Query         gi|254781077|ref|YP_003065490.1| hypothetical protein CLIBASIA_04895 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 111
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 23785
Date          Wed Jun  1 00:28:45 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781077.hhm -d /home/congqian_1/database/pdb/pdb70.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 3ecf_A NTF2-like protein; YP_3  37.9      12 0.00052   17.9   1.8   34   28-61     74-107 (130)
  2 1q8h_A Osteocalcin; helix-turn  35.0     7.2  0.0003   19.2   0.2   13   18-30      7-19  (49)
  3 1dsk_A VPR protein; viral pept  24.3      18 0.00075   17.0   0.7   24   72-95      1-28  (28)
  4 1s29_A LA protein; winged heli  18.3      16 0.00068   17.2  -0.5   40   55-109    21-60  (92)
  5 2voo_A Lupus LA protein; RNA-b  13.4      44  0.0019   14.7   0.7   45   49-109    16-61  (193)
  6 3koj_A Uncharacterized protein  13.2      51  0.0021   14.3   0.9   17   31-47      2-18  (108)
  7 1bde_A VPR protein; AIDS, HIV,  13.1      44  0.0019   14.7   0.6   21   71-91     10-34  (35)
  8 2c7h_A RBBP6, retinoblastoma-b  12.5      71   0.003   13.5   1.5   30   29-62      6-35  (86)
  9 2xi5_A RNA polymerase L, L-pro  12.4      73  0.0031   13.4   1.5   21    6-26     60-81  (184)
 10 1esx_A VPR protein; helix, amp  10.0      68  0.0029   13.6   0.7   24   72-95     59-86  (96)

No 1  
>3ecf_A NTF2-like protein; YP_324687.1, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; 1.90A {Anabaena variabilis atcc 29413} SCOP: d.17.4.21
Probab=37.88  E-value=12  Score=17.90  Aligned_cols=34  Identities=32%  Similarity=0.282  Sum_probs=24.9

Q ss_pred             CCCCEEEEEEEEEEEEEEEEEEEEECCCCCCCCC
Q ss_conf             5430000210000043554003312204561005
Q gi|254781077|r   28 EDSSLFYHFHSTLNLMTLHLPLRLQEEGISQSNL   61 (111)
Q Consensus        28 edsslfyhfhstlnlmtlhlplrlqeegisqsnl   61 (111)
                      ..|++|---...-.+.|+|--.|+.|||||----
T Consensus        74 rAS~v~q~rTTKG~ly~~~nfF~~DEeGis~iWP  107 (130)
T 3ecf_A           74 RASGVWQMRTTKGTLYTLHNFFRLDEEGIVYVWP  107 (130)
T ss_dssp             EEEEEEEEEETTSCEEEEEEEEEEETTEEEEEEC
T ss_pred             CCCCEEEEEECCCEEEEEEHHHEECCCCCEEEEE
T ss_conf             7643178874374189770011325267078874


No 2  
>1q8h_A Osteocalcin; helix-turn-helix-turn-helix, paper-CLIP, hydroxyapatite crystal surface binding protein, calcium binding protein, bone GLA protein; HET: CGU; 2.00A {Sus scrofa} SCOP: g.32.1.1 PDB: 1q3m_A*
Probab=34.98  E-value=7.2  Score=19.25  Aligned_cols=13  Identities=62%  Similarity=1.048  Sum_probs=10.6

Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             6774478876543
Q gi|254781077|r   18 NIPACYPDPLEDS   30 (111)
Q Consensus        18 nipacypdpleds   30 (111)
                      ..||-||||||..
T Consensus         7 G~papypdple~~   19 (49)
T 1q8h_A            7 GAPAPYPDPLEPR   19 (49)
T ss_dssp             ------CCTTHHH
T ss_pred             CCCCCCCCCCHHH
T ss_conf             8998999952023


No 3  
>1dsk_A VPR protein; viral peptide, polypeptide; NMR {Human immunodeficiency virus 1} SCOP: j.11.1.1
Probab=24.31  E-value=18  Score=16.97  Aligned_cols=24  Identities=54%  Similarity=0.714  Sum_probs=15.3

