Query         T0602 3NKZ, Yersinia enterocolitica, 123 residues
Match_columns 123
No_of_seqs    89 out of 91
Neff          5.6 
Searched_HMMs 11830
Date          Mon Jul  5 08:59:14 2010
Command       /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0602.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0602.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PF05400 FliT:  Flagellar prote 100.0 6.8E-35 5.8E-39  230.8   9.6  109    4-112     1-109 (109)
  2 PF05130 FlgN:  FlgN protein;    89.0    0.53 4.5E-05   23.9   6.4  104    8-111    11-137 (143)
  3 PF12535 Nudix_N:  Hydrolase of  59.4     4.7  0.0004   18.1   4.0   32    8-39     25-56  (58)
  4 PF07439 DUF1515:  Protein of u  26.8      16  0.0014   14.8   5.1   38   63-100    16-53  (112)
  5 PF04844 DUF623:  Protein of un  24.5      18  0.0015   14.6   4.0   35   12-46      3-37  (59)
  6 PF10488 PP1c_bdg:  Phosphatase  19.5      23  0.0019   13.9   4.2   43   26-69    263-305 (307)
  7 PF05633 DUF793:  Protein of un  18.0      24  0.0021   13.7   7.3   73    8-81    311-385 (389)
  8 PF08332 CaMKII_AD:  Calcium/ca  17.5      25  0.0021   13.7   3.7   25   15-39      3-27  (128)
  9 PF06884 DUF1264:  Protein of u  17.0      24   0.002   13.8   1.6   21  103-123   104-131 (171)
 10 PF05731 TROVE:  TROVE domain;   15.7      28  0.0023   13.4   3.0   59   30-93    283-341 (385)

No 1  
>PF05400 FliT:  Flagellar protein FliT;  InterPro: IPR008622 This family contains several bacterial flagellar FliT proteins. The flagellar proteins FlgN and FliT have been proposed to act as substrate specific export chaperones, facilitating incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum. In Salmonella typhimurium flgN and fliT mutants, the export of target HAPs is reduced, concomitant with loss of unincorporated flagellin into the surrounding medium .; GO: 0019861 flagellum; PDB: 3h3m_B.
Probab=100.00  E-value=6.8e-35  Score=230.82  Aligned_cols=109  Identities=50%  Similarity=0.718  Sum_probs=108.1

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             66417899999999999999999886238189999999999999998730588999988899999999999864899999
Q T0602             4 MERHQHLLSEYQQILTLSEQMLVLATEGNWDALVDLEMTYLKAVESTANITISSCSSLMLQDLLREKLRAILDNEIEIKR   83 (123)
Q Consensus         4 M~~~~~ll~~Yq~il~lS~~ML~lA~~gdWD~Lv~lE~~y~~~Ve~l~~~~~~~~l~~~~q~~~~~lL~~IL~ndaeIr~   83 (123)
                      |+++.++|+.|++|+++|++||++|++||||+|+++|.+|+.+|+.++..+++++++++++++++++|++||+||++||+
T Consensus         1 M~~~~~ll~~y~~i~~lS~~ML~aA~~gdWd~l~~lE~~y~~~ve~l~~~~~~~~l~~~~~~~~~~lL~~IL~nDaeIr~   80 (109)
T PF05400_consen    1 MNNSQELLARYEAILALSEQMLEAARAGDWDELVELEREYLQLVEQLREAEPPPPLSPAEQERKRELLRRILANDAEIRD   80 (109)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHHHTT-HHHHHH---HHHHHHHHHHHH-------TTT---HHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98567899999999999999999987787777999999999999999746899999999999999999999976999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999999999998535567898766424
Q T0602            84 LLQLRLDRLSDLVGQSTKQQAVNNTYGQF  112 (123)
Q Consensus        84 Llq~rldeL~~li~q~~~q~~l~~aYgqf  112 (123)
                      |++|||++|+.+|+++++++++|+|||+|
T Consensus        81 L~~~rl~~L~~li~~~~~q~~l~~aYg~f  109 (109)
T PF05400_consen   81 LLQPRLDELSQLIGQSRRQRSLNNAYGQF  109 (109)
T ss_dssp             HHHHHHHHHHHH-----------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             98999999999999878889999866779


