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!