Query         T0529 Nucleoprotein structure of lassa fever virus, unknown, 569 residues
Match_columns 569
No_of_seqs    39 out of 41
Neff          2.4 
Searched_HMMs 11830
Date          Fri May 21 18:04:55 2010
Command       /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0529.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0529.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PF00843 Arena_nucleocap:  Aren 100.0       0       0 2216.5  54.1  531    4-543     1-533 (533)
  2 PF00929 Exonuc_X-T:  Exonuclea  75.6     2.1 0.00017   19.8   7.1  140  386-537     2-161 (165)
  3 PF06248 Zw10:  Centromere/kine  60.4     4.1 0.00034   17.6   7.5  122   93-232   118-243 (595)
  4 PF07047 OPA3:  Optic atrophy 3  54.3       5 0.00043   16.9   4.2   72    9-80     42-127 (134)
  5 PF01612 3_5_exonuc:  3'-5' exo  52.7     5.3 0.00045   16.7   5.4  123  370-518     7-136 (174)
  6 PF01853 MOZ_SAS:  MOZ/SAS fami  52.1     5.4 0.00046   16.7   5.3   97   76-212    85-181 (188)
  7 PF10221 DUF2151:  Cell cycle a  48.4     3.8 0.00032   17.8   2.0  135  380-546   423-572 (692)
  8 PF05450 Nicastrin:  Nicastrin;  41.1     4.4 0.00037   17.3   1.4   64  256-324     6-70  (234)
  9 PF04481 DUF561:  Protein of un  38.6     4.6 0.00038   17.2   1.2   68  175-264    23-90  (242)
 10 PF09254 Endonuc-FokI_C:  Restr  37.9     2.6 0.00022   19.0  -0.1   29  479-507    23-51  (193)
 11 PF04522 DUF585:  Protein of un  34.6     3.2 0.00027   18.4  -0.1   14    5-18     11-26  (248)
 12 PF12007 DUF3501:  Protein of u  34.6     9.8 0.00083   14.8   2.7   81  370-454    97-188 (192)
 13 PF11502 BCL9:  B-cell lymphoma  33.4     9.8 0.00083   14.8   2.2   17  128-144     1-17  (40)
 14 PF03223 V-ATPase_C:  V-ATPase   33.2      10 0.00087   14.6   2.4   25   88-114    40-64  (371)
 15 PF05989 Chordopox_A35R:  Chord  32.6     6.1 0.00051   16.3   1.1   25  300-324   144-175 (176)
 16 PF06009 Laminin_II:  Laminin D  32.0      11 0.00091   14.5   5.3   83   29-118    13-106 (140)
 17 PF05813 Orthopox_F7:  Orthopox  28.5     5.8 0.00049   16.5   0.4   31  212-242    35-67  (82)
 18 PF06953 ArsD:  Arsenical resis  28.2     8.2 0.00069   15.4   1.1   43   94-144    21-65  (123)
 19 PF10757 YbaJ:  Biofilm formati  25.9      14  0.0011   13.8   2.2   33  193-225    46-78  (122)
 20 PF11715 Nup160:  Nucleoporin N  24.4     5.3 0.00045   16.7  -0.4   31  186-216    89-119 (547)
 21 PF11041 DUF2612:  Protein of u  24.1      15  0.0012   13.5   3.1   40  245-284   128-169 (187)
 22 PF03410 Peptidase_M44:  Protei  23.9      15  0.0012   13.5   2.1  180   16-233    62-277 (590)
 23 PF06780 Erp_C:  Erp protein C-  21.3      16  0.0014   13.2   2.0   48   65-116    81-128 (141)
 24 PF05677 DUF818:  Chlamydia CHL  20.9      13  0.0011   13.8   1.1  100  227-328   200-307 (365)
 25 PF04609 MCR_C:  Methyl-coenzym  20.4      17  0.0014   13.0   3.1   14  361-374   115-128 (268)
 26 PF02426 MIase:  Muconolactone   20.1      17  0.0015   13.0   2.3   29  154-182    46-74  (91)
 27 PF05415 Peptidase_C36:  Beet n  20.0      17  0.0014   13.0   1.4   16  531-546    51-66  (104)

