Query gi|254780198|ref|YP_003064611.1| hypothetical protein CLIBASIA_00415 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 69
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Mon May 23 10:20:51 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780198.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2647 consensus 40.3 32 0.00081 16.1 3.6 34 11-44 360-396 (444)
2 pfam12031 DUF3518 Domain of un 32.4 20 0.00051 17.2 1.0 34 27-62 71-104 (257)
3 cd02638 R3H_unknown_1 R3H doma 30.6 20 0.00051 17.2 0.8 14 52-65 14-28 (62)
4 cd07064 AlkD_like_1 A new stru 28.0 51 0.0013 15.0 3.3 32 21-52 163-197 (208)
5 TIGR01114 mtrH N5-methyltetrah 26.9 29 0.00074 16.3 1.1 16 24-39 230-246 (323)
6 pfam06388 DUF1075 Protein of u 21.7 68 0.0017 14.3 2.6 20 5-24 91-110 (146)
7 pfam03839 Sec62 Translocation 19.4 77 0.002 14.0 6.6 55 10-64 109-178 (217)
8 pfam09581 Spore_III_AF Stage I 19.0 79 0.002 14.0 3.6 43 12-54 3-45 (185)
9 pfam08713 DNA_alkylation DNA a 18.2 57 0.0015 14.7 1.1 16 21-36 167-182 (212)
10 pfam10831 DUF2556 Protein of u 17.0 87 0.0022 13.7 1.8 10 29-38 5-14 (53)
No 1
>KOG2647 consensus
Probab=40.26 E-value=32 Score=16.13 Aligned_cols=34 Identities=29% Similarity=0.498 Sum_probs=26.0
Q ss_pred HHHHHH---HHHHHHHHCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999---9999985256148999999999999999
Q gi|254780198|r 11 VFVIVA---TIITCFFMNKQCAWWLRVFLPFLLISIM 44 (69)
Q Consensus 11 vfviva---tiitcffmnkqcawwlrvflpfllisim 44 (69)
.|++-| +.|+||+|+-|-.--.--++|++...+-
T Consensus 360 p~~vha~vll~i~~F~mHvQV~tR~lsa~Pl~YW~~A 396 (444)
T KOG2647 360 PFVVHAAVLLLIGCFYMHVQVLTRFLSALPLIYWFLA 396 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHH
T ss_conf 6899999999999854209999999851628999999
No 2
>pfam12031 DUF3518 Domain of unknown function (DUF3518). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 260 amino acids in length. This domain is found associated with pfam01388.
Probab=32.37 E-value=20 Score=17.24 Aligned_cols=34 Identities=26% Similarity=0.689 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECC
Q ss_conf 148999999999999999988762213355665364
Q gi|254780198|r 27 QCAWWLRVFLPFLLISIMIVHITHISGHVNFLLFPP 62 (69)
Q Consensus 27 qcawwlrvflpfllisimivhithisghvnfllfpp 62 (69)
.++||..- |-- +-.-..|-+++|||+.+.-.||.
