Query         T0620 INPPL1B, Homo Sapiens, 312 residues
Match_columns 312
No_of_seqs    117 out of 1623
Neff          9.6 
Searched_HMMs 11830
Date          Thu Jul 22 15:17:10 2010
Command       /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0620.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0620.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PF03372 Exo_endo_phos:  Endonu 100.0   2E-27 1.7E-31  174.0  15.0  266    7-306     1-276 (276)
  2 PF00952 Bunya_nucleocap:  Buny  18.4      16  0.0014   12.1   2.9   23  127-149    56-78  (228)
  3 PF03514 GRAS:  GRAS family tra  10.5      28  0.0023   10.8   3.0   12  267-278   360-371 (374)
  4 PF00919 UPF0004:  Uncharacteri   6.9      40  0.0034    9.9   3.1   43    6-51      1-43  (98)
  5 PF06972 DUF1296:  Protein of u   5.9      20  0.0017   11.7  -2.0   29   35-64     11-40  (60)
  6 PF07853 DUF1648:  Protein of u   5.8      50  0.0042    9.3   0.6   14    2-18     19-32  (51)
  7 PF02076 STE3:  Pheromone A rec   5.2      57  0.0048    9.0   0.6   14  257-271    47-60  (283)
  8 PF10216 ChpXY:  CO2 hydration    5.0      30  0.0025   10.7  -1.6   30  236-275    49-78  (353)
  9 PF03808 Glyco_tran_WecB:  Glyc   5.0      61  0.0052    8.8   1.2   21   34-54     91-115 (172)
 10 PF01937 DUF89:  Protein of unk   4.9      63  0.0053    8.8   0.3   29  164-192   279-307 (354)

No 1  
>PF03372 Exo_endo_phos:  Endonuclease/Exonuclease/phosphatase family Subset of Pfam family Subset of Pfam family;  InterPro: IPR005135    This domain is found in a large number of proteins including magnesium dependent endonucleases and phosphatases involved in intracellular signalling . Proteins this domain is found in include: AP endonuclease proteins (4.2.99.18 from EC), DNase I proteins (3.1.21.1 from EC), Synaptojanin an inositol-1,4,5-trisphosphate phosphatase (3.1.3.56 from EC) and Sphingomyelinase (3.1.4.12 from EC).; PDB: 1si6_X 1ntf_A 2imq_X 1y21_A 1yjh_A 1i9y_A 1i9z_A 3cjc_D 2a42_B 2a40_E ....
Probab=99.95  E-value=2e-27  Score=174.03  Aligned_cols=266  Identities=25%  Similarity=0.206  Sum_probs=153.4

Q ss_pred             EEEEEECCCCCCCCHHHHHHHHHHHCCCHHHHHHCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHC------CCCEEEE
Q ss_conf             9999861577277012345542321010013452057898899972147877789999999987531------7850899
Q T0620             7 VFIGTWNMGSVPPPKNVTSWFTSKGLGKTLDEVTVTIPHDIYVFGTQENSVGDREWLDLLRGGLKEL------TDLDYRP   80 (312)
Q Consensus         7 v~i~TwNVng~~~~~~l~~~l~~~~~~~~~~~~~~~~~~Di~vi~lQE~~~~~~~~~~~~~~~l~~~------~~~~y~~   80 (312)
                      +.|+||||++.........      +.+.+...+...+|||  |||||+..................      ....+..
T Consensus         1 lrv~t~Nv~~~~~~~~~~~------~~~~~~~~i~~~~~Di--i~LQEv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   72 (276)
T PF03372_consen    1 LRVMTWNVNGLSGSDDSEE------RLDELAEVIREQDPDI--ICLQEVWDSSNSNQLQNQLPSGYYYFLNECNYYPYSC   72 (276)
T ss_dssp             EEEEEEEEEECHCHHHHHH------HHHHHHHHHHHHSESE--EEEEEESSHGTGHHHHHHHTCTHEECHEECEEEEEEE
T ss_pred             CEEEEHHHCCCCCCCCCCH------HHHHHHHHHHHCCCCE--EEEEECCCHHCCCCHHHHCCCCCCCCCCCCCCCCCCC
T ss_conf             9999830298988732212------5799999998669988--9998255121033000000124432211212222111


