Query gi|254781001|ref|YP_003065414.1| hypothetical protein CLIBASIA_04510 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 93 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Mon May 30 03:09:59 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781001.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK12862 malic enzyme; Reviewe 32.4 35 0.00089 16.8 2.2 59 22-80 383-453 (761) 2 KOG4268 consensus 27.8 47 0.0012 16.1 2.3 14 4-17 95-108 (189) 3 cd01453 vWA_transcription_fact 22.3 52 0.0013 15.9 1.7 85 4-90 84-178 (183) 4 PRK07232 malic enzyme; Reviewe 21.8 71 0.0018 15.2 2.2 59 22-80 377-447 (753) 5 pfam11355 DUF3157 Protein of u 17.6 44 0.0011 16.3 0.4 16 28-43 147-162 (199) 6 PRK00556 minC septum formation 16.3 10 0.00026 19.6 -3.1 28 40-67 126-153 (195) 7 COG3232 HpaF 5-carboxymethyl-2 15.7 61 0.0016 15.5 0.8 34 40-73 1-34 (127) 8 KOG3181 consensus 15.0 1.2E+02 0.0029 14.1 2.2 34 36-72 75-108 (244) 9 pfam05344 DUF746 Domain of Unk 14.9 1.2E+02 0.003 14.1 2.4 41 19-59 18-64 (65) 10 pfam04056 Ssl1 Ssl1-like. Ssl1 14.4 95 0.0024 14.5 1.5 52 5-58 136-187 (250) No 1 >PRK12862 malic enzyme; Reviewed Probab=32.39 E-value=35 Score=16.81 Aligned_cols=59 Identities=27% Similarity=0.407 Sum_probs=40.8 Q ss_pred HHHCCCHHHHHHHHHHH----HCCCCC----E----EHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCH Q ss_conf 84086311543153665----077886----2----03556777641263788889987641100002532 Q gi|254781001|r 22 FIEGPTKAIVIIWLSIF----SMPSGS----I----EYRDTLDERVANSGLYMIVKKALVRSKKRKIAVPS 80 (93) Q Consensus 22 fiegptkaiviiwlsif----smpsgs----i----eyrdtldervansglymivkkalvrskkrkiavps 80 (93) .|-.|-..-+|.|.+-- .|-||- | .||+.|..|+..|+..|-.--.-.|..+++|..|. T Consensus 383 iip~pfdprl~~~v~~ava~aa~~sgva~~~i~d~~~y~~~L~~~~~~s~~~mr~I~erAK~~PKRIVFaE 453 (761) T PRK12862 383 LIPKPFDPRLILKIAPAVAQAAMDSGVATRPIEDMDAYREQLNQFVYHSGLIMKPVFAAAKAAPKRVVFAE 453 (761) T ss_pred ECCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCEEEECC T ss_conf 52789897426565399999998628876885679999999998867308899999999974886698358 No 2 >KOG4268 consensus Probab=27.82 E-value=47 Score=16.11 Aligned_cols=14 Identities=57% Similarity=1.018 Sum_probs=10.3 Q ss_pred CCCCHHHHHHHHHH Q ss_conf 67256677889999 Q gi|254781001|r 4 SSPSLSDYLKIEHY 17 (93) Q Consensus 4 sspslsdylkiehy 17 (93) .+||++||+..+|| T Consensus 95 t~pS~l~~~t~DiY 108 (189) T KOG4268 95 TSPSLLDYLTMDIY 108 (189) T ss_pred CCHHHHHHHHHHHH T ss_conf 78678888753241 No 3 >cd01453 vWA_transcription_factor_IIH_type Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair, and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear, but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group. Probab=22.31 E-value=52 Score=15.88 Aligned_cols=85 Identities=21% Similarity=0.323 Sum_probs=53.7 Q ss_pred CCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCEEHHHHHHHHHHCC------C--HHHHHHHHHHHHHHHH Q ss_conf 6725667788999999998408631154315366507788620355677764126------3--7888899876411000 Q gi|254781001|r 4 SSPSLSDYLKIEHYMLHSFIEGPTKAIVIIWLSIFSMPSGSIEYRDTLDERVANS------G--LYMIVKKALVRSKKRK 75 (93) Q Consensus 4 sspslsdylkiehymlhsfiegptkaiviiwlsifsmpsgsieyrdtldervans------g--lymivkkalvrskkrk 75 (93) .