T Consensus 71 ~~ewWwd~-L~~-lREN~lV~laNisg~LdLs~~pe 104 (257)
T pfam12031 71 KDEWWWDC-LEV-LRENTLVTLANISGQLDLSFYPE 104 (257)
T ss_pred HHHHHHHH-HHH-HHHCCEEEEEEEEEEEEEEECCH
T ss_conf 77799999-999-86140475160043553000826
No 3
>cd02638 R3H_unknown_1 R3H domain of a group of eukaryotic proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=30.63 E-value=20 Score=17.23 Aligned_cols=14 Identities=50% Similarity=0.721 Sum_probs=9.2
Q ss_pred CCEE-EEEEECCCCE
Q ss_conf 1335-5665364040
Q gi|254780198|r 52 SGHV-NFLLFPPLSM 65 (69)
Q Consensus 52 sghv-nfllfpplsm 65 (69)
+++. .-|+|||++-
T Consensus 14 ~~~~~rVLlFPPl~~ 28 (62)
T cd02638 14 SFQRYRVLLFPPLNS 28 (62)
T ss_pred HCCCCEEEEECCCCC
T ss_conf 346454999578751
No 4
>cd07064 AlkD_like_1 A new structural DNA glycosylase containing HEAT-like repeats. This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity. The known structures for members of this fa
Probab=27.95 E-value=51 Score=14.98 Aligned_cols=32 Identities=28% Similarity=0.511 Sum_probs=20.2
Q ss_pred HHHHCCHHHHHHHHHH---HHHHHHHHHHHHHHHC
Q ss_conf 9852561489999999---9999999998876221
Q gi|254780198|r 21 CFFMNKQCAWWLRVFL---PFLLISIMIVHITHIS 52 (69)
Q Consensus 21 cffmnkqcawwlrvfl---pfllisimivhithis 52 (69)
-||++|-+.|+||-.- |=.++.-+.-|....|
T Consensus 163 e~fIqKAiGW~LRe~~K~dp~~V~~Fl~~~~~~m~ 197 (208)
T cd07064 163 EFFIRKAIGWALREYSKTNPDWVRDFVAAHKLRLS 197 (208)
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCC
T ss_conf 99999999999999975098999999999788677
No 5
>TIGR01114 mtrH N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit H; InterPro: IPR002856 This family of methyltransferases occurs in both archaea and bacteria. In archaea, members of this family (MtrH) are involved in the energy conservation step of methanogenesis, while in prokaryotes, members of this family whose function has been defined (CmuB) are involved in the metabolism of chloromethane. In archaea the enzyme tetrahydromethanopterin S-methyltransferase is composed of eight subunits, MtrA-H. The enzyme is a membrane- associated enzyme complex which catalyzes an energy-conserving, sodium-ion-translocating step in methanogenesis from hydrogen and carbon dioxide . Subunit MtrH catalyzes the methylation reaction and was shown to exhibit methyltetrahydromethanopterin:cob(I)alamin methyltransferase activity . CH3-H4MPT + cob(I)alamin --> H4MPT + CH3-cob(III)alamin (H4MPT = tetrahydromethanopterin) In bacteria, the pathway of chloromethane utilisation allows the microorganisms that possess it to grow with chloromethane as the sole carbon and energy source. It is initiated by a corrinoid-dependent methyltransferase system involving methyltransferase I (CmuA) and methyltransferase II (CmuB), which transfer the methyl group of chloromethane onto tetrahydrofolate . The methyl group of chloromethane is first transferred by the protein CmuA to its corrinoid moiety, from where it is transferred to tetrahydrofolate by CmuB, thereby yielding methyltetrahydrofolate , . CmuB has methylcobalamin:tetrahydrofolate methyltransferase activity, and catalyzes the conversion of methylcobalamin and tetrahydrofolate to cob(I)alamin and methyltetrahydrofolate. CH3-cob(III)alamin + H4F --> CH3-H4F + cob(I)alamin (H4F = tetrahydromethanopterin); GO: 0008168 methyltransferase activity, 0006730 one-carbon compound metabolic process.
Probab=26.88 E-value=29 Score=16.34 Aligned_cols=16 Identities=50% Similarity=0.901 Sum_probs=10.7
Q ss_pred HCCHHHH-HHHHHHHHH
Q ss_conf 2561489-999999999
Q gi|254780198|r 24 MNKQCAW-WLRVFLPFL 39 (69)
Q Consensus 24 mnkqcaw-wlrvflpfl 39 (69)
-|--.|| |||-|---+
T Consensus 230 HN~pSAWDWLR~F~K~~ 246 (323)
T TIGR01114 230 HNVPSAWDWLREFKKKL 246 (323)
T ss_pred CCCCCHHHHHHHHHHCC
T ss_conf 77320457889874137
No 6
>pfam06388 DUF1075 Protein of unknown function (DUF1075). This family consists of several eukaryotic proteins of unknown function.
Probab=21.72 E-value=68 Score=14.30 Aligned_cols=20 Identities=20% Similarity=0.541 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q ss_conf 02488999999999999852
Q gi|254780198|r 5 FWIAVDVFVIVATIITCFFM 24 (69)
Q Consensus 5 fwiavdvfvivatiitcffm 24 (69)
.+|-+--..|..|++.|++|
T Consensus 91 ~RVki~y~Mi~lT~igC~~m 110 (146)
T pfam06388 91 MRVKICYIMIALTVVGCIIM 110 (146)
T ss_pred HHHHHHHHHHHHHHHHHHHH
T ss_conf 33467689999999999999
No 7
>pfam03839 Sec62 Translocation protein Sec62.
