Query gi|254780984|ref|YP_003065397.1| hypothetical protein CLIBASIA_04425 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 125
No_of_seqs 2 out of 4
Neff 1.1
Searched_HMMs 39220
Date Mon May 30 02:27:45 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780984.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2201 consensus 48.9 12 0.00031 18.9 2.0 48 46-93 293-357 (371)
2 KOG0687 consensus 34.7 39 0.00099 15.9 2.8 21 45-65 70-90 (393)
3 TIGR00042 TIGR00042 non-canoni 32.3 4.9 0.00012 21.1 -2.1 42 41-82 83-127 (205)
4 pfam04646 DUF604 Protein of un 29.6 49 0.0012 15.3 2.6 24 17-40 27-51 (256)
5 KOG3877 consensus 25.0 39 0.00099 15.8 1.4 30 90-120 345-374 (393)
6 PRK10040 hypothetical protein; 20.6 73 0.0019 14.2 2.5 44 11-54 7-56 (58)
7 COG5187 RPN7 26S proteasome re 19.7 77 0.002 14.1 3.5 29 45-73 81-109 (412)
8 pfam10464 Peptidase_U40 Peptid 19.6 57 0.0014 14.9 1.4 12 71-82 28-39 (212)
9 TIGR01321 TrpR trp operon repr 19.5 77 0.002 14.1 2.2 22 62-83 70-93 (95)
10 TIGR00591 phr2 deoxyribodipyri 18.6 70 0.0018 14.3 1.7 40 25-64 217-260 (471)
No 1
>KOG2201 consensus
Probab=48.92 E-value=12 Score=18.85 Aligned_cols=48 Identities=33% Similarity=0.475 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHH-------------HHHHHHHHHHHHHCCHHHHHHHH-HHHHH---HHHHCCC
Q ss_conf 7999996300799-------------99999999987624836789999-87877---7751686
Q gi|254780984|r 46 SRLAQLCAENEKR-------------LKEFDKITRELNTLSENEKKAFF-EHEKK---VTSNLNY 93 (125)
Q Consensus 46 srlaqlcaenekr-------------lkefdkITR~~~~L~~~~KKAFF-~HEKK---V~~~LNY 93 (125)
+.+|-|||.++.- .-..+.++-.++-.|+.|.||+| |||-- +-.-|.|
T Consensus 293 GqiAyl~A~~~ni~rV~FgG~fiR~~~itM~tLsyAi~fWSkG~~kAlFLrHEGYlGalGAfL~~ 357 (371)
T KOG2201 293 GQIAYLCALNENIKRVYFGGFFIRGHPITMKTLSYAINFWSKGELKALFLRHEGYLGALGAFLSY 357 (371)
T ss_pred HHHHHHHHHHHCCCEEEEEEEEEECCCEEHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 99999998872763799942687447110478999998743412876755404613778887651
No 2
>KOG0687 consensus
Probab=34.67 E-value=39 Score=15.86 Aligned_cols=21 Identities=29% Similarity=0.457 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 679999963007999999999
Q gi|254780984|r 45 SSRLAQLCAENEKRLKEFDKI 65 (125)
Q Consensus 45 ssrlaqlcaenekrlkefdkI 65 (125)
+++|+.+|+.||.+++|+|.-
T Consensus 70 ~~~l~~m~~~neeki~eld~~ 90 (393)
T KOG0687 70 QDLLNSMKKANEEKIKELDEK 90 (393)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999998528899999999
No 3
>TIGR00042 TIGR00042 non-canonical purine NTP pyrophosphatase, rdgB/HAM1 family; InterPro: IPR002637 This family contains the Saccharomyces cerevisiae HAM1 protein P47119 from SWISSPROT and other hypothetical archaeal, bacterial and Caenorhabditis elegans proteins. Saccharomyces cerevisiae HAM1 protects against the mutagenic effects of the base analog 6-N-hydroxylaminopurine (HAP) which can be a natural product of monooxygenase activity on adenine. HAM1 protein protects the cell from HAP, either on the level of deoxynucleoside triphosphate or the DNA level by a yet unidentified set of reactions .; GO: 0016787 hydrolase activity.
