Query 046512
Match_columns 68
No_of_seqs 107 out of 323
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 12:52:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046512.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046512hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08156 NOP5NT: NOP5NT (NUC12 99.8 3.6E-22 7.8E-27 119.6 0.1 50 18-68 1-51 (67)
2 KOG2573 Ribosome biogenesis pr 99.3 1.9E-13 4.2E-18 105.6 -0.5 53 16-68 1-53 (498)
3 KOG2572 Ribosome biogenesis pr 99.2 7.5E-13 1.6E-17 102.4 -0.9 50 18-68 1-50 (498)
4 PRK00435 ef1B elongation facto 51.9 12 0.00025 23.4 1.7 41 24-67 42-87 (88)
5 PF00516 GP120: Envelope glyco 45.5 8 0.00017 31.0 0.3 16 22-37 196-211 (488)
6 PF05256 UPF0223: Uncharacteri 41.8 8 0.00017 24.4 -0.1 17 18-34 59-75 (88)
7 PF12588 PSDC: Phophatidylseri 41.0 6.8 0.00015 26.4 -0.6 33 23-55 85-118 (141)
8 PRK04387 hypothetical protein; 38.7 8.1 0.00018 24.6 -0.5 17 18-34 59-75 (90)
9 COG3427 Carbon monoxide dehydr 34.8 33 0.00071 23.4 2.0 27 34-60 4-30 (146)
10 cd00292 EF1B Elongation factor 33.6 33 0.00071 21.2 1.7 40 24-66 42-86 (88)
11 COG4476 Uncharacterized protei 31.1 14 0.00029 23.6 -0.3 17 18-34 59-75 (90)
12 PF00736 EF1_GNE: EF-1 guanine 30.1 30 0.00065 21.4 1.1 42 23-66 41-87 (89)
13 PF08132 AdoMetDC_leader: S-ad 29.3 18 0.00039 21.0 0.0 22 18-39 17-38 (54)
14 TIGR00489 aEF-1_beta translati 27.8 45 0.00097 20.8 1.6 41 23-66 41-86 (88)
15 KOG1668 Elongation factor 1 be 26.6 69 0.0015 23.5 2.6 60 6-67 161-230 (231)
16 PF07172 GRP: Glycine rich pro 22.7 1.1E+02 0.0025 19.0 2.8 8 1-8 1-8 (95)
17 PF00639 Rotamase: PPIC-type P 21.4 29 0.00062 20.6 -0.2 14 21-34 81-94 (95)
No 1
>PF08156 NOP5NT: NOP5NT (NUC127) domain; InterPro: IPR012974 This N-terminal domain is found in RNA-binding proteins of the NOP5 family [].
Probab=99.83 E-value=3.6e-22 Score=119.62 Aligned_cols=50 Identities=42% Similarity=0.725 Sum_probs=45.5
Q ss_pred HHhHhhccceehhheec-cccccccchHHHHHHhcCHHhhhcceeeccccCC
Q 046512 18 LYLLYETASNYSLFLVY-GLDQIGQNTKAVRSSIFDLNCFSKVLHFMAFHPF 68 (68)
Q Consensus 18 ~~vLfEtAaGYaLFkv~-~~~~i~~~~~~v~~~~~d~~~f~k~VkL~aF~pF 68 (68)
||||||||+||+||+|+ +.++++.. ++|++.+.|+++|+|+|||++|+||
T Consensus 1 m~vLfEtaaGyaLF~v~~~~~~~~~~-~~v~~~~~~~~~f~k~vkL~aF~pF 51 (67)
T PF08156_consen 1 MLVLFETAAGYALFKVKDEKDEIGSD-EEVQKSFSDPEKFSKIVKLKAFSPF 51 (67)
T ss_pred CEEEEcCCCeeeeeEEechhhhhccH-HHHHHHHcCHHHHhhhhhhhhccCC
Confidence 58999999999999999 55555545 8999999999999999999999999
No 2
>KOG2573 consensus Ribosome biogenesis protein - Nop56p/Sik1p [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=99.32 E-value=1.9e-13 Score=105.62 Aligned_cols=53 Identities=45% Similarity=0.763 Sum_probs=51.1
Q ss_pred HHHHhHhhccceehhheeccccccccchHHHHHHhcCHHhhhcceeeccccCC