No 2  
>PF05130 FlgN:  FlgN protein;  InterPro: IPR007809 This family includes the FlgN protein, an export chaperone involved in flagellar synthesis .; GO: 0009296 flagellum biogenesis, 0019861 flagellum; PDB: 2fup_A.
Probab=89.04  E-value=0.53  Score=23.87  Aligned_cols=104  Identities=21%  Similarity=0.230  Sum_probs=69.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCC---------C-----------CCH---HHH
Q ss_conf             78999999999999999998862381899999999999999987305889---------9-----------998---889
Q T0602             8 QHLLSEYQQILTLSEQMLVLATEGNWDALVDLEMTYLKAVESTANITISS---------C-----------SSL---MLQ   64 (123)
Q Consensus         8 ~~ll~~Yq~il~lS~~ML~lA~~gdWD~Lv~lE~~y~~~Ve~l~~~~~~~---------~-----------l~~---~~q   64 (123)
                      ......|+.+..+..+-..+-..+|++.|.++-..--.+++.+......-         .           ..+   ...
T Consensus        11 ~~~~~~~~~L~~ll~~e~~~l~~~d~~~L~~l~~~k~~l~~~l~~~~~~r~~~~~~~~~~~~~~~l~~l~~~~~~l~~~~   90 (143)
T PF05130_consen   11 EEEIELLQELLELLEQEREALIARDIDELEELTEKKQELLEQLERLEKKRRQLLEALGQQPSEASLSELLEEDEELQALW   90 (143)
T ss_dssp             HHH---HHHHHHHHHHHHHHHHTT--HHHHHH---HHHHHHHHHH---HHHHHHHH----SS----HHHHT---HHHH--
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCHHHHHHH
T ss_conf             99999999999999999999980999999999999999999999999999999998346446216999986449999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998648999999999999999999853556789876642
Q T0602            65 DLLREKLRAILDNEIEIKRLLQLRLDRLSDLVGQSTKQQAVNNTYGQ  111 (123)
Q Consensus        65 ~~~~~lL~~IL~ndaeIr~Llq~rldeL~~li~q~~~q~~l~~aYgq  111 (123)
                      ..+..++.+|-.-...-..+++..++..+..+........-+.+||.
T Consensus        91 ~~l~~~~~~~~~~n~~N~~ll~~~~~~~~~~l~~l~~~~~~~~tY~~  137 (143)
T PF05130_consen   91 DELRELLEELQELNERNGKLLEAALEFIQELLNILRQAADASKTYGA  137 (143)
T ss_dssp             -----HHHHHHHHHHH-------TTT----HHHHH------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf             99999999999999999999999999999999998625777688297


No 3  
>PF12535 Nudix_N:  Hydrolase of X-linked nucleoside diphosphate N terminal 
Probab=59.38  E-value=4.7  Score=18.09  Aligned_cols=32  Identities=16%  Similarity=0.210  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf             78999999999999999998862381899999
Q T0602             8 QHLLSEYQQILTLSEQMLVLATEGNWDALVDL   39 (123)
Q Consensus         8 ~~ll~~Yq~il~lS~~ML~lA~~gdWD~Lv~l   39 (123)
                      ..=...|++|..+|.+|++..-.-+++.+-++
T Consensus        25 ~yD~eRye~Lr~ia~emla~~s~~~~e~v~~l   56 (58)
T PF12535_consen   25 VYDRERYEELREIAAEMLAQYSDLPVEKVKDL   56 (58)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf             61399999999999999997519999999987


No 4  
>PF07439 DUF1515:  Protein of unknown function (DUF1515);  InterPro: IPR010889   This family consists of several hypothetical bacterial proteins of around 130 residues in length. Members of this family seem to be found exclusively in Rhizobium species. The function of this family is unknown.
Probab=26.75  E-value=16  Score=14.82  Aligned_cols=38  Identities=21%  Similarity=0.207  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             89999999999986489999999999999999998535
Q T0602            63 LQDLLREKLRAILDNEIEIKRLLQLRLDRLSDLVGQST  100 (123)
Q Consensus        63 ~q~~~~~lL~~IL~ndaeIr~Llq~rldeL~~li~q~~  100 (123)
                      +-+..|+-|++-.+--+..|.-.-.|+|+|.+.++..-
T Consensus        16 ei~~~Redik~SEdRsd~sR~~M~~R~DELverV~tLE   53 (112)
T PF07439_consen   16 EIKELREDIKRSEDRSDASRASMHRRIDELVERVHTLE   53 (112)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999998788764000888753899999999999