Probab=32.32 E-value=4.9 Score=21.15 Aligned_cols=42 Identities=33% Similarity=0.724 Sum_probs=30.6
Q ss_pred CCC-HHHHHHH--HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf 776-3679999--96300799999999999876248367899998
Q gi|254780984|r 41 KPG-YSSRLAQ--LCAENEKRLKEFDKITRELNTLSENEKKAFFE 82 (125)
Q Consensus 41 kpg-yssrlaq--lcaenekrlkefdkITR~~~~L~~~~KKAFF~ 82 (125)
-|| ||+|.+. ||-....--+-..||-..+.-.+++|++|-|.
T Consensus 83 ~PG~YSary~~eklCkk~~TD~~N~ekiL~~le~~~~e~R~A~F~ 127 (205)
T TIGR00042 83 APGIYSARYAGEKLCKKESTDIKNLEKILKLLEGVEKENRQAYFV 127 (205)
T ss_pred CCCCEEEEECCCEEECCCCCHHHHHHHHHHHHCCCCCCCCCEEEE
T ss_conf 989635000461101113640457999999847973315612999
No 4
>pfam04646 DUF604 Protein of unknown function, DUF604. This family includes a conserved region found in several uncharacterized plant proteins.
Probab=29.57 E-value=49 Score=15.26 Aligned_cols=24 Identities=38% Similarity=0.854 Sum_probs=18.9
Q ss_pred HHHHHHHHHHCCC-CCCHHHHHHHH
Q ss_conf 7775333320777-66434556540
Q gi|254780984|r 17 LNLYDAKARRFPT-YGSEERIATCA 40 (125)
Q Consensus 17 lnlydakarrfpt-ygseeriatca 40 (125)
...-|.--.|+|. |||..||-.|-
T Consensus 27 a~~~D~Ci~RYp~lYGSD~Ri~AC~ 51 (256)
T pfam04646 27 ARMQDGCIERYPALYGSDDRIHACM 51 (256)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHH
T ss_conf 9988789875642127537899999
No 5
>KOG3877 consensus
Probab=25.01 E-value=39 Score=15.84 Aligned_cols=30 Identities=40% Similarity=0.665 Sum_probs=25.0
Q ss_pred HCCCCCCHHHHHHHHHHHHHCCEECCCCHHH
Q ss_conf 1686732023228999972015011671121
Q gi|254780984|r 90 NLNYNARDRKHNINQFYEARGKYRYGNGYYR 120 (125)
Q Consensus 90 ~LNYNA~DRK~NI~~~Y~AR~KYRygngyyr 120 (125)
.|--||+|.++-.+++.++-|+ .||-||-.
T Consensus 345 El~~~a~dt~~~lhv~r~~pg~-kY~pGYna 374 (393)
T KOG3877 345 ELYTNARDTGHFLHVMRKEPGK-KYGPGYNA 374 (393)
T ss_pred HHEECCCCCCHHHHHHHHCCCC-CCCCCCCC
T ss_conf 3141643365199999866587-67897555
No 6
>PRK10040 hypothetical protein; Provisional
Probab=20.61 E-value=73 Score=14.23 Aligned_cols=44 Identities=27% Similarity=0.401 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHC------CCHHHHHHHHHHH
Q ss_conf 9998777775333320777664345565407------7636799999630
Q gi|254780984|r 11 LLISNVLNLYDAKARRFPTYGSEERIATCAK------PGYSSRLAQLCAE 54 (125)
Q Consensus 11 llisnvlnlydakarrfptygseeriatcak------pgyssrlaqlcae 54 (125)
+|+...|--+.|-|.+.|--|+.--|+.|.- .|--|+--+.|..
