Query psy14161
Match_columns 91
No_of_seqs 102 out of 311
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 21:01:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14161.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14161hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00111 pelota probable tran 100.0 1.4E-31 3.1E-36 206.2 12.4 87 1-90 1-87 (351)
2 KOG2869|consensus 100.0 7.3E-29 1.6E-33 190.9 10.0 88 1-89 1-88 (379)
3 COG1537 PelA Predicted RNA-bin 100.0 1.1E-28 2.4E-33 190.6 10.4 87 1-91 1-87 (352)
4 PF03463 eRF1_1: eRF1 domain 1 100.0 9.8E-30 2.1E-34 173.0 1.8 89 1-90 1-90 (132)
5 PF01336 tRNA_anti-codon: OB-f 70.7 7.4 0.00016 22.3 3.2 33 11-44 23-55 (75)
6 PF06019 Phage_30_8: Phage GP3 53.7 43 0.00092 22.8 4.8 22 22-45 22-43 (123)
7 cd05791 S1_CSL4 S1_CSL4: CSL4, 53.4 11 0.00024 23.8 1.9 16 29-44 56-71 (92)
8 PLN00063 photosystem II core c 49.5 5.4 0.00012 29.2 -0.1 26 12-37 159-184 (194)
9 PF10447 EXOSC1: Exosome compo 48.7 15 0.00033 23.1 1.9 15 29-43 64-78 (82)
10 PF10383 Clr2: Transcription-s 47.1 68 0.0015 21.8 5.1 58 31-88 10-69 (139)
11 PTZ00072 40S ribosomal protein 46.8 7.2 0.00016 27.5 0.2 13 19-31 77-89 (148)
12 KOG0400|consensus 46.1 7.5 0.00016 27.2 0.2 14 19-32 80-93 (151)
13 cd04491 SoSSB_OBF SoSSB_OBF: A 43.9 36 0.00079 20.3 3.1 28 12-43 31-58 (82)
14 PRK06807 DNA polymerase III su 32.8 36 0.00078 26.1 2.2 21 14-34 262-282 (313)
15 PF08563 P53_TAD: P53 transact 32.7 15 0.00032 18.5 0.0 11 20-30 11-21 (25)
16 cd05693 S1_Rrp5_repeat_hs1_sc1 32.3 1.1E+02 0.0024 19.4 4.1 16 30-45 63-78 (100)
17 PF10049 DUF2283: Protein of u 30.4 57 0.0012 18.3 2.2 14 72-85 2-15 (50)
18 PRK08561 rps15p 30S ribosomal 29.8 20 0.00043 25.4 0.3 14 19-32 80-93 (151)
19 PF06298 PsbY: Photosystem II 29.4 18 0.0004 19.7 0.0 10 27-36 17-26 (36)
20 cd04320 AspRS_cyto_N AspRS_cyt 27.3 1.1E+02 0.0024 18.9 3.5 34 11-44 24-62 (102)
21 COG4127 Uncharacterized conser 26.9 78 0.0017 24.9 3.1 20 24-43 63-82 (318)
22 smart00357 CSP Cold shock prot 26.9 1.1E+02 0.0024 16.6 3.1 32 13-46 10-49 (64)
23 PF11906 DUF3426: Protein of u 26.8 98 0.0021 20.5 3.3 13 78-90 66-78 (149)
24 PF08142 AARP2CN: AARP2CN (NUC 26.3 1.6E+02 0.0035 18.3 4.0 23 68-90 26-56 (85)
25 PF14641 HTH_44: Helix-turn-he 26.2 23 0.00049 23.9 0.1 12 22-33 82-93 (121)
26 PF08447 PAS_3: PAS fold; Int 25.9 1.4E+02 0.003 17.0 6.0 60 19-88 31-91 (91)
27 cd04454 S1_Rrp4_like S1_Rrp4_l 24.7 1.3E+02 0.0029 17.7 3.3 21 25-45 42-62 (82)
28 cd01234 PH_CADPS CADPS (Ca2+-d 24.0 52 0.0011 22.3 1.5 19 27-45 76-94 (117)
29 TIGR00156 conserved hypothetic 23.9 73 0.0016 21.7 2.2 30 11-43 78-107 (126)
30 COG2904 Uncharacterized protei 23.7 34 0.00073 23.8 0.5 14 20-33 48-61 (137)
31 cd05686 S1_pNO40 S1_pNO40: pNO 23.2 76 0.0016 18.5 2.0 27 16-43 20-58 (73)
32 TIGR00757 RNaseEG ribonuclease 23.1 3.3E+02 0.0071 21.9 6.1 55 30-90 80-134 (414)
33 PF10694 DUF2500: Protein of u 23.0 77 0.0017 20.5 2.1 28 16-43 67-99 (110)
34 KOG1670|consensus 22.2 38 0.00083 25.2 0.6 15 22-36 65-79 (212)
35 cd04482 RPA2_OBF_like RPA2_OBF 21.4 1.2E+02 0.0027 18.8 2.8 36 29-80 43-78 (91)
36 PF08206 OB_RNB: Ribonuclease 21.4 1.7E+02 0.0038 16.6 3.5 34 11-46 7-44 (58)
37 CHL00196 psbY photosystem II p 21.2 32 0.0007 18.7 0.0 9 27-35 17-25 (36)
38 PF03734 YkuD: L,D-transpeptid 20.9 54 0.0012 20.9 1.1 24 15-41 120-143 (144)
No 1
>TIGR00111 pelota probable translation factor pelota. This model describes the Drosophila protein Pelota, the budding yeast protein DOM34 which it can replace, and a set of closely related archaeal proteins. Members contain a proposed RNA binding motif. The meiotic defect in pelota mutants may be a complex result of a protein translation defect, as suggested in yeast by ribosomal protein RPS30A being a multicopy suppressor and by an altered polyribosome profile in DOM34 mutants rescued by RPS30A. This family is homologous to a family of peptide chain release factors. Pelota is proposed to act in protein translation.
