Query gi|254780518|ref|YP_003064931.1| hypothetical protein CLIBASIA_02025 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 48 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Sun May 29 23:43:47 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780518.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 pfam04056 Ssl1 Ssl1-like. Ssl1 37.3 17 0.00044 18.6 1.3 30 2-31 89-121 (250) 2 cd01453 vWA_transcription_fact 23.7 48 0.0012 16.5 1.7 29 2-30 40-71 (183) 3 PHA02107 hypothetical protein 17.6 73 0.0019 15.6 1.6 29 14-42 54-82 (216) 4 PRK02963 hypothetical protein; 11.9 1.5E+02 0.0038 14.2 1.9 30 18-48 109-138 (316) 5 TIGR01925 spIIAB anti-sigma F 10.6 61 0.0015 16.0 -0.5 14 31-44 10-23 (137) 6 PTZ00221 cyclophilin; Provisio 10.4 1.5E+02 0.0039 14.1 1.5 29 12-43 86-114 (249) 7 KOG1106 consensus 10.2 1E+02 0.0026 15.0 0.5 33 8-40 22-57 (177) 8 pfam08943 CsiD CsiD. This fami 9.8 1.9E+02 0.0049 13.7 1.9 30 18-48 96-125 (297) 9 KOG2448 consensus 6.9 1.6E+02 0.0041 14.0 0.4 7 25-31 80-86 (596) 10 TIGR01757 Malate-DH_plant mala 6.6 1.7E+02 0.0043 13.9 0.4 8 26-33 171-178 (390) No 1 >pfam04056 Ssl1 Ssl1-like. Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex. Probab=37.33 E-value=17 Score=18.55 Aligned_cols=30 Identities=20% Similarity=0.556 Sum_probs=24.0 Q ss_pred CCCCCCEEEEEEEEECC---CCCHHCCCCCCCC Q ss_conf 01476114788886244---3600016984210 Q gi|254780518|r 2 YYNSNTVSKLSVACTSE---TGISKLSGNPCNL 31 (48) Q Consensus 2 yynsntvsklsvactse---tgisklsgnpcnl 31 (48) ||..|..|.|++-.+.. .-++.++|||-.. T Consensus 89 fFdqNPiSQlgii~~rn~~a~~ls~lsgnp~~h 121 (250) T pfam04056 89 FFDQNPISQIGLITCKDGRAHRLTDLTGNPRVH 121 (250) T ss_pred HHHCCCCCCEEEEEEECCEEEEEEECCCCHHHH T ss_conf 874398302279999657137833257998999 No 2 >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=23.71 E-value=48 Score=16.46 Aligned_cols=29 Identities=24% Similarity=0.635 Sum_probs=22.9 Q ss_pred CCCCCCEEEEEEEEECCC---CCHHCCCCCCC Q ss_conf 014761147888862443---60001698421 Q gi|254780518|r 2 YYNSNTVSKLSVACTSET---GISKLSGNPCN 30 (48) Q Consensus 2 yynsntvsklsvactset---gisklsgnpcn 30 (48) |+..|..|.+++..+..- -++.++|||-. T Consensus 40 ffdqNPisqlGii~~rn~~a~~ls~lsgn~~~ 71 (183) T cd01453 40 FFDQNPISQLGIISIKNGRAEKLTDLTGNPRK 71 (183) T ss_pred HHCCCCCCEEEEEEEECCEEEEEEECCCCHHH T ss_conf 87079740489999946816997646899899 No 3 >PHA02107 hypothetical protein Probab=17.63 E-value=73 Score=15.60 Aligned_cols=29 Identities=38% Similarity=0.332 Sum_probs=23.3 Q ss_pred EEECCCCCHHCCCCCCCCHHCCCCCEEEE Q ss_conf 86244360001698421011037531557 Q gi|254780518|r 14 ACTSETGISKLSGNPCNLAASRGVSFARV 42 (48) Q Consensus 14 actsetgisklsgnpcnlaasrgvsfarv 42 (48) +-.+.-||+|.+-|--|++|...++.... T Consensus 54 s~G~~~GI~KI~PN~~N~~A~~~~sV~G~ 82 (216) T PHA02107 54 SFGSRFGIAKISPNHINLAAVGTHSVCGT 82 (216) T ss_pred HHCCCCCCCCCCCCEEEEECCCCEEEEEE T ss_conf 31134683313777044411133688778 No 4 >PRK02963 hypothetical protein; Validated Probab=11.88 E-value=1.5e+02 Score=14.18 Aligned_cols=30 Identities=33% Similarity=0.464 Sum_probs=23.7 Q ss_pred CCCCHHCCCCCCCCHHCCCCCEEEEEEEECC Q ss_conf 4360001698421011037531557876429 Q gi|254780518|r 18 ETGISKLSGNPCNLAASRGVSFARVLVFLSD 48 (48) Q Consensus 18 etgisklsgnpcnlaasrgvsfarvlvflsd 48 (48) -|+++.|-|+| |.-|--|--+||-.|--.| T Consensus 109 STAvaHLIG~p-N~DsMsGkYYARF~VKh~D 138 (316) T PRK02963 109 ATAVAHLIGRS-NFDAMSGQYYARFVVKNVD 138 (316) T ss_pred HHHHHHHCCCC-CCCCCCCCEEEEEEEECCC T ss_conf 66789872898-7212477427999994587 No 5 >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=10.55 E-value=61 Score=16.00 Aligned_cols=14 Identities=64% Similarity=0.688 Sum_probs=10.7 Q ss_pred CHHCCCCCEEEEEE Q ss_conf 01103753155787 Q gi|254780518|r 31 LAASRGVSFARVLV 44 (48) Q Consensus 31 laasrgvsfarvlv 44 (48) +|.