Query         gi|254780908|ref|YP_003065321.1| hypothetical protein CLIBASIA_04035 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 35
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 30 03:02:59 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780908.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG4099 Predicted peptidase [G  14.4   1E+02  0.0026   15.1   1.6   30    2-31    193-222 (387)
  2 TIGR02248 mutH_TIGR DNA mismat   8.8 1.7E+02  0.0044   14.1   1.3   26    6-31     55-86  (220)
  3 TIGR01925 spIIAB anti-sigma F    8.3 1.9E+02  0.0047   13.9   1.3   15    1-15      5-19  (137)
  4 COG3870 Uncharacterized protei   7.4 2.5E+02  0.0065   13.3   2.2   33    1-33      1-42  (109)
  5 PRK06293 single-stranded DNA-b   7.3 2.4E+02   0.006   13.4   1.4   20    1-20      1-20  (161)
  6 TIGR00570 cdk7 CDK-activating    6.1 1.2E+02  0.0031   14.7  -0.6   26    3-35     43-68  (322)
  7 KOG0869 consensus                5.9      74  0.0019   15.8  -1.7   15   16-30     30-44  (168)
  8 KOG3321 consensus                5.9 1.9E+02  0.0047   13.9   0.3   19   10-28     16-34  (175)
  9 KOG0808 consensus                4.9 3.5E+02  0.0088   12.7   1.2   16   16-31    181-196 (387)
 10 COG3420 NosD Nitrous oxidase a   4.6      84  0.0021   15.5  -2.2   35    1-35      4-49  (408)

No 1  
>COG4099 Predicted peptidase [General function prediction only]
Probab=14.38  E-value=1e+02  Score=15.10  Aligned_cols=30  Identities=27%  Similarity=0.376  Sum_probs=25.2

Q ss_pred             EEEEEECCCCCCCEEEEEEECCCCEEEECC
Q ss_conf             699984588552012332212553034215
Q gi|254780908|r    2 MLLFLAGSDAESQEMRAVPIANTGAILEKS   31 (35)
Q Consensus         2 mllflagsdaesqemravpiantgaileks   31 (35)
                      ..|||.|+++.+..-+++-..+-|||.+-+
T Consensus       193 LvlfLHgagq~g~dn~~~l~sg~gaiawa~  222 (387)
T COG4099         193 LVLFLHGAGQGGSDNDKVLSSGIGAIAWAG  222 (387)
T ss_pred             EEEEEECCCCCCCHHHHHHHCCCCCEEEEC
T ss_conf             799994488777415666635865135615


No 2  
>TIGR02248 mutH_TIGR DNA mismatch repair endonuclease MutH; InterPro: IPR004230 MutS, MutL and MutH are the three essential proteins for initiation of methyl-directed DNA mismatch repair to correct mistakes made during DNA replication in Escherichia coli. MutH cleaves a newly synthesized and unmethylated daughter strand 5' to the sequence d(GATC) in a hemi-methylated duplex. Activation of MutH requires the recognition of a DNA mismatch by MutS and MutL .; GO: 0004519 endonuclease activity, 0006304 DNA modification.
Probab=8.81  E-value=1.7e+02  Score=14.06  Aligned_cols=26  Identities=38%  Similarity=0.675  Sum_probs=20.7

Q ss_pred             EECCCCCC------CEEEEEEECCCCEEEECC
Q ss_conf             84588552------012332212553034215
Q gi|254780908|r    6 LAGSDAES------QEMRAVPIANTGAILEKS   31 (35)
Q Consensus         6 lagsdaes------qemravpiantgaileks   31 (35)
                      |.||-+|-      -|....||.+.|-=||..
T Consensus        55 LHGsK~EqDF~~LGvELKtiPi~s~G~PLEtT   86 (220)
T TIGR02248        55 LHGSKPEQDFAHLGVELKTIPINSSGYPLETT   86 (220)
T ss_pred             ECCCCCCCCHHHCCEEEEECCCCCCCCCCCCC
T ss_conf             21677322624517362202418877874763


