Query         T0614 Sin1, Homo Sapiens, 135 residues
Match_columns 135
No_of_seqs    67 out of 69
Neff          4.4 
Searched_HMMs 11830
Date          Mon Jul  5 09:00:52 2010
Command       /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0614.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0614.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PF05422 SIN1:  Stress-activate 100.0   6E-36   5E-40  236.3   8.9   95    1-102   428-523 (523)
  2 PF08416 PTB:  Phosphotyrosine-  29.0      15  0.0013   15.2   7.6   80   19-108    39-125 (131)
  3 PF12060 DUF3541:  Domain of un  20.0      22  0.0019   14.1   3.1   50   85-134   136-200 (227)
  4 PF05456 eIF_4EBP:  Eukaryotic   16.6      19  0.0016   14.6   1.0   21   97-117    45-65  (116)
  5 PF07159 DUF1394:  Protein of u  14.9      30  0.0025   13.4   2.8   21   89-109     6-28  (303)
  6 PF05261 Tra_M:  TraM protein;   14.7      18  0.0015   14.7   0.5   17   96-112     8-24  (127)
  7 PF04914 DltD_C:  DltD C-termin  14.6      24   0.002   13.9   1.1   35   77-111    53-88  (130)
  8 PF08878 DUF1837:  Domain of un  12.6      28  0.0024   13.5   1.0   39   13-54     75-116 (236)
  9 PF09330 Lact-deh-memb:  D-lact  11.1      29  0.0024   13.5   0.7   31   86-116   219-250 (291)
 10 PF10496 Syntaxin-18_N:  SNARE-  10.3      41  0.0035   12.5   2.8   28   94-122    41-68  (86)

No 1  
>PF05422 SIN1:  Stress-activated map kinase interacting protein 1 (SIN1);  InterPro: IPR008828 This family consists of several stress-activated map kinase interacting protein 1 (MAPKAP1 OR SIN1) sequences. The Schizosaccharomyces pombe Sty1/Spc1 mitogen-activated protein (MAP) kinase is a member of the eukaryotic stress-activated MAP kinase (SAPK) family. Sin1 interacts with Sty1/Spc1. Cells lacking Sin1 display many, but not all, of the phenotypes of cells lacking the Sty1/Spc1 MAP kinase including sterility, multiple stress sensitivity and a cell-cycle delay. Sin1 is phosphorylated after stress but this is not Sty1/Spc1-dependent .
Probab=100.00  E-value=6e-36  Score=236.27  Aligned_cols=95  Identities=28%  Similarity=0.481  Sum_probs=86.7

Q ss_pred             CCCCCEEEEEEEECCCCCCEEEEEEECCCEEEEECCCCCCCCCEEECCCCCEEECCCCEEEEEEECCCCCCCCEEEEEEE
Q ss_conf             98860478999723656412268875373899735878755531321677013232310344431235888517999985
Q T0614             1 GSHHYKSFKVSMIHRLRFTTDVQLGISGDKVEIDPVTNQKASTKFWIKQKPISIDSDLLCACDLAEEKSPSHAIFKLTYL   80 (135)
Q Consensus         1 ~s~~Yk~y~V~r~~k~~~k~Er~L~IDGdyI~I~P~~~~k~~~~f~~~~Kt~S~~i~~Vv~ckiv~r~~~~~~~Fkiv~~   80 (135)
                      ++++||+|+|||+|+|+|++||+||||||||||||.+++    +||.++||+|+||++||+||+++++   |..|||+|.
T Consensus       428 ~a~~yr~y~V~rkq~m~f~~er~L~idgdyi~I~p~~~~----~~~~~~Kt~s~~~~~V~~ck~s~r~---p~~fki~v~  500 (523)
T PF05422_consen  428 EAGAYRKYTVWRKQPMSFKHERQLAIDGDYIHIMPSESK----KFWEQGKTTSIHISSVVGCKVSRRH---PANFKIVVK  500 (523)
T ss_pred             CCCCCEEEEEEEECCCCCCCCEEEEECCCEEEECCCCCC----CCCCCCCCEEEEHHHEEEEEEECCC---CCEEEEEEE
T ss_conf             354312799999605776531699852756997678876----6545789557730261544672106---742899997


