Query         T0621 3NKG, , 172 residues
Match_columns 172
No_of_seqs    5 out of 7
Neff          2.1 
Searched_HMMs 11830
Date          Thu Jul 22 14:54:11 2010
Command       /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0621.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0621.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PF12245 DUF3607:  Protein of u  47.7     7.5 0.00063   17.3   3.5   57   95-153    58-122 (724)
  2 PF07495 Y_Y_Y:  Y_Y_Y domain;   20.6      23  0.0019   14.4   3.0   34  132-165    30-65  (66)
  3 PF06785 UPF0242:  Uncharacteri  18.8     9.4 0.00079   16.7  -0.1   32  129-160   238-270 (401)
  4 PF04729 ASF1_hist_chap:  ASF1   14.3      32  0.0027   13.5   4.3   74   96-172    22-104 (154)
  5 PF01610 Transposase_12:  Trans  13.3      33  0.0028   13.4   1.5   31   47-77     34-64  (100)
  6 PF02078 Synapsin:  Synapsin, N  12.6      34  0.0029   13.3   1.4   16  141-157    30-45  (105)
  7 PF01812 5-FTHF_cyc-lig:  5-for  10.6      38  0.0032   13.0   1.1   46  113-159   121-171 (186)
  8 PF05941 Chordopox_A20R:  Chord  10.3      43  0.0036   12.7   1.7   23   69-91    199-221 (334)
  9 PF01179 Cu_amine_oxid:  Copper  10.1      44  0.0037   12.6   3.3   67    5-72    213-294 (411)
 10 PF02115 Rho_GDI:  RHO protein    8.7      38  0.0032   13.0   0.5   48    7-54     86-134 (201)

No 1  
>PF12245 DUF3607:  Protein of unknown function (DUF3607)
Probab=47.73  E-value=7.5  Score=17.31  Aligned_cols=57  Identities=25%  Similarity=0.403  Sum_probs=39.5

Q ss_pred             EEEEEEEEEHHHCCCCE-------E-EEEEEEEEECCCCCCHHHHHHHHEECCCCEEEEEEECCHHH
Q ss_conf             56445420111125740-------1-22233355447775011223421000348079998401023
Q T0621            95 VVPIKITIHQINQDNTK-------K-LIADNLYMTKGNGSGAYTRDITTISLDKGKYIFRIENIEAF  153 (172)
Q Consensus        95 vipikltI~qI~~~nt~-------k-~i~d~ly~t~~~g~~~~~r~i~~i~L~kGKY~i~VEt~eaf  153 (172)
                      =+++|++|--+..+.+.       + +.+|-+  +-..|+++|-++|..-+|.+|.|-.+.|++-..
T Consensus        58 GLDRk~kisV~rs~g~~~~st~ts~~~~a~d~--it~~G~eyYGk~ltlPal~eG~ytl~~eiLd~~  122 (724)
T PF12245_consen   58 GLDRKVKISVTRSSGTLMVSTVTSHVLVADDR--ITADGSEYYGKELTLPALGEGTYTLKAEILDSD  122 (724)
T ss_pred             CCCCEEEEEEEECCCEEEEEECCCEEEEEEEE--EEECCCCCCCCEEECCCCCCCCEEEEEEEECCC
T ss_conf             55531799999559859998513307876137--850784200516402446887279999886168


No 2  
>PF07495 Y_Y_Y:  Y_Y_Y domain;  InterPro: IPR011123   This region is mostly found at the end of the beta propellers (IPR011110 from INTERPRO) in a family of two component regulators. However they are also found tandemly repeated in Q891H4 from SWISSPROT without other signal conduction domains being present. It's named after the conserved tyrosines found in the alignment. The exact function is not known.
Probab=20.57  E-value=23  Score=14.37  Aligned_cols=34  Identities=21%  Similarity=0.375  Sum_probs=24.0

Q ss_pred             HHHHEECCCCEEEEEEECCHHHHHHHC--CCEEEEE
Q ss_conf             342100034807999840102355515--8258999
Q T0621           132 DITTISLDKGKYIFRIENIEAFSEMIG--RKVDFTI  165 (172)
Q Consensus       132 ~i~~i~L~kGKY~i~VEt~eaf~Em~~--~~V~f~I  165 (172)
                      .+.--+|..|+|.|.|........-..  +.+.|.|
T Consensus        30 ~~~~~~l~~G~Y~~~v~a~~~~~~~~~~~~~l~i~V   65 (66)
T PF07495_consen   30 SISYTNLPPGKYTFEVRAKDNNGNWSYDEKSLSITV   65 (66)
T ss_pred             EEEEEECCCEEEEEEEEEECCCCCCCCCCEEEEEEE
T ss_conf             999952799789999999999998575548999999


