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!