Probab=99.97 E-value=1.4e-31 Score=206.20 Aligned_cols=87 Identities=34% Similarity=0.538 Sum_probs=82.5
Q ss_pred CeeEeecccCCCCCeeEEEeeCCCchhhhhhhhhcCCCEEEEEeeEEEeeecCCCCccceEEEEEEEEEEEEEeecCCCC
Q psy14161 1 MKLVHKNINDKDKSGVVALVPEESEDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQAC 80 (91)
Q Consensus 1 MKi~~~~~~~k~~~g~i~l~pE~~dDlW~lynli~~GD~V~a~T~Rkv~~~~~~g~~~~~r~~~~L~i~Ve~iefd~~~~ 80 (91)
|||++++. ++++|.|+|+||++||||||||||++||.|+|.|+|+|+++..+|+++ +|++++|+|+||+++|||+++
T Consensus 1 Mki~~~~~--~~~~g~v~l~pe~~dDlw~l~nli~~GD~V~~~T~Rkv~~~~~~g~~~-er~~~~l~i~Ve~ief~~~~~ 77 (351)
T TIGR00111 1 MSIVEESF--NKGGAVIKLLPETLDDLWHLYQIIEKGDVEFAFTKRRTQDLDKIRSDK-SKDTVKLGIEVESVEFDMKTE 77 (351)
T ss_pred Cceeeeec--CCCcEEEEEEeCChHHHHHHHHhCCCCCEEEEEEEEEEeccccCCCcc-eEEEEEEEEEEEEEEecCCCC
Confidence 99999996 677789999999999999999999999999999999999887778877 999999999999999999999
Q ss_pred eEEEEEEEcc
Q psy14161 81 VLRLKGNCGN 90 (91)
Q Consensus 81 ~Lri~G~i~~ 90 (91)
+|||+|+|++
T Consensus 78 ~Lri~G~i~~ 87 (351)
T TIGR00111 78 RLRYKGVIVT 87 (351)
T ss_pred EEEEEEEEec
Confidence 9999999975
No 2
>KOG2869|consensus
Probab=99.96 E-value=7.3e-29 Score=190.87 Aligned_cols=88 Identities=66% Similarity=0.955 Sum_probs=85.7
Q ss_pred CeeEeecccCCCCCeeEEEeeCCCchhhhhhhhhcCCCEEEEEeeEEEeeecCCCCccceEEEEEEEEEEEEEeecCCCC
Q psy14161 1 MKLVHKNINDKDKSGVVALVPEESEDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQAC 80 (91)
Q Consensus 1 MKi~~~~~~~k~~~g~i~l~pE~~dDlW~lynli~~GD~V~a~T~Rkv~~~~~~g~~~~~r~~~~L~i~Ve~iefd~~~~ 80 (91)
||++++++ .+||+|+|+++||++|||||+||+|++||.|+|.|.|||+.+.++|+++++|++++|+|+||+++||+.++
T Consensus 1 MKli~K~~-~rng~G~vtmvpEe~eDmw~~ynli~~gD~v~a~T~rkvq~e~a~G~~~s~rv~~~L~i~VesidfD~~~~ 79 (379)
T KOG2869|consen 1 MKLIRKDI-ERNGSGSVTMVPEESEDLWHLYNLIQVGDSVIASTIRKVQKEEATGKTKSSRVLLKLKIKVESIDFDTKAC 79 (379)
T ss_pred Cccchhhh-hcCCCceEEECcCchhHHHHHHhhccCCceeEEEEEEEeeeccccCcccceEEEEEEEEEEEEeecccccc
Confidence 99999999 99999999999999999999999999999999999999999999998888999999999999999999999
Q ss_pred eEEEEEEEc
Q psy14161 81 VLRLKGNCG 89 (91)
Q Consensus 81 ~Lri~G~i~ 89 (91)
.||++|+.+
T Consensus 80 ~L~~KGrti 88 (379)
T KOG2869|consen 80 VLRLKGRTI 88 (379)
T ss_pred EEEEeeeee
Confidence 999999976
No 3
>COG1537 PelA Predicted RNA-binding proteins [General function prediction only]
Probab=99.96 E-value=1.1e-28 Score=190.56 Aligned_cols=87 Identities=40% Similarity=0.643 Sum_probs=78.6
Q ss_pred CeeEeecccCCCCCeeEEEeeCCCchhhhhhhhhcCCCEEEEEeeEEEeeecCCCCccceEEEEEEEEEEEEEeecCCCC
Q psy14161 1 MKLVHKNINDKDKSGVVALVPEESEDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQAC 80 (91)
Q Consensus 1 MKi~~~~~~~k~~~g~i~l~pE~~dDlW~lynli~~GD~V~a~T~Rkv~~~~~~g~~~~~r~~~~L~i~Ve~iefd~~~~ 80 (91)
|+++.++. ++|.|+|+||++||||||||+|++||.|.|.|.|+.++....++++++|++|+|+|+||++|||++++
T Consensus 1 M~ile~~~----k~g~I~l~pE~lDDLw~L~~Ii~~GD~v~a~T~Rr~~~~d~~r~~~~eri~m~L~IkVe~ieF~~f~n 76 (352)
T COG1537 1 MRILEEDK----KRGVIKLVPETLDDLWHLYNIIEKGDKVFAKTTRRDESSDVIRSKKGERIPMTLGIKVEKIEFDKFAN 76 (352)
T ss_pred Ccceeccc----cCceEEEecCChHHHHHHHHhcCCCCEEEEEEEEecccccccccCcceEEEEEEEEEEEEEEeeeccc
Confidence 89999997 69999999999999999999999999999999999332223347778999999999999999999999
Q ss_pred eEEEEEEEccC
Q psy14161 81 VLRLKGNCGNC 91 (91)
Q Consensus 81 ~Lri~G~i~~~ 91 (91)
+|||+|+|++|
T Consensus 77 rLRi~G~i~~~ 87 (352)
T COG1537 77 RLRIKGPIVEG 87 (352)
T ss_pred EEEEEEEEEEc
Confidence 99999999875
No 4
>PF03463 eRF1_1: eRF1 domain 1; InterPro: IPR005140 This domain is found in the release factor eRF1 which terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known []. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site []. This domain is also found in other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.; PDB: 2VGN_A 2VGM_A 3J16_A 3IZQ 3AGK_A 3AGJ_B 3OBW_A 3E1Y_D 1DT9_A 2LLX_A ....
