Query gi|254781119|ref|YP_003065532.1| hypothetical protein CLIBASIA_05105 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 85
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Mon May 30 05:41:52 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781119.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0753 consensus 57.6 3.5 9E-05 21.8 0.4 40 11-65 259-298 (317)
2 PRK00808 hypothetical protein; 56.9 18 0.00046 17.9 4.6 21 65-85 106-126 (150)
3 KOG1559 consensus 54.8 3.6 9.2E-05 21.8 0.1 32 14-45 203-243 (340)
4 pfam05802 EspB Enterobacterial 38.5 36 0.00091 16.2 4.6 42 23-69 79-121 (317)
5 KOG3304 consensus 36.5 39 0.00098 16.0 3.3 33 14-46 11-48 (148)
6 COG5081 Predicted membrane pro 28.8 25 0.00063 17.1 1.0 15 69-83 44-58 (180)
7 PRK10527 hypothetical protein; 26.3 58 0.0015 15.0 3.0 33 43-75 7-54 (125)
8 TIGR01097 3A0109s02M phosphona 25.3 61 0.0016 14.9 3.8 33 50-83 58-90 (192)
9 pfam01540 Lipoprotein_7 Adhesi 23.8 39 0.001 16.0 1.3 32 17-48 166-197 (353)
10 TIGR00228 ruvC crossover junct 23.4 52 0.0013 15.3 1.8 32 8-39 37-68 (158)
11 COG4397 Mu-like prophage major 20.1 78 0.002 14.3 2.4 20 61-80 50-69 (308)
No 1
>KOG0753 consensus
Probab=57.59 E-value=3.5 Score=21.84 Aligned_cols=40 Identities=40% Similarity=0.684 Sum_probs=29.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCH
Q ss_conf 2378989899999996411466899999998521018999988998873102437
Q gi|254781119|r 11 GEVTLLKQKVDCLIAQFNKQQSVIDEFFTILTTAKGFTAFIKGFISIALPIGSFP 65 (85)
Q Consensus 11 gevtllkqkvdcliaqfnkqqsvidefftilttakgftafikgfisialpigsfp 65 (85)
|..-+.|--+||++--. ...||.||-|||+.--+-.|++.
T Consensus 259 g~~~~Ykgs~DC~~k~v---------------~~EG~~AlYKGF~Psw~RlGpWn 298 (317)
T KOG0753 259 GRGGLYKGSLDCLIKTV---------------KNEGFFALYKGFIPSWLRLGPWN 298 (317)
T ss_pred CCCCCCCCHHHHHHHHH---------------HHCCHHHHHCCCCCCCEECCCEE
T ss_conf 86752146278999999---------------73173988713331010137715
No 2
>PRK00808 hypothetical protein; Provisional
Probab=56.92 E-value=18 Score=17.91 Aligned_cols=21 Identities=14% Similarity=0.271 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHHCCC
Q ss_conf 778999999999999974389
Q gi|254781119|r 65 PALRTWIIHHVVGLLKKLFPF 85 (85)
Q Consensus 65 palrtwiihhvvgllkklfpf 85 (85)
--|+.|++.|+.+-=++..||
T Consensus 106 ~fL~~WL~~HIl~~D~kya~~ 126 (150)
T PRK00808 106 NMLSRWLFNHIRNDDAAYVDA 126 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999858888999999
No 3
>KOG1559 consensus
Probab=54.78 E-value=3.6 Score=21.79 Aligned_cols=32 Identities=41% Similarity=0.598 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHH
Q ss_conf 898989999999641146---------68999999985210
Q gi|254781119|r 14 TLLKQKVDCLIAQFNKQQ---------SVIDEFFTILTTAK 45 (85)
Q Consensus 14 tllkqkvdcliaqfnkqq---------svidefftilttak 45 (85)
-|+|-.+|||.+|+.|-. .....||.|+||..
T Consensus 203 LLkkL~~dcLvmq~Hk~gisp~nF~~N~~Ls~FFnilTT~~ 243 (340)
T KOG1559 203 LLKKLSTDCLVMQNHKFGISPKNFQGNPALSSFFNILTTCT 243 (340)
T ss_pred HHHHHCCCHHEEECCCCCCCHHHCCCCHHHHHHHHHEEEEC
T ss_conf 99873523110003323446230457988997876533301
No 4
>pfam05802 EspB Enterobacterial EspB protein. EspB is a type-III-secreted pore-forming protein of enteropathogenic Escherichia coli (EPEC) which is essential for EPEC pathogenesis. EspB is also found in Citrobacter rodentium.