Q ss_pred             CCCCCEEEEEECCH-HHHHHHHH
Q ss_conf             18860588751787-89999999
Q T0614            81 SNHDYKHLYFESDA-ATVNEIVL  102 (135)
Q Consensus        81 ~~~~~KrYDFEA~~-~~A~EIV~  102 (135)
                      ++++.|||||||.+ .+|+|||.
T Consensus       501 ~~~~~kry~fea~sa~~~~~iv~  523 (523)
T PF05422_consen  501 RNSESKRYDFEATSAPEAAEIVS  523 (523)
T ss_pred             CCCCCCCCEEECCCCHHHHHHCC
T ss_conf             48877654014157045323029


No 2  
>PF08416 PTB:  Phosphotyrosine-binding domain;  InterPro: IPR013625   The phosphotyrosine-binding domain (PTB, also phosphotyrosine-interaction or PI domain) of tensin tends to be found at the C terminus of a protein. Tensin is a multi-domain protein that binds to actin filaments and functions as a focal-adhesion molecule (focal adhesions are regions of plasma membrane through which cells attach to the extracellular matrix). Human tensin has actin-binding sites, an SH2 (IPR000980 from INTERPRO) domain and a region similar to the tumour suppressor PTEN . The PTB domain interacts with the cytoplasmic tails of beta integrin by binding to an NPXY motif . ; PDB: 2gjy_A 1wvh_A 2cy4_A 2cy5_A 2dkq_A.
Probab=29.02  E-value=15  Score=15.16  Aligned_cols=80  Identities=16%  Similarity=0.280  Sum_probs=54.6

Q ss_pred             CEEEEEEECCCEEEEECCCCCCCCCEEECCCCCEEECCCCEEEEEEECCCCCCCCEEEEEEECCC---CCEEEEEEC---
Q ss_conf             12268875373899735878755531321677013232310344431235888517999985188---605887517---
Q T0614            19 TTDVQLGISGDKVEIDPVTNQKASTKFWIKQKPISIDSDLLCACDLAEEKSPSHAIFKLTYLSNH---DYKHLYFES---   92 (135)
Q Consensus        19 k~Er~L~IDGdyI~I~P~~~~k~~~~f~~~~Kt~S~~i~~Vv~ckiv~r~~~~~~~Fkiv~~~~~---~~KrYDFEA---   92 (135)
                      .++.+|-++...|.+.-.+++.    |+     -+++++.|.+|..+.....=++.|.+|+....   +.= +-|-.   
T Consensus        39 ~q~v~lkV~~~gItL~D~~~k~----~~-----e~yp~~~I~~~~~~~~~~~~~~il~fV~r~~~~~~~~~-HlFqc~ev  108 (131)
T PF08416_consen   39 PQEVHLKVSDQGITLTDNERKE----FF-----EHYPLNSITHCGADPNDRRYNSILAFVARKPGSSKDNV-HLFQCDEV  108 (131)
T ss_dssp             -EEEEEEE-SSEEEEEESSTSS----CC-----EEEECCCEEEEECETT--EES-EEEEEEE-TT-TT-EE-EEEE--E-
T ss_pred             CEEEEEEEECCCEEEEECCCCE----EE-----EECCCCCEEECCCCCCCCCCCCEEEEEECCCCCCCCCE-EEEECCCC
T ss_conf             4799999968948999778740----34-----44583030002525898871318999983799999867-89852877


Q ss_pred             CH-HHHHHHHHHHHHHH
Q ss_conf             87-89999999988887
Q T0614            93 DA-ATVNEIVLKVNYIL  108 (135)
Q Consensus        93 ~~-~~A~EIV~kIn~IL  108 (135)
                      ++ ..|+.|++=++-++
T Consensus       109 ~a~~~~~~i~~~~~~~~  125 (131)
T PF08416_consen  109 DAEQPASDIVNFVSKVM  125 (131)
T ss_dssp             -TCSHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHHHH
T ss_conf             87788999999998752


