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!