No 3  
>TIGR01925 spIIAB anti-sigma F factor; InterPro: IPR010194   This entry describes the SpoIIAB anti-sigma F factor. Sigma F regulates spore development in B subtilis. SpoIIAB binds to sigma F, preventing formation of the transcription complex at the promoter . SpoIIAA (anti-anti-sigma F factor) binds to SpoIIAB to inhibit association with sigma F, however SpoIIAB can phosphorylate SpoIIAA, causing disassociation of the SpoIIAA/B complex . The SpoIIE phosphatase dephosphorylates SpoIIAA.; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0016989 sigma factor antagonist activity, 0006468 protein amino acid phosphorylation, 0030435 sporulation, 0045892 negative regulation of transcription DNA-dependent.
Probab=8.25  E-value=1.9e+02  Score=13.92  Aligned_cols=15  Identities=53%  Similarity=0.525  Sum_probs=11.3

Q ss_pred             CEEEEEECCCCCCCE
Q ss_conf             969998458855201
Q gi|254780908|r    1 MMLLFLAGSDAESQE   15 (35)
Q Consensus         1 mmllflagsdaesqe   15 (35)
                      |-|-|+|-|.-||--
T Consensus         5 M~L~F~A~S~NEsFA   19 (137)
T TIGR01925         5 MELEFLAKSENESFA   19 (137)
T ss_pred             EEEEEEEECCCCCCH
T ss_conf             013353101676401


No 4  
>COG3870 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=7.39  E-value=2.5e+02  Score=13.28  Aligned_cols=33  Identities=30%  Similarity=0.477  Sum_probs=22.2

Q ss_pred             CEEEEEECCCCCCC---------EEEEEEECCCCEEEECCCE
Q ss_conf             96999845885520---------1233221255303421541
Q gi|254780908|r    1 MMLLFLAGSDAESQ---------EMRAVPIANTGAILEKSNF   33 (35)
Q Consensus         1 mmllflagsdaesq---------emravpiantgaileksnf   33 (35)
                      |-|++---.|..|+         ..|+...|.||..|.+.|-
T Consensus         1 MKLiiaivqd~da~~l~~~L~d~~fraTkLAsTGGFlkaGNT   42 (109)
T COG3870           1 MKLIIAIVQDQDANELEDALTDKNFRATKLASTGGFLKAGNT   42 (109)
T ss_pred             CEEEEEEEECCCHHHHHHHHHHCCCEEEEEECCCCEEECCCE
T ss_conf             906999973533789999998678406886425760224975


No 5  
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=7.30  E-value=2.4e+02  Score=13.43  Aligned_cols=20  Identities=30%  Similarity=0.388  Sum_probs=16.4

Q ss_pred             CEEEEEECCCCCCCEEEEEE
Q ss_conf             96999845885520123322
Q gi|254780908|r    1 MMLLFLAGSDAESQEMRAVP   20 (35)
Q Consensus         1 mmllflagsdaesqemravp   20 (35)
                      ||.-||.|--...-|+|-.|
T Consensus         1 ~~~~~LvGrLt~DPElR~T~   20 (161)
T PRK06293          1 MMFGYFAGYLGADPEERMTS   20 (161)
T ss_pred             CCCEEEEEECCCCCCEEECC
T ss_conf             91045456146687244889


No 6  
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1; InterPro: IPR004575   MAT1 (menage a trois 1) is a RING finger protein with a characteristic C3HC4 motif located in the N-terminal domain. MAT1 stabilises the cyclin H-CDK7 complex to form a functional CDK-activating kinase (CAK) enzymatic complex which then goes on to activate many of the CDK enzymes intimately involved in the cell cycle . CDK7 forms a stable complex with cyclin H and MAT1 in vivo only when phosphorylated on either one of two residues (Ser164 or Thr170) in its T-loop. The requirement for MAT1 for the activation of CAK can be by-passed by the phosphorylation of CDK7 on the T-loop. The two mechanisms for CDK7 complex stabilisation and activation (MAT1 addition and T-loop phosphorylation), which can operate independently in vitro, actually cooperate under physiological conditions to maintain complex integrity. With prolonged exposure to elevated temperature, dissociation to monomeric subunits occurs in vivo when CDK7 is dephosphorylated, even in the presence of MAT1 .    The Cyclin H-MAT1-CDK7 complex also forms part of TFIIH, a multiprotein complex required for both transcription and DNA repair.; GO: 0007049 cell cycle, 0005634 nucleus.
Probab=6.06  E-value=1.2e+02  Score=14.74  Aligned_cols=26  Identities=42%  Similarity=0.660  Sum_probs=17.2