Probab=19.45 E-value=77 Score=14.02 Aligned_cols=55 Identities=22% Similarity=0.417 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHH-----HCCHHHHHHHHHHHHHHHHHHH---H-----HHH-HH-CCEEEEEEECCCC
Q ss_conf 99999999999985-----2561489999999999999999---8-----876-22-1335566536404
Q gi|254780198|r 10 DVFVIVATIITCFF-----MNKQCAWWLRVFLPFLLISIMI---V-----HIT-HI-SGHVNFLLFPPLS 64 (69)
Q Consensus 10 dvfvivatiitcff-----mnkqcawwlrvflpfllisimi---v-----hit-hi-sghvnfllfppls 64 (69)
...++++.+.-|.| .-|+..|+|-+-.-.++..+.. + -++ .+ .|...|-+||-|.
T Consensus 109 ~~~~v~~v~a~~lFPlWP~~~r~gv~YlSv~~lgll~~~~~lai~R~ilf~i~w~~~~~~~~fWlfPNLf 178 (217)
T pfam03839 109 GVIGVLGIIALVLFPLWPRFMRKGVYYLSIGALGFLAGFFALAILRLILFVIVWAIVGGKPGFWIFPNLT 178 (217)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCHH
T ss_conf 9999999999984126879998878999999999999999999999999999999872897578557501
No 8
>pfam09581 Spore_III_AF Stage III sporulation protein AF (Spore_III_AF). This family represents the stage III sporulation protein AF (Spore_III_AF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of these proteins is poorly conserved.
Probab=18.96 E-value=79 Score=13.96 Aligned_cols=43 Identities=23% Similarity=0.490 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCE
Q ss_conf 9999999999852561489999999999999999887622133
Q gi|254780198|r 12 FVIVATIITCFFMNKQCAWWLRVFLPFLLISIMIVHITHISGH 54 (69)
Q Consensus 12 fvivatiitcffmnkqcawwlrvflpfllisimivhithisgh 54 (69)
|++.+|++.-..-|...--+.|.++-++|+.+|+--+..+-+.
T Consensus 3 ~~~~~~~~~~llp~~~~~ky~~~~~gl~l~~~~l~pi~~l~~~ 45 (185)
T pfam09581 3 FILFATFLEMLLPNSSMKKYVKLVLGLLLIVIILNPVLKLFGK 45 (185)
T ss_pred EEHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 8679999999789633689999999999999999999998447
No 9
>pfam08713 DNA_alkylation DNA alkylation repair enzyme. Proteins in this family are predicted to be DNA alkylation repair enzymes. The structure of a hypothetical protein in this family shows it to adopt a supercoiled alpha helical structure.
Probab=18.25 E-value=57 Score=14.72 Aligned_cols=16 Identities=38% Similarity=0.771 Sum_probs=12.5
Q ss_pred HHHHCCHHHHHHHHHH
Q ss_conf 9852561489999999
Q gi|254780198|r 21 CFFMNKQCAWWLRVFL 36 (69)
Q Consensus 21 cffmnkqcawwlrvfl 36 (69)
-||++|-.+|.||..-
T Consensus 167 e~fiqKAigWaLRe~~ 182 (212)
T pfam08713 167 EFFIQKAIGWALREYS 182 (212)
T ss_pred HHHHHHHHHHHHHHHH
T ss_conf 9999999999999997
No 10
>pfam10831 DUF2556 Protein of unknown function (DUF2556). This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=17.04 E-value=87 Score=13.73 Aligned_cols=10 Identities=50% Similarity=1.092 Sum_probs=5.6
Q ss_pred HHHHHHHHHH
Q ss_conf 8999999999
Q gi|254780198|r 29 AWWLRVFLPF 38 (69)
Q Consensus 29 awwlrvflpf 38 (69)
-|||-||--+
T Consensus 5 ywwlvvfav~ 14 (53)
T pfam10831 5 YWWLVVFAVS 14 (53)
T ss_pred HHHHHHHHHH
T ss_conf 3358999999
Done!