Probab=99.95 E-value=9.8e-30 Score=172.95 Aligned_cols=89 Identities=45% Similarity=0.782 Sum_probs=81.0
Q ss_pred CeeEeecccCCCCCeeEEEeeCCCchhhhhhhhhcCCCEEEEEeeEEEeee-cCCCCccceEEEEEEEEEEEEEeecCCC
Q psy14161 1 MKLVHKNINDKDKSGVVALVPEESEDMWHAYNLITEGDSVRASTIRKVQSE-SNTGSSTSSRVRTMLTISVESIDFDTQA 79 (91)
Q Consensus 1 MKi~~~~~~~k~~~g~i~l~pE~~dDlW~lynli~~GD~V~a~T~Rkv~~~-~~~g~~~~~r~~~~L~i~Ve~iefd~~~ 79 (91)
|||+++++ .++++|.|+++||+.||||||||||.+||.|.|.|+|+|+.+ +.+++..++++++.|+|+|++++|+|++
T Consensus 1 Mki~~~~~-~~~~~~~i~ll~e~~dDlw~L~~li~~gD~v~~~t~Rkv~~~~~~~~~~~~~~v~~~L~i~ve~v~~~~~~ 79 (132)
T PF03463_consen 1 MKIISKDI-EKNGKGLIKLLPEEKDDLWHLYNLIIPGDEVISKTTRKVQEASNIKGSKTRERVQIALTIKVEKVEFDPEN 79 (132)
T ss_dssp -EEEEECH-CHHHHHEEEEETTSHHHHHHHHHHEETTTEEEECCHCHHHHCTCESSHHHHHCEEEEEEEEEEEEEEETTT
T ss_pred Cccchhhh-ccccCceEEEcccccCCcEEEEEEEECCCEEEEEEEEeeeecccccCCcceEEEEEEEEEEEEEeEecCCC
Confidence 99999999 567789999999999999999999999999999999999543 3466777899999999999999999999
Q ss_pred CeEEEEEEEcc
Q psy14161 80 CVLRLKGNCGN 90 (91)
Q Consensus 80 ~~Lri~G~i~~ 90 (91)
+.||++|+|+.
T Consensus 80 ~~Lri~G~i~~ 90 (132)
T PF03463_consen 80 GLLRISGKIVE 90 (132)
T ss_dssp TEEEEEEEEEE
T ss_pred CEEEEEeEEcc
Confidence 99999999975
No 5
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=70.69 E-value=7.4 Score=22.26 Aligned_cols=33 Identities=27% Similarity=0.337 Sum_probs=26.3
Q ss_pred CCCCeeEEEeeCCCchhhhhhhhhcCCCEEEEEe
Q psy14161 11 KDKSGVVALVPEESEDMWHAYNLITEGDSVRAST 44 (91)
Q Consensus 11 k~~~g~i~l~pE~~dDlW~lynli~~GD~V~a~T 44 (91)
.|++|.+.+..-. +++-..++.+.+||.|...-
T Consensus 23 ~D~tg~i~~~~~~-~~~~~~~~~l~~g~~v~v~G 55 (75)
T PF01336_consen 23 EDGTGSIQVVFFN-EEYERFREKLKEGDIVRVRG 55 (75)
T ss_dssp EETTEEEEEEEET-HHHHHHHHTS-TTSEEEEEE
T ss_pred EECCccEEEEEcc-HHhhHHhhcCCCCeEEEEEE
Confidence 3477888888877 77888889999999999883
No 6
>PF06019 Phage_30_8: Phage GP30.8 protein; InterPro: IPR009258 This entry is represented by Bacteriophage T4, Gp30.8; it is a family of uncharacterised viral proteins.
Probab=53.67 E-value=43 Score=22.82 Aligned_cols=22 Identities=41% Similarity=0.629 Sum_probs=18.7
Q ss_pred CCCchhhhhhhhhcCCCEEEEEee
Q psy14161 22 EESEDMWHAYNLITEGDSVRASTI 45 (91)
Q Consensus 22 E~~dDlW~lynli~~GD~V~a~T~ 45 (91)
|-.|-+|||+- ..||.|.|.|.
T Consensus 22 ~~~E~~W~L~~--~qGDiV~cmTp 43 (123)
T PF06019_consen 22 EVNETMWHLRS--EQGDIVACMTP 43 (123)
T ss_pred hhhhhhheeee--eeccEEEEECC
Confidence 55788999984 68999999985
No 7
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=53.40 E-value=11 Score=23.80 Aligned_cols=16 Identities=38% Similarity=0.567 Sum_probs=13.8
Q ss_pred hhhhhhcCCCEEEEEe
Q psy14161 29 HAYNLITEGDSVRAST 44 (91)
Q Consensus 29 ~lynli~~GD~V~a~T 44 (91)
.++..+.+||.|+|.-
T Consensus 56 ~~~~~f~~GDiV~AkV 71 (92)
T cd05791 56 EMYKCFRPGDIVRAKV 71 (92)
T ss_pred HHHhhcCCCCEEEEEE
Confidence 4888899999999973
No 8
>PLN00063 photosystem II core complex proteins psbY; Provisional
Probab=49.52 E-value=5.4 Score=29.18 Aligned_cols=26 Identities=23% Similarity=0.572 Sum_probs=18.6
Q ss_pred CCCeeEEEeeCCCchhhhhhhhhcCC
Q psy14161 12 DKSGVVALVPEESEDMWHAYNLITEG 37 (91)
Q Consensus 12 ~~~g~i~l~pE~~dDlW~lynli~~G 37 (91)
|.+|.+-+..--+-=.|.+|||++|+
T Consensus 159 D~Rg~lll~v~~PaigWVlyNIL~Pa 184 (194)
T PLN00063 159 DSRGLLLLIVVAPAILWVLYNILQPA 184 (194)
T ss_pred CccchhhHHHHHHHHHHHHHHHhhHH
Confidence 45565544455677789999999875
No 9
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=48.69 E-value=15 Score=23.12 Aligned_cols=15 Identities=40% Similarity=0.634 Sum_probs=10.1
Q ss_pred hhhhhhcCCCEEEEE
Q psy14161 29 HAYNLITEGDSVRAS 43 (91)
Q Consensus 29 ~lynli~~GD~V~a~ 43 (91)
.+|.-.+|||+|+|.
