Query T0551 SpR104 , , 74 residues
Match_columns 74
No_of_seqs 84 out of 86
Neff 3.0
Searched_HMMs 11830
Date Fri May 21 18:07:02 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0551.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0551.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09901 DUF2128: Uncharacteri 100.0 6.4E-40 5.5E-44 249.7 6.8 69 4-72 1-69 (70)
2 PF02229 PC4: Transcriptional 72.1 0.49 4.1E-05 25.4 1.0 44 27-71 30-76 (83)
3 PF01269 Fibrillarin: Fibrilla 53.2 1 8.7E-05 23.5 -0.2 32 30-61 35-66 (228)
4 PF03274 Foamy_BEL: Foamy viru 40.1 2.4 0.0002 21.4 -0.0 48 11-58 10-71 (223)
5 PF03830 PTSIIB_sorb: PTS syst 20.9 17 0.0014 16.5 1.6 26 47-72 109-134 (151)
6 PF11314 DUF3117: Protein of u 18.8 21 0.0017 16.0 1.6 17 57-73 33-49 (51)
7 PF05404 TRAP-delta: Transloco 17.1 19 0.0016 16.3 1.1 34 39-73 78-115 (167)
8 PF08145 BOP1NT: BOP1NT (NUC16 16.7 31 0.0027 15.0 2.2 23 52-74 45-67 (260)
9 PF07780 Spb1_C: Spb1 C-termin 15.4 29 0.0025 15.1 1.8 40 29-71 67-108 (218)
10 PF04209 HgmA: homogentisate 1 14.2 18 0.0015 16.4 0.3 24 28-51 256-281 (426)
No 1
>PF09901 DUF2128: Uncharacterized protein conserved in bacteria (DUF2128)
Probab=100.00 E-value=6.4e-40 Score=249.68 Aligned_cols=69 Identities=57% Similarity=0.995 Sum_probs=68.2
Q ss_pred CCCCEEEEEEEEEECCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCHHCCCCCCCCHHHHHHHHHHHC
Q ss_conf 764303454334422589997356654663188998610235784401102765406889999999845
Q T0551 4 MAEFTFEIEEHLLTLSENEKGWTKEINRVSFNGAPAKFDIRAWSPDHTKMGKGITLSNEEFQTMVDAFK 72 (74)
Q Consensus 4 m~e~~yEI~~~igvLS~~~kGW~KELNlvSWNg~~pKyDIR~W~pdh~kMgKGiTLt~eE~~~L~~~L~ 72 (74)
||+|+|||+++|||||++++||+||||+|||||++||||||+|+|||+|||||||||+||+++|+++|+
T Consensus 1 Mae~kyeI~~~igvLSe~~kGW~KELNliSWN~~~pKyDIR~W~pdh~kMgKGITLt~eE~~~Lk~~l~ 69 (70)
T PF09901_consen 1 MAEIKYEIVEHIGVLSESPKGWTKELNLISWNGREPKYDIRDWSPDHEKMGKGITLTEEELKALKELLN 69 (70)
T ss_pred CCCEEEEEEEEEEEECCCCCCCEEEEEEEEECCCCCCCCCCCCCCCHHHCCCCEEECHHHHHHHHHHHH
T ss_conf 984031522436773268987415788887689887660101583422236851505999999999973
No 2
>PF02229 PC4: Transcriptional Coactivator p15 (PC4); InterPro: IPR003173 p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain . The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.; GO: 0003677 DNA binding, 0003713 transcription coactivator activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1pcf_G 2c62_B 2phe_A.