No 3  
>PF06785 UPF0242:  Uncharacterised protein family (UPF0242);  InterPro: IPR009623   This is a group of proteins of unknown function.
Probab=18.81  E-value=9.4  Score=16.71  Aligned_cols=32  Identities=25%  Similarity=0.444  Sum_probs=21.9

Q ss_pred             HHHHHH-HEECCCCEEEEEEECCHHHHHHHCCC
Q ss_conf             122342-10003480799984010235551582
Q T0621           129 YTRDIT-TISLDKGKYIFRIENIEAFSEMIGRK  160 (172)
Q Consensus       129 ~~r~i~-~i~L~kGKY~i~VEt~eaf~Em~~~~  160 (172)
                      -++++. -+.++--|--|+|||+||++-|.+..
T Consensus       238 ~s~~~~~ql~selkkiafk~enieaAsslTasr  270 (401)
T PF06785_consen  238 NSQELPKQLLSELKKIAFKVENIEAASSLTASR  270 (401)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH
T ss_conf             234468999999987973011066787766653


No 4  
>PF04729 ASF1_hist_chap:  ASF1 like histone chaperone;  InterPro: IPR006818 This family includes the yeast ASF1 protein, which derepresses transcriptionally silenced genes. The human ASF1 homologue has been found to possess histone chaperone activity, which may explain the derepressing function of this family .; GO: 0006333 chromatin assembly or disassembly, 0005634 nucleus; PDB: 2io5_A 2i32_A 1tey_A 2iij_A 1wg3_A 1roc_A 2hue_A 2idc_A 2dze_B 2z34_B ....
Probab=14.33  E-value=32  Score=13.45  Aligned_cols=74  Identities=16%  Similarity=0.276  Sum_probs=45.0

Q ss_pred             EEEEEEEEHHHCCCCEEEEEEEEEEECCCCCCHHHHHHHHE---ECCCCEEEEEEECC----HHHH--HHHCCCEEEEEE
Q ss_conf             64454201111257401222333554477750112234210---00348079998401----0235--551582589999
Q T0621            96 VPIKITIHQINQDNTKKLIADNLYMTKGNGSGAYTRDITTI---SLDKGKYIFRIENI----EAFS--EMIGRKVDFTIY  166 (172)
Q Consensus        96 ipikltI~qI~~~nt~k~i~d~ly~t~~~g~~~~~r~i~~i---~L~kGKY~i~VEt~----eaf~--Em~~~~V~f~I~  166 (172)
                      +-.+|+.|-...-...  +-=++.+.-+..+..|+-+.+.+   |+.+|+..|..|.-    +..|  |+-|..|+. |-
T Consensus        22 ~~feI~fE~l~~L~~d--leWkliYVgSa~~~~~DQ~Ld~~~vGPi~~G~~kF~~~a~pPd~~~Ip~~dilGvTvil-lt   98 (154)
T PF04729_consen   22 FQFEITFECLEPLQDD--LEWKLIYVGSAESEEYDQELDSVLVGPIPVGKHKFVFEADPPDPSKIPPDDILGVTVIL-LT   98 (154)
T ss_dssp             EEEEEEEEESSB-SSE--EEEEEEEE--TSSGGGTEEEEEEEE-E-B---EEEEEEE----GGGSSCHHHTSEEEEE-EE
T ss_pred             EEEEEEEEECCCCCCC--EEEEEEEEECCCCCCCCEEEEEEEECCCCCEEEEEEEECCCCCHHHCCHHHCCCEEEEE-EE
T ss_conf             7999999982247887--08999997478877777387899866701206999997589994679810244017999-99


Q ss_pred             EECCCC
Q ss_conf             602589
Q T0621           167 INKRDK  172 (172)
Q Consensus       167 ~~~r~k  172 (172)
                      ..||++
T Consensus        99 ~~Y~~~  104 (154)
T PF04729_consen   99 CSYRGQ  104 (154)
T ss_dssp             EEETTE
T ss_pred             EEECCE
T ss_conf             998885


No 5  
>PF01610 Transposase_12:  Transposase;  InterPro: IPR002560   Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families , , . This family includes the IS204 , IS1001 , IS1096  and IS1165  transposases.   More information about these proteins can be found at Protein of the Month: Transposase .; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=13.30  E-value=33  Score=13.43  Aligned_cols=31  Identities=26%  Similarity=0.224  Sum_probs=11.3