T Consensus 64 ~~~~~FrpGDIVrA~ 78 (82)
T PF10447_consen 64 KMYDCFRPGDIVRAR 78 (82)
T ss_dssp -GGGT--SSSEEEEE
T ss_pred hHHhccCCCCEEEEE
Confidence 346666999999997
No 10
>PF10383 Clr2: Transcription-silencing protein Clr2 ; InterPro: IPR018839 Clr2 (cryptic loci regulator) is a chromatin silencing protein, one of a quartet of proteins forming the core of SHREC, a multienzyme effector complex that mediates hetero-chromatic transcriptional gene silencing in fission yeast []. Clr2 does not have any obvious well-conserved domains but, along with the other core proteins, binds to the histone deacetylase Clr3, and on its own might also have a role in chromatin organisation at the cnt domain, the site of kinetochore assembly.
Probab=47.07 E-value=68 Score=21.81 Aligned_cols=58 Identities=22% Similarity=0.377 Sum_probs=27.6
Q ss_pred hhhhcCCCEEEEEeeEEEee-ecCCCCccceEEEEEEEEEEEEEeecCCCC-eEEEEEEE
Q psy14161 31 YNLITEGDSVRASTIRKVQS-ESNTGSSTSSRVRTMLTISVESIDFDTQAC-VLRLKGNC 88 (91)
Q Consensus 31 ynli~~GD~V~a~T~Rkv~~-~~~~g~~~~~r~~~~L~i~Ve~iefd~~~~-~Lri~G~i 88 (91)
..+|..||.|+-.-...... .+..+....--+.+.-.|.+...+-++... .+|+.|.+
T Consensus 10 AE~I~vGD~VRl~~~~~~~~~~~~~~~~~~tdvMvI~~I~~~~~~~~~~~~~~v~~~G~l 69 (139)
T PF10383_consen 10 AEMIWVGDAVRLKPLNASPSPNQSDGNPDVTDVMVIDEIQLRLINCDPDSPSTVRFRGDL 69 (139)
T ss_pred eEEEEeCCEEEECccCCCcccccccCCCCceeEEEEeEEEEecccCCCCCCceEEEEeEe
Confidence 35788999999843332211 111111111222222334443333333322 79999986
No 11
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=46.82 E-value=7.2 Score=27.49 Aligned_cols=13 Identities=38% Similarity=0.672 Sum_probs=11.4
Q ss_pred EeeCCCchhhhhh
Q psy14161 19 LVPEESEDMWHAY 31 (91)
Q Consensus 19 l~pE~~dDlW~ly 31 (91)
|.||-|||||||-
T Consensus 77 lap~iPeDly~Li 89 (148)
T PTZ00072 77 LAPEIPEDLYFLI 89 (148)
T ss_pred CCCCCchHHHHHH
Confidence 5899999999985
No 12
>KOG0400|consensus
Probab=46.09 E-value=7.5 Score=27.25 Aligned_cols=14 Identities=43% Similarity=0.788 Sum_probs=11.8
Q ss_pred EeeCCCchhhhhhh
Q psy14161 19 LVPEESEDMWHAYN 32 (91)
Q Consensus 19 l~pE~~dDlW~lyn 32 (91)
|.||-+|||+||-.
T Consensus 80 l~PeiPeDLy~lik 93 (151)
T KOG0400|consen 80 LAPEIPEDLYHLIK 93 (151)
T ss_pred CCCCCcHHHHHHHH
Confidence 68999999988753
No 13
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=43.85 E-value=36 Score=20.33 Aligned_cols=28 Identities=21% Similarity=0.379 Sum_probs=21.0
Q ss_pred CCCeeEEEeeCCCchhhhhhhhhcCCCEEEEE
Q psy14161 12 DKSGVVALVPEESEDMWHAYNLITEGDSVRAS 43 (91)
Q Consensus 12 ~~~g~i~l~pE~~dDlW~lynli~~GD~V~a~ 43 (91)
|++|.|.+..=+.++ +..+++||.|...
T Consensus 31 D~TG~i~~~~W~~~~----~~~~~~G~vv~i~ 58 (82)
T cd04491 31 DETGTIRFTLWDEKA----ADDLEPGDVVRIE 58 (82)
T ss_pred CCCCEEEEEEECchh----cccCCCCCEEEEE
Confidence 456777777655554 7889999998777
No 14
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=32.83 E-value=36 Score=26.15 Aligned_cols=21 Identities=19% Similarity=0.235 Sum_probs=18.6
Q ss_pred CeeEEEeeCCCchhhhhhhhh
Q psy14161 14 SGVVALVPEESEDMWHAYNLI 34 (91)
Q Consensus 14 ~g~i~l~pE~~dDlW~lynli 34 (91)
.|..++..+++||||-|.++|
T Consensus 262 ~~~~ri~i~~~~dl~~l~~~i 282 (313)
T PRK06807 262 VGNTRIMLNSLEDVLKLESYI 282 (313)
T ss_pred CCeeEEEeCCHHHHHHHHHHH
Confidence 567899999999999999876
No 15
>PF08563 P53_TAD: P53 transactivation motif; InterPro: IPR013872 The binding of this protein by regulatory proteins regulates p53 transcription activation. This entry is comprised of a single amphipathic alpha helix and contains a highly conserved motif [, ]. ; GO: 0005515 protein binding; PDB: 1YCQ_B 2Z5T_R 3DAB_B 3DAC_B 2Z5S_Q 2K8F_B 2L14_B 1YCR_B.