No 1  
>PF00843 Arena_nucleocap:  Arenavirus nucleocapsid protein;  InterPro: IPR000229 Arenaviruses are single stranded RNA viruses. This family represents the nucleocapsid protein that encapsidates the viral ssRNA .; GO: 0019013 viral nucleocapsid
Probab=100.00  E-value=0  Score=2216.46  Aligned_cols=531  Identities=63%  Similarity=1.051  Sum_probs=521.5

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             64462367789999764320115688998889999842176678999999854057865789998888998777753202
Q T0529             4 SKEIKSFLWTQSLRRELSGYCSNIKLQVVKDAQALLHGLDFSEVSNVQRLMRKERRDDNDLKRLRDLNQAVNNLVELKST   83 (569)
Q Consensus         4 skevpSFrWtQsLRR~Ls~~t~~vK~dVl~Da~~ll~gLDF~~Va~VQR~mRk~KR~D~DL~~LRDlNkeVd~Lm~mkS~   83 (569)
                      ||||||||||||||||||+||++||+|||+||++|++||||+|||||||||||+||+|+||+||||||||||+||+|||+
T Consensus         1 skevpSFrWtQsLRRgLs~~t~~vK~dVlkDa~~l~~~LDF~~Va~VQR~mRk~KR~d~DL~~LRDlNkeVd~Lm~mkS~   80 (533)
T PF00843_consen    1 SKEVPSFRWTQSLRRGLSNWTTPVKADVLKDARALLSGLDFSQVAQVQRMMRKEKRDDSDLTKLRDLNKEVDSLMSMKST   80 (533)
T ss_pred             CCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             99776125579998664125641288999889998720588989999999886227747789999888999888845411


Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEECCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEE
Q ss_conf             45526872577767899999889999999752036778850321664778999999999843676556777788875899
Q T0529            84 QQKSILRVGTLTSDDLLILAADLEKLKSKVIRTERPLSAGVYMGNLSSQQLDQRRALLNMIGMSGGNQGARAGRDGVVRV  163 (569)
Q Consensus        84 Qk~~~lkvG~LskdeLm~LasDLeKLk~Kv~rtEr~~~~gvY~GNLt~~QL~~Rs~iL~~vG~~~~~~~~~~~~~GvVrv  163 (569)
                      |+|++||||+|+|||||||||||||||+||+|+||+++|||||||||++||+||+|||+++||    ++++++++|||||
T Consensus        81 q~~~~lkvG~LskdeLm~LasDLeKLk~Kv~r~er~~~~gvY~GNLt~~QL~~Rs~iL~~~G~----~~~~~~~~GVVrv  156 (533)
T PF00843_consen   81 QKNNVLKVGGLSKDELMELASDLEKLKKKVQRTERSGSPGVYMGNLTQSQLDQRSEILRMVGM----QQPRGGRNGVVRV  156 (533)
T ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEECCCCHHHHHHHHHHHHHHCC----CCCCCCCCCEEEE
T ss_conf             545168735767889999997899999997413578998623056668889999999998476----8887899976999


Q ss_pred             EECCCHHHHHHHCCCCHHHHHHHHHHCCCCCHHHHHHHHHHCCEEEEECCCCHHHHHHHHHCCCEEECCCCCCCCEEEEE
Q ss_conf             73576467764206604678888644056536789998752120034417886799988521871110146543001000
Q T0529           164 WDVKNAELLNNQFGTMPSLTLACLTKQGQVDLNDAVQALTDLGLIYTAKYPNTSDLDRLTQSHPILNMIDTKKSSLNISG  243 (569)
Q Consensus       164 WDvkd~sll~NQFGsmPalTiaCMt~Qgge~lndVVQ~Lt~LGLlYT~KyPNl~DLekLt~~Hp~L~iIt~~~S~iNISG  243 (569)
                      ||||||++|||||||||||||||||+||||+|||||||||+|||+||||||||+|||||+++||||++||+|+|||||||
T Consensus       157 WDvkd~sll~NQFGsmPalTiaCmt~Qg~e~lndvVQ~lt~LGLlYTvKyPNl~DLekLt~~Hp~L~~It~~~S~iNISG  236 (533)
T PF00843_consen  157 WDVKDSSLLNNQFGSMPALTIACMTEQGGETLNDVVQALTDLGLLYTVKYPNLSDLEKLTQKHPCLKIITQEESQINISG  236 (533)
T ss_pred             EECCCHHHHHHCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCEEEEEECCCHHHHHHHHHHCCCEEEECCCCCCEECCC
T ss_conf             74688799874047854999999998358717889987520351576406977889987652983012144512200232


