 Aligned_cols=13 Identities=46% Similarity=0.915 Sum_probs=10.8
Q ss_pred eeeeCCceeeccc
Q psy13914 22 TCGCAEGYSRDAT 34 (87)
Q Consensus 22 t~~~~eg~~reaT 34 (87)
+|-|+|||..|..
T Consensus 19 ~C~CPeGyIlde~ 31 (34)
T PF09064_consen 19 QCFCPEGYILDEG 31 (34)
T ss_pred ceeCCCceEecCC
Confidence 6899999998753
No 5
>PF01826 TIL: Trypsin Inhibitor like cysteine rich domain; InterPro: IPR002919 This domain is found in proteinase inhibitors as well as in many extracellular proteins. The domain typically contains ten cysteine residues that form five disulphide bonds. The cysteine residues that form the disulphide bonds are 1-7, 2-6, 3-5, 4-10 and 8-9. This inhibitor domain belongs to MEROPS inhibitor family I8 (clan IA). Proteins containing this domain inhibit peptidases belonging to families S1 (IPR001254 from INTERPRO), S8 (IPR000209 from INTERPRO), and M4 (IPR001570 from INTERPRO) [] and are restricted to the chordata, nematoda, arthropoda and echinodermata. Examples of proteins containing this domain are: chymotrypsin/elastase inhibitor from Ascaris suum (pig roundworm) Acp62F protein from Drosophila melanogaster Bombina trypsin inhibitor from Bombina maxima (large-webbed bell toad) Bombyx subtilisin inhibitor from Bombyx mori (silk moth) von Willebrand factor ; PDB: 2P3F_N 1HX2_A 1CCV_A 1EAI_D 2H9E_C 1COU_A 1ATE_A 1ATB_A 1ATD_A 1ATA_A ....
Probab=44.48 E-value=18 Score=20.94 Aligned_cols=18 Identities=39% Similarity=0.689 Sum_probs=14.2
Q ss_pred EEEEeeeeeCCceeeccc
Q psy13914 17 LVRVETCGCAEGYSRDAT 34 (87)
Q Consensus 17 LvRVEt~~~~eg~~reaT 34 (87)
..-++.|.|.+||+++..
T Consensus 29 ~~C~~gC~C~~G~v~~~~ 46 (55)
T PF01826_consen 29 EPCVEGCFCPPGYVRNDN 46 (55)
T ss_dssp SS-ESEEEETTTEEEETT
T ss_pred CCCCccCCCCCCeeEcCC
Confidence 346788999999999876
No 6
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=35.42 E-value=15 Score=26.10 Aligned_cols=16 Identities=38% Similarity=0.783 Sum_probs=11.5
Q ss_pred EeeeeeccCccCccce
Q psy13914 57 VFPRLFTCPTLITSNF 72 (87)
Q Consensus 57 vfPRlftCPt~~t~~F 72 (87)
.+|+.||||---.-+-
T Consensus 18 ~L~k~FtCp~Cghe~v 33 (104)
T COG4888 18 VLPKTFTCPRCGHEKV 33 (104)
T ss_pred cCCceEecCccCCeee
Confidence 5899999996544433
No 7
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=33.31 E-value=17 Score=26.65 Aligned_cols=29 Identities=24% Similarity=0.457 Sum_probs=19.7
Q ss_pred EEeeeeeCCceeecc-------cceeeEEEeeCccc
Q psy13914 19 RVETCGCAEGYSRDA-------TEIQNIQIGEGNVF 47 (87)
Q Consensus 19 RVEt~~~~eg~~rea-------TEIQniQIadGdVc 47 (87)
|++...++.-|-+-. =+.|.||+-+|||+
T Consensus 42 ~lk~iqiP~SY~~t~Sksi~mfL~mqgI~LleGDVw 77 (131)
T PF08004_consen 42 NLKAIQIPPSYYKTLSKSIKMFLEMQGIELLEGDVW 77 (131)
T ss_pred CCeEEeCChHHHHHHhHHHHHHHHhcCceeeccccc
Confidence 344555555444332 37899999999999
No 8
>PF02752 Arrestin_C: Arrestin (or S-antigen), C-terminal domain; InterPro: IPR011022 G protein-coupled receptors are a large family of signalling molecules that respond to a wide variety of extracellular stimuli. The receptors relay the information encoded by the ligand through the activation of heterotrimeric G proteins and intracellular effector molecules. To ensure the appropriate regulation of the signalling cascade, it is vital to properly inactivate the receptor. This inactivation is achieved, in part, by the binding of a soluble protein, arrestin, which uncouples the receptor from the downstream G protein after the receptors are phosphorylated by G protein-coupled receptor kinases. In addition to the inactivation of G protein-coupled receptors, arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways. Arrestin (retinal S-antigen) is a major protein of the retinal rod outer segments. It interacts with photo-activated phosphorylated rhodopsin, inhibiting or 'arresting' its ability to interact with transducin []. The protein binds calcium, and shows similarity in its C terminus to alpha-transducin and other purine nucleotide-binding proteins. In mammals, arrestin is associated with autoimmune uveitis. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X) [], which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction [, , ]. The crystal structure of bovine retinal arrestin comprises two domains of antiparallel beta-sheets connected through a hinge region and one short alpha-helix on the back of the amino-terminal fold []. The binding region for phosphorylated light-activated rhodopsin is located at the N-terminal domain, as indicated by the docking of the photoreceptor to the three-dimensional structure of arrestin. The C-terminal domain consists of an immunoglobulin-like beta-sandwich structure. This entry represents proteins with immunoglobulin-like domains that are similar to those found in arrestin.; PDB: 1SUJ_A 3UGX_A 1CF1_B 1AYR_A 3UGU_A 3P2D_B 1ZSH_A 2WTR_B 3GC3_A 1G4R_A ....
Probab=30.33 E-value=1.4e+02 Score=18.55 Aligned_cols=24 Identities=29% Similarity=0.365 Sum_probs=18.1
Q ss_pred ecCCCceeEEEEEEEEeeeeeCCc
Q psy13914 5 QTELPIKSVELQLVRVETCGCAEG 28 (87)
Q Consensus 5 ~s~~pIkSIelQLvRVEt~~~~eg 28 (87)
.|...|++|.+.|+|.-+.....+
T Consensus 31 ~s~~~i~~I~v~L~~~~~~~~~~~ 54 (136)
T PF02752_consen 31 QSKKKIKKIKVSLVERITYKAKGG 54 (136)
T ss_dssp -SSSEEEEEEEEEEEEEEE-SS--
T ss_pred CCCCEEEEEEEEEEEEEEEEEeec
Confidence 567899999999999999987765
No 9
>PF12662 cEGF: Complement Clr-like EGF-like
Probab=23.78 E-value=43 Score=17.70 Aligned_cols=11 Identities=45% Similarity=1.168 Sum_probs=9.0
Q ss_pred eeeeCCceeec
Q psy13914 22 TCGCAEGYSRD 32 (87)
Q Consensus 22 t~~~~eg~~re 32 (87)
+|.|..||...
T Consensus 3 ~C~C~~Gy~l~ 13 (24)
T PF12662_consen 3 TCSCPPGYQLS 13 (24)
T ss_pred EeeCCCCCcCC
Confidence 58999999854
No 10
>PF08290 Hep_core_N: Hepatitis core protein, putative zinc finger; InterPro: IPR013195 This entry represent a short region found at the N terminus of some viral capsid (HBcAg) proteins from various Hepatitis B virus (HBV), which is a major human pathogen. The conservation of four Cys residues suggests that this region acts as a zinc binding domain. Hepatitis virus is composed of an outer envelope of host-derived lipid containing the surface proteins, and an inner protein capsid that contains genomic DNA. The capsid is composed of a single polypeptide, HBcAg, also known as the core antigen. The capsid has a 5-helical fold, where two long helices form a hairpin that dimerises into a 4-helical bundle []; this fold is unusual for icosahedral viruses. The monomer fold is stabilised by a hydrophobic core that is highly conserved among human viral variants. The capsid is assembled from dimers via interactions involving a highly conserved arginine-rich region near the C terminus. This viral capsid acts as a core antigen, the major immunodominant region lying at the tips of the alpha-helical hairpins that form spikes on the capsid surface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005198 structural molecule activity, 0009405 pathogenesis
Probab=22.84 E-value=30 Score=19.35 Aligned_cols=10 Identities=40% Similarity=0.860 Sum_probs=7.5
Q ss_pred eccCccCccc
Q psy13914 62 FTCPTLITSN 71 (87)
Q Consensus 62 ftCPt~~t~~ 71 (87)
-+|||.++..