Probab=72.07 E-value=0.49 Score=25.39 Aligned_cols=44 Identities=20% Similarity=0.511 Sum_probs=32.9
Q ss_pred EEEEEEEECCCCCCCCCCCCCCCCHHC---CCCCCCCHHHHHHHHHHH
Q ss_conf 665466318899861023578440110---276540688999999984
Q T0551 27 KEINRVSFNGAPAKFDIRAWSPDHTKM---GKGITLSNEEFQTMVDAF 71 (74)
Q Consensus 27 KELNlvSWNg~~pKyDIR~W~pdh~kM---gKGiTLt~eE~~~L~~~L 71 (74)
+-+..-.|+|+ .-.|||.|-.+.-++ -|||+|+.++...|++.+
T Consensus 30 rrvtv~~fkG~-~~vdIRe~Y~~~G~~~PgkKGISL~~~qw~~L~~~~ 76 (83)
T PF02229_consen 30 RRVTVREFKGK-TLVDIREYYEKDGELLPGKKGISLTPDQWKKLKENI 76 (83)
T ss_dssp EEEEEEE-----EEEEEEE-EE----EE------EE-HHHHHHHHHTH
T ss_pred EEEEEEEECCE-EEEEEEEEEECCCCCCCCCCCEECCHHHHHHHHHHH
T ss_conf 79999987895-899989788737868766764705999999999989
No 3
>PF01269 Fibrillarin: Fibrillarin; InterPro: IPR000692 Fibrillarin is a component of a nucleolar small nuclear ribonucleoprotein (SnRNP), functioning in vivo in ribosomal RNA processing , . It is associated with U3, U8 and U13 small nuclear RNAs in mammals and is similar to the yeast NOP1 protein . Fibrillarin has a well conserved sequence of around 320 amino acids, and contains 3 domains, an N-terminal Gly/Arg-rich region; a central domain resembling other RNA-binding proteins and containing an RNP-2-like consensus sequence; and a C-terminal alpha-helical domain. An evolutionarily related pre-rRNA processing protein, which lacks the Gly/Arg-rich domain, has been found in various archaebacteria.; GO: 0003723 RNA binding, 0006364 rRNA processing, 0005634 nucleus; PDB: 2nnw_B 1pry_A 1g8a_A 1fbn_A 1g8s_A 1nt2_A 2ipx_A.
Probab=53.19 E-value=1 Score=23.53 Aligned_cols=32 Identities=28% Similarity=0.528 Sum_probs=26.7
Q ss_pred EEEEECCCCCCCCCCCCCCCCHHCCCCCCCCH
Q ss_conf 46631889986102357844011027654068
Q T0551 30 NRVSFNGAPAKFDIRAWSPDHTKMGKGITLSN 61 (74)
Q Consensus 30 NlvSWNg~~pKyDIR~W~pdh~kMgKGiTLt~ 61 (74)
.+|++.+..-|..-|.|+|-++|.+-+|..--
T Consensus 35 k~i~~~~~~~~~eyR~WnP~RSKLaAai~~Gl 66 (228)
T PF01269_consen 35 KRISVEGEGTKCEYRVWNPFRSKLAAAILNGL 66 (228)
T ss_dssp EEEEE------EEEEE--TTT-HHHHHHC---
T ss_pred EEEEECCCCCCCCEEEECCCHHHHHHHHHCCC
T ss_conf 69986378875414666762438999997796
No 4
>PF03274 Foamy_BEL: Foamy virus BEL 1/2 protein; InterPro: IPR004956 Foamy virus (FV) gene expression is strictly dependent on their transactivator proteins called Bel1/Tas. The presence of a functionally active, internal promoter, besides the conventional LTR promoters, is unique to FVs. The nuclear Bel1/Tas protein of primate prototype FV binds DNA target sites directly and consists of at least two functional domains, an N-terminal/central DNA binding and a C-terminal activation domain . ; GO: 0016563 transcription activator activity, 0016032 viral reproduction, 0045941 positive regulation of transcription
Probab=40.08 E-value=2.4 Score=21.42 Aligned_cols=48 Identities=25% Similarity=0.455 Sum_probs=33.6
Q ss_pred EEEEEEECCCCCCCCEE-------EEEEEEECCCC------C-CCCCCCCCCCCHHCCCCCC
Q ss_conf 54334422589997356-------65466318899------8-6102357844011027654
Q T0551 11 IEEHLLTLSENEKGWTK-------EINRVSFNGAP------A-KFDIRAWSPDHTKMGKGIT 58 (74)
Q Consensus 11 I~~~igvLS~~~kGW~K-------ELNlvSWNg~~------p-KyDIR~W~pdh~kMgKGiT 58 (74)
|.++-+.=...++++++ |.-.|||-+.. | -+-+|||-|+-++|+|-+-
T Consensus 10 i~~~p~eNP~~~k~y~~~~~~~p~~~~~vtyh~Yke~edk~p~~iKl~dWiP~PeeMSk~~c 71 (223)
T PF03274_consen 10 IAEEPGENPGRPKRYTQVIKTPPREPSCVTYHGYKEKEDKHPHHIKLRDWIPNPEEMSKSVC 71 (223)
T ss_pred CCCCCCCCCCCHHHHHHHCCCCCCCCCEEEEHHHHHHHHHCCCCCCHHHCCCCHHHHHHHHH
T ss_conf 24687668885013333011124785134303556676508764422105799899989999
No 5
>PF03830 PTSIIB_sorb: PTS system sorbose subfamily IIB component; InterPro: IPR004720 Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This entry is specific for the IIB components of this family of PTS transporters .; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0005737 cytoplasm; PDB: 1vsq_C 2jzo_D 2jzh_A 2jzn_C 1nrz_B 1ble_A 3eye_A.