Probab=38.46 E-value=36 Score=16.22 Aligned_cols=42 Identities=38% Similarity=0.464 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCHHHHH
Q ss_conf 999641146689999999852101899998899887310-24377899
Q gi|254781119|r 23 LIAQFNKQQSVIDEFFTILTTAKGFTAFIKGFISIALPI-GSFPALRT 69 (85)
Q Consensus 23 liaqfnkqqsvidefftilttakgftafikgfisialpi-gsfpalrt 69 (85)
--|-|..|...|+|-- |-.-.|.|.|-||-.|.| |||.|...
T Consensus 79 q~avfesQNKAIeEKK-----A~ATAALvGGaISSvLGILGSFAAins 121 (317)
T pfam05802 79 QQAVFESQNKAIEEKK-----AAATAALVGGAISSVLGILGSFAAINS 121 (317)
T ss_pred HHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999986546777775-----366899985489999999888998764
No 5
>KOG3304 consensus
Probab=36.50 E-value=39 Score=16.04 Aligned_cols=33 Identities=33% Similarity=0.558 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHH
Q ss_conf 89898999999964114-----6689999999852101
Q gi|254781119|r 14 TLLKQKVDCLIAQFNKQ-----QSVIDEFFTILTTAKG 46 (85)
Q Consensus 14 tllkqkvdcliaqfnkq-----qsvidefftilttakg 46 (85)
+-+-+.-..|+-+||+. .|+.|.|+.|+.+||-
T Consensus 11 ~~~~ask~al~k~~~~Rl~ddIkS~~dNF~~Ii~~Akv 48 (148)
T KOG3304 11 PALPASKEALLKSYNKRLKDDIKSIMDNFTEIIKTAKV 48 (148)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 43087899999999999887689999869999999854
No 6
>COG5081 Predicted membrane protein [Function unknown]
Probab=28.85 E-value=25 Score=17.11 Aligned_cols=15 Identities=73% Similarity=1.092 Sum_probs=8.7
Q ss_pred HHHHHHHHHHHHHHC
Q ss_conf 999999999999743
Q gi|254781119|r 69 TWIIHHVVGLLKKLF 83 (85)
Q Consensus 69 twiihhvvgllkklf 83 (85)
.||||-||=+|-|||
T Consensus 44 aWiIHvvvI~lLkl~ 58 (180)
T COG5081 44 AWIIHVVVILLLKLF 58 (180)
T ss_pred CEEHHHHHHHHHHHH
T ss_conf 431589999999999
No 7
>PRK10527 hypothetical protein; Provisional
Probab=26.25 E-value=58 Score=15.04 Aligned_cols=33 Identities=24% Similarity=0.605 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHHHHHC---------------CCCHHHHHHHHHHH
Q ss_conf 2101899998899887310---------------24377899999999
Q gi|254781119|r 43 TAKGFTAFIKGFISIALPI---------------GSFPALRTWIIHHV 75 (85)
Q Consensus 43 takgftafikgfisialpi---------------gsfpalrtwiihhv 75 (85)
-+-|+..+.-|.|.+.||+ -|-|.+..|+++|-
T Consensus 7 ~~lG~~~v~LG~iGi~LP~LPTTpFlLLAa~cFarsS~r~~~WL~~h~ 54 (125)
T PRK10527 7 IIIGWLAVVLGTLGVVLPLLPTTPFILLAAWCFARSSPRFHAWLLYRS 54 (125)
T ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHCC
T ss_conf 999999999999988377888739999999999848999999999591
No 8
>TIGR01097 3A0109s02M phosphonate ABC transporter, permease protein; InterPro: IPR005769 Bacterial binding protein-dependent transport systems , are multicomponent systems typically composed of a periplasmic substrate-binding protein, one or two reciprocally homologous integral inner-membrane proteins and one or two peripheral membrane ATP-binding proteins that couple energy to the active transport system. The integral inner-membrane proteins translocate the substrate across the membrane. It has been shown , that most of these proteins contain a conserved region located about 80 to 100 residues from their C-terminal extremity. This region seems to be located in a cytoplasmic loop between two transmembrane domains. Apart from the conserved region, the sequence of these proteins is quite divergent, and they have a variable number of transmembrane helices. These proteins represent a family of phosphonate uptake transporters., probably responsible for the transport of phosphonate across the inner membrane. ; GO: 0015604 phosphonate transmembrane transporter activity, 0015716 phosphonate transport, 0005887 integral to plasma membrane.
