Query gi|254780906|ref|YP_003065319.1| hypothetical protein CLIBASIA_04025 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 96
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Mon May 30 01:40:33 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780906.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02635 RhaI_grampos L-rhamn 41.9 7.1 0.00018 20.6 -0.0 41 4-55 253-296 (382)
2 TIGR01660 narH nitrate reducta 23.9 43 0.0011 16.4 1.5 18 70-87 42-68 (495)
3 PRK09783 copper/silver efflux 17.9 69 0.0018 15.3 1.5 45 8-52 7-51 (407)
4 TIGR03511 GldH_lipo gliding mo 14.1 51 0.0013 16.0 0.0 43 8-50 7-53 (156)
5 KOG3462 consensus 13.2 86 0.0022 14.8 1.0 13 13-25 38-50 (105)
6 TIGR00819 ydaH AbgT transporte 13.1 83 0.0021 14.9 0.9 25 67-93 240-265 (527)
7 KOG2871 consensus 12.9 1.3E+02 0.0034 13.8 2.4 54 3-58 251-307 (449)
8 pfam10225 DUF2215 Uncharacteri 10.6 79 0.002 15.0 0.1 17 11-27 16-32 (247)
9 TIGR03525 GldK gliding motilit 10.6 71 0.0018 15.2 -0.1 16 8-23 4-19 (449)
10 pfam00658 PABP Poly-adenylate 10.5 1E+02 0.0025 14.5 0.6 6 13-18 38-43 (71)
No 1
>TIGR02635 RhaI_grampos L-rhamnose isomerase; InterPro: IPR013457 The proteins in this entry are closely related to the L-rhamnose isomerases (IPR013451 from INTERPRO) found in Pseudomonas stutzeri and in a number of the Rhizobiales. They are encoded in similar genomic contexts, close to genes apparently involved in rhamnose catabolism such as rhamnulose-1-phosphate aldolase (IPR013454 from INTERPRO), sugar kinases, and sugar transporters..
Probab=41.93 E-value=7.1 Score=20.57 Aligned_cols=41 Identities=32% Similarity=0.481 Sum_probs=32.4
Q ss_pred CCCCEEEEEHHHHHHHHHHHH---HHHHHHHCCCCCCCCEEEEEEEECCCCCCCC
Q ss_conf 566243012265898531001---1001221012454321588874055556686
Q gi|254780906|r 4 SKNQAILFFITGMILSSCGDT---LSDSKQHNKINNTKNHLDLLFPIDDSHNQKP 55 (96)
Q Consensus 4 sknqailffitgmilsscgdt---lsdskqhnkinntknhldllfpiddshnqkp 55 (96)
|-|---||.|---|++.|+|+ +++++. +.-|-+|.+||-+|
T Consensus 253 a~nPyeLFlIf~e~~~a~~d~~Pn~~~~~~-----------~va~MlDqcHn~e~ 296 (382)
T TIGR02635 253 AINPYELFLIFKEIVRAGRDSEPNLRDLAS-----------DVAYMLDQCHNLEP 296 (382)
T ss_pred HCCHHHHHHHHHHHHCCCCCCCHHHHHHHC-----------CCEEECCCCCCCHH
T ss_conf 017579999999997068998522333002-----------20100101025211
No 2
>TIGR01660 narH nitrate reductase, beta subunit; InterPro: IPR006547 The nitrate reductase enzyme complex allows bacteria to use nitrate as an electron acceptor during anaerobic growth. The enzyme complex consists of a tetramer that has an alpha, beta and 2 gamma subunits. The alpha and beta subunits have catalytic activity and the gamma subunits attach the enzyme to the membrane and are b-type cytochromes that receive electrons from the quinone pool and transfers them to the beta subunit. The sequences in this family are the beta subunit for nitrate reductase I (narH) and nitrate reductase II (narY) for Gram-positive and Gram-negative bacteria. A few thermophiles and archaea also match the model. A number of the sequences in this set are experimentally characterised, these include: E.Coli NarH (P11349 from SWISSPROT) and NarY (P19318 from SWISSPROT) , , P42176 from SWISSPROT from Bacillus subtilis, and related proteins from Psuedomonas fluorescens, Paracoccus denitrificans, and Halomonas halodenitrificans.; GO: 0008940 nitrate reductase activity, 0042126 nitrate metabolic process, 0009325 nitrate reductase complex.