Q ss_pred             EECCCCCEEEEEEEECCCCCCCCCCCCCCCEEECCCCCCCCCCCEEEEEEECCEEEEEEEEECCCCCCCHHHHHHHHHHH
Q ss_conf             83147540267888525320112445513213426875668783899999848289999710477874014678999999
Q T0620            81 IAMQSLWNIKVAVLVKPEHENRISHVSTSSVKTGIANTLGNKGAVGVSFMFNGTSFGFVNCHLTSGNEKTARRNQNYLDI  160 (312)
Q Consensus        81 ~~~~~~~~~gv~vf~r~~~~~~i~~~~~~~~~~g~~~~~~~kG~v~i~~~~~~~~i~~in~hl~a~~~~~~~R~~~~~~i  160 (312)
                      .........|+++++|.+............       .......+.......+..+.++|+|++++......|..++..+
T Consensus        73 ~~~~~~~~~gv~i~~r~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~v~~~H~~~~~~~~~~r~~~~~~l  145 (276)
T PF03372_consen   73 YSGSGGGDGGVAIFSRYPIFSLFSHIFPRN-------RLSSRIIVVVRIKINGRSFTVINVHLPAGGESSDQRLSQAKEL  145 (276)
T ss_dssp             EETSTSSTS-EEEEESSTESEEEEECCEEE-------CESTTTTEEEEEEEETCEEEEEEEEEECC-HHHHHHHHHHHHH
T ss_pred             CCCCCCCCCEEEEEEECCCCCCCCCCCCCC-------CCCCCCEEEEEEECCCCEEEEEEEECCCCCCCHHHHHHHHHHH
T ss_conf             126788764599997327211123333323-------3555516999982488349999986375443303579999999


Q ss_pred             HHHHCCCHHHHHHHHHHHCCCCEEEECCCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf             98730003444556653004644775456545467736899873024601466766567998625411433248885366
Q T0620           161 LRLLSLGDRQLNAFDISLRFTHLFWFGDLNYRLDMDIQEILNYISRKEFEPLLRVDQLNLEREKHKVFLRFSEEEISFPP  240 (312)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~v~~~GD~N~~~~~~~~~~~~~~~~~~~~~l~~~d~~~~~~~~~~~~~~~~e~~i~F~p  240 (312)
                      .+.+....       ......++|++||||.+.......................+.....+..........+....+.+
T Consensus       146 ~~~~~~~~-------~~~~~~~~il~GDfN~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  218 (276)
T PF03372_consen  146 LDFLSEFI-------KNPPGDPIILAGDFNSRPDSDDYRNLSSRSDSSQDRLDWRDSLELPKEGGFDDYGRDELPIGFPP  218 (276)
T ss_dssp             HHHHHHHH-------HHTTTSEEEEE---SSSHSGGHCHHHHHHHHHHHHHHHHHHHHHHHHTTCEEHHHHHHTTEESSB
T ss_pred             HHHHHHCC-------CCCCCCCEEEECCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHCCCCCC
T ss_conf             76533102-------34555632587304878540011111103432124402345566651354202222220246753


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEEC----CCCCCCCCCCEEEEE
Q ss_conf             247648788865343456776666777230146664175440378740002----776768985579999
Q T0620           241 TYRYERGSRDTYAWHKQKPTGVRTNVPSWCDRILWKSYPETHIICNSYGCT----DDIVTSDHSPVFGTF  306 (312)
Q Consensus       241 tyk~~~~~~~~~t~~~~~~~~~~~r~p~w~DRIly~~~~~~~~~~~~y~~~----~~~~~SDH~PV~a~f  306 (312)
                      ||+...+.            ......|+|+|||++...-............    .....|||+||.|+|
T Consensus       219 T~~~~~~~------------~~~~~~~~~lD~il~s~~~~~~~~~~~~~~~~~~~~~~~~SDH~pV~~~f  276 (276)
T PF03372_consen  219 TYKFWRNN------------SDKGGFPSRLDYILVSGSLTQRIQDVSVDSTSDKPDGFSLSDHLPVVAEF  276 (276)
T ss_dssp             SBESTTCH------------CTTTTEEB--S-EEEEHHHHTTEEEEEEETTHCEETSSSSSSB-EEEEEE
T ss_pred             CCCCCCCC------------CCCCCCCCCCCEEEEECHHHHHCEEEEECCCCCCCCCCCCCCCHHHEEEC
T ss_conf             22155432------------23448986305599734354203554430332235789899884309979