Q ss_pred             HHHHHHHHHHHC----CCCHHHHHHHHH
Q ss_conf             077899874100----000455566676
Q gi|254781077|r   72 AITPILQMLDLT----NCRHSRVNQWRQ   95 (111)
Q Consensus        72 aitpilqmldlt----ncrhsrvnqwrq   95 (111)
                      ||..|||-|-..    .|+|||..--||
T Consensus         1 AiirilQqllfiHfRigc~hSrIgi~~q   28 (28)
T 1dsk_A            1 AIIRILQQLLFIHFRIGCRHSRIGVTRQ   28 (28)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTTTGGGSCC
T ss_pred             CHHHHHHHHHHHHEECCCCCCCCCCCCC
T ss_conf             9889999998885020564142032469


No 4  
>1s29_A LA protein; winged helix-turn-helix, autoantigen, RNA-binding, RNA binding protein; 1.60A {Trypanosoma brucei} SCOP: a.4.5.46
Probab=18.32  E-value=16  Score=17.20  Aligned_cols=40  Identities=15%  Similarity=0.332  Sum_probs=27.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHEECC
Q ss_conf             4561005410013354007789987410000045556667686543223210004
Q gi|254781077|r   55 GISQSNLRTDHNVKQHVAITPILQMLDLTNCRHSRVNQWRQISNIIGYKKIKRIN  109 (111)
Q Consensus        55 gisqsnlrtdhnvkqhvaitpilqmldltncrhsrvnqwrqisniigykkikrin  109 (111)
                      -.|.+||+.|.-..+++.-               .-..|-.|+.|..++|+|.+.
T Consensus        21 YFSd~NL~~D~fLr~~~~~---------------~~~g~Vpl~~i~~F~r~k~l~   60 (92)
T 1s29_A           21 YFSDVNVQRDIFLKGKMAE---------------NAEGFVSLETLLTFKRVNSVT   60 (92)
T ss_dssp             HTSHHHHTTCHHHHHHHTT---------------STTCCEEHHHHTTSHHHHTTC
T ss_pred             HCCHHHHCCCHHHHHHHHC---------------CCCCCEEHHHHHCCCCHHHHC
T ss_conf             7367441328999999836---------------689869659986784788874


No 5  
>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A
Probab=13.45  E-value=44  Score=14.68  Aligned_cols=45  Identities=20%  Similarity=0.371  Sum_probs=25.6

Q ss_pred             EEEECC-CCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHEECC
Q ss_conf             331220-4561005410013354007789987410000045556667686543223210004
Q gi|254781077|r   49 LRLQEE-GISQSNLRTDHNVKQHVAITPILQMLDLTNCRHSRVNQWRQISNIIGYKKIKRIN  109 (111)
Q Consensus        49 lrlqee-gisqsnlrtdhnvkqhvaitpilqmldltncrhsrvnqwrqisniigykkikrin  109 (111)
                      ++-|-| =.|.+||++|.-.+.++.                +-..|-.|+-|..++++|...
T Consensus        16 i~~QvEfYFSd~NL~~D~fL~~~~~----------------~~~g~V~i~~i~~F~r~k~l~   61 (193)
T 2voo_A           16 ICHQIEYYFGDFNLPRDKFLKEQIK----------------LDEGWVPLEIMIKFNRLNRLT   61 (193)
T ss_dssp             HHHHHHHHTSTTTGGGCHHHHHHHH----------------HTTTCEEHHHHTTSHHHHHHC
T ss_pred             HHHHHHHHCCCCCCCCCHHHHHHHC----------------CCCCCEEHHHHHHHHHHHHHC
T ss_conf             9998786357541223889999844----------------689958599999789999747


No 6  
>3koj_A Uncharacterized protein YCF41; single-strand binding protein family, PF00436, SNR59A, NESG, structural genomics, PSI-2; 1.90A {Synechococcus elongatus pcc 6301}
Probab=13.17  E-value=51  Score=14.32  Aligned_cols=17  Identities=29%  Similarity=0.335  Sum_probs=13.8

Q ss_pred             CEEEEEEEEEEEEEEEE
Q ss_conf             00002100000435540
Q gi|254781077|r   31 SLFYHFHSTLNLMTLHL   47 (111)
Q Consensus        31 slfyhfhstlnlmtlhl   47 (111)
                      .+|-||||.+|-.+|.-
T Consensus         2 ~~~~~~~s~MN~v~l~G   18 (108)
T 3koj_A            2 GHHHHHHSHMNSCILQA   18 (108)
T ss_dssp             -----CCSSCEEEEEEE
T ss_pred             CCCCCCHHHCCEEEEEE
T ss_conf             84445631279999999