Q 046512 16 IALYLLYETASNYSLFLVYGLDQIGQNTKAVRSSIFDLNCFSKVLHFMAFHPF 68 (68)
Q Consensus 16 m~~~vLfEtAaGYaLFkv~~~~~i~~~~~~v~~~~~d~~~f~k~VkL~aF~pF 68 (68)
|..|+|||+|+||+||++.+.|+|+...++|+.++.|+.+|+++|+|.+|.||
T Consensus 1 ~~~~ll~E~a~GY~lf~~~~~dei~~~~~~v~~s~~D~~kf~~vv~l~sf~pF 53 (498)
T KOG2573|consen 1 MMEYLLFESATGYGLFKVKEQDEIGLHLKEVRSSVDDLSKFTQVVQLASFAPF 53 (498)
T ss_pred CcceEEEeccCceeEEEEechhHhhhhhHHHHHHHHhHHHHHhHhhhhccCCc
Confidence 34799999999999999999999999999999999999999999999999999
No 3
>KOG2572 consensus Ribosome biogenesis protein - Nop58p/Nop5p [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=99.24 E-value=7.5e-13 Score=102.39 Aligned_cols=50 Identities=26% Similarity=0.464 Sum_probs=47.2
Q ss_pred HHhHhhccceehhheeccccccccchHHHHHHhcCHHhhhcceeeccccCC
Q 046512 18 LYLLYETASNYSLFLVYGLDQIGQNTKAVRSSIFDLNCFSKVLHFMAFHPF 68 (68)
Q Consensus 18 ~~vLfEtAaGYaLFkv~~~~~i~~~~~~v~~~~~d~~~f~k~VkL~aF~pF 68 (68)
|+||||||+|||||++.|+..+ .+++++++.|.+++++.++|||++|.+|
T Consensus 1 mlvL~Eta~Gya~fk~~de~kl-~~v~~l~~ef~s~e~a~~~~kl~~f~kf 50 (498)
T KOG2572|consen 1 MLVLFETAAGYALFKVLDEKKL-ANVDDLWKEFSSAEKALKMVKLVAFEKF 50 (498)
T ss_pred CeEEEeeccceeeeeecchhhH-hhHHHHHHHhcCHHHHHHHHHHHHHHhh
Confidence 4899999999999999988887 5899999999999999999999999998
No 4
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=51.93 E-value=12 Score=23.41 Aligned_cols=41 Identities=7% Similarity=0.085 Sum_probs=29.9
Q ss_pred ccceehhheec-----cccccccchHHHHHHhcCHHhhhcceeeccccC
Q 046512 24 TASNYSLFLVY-----GLDQIGQNTKAVRSSIFDLNCFSKVLHFMAFHP 67 (68)
Q Consensus 24 tAaGYaLFkv~-----~~~~i~~~~~~v~~~~~d~~~f~k~VkL~aF~p 67 (68)
-|.||+|.++. ++++ ..++++++.+++.+. -+.|...+|++
T Consensus 42 ePIaFGLkaL~i~~vv~D~~--~~td~lee~i~~~e~-Vqsvei~~~~r 87 (88)
T PRK00435 42 EPIAFGLKALKLYVIMPDEE--GGTEPVEEAFANVEG-VESVEVEEVSR 87 (88)
T ss_pred EEeeccceeEEEEEEEEcCC--cCcHHHHHHHhccCC-CcEEEEEEEec
Confidence 47899998863 3333 357999999999888 66677666654
No 5
>PF00516 GP120: Envelope glycoprotein GP120; InterPro: IPR000777 The entry represents Gp160 of HIV1. Gp160 is cleaved into the surface protein Gp120 and the transmembrane protein Gp41. ; GO: 0019031 viral envelope; PDB: 2NY4_A 2NY0_A 2NY5_G 2NXZ_A 3ECB_P 2NY2_A 3E6F_P 3MLT_C 2NXY_A 1U6V_A ....
Probab=45.50 E-value=8 Score=30.95 Aligned_cols=16 Identities=6% Similarity=0.277 Sum_probs=10.9
Q ss_pred hhccceehhheecccc
Q 046512 22 YETASNYSLFLVYGLD 37 (68)
Q Consensus 22 fEtAaGYaLFkv~~~~ 37 (68)
|=+||||||+|+.|.+
T Consensus 196 YCAPaGfAiLKCndk~ 211 (488)
T PF00516_consen 196 YCAPAGFAILKCNDKK 211 (488)
T ss_dssp EBS-TTEEEEEE-STT
T ss_pred cccCCceEEEeecccc
Confidence 4479999999997543
No 6
>PF05256 UPF0223: Uncharacterised protein family (UPF0223); InterPro: IPR007920 This family of proteins is functionally uncharacterised.; PDB: 2OY9_B.