Probab=32.69 E-value=15 Score=18.53 Aligned_cols=11 Identities=27% Similarity=0.649 Sum_probs=8.4
Q ss_pred eeCCCchhhhh
Q psy14161 20 VPEESEDMWHA 30 (91)
Q Consensus 20 ~pE~~dDlW~l 30 (91)
--|+-+|||++
T Consensus 11 SQeTF~~LW~~ 21 (25)
T PF08563_consen 11 SQETFSDLWNL 21 (25)
T ss_dssp STCCHHHHHHT
T ss_pred cHHHHHHHHHh
Confidence 34788999986
No 16
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=32.35 E-value=1.1e+02 Score=19.41 Aligned_cols=16 Identities=25% Similarity=0.420 Sum_probs=13.7
Q ss_pred hhhhhcCCCEEEEEee
Q psy14161 30 AYNLITEGDSVRASTI 45 (91)
Q Consensus 30 lynli~~GD~V~a~T~ 45 (91)
+++.+.+||.|+|.-.
T Consensus 63 ~~~~f~vGd~V~~kVi 78 (100)
T cd05693 63 LEDLFSVGQLVRCKVV 78 (100)
T ss_pred HHHhccCCCEEEEEEE
Confidence 7788999999999843
No 17
>PF10049 DUF2283: Protein of unknown function (DUF2283); InterPro: IPR019270 Members of this family of hypothetical proteins have no known function.
Probab=30.37 E-value=57 Score=18.26 Aligned_cols=14 Identities=29% Similarity=0.605 Sum_probs=11.0
Q ss_pred EEeecCCCCeEEEE
Q psy14161 72 SIDFDTQACVLRLK 85 (91)
Q Consensus 72 ~iefd~~~~~Lri~ 85 (91)
+++|||.++.|.|.
T Consensus 2 ki~YD~~~D~lyi~ 15 (50)
T PF10049_consen 2 KIEYDPEADALYIR 15 (50)
T ss_pred EeEEcCcCCEEEEE
Confidence 57889988888774
No 18
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=29.78 E-value=20 Score=25.37 Aligned_cols=14 Identities=36% Similarity=0.539 Sum_probs=12.1
Q ss_pred EeeCCCchhhhhhh
Q psy14161 19 LVPEESEDMWHAYN 32 (91)
Q Consensus 19 l~pE~~dDlW~lyn 32 (91)
+.||-||||++|..
T Consensus 80 l~p~iPEDL~~L~~ 93 (151)
T PRK08561 80 LAPEIPEDLRNLIK 93 (151)
T ss_pred CCCCCcHHHHHHHH
Confidence 68999999999864
No 19
>PF06298 PsbY: Photosystem II protein Y (PsbY); InterPro: IPR009388 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbY found in PSII. In higher plants, two related PsbY proteins exist, PsbY-1 and PsbY-2, which appear to function as a heterodimer. In spinach and Arabidopsis, these two proteins arise from a single-copy nuclear gene that is processed in the chloroplast. By contrast, prokaryotic and organellar chromosomes encode a single PsbY protein, as found in cyanobacteria and red algae, indicating a duplication event in the evolution of higher plants []. PsbY has two low manganese-dependent activities: a catalase-like activity and an L-arginine metabolising activity that converts L-arginine into ornithine and urea []. In addition, a redox-active group is thought to be present in the protein. In cyanobacteria, PsbY deletion mutants have a slightly impaired PSII that is less capable of coping with low levels of calcium ions than the wild-type.; GO: 0030145 manganese ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0016021 integral to membrane
Probab=29.40 E-value=18 Score=19.68 Aligned_cols=10 Identities=20% Similarity=0.524 Sum_probs=7.9
Q ss_pred hhhhhhhhcC
Q psy14161 27 MWHAYNLITE 36 (91)
Q Consensus 27 lW~lynli~~ 36 (91)
=|.+|||.++
T Consensus 17 gWa~fNIg~~ 26 (36)
T PF06298_consen 17 GWALFNIGRA 26 (36)
T ss_pred HHHHHHhHHH
Confidence 4999998754
No 20
>cd04320 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis.
Probab=27.27 E-value=1.1e+02 Score=18.94 Aligned_cols=34 Identities=12% Similarity=0.042 Sum_probs=24.4
Q ss_pred CCCCeeEEEeeC-----CCchhhhhhhhhcCCCEEEEEe
Q psy14161 11 KDKSGVVALVPE-----ESEDMWHAYNLITEGDSVRAST 44 (91)
Q Consensus 11 k~~~g~i~l~pE-----~~dDlW~lynli~~GD~V~a~T 44 (91)
.+++|.+-++.. ..+++|....-+..||.|...=
T Consensus 24 rD~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G 62 (102)
T cd04320 24 RQQGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEG 62 (102)
T ss_pred ecCCceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEE
Confidence 345666655553 2478888888899999998874
No 21
>COG4127 Uncharacterized conserved protein [Function unknown]
Probab=26.91 E-value=78 Score=24.87 Aligned_cols=20 Identities=30% Similarity=0.504 Sum_probs=17.1
Q ss_pred CchhhhhhhhhcCCCEEEEE
Q psy14161 24 SEDMWHAYNLITEGDSVRAS 43 (91)
Q Consensus 24 ~dDlW~lynli~~GD~V~a~ 43 (91)
+--+|.+-|=|++||.|-..