Q ss_pred             ECHHHHHHHHHCCEEECCCCCEEEEEECHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCHHHHHHHHEECCCCCCCEEEC
Q ss_conf             02136666541400110666035676352128899999999886606421178778884454450110157986300012
Q T0529           244 YNFSLGAAVKAGACMLDGGNMLETIKVSPQTMDGILKSILKVKKALGMFISDTPGERNPYENILYKICLSGDGWPYIASR  323 (569)
Q Consensus       244 YNlSLsAAVKAGA~liDGGNMLETIkv~p~~f~~iiK~~L~vK~~e~MFv~~~PG~RNPYENlLYKlCLSGeGWPYI~SR  323 (569)
                      |||||||||||||||||||||||||+|+|+||++|||++|+||++|+||||++||+||||||||||||||||||||||||
T Consensus       237 YNlSLsAAVKAGAcliDGGNMLETIkv~p~~f~~iiK~~L~vK~~e~MFV~~~pg~RNPYENlLYKlCLSGeGWPYIgSR  316 (533)
T PF00843_consen  237 YNLSLSAAVKAGACLIDGGNMLETIKVTPSNFSTIIKAVLQVKNREGMFVSETPGQRNPYENLLYKLCLSGEGWPYIGSR  316 (533)
T ss_pred             CCCCHHHHHHCCCEEECCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCEEEC
T ss_conf             24117888750743751774167787255318999999998777418511799988780888799985078897643331


Q ss_pred             CEEEEEEECCEEEEECCCC-CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCEEEEE
Q ss_conf             4010011034068707888-877888888765545556556788889999999986138998657860478989647888
Q T0529           324 TSITGRAWENTVVDLESDG-KPQKADSNNSSKSLQSAGFTAGLTYSQLMTLKDAMLQLDPNAKTWMDIEGRPEDPVEIAL  402 (569)
Q Consensus       324 SqI~GRAWDNT~VDl~~~~-~p~~p~~~~~~~~~~~~~~~~~Lt~~qe~~ik~~m~~Ldp~~tTWiDIEG~p~DPVElAi  402 (569)
                      |||+|||||||+|||+.+| .++++|.+||+.+     ++++|+++||++||++|++|||++||||||||||+|||||||
T Consensus       317 SqI~GRAWDNT~VDl~~~~~~~~~~p~~ng~~~-----~l~~Lt~~qe~~vk~am~~Ldp~~ttWiDIEGpp~DPVElAi  391 (533)
T PF00843_consen  317 SQIKGRAWDNTTVDLSGKPDSGPPPPVRNGGNP-----RLSGLTESQEMQVKEAMEKLDPNATTWIDIEGPPNDPVELAI  391 (533)
T ss_pred             CCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCC-----CCCCCCHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCEEEEE
T ss_conf             544444457856847889998999865778997-----877889889999999997179899836826789999757888


Q ss_pred             EECCCCCEEEEEECCCCHHHHHCCCCCCCCCHHHHHHCCCCCHHHHHHHHCCCCCEEEECCHHHHHHHHHHCCCCCEEEE
Q ss_conf             70799867888507551002121264100111655402475368999974586648981382899999984499622678
Q T0529           403 YQPSSGCYIHFFREPTDLKQFKQDAKYSHGIDVTDLFATQPGLTSAVIDALPRNMVITCQGSDDIRKLLESQGRKDIKLI  482 (569)
Q Consensus       403 yQP~sg~YIHcyR~P~D~K~FK~~SKysHGillkDl~~aqPGL~S~vI~~LP~~MVlT~QGsDDIrkLld~hGRkDiKli  482 (569)
                      |||++|+||||||+|||+|||||||||||||||||||+|||||+||||++||+|||||||||||||||||||||||||+|
T Consensus       392 yQP~sg~YIHcyR~PhDeK~FK~~SKysHGillkDle~aqPGL~S~ii~~LP~~MVlT~QGsDD