+|||.+-|...+-+|.+-----+|.|++|+-|+.+--.|.|. +|++.-+.+. | --+-+-|.+.+...-. T Consensus 84 G~~SLqN~Le~A~~~L~~~P~~~sREILiI~~Sl~t~DpgdI~--~ti~~lk~~~IrvsvI~l~aEv~I~k~l~~~TgG~ 161 (183) T cd01453 84 GEPSLQNGLEMALESLKHMPSHGSREVLIIFSSLSTCDPGNIY--ETIDKLKKENIRVSVIGLSAEMHICKEICKATNGT 161 (183) T ss_pred CCHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCHH--HHHHHHHHCCCEEEEEEECHHHHHHHHHHHHHCCE T ss_conf 9813999999999998208987844899997565347976499--99999998397899997427899999999983997 Q ss_pred CCCC--HHHHHHHHHHH Q ss_conf 0253--25788898751 Q gi|254781001|r 76 IAVP--SRQVTDLYKET 90 (93) Q Consensus 76 iavp--srqvtdlyket 90 (93) -.|+ ..+..++.-+. T Consensus 162 y~V~lde~H~~~ll~~~ 178 (183) T cd01453 162 YKVILDETHLKELLLEH 178 (183) T ss_pred EEEECCHHHHHHHHHHC T ss_conf 68753999999999956 No 4 >PRK07232 malic enzyme; Reviewed Probab=21.81 E-value=71 Score=15.20 Aligned_cols=59 Identities=25% Similarity=0.386 Sum_probs=40.4 Q ss_pred HHHCCCHHHHHHHHHH----HHCCCC----CE----EHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCH Q ss_conf 8408631154315366----507788----62----03556777641263788889987641100002532 Q gi|254781001|r 22 FIEGPTKAIVIIWLSI----FSMPSG----SI----EYRDTLDERVANSGLYMIVKKALVRSKKRKIAVPS 80 (93) Q Consensus 22 fiegptkaiviiwlsi----fsmpsg----si----eyrdtldervansglymivkkalvrskkrkiavps 80 (93) .|-.|-..-+|.|.+- -.|-|| .| .||+.|..|+..|+..|-.--.-.|...++|..|. T Consensus 377 ~ip~pfd~r~~~~v~~ava~aa~~~gva~~~i~d~~~Y~~~L~~rl~~s~~~mr~I~erAK~~pKRIVFpE 447 (753) T PRK07232 377 IIPKPFDPRLIVKIAPAVAKAAMDSGVATRPIADMDAYREKLEAFVYRTGLVMKPIFAKAKKDPKRVVFAE 447 (753) T ss_pred CCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCEEEECC T ss_conf 26889897315354299999999748887885559999999998767408899999999974886698258 No 5 >pfam11355 DUF3157 Protein of unknown function (DUF3157). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. Probab=17.55 E-value=44 Score=16.28 Aligned_cols=16 Identities=38% Similarity=0.617 Sum_probs=12.3 Q ss_pred HHHHHHHHHHHHCCCC Q ss_conf 1154315366507788 Q gi|254781001|r 28 KAIVIIWLSIFSMPSG 43 (93) Q Consensus 28 kaiviiwlsifsmpsg 43 (93) +.-|-+|-|||.||.- T Consensus 147 ~e~v~vWqsIkRMpdT 162 (199) T pfam11355 147 TEEVTVWQSIKRMPET 162 (199) T ss_pred EEEEHHHHHHHHCHHH T ss_conf 5003276655328342 No 6 >PRK00556 minC septum formation inhibitor; Reviewed Probab=16.33 E-value=10 Score=19.61 Aligned_cols=28 Identities=25% Similarity=0.444 Sum_probs=24.6 Q ss_pred CCCCCEEHHHHHHHHHHCCCHHHHHHHH Q ss_conf 7788620355677764126378888998 Q gi|254781001|r 40 MPSGSIEYRDTLDERVANSGLYMIVKKA 67 (93) Q Consensus 40 mpsgsieyrdtldervansglymivkka 67 (93) +..|+|.-..+++-+|--.