Probab=41.78 E-value=8 Score=24.42 Aligned_cols=17 Identities=35% Similarity=0.495 Sum_probs=12.7
Q ss_pred HHhHhhccceehhheec
Q 046512 18 LYLLYETASNYSLFLVY 34 (68)
Q Consensus 18 ~~vLfEtAaGYaLFkv~ 34 (68)
+.-=||..+||.+|++.
T Consensus 59 l~r~Fe~~SGYs~Y~~v 75 (88)
T PF05256_consen 59 LDREFEEQSGYSIYRVV 75 (88)
T ss_dssp HHHHHHCCSS--HHHHH
T ss_pred HHHHHHHHhCCcHHHHH
Confidence 46779999999999985
No 7
>PF12588 PSDC: Phophatidylserine decarboxylase ; InterPro: IPR022237 This domain family is found in bacteria and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with PF02666 from PFAM. Phosphatidylserine decarboxylase (PSD) is an important enzyme in the synthesis of phosphatidylethanolamine in both prokaryotes and eukaryotes.
Probab=41.00 E-value=6.8 Score=26.44 Aligned_cols=33 Identities=15% Similarity=0.165 Sum_probs=18.6
Q ss_pred hccceehhheeccccc-cccchHHHHHHhcCHHh
Q 046512 23 ETASNYSLFLVYGLDQ-IGQNTKAVRSSIFDLNC 55 (68)
Q Consensus 23 EtAaGYaLFkv~~~~~-i~~~~~~v~~~~~d~~~ 55 (68)
-|++||++|.-.+.+. +..-++...+.+.+++.
T Consensus 85 ~T~sG~a~F~~p~vN~~lK~ILn~W~~fL~sp~S 118 (141)
T PF12588_consen 85 GTPSGYAFFLDPDVNAQLKKILNEWGEFLSSPAS 118 (141)
T ss_pred cChHHHHHHcCHHHHHHHHHHHHHHHHHcCChhh
Confidence 5899999998643322 22233444444555443
No 8
>PRK04387 hypothetical protein; Provisional
Probab=38.70 E-value=8.1 Score=24.56 Aligned_cols=17 Identities=24% Similarity=0.417 Sum_probs=14.4
Q ss_pred HHhHhhccceehhheec
Q 046512 18 LYLLYETASNYSLFLVY 34 (68)
Q Consensus 18 ~~vLfEtAaGYaLFkv~ 34 (68)
++-=||..+||.+|++.
T Consensus 59 l~reFe~~SGYS~Y~~V 75 (90)
T PRK04387 59 IDREFEKVSGYSIYRAV 75 (90)
T ss_pred HHHHHHHHcCCcHHHHH
Confidence 35668999999999985
No 9
>COG3427 Carbon monoxide dehydrogenase subunit G, CoxG [Energy production and conversion]
Probab=34.76 E-value=33 Score=23.39 Aligned_cols=27 Identities=15% Similarity=0.116 Sum_probs=21.7
Q ss_pred ccccccccchHHHHHHhcCHHhhhcce
Q 046512 34 YGLDQIGQNTKAVRSSIFDLNCFSKVL 60 (68)
Q Consensus 34 ~~~~~i~~~~~~v~~~~~d~~~f~k~V 60 (68)
..+..|....++||+.++||+++...+
T Consensus 4 ~G~f~V~~p~e~Vw~~L~dpe~~a~ci 30 (146)
T COG3427 4 EGTFRVAAPPEAVWEFLNDPEQVAACI 30 (146)
T ss_pred cceEEecCCHHHHHHHhcCHHHHHhhc
Confidence 345667778899999999999987654
No 10
>cd00292 EF1B Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this exchange reaction.
Probab=33.61 E-value=33 Score=21.22 Aligned_cols=40 Identities=15% Similarity=0.189 Sum_probs=26.0
Q ss_pred ccceehhheec-----cccccccchHHHHHHhcCHHhhhcceeecccc
Q 046512 24 TASNYSLFLVY-----GLDQIGQNTKAVRSSIFDLNCFSKVLHFMAFH 66 (68)
Q Consensus 24 tAaGYaLFkv~-----~~~~i~~~~~~v~~~~~d~~~f~k~VkL~aF~ 66 (68)
-|.||+|.++. ++++ ..++++++.++..+. -+.|...+|.