No 5  
>PF04844 DUF623:  Protein of unknown function, DUF623;  InterPro: IPR006458    This group of sequences contain an uncharacterised domain of about 70 residues found exclusively in plants, generally toward the C terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana. Other regions of these proteins tend to consist largely of low-complexity sequence. Function is not known. 
Probab=24.51  E-value=18  Score=14.56  Aligned_cols=35  Identities=23%  Similarity=0.372  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH
Q ss_conf             99999999999999988623818999999999999
Q T0602            12 SEYQQILTLSEQMLVLATEGNWDALVDLEMTYLKA   46 (123)
Q Consensus        12 ~~Yq~il~lS~~ML~lA~~gdWD~Lv~lE~~y~~~   46 (123)
                      +.|..--.--.+|...-.-.+|+.|-+|-..|+.+
T Consensus         3 DPy~DFR~SM~EMI~~~~i~~~~~LeeLL~cYL~L   37 (59)
T PF04844_consen    3 DPYEDFRRSMVEMIEENGIRDWDDLEELLACYLSL   37 (59)
T ss_pred             CHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHC
T ss_conf             67899999999999985778999999999999870


No 6  
>PF10488 PP1c_bdg:  Phosphatase-1 catalytic subunit binding region
Probab=19.49  E-value=23  Score=13.94  Aligned_cols=43  Identities=14%  Similarity=0.336  Sum_probs=32.7

Q ss_pred             HHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH
Q ss_conf             98862381899999999999999987305889999888999999
Q T0602            26 VLATEGNWDALVDLEMTYLKAVESTANITISSCSSLMLQDLLRE   69 (123)
Q Consensus        26 ~lA~~gdWD~Lv~lE~~y~~~Ve~l~~~~~~~~l~~~~q~~~~~   69 (123)
                      .+||.|.|+.+..=-.++..-|..+... ....+++.-+++...
T Consensus       263 RaARKG~Weq~ArDR~RFqrRI~~~E~~-L~~~Lsp~HR~kv~~  305 (307)
T PF10488_consen  263 RAARKGPWEQMARDRDRFQRRIAETEPV-LGPCLSPEHREKVYA  305 (307)
T ss_pred             HHHHCCHHHHHHHHHHHHHHHHHHHHHH-HHHHCCHHHHHHHHH
T ss_conf             7763371999887699999999999998-875159999999986


No 7  
>PF05633 DUF793:  Protein of unknown function (DUF793);  InterPro: IPR008511 This family consists of several plant proteins of unknown function.
Probab=18.03  E-value=24  Score=13.73  Aligned_cols=73  Identities=22%  Similarity=0.186  Sum_probs=46.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCC--CCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             789999999999999999988623818999999999999999873058--89999888999999999998648999
Q T0602             8 QHLLSEYQQILTLSEQMLVLATEGNWDALVDLEMTYLKAVESTANITI--SSCSSLMLQDLLREKLRAILDNEIEI   81 (123)
Q Consensus         8 ~~ll~~Yq~il~lS~~ML~lA~~gdWD~Lv~lE~~y~~~Ve~l~~~~~--~~~l~~~~q~~~~~lL~~IL~ndaeI   81 (123)
                      ..+|..++++-+..+.+-+++....-+.--+.+.+-...|+.|...-.  ..++. +...+.+++.++|+.-=.++
T Consensus       311 ~gLLkEL~~vea~vr~L~elid~~~fp~~~Ek~eEvr~~V~EL~~~~e~L~~GLd-pLe~QVrEvFh~IV~sR~el  385 (389)
T PF05633_consen  311 CGLLKELDQVEACVRRLHELIDGFQFPLEEEKEEEVREAVEELAEVCERLSEGLD-PLERQVREVFHRIVRSRTEL  385 (389)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHH
T ss_conf             7799999999999999999997056886265899999999999999999972006-89999999999999989988