|-|||+++- T Consensus 126 ~A~Gni~v~G~~~G~v~C~GeYmIlk~i 153 (195) T PRK00556 126 ISEGNVSVLGVCEGAIECFGEYMILKKV 153 (195) T ss_pred EECCCEEEEEECCEEEEECCEEEEECCC T ss_conf 8288589998624079987718997356 No 7 >COG3232 HpaF 5-carboxymethyl-2-hydroxymuconate isomerase [Amino acid transport and metabolism] Probab=15.66 E-value=61 Score=15.52 Aligned_cols=34 Identities=38% Similarity=0.467 Sum_probs=27.6 Q ss_pred CCCCCEEHHHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 7788620355677764126378888998764110 Q gi|254781001|r 40 MPSGSIEYRDTLDERVANSGLYMIVKKALVRSKK 73 (93) Q Consensus 40 mpsgsieyrdtldervansglymivkkalvrskk 73 (93) ||.=-+||.|.+++++.-.||.--|..+|.-|-- T Consensus 1 MPHli~EyT~Nl~~~~~~~~L~~~vn~~l~asG~ 34 (127) T COG3232 1 MPHLIMEYTDNLREEADLPGLLEKVNAALIASGL 34 (127) T ss_pred CCCEEHHHHCCCCCCCCCHHHHHHHHHHHHHCCC T ss_conf 9846020202766447808999999999986388 No 8 >KOG3181 consensus Probab=15.02 E-value=1.2e+02 Score=14.08 Aligned_cols=34 Identities=41% Similarity=0.642 Sum_probs=25.8 Q ss_pred HHHHCCCCCEEHHHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 6650778862035567776412637888899876411 Q gi|254781001|r 36 SIFSMPSGSIEYRDTLDERVANSGLYMIVKKALVRSK 72 (93) Q Consensus 36 sifsmpsgsieyrdtldervansglymivkkalvrsk 72 (93) .-|..|.||+|. ..|+|+|.||.-+..-.-.|-| T Consensus 75 kRf~f~~~svel---yaEkV~~rGLcAiaQaeslryK 108 (244) T KOG3181 75 KRFKFPEGSVEL---YAEKVANRGLCAIAQAESLRYK 108 (244) T ss_pred HHCCCCCCCEEE---EHHHHHCCCHHHHHHHHHHHHH T ss_conf 871899874787---4664311442487877789999 No 9 >pfam05344 DUF746 Domain of Unknown Function (DUF746). This is a short conserved region found in some transposons. Probab=14.92 E-value=1.2e+02 Score=14.07 Aligned_cols=41 Identities=29% Similarity=0.427 Sum_probs=32.1 Q ss_pred HHHHHHCCCHHHHHHHHHHHH------CCCCCEEHHHHHHHHHHCCC Q ss_conf 999840863115431536650------77886203556777641263 Q gi|254781001|r 19 LHSFIEGPTKAIVIIWLSIFS------MPSGSIEYRDTLDERVANSG 59 (93) Q Consensus 19 lhsfiegptkaiviiwlsifs------mpsgsieyrdtldervansg 59 (93) --+.+-|-...++..|+..|. -|||+.|-|--|.-|.++.. T Consensus 18 qaa~~lg~~~~~i~~wv~~fr~~ll~LDPSG~~e~RVRLG~rpa~~~ 64 (65) T pfam05344 18 QAADQLGTDEGIIRKWVRMFRRWLLQLDPSGHLERRIRLGGRPAAAT 64 (65) T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCC T ss_conf 99999787888999999999999986198877188765277756679 No 10 >pfam04056 Ssl1 Ssl1-like. Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex. Probab=14.41 E-value=95 Score=14.51 Aligned_cols=52 Identities=23% Similarity=0.340 Sum_probs=0.0 Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCEEHHHHHHHHHHCC Q ss_conf 725667788999999998408631154315366507788620355677764126 Q gi|254781001|r 5 SPSLSDYLKIEHYMLHSFIEGPTKAIVIIWLSIFSMPSGSIEYRDTLDERVANS 58 (93) Q Consensus 5 spslsdylkiehymlhsfiegptkaiviiwlsifsmpsgsieyrdtldervans 58 (93) .|||-.-|..-+-.|...----|+-|+||+-|+.+--.|.|. +|++.-+.+. T Consensus 136 ~pSLqN~Le~a~~~L~~~P~~~sREILii~gSL~T~DPgdI~--~tI~~l~~~~ 187 (250) T pfam04056 136 DPSLQNALELARASLKHVPSHGSREVLIIFGSLSTCDPGDIY--STIDTLKKEK 187 (250) T ss_pred CHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCCCHH--HHHHHHHHCC T ss_conf 920899999999887508987854899998204445886599--9999999759 Done!