T Consensus 63 Agqiw~FvneI~KGDlvi~y 82 (318)
T COG4127 63 AGQIWRFVNEIQKGDLVITY 82 (318)
T ss_pred HHHHHHHHHHhccCcEEEee
Confidence 34689999999999999765
No 22
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=26.88 E-value=1.1e+02 Score=16.56 Aligned_cols=32 Identities=22% Similarity=0.459 Sum_probs=20.9
Q ss_pred CCeeEEEeeCCC-chhhhhhhh-------hcCCCEEEEEeeE
Q psy14161 13 KSGVVALVPEES-EDMWHAYNL-------ITEGDSVRASTIR 46 (91)
Q Consensus 13 ~~g~i~l~pE~~-dDlW~lynl-------i~~GD~V~a~T~R 46 (91)
+.|++ .|++. .|++.-.+- +..||.|.+.-..
T Consensus 10 g~gfv--~~~~~~~~i~v~~~~~~~~~~~~~~Gd~V~~~i~~ 49 (64)
T smart00357 10 GFGFI--RPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVS 49 (64)
T ss_pred CeeEE--ecCCCCccEEEEhHHhhcCCCcCCCCCEEEEEEEE
Confidence 45665 56644 577774333 5779999998543
No 23
>PF11906 DUF3426: Protein of unknown function (DUF3426); InterPro: IPR021834 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 262 to 463 amino acids in length.
Probab=26.78 E-value=98 Score=20.49 Aligned_cols=13 Identities=31% Similarity=0.345 Sum_probs=10.9
Q ss_pred CCCeEEEEEEEcc
Q psy14161 78 QACVLRLKGNCGN 90 (91)
Q Consensus 78 ~~~~Lri~G~i~~ 90 (91)
..+.+.++|.+.|
T Consensus 66 ~~~~l~v~g~i~N 78 (149)
T PF11906_consen 66 GPGVLVVSGTIRN 78 (149)
T ss_pred CCCEEEEEEEEEe
Confidence 5688999999887
No 24
>PF08142 AARP2CN: AARP2CN (NUC121) domain; InterPro: IPR012948 This domain is the central domain of AARP2 (asparagine and aspartate rich protein 2). It is weakly similar to the GTP-binding domain of elongation factor TU []. PfAARP2 is an antigen from Plasmodium falciparum of 150 kDa, which is encoded by a unique gene on chromosome 1 []. The central region of Pfaarp2 contains blocks of repetitions encoding asparagine and aspartate residues. ; GO: 0042254 ribosome biogenesis, 0005634 nucleus
Probab=26.33 E-value=1.6e+02 Score=18.32 Aligned_cols=23 Identities=13% Similarity=0.323 Sum_probs=15.7
Q ss_pred EEEEEEeecCCCC--------eEEEEEEEcc
Q psy14161 68 ISVESIDFDTQAC--------VLRLKGNCGN 90 (91)
Q Consensus 68 i~Ve~iefd~~~~--------~Lri~G~i~~ 90 (91)
+-+++++|.+..+ .|.|.|-+.+
T Consensus 26 ~lad~~e~~~~~~~~~~~~~~~l~v~GyvRG 56 (85)
T PF08142_consen 26 MLADRVEFVPDPEDESENEDGTLKVYGYVRG 56 (85)
T ss_pred EEEEEEEecCCccccccCCceEEEEEEEEcc
Confidence 3456677766543 8999998764
No 25
>PF14641 HTH_44: Helix-turn-helix DNA-binding domain of SPT6; PDB: 3PSI_A 3PSF_A.
Probab=26.24 E-value=23 Score=23.86 Aligned_cols=12 Identities=33% Similarity=1.013 Sum_probs=8.9
Q ss_pred CCCchhhhhhhh
Q psy14161 22 EESEDMWHAYNL 33 (91)
Q Consensus 22 E~~dDlW~lynl 33 (91)
=+.+|||-+|.+
T Consensus 82 L~~~DLWrI~~l 93 (121)
T PF14641_consen 82 LNEDDLWRIYDL 93 (121)
T ss_dssp --HHHHHHHHHH
T ss_pred ccHHHHHHHHHh
Confidence 468999999975
No 26
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=25.86 E-value=1.4e+02 Score=17.03 Aligned_cols=60 Identities=17% Similarity=0.189 Sum_probs=37.1
Q ss_pred EeeCCCchhhhhhhh-hcCCCEEEEEeeEEEeeecCCCCccceEEEEEEEEEEEEEeecCCCCeEEEEEEE
Q psy14161 19 LVPEESEDMWHAYNL-ITEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQACVLRLKGNC 88 (91)
Q Consensus 19 l~pE~~dDlW~lynl-i~~GD~V~a~T~Rkv~~~~~~g~~~~~r~~~~L~i~Ve~iefd~~~~~Lri~G~i 88 (91)
+.||+.+-++....- ...++......+|-..+ .| +-+-+..+.. -+ ||+.++..++.|++
T Consensus 31 ihpdD~~~~~~~~~~~~~~~~~~~~~e~R~~~~---~G----~~~wi~~~~~--~~-~d~~g~~~~~~Gv~ 91 (91)
T PF08447_consen 31 IHPDDRERVRQAIQQAALQNGEPFEIEYRIRRK---DG----EYRWIEVRGR--PI-FDENGKPIRIIGVI 91 (91)
T ss_dssp B-TTTHHHHHHHHHHHHHHTT-EEEEEEEEEGT---TS----TEEEEEEEEE--EE-ETTTS-EEEEEEEE
T ss_pred cCHHHHHHHHHHHHHHhhccCcceEEEEEEECC---CC----CEEEEEEEEE--EE-ECCCCCEEEEEEEC
Confidence 467888888777776 55566666667787754 22 3334433333 33 48999999999986
No 27
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=24.72 E-value=1.3e+02 Score=17.72 Aligned_cols=21 Identities=24% Similarity=0.262 Sum_probs=15.6
Q ss_pred chhhhhhhhhcCCCEEEEEee
Q psy14161 25 EDMWHAYNLITEGDSVRASTI 45 (91)
Q Consensus 25 dDlW~lynli~~GD~V~a~T~ 45 (91)
++.-.+...+.+||.+.|.-.
