Query gi|254781205|ref|YP_003065618.1| hypothetical protein CLIBASIA_05560 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 171
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Mon May 30 06:11:44 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781205.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00591 phr2 deoxyribodipyri 65.7 2.5 6.4E-05 22.3 0.9 56 20-77 334-389 (471)
2 TIGR02317 prpB methylisocitrat 62.4 6.7 0.00017 19.9 2.6 92 41-136 24-130 (287)
3 pfam01771 Herpes_alk_exo Herpe 33.8 16 0.0004 17.9 0.7 19 77-95 184-202 (458)
4 TIGR03132 malonate_mdcB tripho 33.0 27 0.00068 16.7 1.7 18 151-168 141-158 (272)
5 pfam07037 DUF1323 Putative tra 30.8 23 0.00058 17.0 1.1 24 112-135 14-37 (122)
6 PRK10096 citG triphosphoribosy 30.6 23 0.00059 17.0 1.1 18 151-168 162-179 (292)
7 TIGR01345 malate_syn_G malate 25.9 20 0.00052 17.3 0.1 14 40-53 47-60 (726)
8 PRK03692 putative UDP-N-acetyl 23.7 42 0.0011 15.5 1.4 13 35-47 52-64 (246)
9 COG3803 Uncharacterized protei 21.5 25 0.00064 16.8 -0.1 43 88-130 63-107 (182)
10 pfam04369 Lactococcin Lactococ 19.7 33 0.00084 16.1 0.2 45 79-123 13-57 (60)
No 1
>TIGR00591 phr2 deoxyribodipyrimidine photolyase; InterPro: IPR008148 Deoxyribodipyrimidine photolyase (DNA photolyase) is a DNA repair enzyme. It binds to UV-damaged DNA containing pyrimidine dimers and, upon absorbing a near-UV photon (300 to 500 nm), breaks the cyclobutane ring joining the two pyrimidines of the dimer. DNA photolyase is an enzyme that requires two choromophore-cofactors for its activity: a reduced FADH2 and either 5,10-methenyltetrahydrofolate (5,10-MTFH) or an oxidized 8-hydroxy-5- deazaflavin (8-HDF) derivative (F420). The folate or deazaflavin chromophore appears to function as an antenna, while the FADH2 chromophore is thought to be responsible for electron transfer. On the basis of sequence similarities DNA photolyases can be grouped into two classes. The second class contains enzymes from Myxococcus xanthus, methanogenic archaebacteria, insects, fish and marsupial mammals. It is not yet known what second cofactor is bound to class 2 enzymes. There are a number of conserved sequence regions in all known class 2 DNA photolyases, especially in the C-terminal part. ; GO: 0003904 deoxyribodipyrimidine photo-lyase activity, 0006281 DNA repair.
Probab=65.70 E-value=2.5 Score=22.31 Aligned_cols=56 Identities=34% Similarity=0.379 Sum_probs=46.7
Q ss_pred HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEECCCHHHHHHHHHHHHHHHH
Q ss_conf 0440013466665532124678888754210000023441203676640133427889
Q gi|254781205|r 20 GAGLRISSTLASHRSSIRDHEYRSLLAEENALRADVLYLDREDQARREGIMDTGVFRM 77 (171)
Q Consensus 20 gaglrisstlashrssirdheyrsllaeenalradvlyldredqarregimdtgvfrm 77 (171)
|+--=-..||..|.+--|+|.| ||--=|+|..+|-|.=--.-|--.+|-|. |-.||
T Consensus 334 gl~~WA~~TL~~H~kD~Re~~Y-SleqLE~a~T~D~LWNAAQ~elV~~GKmH-GfLRM 389 (471)
T TIGR00591 334 GLYEWAQKTLMDHAKDKREHLY-SLEQLEKAKTHDPLWNAAQLELVEEGKMH-GFLRM 389 (471)
T ss_pred CCCHHHHHHHHHHHCCCCCCCH-HHHHHHCCCCCCHHHHHHHHHHHHCCCCC-CCHHH
T ss_conf 6627899998754216877301-28973064676610569999998707603-21366
No 2