Probab=23.92 E-value=43 Score=16.43 Aligned_cols=18 Identities=44% Similarity=1.180 Sum_probs=11.4
Q ss_pred CCCCCCCC---C------CCCCCCCCH
Q ss_conf 30078998---3------223577675
Q gi|254780906|r 70 NIIEPQPG---P------SRWEGGWNG 87 (96)
Q Consensus 70 niiepqpg---p------srweggwng 87 (96)
|-+|..|| | .+|.|||--
T Consensus 42 NNVEtKPGiGyPk~WEnQ~k~kGGW~r 68 (495)
T TIGR01660 42 NNVETKPGIGYPKDWENQDKYKGGWVR 68 (495)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCEEE
T ss_conf 351368777888663012112676053
No 3
>PRK09783 copper/silver efflux system membrane fusion protein CusB; Provisional
Probab=17.94 E-value=69 Score=15.29 Aligned_cols=45 Identities=22% Similarity=0.170 Sum_probs=30.0
Q ss_pred EEEEEHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCC
Q ss_conf 430122658985310011001221012454321588874055556
Q gi|254780906|r 8 AILFFITGMILSSCGDTLSDSKQHNKINNTKNHLDLLFPIDDSHN 52 (96)
Q Consensus 8 ailffitgmilsscgdtlsdskqhnkinntknhldllfpiddshn 52 (96)
.|+|+|-|-+++..|-+.+.+.+..+-++....-..||=.+--|-
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~er~~lyw~~pM~P 51 (407)
T PRK09783 7 IIGSMIAGGIISAAGFTWVAKAEPPAEKTSTAERKVLFWYDPMYP 51 (407)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEECCCCCC
T ss_conf 599999988777775655632788766778777640698689898
No 4
>TIGR03511 GldH_lipo gliding motility-associated lipoprotein GldH. Members of this protein family are predicted lipoproteins, exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). Members include GldH, a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Not all Bacteroidetes with members of this protein family may have gliding motility.
Probab=14.10 E-value=51 Score=16.02 Aligned_cols=43 Identities=30% Similarity=0.522 Sum_probs=23.5
Q ss_pred EEEEEHHHHHHHHHHHH--HHHHHHHCCCC--CCCCEEEEEEEECCC
Q ss_conf 43012265898531001--10012210124--543215888740555
Q gi|254780906|r 8 AILFFITGMILSSCGDT--LSDSKQHNKIN--NTKNHLDLLFPIDDS 50 (96)
Q Consensus 8 ailffitgmilsscgdt--lsdskqhnkin--ntknhldllfpidds 50 (96)
.|+||+...+|.||.|. .-+.-|+-.-. ....-+..-||+.|+
T Consensus 7 ~i~~~l~~~ll~SC~~~~~vy~~y~~~~~~gW~~~d~l~F~~~~~d~ 53 (156)
T TIGR03511 7 SISFFLGACVLVSCTENTDVYHSYQSTPHGGWQKSDTLDFEIPITDY 53 (156)
T ss_pred HHHHHHHHHHEEEECCCCCEEEEEEECCCCCCCCCCCEEEEEECCCC
T ss_conf 49999999970763899633567679775788889978999761778
No 5
>KOG3462 consensus
Probab=13.24 E-value=86 Score=14.81 Aligned_cols=13 Identities=46% Similarity=0.843 Sum_probs=9.3
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 2658985310011
Q gi|254780906|r 13 ITGMILSSCGDTL 25 (96)
Q Consensus 13 itgmilsscgdtl 25 (96)
+-|||+|-||--+
T Consensus 38 ~lgmIfsmcGlM~ 50 (105)
T KOG3462 38 FLGMIFSMCGLMF 50 (105)
T ss_pred HHHHHHHHHHHHH
T ss_conf 9999999989999
No 6
>TIGR00819 ydaH AbgT transporter family; InterPro: IPR011540 The p-aminobenzoyl-glutamate transporter family includes two putative transporters, the AbgT protein of Escherichia coli and MtrF of Neisseria gonorrhoeae. AbgT expression is apparently cryptic in wild type cells, but when present on a high copy number plasmid, or when expressed at higher levels due to mutation, it allows utilization of p-aminobenzoyl-glutamate as a source of p-aminobenzoate for p-aminobenzoate auxotrophs . p-Aminobenzoate is a constituent of, and a precursor for, the biosynthesis of folic acid. It is not currently known if AbgT is naturally involved in transporting p-aminobenzoyl-glutamate, or if it only becomes involved when under altered regulation. MtrF is an inner membrane protein which, together with the MtrCDE efflux pump, is required for high-level resistance to hydrophobic antimicrobial agents in N. gonorrhoeae . Its role in this process is not known, but it has been suggested that it may be a component of the efflux pump which is dispensible for basal activity, but required for high-level activity ..
Probab=13.11 E-value=83 Score=14.89 Aligned_cols=25 Identities=20% Similarity=0.617 Sum_probs=16.1
Q ss_pred ECCCCCCCCCCCCCCCCCCCHHHH-HHH
Q ss_conf 402300789983223577675567-675
Q gi|254780906|r 67 IKNNIIEPQPGPSRWEGGWNGERY-VRE 93 (96)
Q Consensus 67 iknniiepqpgpsrweggwngery-vre 93 (96)
|.+.|||||-|| |.|.-|.|.- +|.