No 2  
>PF00952 Bunya_nucleocap:  Bunyavirus nucleocapsid (N) protein;  InterPro: IPR001784 Orthobunyavirus are enveloped viruses with a genome consisting of 3 ssRNA segments (called L, M and S). The nucleocapsid protein is encode on the small (S) genomic RNA. The N protein is the major component of the nucleocapsids. This protein is thought to interact with the L protein, virus RNA and/or other N proteins .; GO: 0019013 viral nucleocapsid
Probab=18.38  E-value=16  Score=12.13  Aligned_cols=23  Identities=26%  Similarity=0.494  Sum_probs=18.3

Q ss_pred             EEEEECCEEEEEEEEECCCCCCC
Q ss_conf             99998482899997104778740
Q T0620           127 VSFMFNGTSFGFVNCHLTSGNEK  149 (312)
Q Consensus       127 i~~~~~~~~i~~in~hl~a~~~~  149 (312)
                      +.+++.+-.+.++|.|.|.+..+
T Consensus        56 v~l~fG~~~~~vvNthfP~n~~n   78 (228)
T PF00952_consen   56 VTLKFGGWKIEVVNTHFPGNRNN   78 (228)
T ss_pred             EEEEECCEEEEEEECCCCCCCCC
T ss_conf             51342667899872578553579


No 3  
>PF03514 GRAS:  GRAS family transcription factor;  InterPro: IPR005202   Sequence analysis of the products of the GRAS (GAI, RGA, SCR) gene family indicates that they share a variable N-terminus and a highly conserved C-terminus that contains five recognizable motifs . Proteins in the GRAS family are transcription factors that seem to be involved in development and other processes. Mutation of the SCARECROW (SCR) gene results in a radial pattern defect, loss of a ground tissue layer, in the root. The PAT1 protein is involved in phytochrome A signal transduction .    GRAS proteins contain a conserved region of about 350 amino acids that can be divided in 5 motifs, found in the following order: leucine heptad repeat I, the VHIID motif, leucine heptad repeat II, the PFYRE motif and the SAW motif , . Plant specific GRAS proteins have parallels in their motif structure to the animal Signal Transducers and Activators of Transcription (STAT) family of proteins  which suggests also some parallels in their functions.
Probab=10.48  E-value=28  Score=10.82  Aligned_cols=12  Identities=25%  Similarity=0.346  Sum_probs=7.1

Q ss_pred             CCCCEEEEEEEC
Q ss_conf             723014666417
Q T0620           267 PSWCDRILWKSY  278 (312)
Q Consensus       267 p~w~DRIly~~~  278 (312)
                      -+|.+|.+|.++
T Consensus       360 L~Wk~~pL~~~S  371 (374)
T PF03514_consen  360 LGWKGRPLVSAS  371 (374)
T ss_pred             EEECCCEEEEEE
T ss_conf             865896689993


No 4  
>PF00919 UPF0004:  Uncharacterized protein family UPF0004;  InterPro: IPR013848   This entry represents an N-terminal domain found in a family of proteins defined by sequence similarity. Most of these proteins are not yet characterised, but those that are include  CDK5 regulatory subunit-associated protein 1, which specifically inhibits CDK5 activation by CDK5R1 . MiaB, a tRNA modification enzyme .  It is almost always found in conjunction with a radical SAM domain (IPR006638 from INTERPRO) and a TRAM domain (IPR002792 from INTERPRO). 
Probab=6.90  E-value=40  Score=9.88  Aligned_cols=43  Identities=12%  Similarity=0.042  Sum_probs=21.9