Q ss_pred             CCHHHHHHHHCCCCCCCCCCCEEEEECCHHH
Q ss_conf             0056787761322247345715552041000
Q T0621            47 LDGKRVWKFLGFNSYDPRDGKQVGYVDYRLA   77 (172)
Q Consensus        47 ~dg~~v~k~~G~~~~~p~ngk~~~~~~~~~a   77 (172)
                      ++.+-+..||-..+...+...+.--.|-..+
T Consensus        34 R~~~~l~~~l~~~~~~~r~~V~~V~~Dm~~~   64 (100)
T PF01610_consen   34 RDKETLKEFLKQLPEEARDSVKVVSMDMSPA   64 (100)
T ss_pred             CCHHHHHHHHHHHHHHHHHHEEEEEECCCHH
T ss_conf             4758999999875066764436776246453


No 6  
>PF02078 Synapsin:  Synapsin, N-terminal domain;  InterPro: IPR001359 Synapsins are neuronal phosphoproteins that coat synaptic vesicles, bind to several elements of the cytoskeleton (including actin filaments), and are believed to function in the regulation of neurotransmitter release , . The synapsin family currently includes the highly related synapsin I and II. Both synapsins exist in two alternatively spliced variants, IA and IB and IIA and IIB, that only differ at the C-terminus. It also includes synapsin III.; GO: 0007269 neurotransmitter secretion, 0008021 synaptic vesicle; PDB: 2p0a_B 1pk8_B 1px2_A 1aux_A 1auv_B 1i7l_B 1i7n_A.
Probab=12.57  E-value=34  Score=13.34  Aligned_cols=16  Identities=50%  Similarity=0.823  Sum_probs=10.7

Q ss_pred             CEEEEEEECCHHHHHHH
Q ss_conf             80799984010235551
Q T0621           141 GKYIFRIENIEAFSEMI  157 (172)
Q Consensus       141 GKY~i~VEt~eaf~Em~  157 (172)
                      |-|-||||-.| |+||+
T Consensus        30 g~ydIrVEQAe-FsEin   45 (105)
T PF02078_consen   30 GDYDIRVEQAE-FSEIN   45 (105)
T ss_dssp             --EEEEEEEE--GGGEE
T ss_pred             CCEEEEEEEEC-CEEEE
T ss_conf             85668998733-10578


No 7  
>PF01812 5-FTHF_cyc-lig:  5-formyltetrahydrofolate cyclo-ligase family;  InterPro: IPR002698 5-formyltetrahydrofolate cyclo-ligase or methenyl-THF synthetase 6.3.3.2 from EC catalyses the interchange of 5-formyltetrahydrofolate (5-FTHF) to 5-10-methenyltetrahydrofolate, this requires ATP and Mg^2+ . 5-FTHF is used in chemotherapy where it is clinically known as Leucovorin .; GO: 0005524 ATP binding, 0030272 5-formyltetrahydrofolate cyclo-ligase activity, 0009396 folic acid and derivative biosynthetic process; PDB: 1ydm_B 2jcb_A 1sou_A 1u3f_A 1u3g_A 1sbq_B 1wkc_A.
Probab=10.61  E-value=38  Score=13.05  Aligned_cols=46  Identities=22%  Similarity=0.218  Sum_probs=29.7

Q ss_pred             EEEEEEEEE-----CCCCCCHHHHHHHHEECCCCEEEEEEECCHHHHHHHCC
Q ss_conf             222333554-----47775011223421000348079998401023555158
Q T0621           113 LIADNLYMT-----KGNGSGAYTRDITTISLDKGKYIFRIENIEAFSEMIGR  159 (172)
Q Consensus       113 ~i~d~ly~t-----~~~g~~~~~r~i~~i~L~kGKY~i~VEt~eaf~Em~~~  159 (172)
                      +++--+-++     =|+|.|+|+|..+..+= .++-..+|-..-+++.+...
T Consensus       121 iiVP~lafD~~G~RLG~G~GyYDR~L~~~~~-~~~~~~~igl~~~~q~~~~l  171 (186)
T PF01812_consen  121 IIVPGLAFDRNGYRLGYGGGYYDRFLARLPP-AGKRPLKIGLAFDEQIVDEL  171 (186)
T ss_dssp             EEE---EEETTSBEE------HHHHHCC--S------EEEEEB-GGGEES--
T ss_pred             EEECCEEECCCCCEECCCCCHHHHHHHHCCC-CCCCCEEEEEEEHHEEECCC
T ss_conf             9979478989996603888768878665233-45566399998853088787