T Consensus 42 epiaFGlk~L~i~~vv~D~~--~~td~lee~i~~~d~-VqsveI~~~~ 86 (88)
T cd00292 42 EPIAFGLKALQIYCVVEDDE--GGTDELEEAISEEDG-VQSVDVEAFN 86 (88)
T ss_pred EEeeeEeeEEEEEEEEEeCC--cCcHHHHHHHhccCC-ceEEEEEEEE
Confidence 46899999863 3344 357999999888444 3445555544
No 11
>COG4476 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.07 E-value=14 Score=23.64 Aligned_cols=17 Identities=35% Similarity=0.448 Sum_probs=14.8
Q ss_pred HHhHhhccceehhheec
Q 046512 18 LYLLYETASNYSLFLVY 34 (68)
Q Consensus 18 ~~vLfEtAaGYaLFkv~ 34 (68)
+..=||.++||.+|++.
T Consensus 59 l~r~FE~~SgyS~Y~~v 75 (90)
T COG4476 59 LGRDFEKSSGYSLYQAV 75 (90)
T ss_pred HhHHHHHhcCccHHHHH
Confidence 46779999999999985
No 12
>PF00736 EF1_GNE: EF-1 guanine nucleotide exchange domain; InterPro: IPR014038 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents the guanine nucleotide exchange domain of the beta (EF-1beta, also known as EF1B-alpha) and delta (EF-1delta, also known as EF1B-beta) chains of EF1B proteins from eukaryotes and archaea. The beta and delta chains have exchange activity, which mainly resides in their homologous guanine nucleotide exchange domains, found in the C-terminal region of the peptides. Their N-terminal regions may be involved in interactions with the gamma chain (EF-1gamma). More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005853 eukaryotic translation elongation factor 1 complex; PDB: 2YY3_B 1GH8_A 1B64_A 1IJE_B 1IJF_B 1F60_B 1G7C_B 2B7B_B 2B7C_B.
Probab=30.13 E-value=30 Score=21.36 Aligned_cols=42 Identities=14% Similarity=0.131 Sum_probs=25.4
Q ss_pred hccceehhheec-----cccccccchHHHHHHhcCHHhhhcceeecccc
Q 046512 23 ETASNYSLFLVY-----GLDQIGQNTKAVRSSIFDLNCFSKVLHFMAFH 66 (68)
Q Consensus 23 EtAaGYaLFkv~-----~~~~i~~~~~~v~~~~~d~~~f~k~VkL~aF~ 66 (68)
+-|.||+|.++. ++++. .++++++.+.....--+.|...+|.
T Consensus 41 ~epIaFGlk~L~v~~vv~D~~~--~~d~lee~i~~~~e~Vqsvei~~~~ 87 (89)
T PF00736_consen 41 EEPIAFGLKALQVSCVVEDDEG--STDDLEEAIESFEEGVQSVEIESFN 87 (89)
T ss_dssp EEEECTTEEEEEEEEEECTTTC--GHHHHHHHHTTCTTTEEEEEEEEEE
T ss_pred eeeecccEEEEEEEEEEEcCcc--ChHHHHHHHHhcCCCccEEEEEEEE
Confidence 347889988874 33443 6899999993333333444555443
No 13
>PF08132 AdoMetDC_leader: S-adenosyl-l-methionine decarboxylase leader peptide; InterPro: IPR012511 This family consists of the S-adenosyl-l-methionine decarboxylase (AdoMetDC) leader peptides. AdoMetDC is a key regulatory enzyme in the biosynthesis of polyamines. All expressed plant AdoMetDC mRNA 5, leader sequences contain a highly conserved pair of overlapping upstream ORFs (uORFs) that overlap by one base. Sequences of the small uORFs are highly conserved between monocot, dicot and gymnosperm AdoMetDC mRNA species, suggesting a translational regulatory mechanism [].
Probab=29.29 E-value=18 Score=21.00 Aligned_cols=22 Identities=32% Similarity=0.255 Sum_probs=17.1
Q ss_pred HHhHhhccceehhheecccccc
Q 046512 18 LYLLYETASNYSLFLVYGLDQI 39 (68)
Q Consensus 18 ~~vLfEtAaGYaLFkv~~~~~i 39 (68)
..+.||+|.||.+=.|....-|
T Consensus 17 ~s~~yeaPLgYsIEDvRP~Ggi 38 (54)
T PF08132_consen 17 NSLFYEAPLGYSIEDVRPNGGI 38 (54)
T ss_pred cceEEeccccceeeecccCCcH
Confidence 4688999999998777655554
No 14
>TIGR00489 aEF-1_beta translation elongation factor aEF-1 beta. This model describes the archaeal translation elongation factor aEF-1 beta. The member from Sulfolobus solfataricus was demonstrated experimentally. It is a dimer that catalyzes the exchange of GDP for GTP on aEF-1 alpha.
