Query         T0561 JBP1 , Leishmania Tarentolae, 161 residues
Match_columns 161
No_of_seqs    4 out of 6
Neff          1.7 
Searched_HMMs 11830
Date          Wed May 26 17:44:45 2010
Command       /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0561.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0561.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PF10987 DUF2806:  Protein of u  43.0     8.3  0.0007   16.8   3.1   61   45-143    34-94  (219)
  2 PF06292 DUF1041:  Domain of Un  28.9      10 0.00086   16.2   1.7   14   91-104    90-103 (106)
  3 PF11304 DUF3106:  Protein of u  23.2      13  0.0011   15.5   1.4   10  134-143    74-83  (107)
  4 PF04553 Tis11B_N:  Tis11B like  19.6      15  0.0013   15.2   1.1   14   57-71      2-15  (109)
  5 PF11240 DUF3042:  Protein of u  17.4      19  0.0016   14.5   1.2   17  138-160    33-49  (54)
  6 PF00982 Glyco_transf_20:  Glyc  17.1      25  0.0021   13.8   1.7   42   64-110   180-221 (473)
  7 PF10265 DUF2217:  Uncharacteri  16.8      26  0.0022   13.6   3.3   39   67-108   319-357 (514)
  8 PF04838 Baculo_LEF5:  Baculovi  15.1      15  0.0013   15.1   0.3   15  119-133    30-44  (159)
  9 PF12478 DUF3697:  Ubiquitin-as  15.1      18  0.0015   14.7   0.6   24  107-130     9-32  (33)
 10 PF02603 Hpr_kinase_N:  HPr Ser  13.7      30  0.0026   13.2   1.5   24  126-149    54-77  (127)

No 1  
>PF10987 DUF2806:  Protein of unknown function (DUF2806)
Probab=43.01  E-value=8.3  Score=16.80  Aligned_cols=61  Identities=31%  Similarity=0.441  Sum_probs=42.0

Q ss_pred             CCCCHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHEEEEE
Q ss_conf             18610000105653135788989999999987441343457201357788999886278887513412320223101210
Q T0561            45 LNPERKDFLWKNQSEMNSAFFDLCEVGKQVMLGLLGKEVALPKEEQAFWIMYAVHLSAACAEELHMEVAMSLRKLNVKLK  124 (161)
Q Consensus        45 ~~PeRt~F~W~N~S~MN~AFFDLCeVaKQ~M~Gll~ke~~~~~Ee~~FW~~~AaHL~~AC~~e~~M~~am~m~KLNVKLK  124 (161)
                      ...+..|.-|-      ..|||+|+             ..+..+=|..|+--       -+.|+.-|++.|++-|.+   
T Consensus        34 ~~~~~~D~DWl------~rFf~~A~-------------~isn~~mQ~LWakI-------LA~Ei~~PGs~S~rtL~~---   84 (219)
T PF10987_consen   34 VSGEPLDPDWL------YRFFDMAE-------------DISNEEMQELWAKI-------LAGEITNPGSFSLRTLDT---   84 (219)
T ss_pred             CCCCCCCHHHH------HHHHHHHH-------------HHCHHHHHHHHHHH-------HHHHHCCCCCCCHHHHHH---
T ss_conf             36899985799------99999998-------------75619999999999-------998724898757899999---


Q ss_pred             CCCCCCHHHHHCCCCHHHH
Q ss_conf             1234301221138940688
Q T0561           125 DFNFGGTRYFKDMPPEEKK  143 (161)
Q Consensus       125 Df~FGGTRY~KDMPpEEqe  143 (161)
                               ||+|-+.|-+
T Consensus        85 ---------Lk~mt~~eA~   94 (219)
T PF10987_consen   85 ---------LKSMTKREAQ   94 (219)
T ss_pred             ---------HHHCCHHHHH
T ss_conf             ---------9717999999


No 2  
>PF06292 DUF1041:  Domain of Unknown Function (DUF1041);  InterPro: IPR010439   This domain is often found in tandem repeats and co-occur with C2 domains IPR000008 from INTERPRO, Protein kinase C, phorbol ester/diacylglycerol binding regions IPR002219 from INTERPRO and PH domains IPR001849 from INTERPRO.
Probab=28.90  E-value=10  Score=16.24  Aligned_cols=14  Identities=36%  Similarity=0.859  Sum_probs=12.2

Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             77889998862788
Q T0561            91 AFWIMYAVHLSAAC  104 (161)
Q Consensus        91 ~FW~~~AaHL~~AC  104 (161)
                      .||++||+-+++|-
T Consensus        90 ~~WsLfa~Dm~~aL  103 (106)
T PF06292_consen   90 TFWSLFAVDMDYAL  103 (106)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             99999999899998