>TIGR02317 prpB methylisocitrate lyase; InterPro: IPR012695 Propionate is the second most abundant low molecular mass carbon source found in soil, being generated by the degradation of several amino acids, fementation of crabohydrates and the oxidation of odd-chain fatty acids. Many different organisms are capable of metabolising propionate and several distinct pathways for utilising this compound exist, all of which begin with its activation to propionyl-CoA . Many bacteria metabolise propionate to pyruvate by the 2-methylcitric acid cycle. In the first step, catalysed by methycitrate synthase, oxaloacetate and propionyl-CoA are condensed to form 2-methylcitrate and CoA. The 2-methylcitrate is subsequently converted to 2-methylisocitrate by the combined actions of a dehydratase and an aconitase. In the final step, 2-methylisocitrate lyase cleaves a C-C bond within this compound to form succinate and pyruvate. The succinate is further oxidised to oxaloacetate which re-enters the cycle, while the pyruvate can be used further for either energy generation or biomass synthesis. Proteins in this entry are mostly 2-methylisocitrate lyases. Some of them have been annotated (incorrectly it seems) as the related protein carboxyphosphoenolpyruvate phosphomutase, which is involved in synthesizing the antibiotic bialaphos in Streptomyces hygroscopicus. Structural studies indicate that these enzymes belong to the isocitrate lyase family, binding a Mg(2+) cofactor and forming a TIM barrel fold , . As with other enzymes in this family, substrate-binding induces a conformational change that prevents solvent access to the active site and which is important for catalysis. .
Probab=62.42 E-value=6.7 Score=19.95 Aligned_cols=92 Identities=33% Similarity=0.405 Sum_probs=70.5
Q ss_pred HHHHHHHHHHHHHEEEEECCCHHHH-HHHHHHHHHHHHHHHHHCCC----CCCEEEEEECCCCHHHCCCHHHHHHHHHHH
Q ss_conf 8888754210000023441203676-64013342788998860466----551366651464102203313445678899
Q gi|254781205|r 41 YRSLLAEENALRADVLYLDREDQAR-REGIMDTGVFRMKAVLSGVS----GASLDLLVGQNTRNAYKGINTARTAREQTV 115 (171)
Q Consensus 41 yrsllaeenalradvlyldredqar-regimdtgvfrmkavlsgvs----gasldllvgqntrnaykgintartareqtv 115 (171)
+-+|+||+--. +-+||-----+- --|+-|-|+--..-|+.-.. -.+|-|||--.|---= -+|-+||.||-.-
T Consensus 24 ~~AL~Ae~aGF--~A~YLSGaa~aa~sLGlPDLG~~tL~Eva~~~r~Itr~~~LPlLVD~DTGFGe-a~nvaRTVreme~ 100 (287)
T TIGR02317 24 LVALLAERAGF--EAIYLSGAAVAAGSLGLPDLGITTLTEVAERARRITRVTDLPLLVDADTGFGE-ALNVARTVREMED 100 (287)
T ss_pred HHHHHHHHCCC--CEEEEHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCC-HHHHHHHHHHHHH
T ss_conf 99999986375--56610168774132067767667878999998877753048727863328983-5449999999998
Q ss_pred HHHH----------HHHCHHHHHHHHHHCCC
Q ss_conf 9988----------64121121066642154
Q gi|254781205|r 116 ARFA----------KEAGWHRANKEAVKNNR 136 (171)
Q Consensus 116 arfa----------keagwhrankeavknnr 136 (171)
|+-| |..| |+-||+-|..|-
T Consensus 101 AGaAa~HiEDQv~pKrCG-HL~gK~lv~~~e 130 (287)
T TIGR02317 101 AGAAAVHIEDQVLPKRCG-HLNGKELVSRDE 130 (287)
T ss_pred HHHHHCCHHHHCCCCCCC-CCCCCCCCCHHH
T ss_conf 445400467742544267-898874048877
No 3
>pfam01771 Herpes_alk_exo Herpesvirus alkaline exonuclease. This family includes various alkaline exonucleases from members of the herpesviridae. Alkaline exonuclease appears to have an important role in the replication of herpes simplex virus.