Q ss_pred             EEEEEEECCCCCCCCHHHHHHHHHHHCCCHHHHHHCCCCCCEEEEE
Q ss_conf             9999986157727701234554232101001345205789889997
Q T0620             6 SVFIGTWNMGSVPPPKNVTSWFTSKGLGKTLDEVTVTIPHDIYVFG   51 (312)
Q Consensus         6 ~v~i~TwNVng~~~~~~l~~~l~~~~~~~~~~~~~~~~~~Di~vi~   51 (312)
                      |++|.|+-|.--..+.+   .+........+.......++|+++|-
T Consensus         1 kv~i~T~GC~~N~~dse---~~~~~L~~~G~~~v~~~e~ADviiiN   43 (98)
T PF00919_consen    1 KVYIETLGCQMNQYDSE---RMAGILKAAGYEIVDDPEEADVIIIN   43 (98)
T ss_pred             CEEEEECCCCCCHHHHH---HHHHHHHHCCCCCCCCCCCCCEEEEE
T ss_conf             98999779984789999---99999975698545776779999998


No 5  
>PF06972 DUF1296:  Protein of unknown function (DUF1296);  InterPro: IPR009719   This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=5.88  E-value=20  Score=11.65  Aligned_cols=29  Identities=17%  Similarity=0.339  Sum_probs=16.5

Q ss_pred             HHHHHHCC-CCCCEEEEEEECCCCCHHHHHH
Q ss_conf             01345205-7898899972147877789999
Q T0620            35 TLDEVTVT-IPHDIYVFGTQENSVGDREWLD   64 (312)
Q Consensus        35 ~~~~~~~~-~~~Di~vi~lQE~~~~~~~~~~   64 (312)
                      .+.++... .++|||+. |+|+.|...+..+
T Consensus        11 ~iKEiv~~hSd~eIya~-L~ec~MDPnEtvq   40 (60)
T PF06972_consen   11 SIKEIVGKHSDEEIYAM-LKECNMDPNETVQ   40 (60)
T ss_pred             HHHHHHCCCCHHHHHHH-HHHHCCCHHHHHH
T ss_conf             99999848977999999-9996798789999


No 6  
>PF07853 DUF1648:  Protein of unknown function (DUF1648);  InterPro: IPR012867   This entry contains hypothetical proteins expressed by either bacterial or archaeal species. Some of these are annotated as being transmembrane proteins, and many contain a high proportion of hydrophobic residues. 
Probab=5.84  E-value=50  Score=9.34  Aligned_cols=14  Identities=43%  Similarity=0.914  Sum_probs=6.7

Q ss_pred             CCEEEEEEEEECCCCCC
Q ss_conf             97379999986157727
Q T0620             2 PDMISVFIGTWNMGSVP   18 (312)
Q Consensus         2 p~~l~v~i~TwNVng~~   18 (312)
                      |+++.++   ||.+|..
T Consensus        19 P~~ip~H---~~~~G~~   32 (51)
T PF07853_consen   19 PDEIPTH---WNANGEP   32 (51)
T ss_pred             CHHHCEE---ECCCCCC
T ss_conf             5644321---5889987


No 7  
>PF02076 STE3:  Pheromone A receptor;  InterPro: IPR001499   G-protein-coupled receptors, GPCRs, constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence . The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. There is a specialised database for GPCRs: http://www.gpcr.org/7tm/.    Little is known about the structure and function of the mating factor receptors, STE2 and STE3. It is believed, however, that they are integral membrane proteins that may be involved in the response to mating factors on the cell membrane , , . The amino acid sequences of both receptors contain high proportions of hydrophobic residues grouped into 7 domains, in a manner reminiscent of the rhodopsins and other receptors believed to interact with G-proteins. However, while a similar 3D framework has been proposed to account for this, there is no significant sequence similarity either between STE2 and STE3, or between these and the rhodopsin-type family: the receptors thus bear their own unique '7TM' signatures.   The STE3 gene of Saccharomyces cerevisiae is the cell-surface receptor that binds the 13-residue lipopeptide a-factor. Several related fungal pheromone receptor sequences are known: these include pheromone B alpha 1 and B alpha 3, and pheromone B beta 1 receptors from Schizophyllum commune; pheromone receptor 1 from Ustilago hordei; and pheromone receptors 1 and 2 from Ustilago maydis. Members of the family share about 20% sequence identity.; GO: 0004932 mating-type factor pheromone receptor activity, 0007186 G-protein coupled receptor protein signaling pathway, 0016021 integral to membrane
Probab=5.24  E-value=57  Score=9.00  Aligned_cols=14  Identities=29%  Similarity=0.636  Sum_probs=0.0