T Consensus 240 ~T~KI~EP~LG~--yQ~dl~~~EKdirh 265 (527)
T TIGR00819 240 VTDKIVEPRLGQ--YQSDLSSDEKDIRH 265 (527)
T ss_pred HHCCEECCCCCC--CCCCCCHHHHHHHH
T ss_conf 740101688886--43444401456666
No 7
>KOG2871 consensus
Probab=12.87 E-value=1.3e+02 Score=13.77 Aligned_cols=54 Identities=26% Similarity=0.404 Sum_probs=40.6
Q ss_pred CCCCCEEEEEHHHHHH---HHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCCCCCCCC
Q ss_conf 2566243012265898---5310011001221012454321588874055556686212
Q gi|254780906|r 3 ISKNQAILFFITGMIL---SSCGDTLSDSKQHNKINNTKNHLDLLFPIDDSHNQKPTEK 58 (96)
Q Consensus 3 isknqailffitgmil---sscgdtlsdskqhnkinntknhldllfpiddshnqkptek 58 (96)
|+++-++- |+|+|-+ .+.|..+..+||---+-.+.+|+-.||..|. |-+.|-++
T Consensus 251 I~e~~dvg-fltlle~l~~ckvgs~lk~pr~Piwv~gSeth~tvlfs~d~-~l~~~~~~ 307 (449)
T KOG2871 251 IPEQGDVG-FLTLLELLRYCKVGSALKQPRQPIWVLGSETHLTVLFSCDG-HLVVPENP 307 (449)
T ss_pred CCCCCCHH-HHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCEEEEEECCC-CCCCCCCC
T ss_conf 54013156-99999998787777764499886047458873489991376-31277897
No 8
>pfam10225 DUF2215 Uncharacterized conserved protein (DUF2215). This entry is the central 200 residues of a family of proteins conserved from worms to humans. The function is unknown.
Probab=10.63 E-value=79 Score=14.99 Aligned_cols=17 Identities=24% Similarity=0.356 Sum_probs=6.7
Q ss_pred EEHHHHHHHHHHHHHHH
Q ss_conf 12265898531001100
Q gi|254780906|r 11 FFITGMILSSCGDTLSD 27 (96)
Q Consensus 11 ffitgmilsscgdtlsd 27 (96)
+|+.|++|-.++++||+
T Consensus 16 ~f~~Gi~lf~~A~~LS~ 32 (247)
T pfam10225 16 VLVLGIVLFLLAPLLSR 32 (247)
T ss_pred HHHHHHHHHHHHHHHCC
T ss_conf 99999999995498716
No 9
>TIGR03525 GldK gliding motility-associated lipoprotein GldK. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldK is a lipoprotein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae. Knockouts of GldK abolish the gliding phenotype. GldK is homologous to GldJ. There is a GldK homolog in Cytophaga hutchinsonii and several other species that has a different, shorter architecture and is represented by a separate model. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.
Probab=10.63 E-value=71 Score=15.24 Aligned_cols=16 Identities=25% Similarity=0.559 Sum_probs=10.0
Q ss_pred EEEEEHHHHHHHHHHH
Q ss_conf 4301226589853100
Q gi|254780906|r 8 AILFFITGMILSSCGD 23 (96)
Q Consensus 8 ailffitgmilsscgd 23 (96)
.++|++...+++|||.
T Consensus 4 ~~~~~~~~~~~~SCg~ 19 (449)
T TIGR03525 4 YLVFAALVVLVYSCGS 19 (449)
T ss_pred HHHHHHHHHHHHHCCC
T ss_conf 4899999998721058
No 10
>pfam00658 PABP Poly-adenylate binding protein, unique domain. The region featured in this family is found towards the C-terminus of poly(A)-binding proteins (PABPs). These are eukaryotic proteins that, through their binding of the 3' poly(A) tail on mRNA, have very important roles in the pathways of gene expression. They seem to provide a scaffold on which other proteins can bind and mediate processes such as export, translation and turnover of the transcripts. Moreover, they may act as antagonists to the binding of factors that allow mRNA degradation, regulating mRNA longevity. PABPs are also involved in nuclear transport. PABPs interact with poly(A) tails via RNA-recognition motifs (pfam00076). Note that the PABP C-terminal region is also found in members of the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains - these are also included in this family.
Probab=10.50 E-value=1e+02 Score=14.46 Aligned_cols=6 Identities=83% Similarity=1.342 Sum_probs=0.0
Q ss_pred HHHHHH
Q ss_conf 265898
Q gi|254780906|r 13 ITGMIL 18 (96)
Q Consensus 13 itgmil 18 (96)
||||+|
T Consensus 38 ITGMLL 43 (71)
T pfam00658 38 ITGMLL 43 (71)
T ss_pred HHHHHH
T ss_conf 668775
Done!