No 3  
>PF12060 DUF3541:  Domain of unknown function (DUF3541)
Probab=20.04  E-value=22  Score=14.11  Aligned_cols=50  Identities=18%  Similarity=0.304  Sum_probs=38.5

Q ss_pred             CEEEEEEC---CHH----HHHHHHHHHHHHHHHCCCHHHHHHHH--------HHHHHHHHHHCCC
Q ss_conf             05887517---878----99999999888876115524688898--------8888767642379
Q T0614            85 YKHLYFES---DAA----TVNEIVLKVNYILESRASTARADYFA--------QKQRKLNRRTSGN  134 (135)
Q Consensus        85 ~KrYDFEA---~~~----~A~EIV~kIn~ILe~R~s~~r~e~~~--------~r~rk~~~~~~~~  134 (135)
                      .|+|||+.   |++    =|+++.+-.=|+-++--.++-.+|..        .++.|++++-=||
T Consensus       136 lrr~Df~~~~Td~~MI~aWAAQLaN~VYW~kQlG~~D~v~~f~~AF~~tYPD~~D~kLsk~Qy~N  200 (227)
T PF12060_consen  136 LRRYDFKKYLTDKAMIKAWAAQLANQVYWLKQLGEQDVVNDFKQAFRKTYPDNKDKKLSKQQYRN  200 (227)
T ss_pred             HHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHCC
T ss_conf             99805301269999999999999999999999471157999999999858984044532998512


No 4  
>PF05456 eIF_4EBP:  Eukaryotic translation initiation factor 4E binding protein (EIF4EBP);  InterPro: IPR008606 This family consists of several eukaryotic translation initiation factor 4E binding proteins (EIF4EBP1, -2 and -3). Translation initiation in eukaryotes is mediated by the cap structure (m7GpppN, where N is any nucleotide) present at the 5' end of all cellular mRNAs, except organellar. The cap is recognised by eukaryotic initiation factor 4F (eIF4F), which consists of three polypeptides, including eIF4E, the cap-binding protein subunit. The interaction of the cap with eIF4E facilitates the binding of the ribosome to the mRNA. eIF4E activity is regulated in part by translational repressors, 4E-BP1, 4E-BP2 and 4E-BP3 which bind to it and prevent its assembly into eIF4F .; GO: 0008190 eukaryotic initiation factor 4E binding, 0045947 negative regulation of translational initiation; PDB: 2v8w_F 2v8x_F 2jgc_B 2jgb_B 1wkw_B 2v8y_B.
Probab=16.59  E-value=19  Score=14.55  Aligned_cols=21  Identities=19%  Similarity=0.338  Sum_probs=17.0

Q ss_pred             HHHHHHHHHHHHHHCCCHHHH
Q ss_conf             999999988887611552468
Q T0614            97 VNEIVLKVNYILESRASTARA  117 (135)
Q Consensus        97 A~EIV~kIn~ILe~R~s~~r~  117 (135)
                      -.-|+..=+++|++|.|++-+
T Consensus        45 GTRIIYdR~FLl~~RnSPlar   65 (116)
T PF05456_consen   45 GTRIIYDRKFLLNCRNSPLAR   65 (116)
T ss_dssp             -------HHHHHHTCG-----
T ss_pred             CCEEEEEHHHHHHHCCCCCCC
T ss_conf             747887679998740797545


No 5  
>PF07159 DUF1394:  Protein of unknown function (DUF1394);  InterPro: IPR009828   This family consists of several hypothetical eukaryotic proteins of around 320 residues in length. The function of this family is unknown.
Probab=14.93  E-value=30  Score=13.37  Aligned_cols=21  Identities=33%  Similarity=0.444  Sum_probs=9.1

Q ss_pred             EEE-CCH-HHHHHHHHHHHHHHH
Q ss_conf             751-787-899999999888876
Q T0614            89 YFE-SDA-ATVNEIVLKVNYILE  109 (135)
Q Consensus        89 DFE-A~~-~~A~EIV~kIn~ILe  109 (135)
                      ||| |.| .+-.||.+.+|-+|+
T Consensus         6 DfenA~Pt~~E~ev~~~vn~vL~   28 (303)
T PF07159_consen    6 DFENAQPTEEEREVYEQVNEVLE   28 (303)
T ss_pred             ECCCCCCCHHHHHHHHHHHHHHH
T ss_conf             46679999899999999999999