Probab=33.79 E-value=16 Score=17.90 Aligned_cols=19 Identities=37% Similarity=0.497 Sum_probs=15.6
Q ss_pred HHHHHHCCCCCCEEEEEEC
Q ss_conf 9988604665513666514
Q gi|254781205|r 77 MKAVLSGVSGASLDLLVGQ 95 (171)
Q Consensus 77 mkavlsgvsgasldllvgq 95 (171)
|--..+|+-|||||++++-
T Consensus 184 LiDp~tGi~GaSLD~~~~~ 202 (458)
T pfam01771 184 LIDPRTGIFGASLDMCVNV 202 (458)
T ss_pred EECCCCCCCEEEEHEEECC
T ss_conf 5568877440120004412
No 4
>TIGR03132 malonate_mdcB triphosphoribosyl-dephospho-CoA synthase MdcB. This protein acts in cofactor biosynthesis, preparing the coenzyme A derivative that becomes attached to the malonate decarboxylase acyl carrier protein (or delta subunit). The closely related protein CitG of citrate lyase produces the same molecule, but the two families are nonetheless readily separated.
Probab=32.99 E-value=27 Score=16.66 Aligned_cols=18 Identities=39% Similarity=0.637 Sum_probs=15.0
Q ss_pred CHHHHHHHHHHHHCCCCC
Q ss_conf 001356888876245776
Q gi|254781205|r 151 SASSAGMKMFRRYNVKGK 168 (171)
Q Consensus 151 sassagmkmfrrynvkgk 168 (171)
...|.|-++|++|.+.|-
T Consensus 141 ~~~T~Ge~~~~~yg~~G~ 158 (272)
T TIGR03132 141 DADSHGQRVRQRYGVGGA 158 (272)
T ss_pred CCCCCHHHHHHHHCCCCH
T ss_conf 999947999998389958
No 5
>pfam07037 DUF1323 Putative transcription regulator (DUF1323). This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. This family appears to have an HTH domain and is therefore likely to act as a transcriptional regulator.
Probab=30.84 E-value=23 Score=17.04 Aligned_cols=24 Identities=33% Similarity=0.732 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHCHHHHHHHHHHCC
Q ss_conf 889999886412112106664215
Q gi|254781205|r 112 EQTVARFAKEAGWHRANKEAVKNN 135 (171)
Q Consensus 112 eqtvarfakeagwhrankeavknn 135 (171)
-|||-+.+++-||.+..+..||..
T Consensus 14 rQtINkwaRkeGW~t~~~~GVQGG 37 (122)
T pfam07037 14 RQTINRWVRKEGWKTSPKPGVKGG 37 (122)
T ss_pred HHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf 999999999738704887886576
No 6
>PRK10096 citG triphosphoribosyl-dephospho-CoA synthase; Provisional
Probab=30.57 E-value=23 Score=17.00 Aligned_cols=18 Identities=22% Similarity=0.584 Sum_probs=14.7
Q ss_pred CHHHHHHHHHHHHCCCCC
Q ss_conf 001356888876245776
Q gi|254781205|r 151 SASSAGMKMFRRYNVKGK 168 (171)
Q Consensus 151 sassagmkmfrrynvkgk 168 (171)
+..++|-+.|++|.+.|-
T Consensus 162 ~~~T~Ger~~~~yG~~Ga 179 (292)
T PRK10096 162 SQLTAGQRLYQQLGLTGA 179 (292)
T ss_pred CCCCHHHHHHHHHCCCCH
T ss_conf 889879999998299838
No 7
>TIGR01345 malate_syn_G malate synthase G; InterPro: IPR006253 These sequences represent the G isozyme of malate synthase. Malate synthase G (MSG, 723 residues) is an enzyme of the glyoxylate pathway, that catalyzes the condensation and subsequent hydrolysis of acetyl-coenzyme A (acetyl-CoA) and glyoxylate to form malate and CoA , this biochemical bypass is used by microorganisms (bacteria, yeast, and fungi) for biosynthesis under anaerobic conditions . Enzymes of the glyoxylate bypass have been implicated as virulence factors in several pathogens, including Mycobacterium tuberculosis , , . The X-ray structure of the ternary abortive complex of MSG with pyruvate (glyoxylate mimic) and acetyl-CoA has been determined and shown to have the same structure as in the complex with glyoxylate .; GO: 0004474 malate synthase activity, 0006097 glyoxylate cycle.