Q ss_pred             EEEEECCCCCCCEEEEEEECCCCEEEECCCEEC
Q ss_conf             999845885520123322125530342154109
Q gi|254780908|r    3 LLFLAGSDAESQEMRAVPIANTGAILEKSNFIV   35 (35)
Q Consensus         3 llflagsdaesqemravpiantgaileksnfiv   35 (35)
                      +||+-||.+       -|...-+.+|-|+||-|
T Consensus        43 lLF~~Gsg~-------CPyk~C~~pLRkn~Frv   68 (322)
T TIGR00570        43 LLFVRGSGS-------CPYKECDTPLRKNNFRV   68 (322)
T ss_pred             HHHHCCCCC-------CCCCCCCCCCCCCCCCE
T ss_conf             887348888-------88546787443456502


No 7  
>KOG0869 consensus
Probab=5.95  E-value=74  Score=15.77  Aligned_cols=15  Identities=47%  Similarity=0.667  Sum_probs=11.6

Q ss_pred             EEEEEECCCCEEEEC
Q ss_conf             233221255303421
Q gi|254780908|r   16 MRAVPIANTGAILEK   30 (35)
Q Consensus        16 mravpiantgailek   30 (35)
                      -|-.||||.+-|..|
T Consensus        30 Dr~LPIANV~RIMK~   44 (168)
T KOG0869          30 DRFLPIANVSRIMKK   44 (168)
T ss_pred             HHHCCHHHHHHHHHH
T ss_conf             000137789999874


No 8  
>KOG3321 consensus
Probab=5.92  E-value=1.9e+02  Score=13.91  Aligned_cols=19  Identities=42%  Similarity=0.721  Sum_probs=14.7

Q ss_pred             CCCCCEEEEEEECCCCEEE
Q ss_conf             8552012332212553034
Q gi|254780908|r   10 DAESQEMRAVPIANTGAIL   28 (35)
Q Consensus        10 daesqemravpiantgail   28 (35)
                      ..+||-||.+|..|+.+..
T Consensus        16 ~~~s~~~r~l~~vNv~a~~   34 (175)
T KOG3321          16 NSESQSMRQLPFVNVAAVY   34 (175)
T ss_pred             CCCCCCCCCCCCCCCCCCC
T ss_conf             4557664426764423000


No 9  
>KOG0808 consensus
Probab=4.93  E-value=3.5e+02  Score=12.67  Aligned_cols=16  Identities=38%  Similarity=0.530  Sum_probs=12.7

Q ss_pred             EEEEEECCCCEEEECC
Q ss_conf             2332212553034215
Q gi|254780908|r   16 MRAVPIANTGAILEKS   31 (35)
Q Consensus        16 mravpiantgaileks   31 (35)
                      -.||-|.|+|+++.|+
T Consensus       181 ntavvisn~g~vigk~  196 (387)
T KOG0808         181 NTAVVISNNGNVIGKH  196 (387)
T ss_pred             EEEEEECCCCCEECCC
T ss_conf             4469982687533321


No 10 
>COG3420 NosD Nitrous oxidase accessory protein [Inorganic ion transport and metabolism]
Probab=4.60  E-value=84  Score=15.49  Aligned_cols=35  Identities=37%  Similarity=0.482  Sum_probs=0.0

Q ss_pred             CEEEEEECCCCCCCEEEEEEEC------CCCEEEECC-----CEEC
Q ss_conf             9699984588552012332212------553034215-----4109
Q gi|254780908|r    1 MMLLFLAGSDAESQEMRAVPIA------NTGAILEKS-----NFIV   35 (35)
Q Consensus         1 mmllflagsdaesqemravpia------ntgaileks-----nfiv   35 (35)
                      +|+|+|+|--|-+|.-+.-++.      ..|..++-+     ||++
T Consensus         4 ~~~llla~l~a~~qaa~v~v~dg~plqa~pgd~~~i~g~~~g~~vI   49 (408)
T COG3420           4 RMLLLLAGLAAGAQAATVRVIDGLPLQAKPGDYYGISGRYAGNFVI   49 (408)
T ss_pred             HHHHHHHHHHHHHHHCEEEECCCCCCCCCCCCEEEEEEEECCCEEE
T ss_conf             5689999997443012477315873325899589996652264797


Done!