Probab=27.80 E-value=45 Score=20.75 Aligned_cols=41 Identities=17% Similarity=0.285 Sum_probs=27.3
Q ss_pred hccceehhheec-----cccccccchHHHHHHhcCHHhhhcceeecccc
Q 046512 23 ETASNYSLFLVY-----GLDQIGQNTKAVRSSIFDLNCFSKVLHFMAFH 66 (68)
Q Consensus 23 EtAaGYaLFkv~-----~~~~i~~~~~~v~~~~~d~~~f~k~VkL~aF~ 66 (68)
+-|.||+|..+. ++++ + .++++++.+++.+. -+.+...+|.
T Consensus 41 ~ePiaFGLkaL~~~~vv~D~~-g-~td~lee~i~~ve~-V~svev~~~~ 86 (88)
T TIGR00489 41 EEPIAFGLVAINVMVVMGDAE-G-GTEAAEESLSGIEG-VESVEVTDVR 86 (88)
T ss_pred EEeeeccceeeEEEEEEecCC-c-ChHHHHHHHhcCCC-ccEEEEEEEE
Confidence 347889988874 3333 3 57999999999886 3444544443
No 15
>KOG1668 consensus Elongation factor 1 beta/delta chain [Transcription]
Probab=26.58 E-value=69 Score=23.51 Aligned_cols=60 Identities=17% Similarity=0.125 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHHHHhHhhcc-----ceehhheec-----cccccccchHHHHHHhcCHHhhhcceeeccccC
Q 046512 6 MLLQQLAAASIALYLLYETA-----SNYSLFLVY-----GLDQIGQNTKAVRSSIFDLNCFSKVLHFMAFHP 67 (68)
Q Consensus 6 ~~~~~~~~~~m~~~vLfEtA-----aGYaLFkv~-----~~~~i~~~~~~v~~~~~d~~~f~k~VkL~aF~p 67 (68)
|--|+-+.++|.|=.|++-+ .||++=|.. +.+.+ ..+.+++.+...+.+-+.|-..+|.+
T Consensus 161 m~~~e~~vrsi~~~gl~wgasklvpvGygikKlqi~~vveddkv--s~D~l~e~i~~~e~~Vqs~di~afnk 230 (231)
T KOG1668|consen 161 MKELEECVRSIEMDGLVWGASKLVPVGYGIKKLQIQCVVEDDKV--SIDDLIEEITKFEDHVQSVDIAAFNK 230 (231)
T ss_pred HHHHHHHHHHhhhccceeccccccccccceeeEEEEEEEEcCcc--ccchhHHHhhhhhcceeeehhhhccc
Confidence 44566677777777777765 899987762 44554 68899999999999999998888865
No 16
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=22.72 E-value=1.1e+02 Score=19.05 Aligned_cols=8 Identities=63% Similarity=0.870 Sum_probs=6.2
Q ss_pred CchhhHHH
Q 046512 1 MGSKSMLL 8 (68)
Q Consensus 1 ~~~~~~~~ 8 (68)
|+||..||
T Consensus 1 MaSK~~ll 8 (95)
T PF07172_consen 1 MASKAFLL 8 (95)
T ss_pred CchhHHHH
Confidence 88998665
No 17
>PF00639 Rotamase: PPIC-type PPIASE domain; InterPro: IPR000297 Peptidylprolyl isomerase (5.2.1.8 from EC) is an enzyme that accelerates protein folding by catalyzing the cis-trans isomerization of proline imidic peptide bonds in oligopeptides []. It has been reported in bacteria and eukayotes. Synonyms for proteins with this domain are: Peptidylprolyl isomerase, Peptidyl-prolyl cis-trans isomerase, PPIase, rotamase, cyclophilin, FKBP65.; GO: 0016853 isomerase activity; PDB: 2JZV_A 2PV3_B 1M5Y_A 2PV2_B 2PV1_A 1JNS_A 1JNT_A 3KAB_A 2ZR6_A 2XPB_A ....
Probab=21.41 E-value=29 Score=20.60 Aligned_cols=14 Identities=29% Similarity=0.337 Sum_probs=11.7
Q ss_pred Hhhccceehhheec
Q 046512 21 LYETASNYSLFLVY 34 (68)
Q Consensus 21 LfEtAaGYaLFkv~ 34 (68)
.++|..||-+++|.
T Consensus 81 pi~t~~G~~Ii~v~ 94 (95)
T PF00639_consen 81 PIETDNGYHIIKVE 94 (95)
T ss_dssp EEEETTEEEEEEEE
T ss_pred CEEECCEEEEEEEE
Confidence 35899999999986
Done!