|..-|||||-| T Consensus 10 ~A~S~NEsFARVtV 23 (137) T TIGR01925 10 LAKSENESFARVTV 23 (137) T ss_pred EEECCCCCCHHHHH T ss_conf 31016764013445 No 6 >PTZ00221 cyclophilin; Provisional Probab=10.44 E-value=1.5e+02 Score=14.12 Aligned_cols=29 Identities=17% Similarity=0.093 Sum_probs=22.4 Q ss_pred EEEEECCCCCHHCCCCCCCCHHCCCCCEEEEE Q ss_conf 88862443600016984210110375315578 Q gi|254780518|r 12 SVACTSETGISKLSGNPCNLAASRGVSFARVL 43 (48) Q Consensus 12 svactsetgisklsgnpcnlaasrgvsfarvl 43 (48) -.-||.|.|+.+.+|.|-.. .|-.|-||. T Consensus 86 RaLCTGEkG~~~~~G~~L~Y---kgs~FHRVi 114 (249) T PTZ00221 86 RALITGSCGIDTNTGVKLDY---LYTPVHHVD 114 (249) T ss_pred HHHHCCCCCCCCCCCCCCCC---CCCEEEEEE T ss_conf 98853788778888985351---697160783 No 7 >KOG1106 consensus Probab=10.19 E-value=1e+02 Score=14.95 Aligned_cols=33 Identities=36% Similarity=0.508 Sum_probs=24.9 Q ss_pred EEEEEEEEECCCCCHHCC---CCCCCCHHCCCCCEE Q ss_conf 147888862443600016---984210110375315 Q gi|254780518|r 8 VSKLSVACTSETGISKLS---GNPCNLAASRGVSFA 40 (48) Q Consensus 8 vsklsvactsetgiskls---gnpcnlaasrgvsfa 40 (48) .+.-++.||.||+|-.|. --|-.+++.++|... T Consensus 22 a~~~ki~ct~e~~i~~lgfl~~~~~~~~~g~kVelP 57 (177) T KOG1106 22 ASGEKIPCTFETKIPNLGFLQAPPRELPAGRKVELP 57 (177) T ss_pred HCCCCCCCEEEECCCCCCCCCCCCCCCCCCCEECCH T ss_conf 079744654650588877567886638999720532 No 8 >pfam08943 CsiD CsiD. This family consists of various bacterial proteins pertaining to the non-haem Fe(II)-dependent oxygenase family. Exact function is unknown, but a putative role includes involvement in the control of utilisation of gamma-aminobutyric acid. Probab=9.77 E-value=1.9e+02 Score=13.66 Aligned_cols=30 Identities=37% Similarity=0.557 Sum_probs=23.3 Q ss_pred CCCCHHCCCCCCCCHHCCCCCEEEEEEEECC Q ss_conf 4360001698421011037531557876429 Q gi|254780518|r 18 ETGISKLSGNPCNLAASRGVSFARVLVFLSD 48 (48) Q Consensus 18 etgisklsgnpcnlaasrgvsfarvlvflsd 48 (48) -|.|+.|-|+| |..+--|--+||-.|--.| T Consensus 96 STAi~hLiG~P-N~DsM~GKYYARF~VKh~D 125 (297) T pfam08943 96 STAVAHLIGRP-NFDAMSGKYYARFVVKNED 125 (297) T ss_pred HHHHHHHHCCC-CHHHCCCCEEEEEEEECCC T ss_conf 76679871898-7112056237999996587 No 9 >KOG2448 consensus Probab=6.86 E-value=1.6e+02 Score=14.00 Aligned_cols=7 Identities=71% Similarity=1.725 Sum_probs=0.0 Q ss_pred CCCCCCC Q ss_conf 6984210 Q gi|254780518|r 25 SGNPCNL 31 (48) Q Consensus 25 sgnpcnl 31 (48) +|||||. T Consensus 80 egnpcnm 86 (596) T KOG2448 80 EGNPCNM 86 (596) T ss_pred CCCCCCH T ss_conf 4886521 No 10 >TIGR01757 Malate-DH_plant malate dehydrogenase, NADP-dependent; InterPro: IPR011273 This entry represents the NADP-dependent malate dehydrogenase found in plants, mosses and green algae and localised to the chloroplast. Malate dehydrogenase converts oxaloacetate into malate, a critical step in the C4 cycle which allows circumvention of the effects of photorespiration. Malate is subsequently transported from the chloroplast to the cytoplasm (and then to the bundle sheath cells in C4 plants). The plant and moss enzymes are light regulated via cysteine diisulphide bonds. The enzyme from sorghum has been crystallised .; GO: 0046554 malate dehydrogenase (NADP+) activity, 0006108 malate metabolic process. Probab=6.61 E-value=1.7e+02 Score=13.94 Aligned_cols=8 Identities=75% Similarity=1.419 Sum_probs=0.0 Q ss_pred CCCCCCHH Q ss_conf 98421011 Q gi|254780518|r 26 GNPCNLAA 33 (48) Q Consensus 26 gnpcnlaa 33 (48) |||||-.| T Consensus 171 GnPCntna 178 (390) T TIGR01757 171 GNPCNTNA 178 (390) T ss_pred CCCCCHHH T ss_conf 28754146 Done!