No 8  
>PF05941 Chordopox_A20R:  Chordopoxvirus A20R protein;  InterPro: IPR010267   This family consists of several Chordopoxvirus A20R proteins. The A20R protein is required for DNA replication, is associated with the processive form of the viral DNA polymerase, and directly interacts with the viral proteins encoded by the D4R, D5R, and H5R open reading frames. A20R may contribute to the assembly or stability of the multiprotein DNA replication complex .
Probab=10.34  E-value=43  Score=12.69  Aligned_cols=23  Identities=13%  Similarity=0.377  Sum_probs=12.9

Q ss_pred             EEEECCHHHHHHHHHHCCCCCCC
Q ss_conf             55204100011110000135677
Q T0621            69 VGYVDYRLAKSELGDLIDETYDC   91 (172)
Q Consensus        69 ~~~~~~~~a~~~~~~~i~~t~~~   91 (172)
                      +-++--+.+.+...|.-..+|.|
T Consensus       199 ~c~ik~G~~~R~viDf~~~~y~~  221 (334)
T PF05941_consen  199 LCCIKEGYSRRNVIDFFKREYVC  221 (334)
T ss_pred             EEEEECCCHHHHHHHHCCCCEEE
T ss_conf             89995384044444435542489


No 9  
>PF01179 Cu_amine_oxid:  Copper amine oxidase, enzyme domain;  InterPro: IPR015798   Amine oxidases (AO) are enzymes that catalyse the oxidation of a wide range of biogenic amines including many neurotransmitters, histamine and xenobiotic amines. There are two classes of amine oxidases: flavin-containing (1.4.3.4 from EC) and copper-containing (1.4.3.6 from EC). Copper-containing AO act as a disulphide-linked homodimer. They catalyse the oxidation of primary amines to aldehydes, with the subsequent release of ammonia and hydrogen peroxide, which requires one copper ion per subunit and topaquinone as cofactor : RCH_2NH_2 + H_2O + O_2 = RCHO + NH_3 + H_2O_2   Copper-containing amine oxidases are found in bacteria, fungi, plants and animals. In prokaryotes, the enzyme enables various amine substrates to be used as sources of carbon and nitrogen , . In eukaryotes they have a broader range of functions, including cell differentiation and growth, wound healing, detoxification and cell signalling .   The copper amine oxidases occur as mushroom-shaped homodimers of 70-95 kDa, each monomer containing a copper ion and a covalently bound redox cofactor, topaquinone (TPQ). TPQ is formed by post-translational modification of a conserved tyrosine residue. The copper ion is coordinated with three histidine residues and two water molecules in a distorted square pyramidal geometry, and has a dual function in catalysis and TPQ biogenesis. The catalytic domain is the largest of the 3-4 domains found in copper amine oxidases, and consists of a beta sandwich of 18 strands in two sheets. The active site is buried and requires a conformational change to allow the substrate access. The two N-terminal domains share a common structural fold, its core consisting of a five-stranded antiparallel beta sheet twisted around an alpha helix. The D1 domains from the two subunits comprise the stalk, of the mushroom-shaped dimer, and interact with each other but do not pack tightly against each other , .    This entry represents the C-terminal catalytic domain of copper amine oxidases, and has a super-sandwich fold consisting of 18 beta-strands in 2 sheets . A domain with a similar structural fold can be found as the third domain in lysyl oxidase PplO .; GO: 0005507 copper ion binding, 0008131 amine oxidase activity, 0048038 quinone binding, 0009308 amine metabolic process; PDB: 2oqe_A 1ekm_B 2oov_B 1a2v_B 1ksi_B 1w2z_B 2wgq_A 1d6u_B 1oac_A 1d6y_B ....
Probab=10.10  E-value=44  Score=12.64  Aligned_cols=67  Identities=27%  Similarity=0.479  Sum_probs=46.3

