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!