No 6  
>PF05261 Tra_M:  TraM protein;  InterPro: IPR007925   The TraM protein is an essential part of the DNA transfer machinery of the conjugative resistance plasmid R1 (IncFII). On the basis of mutational analyses, it was shown that the essential transfer protein TraM has at least two functions. First, a functional TraM protein was found to be required for normal levels of transfer gene expression. Second, experimental evidence was obtained that TraM stimulates efficient site-specific single-stranded DNA cleavage at the oriT, in vivo. Furthermore, a specific interaction of the cytoplasmic TraM protein with the membrane protein TraD was demonstrated, suggesting that the TraM protein creates a physical link between the relaxosomal nucleoprotein complex and the membrane-bound DNA transfer apparatus .; GO: 0003677 DNA binding, 0000746 conjugation; PDB: 3d8a_B 2g9e_A 2g7o_A 1dp3_A.
Probab=14.68  E-value=18  Score=14.68  Aligned_cols=17  Identities=35%  Similarity=0.497  Sum_probs=10.0

Q ss_pred             HHHHHHHHHHHHHHHCC
Q ss_conf             99999999888876115
Q T0614            96 TVNEIVLKVNYILESRA  112 (135)
Q Consensus        96 ~A~EIV~kIn~ILe~R~  112 (135)
                      +-.+++.+||.|.|-|.
T Consensus         8 vsn~v~e~I~~iveeRr   24 (127)
T PF05261_consen    8 VSNQVYEKINAIVEERR   24 (127)
T ss_dssp             ---THHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
T ss_conf             51468999999999999


No 7  
>PF04914 DltD_C:  DltD C-terminal region;  InterPro: IPR006998   The dlt operon (dltA to dltD) of Lactobacillus rhamnosus 7469 encodes four proteins responsible for the esterification of lipoteichoic acid (LTA) by D-alanine. These esters play an important role in controlling the net anionic charge of the poly (GroP) moiety of LTA. DltA and DltC encode the D-alanine-D-alanyl carrier protein ligase (Dcl) and D-alanyl carrier protein (Dcp), respectively. Whereas the functions of DltA and DltC are defined, the functions of DltB and DltD are unknown. In vitro assays showed that DltD bound Dcp for ligation with D-alanine by Dcl in the presence of ATP. In contrast, the homologue of Dcp, the Escherichia coli acyl carrier protein (ACP), involved in fatty acid biosynthesis, was not bound to DltD and thus was not ligated with D-alanine. DltD also catalyzed the hydrolysis of the mischarged D-alanyl-ACP. The hydrophobic N-terminal sequence of DltD was required for anchoring the protein in the membrane. It is hypothesized that this membrane-associated DltD facilitates the binding of Dcp and Dcl for ligation of Dcp with D-alanine and that the resulting D-alanyl-Dcp is translocated to the primary site of D-alanylation .   These sequences contain the C-terminal region of DltD.; PDB: 3bma_C.
Probab=14.61  E-value=24  Score=13.93  Aligned_cols=35  Identities=17%  Similarity=0.216  Sum_probs=29.8

Q ss_pred             EEEECCCCCEEEEEEC-CHHHHHHHHHHHHHHHHHC
Q ss_conf             9985188605887517-8789999999988887611
Q T0614            77 LTYLSNHDYKHLYFES-DAATVNEIVLKVNYILESR  111 (135)
Q Consensus        77 iv~~~~~~~KrYDFEA-~~~~A~EIV~kIn~ILe~R  111 (135)
                      |++..+...|-||+.. +...-++.+.||+..|+..
T Consensus        53 lfIi~PvNgkWydytG~~~~~r~~~y~kI~~~~~~~   88 (130)
T PF04914_consen   53 LFIIPPVNGKWYDYTGLSKEMRQQYYKKIKYQLKSQ   88 (130)
T ss_dssp             EEEE----HHHHHH--B-HHHHHHHHHHHHHHHHT-
T ss_pred             EEEECCCCCHHHHHHCCCHHHHHHHHHHHHHHHHHC
T ss_conf             798557871588880889999999999999999987