No 3  
>PF11304 DUF3106:  Protein of unknown function (DUF3106)
Probab=23.17  E-value=13  Score=15.46  Aligned_cols=10  Identities=50%  Similarity=1.271  Sum_probs=5.8

Q ss_pred             HHCCCCHHHH
Q ss_conf             1138940688
Q T0561           134 FKDMPPEEKK  143 (161)
Q Consensus       134 ~KDMPpEEqe  143 (161)
                      |+.+||++++
T Consensus        74 ~~~Lpp~~r~   83 (107)
T PF11304_consen   74 FKSLPPEQRQ   83 (107)
T ss_pred             HHCCCHHHHH
T ss_conf             8708999999


No 4  
>PF04553 Tis11B_N:  Tis11B like protein, N terminus;  InterPro: IPR007635 All proteins of containing this domain also contain a tandem repeat of CCCH zinc fingers (IPR000571 from INTERPRO). Tis11B, Tis11D and their homologues are thought to be regulatory proteins involved in the response to growth factors . Tis11B (Q07352 from SWISSPROT) is thought to be involved in calcium signalling-induced apoptosis in B cells . The function of this N-terminal domain is unknown.
Probab=19.55  E-value=15  Score=15.19  Aligned_cols=14  Identities=43%  Similarity=0.672  Sum_probs=10.1

Q ss_pred             CCHHHHHHHHHHHHH
Q ss_conf             531357889899999
Q T0561            57 QSEMNSAFFDLCEVG   71 (161)
Q Consensus        57 ~S~MN~AFFDLCeVa   71 (161)
                      +++|-++|||+ ||-
T Consensus         2 SttllSaF~D~-e~L   15 (109)
T PF04553_consen    2 STTLLSAFYDI-EVL   15 (109)
T ss_pred             CCCHHHHHHHH-HHH
T ss_conf             42023334548-988


No 5  
>PF11240 DUF3042:  Protein of unknown function (DUF3042)
Probab=17.38  E-value=19  Score=14.55  Aligned_cols=17  Identities=47%  Similarity=0.638  Sum_probs=9.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             94068899999887898875068
Q T0561           138 PPEEKKRRMERKQRIEEARRHGM  160 (161)
Q Consensus       138 PpEEqeRR~~Rk~~IEeARRr~~  160 (161)
                      |.|+||-      .|||-|++++
T Consensus        33 P~e~ke~------~ieenRk~A~   49 (54)
T PF11240_consen   33 PIEEKEE------FIEENRKKAA   49 (54)
T ss_pred             CHHHHHH------HHHHHHHHHH
T ss_conf             1888999------9999889987


No 6  
>PF00982 Glyco_transf_20:  Glycosyltransferase family 20;  InterPro: IPR001830   The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described . This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site . The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'.   Glycosyltransferase family 20 GT20 from CAZY comprises enzymes with only one known activity; alpha, alpha-trehalose-phosphate synthase [UDP-forming] (2.4.1.15 from EC).    Synthesis of trehalose in the yeast Saccharomyces cerevisiae is catalysed by the trehalose-6-phosphate (Tre6P) synthase/phosphatase complex, which is composed of at least three different subunits encoded by the genes TPS1, TPS2, and TSL1. Tps1 and Tps2 carry the catalytic activities of trehalose synthesis, namely Tre6P synthase (Tps1) and Tre6P phosphatase (Tps2), while TsI1 has regulatory functions. There is some evidence that TsI1 and Tps3 may share a common function with respect to regulation and/or structural stabilisation of the Tre6P synthase/phosphatase complex in exponentially growing, heat-shocked cells .   OtsA (trehalose-6-phosphate synthase) from Escherichia coli has homology to the full-length TPS1, the N-terminal part of TPS2 and an internal region of TPS3 (TSL1) of yeast .; GO: 0003824 catalytic activity, 0005992 trehalose biosynthetic process; PDB: 1gz5_C 1uqu_B 1uqt_B.
Probab=17.10  E-value=25  Score=13.79  Aligned_cols=42  Identities=21%  Similarity=0.380  Sum_probs=17.9

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             89899999999874413434572013577889998862788875134
Q T0561            64 FFDLCEVGKQVMLGLLGKEVALPKEEQAFWIMYAVHLSAACAEELHM  110 (161)
Q Consensus        64 FFDLCeVaKQ~M~Gll~ke~~~~~Ee~~FW~~~AaHL~~AC~~e~~M  110 (161)
                      .|-..-+.++++-|+|+-....=-.     --|+.|.-.+|..-++.
T Consensus       180 ifr~LP~r~~iL~glL~aDlIGF~t-----~~y~~~Fl~~~~~~l~~  221 (473)
T PF00982_consen  180 IFRCLPWREEILRGLLGADLIGFQT-----FDYARNFLSCCRRLLGL  221 (473)
T ss_dssp             HHTTSTTHHHHHHHHTTSSEE---S-----HHHHHHHHHHHHHHS-E
T ss_pred             HHHHCCCHHHHHHHHHCCCEEEEEC-----HHHHHHHHHHHHHHCCC
T ss_conf             9975963899999986189799965-----89999999999997097