Probab=25.26 E-value=61 Score=14.93 Aligned_cols=33 Identities=33% Similarity=0.674 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf 9988998873102437789999999999999743
Q gi|254781119|r 50 FIKGFISIALPIGSFPALRTWIIHHVVGLLKKLF 83 (85)
Q Consensus 50 fikgfisialpigsfpalrtwiihhvvgllkklf 83 (85)
-+-+|--.++..|.||+.-.--|| ..|.|.|||
T Consensus 58 V~A~lF~~~~~LGP~~~~~A~~IH-T~G~L~KLl 90 (192)
T TIGR01097 58 VIAGLFLVILSLGPIAAVLALFIH-TIGVLSKLL 90 (192)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHH-HHHHHHHHH
T ss_conf 999999999950518999999999-998999999
No 9
>pfam01540 Lipoprotein_7 Adhesin lipoprotein. This family consists of the p50 and variable adherence-associated antigen (Vaa) adhesins from Mycoplasma hominis. M. hominis is a mycoplasma associated with human urogenital diseases, pneumonia, and septic arthritis. An adhesin is a cell surface molecule that mediates adhesion to other cells or to the surrounding surface or substrate. The Vaa antigen is a 50-kDa surface lipoprotein that has four tandem repetitive DNA sequences encoding a periodic peptide structure, and is highly immunogenic in the human host. p50 is also a 50-kDa lipoprotein, having three repeats A,B and C, that may be a tetramer of 191-kDa in its native environment.
Probab=23.75 E-value=39 Score=16.00 Aligned_cols=32 Identities=31% Similarity=0.552 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 98999999964114668999999985210189
Q gi|254781119|r 17 KQKVDCLIAQFNKQQSVIDEFFTILTTAKGFT 48 (85)
Q Consensus 17 kqkvdcliaqfnkqqsvidefftilttakgft 48 (85)
|...+..+.+.|+...-||+|-|.-++-+||+
T Consensus 166 K~qL~~~~d~L~~KS~qI~~F~Tv~s~qe~F~ 197 (353)
T pfam01540 166 KEQLENFADDLLDKSRQIDEFTTVTSTQEGFT 197 (353)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHEEECCCCCEE
T ss_conf 99999999999887875324312220233200
No 10
>TIGR00228 ruvC crossover junction endodeoxyribonuclease RuvC; InterPro: IPR002176 The Escherichia coli ruvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination . RuvC protein (3.1.22.4 from EC) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo . RucC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli ruvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices .; GO: 0004520 endodeoxyribonuclease activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=23.43 E-value=52 Score=15.31 Aligned_cols=32 Identities=19% Similarity=0.355 Sum_probs=24.9
Q ss_pred EECCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 30023789898999999964114668999999
Q gi|254781119|r 8 EMKGEVTLLKQKVDCLIAQFNKQQSVIDEFFT 39 (85)
Q Consensus 8 emkgevtllkqkvdcliaqfnkqqsvidefft 39 (85)
++......+-.-|||+|.||.-..--|++.|-
T Consensus 37 ~L~~~l~~~~~~~~~~~~~f~~n~~AIE~vF~ 68 (158)
T TIGR00228 37 DLPERLKDIYAGVTEIITQFQPNEFAIEQVFM 68 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
T ss_conf 68899999999999998430666001212432
No 11
>COG4397 Mu-like prophage major head subunit gpT [General function prediction only]
Probab=20.07 E-value=78 Score=14.33 Aligned_cols=20 Identities=40% Similarity=0.914 Sum_probs=16.2
Q ss_pred CCCCHHHHHHHHHHHHHHHH
Q ss_conf 02437789999999999999
Q gi|254781119|r 61 IGSFPALRTWIIHHVVGLLK 80 (85)
Q Consensus 61 igsfpalrtwiihhvvgllk 80 (85)
.|.||++|.||-..|..-.|
T Consensus 50 LGQ~P~frEWiGdRv~~~mk 69 (308)
T COG4397 50 LGQFPQFREWIGDRVIEKMK 69 (308)
T ss_pred HCCCHHHHHHHHHHHHHHHH
T ss_conf 20572588887489999998
Done!