No 8  
>PF08878 DUF1837:  Domain of unknown function (DUF1837);  InterPro: IPR014976   This group of proteins are functionally uncharacterised. 
Probab=12.63  E-value=28  Score=13.53  Aligned_cols=39  Identities=15%  Similarity=0.133  Sum_probs=22.9

Q ss_pred             ECCCCCCEE---EEEEECCCEEEEECCCCCCCCCEEECCCCCEEE
Q ss_conf             236564122---688753738997358787555313216770132
Q T0614            13 IHRLRFTTD---VQLGISGDKVEIDPVTNQKASTKFWIKQKPISI   54 (135)
Q Consensus        13 ~~k~~~k~E---r~L~IDGdyI~I~P~~~~k~~~~f~~~~Kt~S~   54 (135)
                      .-+|.+|+.   -+-|.||  |||.+-.++. ...+|..+|.-+-
T Consensus        75 ~~K~~lKt~~~~~~~G~D~--VHi~~~~~~~-~~L~lGESKly~d  116 (236)
T PF08878_consen   75 LSKMYLKTSSNMHVHGFDG--VHIVVDNDNG-LQLWLGESKLYKD  116 (236)
T ss_pred             EEEEEEECCCCCCCCCCCE--EEEEECCCCC-CEEEEEEEEECCC
T ss_conf             4789872488872026762--7997428988-6899986100036


No 9  
>PF09330 Lact-deh-memb:  D-lactate dehydrogenase, membrane binding;  InterPro: IPR015409   Members of this entry are predominantly found in prokaryotic D-lactate dehydrogenase, forming the cap-membrane-binding domain, which consists of a large seven-stranded antiparallel beta-sheet flanked on both sides by alpha-helices. They allow for membrane association . ; GO: 0008720 D-lactate dehydrogenase activity, 0009055 electron carrier activity, 0050660 FAD binding, 0055085 transmembrane transport, 0000300 peripheral to membrane of membrane fraction; PDB: 1f0x_B.
Probab=11.07  E-value=29  Score=13.46  Aligned_cols=31  Identities=10%  Similarity=0.133  Sum_probs=17.7

Q ss_pred             EEEEEECC-HHHHHHHHHHHHHHHHHCCCHHH
Q ss_conf             58875178-78999999998888761155246
Q T0614            86 KHLYFESD-AATVNEIVLKVNYILESRASTAR  116 (135)
Q Consensus        86 KrYDFEA~-~~~A~EIV~kIn~ILe~R~s~~r  116 (135)
                      =|-|+-.. ..-|.++-.++-.+|+-|-.-+-
T Consensus       219 fHQDYi~KkGvD~~~lk~~ml~lLd~RgA~YP  250 (291)
T PF09330_consen  219 FHQDYIVKKGVDAKALKHEMLALLDARGAEYP  250 (291)
T ss_dssp             EEEEEEEE----HHHHHHHHHHHHHH---BSS
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf             14766640587889999999999987078788


No 10 
>PF10496 Syntaxin-18_N:  SNARE-complex protein Syntaxin-18 N-terminus 
Probab=10.28  E-value=41  Score=12.49  Aligned_cols=28  Identities=14%  Similarity=0.186  Sum_probs=23.2

Q ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             78999999998888761155246888988
Q T0614            94 AATVNEIVLKVNYILESRASTARADYFAQ  122 (135)
Q Consensus        94 ~~~A~EIV~kIn~ILe~R~s~~r~e~~~~  122 (135)
                      .++|-+|..-|..++. -...+|..||+-
T Consensus        41 ~KeA~~i~~~I~~L~~-fL~~iR~~Yls~   68 (86)
T PF10496_consen   41 LKEAYRINSHITSLLT-FLKSIRKAYLSI   68 (86)
T ss_pred             HHHHHHHHHHHHHHHH-HHHHHHHHHHHC
T ss_conf             9999999999999999-999982999705


Done!