T Consensus 7 ~l~l~~l~s~~a~a~n~PCSG~KGGis~C~g~~FvCnDGsiS~Sk~~C~~ 56 (58)
T PRK10040 7 ILFLGTLVSFYADAGNKPCSGKKGGISHCAGGKFVCNDGSISASKKTCTN 56 (58)
T ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHH
T ss_conf 35676789875753589888887882514699788779970166645431
No 7
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=19.65 E-value=77 Score=14.10 Aligned_cols=29 Identities=28% Similarity=0.442 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 67999996300799999999999876248
Q gi|254780984|r 45 SSRLAQLCAENEKRLKEFDKITRELNTLS 73 (125)
Q Consensus 45 ssrlaqlcaenekrlkefdkITR~~~~L~ 73 (125)
+.++..||..||.+++|||+--|+...+.
T Consensus 81 ~~~~n~l~kkneeki~Elde~i~~~eedn 109 (412)
T COG5187 81 RGRMNTLLKKNEEKIEELDERIREKEEDN 109 (412)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 68899998701889999999999876215
No 8
>pfam10464 Peptidase_U40 Peptidase U40. This family contains P5 murein endopeptidase from bacteriophage phi-6. P5 murein endopeptidase has lytic activity against several gram-negative bacteria. It is thought that the enzyme cleaves the cell wall peptide bridge formed by meso-2,6-diaminopimelic acid and D-Ala
Probab=19.60 E-value=57 Score=14.87 Aligned_cols=12 Identities=58% Similarity=0.767 Sum_probs=4.6
Q ss_pred HCCHHHHHHHHH
Q ss_conf 248367899998
Q gi|254780984|r 71 TLSENEKKAFFE 82 (125)
Q Consensus 71 ~L~~~~KKAFF~ 82 (125)
.||+|||||..+
T Consensus 28 alpenqkkaive 39 (212)
T pfam10464 28 ALPENQKKAIVE 39 (212)
T ss_pred HCCHHHHHHHHH
T ss_conf 375123668898
No 9
>TIGR01321 TrpR trp operon repressor; InterPro: IPR013335 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan . The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit. This entry represents Trp repressors found in proteobacterial and chlamydial species.; GO: 0016564 transcription repressor activity, 0006355 regulation of transcription DNA-dependent.
Probab=19.54 E-value=77 Score=14.09 Aligned_cols=22 Identities=36% Similarity=0.508 Sum_probs=16.4
Q ss_pred HHHHHHHHHHCC--HHHHHHHHHH
Q ss_conf 999999876248--3678999987
Q gi|254780984|r 62 FDKITRELNTLS--ENEKKAFFEH 83 (125)
Q Consensus 62 fdkITR~~~~L~--~~~KKAFF~H 83 (125)
.-+||||-|.|- .++=|-|.+.
T Consensus 70 iA~ITRGSn~Lk~~D~~~~~fL~~ 93 (95)
T TIGR01321 70 IATITRGSNALKALDPEFKQFLKK 93 (95)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 667878788751698788999884
No 10
>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=18.63 E-value=70 Score=14.35 Aligned_cols=40 Identities=28% Similarity=0.316 Sum_probs=29.1
Q ss_pred HHCCCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHH
Q ss_conf 20777664345565407763679999963----00799999999
Q gi|254780984|r 25 RRFPTYGSEERIATCAKPGYSSRLAQLCA----ENEKRLKEFDK 64 (125)
Q Consensus 25 rrfptygseeriatcakpgyssrlaqlca----enekrlkefdk 64 (125)
..|-.-|.|-.-...|+||.++-|.+|-+ =-.+||+.|+.
T Consensus 217 ~~l~~dG~~V~E~~~a~pG~~agl~~L~~nkdGF~~~RL~~f~~ 260 (471)
T TIGR00591 217 ASLQVDGREVAEVQWAKPGTKAGLEMLQSNKDGFISQRLELFET 260 (471)
T ss_pred HHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHCCCC
T ss_conf 97168988388600006843899999872013316666400146
Done!