T Consensus 42 ~~~~~~~~~~~~GD~i~~~V~ 62 (82)
T cd04454 42 KDKKEIRKSLQPGDLILAKVI 62 (82)
T ss_pred cchHHHHhcCCCCCEEEEEEE
Confidence 334556677899999999844
No 28
>cd01234 PH_CADPS CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS is a calcium-dependent activator involved in secretion. It contains a central PH domain that binds to phosphoinositide 4,5 bisphosphate containing liposomes. However, membrane association may also be mediated by binding to phosphatidlyserine via general electrostatic interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=24.00 E-value=52 Score=22.26 Aligned_cols=19 Identities=32% Similarity=0.468 Sum_probs=15.7
Q ss_pred hhhhhhhhcCCCEEEEEee
Q psy14161 27 MWHAYNLITEGDSVRASTI 45 (91)
Q Consensus 27 lW~lynli~~GD~V~a~T~ 45 (91)
==+++|.+.+||.|...|.
T Consensus 76 g~~ff~avkegd~~~fa~~ 94 (117)
T cd01234 76 GRHFFNAVKEGDELKFATD 94 (117)
T ss_pred chhhhheeccCcEEEEecc
Confidence 3578999999999987753
No 29
>TIGR00156 conserved hypothetical protein TIGR00156. As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae.
Probab=23.91 E-value=73 Score=21.71 Aligned_cols=30 Identities=27% Similarity=0.451 Sum_probs=22.0
Q ss_pred CCCCeeEEEeeCCCchhhhhhhhhcCCCEEEEE
Q psy14161 11 KDKSGVVALVPEESEDMWHAYNLITEGDSVRAS 43 (91)
Q Consensus 11 k~~~g~i~l~pE~~dDlW~lynli~~GD~V~a~ 43 (91)
+|+.|.|. .|-.+++|.=.+ +.|+|.|+-.
T Consensus 78 ~D~TG~I~--VeId~~~w~G~~-v~p~d~V~I~ 107 (126)
T TIGR00156 78 RDKSGEIN--VVIPAAVWNGRE-VQPKDMVNIS 107 (126)
T ss_pred ECCCCCEE--EEECHHHcCCCc-CCCCCEEEEE
Confidence 46778764 455889996554 5899999876
No 30
>COG2904 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.66 E-value=34 Score=23.77 Aligned_cols=14 Identities=36% Similarity=0.926 Sum_probs=12.1
Q ss_pred eeCCCchhhhhhhh
Q psy14161 20 VPEESEDMWHAYNL 33 (91)
Q Consensus 20 ~pE~~dDlW~lynl 33 (91)
.|.--.|+|++|.|
T Consensus 48 lpf~G~DiW~~YEl 61 (137)
T COG2904 48 LPFHGADIWTLYEL 61 (137)
T ss_pred CCccccchhhhhhh
Confidence 57778999999987
No 31
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=23.21 E-value=76 Score=18.52 Aligned_cols=27 Identities=19% Similarity=0.398 Sum_probs=14.5
Q ss_pred eEEEeeCC-Cchhhhhhhh-----------hcCCCEEEEE
Q psy14161 16 VVALVPEE-SEDMWHAYNL-----------ITEGDSVRAS 43 (91)
Q Consensus 16 ~i~l~pE~-~dDlW~lynl-----------i~~GD~V~a~ 43 (91)
++.+ ++. .|=|+|..++ ++.||.|++.
T Consensus 20 fv~l-~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vk 58 (73)
T cd05686 20 FVKI-PGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVK 58 (73)
T ss_pred EEEE-CCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEE
Confidence 4554 332 4566666555 4556666654
No 32
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=23.05 E-value=3.3e+02 Score=21.91 Aligned_cols=55 Identities=13% Similarity=0.201 Sum_probs=39.9
Q ss_pred hhhhhcCCCEEEEEeeEEEeeecCCCCccceEEEEEEEEEEEEEeecCCCCeEEEEEEEcc
Q psy14161 30 AYNLITEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQACVLRLKGNCGN 90 (91)
Q Consensus 30 lynli~~GD~V~a~T~Rkv~~~~~~g~~~~~r~~~~L~i~Ve~iefd~~~~~Lri~G~i~~ 90 (91)
..+++.+||.|...-. +++- +.+.-+....+++.=.-+-|-|+.+.+.||-+|.+
T Consensus 80 i~~~l~~G~~IlVQV~----Ke~~--~~Kgp~lT~~Isl~GrylVl~P~~~~v~ISrkI~d 134 (414)
T TIGR00757 80 ISELLRPGQSVLVQVV----KEPR--GNKGARLTTDISLPGRYLVLMPNNSHVGVSRRIES 134 (414)
T ss_pred HHHhCcCCCEEEEEEe----eCCc--CCCCCeEEEEEEeccceEEEecCCCCceeecccCC
Confidence 3457999999998844 4332 22345777777777777788899999999988764
No 33
>PF10694 DUF2500: Protein of unknown function (DUF2500); InterPro: IPR019635 This entry represents a group of proteins that is largely confined to the Gammaproteobacteria. The function is not known. ; PDB: 3RD4_D 2L0C_A 3Q6C_N.
Probab=22.97 E-value=77 Score=20.47 Aligned_cols=28 Identities=25% Similarity=0.330 Sum_probs=21.3
Q ss_pred eEEEeeCCCchhh-----hhhhhhcCCCEEEEE
Q psy14161 16 VVALVPEESEDMW-----HAYNLITEGDSVRAS 43 (91)
Q Consensus 16 ~i~l~pE~~dDlW-----~lynli~~GD~V~a~ 43 (91)
++++.+|+-+.+. +.|+.+.+||.-+-.
