Query gi|254781214|ref|YP_003065627.1| hypothetical protein CLIBASIA_05605 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 110 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Mon May 30 06:28:07 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781214.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR02488 flgG_G_neg flagellar 44.6 6.8 0.00017 20.6 0.2 16 80-95 236-251 (263) 2 COG4395 Uncharacterized protei 42.5 15 0.00039 18.8 1.7 25 27-55 33-57 (281) 3 PHA00437 tail assembly protein 35.1 9 0.00023 20.0 -0.4 21 21-41 14-34 (92) 4 COG4256 HemP Hemin uptake prot 24.3 26 0.00067 17.5 0.5 27 82-108 12-38 (63) 5 cd00321 SO_family_Moco Sulfite 24.0 21 0.00055 18.0 -0.1 25 73-97 104-128 (156) 6 KOG0466 consensus 23.0 30 0.00077 17.2 0.5 24 81-104 230-253 (466) 7 cd01492 Aos1_SUMO Ubiquitin ac 22.9 38 0.00098 16.6 1.1 22 18-39 149-170 (197) 8 PTZ00249 variable surface prot 22.1 41 0.001 16.5 1.1 45 10-54 409-467 (516) 9 pfam10439 Bacteriocin_IIc Bact 21.2 28 0.00072 17.3 0.1 32 10-41 29-61 (65) 10 cd02108 bact_SO_family_Moco ba 18.8 54 0.0014 15.9 1.1 24 73-96 112-135 (185) No 1 >TIGR02488 flgG_G_neg flagellar basal-body rod protein FlgG; InterPro: IPR012834 This family consists of the FlgG protein of the flagellar apparatus in the proteobacteria and spirochetes. The basal body constitutes a major portion of the flagellar organelle and consists of four rings (L,P,S, and M) mounted on a central rod . The rod consists of about 26 subunits of flgG in the distal portion, and flgB, flgC and flgF are thought to build up the proximal portion of the rod with about 6 subunits each.; GO: 0006928 cell motility, 0043064 flagellum organization and biogenesis, 0009426 flagellin-based flagellum basal body distal rod. Probab=44.59 E-value=6.8 Score=20.60 Aligned_cols=16 Identities=50% Similarity=0.547 Sum_probs=11.2 Q ss_pred HHHHHHHHCCCCCCCH Q ss_conf 6423343302576613 Q gi|254781214|r 80 QESLRAYEMNRIPIPA 95 (110) Q Consensus 80 qeslrayemnripipa 95 (110) -+.=||||||---|-| T Consensus 236 I~aQRAYE~NSK~i~a 251 (263) T TIGR02488 236 ITAQRAYEMNSKVIQA 251 (263) T ss_pred HHHHHHHHHHHHHHHH T ss_conf 3688898775388887 No 2 >COG4395 Uncharacterized protein conserved in bacteria [Function unknown] Probab=42.50 E-value=15 Score=18.75 Aligned_cols=25 Identities=48% Similarity=0.725 Sum_probs=11.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 67888776312322122344444442152 Q gi|254781214|r 27 VGGVIGGLMGGAAGLYSEWDTIGGFFGSS 55 (110) Q Consensus 27 vggvigglmggaaglysewdtiggffgss 55 (110) .||.+|||+.| | +--+.+++|||-- T Consensus 33 ~g~l~ggl~~g---l-~~~~~~~~f~gia 57 (281) T COG4395 33 LGGLAGGLLMG---L-SGMFFGGLFFGIA 57 (281) T ss_pred HHHHHHHHHHH---H-HHHHHHHHHHHHH T ss_conf 66789999876---8-9999998999999 No 3 >PHA00437 tail assembly protein Probab=35.13 E-value=9 Score=19.97 Aligned_cols=21 Identities=48% Similarity=0.771 Sum_probs=16.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHH Q ss_conf 234434678887763123221 Q gi|254781214|r 21 GSIFGPVGGVIGGLMGGAAGL 41 (110) Q Consensus 21 gsifgpvggvigglmggaagl 41 (110) -++.+|++++.||+.