No 8  
>PF08332 CaMKII_AD:  Calcium/calmodulin dependent protein kinase II Association;  InterPro: IPR013543   Protein kinases are a group of enzymes that possess a catalytic subunit which transfers the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. The enzymes fall into two broad classes, characterised with respect to substrate specificity: serine/threonine specific and tyrosine specific .   Protein kinase function has been evolutionarily conserved from Escherichia coli to Homo sapiens. Protein kinases play a role in a mulititude of cellular processes, including division, proliferation, apoptosis, and differentiation . Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins.   The catalytic subunits of protein kinases are highly conserved, and several structures have been solved , leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases .   This domain is found at the C terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (IPR000719 from INTERPRO) at their N terminus . The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers . ; PDB: 2ux0_D 2w2c_L 1hkx_M 2f86_B 3h51_A 3f7s_A.
Probab=17.48  E-value=25  Score=13.66  Aligned_cols=25  Identities=28%  Similarity=0.320  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf             9999999999998862381899999
Q T0602            15 QQILTLSEQMLVLATEGNWDALVDL   39 (123)
Q Consensus        15 q~il~lS~~ML~lA~~gdWD~Lv~l   39 (123)
                      ++|..+.++...+-..||+|.+.++
T Consensus         3 ~eI~~l~~~~~~A~~~~D~~~~~~l   27 (128)
T PF08332_consen    3 QEIRALFDAWNEALATGDIDAVMAL   27 (128)
T ss_dssp             HHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf             8999999999999980899999975


No 9  
>PF06884 DUF1264:  Protein of unknown function (DUF1264);  InterPro: IPR010686   This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 200 residues long. Some family members are annotated as putative lipoproteins.
Probab=17.02  E-value=24  Score=13.80  Aligned_cols=21  Identities=33%  Similarity=0.536  Sum_probs=16.3

Q ss_pred             HHHHHHHHHC-------CCCCCCCCCCC
Q ss_conf             7898766424-------79844789899
Q T0602           103 QAVNNTYGQF-------PDHALLLGETQ  123 (123)
Q Consensus       103 ~~l~~aYgqf-------~~~~l~~~~~~  123 (123)
                      +.+.++||+|       .|+.|=.|.||
T Consensus       104 ~~~~~tYGKtwH~WqvDrgd~LPLG~P~  131 (171)
T PF06884_consen  104 EDLAKTYGKTWHTWQVDRGDKLPLGPPQ  131 (171)
T ss_pred             HHHHHHHCCEEEECCCCCCCCCCCCCHH
T ss_conf             9999750871680406999978898303


No 10 
>PF05731 TROVE:  TROVE domain;  InterPro: IPR008858   The TROVE (Telomerase, Ro and Vault) domain is a module of ~300-500 residues that is found in TEP1 and Ro60 the protein components of three ribonucleoprotein particles. The TROVE domain is also found in bacterial ribonucleoproteins suggesting an ancient origin of these ribonucleoproteins. The TROVE domain can be found associated with other domains, such as the VWFA domain, the TEP1 N-terminal domain, the NACHT-NTPase domain, and WD-40 repeats. The TROVE domain may be involved in binding the RNA components of the three RNPs, which are telomerase RNA, Y RNA and vault RNA .   The TROVE domain contains a few absolutely conserved residues. As none of these conserved residues are the polar type of amino acids found in active sites, it seems unlikely that this region has an enzymatic function .; GO: 0003723 RNA binding, 0030529 ribonucleoprotein complex; PDB: 1yvp_B 2i91_B 1yvr_A 2nvo_A.
Probab=15.69  E-value=28  Score=13.38  Aligned_cols=59  Identities=20%  Similarity=0.318  Sum_probs=34.5

Q ss_pred             HCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2381899999999999999987305889999888999999999998648999999999999999
Q T0602            30 EGNWDALVDLEMTYLKAVESTANITISSCSSLMLQDLLREKLRAILDNEIEIKRLLQLRLDRLS   93 (123)
Q Consensus        30 ~gdWD~Lv~lE~~y~~~Ve~l~~~~~~~~l~~~~q~~~~~lL~~IL~ndaeIr~Llq~rldeL~   93 (123)
                      ..-|+.|+...+.|..++.+|..+...- .....-.    .+-..|.|+.+|+.==+-=+.-|+
T Consensus       283 ~~~We~Li~~~mp~~AllRNL~nl~~~g-v~~~~~~----~V~~rL~d~~~v~~sr~~P~~~l~  341 (385)
T PF05731_consen  283 KEVWEALIPSKMPYMALLRNLRNLLRAG-VSDEAHE----RVAARLSDPEAVRKSRQHPFRFLS  341 (385)
T ss_dssp             HHHHHHHHTT---HHHHHHC---TTTTT-TT-TT-H----HHHHHHT-HHHHHHTT--HHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHCC-CCHHHHH----HHHHHHCCHHHHHHHCCCHHHHHH
T ss_conf             9999999986288999999898898869-9856799----999984899999983339699999


Done!