No 7  
>PF10265 DUF2217:  Uncharacterized conserved protein (DUF2217)
Probab=16.83  E-value=26  Score=13.62  Aligned_cols=39  Identities=33%  Similarity=0.396  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999998744134345720135778899988627888751
Q T0561            67 LCEVGKQVMLGLLGKEVALPKEEQAFWIMYAVHLSAACAEEL  108 (161)
Q Consensus        67 LCeVaKQ~M~Gll~ke~~~~~Ee~~FW~~~AaHL~~AC~~e~  108 (161)
                      ++|||+|+..+|+-+-..+||.   |-..|-.-|++.--.++
T Consensus       319 ~~~~Gr~~l~~ll~~a~k~p~~---F~~~y~~ml~~~~~~~~  357 (514)
T PF10265_consen  319 LAEVGRQMLSDLLCKANKDPKD---FLEAYEEMLEYLENPDN  357 (514)
T ss_pred             HHHHHHHHHHHHHHHCCCCHHH---HHHHHHHHHHHHHCCCC
T ss_conf             4975489999999975798789---99999999999838540


No 8  
>PF04838 Baculo_LEF5:  Baculoviridae late expression factor 5 ;  InterPro: IPR006923   This is a family of Baculoviridae late expression factor 5, required for late and very late gene expression.; GO: 0030528 transcription regulator activity, 0045449 regulation of transcription
Probab=15.11  E-value=15  Score=15.10  Aligned_cols=15  Identities=53%  Similarity=0.589  Sum_probs=9.8

Q ss_pred             HEEEEECCCCCCHHH
Q ss_conf             101210123430122
Q T0561           119 LNVKLKDFNFGGTRY  133 (161)
Q Consensus       119 LNVKLKDf~FGGTRY  133 (161)
                      -|||-|.|||-||.-
T Consensus        30 ~nVKNkTFNF~nTGH   44 (159)
T PF04838_consen   30 KNVKNKTFNFANTGH   44 (159)
T ss_pred             CCCCCCEEECCCCCH
T ss_conf             211347320477762


No 9  
>PF12478 DUF3697:  Ubiquitin-associated protein 2 
Probab=15.05  E-value=18  Score=14.71  Aligned_cols=24  Identities=21%  Similarity=0.486  Sum_probs=19.8

Q ss_pred             HHCCHHHHHHHHHEEEEECCCCCC
Q ss_conf             513412320223101210123430
Q T0561           107 ELHMEVAMSLRKLNVKLKDFNFGG  130 (161)
Q Consensus       107 e~~M~~am~m~KLNVKLKDf~FGG  130 (161)
                      -.-||+++..--|||..--.+||.
T Consensus         9 AVEMPGs~~i~~L~vQfgal~fGs   32 (33)
T PF12478_consen    9 AVEMPGSADIDGLDVQFGALDFGS   32 (33)
T ss_pred             HHCCCCCCCCCCEEEEECCCCCCC
T ss_conf             732788777773045632111357


No 10 
>PF02603 Hpr_kinase_N:  HPr Serine kinase N terminus;  InterPro: IPR011126   This entry represents the N-terminal region of Hpr Serine/threonine kinase PtsK. This kinase is the sensor in a multicomponent phosphorelay system in control of carbon catabolic repression in bacteria . This kinase in unusual in that it recognises the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating enzymes . X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller. The blades are formed by two N-terminal domains each, and the compact central hub assembles the C-terminal kinase domains . ; GO: 0000155 two-component sensor activity, 0004672 protein kinase activity, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0006109 regulation of carbohydrate metabolic process; PDB: 1ko7_A 1knx_A.
Probab=13.71  E-value=30  Score=13.22  Aligned_cols=24  Identities=25%  Similarity=0.479  Sum_probs=18.5

Q ss_pred             CCCCCHHHHHCCCCHHHHHHHHHH
Q ss_conf             234301221138940688999998
Q T0561           126 FNFGGTRYFKDMPPEEKKRRMERK  149 (161)
Q Consensus       126 f~FGGTRY~KDMPpEEqeRR~~Rk  149 (161)
                      +.-.-..|++.+++|+++.|+++=
T Consensus        54 lG~~E~~yl~~l~~e~r~~~~~~l   77 (127)
T PF02603_consen   54 LGNTELAYLETLSEEERKERLEKL   77 (127)
T ss_dssp             E--CCHHHHCCS-HHHHHHHHHHH
T ss_pred             ECHHHHHHHHHCCHHHHHHHHHHH
T ss_conf             868999999968999999999998


Done!