No 7  
>1bde_A VPR protein; AIDS, HIV, viral protein, VPR fragment, helix; NMR {Synthetic} SCOP: j.11.1.1 PDB: 1dsj_A
Probab=13.12  E-value=44  Score=14.69  Aligned_cols=21  Identities=52%  Similarity=0.748  Sum_probs=14.2

Q ss_pred             HHHHHHHHHHHHC----CCCHHHHH
Q ss_conf             0077899874100----00045556
Q gi|254781077|r   71 VAITPILQMLDLT----NCRHSRVN   91 (111)
Q Consensus        71 vaitpilqmldlt----ncrhsrvn   91 (111)
                      -||.-|||-+-.+    .|+|||..
T Consensus        10 eaiiriLQqlLFiHFRiGC~hSRIG   34 (35)
T 1bde_A           10 EAIIRILQQLLFIHFRIGCRHSRIG   34 (35)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSCCC
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9999999999999986367626578


No 8  
>2c7h_A RBBP6, retinoblastoma-binding protein 6, isoform 3; P53-associated, mRNA processing, splicing-associated, oesophageal cancer; NMR {Homo sapiens}
Probab=12.54  E-value=71  Score=13.48  Aligned_cols=30  Identities=33%  Similarity=0.414  Sum_probs=20.7

Q ss_pred             CCCEEEEEEEEEEEEEEEEEEEEECCCCCCCCCC
Q ss_conf             4300002100000435540033122045610054
Q gi|254781077|r   29 DSSLFYHFHSTLNLMTLHLPLRLQEEGISQSNLR   62 (111)
Q Consensus        29 dsslfyhfhstlnlmtlhlplrlqeegisqsnlr   62 (111)
                      -|+.||.|.|..+.-++..+    ..+||-+.|.
T Consensus         6 mSsV~YKFkS~k~~~~I~fd----G~~Isv~dLK   35 (86)
T 2c7h_A            6 MSCVHYKFSSKLNYDTVTFD----GLHISLCDLK   35 (86)
T ss_dssp             BEEEEEEETTCSSEEEEEES----SSEEEHHHHH
T ss_pred             EEEEEEEECCCCCCCEEEEC----CCEEEHHHHH
T ss_conf             50699997136876268875----9888899999


No 9  
>2xi5_A RNA polymerase L, L-protein; transferase, bunyaviridae, orthobunyavirus, aedes triseriatu hydrolase; 2.20A {Bunyavirus la crosse} PDB: 2xi7_A*
Probab=12.38  E-value=73  Score=13.43  Aligned_cols=21  Identities=19%  Similarity=0.381  Sum_probs=14.1

Q ss_pred             HHHHHHHC-CCCCCCCCCCCCC
Q ss_conf             58888732-7666677447887
Q gi|254781077|r    6 CLSVISSM-GINYNIPACYPDP   26 (111)
Q Consensus         6 clsvissm-ginynipacypdp   26 (111)
                      ||.+.... ..||+||-|-||-
T Consensus        60 iLd~~P~~~~~~~~ip~~TPDN   81 (184)
T 2xi5_A           60 ILDIRPEVDPLTIDAPHITPDN   81 (184)
T ss_dssp             HHHHSTTSCTTTCCCCCCCCSE
T ss_pred             HHHHCCCCCCCCCCCCCCCCCC
T ss_conf             8664489883225488758875


No 10 
>1esx_A VPR protein; helix, amphipatic, turn, viral protein; NMR {Synthetic} SCOP: j.11.1.1 PDB: 1m8l_A 1vpc_A 1x9v_A
Probab=10.02  E-value=68  Score=13.59  Aligned_cols=24  Identities=46%  Similarity=0.671  Sum_probs=16.8

Q ss_pred             HHHHHHHHHHHC----CCCHHHHHHHHH
Q ss_conf             077899874100----000455566676
Q gi|254781077|r   72 AITPILQMLDLT----NCRHSRVNQWRQ   95 (111)
Q Consensus        72 aitpilqmldlt----ncrhsrvnqwrq   95 (111)
                      ||.-|||-+-..    .|+|||...-+|
T Consensus        59 a~IriLQq~LFiHfR~GC~hSRIGi~~~   86 (96)
T 1esx_A           59 ALIRILQQLLFIHFRIGCRHSRIGIIQQ   86 (96)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTTTSS
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             9999999999999884797553267755


Done!