Probab=25.87 E-value=20 Score=17.30 Aligned_cols=14 Identities=43% Similarity=0.667 Sum_probs=5.6
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 78888754210000
Q gi|254781205|r 40 EYRSLLAEENALRA 53 (171)
Q Consensus 40 eyrsllaeenalra 53 (171)
|-|.|||+-.-+.+
T Consensus 47 eNr~LLA~RdeiQa 60 (726)
T TIGR01345 47 ENRELLAKRDEIQA 60 (726)
T ss_pred CCHHHHHHHHHHHH
T ss_conf 00788877889999
No 8
>PRK03692 putative UDP-N-acetyl-D-mannosaminuronic acid transferase; Provisional
Probab=23.75 E-value=42 Score=15.53 Aligned_cols=13 Identities=23% Similarity=0.337 Sum_probs=6.3
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 2124678888754
Q gi|254781205|r 35 SIRDHEYRSLLAE 47 (171)
Q Consensus 35 sirdheyrsllae 47 (171)
+.+|.+|+.++..
T Consensus 52 A~~dp~~~~~l~~ 64 (246)
T PRK03692 52 AEDNPEVRELINA 64 (246)
T ss_pred HCCCHHHHHHHHH
T ss_conf 6209999999983
No 9
>COG3803 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.49 E-value=25 Score=16.79 Aligned_cols=43 Identities=35% Similarity=0.363 Sum_probs=32.8
Q ss_pred CEEEEEECCCCHHHCCCHH--HHHHHHHHHHHHHHHHCHHHHHHH
Q ss_conf 1366651464102203313--445678899998864121121066
Q gi|254781205|r 88 SLDLLVGQNTRNAYKGINT--ARTAREQTVARFAKEAGWHRANKE 130 (171)
Q Consensus 88 sldllvgqntrnaykgint--artareqtvarfakeagwhranke 130 (171)
.|-+|..|-.||.|.|.-- +..+.-+-|||-|-.+||.++-..
T Consensus 63 Al~iLlDQfPRN~fRGTpr~yatD~lA~~~Ar~ai~ag~D~~~~~ 107 (182)
T COG3803 63 ALIILLDQFPRNMFRGTPRAYATDALALRVAREAIAAGHDRQLPP 107 (182)
T ss_pred HHHHHHHHCHHHHHCCCCHHHCCCHHHHHHHHHHHHCCCCCCCCH
T ss_conf 999999775287757993443057989999999985666445897
No 10
>pfam04369 Lactococcin Lactococcin-like family. Family of bacteriocins from lactic acid bacteria.
Probab=19.74 E-value=33 Score=16.14 Aligned_cols=45 Identities=22% Similarity=0.324 Sum_probs=35.7
Q ss_pred HHHHCCCCCCEEEEEECCCCHHHCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf 886046655136665146410220331344567889999886412
Q gi|254781205|r 79 AVLSGVSGASLDLLVGQNTRNAYKGINTARTAREQTVARFAKEAG 123 (171)
Q Consensus 79 avlsgvsgasldllvgqntrnaykgintartareqtvarfakeag 123 (171)
.-||-++|.+|........-.-|+--+|+.|.-.||...|.-.++
T Consensus 13 eELse~nGGklqfi~s~g~~~wy~~t~t~kt~~qQt~~~~~a~~~ 57 (60)
T pfam04369 13 EELSEINGGKLQFIMSKGVLGWYSMTSTAKTGPQQTNSPWLAKIK 57 (60)
T ss_pred HHHHHCCCCCEEEEEECCCEEEEECCCCCCCCCCCCCCHHHHHHH
T ss_conf 674222487168886136302222044441135678984787641
Done!