T Consensus 12 cscpt~qask 21 (27)
T PF08290_consen 12 CSCPTVQASK 21 (27)
T ss_pred ccCCcchhhh
Confidence 4799988764
No 11
>PF00399 PIR: Yeast PIR protein repeat; InterPro: IPR000420 A number of yeast cell wall glycoproteins are characterised by the presence of tandem repeats of a region of 18 to 19 residues [, ].; GO: 0005199 structural constituent of cell wall, 0005618 cell wall
Probab=21.96 E-value=33 Score=17.58 Aligned_cols=7 Identities=57% Similarity=1.256 Sum_probs=5.5
Q ss_pred EEeeCcc
Q psy13914 40 QIGEGNV 46 (87)
Q Consensus 40 QIadGdV 46 (87)
||.||.+
T Consensus 6 QI~DGQi 12 (18)
T PF00399_consen 6 QIGDGQI 12 (18)
T ss_pred cccCCce
Confidence 7888865
No 12
>KOG0443|consensus
Probab=21.68 E-value=54 Score=30.27 Aligned_cols=26 Identities=27% Similarity=0.347 Sum_probs=18.7
Q ss_pred ccCeEEEeeeeeccCccCccceEEEEEe
Q psy13914 51 PIPIYMVFPRLFTCPTLITSNFKIGERL 78 (87)
Q Consensus 51 ~IPiymvfPRlftCPt~~t~~FkveFev 78 (87)
.-+.--.-||||+|- ..++-|.++ |+
T Consensus 612 ~~~~~~~~PrLF~Cs-~~~g~f~~~-EI 637 (827)
T KOG0443|consen 612 LEEKPERDPRLFSCS-NKTGSFVVE-EI 637 (827)
T ss_pred ccccCCCCCcEEEEE-ecCCcEEEE-Ee
Confidence 335555779999995 467788888 44
No 13
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=20.73 E-value=26 Score=22.93 Aligned_cols=16 Identities=38% Similarity=0.895 Sum_probs=11.1
Q ss_pred EEee-eeeccCccCccc
Q psy13914 56 MVFP-RLFTCPTLITSN 71 (87)
Q Consensus 56 mvfP-RlftCPt~~t~~ 71 (87)
|++| |=|||-+..+.-
T Consensus 1 MiiPiRCFsCGkvi~~~ 17 (63)
T COG1644 1 MIIPVRCFSCGKVIGHK 17 (63)
T ss_pred CCCceEeecCCCCHHHH
Confidence 4455 889998876543
No 14
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=20.49 E-value=36 Score=21.79 Aligned_cols=17 Identities=41% Similarity=0.954 Sum_probs=9.6
Q ss_pred EEee-eeeccCccCccce
Q psy13914 56 MVFP-RLFTCPTLITSNF 72 (87)
Q Consensus 56 mvfP-RlftCPt~~t~~F 72 (87)
|++| |=|||-......+
T Consensus 1 MiiPVRCFTCGkvi~~~~ 18 (60)
T PF01194_consen 1 MIIPVRCFTCGKVIGNKW 18 (60)
T ss_dssp ---SSS-STTTSBTCGHH
T ss_pred CCCceecCCCCCChhHhH
Confidence 4555 8899988876543
Done!