Q ss_pred             CCCCCCCCCCCCCCE
Q ss_conf             567766667772301
Q T0620           257 QKPTGVRTNVPSWCD  271 (312)
Q Consensus       257 ~~~~~~~~r~p~w~D  271 (312)
                      ..++. ..+.|+|||
T Consensus        47 W~~~~-~~~~~~wCD   60 (283)
T PF02076_consen   47 WSGND-INWWPGWCD   60 (283)
T ss_pred             CCCCC-CCCCEEEEH
T ss_conf             38997-311601310


No 8  
>PF10216 ChpXY:  CO2 hydration protein (ChpXY)
Probab=4.99  E-value=30  Score=10.66  Aligned_cols=30  Identities=23%  Similarity=0.419  Sum_probs=0.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEE
Q ss_conf             8536624764878886534345677666677723014666
Q T0620           236 ISFPPTYRYERGSRDTYAWHKQKPTGVRTNVPSWCDRILW  275 (312)
Q Consensus       236 i~F~ptyk~~~~~~~~~t~~~~~~~~~~~r~p~w~DRIly  275 (312)
                      +.+-|-|||.+|....--.|.++          |-|||-|
T Consensus        49 L~~fP~FKyF~Ge~~~~kLl~Hl----------~hDRIN~   78 (353)
T PF10216_consen   49 LNPFPFFKYFNGEISLPKLLHHL----------WHDRINF   78 (353)
T ss_pred             CCCCHHHHHHCCCCCHHHHHHHH----------HHCHHHH
T ss_conf             03225877717887889999997----------3111015


No 9  
>PF03808 Glyco_tran_WecB:  Glycosyl transferase WecB/TagA/CpsF family;  InterPro: IPR004629   The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=4.97  E-value=61  Score=8.82  Aligned_cols=21  Identities=29%  Similarity=0.275  Sum_probs=0.0

Q ss_pred             CHHHHHHCCCCCCEEEEEE----EC
Q ss_conf             0013452057898899972----14
Q T0620            34 KTLDEVTVTIPHDIYVFGT----QE   54 (312)
Q Consensus        34 ~~~~~~~~~~~~Di~vi~l----QE   54 (312)
                      ..+.+.+....|||+++||    ||
T Consensus        91 ~~i~~~I~~s~pdiv~vglG~PkQE  115 (172)
T PF03808_consen   91 EAIIEAINASGPDIVFVGLGSPKQE  115 (172)
T ss_pred             HHHHHHHHHCCCCEEEEECCCCHHH
T ss_conf             9999999972969999988998789


No 10 
>PF01937 DUF89:  Protein of unknown function DUF89;  InterPro: IPR002791   This entry contains uncharacterised proteins. Those with structural information consist of two domains: an all-alpha domain with a 3-helical bundle immunoglobulin-like fold, and an alpha-beta domain in 3 layers, alpha/beta/alpha. ; PDB: 2ffj_A 1xfi_A 2q40_A 2g8l_B.
Probab=4.86  E-value=63  Score=8.76  Aligned_cols=29  Identities=24%  Similarity=0.329  Sum_probs=0.0

Q ss_pred             HCCCHHHHHHHHHHHCCCCEEEECCCCCC
Q ss_conf             30003444556653004644775456545
Q T0620           164 LSLGDRQLNAFDISLRFTHLFWFGDLNYR  192 (312)
Q Consensus       164 ~~~~~~~~~~~~~~~~~~~v~~~GD~N~~  192 (312)
                      ..+........+.....+-||.=||.|||
T Consensus       279 ~~~~~~~~~l~~~l~~adLVI~KG~~Nyr  307 (354)
T PF01937_consen  279 TDLWRMSPELYEALKEADLVIFKGDLNYR  307 (354)
T ss_dssp             --TTCS-HHHHHHHHH-SEEEE---HHHH
T ss_pred             CCHHHHCHHHHHHHCCCCEEEEECCHHHH
T ss_conf             79888599999997109989995747887


Done!