Probab=20.93 E-value=17 Score=16.54 Aligned_cols=26 Identities=19% Similarity=0.319 Sum_probs=22.5
Q ss_pred CCCCHHCCCCCCCCHHHHHHHHHHHC
Q ss_conf 84401102765406889999999845
Q T0551 47 SPDHTKMGKGITLSNEEFQTMVDAFK 72 (74)
Q Consensus 47 ~pdh~kMgKGiTLt~eE~~~L~~~L~ 72 (74)
.|+..+.++.+.++.||+.+|+++..
T Consensus 109 ~~g~~~v~~~v~v~~ee~~~l~~l~~ 134 (151)
T PF03830_consen 109 REGRKKVTKNVYVSEEEIEALKELAD 134 (151)
T ss_dssp -TTSEEECTTEEE-HHHHHHHHHHHH
T ss_pred CCCCEEECCCEEECHHHHHHHHHHHH
T ss_conf 88863873726318999999999997
No 6
>PF11314 DUF3117: Protein of unknown function (DUF3117)
Probab=18.79 E-value=21 Score=16.03 Aligned_cols=17 Identities=29% Similarity=0.544 Sum_probs=14.8
Q ss_pred CCCCHHHHHHHHHHHCC
Q ss_conf 54068899999998457
Q T0551 57 ITLSNEEFQTMVDAFKG 73 (74)
Q Consensus 57 iTLt~eE~~~L~~~L~G 73 (74)
|-|+.+|+..|.++|.+
T Consensus 33 vEl~~~Ea~eL~~~l~~ 49 (51)
T PF11314_consen 33 VELNADEAAELGEALKG 49 (51)
T ss_pred EEECHHHHHHHHHHHHC
T ss_conf 99489999999999860
No 7
>PF05404 TRAP-delta: Translocon-associated protein, delta subunit precursor (TRAP-delta); InterPro: IPR008855 This family consists of several eukaryotic translocon-associated protein, delta subunit precursors (TRAP-delta or SSR-delta). The exact function of this protein is unknown .; GO: 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=17.09 E-value=19 Score=16.27 Aligned_cols=34 Identities=26% Similarity=0.637 Sum_probs=24.9
Q ss_pred CCCCCCCCCCCCHHCCCCC---CCCHHH-HHHHHHHHCC
Q ss_conf 8610235784401102765---406889-9999998457
Q T0551 39 AKFDIRAWSPDHTKMGKGI---TLSNEE-FQTMVDAFKG 73 (74)
Q Consensus 39 pKyDIR~W~pdh~kMgKGi---TLt~eE-~~~L~~~L~G 73 (74)
-||.. +|+.||.+++.|- .|=.|| ..+|+++.+.