T Consensus 67 yvtFe~e~G~r~ef~V~~~~Y~~l~eGd~G~Lt 99 (110)
T PF10694_consen 67 YVTFEFESGDRREFRVSGHEYGQLAEGDKGTLT 99 (110)
T ss_dssp EEEEEESSSSSEEEEE-HHHHHTS-TT-EEEEE
T ss_pred EEEEEECCCCEEEEEECHHHcCCCCCCCEEEEE
Confidence 6889999888775 689999999987654
No 34
>KOG1670|consensus
Probab=22.17 E-value=38 Score=25.21 Aligned_cols=15 Identities=33% Similarity=0.767 Sum_probs=13.3
Q ss_pred CCCchhhhhhhhhcC
Q psy14161 22 EESEDMWHAYNLITE 36 (91)
Q Consensus 22 E~~dDlW~lynli~~ 36 (91)
.+-||+|.|||-|.+
T Consensus 65 ~TVeeFW~Ly~~I~~ 79 (212)
T KOG1670|consen 65 DTVEEFWSLYNNIKP 79 (212)
T ss_pred ccHHHHHHHHhccCC
Confidence 567999999999988
No 35
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=21.38 E-value=1.2e+02 Score=18.82 Aligned_cols=36 Identities=22% Similarity=0.293 Sum_probs=22.5
Q ss_pred hhhhhhcCCCEEEEEeeEEEeeecCCCCccceEEEEEEEEEEEEEeecCCCC
Q psy14161 29 HAYNLITEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQAC 80 (91)
Q Consensus 29 ~lynli~~GD~V~a~T~Rkv~~~~~~g~~~~~r~~~~L~i~Ve~iefd~~~~ 80 (91)
.+.-.+.+||.|.+.-. +.. .+ .+.||+++-...+.
T Consensus 43 ~~~~~l~~Gd~V~v~G~--v~~--------y~------ql~ve~l~~~glg~ 78 (91)
T cd04482 43 DVVRLLIPGDEVTVYGS--VRP--------GT------TLNLEKLRVIRLAR 78 (91)
T ss_pred cccCCCCCCCEEEEEEE--Eec--------CC------EEEEEEEEECCCcc
Confidence 45566899999988743 211 01 57777777655444
No 36
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=21.36 E-value=1.7e+02 Score=16.55 Aligned_cols=34 Identities=26% Similarity=0.424 Sum_probs=20.3
Q ss_pred CCCCeeEEEeeCC-Cchhhhhh---hhhcCCCEEEEEeeE
Q psy14161 11 KDKSGVVALVPEE-SEDMWHAY---NLITEGDSVRASTIR 46 (91)
Q Consensus 11 k~~~g~i~l~pE~-~dDlW~ly---nli~~GD~V~a~T~R 46 (91)
+++-|++ .|++ .+|+|.-- +=.-.||.|.+.-..
T Consensus 7 ~~GfGFv--~~~~~~~DifIp~~~l~~A~~gD~V~v~i~~ 44 (58)
T PF08206_consen 7 PKGFGFV--IPDDGGEDIFIPPRNLNGAMDGDKVLVRITP 44 (58)
T ss_dssp SSS-EEE--EECT-TEEEEE-HHHHTTS-TT-EEEEEEEE
T ss_pred cCCCEEE--EECCCCCCEEECHHHHCCCCCCCEEEEEEec
Confidence 3456776 5766 88988433 334579999997543
No 37
>CHL00196 psbY photosystem II protein Y; Provisional
Probab=21.24 E-value=32 Score=18.72 Aligned_cols=9 Identities=22% Similarity=0.660 Sum_probs=7.0
Q ss_pred hhhhhhhhc
Q psy14161 27 MWHAYNLIT 35 (91)
Q Consensus 27 lW~lynli~ 35 (91)
=|.+|||-+
T Consensus 17 ~Wa~fNIg~ 25 (36)
T CHL00196 17 SWALFNIGR 25 (36)
T ss_pred HHHHHHhHH
Confidence 499999864
No 38
>PF03734 YkuD: L,D-transpeptidase catalytic domain; InterPro: IPR005490 This family of proteins are found in a range of bacteria. The conserved region contains a conserved histidine and cysteine, suggesting that these proteins have an enzymatic activity. Several members of this family contain peptidoglycan binding domains. So these proteins may use peptidoglycan or a precursor as a substrate. The molecular structure of YkuD protein shows this domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This domain contains a putative catalytic site with a tetrad of invariant His123, Gly124, Cys139, and Arg141. The stereochemistry of this active site shows similarities to peptidotransferases and sortases, and suggests that the enzymes of this family may play an important role in cell wall biology. This family was formerly called the ErfK/YbiS/YcfS/YnhG family, but is now named after the first protein of known structure.; GO: 0016740 transferase activity; PDB: 3ZQD_A 1Y7M_B 4A52_A 2HKL_C 1ZAT_A.
Probab=20.91 E-value=54 Score=20.87 Aligned_cols=24 Identities=29% Similarity=0.437 Sum_probs=17.3
Q ss_pred eeEEEeeCCCchhhhhhhhhcCCCEEE
Q psy14161 15 GVVALVPEESEDMWHAYNLITEGDSVR 41 (91)
Q Consensus 15 g~i~l~pE~~dDlW~lynli~~GD~V~ 41 (91)
|=|.|. .+|+-.||+.+.+|+.|.
T Consensus 120 GCIrl~---~~d~~~l~~~v~~gt~V~ 143 (144)
T PF03734_consen 120 GCIRLS---NEDAKWLYDNVPVGTPVI 143 (144)
T ss_dssp SSEEE----HHHHHHHHHHS-TTEEEE
T ss_pred CEeccC---HHHHHHHHhhCCCCCEEe
Confidence 556663 478888899999998874
Done!