|+++|- T Consensus 14 K~v~k~~~~~~gg~~G~a~g~ 34 (92) T PHA00437 14 KSVSKPVGKVVGGALGLAGGA 34 (92) T ss_pred HCCCCCCCCCCCCHHCCCCCC T ss_conf 233222100000010012478 No 4 >COG4256 HemP Hemin uptake protein [Inorganic ion transport and metabolism] Probab=24.27 E-value=26 Score=17.49 Aligned_cols=27 Identities=33% Similarity=0.487 Sum_probs=22.1 Q ss_pred HHHHHHCCCCCCCHHHHCHHHHHCCCC Q ss_conf 233433025766133304044402522 Q gi|254781214|r 82 SLRAYEMNRIPIPARRFTSSSLLSGVH 108 (110) Q Consensus 82 slrayemnripiparrftsssllsgvh 108 (110) |-.|-.|.++|-|+|+.+|..|+.|-+ T Consensus 12 s~da~~~~~~p~~~r~v~S~~Lfgg~~ 38 (63) T COG4256 12 STDANHKTALPQPIRRVSSQTLFGGDG 38 (63) T ss_pred CCCCCCCCCCCCCCCEECHHHCCCCCC T ss_conf 767774344777501210423006887 No 5 >cd00321 SO_family_Moco Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the terminal reaction in the oxidative degradation of the sulfur-containing amino acids cysteine and methionine. Assimilatory NRs catalyze the reduction of nitrate to nitrite which is subsequently converted to NH4+ by nitrite reductase. Common features of all known members of this family are that they contain one single pterin cofactor and part of the coordination of the metal (Mo) is a cysteine ligand of the protein and that they catalyze the transfer of an oxygen to or from a lone pair of electrons on the substrate. Probab=23.97 E-value=21 Score=17.97 Aligned_cols=25 Identities=36% Similarity=0.566 Sum_probs=20.4 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHHH Q ss_conf 7999886642334330257661333 Q gi|254781214|r 73 ELAEVRRQESLRAYEMNRIPIPARR 97 (110) Q Consensus 73 elaevrrqeslrayemnripiparr 97 (110) .|.++...+.+-||+||--|+|... T Consensus 104 pl~~~~~~~~lLA~~~nGepL~~~h 128 (156) T cd00321 104 PLEKALDPDVLLAYEMNGEPLPPDH 128 (156) T ss_pred EHHHHHCCCCEEEEEECCEECCHHC T ss_conf 9999528772998455882885650 No 6 >KOG0466 consensus Probab=22.99 E-value=30 Score=17.18 Aligned_cols=24 Identities=38% Similarity=0.731 Sum_probs=18.9 Q ss_pred HHHHHHHCCCCCCCHHHHCHHHHH Q ss_conf 423343302576613330404440 Q gi|254781214|r 81 ESLRAYEMNRIPIPARRFTSSSLL 104 (110) Q Consensus 81 eslrayemnripiparrftsssll 104 (110) +.+-.|-.+.||+|.|.|+|..-+ T Consensus 230 d~v~eyivkkIPvPvRdf~s~prl 253 (466) T KOG0466 230 DVVCEYIVKKIPVPVRDFTSPPRL 253 (466) T ss_pred HHHHHHHHHCCCCCCCCCCCCCCE T ss_conf 799999986189882014789728 No 7 >cd01492 Aos1_SUMO Ubiquitin activating enzyme (E1) subunit Aos1. Aos1 is part of the heterodimeric activating enzyme (E1), specific for the SUMO family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. The E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by SUMO family of ubiquitin-like proteins (Ublps) is involved in cell division, nuclear transport, the stress response and signal transduction. Aos1 contains part of the adenylation domain. Probab=22.91 E-value=38 Score=16.63 Aligned_cols=22 Identities=27% Similarity=0.761 Sum_probs=16.0 Q ss_pred CCHHHHHHHHHHHHHHHHHHHH Q ss_conf 1112344346788877631232 Q gi|254781214|r 18 FKLGSIFGPVGGVIGGLMGGAA 39 (110) Q Consensus 18 fklgsifgpvggvigglmggaa 39 (110) +-.-.+|+||-||||++|.-.| T Consensus 149 ~vf~dv~~pv~gviGsl~A~Ea 170 (197) T cd01492 149 FVFADLLAPVAAVVGGILAQDV 170 (197) T ss_pred EEECCCCCCHHHHHHHHHHHHH T ss_conf 3676877336689999999999 No 8 >PTZ00249 variable surface protein Vir28; Provisional Probab=22.06 E-value=41 Score=16.47 Aligned_cols=45 Identities=31% Similarity=0.620 Sum_probs=22.5 Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHH------------H--HHHHHHHHHHHHHHHHCC Q ss_conf 00122001111234434678887763------------1--232212234444444215 Q gi|254781214|r 10 FGSSLSSGFKLGSIFGPVGGVIGGLM------------G--GAAGLYSEWDTIGGFFGS 54 (110) Q Consensus 10 fgsslssgfklgsifgpvggvigglm------------g--gaaglysewdtiggffgs 54 (110) ..