T Consensus 78 ~kyQV-SW~~e~K~a~sG~y~V~~fDEegy~alrKAqR~ 115 (167)
T PF05404_consen 78 NKYQV-SWSEEHKKASSGTYQVRFFDEEGYAALRKAQRN 115 (167)
T ss_pred CEEEE-EEEEECCCCCCCCEEEEEECHHHHHHHHHHHHC
T ss_conf 70799-998300416688579999672889999998646
No 8
>PF08145 BOP1NT: BOP1NT (NUC169) domain; InterPro: IPR012953 This N-terminal domain is found in BOP1-like WD40 proteins .; GO: 0006364 rRNA processing, 0005634 nucleus
Probab=16.75 E-value=31 Score=14.97 Aligned_cols=23 Identities=26% Similarity=0.530 Sum_probs=19.5
Q ss_pred HCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 10276540688999999984579
Q T0551 52 KMGKGITLSNEEFQTMVDAFKGN 74 (74)
Q Consensus 52 kMgKGiTLt~eE~~~L~~~L~G~ 74 (74)
+-|+-|+||.||+..+..+..|.
T Consensus 45 ~~~~~v~Ltdedl~lI~ri~~g~ 67 (260)
T PF08145_consen 45 KNGREVVLTDEDLELIRRIQKGE 67 (260)
T ss_pred CCCCEEEECHHHHHHHHHHHCCC
T ss_conf 88944445899999999998489
No 9
>PF07780 Spb1_C: Spb1 C-terminal domain; InterPro: IPR012920 This presumed domain is found at the C-terminus of a family of FtsJ-like methyltransferases. Members of this family are involved in 60S ribosomal biogenesis, for example P25582 from SWISSPROT . ; GO: 0008168 methyltransferase activity, 0006364 rRNA processing, 0005634 nucleus
Probab=15.43 E-value=29 Score=15.13 Aligned_cols=40 Identities=20% Similarity=0.399 Sum_probs=31.0
Q ss_pred EEEEEECCCCCCCCCCCCC--CCCHHCCCCCCCCHHHHHHHHHHH
Q ss_conf 5466318899861023578--440110276540688999999984
Q T0551 29 INRVSFNGAPAKFDIRAWS--PDHTKMGKGITLSNEEFQTMVDAF 71 (74)
Q Consensus 29 LNlvSWNg~~pKyDIR~W~--pdh~kMgKGiTLt~eE~~~L~~~L 71 (74)
.|+-|||+.+ ++-+|= .+...|-.-+-+|.|++.+++.-+
T Consensus 67 ~NRysF~D~d---~LP~WFveDE~kh~k~~~PiTKe~~~~~k~k~ 108 (218)
T PF07780_consen 67 FNRYSFNDDD---GLPDWFVEDEKKHNKPQIPITKEAVAAYKEKL 108 (218)
T ss_pred CCCCCCCCCC---CCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHH
T ss_conf 0121236877---88477799899864688986999999999999
No 10
>PF04209 HgmA: homogentisate 1,2-dioxygenase; InterPro: IPR005708 Alkaptonuria (AKU), a rare hereditary disorder, was the first disease to be interpreted as an inborn error of metabolism. The deficiency causes homogentisic aciduria, ochronosis, and arthritis. AKU patients are deficient for homogentisate 1,2 dioxygenase (1.13.11.5 from EC), the enzyme that mediates the conversion of homogentisate to maleylacetoacetate; a step in the catabolism of both tyrosine and phenylalanine. Homogentisate + O(2) = 4-maleylacetoacetate. ; GO: 0004411 homogentisate 1,2-dioxygenase activity, 0006559 L-phenylalanine catabolic process, 0006570 tyrosine metabolic process; PDB: 1ey2_A 1eyb_A.
Probab=14.15 E-value=18 Score=16.42 Aligned_cols=24 Identities=29% Similarity=0.715 Sum_probs=18.8
Q ss_pred EEEEEEECCC--CCCCCCCCCCCCCH
Q ss_conf 6546631889--98610235784401
Q T0551 28 EINRVSFNGA--PAKFDIRAWSPDHT 51 (74)
Q Consensus 28 ELNlvSWNg~--~pKyDIR~W~pdh~ 51 (74)
-++.|.|.|. +=|||||+..|=.+
T Consensus 256 PfDVVgWhGn~~Pykydl~~F~pi~s 281 (426)
T PF04209_consen 256 PFDVVGWHGNYYPYKYDLRDFEPINS 281 (426)
T ss_dssp S--EEEEE-----EEEEGGG------
T ss_pred CCEECCCCCCCCCEEEEHHHEEECCC
T ss_conf 84061262655476960567142132
Done!