Q ss_pred             EEEECCCCCCC---CEEEEEEECCCC--------EEEEEEEEEEEEHHHHCCC----CCHHHHHHHHCCCCCCCCCCCEE
Q ss_conf             36430433246---511213313401--------4677778730001111035----00567877613222473457155
Q T0621             5 ISIPIDLSQAG---SVVEKEVKIEES--------WSYHLILQFAVHDRKEDGG----LDGKRVWKFLGFNSYDPRDGKQV   69 (172)
Q Consensus         5 ~tiPIDlSkAG---svvE~eirI~E~--------~~y~~~l~f~~r~rk~~g~----~dg~~v~k~~G~~~~~p~ngk~~   69 (172)
                      |+.-|||.-+|   ||++.++.-.+.        +..++.+.-...++-.++.    ....|.|++.--++.|+. |+.+
T Consensus       213 f~~RlD~dIdG~~Nsv~~~d~~~~~~~~~~~~np~g~~~~~~~t~~~~E~~a~~~~~~~~~r~~~i~N~~~~N~~-G~p~  291 (411)
T PF01179_consen  213 FNFRLDLDIDGTKNSVVEVDIVPEPITYPWSPNPYGNAFKVERTVLETESEAAFDFDPNTPRYWKIVNPNKKNPW-GHPV  291 (411)
T ss_dssp             EEEEEEE-----BEEEEEEEEEEEEEEETTECCCEEEEEEEEEEEE-BGGGGEEE--TT-EEEEEEEEEEEE-TT-S-EE
T ss_pred             EEEEECCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCEEEEEEEEECCHHHHHHCCCCCCCEEEEEECCCCCCCC-CCCC
T ss_conf             999974665799776999985863444578877524336898887187667632258879449999889874777-8852


Q ss_pred             EEE
Q ss_conf             520
Q T0621            70 GYV   72 (172)
Q Consensus        70 ~~~   72 (172)
                      ||-
T Consensus       292 gYk  294 (411)
T PF01179_consen  292 GYK  294 (411)
T ss_dssp             EEE
T ss_pred             EEE
T ss_conf             289


No 10 
>PF02115 Rho_GDI:  RHO protein GDP dissociation inhibitor;  InterPro: IPR000406 The GDP dissociation inhibitor for rho proteins, rho GDI, regulates GDP/GTP exchange. The protein contains 204 amino acids, with a calculated Mr value of 23,421. Hydropathy analysis shows it to be largely hydrophilic, with a single hydrophobic region. Results of database searches suggest rho GDI is a novel protein, currently with no known homologue. The protein plays an important role in the activation of the superoxide (O2-)-generating NADPH oxidase of phagocytes. This process requires the interaction of membrane-associated cytochrome b559 with 3 cytosolic components: p47-phox, p67-phox and a heterodimer of the small G-protein p21rac1 and rho GDI . The association of p21rac and GDI inhibits dissociation of GDP from p21rac, thereby maintaining it in an inactive form. The proteins are attached via a lipid tail on p21rac that binds to the hydrophobic region of GDI . Dissociation of these proteins might be mediated by the release of lipids (e.g., arachidonate and phosphatidate) from membranes through the action of phospholipases . The lipids may then compete with the lipid tail on p21rac for the hydrophobic pocket on GDI.; GO: 0005094 Rho GDP-dissociation inhibitor activity, 0005737 cytoplasm; PDB: 1ajw_A 1doa_B 1gdf_A 1qvy_C 1fso_A 2jhx_B 1hh4_E 2bxw_B 1ft0_B 2jhy_A ....
Probab=8.74  E-value=38  Score=13.05  Aligned_cols=48  Identities=25%  Similarity=0.292  Sum_probs=31.5

Q ss_pred             EECCCCC-CCCEEEEEEECCCCEEEEEEEEEEEEHHHHCCCCCHHHHHH
Q ss_conf             4304332-46511213313401467777873000111103500567877
Q T0621             7 IPIDLSQ-AGSVVEKEVKIEESWSYHLILQFAVHDRKEDGGLDGKRVWK   54 (172)
Q Consensus         7 iPIDlSk-AGsvvE~eirI~E~~~y~~~l~f~~r~rk~~g~~dg~~v~k   54 (172)
                      |.+||+. .++.-.+-|.|.|--.|.+-+.|.|..+--+|=++--.|||
T Consensus        86 i~ldl~~~~~~~k~~~F~IKEGs~Y~lki~F~V~~eivsGLkY~q~Vkr  134 (201)
T PF02115_consen   86 IVLDLPGDLENLKKKPFTIKEGSEYRLKITFKVQHEIVSGLKYVQTVKR  134 (201)
T ss_dssp             EEEE----HCCCCCSEEEEE---EEEEEEEEEEESSEB--EEEEEEEEE
T ss_pred             EEEECCCCCCCCCCCCEEECCCCEEEEEEEEEEECCCCCCCEEEEEEEE
T ss_conf             7875777655446874895799789999999990741137189999997


Done!