+|..+.+.-|+|+|.+-+.|-|.+ | ||-=|.=.+.-+|-||+- T Consensus 409 ~~~s~~~~~d~~ti~~~i~~aiS~vL~~VDPVPVvGVSGGMGALFLLFRYTPvGsFFrG 467 (516) T PTZ00249 409 PAGSMQSTFDTGTIMGTIKGAVSNVLEAVEPVPVLGVSGGMGALYLLLKYTPIGSLFRR 467 (516) T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEECCCHHHHHHHHHCCCCCCCCCC T ss_conf 76654555454420001235776530457887711114723568887600665330278 No 9 >pfam10439 Bacteriocin_IIc Bacteriocin class II with double-glycine leader peptide. This is a family of bacteriocidal bacteriocins secreted by Streptococcal species in order to kill off closely-related competitor Gram-positives. The sequence includes the peptide precursor, this being cleaved off proteolytically at the double-glycine. The family does not carry the YGNGVXC motif characteristic of pediocin-like Bacteriocins, Bacteriocin_II pfam01721. The producer bacteria are protected from the effects of their own bacteriocins by production of a specific immunity protein which is co-transcribed with the genes encoding the bacteriocins, eg family EntA_Immun pfam08951. The bacteriocins are structurally more specific than their immunity-protein counterparts. Typically, production of the bacteriocin gene is from within an operon carrying up to 6 genes including a typical two-component regulatory system (R and H), a small peptide pheromone (C), and a dedicated ABC transporter (A and -B) as wel Probab=21.21 E-value=28 Score=17.34 Aligned_cols=32 Identities=38% Similarity=0.694 Sum_probs=23.6 Q ss_pred HHHHHHCCCCHHHHHHH-HHHHHHHHHHHHHHH Q ss_conf 00122001111234434-678887763123221 Q gi|254781214|r 10 FGSSLSSGFKLGSIFGP-VGGVIGGLMGGAAGL 41 (110) Q Consensus 10 fgsslssgfklgsifgp-vggvigglmggaagl 41 (110) ...+..+|+..|..+++ +++++|.+.|+..|. T Consensus 29 ~~g~~~~G~~~G~~~g~~~g~~~Ga~~G~~~G~ 61 (65) T pfam10439 29 IGGGAAAGAVAGAAGGGPVGGLAGALVGGVVGA 61 (65) T ss_pred CCCHHHHHHHCCCCCCCCCCHHHHHHHHCEEEC T ss_conf 574045433301557886510567665010112 No 10 >cd02108 bact_SO_family_Moco bacterial subgroup of the sulfite oxidase (SO) family of molybdopterin binding domains. This domain is found in a variety of oxidoreductases. Common features of all known members of this family, like sulfite oxidase and nitrite reductase, are that they contain one single pterin cofactor and part of the coordination of the metal (Mo) is a cysteine ligand of the protein and that they catalyze the transfer of an oxygen to or from a lone pair of electrons on the substrate. The specific function of this subgroup is unknown. Probab=18.82 E-value=54 Score=15.86 Aligned_cols=24 Identities=38% Similarity=0.699 Sum_probs=19.4 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCHH Q ss_conf 799988664233433025766133 Q gi|254781214|r 73 ELAEVRRQESLRAYEMNRIPIPAR 96 (110) Q Consensus 73 elaevrrqeslrayemnripipar 96 (110) .+.+....+.|-||+||--|+|.. T Consensus 112 pl~~a~~~~~LlA~~mNGepL~~~ 135 (185) T cd02108 112 DMASALHPQTLLAYEMNGQPLPIK 135 (185) T ss_pred CHHHHHCCCCCHHHHCCCCCCCHH T ss_conf 289964922130343079489666 Done!